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-rw-r--r--README.md33
-rw-r--r--app-office/visidata/visidata-2.8.ebuild2
-rw-r--r--dev-cpp/blitz/blitz-1.0.3_pre20200524.ebuild6
-rw-r--r--dev-cpp/castxml/Manifest2
-rw-r--r--dev-cpp/castxml/castxml-0.3.6.ebuild35
-rw-r--r--dev-cpp/castxml/castxml-0.4.3.ebuild35
-rw-r--r--dev-cpp/castxml/castxml-9999.ebuild33
-rw-r--r--dev-cpp/castxml/files/castxml-0.3.6-install-paths.patch12
-rw-r--r--dev-java/jeuclid-core/Manifest1
-rw-r--r--dev-java/jeuclid-core/files/jeuclid-core-no-freehep.patch10
-rw-r--r--dev-java/jeuclid-core/jeuclid-core-3.1.14.ebuild55
-rw-r--r--dev-java/jeuclid-core/metadata.xml21
-rw-r--r--dev-libs/optix/Manifest1
-rw-r--r--dev-libs/optix/metadata.xml10
-rw-r--r--dev-libs/optix/optix-7.4.0.ebuild37
-rw-r--r--dev-python/anys/anys-0.2.0.ebuild2
-rw-r--r--dev-python/anys/anys-0.2.1.ebuild3
-rw-r--r--dev-python/bokeh/bokeh-2.4.2.ebuild2
-rw-r--r--dev-python/cadquery-pywrap/cadquery-pywrap-7.5.2_rc20210526.ebuild2
-rw-r--r--dev-python/cadquery-pywrap/cadquery-pywrap-7.5.3_rc20220113.ebuild2
-rw-r--r--dev-python/cadquery/cadquery-2.2_rc20210804.ebuild2
-rw-r--r--dev-python/cadquery/cadquery-2.2_rc20220506.ebuild2
-rw-r--r--dev-python/dandi-schema/Manifest1
-rw-r--r--dev-python/dandi-schema/dandi-schema-0.7.1.ebuild42
-rw-r--r--dev-python/delegator/delegator-0.1.1.ebuild6
-rw-r--r--dev-python/fslpy/fslpy-3.8.1.ebuild8
-rw-r--r--dev-python/grabbit/grabbit-0.2.6.ebuild6
-rw-r--r--dev-python/hdf5storage/Manifest3
-rw-r--r--dev-python/hdf5storage/hdf5storage-0.1.17.ebuild (renamed from dev-python/hdf5storage/hdf5storage-0.1.15_p1.ebuild)17
-rw-r--r--dev-python/hdf5storage/hdf5storage-0.1.18.ebuild24
-rw-r--r--dev-python/hdf5storage/hdf5storage-9999.ebuild6
-rw-r--r--dev-python/hdmf/Manifest1
-rw-r--r--dev-python/hdmf/files/hdmf-3.3.2-versions.patch20
-rw-r--r--dev-python/hdmf/hdmf-3.1.1-r1.ebuild8
-rw-r--r--dev-python/hdmf/hdmf-3.3.2-r1.ebuild32
-rw-r--r--dev-python/hdmf/metadata.xml4
-rw-r--r--dev-python/keyrings_alt/Manifest1
-rw-r--r--dev-python/keyrings_alt/files/keyrings_alt-4.1.0-pycryptodome.patch90
-rw-r--r--dev-python/keyrings_alt/keyrings_alt-4.1.0-r1.ebuild31
-rw-r--r--dev-python/keyrings_alt/metadata.xml24
-rw-r--r--dev-python/llvmlite/Manifest3
-rw-r--r--dev-python/llvmlite/files/llvmlite-0.37.0-llvm12.patch91
-rw-r--r--dev-python/llvmlite/files/llvmlite-0.39.0-llvm12.patch (renamed from dev-python/llvmlite/files/llvmlite-0.38.0-llvm12.patch)57
-rw-r--r--dev-python/llvmlite/llvmlite-0.38.0-r1.ebuild62
-rw-r--r--dev-python/llvmlite/llvmlite-0.39.0.ebuild (renamed from dev-python/llvmlite/llvmlite-0.37.0-r1.ebuild)4
-rw-r--r--dev-python/num2words/num2words-0.5.10.ebuild6
-rw-r--r--dev-python/numba/Manifest3
-rw-r--r--dev-python/numba/numba-0.54.0.ebuild84
-rw-r--r--dev-python/numba/numba-0.56.0.ebuild (renamed from dev-python/numba/numba-0.55.0.ebuild)6
-rw-r--r--dev-python/numcodecs/Manifest1
-rw-r--r--dev-python/numcodecs/numcodecs-0.10.0.ebuild35
-rw-r--r--dev-python/nwbinspector/Manifest2
-rw-r--r--dev-python/nwbinspector/nwbinspector-0.3.9.ebuild1
-rw-r--r--dev-python/nwbinspector/nwbinspector-0.4.12.ebuild39
-rw-r--r--dev-python/nwbinspector/nwbinspector-0.4.14.ebuild39
-rw-r--r--dev-python/pynrrd/Manifest1
-rw-r--r--dev-python/pynrrd/pynrrd-0.4.2.ebuild6
-rw-r--r--dev-python/pynrrd/pynrrd-0.4.3.ebuild26
-rw-r--r--dev-python/pynwb/Manifest3
-rw-r--r--dev-python/pynwb/files/pynwb-2.1.0-versions.patch21
-rw-r--r--dev-python/pynwb/metadata.xml4
-rw-r--r--dev-python/pynwb/pynwb-2.0.0.ebuild4
-rw-r--r--dev-python/pynwb/pynwb-2.0.1.ebuild39
-rw-r--r--dev-python/pynwb/pynwb-2.1.0-r1.ebuild (renamed from dev-python/pynwb/pynwb-2.0.0_p0.ebuild)16
-rw-r--r--dev-python/pysolar/pysolar-0.8.ebuild6
-rw-r--r--dev-python/python-gantt/python-gantt-0.6.0_p20200809.ebuild8
-rw-r--r--dev-python/python-igraph/Manifest1
-rw-r--r--dev-python/python-igraph/python-igraph-0.9.11.ebuild53
-rw-r--r--dev-python/traits/traits-6.0.0.ebuild6
-rw-r--r--dev-python/traits/traits-6.1.1.ebuild6
-rw-r--r--dev-python/visvis/visvis-1.13.0.ebuild2
-rw-r--r--dev-python/wraps/Manifest1
-rw-r--r--dev-python/wraps/files/wraps-0.1.0-includes.patch16
-rw-r--r--dev-python/wraps/files/wraps-0.1.0-poetry_groups.patch61
-rw-r--r--dev-python/wraps/metadata.xml (renamed from dev-cpp/castxml/metadata.xml)8
-rw-r--r--dev-python/wraps/wraps-0.1.0.ebuild31
-rw-r--r--dev-vcs/dandi-cli/Manifest6
-rw-r--r--dev-vcs/dandi-cli/dandi-cli-0.38.0.ebuild4
-rw-r--r--dev-vcs/dandi-cli/dandi-cli-0.39.4.ebuild5
-rw-r--r--dev-vcs/dandi-cli/dandi-cli-0.45.1.ebuild (renamed from dev-vcs/dandi-cli/dandi-cli-0.37.0.ebuild)27
-rw-r--r--dev-vcs/datalad/Manifest3
-rw-r--r--dev-vcs/datalad/datalad-0.15.1.ebuild6
-rw-r--r--dev-vcs/datalad/datalad-0.15.2.ebuild6
-rw-r--r--dev-vcs/datalad/datalad-0.16.1.ebuild72
-rw-r--r--dev-vcs/datalad/datalad-0.17.0.ebuild75
-rw-r--r--dev-vcs/datalad/datalad-0.17.2.ebuild73
-rw-r--r--dev-vcs/datalad/files/datalad-0.16.1-input.patch94
-rw-r--r--dev-vcs/datalad/files/datalad-0.17.0-skip.patch162
-rw-r--r--media-libs/charls/Manifest1
-rw-r--r--media-libs/charls/charls-2.3.4.ebuild30
-rw-r--r--media-libs/charls/metadata.xml11
-rw-r--r--net-misc/cernbox-client/Manifest3
-rw-r--r--net-misc/cernbox-client/cernbox-client-2.11.1.8438.ebuild (renamed from net-misc/cernbox-client/cernbox-client-2.10.0.6519.ebuild)18
-rw-r--r--profiles/package.mask12
-rw-r--r--profiles/package.use.mask10
-rw-r--r--sci-biology/ants/Manifest3
-rw-r--r--sci-biology/ants/ants-2.3.4.ebuild78
-rw-r--r--sci-biology/ants/ants-2.4.1-r1.ebuild60
-rw-r--r--sci-biology/ants/files/ants-2.3.1_p20191013-logic.patch37
-rw-r--r--sci-biology/ants/files/ants-2.3.1_p20191013-paths.patch40
-rw-r--r--sci-biology/ants/files/ants-2.3.4-libdir.patch117
-rw-r--r--sci-biology/ants/files/ants-2.3.4-version.patch17
-rw-r--r--sci-biology/ants/files/ants-2.4.1-fix-compile.patch13
-rw-r--r--sci-biology/bidsschematools/Manifest2
-rw-r--r--sci-biology/bidsschematools/bidsschematools-0.4.0.ebuild37
-rw-r--r--sci-biology/bidsschematools/bidsschematools-0.5.1.ebuild37
-rw-r--r--sci-biology/bidsschematools/metadata.xml19
-rw-r--r--sci-biology/bruker2nifti/bruker2nifti-1.0.4.ebuild6
-rw-r--r--sci-biology/dcmstack/Manifest1
-rw-r--r--sci-biology/dcmstack/dcmstack-0.8.ebuild15
-rw-r--r--sci-biology/dipy/dipy-1.1.1.ebuild6
-rw-r--r--sci-biology/dipy/dipy-9999.ebuild37
-rw-r--r--sci-biology/nilearn/nilearn-0.8.1.ebuild2
-rw-r--r--sci-biology/nilearn/nilearn-0.9.1.ebuild3
-rw-r--r--sci-biology/open-ephys-gui/Manifest1
-rw-r--r--sci-biology/open-ephys-gui/files/open-ephys-gui-0.6.1.patch15
-rw-r--r--sci-biology/open-ephys-gui/files/open-ephys-gui-9999.patch12
-rw-r--r--sci-biology/open-ephys-gui/files/open-ephys-gui-99999999.patch12
-rw-r--r--sci-biology/open-ephys-gui/metadata.xml4
-rw-r--r--sci-biology/open-ephys-gui/open-ephys-gui-0.6.1.ebuild83
-rw-r--r--sci-biology/open-ephys-gui/open-ephys-gui-9999.ebuild13
-rw-r--r--sci-biology/open-ephys-gui/open-ephys-gui-99999999.ebuild13
-rw-r--r--sci-biology/samri/samri-0.5.ebuild4
-rw-r--r--sci-electronics/minipro/Manifest2
-rw-r--r--sci-electronics/minipro/files/minipro-0.5-makefile.patch12
-rw-r--r--sci-electronics/minipro/metadata.xml7
-rw-r--r--sci-electronics/minipro/minipro-0.5.ebuild (renamed from sci-electronics/minipro/minipro-0.4.ebuild)19
-rw-r--r--sci-libs/HDF5Plugin-Zstandard/HDF5Plugin-Zstandard-0_pre20201121-r1.ebuild (renamed from sci-libs/HDF5Plugin-Zstandard/HDF5Plugin-Zstandard-0_pre20201121.ebuild)4
-rw-r--r--sci-libs/bids-validator/bids-validator-1.4.4.ebuild6
-rw-r--r--sci-libs/gdcm/Manifest2
-rw-r--r--sci-libs/gdcm/files/gdcm-3.0.14-include-math-h.patch15
-rw-r--r--sci-libs/gdcm/files/gdcm_support_vtk9.patch70
-rw-r--r--sci-libs/gdcm/gdcm-3.0.14.ebuild121
-rw-r--r--sci-libs/gdcm/metadata.xml14
-rw-r--r--sci-libs/itk/Manifest17
-rw-r--r--sci-libs/itk/files/0001-BUG-Wrap-TransformFileReader-TransformFileWriter.patch50
-rw-r--r--sci-libs/itk/files/0002-COMP-Fixed-itkQuasiNewtonOptimizerv4-wrapping-warnin.patch28
-rw-r--r--sci-libs/itk/files/0003-COMP-Fixed-itkGradientDescentOptimizerv4-wrapping-wa.patch73
-rw-r--r--sci-libs/itk/files/0004-COMP-Warp-OptimizerParameterScalesEstimatorTemplate.patch30
-rw-r--r--sci-libs/itk/files/0005-make-gdcm-helper-library-static.patch11
-rw-r--r--sci-libs/itk/files/ITKModuleRemote.patch45
-rw-r--r--sci-libs/itk/files/itk-5.1.0-downloads.patch20
-rw-r--r--sci-libs/itk/files/itk-5.1.0-include_limits.patch10
-rw-r--r--sci-libs/itk/files/itk-5.2.1-fix-castxml-clang-attr-malloc.patch25
-rw-r--r--sci-libs/itk/files/itk-5.2.1-system-openjpeg.patch558
-rw-r--r--sci-libs/itk/files/itk-5.2.1-system-tiff-has-64.patch18
-rw-r--r--sci-libs/itk/files/itk-5.2.1-upstream-fixes.patch309
-rw-r--r--sci-libs/itk/files/nrrdio-linking.patch15
-rw-r--r--sci-libs/itk/files/tests.patch41
-rw-r--r--sci-libs/itk/itk-5.0.1.ebuild178
-rw-r--r--sci-libs/itk/itk-5.2.1-r2.ebuild (renamed from sci-libs/itk/itk-5.1.0.ebuild)111
-rw-r--r--sci-libs/labbookdb/labbookdb-0.1.ebuild6
-rw-r--r--sci-libs/mlpack/Manifest2
-rw-r--r--sci-libs/mlpack/metadata.xml27
-rw-r--r--sci-libs/mlpack/mlpack-3.4.1.ebuild112
-rw-r--r--sci-libs/mlpack/mlpack-3.4.2.ebuild118
-rw-r--r--sci-libs/nibabel/Manifest1
-rw-r--r--sci-libs/nibabel/nibabel-2.5.1.ebuild42
-rw-r--r--sci-libs/nibabel/nibabel-3.0.2.ebuild6
-rw-r--r--sci-libs/nibabel/nibabel-3.2.1.ebuild15
-rw-r--r--sci-libs/nibabel/nibabel-9999.ebuild37
-rw-r--r--sci-libs/nipy/Manifest3
-rw-r--r--sci-libs/nipy/nipy-0.4.2.ebuild10
-rw-r--r--sci-libs/nipy/nipy-0.5.0.ebuild52
-rw-r--r--sci-libs/nipy/nipy-9999.ebuild54
-rw-r--r--sci-libs/nipype/files/nipype-1.5.0-collections.patch28
-rw-r--r--sci-libs/nipype/nipype-1.5.0.ebuild20
-rw-r--r--sci-libs/pybids/Manifest1
-rw-r--r--sci-libs/pybids/pybids-0.10.2.ebuild16
-rw-r--r--sci-libs/pybids/pybids-0.11.1.ebuild40
-rw-r--r--sci-libs/pybids/pybids-0.12.4.ebuild12
-rw-r--r--sci-libs/pybids/pybids-0.6.5.ebuild6
-rw-r--r--sci-libs/simpleitk/simpleitk-1.2.4.ebuild6
-rw-r--r--sci-libs/torchvision/torchvision-0.11.2.ebuild2
-rw-r--r--sci-misc/elmer-fem/elmer-fem-9.0-r2.ebuild (renamed from sci-misc/elmer-fem/elmer-fem-9.0-r1.ebuild)2
-rw-r--r--sci-misc/elmer-fem/files/elmer-fem-9.0-qwt-6.2.patch35
-rw-r--r--sci-misc/elmer-fem/files/elmer-fem-rpath.patch11
-rw-r--r--sci-physics/feynarts/Manifest1
-rw-r--r--sci-physics/feynarts/feynarts-3.11.ebuild29
-rw-r--r--sci-physics/feynarts/metadata.xml19
-rw-r--r--sci-physics/feyncalc/Manifest2
-rw-r--r--sci-physics/feyncalc/feyncalc-9.3.1.ebuild43
-rw-r--r--sci-physics/feyncalc/feyncalc-9999.ebuild47
-rw-r--r--sci-physics/feyncalc/metadata.xml22
-rw-r--r--sci-physics/formcalc/Manifest2
-rw-r--r--sci-physics/formcalc/files/formcalc-9.9-compile.patch50
-rw-r--r--sci-physics/formcalc/formcalc-9.10-r1.ebuild52
-rw-r--r--sci-physics/formcalc/formcalc-9.9-r1.ebuild54
-rw-r--r--sci-physics/formcalc/metadata.xml19
-rw-r--r--sci-physics/rivet/Manifest2
-rw-r--r--sci-physics/rivet/files/rivet-3.1.5-doc.patch38
-rw-r--r--sci-physics/rivet/files/rivet-3.1.5-test.patch11
-rw-r--r--sci-physics/rivet/files/rivet-3.1.6-binreloc.patch12
-rw-r--r--sci-physics/rivet/metadata.xml20
-rw-r--r--sci-physics/rivet/rivet-3.1.5.ebuild75
-rw-r--r--sci-physics/rivet/rivet-3.1.6.ebuild75
-rw-r--r--sci-physics/spheno/Manifest1
-rw-r--r--sci-physics/spheno/files/spheno-3.3.8-gfortran.patch32
-rw-r--r--sci-physics/spheno/metadata.xml19
-rw-r--r--sci-physics/spheno/spheno-3.3.8.ebuild43
-rw-r--r--sci-visualization/fsleyes-props/fsleyes-props-1.7.3.ebuild8
-rw-r--r--sci-visualization/fsleyes-widgets/fsleyes-widgets-0.12.2.ebuild8
202 files changed, 3627 insertions, 2221 deletions
diff --git a/README.md b/README.md
index 3904770a0..cd47d84a4 100644
--- a/README.md
+++ b/README.md
@@ -17,6 +17,7 @@
### Contents
1. [Installation](#install)
+ - [Eselect](#install-eselect)
- [Manual](#install-manual)
- [Layman](#install-layman)
2. [Usage](#usage)
@@ -28,25 +29,35 @@
## Installation <a name="install"></a>
-### Eselect-repository install <a name="install-eselect"></a>
+As per the current [Portage specification](https://dev.gentoo.org/~zmedico/portage/doc/man/portage.5.html), ebuild repositories (a.k.a. overlays) can be managed via file collections under `/etc/portage/repos.conf/`, via the new [plug-in sync system](https://wiki.gentoo.org/wiki/Project:Portage/Sync).
+
+### Eselect-repository Install <a name="install-eselect"></a>
+
+The overlay can be enabled via the `repository` extension of the Gentoo `eselect` utility.
-The easiest way to enable the overlay is to:
```console
-emerge --noreplace eselect-repository && eselect repository enable science && emerge --sync
+emerge --ask --noreplace --verbose eselect-repository
+eselect repository enable science
```
-and emerge the package as usual.
-### Manual Install <a name="install-manual"></a>
+### Eselect-repository Uninstall
+
+To disable and remove the overlay, run:
-As per the current [Portage specifications](https://dev.gentoo.org/~zmedico/portage/doc/man/portage.5.html), ebuild repositories (a.k.a. overlays) can be managed via file collections under `/etc/portage/repos.conf/`, via the new [plug-in sync system](https://wiki.gentoo.org/wiki/Project:Portage/Sync).
+```console
+eselect repository disable science
+eselect repository remove science
+```
+
+### Manual Install <a name="install-manual"></a>
-To enable the overlay without the need for additional software, you first need to have `git` installed:
+To enable the overlay without the need for dedicated repository software, you need to have `git` installed:
```console
-emerge --ask --verbose dev-vcs/git
+emerge --ask --noreplace --verbose dev-vcs/git
````
-Then you need to add the science repository configuration by downloading the [science.conf](metadata/science.conf) file:
+Then you can simply download the science repository configuration file, [science.conf](metadata/science.conf):
```console
wget https://gitweb.gentoo.org/proj/sci.git/plain/metadata/science.conf \
@@ -55,7 +66,7 @@ wget https://gitweb.gentoo.org/proj/sci.git/plain/metadata/science.conf \
### Manual Uninstall
-To uninstall the overlay, simply run:
+To disable and remove the overlay, run:
```console
rm /etc/portage/repos.conf/science
@@ -67,7 +78,7 @@ rm /var/db/repos/science -rf
You can also install the overlay via the [layman](https://wiki.gentoo.org/wiki/Layman) overlay manager.
```console
-emerge --ask --verbose app-portage/layman
+emerge --ask --noreplace --verbose app-portage/layman
layman --add science
```
diff --git a/app-office/visidata/visidata-2.8.ebuild b/app-office/visidata/visidata-2.8.ebuild
index bb35b1c03..ab4d506ab 100644
--- a/app-office/visidata/visidata-2.8.ebuild
+++ b/app-office/visidata/visidata-2.8.ebuild
@@ -3,7 +3,7 @@
EAPI=8
-PYTHON_COMPAT=( python3_{8..9} )
+PYTHON_COMPAT=( python3_{8..10} )
DISTUTILS_USE_SETUPTOOLS=rdepend
inherit distutils-r1 optfeature
diff --git a/dev-cpp/blitz/blitz-1.0.3_pre20200524.ebuild b/dev-cpp/blitz/blitz-1.0.3_pre20200524.ebuild
index 389e5430d..432004f11 100644
--- a/dev-cpp/blitz/blitz-1.0.3_pre20200524.ebuild
+++ b/dev-cpp/blitz/blitz-1.0.3_pre20200524.ebuild
@@ -1,14 +1,12 @@
# Copyright 1999-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=7
-
-PYTHON_COMPAT=( python3_{7..9} )
+EAPI=8
+PYTHON_COMPAT=( python3_{8..11} )
inherit cmake python-any-r1
COMMIT="39f885951a9b8b11f931f917935a16066a945056"
-
DESCRIPTION="Multi-dimensional array library for C++"
HOMEPAGE="https://github.com/blitzpp/blitz"
SRC_URI="https://github.com/blitzpp/blitz/archive/${COMMIT}.tar.gz -> ${P}.tar.gz"
diff --git a/dev-cpp/castxml/Manifest b/dev-cpp/castxml/Manifest
deleted file mode 100644
index a7d756e8b..000000000
--- a/dev-cpp/castxml/Manifest
+++ /dev/null
@@ -1,2 +0,0 @@
-DIST castxml-0.3.6.tar.gz 95844 BLAKE2B c0ab3c7ba29b2abb4755320d97c36ee850135fff6fd5bb7a9436d68f50e9c6a80108ac95958fe9b51afaf6b4ebdde7db825a9cdf047c5e8f47f4f57fba77dcc1 SHA512 c850ce9ce0ef716cf64139d4311955deb8373db691e3cb7348932bbd3945056366838187603e5850a088911a8be6b0e5b53e2c700c0b5c8fed71008de7ab2350
-DIST castxml-0.4.3.tar.gz 103188 BLAKE2B ceaeaa0e228865847fc9627e93366c9dc2d33f89c97621af25ce84746ffe79b0db7cf52a93aed3ac297ce116e1f63f4bcc636dc21419aabf3ba737f545b240c1 SHA512 af2c03e148d42615a9ad0366a224ebeb06ca0348c0b5fcc0a93cba4871710dd8901874e5e30968532cdb1254e63a7ab596403bf2f3c836eed57be287203ddbed
diff --git a/dev-cpp/castxml/castxml-0.3.6.ebuild b/dev-cpp/castxml/castxml-0.3.6.ebuild
deleted file mode 100644
index 6fb7ac720..000000000
--- a/dev-cpp/castxml/castxml-0.3.6.ebuild
+++ /dev/null
@@ -1,35 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit cmake llvm
-
-MY_PN="CastXML"
-
-DESCRIPTION="CastXML is a C-family abstract syntax tree XML output tool."
-HOMEPAGE="https://github.com/CastXML/CastXML"
-if [[ ${PV} == 9999 ]]; then
- inherit git-r3
- EGIT_REPO_URI="https://github.com/CastXML/CastXML"
-else
- SRC_URI="https://github.com/CastXML/CastXML/archive/v${PV}.tar.gz -> ${P}.tar.gz"
- KEYWORDS="~amd64 ~x86"
-fi
-
-LICENSE="Apache-2.0"
-SLOT="0"
-IUSE="test"
-RESTRICT="!test? ( test )"
-
-DEPEND="${RDEPEND}"
-RDEPEND="
- dev-libs/glib:2
- dev-libs/libxml2
- sys-devel/llvm:=
- sys-devel/clang:=
-"
-
-S="${WORKDIR}/${MY_PN}-${PV}"
-
-PATCHES=( "${FILESDIR}"/${PN}-0.3.6-install-paths.patch )
diff --git a/dev-cpp/castxml/castxml-0.4.3.ebuild b/dev-cpp/castxml/castxml-0.4.3.ebuild
deleted file mode 100644
index 6fb7ac720..000000000
--- a/dev-cpp/castxml/castxml-0.4.3.ebuild
+++ /dev/null
@@ -1,35 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit cmake llvm
-
-MY_PN="CastXML"
-
-DESCRIPTION="CastXML is a C-family abstract syntax tree XML output tool."
-HOMEPAGE="https://github.com/CastXML/CastXML"
-if [[ ${PV} == 9999 ]]; then
- inherit git-r3
- EGIT_REPO_URI="https://github.com/CastXML/CastXML"
-else
- SRC_URI="https://github.com/CastXML/CastXML/archive/v${PV}.tar.gz -> ${P}.tar.gz"
- KEYWORDS="~amd64 ~x86"
-fi
-
-LICENSE="Apache-2.0"
-SLOT="0"
-IUSE="test"
-RESTRICT="!test? ( test )"
-
-DEPEND="${RDEPEND}"
-RDEPEND="
- dev-libs/glib:2
- dev-libs/libxml2
- sys-devel/llvm:=
- sys-devel/clang:=
-"
-
-S="${WORKDIR}/${MY_PN}-${PV}"
-
-PATCHES=( "${FILESDIR}"/${PN}-0.3.6-install-paths.patch )
diff --git a/dev-cpp/castxml/castxml-9999.ebuild b/dev-cpp/castxml/castxml-9999.ebuild
deleted file mode 100644
index dbf7fff49..000000000
--- a/dev-cpp/castxml/castxml-9999.ebuild
+++ /dev/null
@@ -1,33 +0,0 @@
-# Copyright 1999-2020 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit cmake llvm
-
-MY_PN="CastXML"
-
-DESCRIPTION="CastXML is a C-family abstract syntax tree XML output tool."
-HOMEPAGE="https://github.com/CastXML/CastXML"
-if [[ ${PV} == 9999 ]]; then
- inherit git-r3
- EGIT_REPO_URI="https://github.com/CastXML/CastXML"
-else
- SRC_URI="https://github.com/CastXML/CastXML/archive/v${PV}.tar.gz -> ${P}.tar.gz"
- KEYWORDS="~amd64 ~x86"
-fi
-
-LICENSE="Apache-2.0"
-SLOT="0"
-IUSE="test"
-RESTRICT="!test? ( test )"
-
-DEPEND="${RDEPEND}"
-RDEPEND="
- dev-libs/glib:2
- dev-libs/libxml2
- sys-devel/llvm:=
- sys-devel/clang:=
-"
-
-PATCHES=( "${FILESDIR}"/${PN}-0.3.6-install-paths.patch )
diff --git a/dev-cpp/castxml/files/castxml-0.3.6-install-paths.patch b/dev-cpp/castxml/files/castxml-0.3.6-install-paths.patch
deleted file mode 100644
index 0b72085b4..000000000
--- a/dev-cpp/castxml/files/castxml-0.3.6-install-paths.patch
+++ /dev/null
@@ -1,12 +0,0 @@
-diff --git a/CMakeLists.txt b/CMakeLists.txt
-index 90feea4..4b058a8 100644
---- a/CMakeLists.txt
-+++ b/CMakeLists.txt
-@@ -194,5 +194,5 @@ install(DIRECTORY share/castxml/ DESTINATION "${CastXML_INSTALL_DATA_DIR}")
- install(FILES
- "LICENSE"
- "NOTICE"
-- DESTINATION "${CastXML_INSTALL_DOC_DIR}"
-+ DESTINATION "${CastXML_INSTALL_DATA_DIR}"
- )
-
diff --git a/dev-java/jeuclid-core/Manifest b/dev-java/jeuclid-core/Manifest
deleted file mode 100644
index 6df1751b1..000000000
--- a/dev-java/jeuclid-core/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST jeuclid-core-3.1.14.tar.gz 7244186 BLAKE2B 9cada848e516aba942ef87e7b746296f9565d5271a1ce6635e80e6559edcedac3245c4bde28e8d1053cacc5774e6a015079b0281802559e86366a75223b8ea2c SHA512 7b52491d7fac40a13f41176a49f36411681c957aba95c23bb6396f4e1248f5463afcd5394b0bb8e3dfbdd498d3290ac5f787e876636f5f282b703a72799eff4e
diff --git a/dev-java/jeuclid-core/files/jeuclid-core-no-freehep.patch b/dev-java/jeuclid-core/files/jeuclid-core-no-freehep.patch
deleted file mode 100644
index daf123c92..000000000
--- a/dev-java/jeuclid-core/files/jeuclid-core-no-freehep.patch
+++ /dev/null
@@ -1,10 +0,0 @@
---- a/build.xml 2010-01-22 17:46:35.000000000 +0000
-+++ b/build.xml 2010-01-22 17:49:07.000000000 +0000
-@@ -113,6 +113,7 @@
- <src>
- <pathelement location="src/main/java"/>
- </src>
-+ <exclude name="**/FreeHep*" />
- <classpath refid="libs-build-classpath"/>
- </javac>
- <copy todir="${build.output}">
diff --git a/dev-java/jeuclid-core/jeuclid-core-3.1.14.ebuild b/dev-java/jeuclid-core/jeuclid-core-3.1.14.ebuild
deleted file mode 100644
index a64ebcd74..000000000
--- a/dev-java/jeuclid-core/jeuclid-core-3.1.14.ebuild
+++ /dev/null
@@ -1,55 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-JAVA_PKG_IUSE="source"
-
-inherit java-pkg-2 java-ant-2
-
-DESCRIPTION="Core module of MathML rendering solution"
-HOMEPAGE="https://github.com/rototor/jeuclid"
-SRC_URI="https://github.com/rototor/jeuclid/archive/jeuclid-parent-${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="Apache-2.0"
-SLOT="0"
-KEYWORDS="~amd64"
-
-COMMON_DEPEND="
- dev-java/ant-core:0
- dev-java/batik:1.9
- dev-java/commons-logging:0
- dev-java/jcip-annotations:0
- dev-java/jsr305:0
- dev-java/xml-commons-external:1.3
- dev-java/xmlgraphics-commons:2
-"
-
-RDEPEND=">=virtual/jre-1.7
- ${COMMON_DEPEND}"
-
-DEPEND=">=virtual/jdk-1.7
- ${COMMON_DEPEND}"
-
-S="${WORKDIR}/jeuclid-jeuclid-parent-${PV}/${PN}"
-
-PATCHES=(
- "${FILESDIR}"/${PN}-no-freehep.patch
-)
-
-src_prepare() {
- default
-
- # create directory for dependencies
- mkdir lib && cd lib || die
-
- # add dependencies into the lib dir
- java-pkg_jar-from ant-core ant.jar
- java-pkg_jar-from batik-1.9 batik-all.jar
- java-pkg_jar-from commons-logging,jcip-annotations,xml-commons-external-1.3
- java-pkg_jar-from xml-commons-external-1.3,xmlgraphics-commons-2
- java-pkg_jar-from jsr305
-}
-
-src_install() {
- java-pkg_dojar target/${PN}.jar
-}
diff --git a/dev-java/jeuclid-core/metadata.xml b/dev-java/jeuclid-core/metadata.xml
deleted file mode 100644
index 8b5c039f5..000000000
--- a/dev-java/jeuclid-core/metadata.xml
+++ /dev/null
@@ -1,21 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <maintainer type="project">
- <email>sci@gentoo.org</email>
- <name>Gentoo Science Project</name>
- </maintainer>
- <longdescription lang="en">
-JEuclid is a complete MathML rendering solution, consisting of:
-* A MathViewer application
-* Command line converters from MathML to other formats
-* An ant task for automated conversion
-* Display components for AWT and Swing
-* A component for Apache Cocoon
-This package contains the basic JEuclid rendering and document
-handling classes.
-</longdescription>
- <upstream>
- <remote-id type="sourceforge">jeuclid</remote-id>
- </upstream>
-</pkgmetadata>
diff --git a/dev-libs/optix/Manifest b/dev-libs/optix/Manifest
deleted file mode 100644
index 0a6859644..000000000
--- a/dev-libs/optix/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST NVIDIA-OptiX-SDK-7.4.0-linux64-x86_64.sh 57923655 BLAKE2B c3e159106ec6c8c446090ebd182fd3b0a75ec48b62e6984ae6559578688fd9a6cb29ea6065cb89aecdeb02247acbf3fb3bb0cbf69b10c29c222eb9fcbb0c6d90 SHA512 04f50c49d08c5e4e9be73ee322c4bff4f10a5e30445bc431e213c879a35cc5e36e0ceb8c864313f417628575a3c71593e65467ea13dd111b432fdf1db9383ae0
diff --git a/dev-libs/optix/metadata.xml b/dev-libs/optix/metadata.xml
deleted file mode 100644
index 43be4e4e4..000000000
--- a/dev-libs/optix/metadata.xml
+++ /dev/null
@@ -1,10 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <maintainer type="person">
- <email>heroxbd@gentoo.org</email>
- </maintainer>
- <maintainer type="person">
- <email>rich@warfaresdl.com</email>
- </maintainer>
-</pkgmetadata>
diff --git a/dev-libs/optix/optix-7.4.0.ebuild b/dev-libs/optix/optix-7.4.0.ebuild
deleted file mode 100644
index a3f61205e..000000000
--- a/dev-libs/optix/optix-7.4.0.ebuild
+++ /dev/null
@@ -1,37 +0,0 @@
-# Copyright 2021-2022 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-DESCRIPTION="NVIDIA Ray Tracing Engine"
-HOMEPAGE="https://developer.nvidia.com/optix"
-SRC_URI="NVIDIA-OptiX-SDK-${PV}-linux64-x86_64.sh"
-S="${WORKDIR}"
-
-SLOT="0/7"
-KEYWORDS="~amd64"
-RESTRICT="fetch mirror"
-LICENSE="NVIDIA-r2"
-
-RDEPEND="
- dev-util/nvidia-cuda-toolkit:=
- media-libs/freeglut
- virtual/opengl
-"
-
-pkg_nofetch() {
- einfo "Please download ${SRC_URI} from:"
- einfo " ${HOMEPAGE}"
- einfo "and move it to your DISTDIR directory."
- einfo 'DISTDIR value is available from `emerge --info`'
-}
-
-src_unpack() {
- tail -n +223 "${DISTDIR}"/${A} | tar -zx || die
-}
-
-src_install() {
- insinto /opt/${PN}
- dodoc -r doc
- doins -r include SDK
-}
diff --git a/dev-python/anys/anys-0.2.0.ebuild b/dev-python/anys/anys-0.2.0.ebuild
index 0d2fec35f..0f1bb884f 100644
--- a/dev-python/anys/anys-0.2.0.ebuild
+++ b/dev-python/anys/anys-0.2.0.ebuild
@@ -4,7 +4,7 @@
EAPI=8
PYTHON_COMPAT=( python3_{8..9} )
-DISTUTILS_USE_SETUPTOOLS=pyproject.toml
+DISTUTILS_USE_PEP517=setuptools
inherit distutils-r1
DESCRIPTION="Matchers for pytest"
diff --git a/dev-python/anys/anys-0.2.1.ebuild b/dev-python/anys/anys-0.2.1.ebuild
index 783fc75ce..d74bb76f9 100644
--- a/dev-python/anys/anys-0.2.1.ebuild
+++ b/dev-python/anys/anys-0.2.1.ebuild
@@ -4,7 +4,7 @@
EAPI=8
PYTHON_COMPAT=( python3_{8..10} )
-DISTUTILS_USE_SETUPTOOLS=pyproject.toml
+DISTUTILS_USE_PEP517=setuptools
inherit distutils-r1
DESCRIPTION="Matchers for pytest"
@@ -18,6 +18,7 @@ IUSE="test"
RESTRICT="!test? ( test )"
RDEPEND="
+ dev-python/deprecated[${PYTHON_USEDEP}]
dev-python/wheel[${PYTHON_USEDEP}]
"
diff --git a/dev-python/bokeh/bokeh-2.4.2.ebuild b/dev-python/bokeh/bokeh-2.4.2.ebuild
index d6dfa1901..263546dbf 100644
--- a/dev-python/bokeh/bokeh-2.4.2.ebuild
+++ b/dev-python/bokeh/bokeh-2.4.2.ebuild
@@ -25,7 +25,7 @@ RDEPEND="
>=dev-python/pillow-7.1.0[${PYTHON_USEDEP}]
>=dev-python/pyyaml-3.10[${PYTHON_USEDEP}]
>=dev-python/typing-extensions-3.10.0[${PYTHON_USEDEP}]
- >=www-servers/tornado-5.1[${PYTHON_USEDEP}]
+ >=dev-python/tornado-5.1[${PYTHON_USEDEP}]
"
BDEPEND="
test? (
diff --git a/dev-python/cadquery-pywrap/cadquery-pywrap-7.5.2_rc20210526.ebuild b/dev-python/cadquery-pywrap/cadquery-pywrap-7.5.2_rc20210526.ebuild
index 19494930c..3217b8774 100644
--- a/dev-python/cadquery-pywrap/cadquery-pywrap-7.5.2_rc20210526.ebuild
+++ b/dev-python/cadquery-pywrap/cadquery-pywrap-7.5.2_rc20210526.ebuild
@@ -29,7 +29,7 @@ SLOT="0"
RDEPEND="
dev-python/click[${PYTHON_USEDEP}]
dev-python/logzero[${PYTHON_USEDEP}]
- dev-python/path-py[${PYTHON_USEDEP}]
+ dev-python/path[${PYTHON_USEDEP}]
dev-python/clang-python[${PYTHON_USEDEP}]
dev-python/cymbal[${PYTHON_USEDEP}]
dev-python/toml[${PYTHON_USEDEP}]
diff --git a/dev-python/cadquery-pywrap/cadquery-pywrap-7.5.3_rc20220113.ebuild b/dev-python/cadquery-pywrap/cadquery-pywrap-7.5.3_rc20220113.ebuild
index b2213cef7..3197a52ea 100644
--- a/dev-python/cadquery-pywrap/cadquery-pywrap-7.5.3_rc20220113.ebuild
+++ b/dev-python/cadquery-pywrap/cadquery-pywrap-7.5.3_rc20220113.ebuild
@@ -29,7 +29,7 @@ SLOT="0"
RDEPEND="
dev-python/click[${PYTHON_USEDEP}]
dev-python/logzero[${PYTHON_USEDEP}]
- dev-python/path-py[${PYTHON_USEDEP}]
+ dev-python/path[${PYTHON_USEDEP}]
dev-python/clang-python[${PYTHON_USEDEP}]
dev-python/cymbal[${PYTHON_USEDEP}]
dev-python/toml[${PYTHON_USEDEP}]
diff --git a/dev-python/cadquery/cadquery-2.2_rc20210804.ebuild b/dev-python/cadquery/cadquery-2.2_rc20210804.ebuild
index 3eafde559..e31f8d37c 100644
--- a/dev-python/cadquery/cadquery-2.2_rc20210804.ebuild
+++ b/dev-python/cadquery/cadquery-2.2_rc20210804.ebuild
@@ -31,7 +31,7 @@ BDEPEND="
$(python_gen_cond_dep '
dev-python/pytest[${PYTHON_USEDEP}]
dev-python/docutils[${PYTHON_USEDEP}]
- dev-python/path-py[${PYTHON_USEDEP}]
+ dev-python/path[${PYTHON_USEDEP}]
')
)
"
diff --git a/dev-python/cadquery/cadquery-2.2_rc20220506.ebuild b/dev-python/cadquery/cadquery-2.2_rc20220506.ebuild
index 26aa07b6d..a40a5c69a 100644
--- a/dev-python/cadquery/cadquery-2.2_rc20220506.ebuild
+++ b/dev-python/cadquery/cadquery-2.2_rc20220506.ebuild
@@ -31,7 +31,7 @@ BDEPEND="
test? (
$(python_gen_cond_dep '
dev-python/docutils[${PYTHON_USEDEP}]
- dev-python/path-py[${PYTHON_USEDEP}]
+ dev-python/path[${PYTHON_USEDEP}]
')
)
"
diff --git a/dev-python/dandi-schema/Manifest b/dev-python/dandi-schema/Manifest
index cb098f9b4..041d6cab7 100644
--- a/dev-python/dandi-schema/Manifest
+++ b/dev-python/dandi-schema/Manifest
@@ -2,3 +2,4 @@ DIST dandi-schema-0.4.3.tar.gz 51831 BLAKE2B 177a0ec148c1e823abdaa2b7e60d971c17a
DIST dandi-schema-0.5.1.tar.gz 55945 BLAKE2B b9af1b34c7e4ce07b2fdac1d74dd746684f9e5e4667890931bbf2cb2421a01690eaed5114f2d077c46304f1298475739acef5a256430cac470ceb9fc1884e182 SHA512 699e9fb6626dd87576f29b908cd259748a6ebbd94391d8c5ba821273496323a3b4b9e88ee337809abc65c9aaeadca8aee4d986c173b055914c4ca67ddfd88804
DIST dandi-schema-0.5.3.tar.gz 56222 BLAKE2B 3b23c93330f621a5a050c9e5b597fd8b9046a66465c16f26b5216d443547a0c8d07a491213cde90c411f5cda6f6c6b2a23d1c0f4b2d7a1e7336c55e5768d3338 SHA512 bf0d434ac6d8e5584ba9f31dd179e5402c13c89257bc87c2d34b03483e9ab85d9b616391a40c64ad853e6774f950ecc58d3f3fde29305586d5faa387dc5b3e80
DIST dandi-schema-0.6.0.tar.gz 57102 BLAKE2B eb4ef024ef87e234c4c9e741fa2e70920aa13e0ab661aa179553b81ae8d28853274102b49532fc542368ebb43be9779a96434134e35b7c3380609511bed5ce8c SHA512 e2846e3e573264b83e95d92e7d2f2e4177721f32228beb63c701280312611bc668d1042248f4c65ed8f07b8c80991c398a4d29969513f235b4d37369cae0ddcd
+DIST dandi-schema-0.7.1.tar.gz 57312 BLAKE2B 5aa77c4c98633f82511a964f0b202b44acdb63e162cff62785f44fab64fdf97c04f10b10b3c1329ea7176d7ee1b12eeabd64d467d9646550b1db14b2fcc36a2b SHA512 04e0bf6caa9183cdac021430869be884ba8db207e7056a145ecac11858e9ecf051212cee10f5b4d501ca513838edc112dde014e256ab2256729c810d0c2c6cdf
diff --git a/dev-python/dandi-schema/dandi-schema-0.7.1.ebuild b/dev-python/dandi-schema/dandi-schema-0.7.1.ebuild
new file mode 100644
index 000000000..19a906634
--- /dev/null
+++ b/dev-python/dandi-schema/dandi-schema-0.7.1.ebuild
@@ -0,0 +1,42 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DISTUTILS_USE_PEP517=setuptools
+PYTHON_COMPAT=( python3_{8..10} )
+
+inherit distutils-r1
+
+DESCRIPTION="Schemata for DANDI archive project"
+HOMEPAGE="https://github.com/dandi/dandi-schema"
+SRC_URI="https://github.com/dandi/dandi-schema/archive/refs/tags/${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="Apache-2.0"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+RDEPEND="
+ dev-python/wheel[${PYTHON_USEDEP}]
+ dev-python/jsonschema[${PYTHON_USEDEP}]
+ dev-python/pydantic[${PYTHON_USEDEP}]
+ dev-python/python-email-validator[${PYTHON_USEDEP}]
+ dev-python/requests[${PYTHON_USEDEP}]
+"
+
+PATCHES=(
+ "${FILESDIR}/${PN}-0.3.4-coverage.patch"
+)
+
+src_configure() {
+ echo "__version__ = '${PV}'" >> dandischema/_version.py
+}
+
+distutils_enable_tests pytest
+
+python_test() {
+ export DANDI_TESTS_NONETWORK=1
+ pushd dandischema || die
+ epytest tests
+ popd
+}
diff --git a/dev-python/delegator/delegator-0.1.1.ebuild b/dev-python/delegator/delegator-0.1.1.ebuild
index f56de2340..1ae0a527a 100644
--- a/dev-python/delegator/delegator-0.1.1.ebuild
+++ b/dev-python/delegator/delegator-0.1.1.ebuild
@@ -1,9 +1,9 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=7
+EAPI=8
-PYTHON_COMPAT=( python3_{7..9} )
+PYTHON_COMPAT=( python3_{8..10} )
inherit distutils-r1
diff --git a/dev-python/fslpy/fslpy-3.8.1.ebuild b/dev-python/fslpy/fslpy-3.8.1.ebuild
index 5bff5ed60..f28e7283e 100644
--- a/dev-python/fslpy/fslpy-3.8.1.ebuild
+++ b/dev-python/fslpy/fslpy-3.8.1.ebuild
@@ -3,7 +3,7 @@
EAPI=8
-PYTHON_COMPAT=( python3_{8..9} )
+PYTHON_COMPAT=( python3_{8..10} )
inherit distutils-r1 virtualx
@@ -34,6 +34,10 @@ PATCHES=(
distutils_enable_tests pytest
distutils_enable_sphinx doc dev-python/sphinx_rtd_theme
+src_test() {
+ virtx distutils-r1_src_test
+}
+
python_test() {
- virtx epytest --niters=50 -m "not (dicomtest or longtest or fsltest)"
+ epytest --niters=50 -m "not (dicomtest or longtest or fsltest)" || die "Tests failed with ${EPYTHON}"
}
diff --git a/dev-python/grabbit/grabbit-0.2.6.ebuild b/dev-python/grabbit/grabbit-0.2.6.ebuild
index 045f26d06..93e08ccf4 100644
--- a/dev-python/grabbit/grabbit-0.2.6.ebuild
+++ b/dev-python/grabbit/grabbit-0.2.6.ebuild
@@ -1,9 +1,9 @@
-# Copyright 1999-2020 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=7
+EAPI=8
-PYTHON_COMPAT=( python3_{7..9} )
+PYTHON_COMPAT=( python3_{8..10} )
inherit distutils-r1
diff --git a/dev-python/hdf5storage/Manifest b/dev-python/hdf5storage/Manifest
index b9aa0d469..dee5fa709 100644
--- a/dev-python/hdf5storage/Manifest
+++ b/dev-python/hdf5storage/Manifest
@@ -1 +1,2 @@
-DIST hdf5storage-0.1.15_p1.tar.gz 117372 BLAKE2B 56839673864fbb41ea96b535293dc35cff99635f2d8f37b4b57c184a62a4a957a12f99387f43f53061ce5b49c8dcbc6816db6eaa43d0f98ac7f54d530675b487 SHA512 38b71b5e061da3ea259decefeb0f0dd4812f92839dd06b24b6cdf11a225b8dd7446e37972987f9be914448fd05ca780ca0239d0275464e64775a867420c3c819
+DIST hdf5storage-0.1.17.tar.gz 91008 BLAKE2B 7956573a1b9531146f5e5509788a9894317e77afcc4c12faf9ba197744bc4a1e2cc28e063bb51f94bcebbc26d876edefdc2f113dbf4ad26d559d77cefcf8cc1d SHA512 5a0781ac93bfc486025022c04aa6d7253910194b2d4b5e00d2a396a5865e1eccb6bde1565c66dde5a9798d16441461c539586a7a67f039ca960bce1cdcb8bbd9
+DIST hdf5storage-0.1.18.tar.gz 91599 BLAKE2B 822dde832ab5abb0def1d6b478e6b02cbe5597b009a3be9c76f1d0583f44aa28bfc0cedb10eadac6619daabc08d4642815779e1380e69d601e8e55500cba595e SHA512 5c8df3768b3fca0cd600acff65b96faf29e517e2375ed2dd7c1a516f30929ec21c70a6c9dc8b17271d5643ea94ffa01e8ed9963a2fa161e2af14aab57851b59e
diff --git a/dev-python/hdf5storage/hdf5storage-0.1.15_p1.ebuild b/dev-python/hdf5storage/hdf5storage-0.1.17.ebuild
index 8a7b76420..22f9151e0 100644
--- a/dev-python/hdf5storage/hdf5storage-0.1.15_p1.ebuild
+++ b/dev-python/hdf5storage/hdf5storage-0.1.17.ebuild
@@ -1,23 +1,16 @@
-# Copyright 1999-2020 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=7
-PYTHON_COMPAT=( python3_{7..9} )
+EAPI=8
+PYTHON_COMPAT=( python3_{8..10} )
inherit distutils-r1
DESCRIPTION="Read/write Python types to/from HDF5 files, including MATLAB v7.3 MAT files"
HOMEPAGE="https://github.com/frejanordsiek/hdf5storage"
-if [[ ${PV} == 9999 ]]; then
- inherit git-r3
- EGIT_REPO_URI="https://github.com/frejanordsiek/hdf5storage"
-else
- COMMIT=09dfc5fb3a6a3f9c32c2479a896c7f14d3c8d830
- SRC_URI="https://github.com/frejanordsiek/hdf5storage/archive/${COMMIT}.tar.gz -> ${P}.tar.gz"
- S="${WORKDIR}"/${PN}-${COMMIT}
- KEYWORDS="~amd64"
-fi
+SRC_URI="https://github.com/frejanordsiek/hdf5storage/archive/refs/tags/${PV}.tar.gz -> ${P}.tar.gz"
+KEYWORDS="~amd64 ~x86"
LICENSE="BSD"
SLOT="0"
diff --git a/dev-python/hdf5storage/hdf5storage-0.1.18.ebuild b/dev-python/hdf5storage/hdf5storage-0.1.18.ebuild
new file mode 100644
index 000000000..22f9151e0
--- /dev/null
+++ b/dev-python/hdf5storage/hdf5storage-0.1.18.ebuild
@@ -0,0 +1,24 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+PYTHON_COMPAT=( python3_{8..10} )
+
+inherit distutils-r1
+
+DESCRIPTION="Read/write Python types to/from HDF5 files, including MATLAB v7.3 MAT files"
+HOMEPAGE="https://github.com/frejanordsiek/hdf5storage"
+
+SRC_URI="https://github.com/frejanordsiek/hdf5storage/archive/refs/tags/${PV}.tar.gz -> ${P}.tar.gz"
+KEYWORDS="~amd64 ~x86"
+
+LICENSE="BSD"
+SLOT="0"
+
+RDEPEND="
+ dev-python/numpy[${PYTHON_USEDEP}]
+ dev-python/h5py[${PYTHON_USEDEP}]
+"
+DEPEND="${RDEPEND}"
+
+distutils_enable_tests nose
diff --git a/dev-python/hdf5storage/hdf5storage-9999.ebuild b/dev-python/hdf5storage/hdf5storage-9999.ebuild
index 8a7b76420..3a6391eb0 100644
--- a/dev-python/hdf5storage/hdf5storage-9999.ebuild
+++ b/dev-python/hdf5storage/hdf5storage-9999.ebuild
@@ -1,8 +1,8 @@
-# Copyright 1999-2020 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=7
-PYTHON_COMPAT=( python3_{7..9} )
+EAPI=8
+PYTHON_COMPAT=( python3_{8..10} )
inherit distutils-r1
diff --git a/dev-python/hdmf/Manifest b/dev-python/hdmf/Manifest
index 67e1f4b6c..683f37a69 100644
--- a/dev-python/hdmf/Manifest
+++ b/dev-python/hdmf/Manifest
@@ -1 +1,2 @@
DIST hdmf-3.1.1.tar.gz 292419 BLAKE2B eed1b1c282f022f7e1bd3af63c3078563a74895bf177244841ee0cabd3ab391e2d7a48c9a111a909f5982bf1a1c9b44f1b82fd710f9729681bcada396d3c3d7b SHA512 41776932b1150126a162e9f87072d6626a28bb3f0e05f75337e4f6529c27005ca9db932fdff0c45bb16cbebf68388c7cbf575bbd17950c29c300702a37afacf0
+DIST hdmf-3.3.2.tar.gz 312991 BLAKE2B 6765f1543e73746fd07279104d70ccf069795140781375427b14586d4ab0d433f7769051436618791db7d2eb09cf4515d983c0232c76aa8a67bacd65b9e9bc2a SHA512 b769216b048df8f9fb220c38053d2f1c7976b0ad9cfcac5f36656fcf5cabfab25f910c9a1fec7fbb20ad919bf4c791751e92e485e02b3e26314e7f396e45549b
diff --git a/dev-python/hdmf/files/hdmf-3.3.2-versions.patch b/dev-python/hdmf/files/hdmf-3.3.2-versions.patch
new file mode 100644
index 000000000..aaf62e115
--- /dev/null
+++ b/dev-python/hdmf/files/hdmf-3.3.2-versions.patch
@@ -0,0 +1,20 @@
+--- a/setup.py 2022-01-31 02:48:24.645837186 -0500
++++ b/setup.py 2022-01-31 02:49:55.066949247 -0500
+@@ -18,12 +18,12 @@
+ schema_dir = 'common/hdmf-common-schema/common'
+
+ reqs = [
+- 'h5py>=2.10,<4',
+- 'jsonschema>=2.6.0,<5',
+- 'numpy>=1.16,<1.23',
+- 'pandas>=1.0.5,<2',
+- 'ruamel.yaml>=0.16,<1',
+- 'scipy>=1.1,<2',
++ 'h5py',
++ 'jsonschema',
++ 'numpy',
++ 'pandas',
++ 'ruamel.yaml',
++ 'scipy',
+ 'setuptools',
+ ]
diff --git a/dev-python/hdmf/hdmf-3.1.1-r1.ebuild b/dev-python/hdmf/hdmf-3.1.1-r1.ebuild
index 76d40c95f..866b5e553 100644
--- a/dev-python/hdmf/hdmf-3.1.1-r1.ebuild
+++ b/dev-python/hdmf/hdmf-3.1.1-r1.ebuild
@@ -27,6 +27,12 @@ BDEPEND=""
distutils_enable_tests pytest
+# Known to upstream:
+# https://github.com/hdmf-dev/hdmf/issues/687
+EPYTEST_DESELECT=(
+ tests/unit/utils_test/test_labelleddict.py::TestLabelledDict::test_set_key_attr
+)
+
PATCHES=(
- "${FILESDIR}/${PN}-3.1.1-versions.patch"
+ "${FILESDIR}/${P}-versions.patch"
)
diff --git a/dev-python/hdmf/hdmf-3.3.2-r1.ebuild b/dev-python/hdmf/hdmf-3.3.2-r1.ebuild
new file mode 100644
index 000000000..1bec3913c
--- /dev/null
+++ b/dev-python/hdmf/hdmf-3.3.2-r1.ebuild
@@ -0,0 +1,32 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DISTUTILS_USE_PEP517=setuptools
+PYTHON_COMPAT=( python3_{8..10} )
+inherit distutils-r1
+
+DESCRIPTION="The Hierarchical Data Modeling Framework"
+HOMEPAGE="https://github.com/hdmf-dev/hdmf"
+SRC_URI="https://github.com/hdmf-dev/hdmf/releases/download/${PV}/${P}.tar.gz"
+
+SLOT="0"
+LICENSE="BSD"
+KEYWORDS="~amd64 ~x86"
+
+RDEPEND="
+ dev-python/h5py[${PYTHON_USEDEP}]
+ dev-python/jsonschema[${PYTHON_USEDEP}]
+ dev-python/numpy[${PYTHON_USEDEP}]
+ dev-python/pandas[${PYTHON_USEDEP}]
+ dev-python/ruamel-yaml[${PYTHON_USEDEP}]
+ dev-python/scipy[${PYTHON_USEDEP}]
+ "
+BDEPEND=""
+
+PATCHES=(
+ "${FILESDIR}/${P}-versions.patch"
+)
+
+distutils_enable_tests pytest
diff --git a/dev-python/hdmf/metadata.xml b/dev-python/hdmf/metadata.xml
index 82da7c426..ac3f7a6cb 100644
--- a/dev-python/hdmf/metadata.xml
+++ b/dev-python/hdmf/metadata.xml
@@ -15,4 +15,8 @@
data models, reading and writing data to different storage backends,
and representing data with Python object.
</longdescription>
+ <upstream>
+ <remote-id type="github">hdmf-dev/hdmf</remote-id>
+ <remote-id type="pypi">hdmf</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/dev-python/keyrings_alt/Manifest b/dev-python/keyrings_alt/Manifest
deleted file mode 100644
index ec1eff845..000000000
--- a/dev-python/keyrings_alt/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST keyrings.alt-4.1.0.tar.gz 28581 BLAKE2B bb4c8c5faa130c4cfb377985ee8692bcce802f0e03d1121281a8d73ac1c4ced4c6f913e6ab9ff39b1b7d37ff41b37905910d3a02e91fa4160fbe109aa16c2ae0 SHA512 6c2a7637bc73971081b95851898dcc2fafe5fd155333cee7032983b16f668d8db941c972747c7c4a2e20b4d6a5fe52d8ad96448f8ae7d372cd1c32e2a0d344f9
diff --git a/dev-python/keyrings_alt/files/keyrings_alt-4.1.0-pycryptodome.patch b/dev-python/keyrings_alt/files/keyrings_alt-4.1.0-pycryptodome.patch
deleted file mode 100644
index e0ca3a012..000000000
--- a/dev-python/keyrings_alt/files/keyrings_alt-4.1.0-pycryptodome.patch
+++ /dev/null
@@ -1,90 +0,0 @@
-diff --git a/keyrings/alt/file.py b/keyrings/alt/file.py
-index 37c837f..866e8d0 100644
---- a/keyrings/alt/file.py
-+++ b/keyrings/alt/file.py
-@@ -44,8 +44,12 @@ class Encrypted:
- """
- Create the cipher object to encrypt or decrypt a payload.
- """
-- from Cryptodome.Protocol.KDF import PBKDF2
-- from Cryptodome.Cipher import AES
-+ try:
-+ from Cryptodome.Protocol.KDF import PBKDF2
-+ from Cryptodome.Cipher import AES
-+ except ImportError:
-+ from Crypto.Protocol.KDF import PBKDF2
-+ from Crypto.Cipher import AES
-
- pw = PBKDF2(password, salt, dkLen=self.block_size)
- return AES.new(pw[: self.block_size], AES.MODE_CFB, IV)
-@@ -79,7 +83,12 @@ class EncryptedKeyring(Encrypted, Keyring):
- __import__('Cryptodome.Protocol.KDF')
- __import__('Cryptodome.Random')
- except ImportError: # pragma: no cover
-- raise RuntimeError("pycryptodomex required")
-+ try:
-+ __import__('Crypto.Cipher.AES')
-+ __import__('Crypto.Protocol.KDF')
-+ __import__('Crypto.Random')
-+ except ImportError:
-+ raise RuntimeError("pycryptodomex or pycryptodome required")
- if not json: # pragma: no cover
- raise RuntimeError("JSON implementation such as simplejson required.")
- return 0.6
-@@ -190,10 +199,16 @@ class EncryptedKeyring(Encrypted, Keyring):
-
- def encrypt(self, password, assoc=None):
- # encrypt password, ignore associated data
-- from Cryptodome.Random import get_random_bytes
-+ try:
-+ from Cryptodome.Random import get_random_bytes
-+ except ImportError:
-+ from Crypto.Random import get_random_bytes
-
- salt = get_random_bytes(self.block_size)
-- from Cryptodome.Cipher import AES
-+ try:
-+ from Cryptodome.Cipher import AES
-+ except ImportError:
-+ from Crypto.Cipher import AES
-
- IV = get_random_bytes(AES.block_size)
- cipher = self._create_cipher(self.keyring_key, salt, IV)
-diff --git a/tests/test_crypto.py b/tests/test_crypto.py
-index cfc782a..7396023 100644
---- a/tests/test_crypto.py
-+++ b/tests/test_crypto.py
-@@ -14,7 +14,12 @@ def is_crypto_supported():
- __import__('Cryptodome.Protocol.KDF')
- __import__('Cryptodome.Random')
- except ImportError:
-- return False
-+ try:
-+ __import__('Crypto.Cipher.AES')
-+ __import__('Crypto.Protocol.KDF')
-+ __import__('Crypto.Random')
-+ except ImportError:
-+ return False
- return True
-
-
-diff --git a/tests/test_file.py b/tests/test_file.py
-index 62192da..3f813f0 100644
---- a/tests/test_file.py
-+++ b/tests/test_file.py
-@@ -157,7 +157,14 @@ class FileKeyringTests(BackendBasicTests):
- class TestEncryptedFileKeyring(FileKeyringTests):
- @pytest.fixture(autouse=True)
- def crypt_fixture(self, monkeypatch):
-- pytest.importorskip('Cryptodome')
-+ try:
-+ import Cryptodome
-+ except ImportError:
-+ try:
-+ import Crypto
-+ except ImportError:
-+ pytest.skip("Neither pycryptodome nor pycryptodomex are available",
-+ allow_module_level=True)
- fake_getpass = mock.Mock(return_value='abcdef')
- monkeypatch.setattr(getpass, 'getpass', fake_getpass)
-
diff --git a/dev-python/keyrings_alt/keyrings_alt-4.1.0-r1.ebuild b/dev-python/keyrings_alt/keyrings_alt-4.1.0-r1.ebuild
deleted file mode 100644
index 290c2f434..000000000
--- a/dev-python/keyrings_alt/keyrings_alt-4.1.0-r1.ebuild
+++ /dev/null
@@ -1,31 +0,0 @@
-# Copyright 1999-2022 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-DISTUTILS_USE_PEP517=setuptools
-PYTHON_COMPAT=( pypy3 python3_{8..10} )
-
-inherit distutils-r1
-
-MY_PN="keyrings.alt"
-MY_P="${MY_PN}-${PV}"
-
-DESCRIPTION="Alternate keyring backend implementations used with dev-python/keyring"
-HOMEPAGE="https://github.com/jaraco/keyrings.alt/"
-SRC_URI="mirror://pypi/${MY_P:0:1}/${MY_PN}/${MY_P}.tar.gz"
-
-SLOT="0"
-LICENSE="MIT"
-KEYWORDS="~alpha ~amd64 ~arm ~arm64 ~x86"
-
-DEPEND=""
-
-S="${WORKDIR}/${MY_P}"
-
-# Patch sumbitted upstream:
-# https://github.com/jaraco/keyrings.alt/pull/46
-PATCHES=( "${FILESDIR}/${P}-pycryptodome.patch" )
-
-distutils_enable_tests pytest
-distutils_enable_sphinx docs
diff --git a/dev-python/keyrings_alt/metadata.xml b/dev-python/keyrings_alt/metadata.xml
deleted file mode 100644
index 59728c331..000000000
--- a/dev-python/keyrings_alt/metadata.xml
+++ /dev/null
@@ -1,24 +0,0 @@
-<?xml version='1.0' encoding='UTF-8'?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <maintainer type="person">
- <email>gentoo@chymera.eu</email>
- <name>Horea Christian</name>
- </maintainer>
- <maintainer type="project">
- <email>sci@gentoo.org</email>
- <name>Gentoo Science Project</name>
- </maintainer>
- <longdescription lang="en">
- This package distributes backends extracted from the main Python keyring
- project to make them available for those who wish to employ them, but
- are discouraged for general production use. Include this module and use
- its backends at your own risk.
- For example, the PlaintextKeyring stores passwords in plain text on the
- file system, defeating the intended purpose of this library to encourage
- best practices for security.
- </longdescription>
- <upstream>
- <remote-id type="github">jaraco/keyrings.alt</remote-id>
- </upstream>
-</pkgmetadata>
diff --git a/dev-python/llvmlite/Manifest b/dev-python/llvmlite/Manifest
index ea7fa3ead..1749985b0 100644
--- a/dev-python/llvmlite/Manifest
+++ b/dev-python/llvmlite/Manifest
@@ -1,2 +1 @@
-DIST llvmlite-0.37.0.gh.tar.gz 223602 BLAKE2B 74f975d5ac1782528f60f1c0d5c6230a02953e0d494d8323e4caa6651f642ad791ad51df44f6593da41edc5c34bd883f144e95b16f9b8962393d16de013fdbc5 SHA512 665f486fd38c9cc4ee91b15fc75f33451ada6391fc9f1b371091ece844693e0cd8e23766400bf76d9879e8f10f53f4e21f8bb19f3ff1e01c4a95ce9004b0884a
-DIST llvmlite-0.38.0.gh.tar.gz 230044 BLAKE2B b027f34a6ba4c6d8a4fe8963501a49b1f87cc86976c131c94c597383ab47aef1faf6bb05f27f148f03b2d6673e12b04fdfbdab20658de32b18c257bb1cd16fee SHA512 014e2ba08a451ff8bb76ea4b25d2d6605bc048cae560ad367a3bb3afd13421aaf151862116e73e7606d800638d2a2df713cc0e187a6acc483b80df1290c81743
+DIST llvmlite-0.39.0.gh.tar.gz 237009 BLAKE2B 41e485c636d285d039cd559c6386f79d05d51c266b31e24c68a30a921e9131d422e5782befdbdac7407b61fd44cab4b14863fdefa1c76ced235dd89eb0328110 SHA512 3493afc14c08b06bfb26230409d678b9a72d3957e412a4a6a6367aea0bc743fc46191ba050aa70e403424567038ab9fc2721c839df8035e4511dbf9ee4caddfa
diff --git a/dev-python/llvmlite/files/llvmlite-0.37.0-llvm12.patch b/dev-python/llvmlite/files/llvmlite-0.37.0-llvm12.patch
deleted file mode 100644
index ed104ab99..000000000
--- a/dev-python/llvmlite/files/llvmlite-0.37.0-llvm12.patch
+++ /dev/null
@@ -1,91 +0,0 @@
-From 1d928ebcd59b23b5050234a2bf71f9be7f5f6bd1 Mon Sep 17 00:00:00 2001
-From: Richard Barnes <rbarnes@umn.edu>
-Date: Wed, 1 Dec 2021 10:29:08 -0700
-Subject: [PATCH] Enable LLVM-12 and LLVM-13
-
----
- ffi/build.py | 5 ++---
- ffi/targets.cpp | 2 ++
- llvmlite/tests/test_binding.py | 19 ++++++++++++++++---
- 3 files changed, 20 insertions(+), 6 deletions(-)
-
-diff --git a/ffi/build.py b/ffi/build.py
-index 6408bf5f..95e33c64 100755
---- a/ffi/build.py
-+++ b/ffi/build.py
-@@ -162,9 +162,8 @@ def main_posix(kind, library_ext):
- print(msg)
- print(warning + '\n')
- else:
--
-- if not out.startswith('11'):
-- msg = ("Building llvmlite requires LLVM 11.x.x, got "
-+ if not (out.startswith('11') or out.startswith('12') or out.startswith('13')):
-+ msg = ("Building llvmlite requires LLVM 11-13.x.x, got "
- "{!r}. Be sure to set LLVM_CONFIG to the right executable "
- "path.\nRead the documentation at "
- "http://llvmlite.pydata.org/ for more information about "
-diff --git a/ffi/targets.cpp b/ffi/targets.cpp
-index 1ce472c2..4ba33e79 100644
---- a/ffi/targets.cpp
-+++ b/ffi/targets.cpp
-@@ -233,6 +233,8 @@ LLVMPY_CreateTargetMachine(LLVMTargetRef T,
- rm = Reloc::DynamicNoPIC;
-
- TargetOptions opt;
-+#if LLVM_VERSION_MAJOR < 12
- opt.PrintMachineCode = PrintMC;
-+#endif
-
- bool jit = JIT;
-diff --git a/llvmlite/tests/test_binding.py b/llvmlite/tests/test_binding.py
-index 80495787..fee2372a 100644
---- a/llvmlite/tests/test_binding.py
-+++ b/llvmlite/tests/test_binding.py
-@@ -18,6 +18,16 @@
- from llvmlite.tests import TestCase
-
-
-+def clean_string_whitespace(x: str) -> str:
-+ # Remove trailing whitespace from the end of each line
-+ x = re.sub(r"\s+$", "", x, flags=re.MULTILINE)
-+ # Remove intermediate blank lines
-+ x = re.sub(r"\n\s*\n", r"\n", x, flags=re.MULTILINE)
-+ # Remove extraneous whitespace from the beginning and end of the string
-+ x = x.strip()
-+ return x
-+
-+
- # arvm7l needs extra ABI symbols to link successfully
- if platform.machine() == 'armv7l':
- llvm.load_library_permanently('libgcc_s.so.1')
-@@ -158,7 +168,7 @@ def no_de_locale():
- target triple = "unknown-unknown-unknown"
- target datalayout = ""
-
--define i32 @"foo"()
-+define i32 @"foo"()
- {
- "<>!*''#":
- ret i32 12345
-@@ -424,7 +434,10 @@ def test_nonalphanum_block_name(self):
- bd = ir.IRBuilder(fn.append_basic_block(name="<>!*''#"))
- bd.ret(ir.Constant(ir.IntType(32), 12345))
- asm = str(mod)
-- self.assertEqual(asm, asm_nonalphanum_blocklabel)
-+ self.assertEqual(
-+ clean_string_whitespace(asm),
-+ clean_string_whitespace(asm_nonalphanum_blocklabel)
-+ )
-
- def test_global_context(self):
- gcontext1 = llvm.context.get_global_context()
-@@ -509,7 +522,7 @@ def test_set_option(self):
- def test_version(self):
- major, minor, patch = llvm.llvm_version_info
- # one of these can be valid
-- valid = [(11,)]
-+ valid = [(11,), (12,), (13,)]
- self.assertIn((major,), valid)
- self.assertIn(patch, range(10))
-
diff --git a/dev-python/llvmlite/files/llvmlite-0.38.0-llvm12.patch b/dev-python/llvmlite/files/llvmlite-0.39.0-llvm12.patch
index 6630652c2..17eb80e87 100644
--- a/dev-python/llvmlite/files/llvmlite-0.38.0-llvm12.patch
+++ b/dev-python/llvmlite/files/llvmlite-0.39.0-llvm12.patch
@@ -9,11 +9,11 @@ Subject: [PATCH] Enable LLVM-12 and LLVM-13
llvmlite/tests/test_binding.py | 19 ++++++++++++++++---
3 files changed, 20 insertions(+), 6 deletions(-)
-diff --git a/ffi/build.py b/ffi/build.py
-index 6408bf5f..95e33c64 100755
---- a/ffi/build.py
-+++ b/ffi/build.py
-@@ -162,9 +162,8 @@ def main_posix(kind, library_ext):
+Index: llvmlite-0.39.0/ffi/build.py
+===================================================================
+--- llvmlite-0.39.0.orig/ffi/build.py
++++ llvmlite-0.39.0/ffi/build.py
+@@ -163,9 +163,8 @@ def main_posix(kind, library_ext):
print(msg)
print(warning + '\n')
else:
@@ -25,11 +25,11 @@ index 6408bf5f..95e33c64 100755
"{!r}. Be sure to set LLVM_CONFIG to the right executable "
"path.\nRead the documentation at "
"http://llvmlite.pydata.org/ for more information about "
-diff --git a/ffi/targets.cpp b/ffi/targets.cpp
-index 1ce472c2..4ba33e79 100644
---- a/ffi/targets.cpp
-+++ b/ffi/targets.cpp
-@@ -233,7 +233,9 @@ LLVMPY_CreateTargetMachine(LLVMTargetRef T,
+Index: llvmlite-0.39.0/ffi/targets.cpp
+===================================================================
+--- llvmlite-0.39.0.orig/ffi/targets.cpp
++++ llvmlite-0.39.0/ffi/targets.cpp
+@@ -204,7 +204,9 @@ LLVMPY_CreateTargetMachine(LLVMTargetRef
rm = Reloc::DynamicNoPIC;
TargetOptions opt;
@@ -39,11 +39,11 @@ index 1ce472c2..4ba33e79 100644
opt.MCOptions.ABIName = ABIName;
bool jit = JIT;
-diff --git a/llvmlite/tests/test_binding.py b/llvmlite/tests/test_binding.py
-index 80495787..fee2372a 100644
---- a/llvmlite/tests/test_binding.py
-+++ b/llvmlite/tests/test_binding.py
-@@ -18,6 +18,16 @@
+Index: llvmlite-0.39.0/llvmlite/tests/test_binding.py
+===================================================================
+--- llvmlite-0.39.0.orig/llvmlite/tests/test_binding.py
++++ llvmlite-0.39.0/llvmlite/tests/test_binding.py
+@@ -18,6 +18,16 @@ from llvmlite.binding import ffi
from llvmlite.tests import TestCase
@@ -60,16 +60,7 @@ index 80495787..fee2372a 100644
# arvm7l needs extra ABI symbols to link successfully
if platform.machine() == 'armv7l':
llvm.load_library_permanently('libgcc_s.so.1')
-@@ -158,7 +168,7 @@ def no_de_locale():
- target triple = "unknown-unknown-unknown"
- target datalayout = ""
-
--define i32 @"foo"()
-+define i32 @"foo"()
- {
- "<>!*''#":
- ret i32 12345
-@@ -424,7 +434,10 @@ def test_nonalphanum_block_name(self):
+@@ -555,7 +565,10 @@ class TestMisc(BaseTest):
bd = ir.IRBuilder(fn.append_basic_block(name="<>!*''#"))
bd.ret(ir.Constant(ir.IntType(32), 12345))
asm = str(mod)
@@ -81,7 +72,7 @@ index 80495787..fee2372a 100644
def test_global_context(self):
gcontext1 = llvm.context.get_global_context()
-@@ -509,7 +522,7 @@ def test_set_option(self):
+@@ -640,7 +653,7 @@ class TestMisc(BaseTest):
def test_version(self):
major, minor, patch = llvm.llvm_version_info
# one of these can be valid
@@ -90,3 +81,17 @@ index 80495787..fee2372a 100644
self.assertIn((major,), valid)
self.assertIn(patch, range(10))
+Index: llvmlite-0.39.0/ffi/passmanagers.cpp
+===================================================================
+--- llvmlite-0.39.0.orig/ffi/passmanagers.cpp
++++ llvmlite-0.39.0/ffi/passmanagers.cpp
+@@ -17,9 +17,6 @@
+ #include "llvm-c/Transforms/IPO.h"
+ #include "llvm-c/Transforms/Scalar.h"
+ #include "llvm/IR/LegacyPassManager.h"
+-#if LLVM_VERSION_MAJOR > 11
+-#include "llvm/IR/RemarkStreamer.h"
+-#endif
+ #include "llvm/IR/LLVMRemarkStreamer.h"
+ #include "llvm/Remarks/RemarkStreamer.h"
+ #include "llvm/Transforms/IPO.h"
diff --git a/dev-python/llvmlite/llvmlite-0.38.0-r1.ebuild b/dev-python/llvmlite/llvmlite-0.38.0-r1.ebuild
deleted file mode 100644
index 607c1bb0b..000000000
--- a/dev-python/llvmlite/llvmlite-0.38.0-r1.ebuild
+++ /dev/null
@@ -1,62 +0,0 @@
-# Copyright 1999-2022 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-PYTHON_COMPAT=( python3_{8..10} )
-inherit distutils-r1 llvm
-
-DESCRIPTION="Python wrapper around the llvm C++ library"
-HOMEPAGE="https://llvmlite.pydata.org/"
-SRC_URI="https://github.com/numba/llvmlite/archive/v${PV/_/}.tar.gz -> ${P/_/}.gh.tar.gz"
-S="${WORKDIR}/${P/_/}"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS="~amd64 ~arm ~arm64 ~x86"
-IUSE="examples"
-
-LLVM_MAX_SLOT=12
-
-RDEPEND="
- sys-devel/llvm:${LLVM_MAX_SLOT}
- sys-libs/zlib:0=
-"
-DEPEND="${RDEPEND}"
-
-PATCHES=( "${FILESDIR}/${P}-llvm12.patch" )
-
-src_prepare() {
- sed -i -e '/max_python/s:3\.10:3.11:' setup.py || die
- distutils-r1_src_prepare
-}
-
-python_configure_all() {
- # upstream's build system is just horrible, and they ignored the PR
- # fixing it, so let's build the shared lib properly using implicit
- # make rules
-
- export LDLIBS=$(llvm-config --libs all)
- export CXXFLAGS="$(llvm-config --cxxflags) -fPIC ${CXXFLAGS}"
- export LDFLAGS="$(llvm-config --ldflags) ${LDFLAGS}"
-
- local files=( ffi/*.cpp )
- emake -f - <<EOF
-ffi/libllvmlite.so: ${files[*]/.cpp/.o}
- \$(CXX) -shared \$(CXXFLAGS) \$(LDFLAGS) -o \$@ \$^ \$(LDLIBS)
-EOF
-
- export LLVMLITE_SKIP_LLVM_VERSION_CHECK=1
-}
-
-python_test() {
- "${EPYTHON}" runtests.py -v || die "Tests failed under ${EPYTHON}"
-}
-
-python_install_all() {
- distutils-r1_python_install_all
- if use examples; then
- dodoc -r examples
- docompress -x /usr/share/doc/${PF}/examples
- fi
-}
diff --git a/dev-python/llvmlite/llvmlite-0.37.0-r1.ebuild b/dev-python/llvmlite/llvmlite-0.39.0.ebuild
index 607c1bb0b..a2c3a6750 100644
--- a/dev-python/llvmlite/llvmlite-0.37.0-r1.ebuild
+++ b/dev-python/llvmlite/llvmlite-0.39.0.ebuild
@@ -1,7 +1,7 @@
# Copyright 1999-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=7
+EAPI=8
PYTHON_COMPAT=( python3_{8..10} )
inherit distutils-r1 llvm
@@ -16,7 +16,7 @@ SLOT="0"
KEYWORDS="~amd64 ~arm ~arm64 ~x86"
IUSE="examples"
-LLVM_MAX_SLOT=12
+LLVM_MAX_SLOT=13
RDEPEND="
sys-devel/llvm:${LLVM_MAX_SLOT}
diff --git a/dev-python/num2words/num2words-0.5.10.ebuild b/dev-python/num2words/num2words-0.5.10.ebuild
index 7e62a328d..e846480bd 100644
--- a/dev-python/num2words/num2words-0.5.10.ebuild
+++ b/dev-python/num2words/num2words-0.5.10.ebuild
@@ -1,9 +1,9 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=7
+EAPI=8
-PYTHON_COMPAT=( python3_{7..9} )
+PYTHON_COMPAT=( python3_{8..10} )
inherit distutils-r1
diff --git a/dev-python/numba/Manifest b/dev-python/numba/Manifest
index a4d39c09c..6282580a9 100644
--- a/dev-python/numba/Manifest
+++ b/dev-python/numba/Manifest
@@ -1,2 +1 @@
-DIST numba-0.54.0.tar.gz 2263302 BLAKE2B 24747fcf23f686460fdd8df4784a3bccd6c41f07ff7e657f797a2959066254c079b05ec4460a7cbafef9482f463aa000ee28f8f09339cd7568a0c85b52bc4437 SHA512 ad1142e8c772660b7cbbd17566b9dc96784057467b5cc546f88e2215c9428905e1f6da05ffe104f4ad526f5131fedfa9057745d5458c3293a8cd8e01a49d0fad
-DIST numba-0.55.0.tar.gz 2335687 BLAKE2B 439206cb94149226f54eb988bcc9cefb815f734b0bfa01888f7ba16525ae2cbab39ee929a655086a47a3c3bc540e8589bdbf119cc084e876d9b61da1017bdfe9 SHA512 3651d1d06c5f325459ab73c07f501c12b3081d97d0f92d0120c8cfb312092658bbebc91f8340786f7b10cd43a95e278085cbba6d199cb3d0b5f71987ee7e5776
+DIST numba-0.56.0.tar.gz 2488023 BLAKE2B ebfc00e2f131de54cf97db0f7bb6034a650c76db1b001fc68adec7800f4890b598d83cbcf8e5beb7f8023b770b310a2d837bfc0a43d5b901f2e09a40908ec307 SHA512 cedeb683120505a02ce2911efc46c0137cc03a25b1a6864b1ff68fe69655abfbe1d9880785ea718cd14577c985e1baa8b2cb3ecaf5c591c843b9021fa182c284
diff --git a/dev-python/numba/numba-0.54.0.ebuild b/dev-python/numba/numba-0.54.0.ebuild
deleted file mode 100644
index 125b20daf..000000000
--- a/dev-python/numba/numba-0.54.0.ebuild
+++ /dev/null
@@ -1,84 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-PYTHON_COMPAT=( python3_{8..9} )
-
-DISTUTILS_USE_SETUPTOOLS=rdepend
-inherit optfeature multiprocessing distutils-r1
-
-DESCRIPTION="NumPy aware dynamic Python compiler using LLVM"
-HOMEPAGE="https://numba.pydata.org/
- https://github.com/numba"
-SRC_URI="https://github.com/numba/numba/archive/${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS="~amd64 ~arm ~arm64 ~x86"
-IUSE="openmp threads"
-
-RDEPEND="
- >=dev-python/llvmlite-0.37.0[${PYTHON_USEDEP}]
- <dev-python/llvmlite-0.38.0
- >=dev-python/numpy-1.17.0[${PYTHON_USEDEP}]
- threads? ( >=dev-cpp/tbb-2019.5 )
-"
-BDEPEND="
- dev-python/pip[${PYTHON_USEDEP}]
- dev-python/versioneer[${PYTHON_USEDEP}]
-"
-
-DISTUTILS_IN_SOURCE_BUILD=1
-distutils_enable_tests unittest
-distutils_enable_sphinx docs/source dev-python/numpydoc dev-python/sphinx_rtd_theme
-
-PATCHES=(
- "${FILESDIR}/${PN}-0.52.0-skip_tests.patch"
-)
-
-pkg_setup() {
- if ! use openmp; then
- export NUMBA_DISABLE_OPENMP=1 || die
- else
- unset NUMBA_DISABLE_OPENMP || die
- fi
- if ! use threads; then
- export NUMBA_DISABLE_TBB=1 || die
- else
- unset NUMBA_DISABLE_TBB || die
- export TBBROOT="${EPREFIX}/usr" || die
- fi
-}
-
-python_prepare_all() {
- # This conf.py only works in a git repo
- if use doc; then
- git init -q || die
- git config user.email "larry@gentoo.org" || die
- git config user.name "Larry the Cow" || die
- git add . || die
- git commit -m "init" || die
- fi
- distutils-r1_python_prepare_all
-}
-
-python_compile() {
- # FIXME: parallel python building fails. See Portage bug #614464 and
- # gentoo/sci issue #1080.
- export MAKEOPTS=-j1 || die
- distutils-r1_python_compile
-}
-
-# https://numba.pydata.org/numba-doc/latest/developer/contributing.html?highlight=test#running-tests
-python_test() {
- distutils_install_for_testing
- ${EPYTHON} setup.py build_ext --inplace || die \
- "${EPYTHON} failed to build_ext"
- ${EPYTHON} runtests.py -m $(makeopts_jobs) || die \
- "${EPYTHON} failed unittests"
-}
-
-pkg_postinst() {
- optfeature "compile cuda code" dev-util/nvidia-cuda-sdk
-}
diff --git a/dev-python/numba/numba-0.55.0.ebuild b/dev-python/numba/numba-0.56.0.ebuild
index 342c3894f..15eae53a7 100644
--- a/dev-python/numba/numba-0.55.0.ebuild
+++ b/dev-python/numba/numba-0.56.0.ebuild
@@ -19,10 +19,10 @@ KEYWORDS="~amd64 ~arm ~arm64 ~x86"
IUSE="openmp threads"
RDEPEND="
- >=dev-python/llvmlite-0.38.0[${PYTHON_USEDEP}]
- <=dev-python/llvmlite-0.39.0
+ >=dev-python/llvmlite-0.39.0[${PYTHON_USEDEP}]
+ <=dev-python/llvmlite-0.40.0
>=dev-python/numpy-1.18.0[${PYTHON_USEDEP}]
- <dev-python/numpy-1.22[${PYTHON_USEDEP}]
+ <dev-python/numpy-1.23[${PYTHON_USEDEP}]
threads? ( >=dev-cpp/tbb-2021.1 )
"
BDEPEND="
diff --git a/dev-python/numcodecs/Manifest b/dev-python/numcodecs/Manifest
index 761068546..8527c31e4 100644
--- a/dev-python/numcodecs/Manifest
+++ b/dev-python/numcodecs/Manifest
@@ -1,2 +1,3 @@
+DIST numcodecs-0.10.0.tar.gz 4519035 BLAKE2B c94edb258d23b815048c758fb1f36f6291e6b0f5b8ae9f72ea9d7a6bfd5a35891882380f309f1c26ca47b62d1825a11b1bbff289d2970d739ccfad7a5f4d610d SHA512 098602d79ac4d7cbb6c261f513b0ab6206c4b74f5f5cbb6e500434bcdeb6b2c023b0afa272c2a300081abf8bd0ec363ca0985e954b284e96fb70e95c369abf77
DIST numcodecs-0.9.0.tar.gz 4514267 BLAKE2B d7042ff0296a8246f063f55f31d790fcfbd59de07c08ff0d57e1bd4c7094c6f375ef55714866061f449dcca87d39abd36c56218d23aca0fd6bcfae491fb10097 SHA512 1525e5a7f7a7427752d3ccfbbb82b7afbfc90fcbc2c9e886e31d286c64478d85747de7e6bf16a8e980af96cf952d1202a15affa02cf6a22b4aac3725a0c8a65f
DIST numcodecs-0.9.1.tar.gz 4514374 BLAKE2B b418ee0fd27cb5f7bf8def3b124f31af7c0e2e2610dca55351c105933f7471e2465f24fa24e53ee607abcf26d690ba2b368e77618c703a4dbc8a926be48c9c1d SHA512 639cc5a5656e026f85e893009831f98420e3818f73bab95f0afd0a5bd64c901082826921e40c1b6e1f75cad82b3be2cf36787fa74ba7f0fd011dac070b24e0f8
diff --git a/dev-python/numcodecs/numcodecs-0.10.0.ebuild b/dev-python/numcodecs/numcodecs-0.10.0.ebuild
new file mode 100644
index 000000000..7219b5b7b
--- /dev/null
+++ b/dev-python/numcodecs/numcodecs-0.10.0.ebuild
@@ -0,0 +1,35 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{8..10} )
+inherit distutils-r1
+
+DESCRIPTION="Data storage buffer compression and transformation codecs"
+HOMEPAGE="https://github.com/zarr-developers/numcodecs"
+SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="test"
+# Fails to collect tests for yet unknown reasons:
+# https://github.com/zarr-developers/numcodecs/issues/304
+RESTRICT="test"
+
+RDEPEND="
+ dev-python/cython[${PYTHON_USEDEP}]
+ dev-python/msgpack[${PYTHON_USEDEP}]
+ dev-python/numpy[${PYTHON_USEDEP}]
+ dev-python/cython[${PYTHON_USEDEP}]
+"
+
+DEPEND="
+ test? (
+ ${RDEPEND}
+ dev-python/entrypoints[${PYTHON_USEDEP}]
+ )
+"
+
+distutils_enable_tests pytest
diff --git a/dev-python/nwbinspector/Manifest b/dev-python/nwbinspector/Manifest
index f5e2c79b7..ba201f8da 100644
--- a/dev-python/nwbinspector/Manifest
+++ b/dev-python/nwbinspector/Manifest
@@ -1 +1,3 @@
DIST nwbinspector-0.3.9.tar.gz 443247 BLAKE2B 4d1adbca50ff0f5d8278d71063d1248a4b22da952de6dc3e4984d58285d1acecf5adfe85b2a624df20e8064a69fa2ffe2c4a23ec1d2a579446fc451e7cd04bd5 SHA512 e8752fadbfcdb9a46f5c16771d789995fdab378720861dbe15b100f8e07cfad58f99a75fbda8e7631f06ec5671e16b3ac48a002606b658b018d50dd62151cc5e
+DIST nwbinspector-0.4.12.tar.gz 455926 BLAKE2B 4bb8b493367593fdd575535e574b8494980a60a6ed1983a08f895c106e03e25ad6cd76b6c72cfcc42a34778d5059c90940bc9907dc9d87569df79aeae1698135 SHA512 60bb799beaff61612e7993069a34f62e0b6053dc3e820474f33c020c02f8c7b11bed0bca7e2bb335edfd60b06159be90b1a50dfcd497f6a3fb0916dc49cf17b7
+DIST nwbinspector-0.4.14.tar.gz 469679 BLAKE2B 96fc92be4b52626b6533ca3d6f9584991543b2de392733af70d7d71d2a98bc8c1455a78ea0a8a6682cd4c52d0e8ed7ebcb0ac439aea9e4a5503f1dbd8b8ef148 SHA512 a1199460420b092a1e9a8803d0f881c7998e4a75e3878cb80b1b44624b1984a63aca39d4b2631339f25a00fb46982289463a062324388edfdebff27e0b8c9faa
diff --git a/dev-python/nwbinspector/nwbinspector-0.3.9.ebuild b/dev-python/nwbinspector/nwbinspector-0.3.9.ebuild
index 1e0352b88..e248266d4 100644
--- a/dev-python/nwbinspector/nwbinspector-0.3.9.ebuild
+++ b/dev-python/nwbinspector/nwbinspector-0.3.9.ebuild
@@ -20,6 +20,7 @@ RESTRICT="!test? ( test )"
DEPEND=""
RDEPEND="
dev-python/jsonschema[${PYTHON_USEDEP}]
+ dev-python/natsort[${PYTHON_USEDEP}]
dev-python/pynwb[${PYTHON_USEDEP}]
dev-python/pyyaml[${PYTHON_USEDEP}]
"
diff --git a/dev-python/nwbinspector/nwbinspector-0.4.12.ebuild b/dev-python/nwbinspector/nwbinspector-0.4.12.ebuild
new file mode 100644
index 000000000..a2b20f5af
--- /dev/null
+++ b/dev-python/nwbinspector/nwbinspector-0.4.12.ebuild
@@ -0,0 +1,39 @@
+# Copyright 2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DISTUTILS_USE_PEP517=setuptools
+PYTHON_COMPAT=( python3_{8..10} )
+inherit distutils-r1
+
+DESCRIPTION="Inspect NWB files for compliance with NWB Best Practices"
+HOMEPAGE="https://github.com/NeurodataWithoutBorders/nwbinspector"
+SRC_URI="https://github.com/NeurodataWithoutBorders/nwbinspector/archive/refs/tags/v${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="test"
+RESTRICT="!test? ( test )"
+
+DEPEND=""
+RDEPEND="
+ dev-python/click[${PYTHON_USEDEP}]
+ dev-python/jsonschema[${PYTHON_USEDEP}]
+ dev-python/natsort[${PYTHON_USEDEP}]
+ dev-python/pynwb[${PYTHON_USEDEP}]
+ dev-python/pyyaml[${PYTHON_USEDEP}]
+ dev-python/tqdm[${PYTHON_USEDEP}]
+"
+BDEPEND=""
+
+distutils_enable_tests pytest
+
+python_test() {
+ local EPYTEST_IGNORE=(
+ tests/test_inspector.py
+ tests/unit_tests/test_time_series.py
+ )
+ epytest
+}
diff --git a/dev-python/nwbinspector/nwbinspector-0.4.14.ebuild b/dev-python/nwbinspector/nwbinspector-0.4.14.ebuild
new file mode 100644
index 000000000..a2b20f5af
--- /dev/null
+++ b/dev-python/nwbinspector/nwbinspector-0.4.14.ebuild
@@ -0,0 +1,39 @@
+# Copyright 2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DISTUTILS_USE_PEP517=setuptools
+PYTHON_COMPAT=( python3_{8..10} )
+inherit distutils-r1
+
+DESCRIPTION="Inspect NWB files for compliance with NWB Best Practices"
+HOMEPAGE="https://github.com/NeurodataWithoutBorders/nwbinspector"
+SRC_URI="https://github.com/NeurodataWithoutBorders/nwbinspector/archive/refs/tags/v${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="test"
+RESTRICT="!test? ( test )"
+
+DEPEND=""
+RDEPEND="
+ dev-python/click[${PYTHON_USEDEP}]
+ dev-python/jsonschema[${PYTHON_USEDEP}]
+ dev-python/natsort[${PYTHON_USEDEP}]
+ dev-python/pynwb[${PYTHON_USEDEP}]
+ dev-python/pyyaml[${PYTHON_USEDEP}]
+ dev-python/tqdm[${PYTHON_USEDEP}]
+"
+BDEPEND=""
+
+distutils_enable_tests pytest
+
+python_test() {
+ local EPYTEST_IGNORE=(
+ tests/test_inspector.py
+ tests/unit_tests/test_time_series.py
+ )
+ epytest
+}
diff --git a/dev-python/pynrrd/Manifest b/dev-python/pynrrd/Manifest
index b9c8e53d7..72f9e8c2a 100644
--- a/dev-python/pynrrd/Manifest
+++ b/dev-python/pynrrd/Manifest
@@ -1 +1,2 @@
DIST pynrrd-0.4.2.tar.gz 43129 BLAKE2B 2001d151e38bbd02a648759475af13dd1be4bb7c12b7f8a3c7294e7fe1c281aeb9b35e39cce8254088b1c2f766aabe7343be0da4d48208375bb21be6dce9ba61 SHA512 8c5e4c1cb89dc84be3cf06e40d3f5bd45ea355c4e103027a62b088c4a73b03d1032cea1de0b153ef13fefd9b06d5a9b1954456a4542ae27cb74a278835b759ca
+DIST pynrrd-0.4.3.tar.gz 43162 BLAKE2B 266c57029e48e923dd5371184f59471e069890668ac15a75cfafc178cfe1a718f33bc6bcc704172e0fca0bdc9c52091da79e404b6bfb85838eef0c3e0807409c SHA512 d6264fce3b270e5ae9d889e7d58a18ae7bf3fecf5a1fe168dc584dece2052efd32170b21a02fa630c35e0e45e7109c745069710169ec38819639a4585344e0f6
diff --git a/dev-python/pynrrd/pynrrd-0.4.2.ebuild b/dev-python/pynrrd/pynrrd-0.4.2.ebuild
index c877ed1f3..aa922e6ed 100644
--- a/dev-python/pynrrd/pynrrd-0.4.2.ebuild
+++ b/dev-python/pynrrd/pynrrd-0.4.2.ebuild
@@ -1,9 +1,9 @@
-# Copyright 1999-2020 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=7
+EAPI=8
-PYTHON_COMPAT=( python3_{7..9} )
+PYTHON_COMPAT=( python3_{8..10} )
inherit distutils-r1
diff --git a/dev-python/pynrrd/pynrrd-0.4.3.ebuild b/dev-python/pynrrd/pynrrd-0.4.3.ebuild
new file mode 100644
index 000000000..aa922e6ed
--- /dev/null
+++ b/dev-python/pynrrd/pynrrd-0.4.3.ebuild
@@ -0,0 +1,26 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{8..10} )
+
+inherit distutils-r1
+
+DESCRIPTION="Simple pure-python module for reading and writing nrrd files"
+HOMEPAGE="https://github.com/mhe/pynrrd"
+SRC_URI="https://github.com/mhe/pynrrd/archive/v${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64"
+
+RDEPEND="dev-python/numpy[${PYTHON_USEDEP}]"
+DEPEND="test? ( ${RDEPEND} )"
+
+distutils_enable_tests unittest
+
+python_test() {
+ ${EPYTHON} -m unittest discover -v nrrd/tests || \
+ die "unittests failed for ${EPYTHON}"
+}
diff --git a/dev-python/pynwb/Manifest b/dev-python/pynwb/Manifest
index 16b7c7287..ddb67415a 100644
--- a/dev-python/pynwb/Manifest
+++ b/dev-python/pynwb/Manifest
@@ -1,2 +1,3 @@
-DIST pynwb-2.0.0.post0.dev5.tar.gz 450799 BLAKE2B 02aef74992dda44139e776eebf3d29924caa46bfc2a12da400ceaadff5856295b6205c6ad230483935e713eed9dd868b9109c2d51d7c69291dc93db806ef4761 SHA512 840a33cd0a2de5c491e785530e4dab589945015b9a60384ed127a27fbfe4c527b1b10d74a9ffe2a795a29c3bba65aafd007975973a2da68fca73bf71260b7b8b
DIST pynwb-2.0.0.tar.gz 450082 BLAKE2B 3bfd17b8cbe5f12992630bc5a97144dbc7b3d583238e1fe0d59576029ae7a30acbd05b7af18ca89d6cba389df1bf543c97e75e83e04aeb4a4e44c4cd1a26be9d SHA512 4afc319fd9cce0c1e81589236237f9a28b69dd846d96849ae5cc554287a6dd124fd421f700736dbb714cfbe6f260e79f374d1dd63ee92c2776f5173654d61f9a
+DIST pynwb-2.0.1.tar.gz 452718 BLAKE2B d29347d748bd37bdf9326e0f9cc88b84742714ba78e6b0c56a923a4dd723c94e69ab3f325b5a5c66aef3ef819228abd64704268240fbdd369dac41b25e226b43 SHA512 897fa3bce93e733222a94bf9f043ed39c606c29f392f932a21c1004eebc1866d4caf50905a8e59baca87744af04d93e9957a7efb7e775422af5022787c4d086e
+DIST pynwb-2.1.0.tar.gz 459375 BLAKE2B 3645c4cac9a9c8e8726d6a6bf38d1fa8946237c7496fde76162ee5dec66de4d0c86241a7f076d44ce857c8b411a33e9e52af47c1c5e74cf4eb84da484950c61c SHA512 11d5b23809de1e5b13baf4d02420200baf215aa99237b8e747a9d401830bef5356306eb7f9a464be36e88e64e8c50018606102b126daa450a7ee624c5babb025
diff --git a/dev-python/pynwb/files/pynwb-2.1.0-versions.patch b/dev-python/pynwb/files/pynwb-2.1.0-versions.patch
new file mode 100644
index 000000000..8c816d226
--- /dev/null
+++ b/dev-python/pynwb/files/pynwb-2.1.0-versions.patch
@@ -0,0 +1,21 @@
+diff --git a/setup.py b/tmp/setup.py
+index 39e75824..f7948f64 100755
+--- a/setup.py
++++ b/setup.py
+@@ -19,11 +19,11 @@ print('found these packages:', pkgs)
+ schema_dir = 'nwb-schema/core'
+
+ reqs = [
+- 'h5py>=2.10,<4',
+- 'hdmf>=3.3.2,<4',
+- 'numpy>=1.16,<1.23',
+- 'pandas>=1.0.5,<2',
+- 'python-dateutil>=2.7,<3',
++ 'h5py',
++ 'hdmf',
++ 'numpy',
++ 'pandas',
++ 'python-dateutil',
+ 'setuptools'
+ ]
+
diff --git a/dev-python/pynwb/metadata.xml b/dev-python/pynwb/metadata.xml
index 99512b574..1e30097b2 100644
--- a/dev-python/pynwb/metadata.xml
+++ b/dev-python/pynwb/metadata.xml
@@ -17,4 +17,8 @@
data, focused on the dynamics of groups of neurons measured under a
large range of experimental conditions.
</longdescription>
+ <upstream>
+ <remote-id type="pypi">pynwb</remote-id>
+ <remote-id type="github">NeurodataWithoutBorders/pynwb</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/dev-python/pynwb/pynwb-2.0.0.ebuild b/dev-python/pynwb/pynwb-2.0.0.ebuild
index d9afd62e7..e133d027b 100644
--- a/dev-python/pynwb/pynwb-2.0.0.ebuild
+++ b/dev-python/pynwb/pynwb-2.0.0.ebuild
@@ -16,7 +16,7 @@ KEYWORDS="~amd64 ~x86"
RDEPEND="
sci-libs/hdf5[ros3(-)]
- dev-python/hdmf[${PYTHON_USEDEP}]
+ <dev-python/hdmf-3.3.2[${PYTHON_USEDEP}]
dev-python/h5py[${PYTHON_USEDEP}]
dev-python/numpy[${PYTHON_USEDEP}]
dev-python/pandas[${PYTHON_USEDEP}]
@@ -30,7 +30,7 @@ PATCHES=(
EPYTEST_DESELECT=(
# Reported upsream:
- # https://github.com/dandi/dandischema/issues/87
+ # https://github.com/NeurodataWithoutBorders/pynwb/issues/1425
tests/validation/test_validate.py::TestValidateScript::test_validate_file_cached
tests/validation/test_validate.py::TestValidateScript::test_validate_file_cached_bad_ns
tests/validation/test_validate.py::TestValidateScript::test_validate_file_cached_hdmf_common
diff --git a/dev-python/pynwb/pynwb-2.0.1.ebuild b/dev-python/pynwb/pynwb-2.0.1.ebuild
new file mode 100644
index 000000000..3fe21370f
--- /dev/null
+++ b/dev-python/pynwb/pynwb-2.0.1.ebuild
@@ -0,0 +1,39 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DISTUTILS_USE_PEP517=setuptools
+PYTHON_COMPAT=( python3_{8..10} )
+inherit distutils-r1
+
+DESCRIPTION="A Python API for working with Neurodata stored in the NWB Format "
+HOMEPAGE="https://github.com/NeurodataWithoutBorders/pynwb"
+SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
+
+SLOT="0"
+LICENSE="BSD"
+KEYWORDS="~amd64 ~x86"
+
+RDEPEND="
+ sci-libs/hdf5[ros3(-)]
+ <dev-python/hdmf-3.3.2[${PYTHON_USEDEP}]
+ dev-python/h5py[${PYTHON_USEDEP}]
+ dev-python/numpy[${PYTHON_USEDEP}]
+ dev-python/pandas[${PYTHON_USEDEP}]
+ dev-python/python-dateutil[${PYTHON_USEDEP}]
+ "
+BDEPEND=""
+
+EPYTEST_DESELECT=(
+ # Reported upsream:
+ # https://github.com/NeurodataWithoutBorders/pynwb/issues/1425
+ tests/validation/test_validate.py::TestValidateScript::test_validate_file_cached
+ tests/validation/test_validate.py::TestValidateScript::test_validate_file_cached_bad_ns
+ tests/validation/test_validate.py::TestValidateScript::test_validate_file_cached_hdmf_common
+ tests/validation/test_validate.py::TestValidateScript::test_validate_file_cached_ignore
+ tests/validation/test_validate.py::TestValidateScript::test_validate_file_no_cache
+ tests/validation/test_validate.py::TestValidateScript::test_validate_file_no_cache_bad_ns
+)
+
+distutils_enable_tests pytest
diff --git a/dev-python/pynwb/pynwb-2.0.0_p0.ebuild b/dev-python/pynwb/pynwb-2.1.0-r1.ebuild
index 25672015c..c24dae23a 100644
--- a/dev-python/pynwb/pynwb-2.0.0_p0.ebuild
+++ b/dev-python/pynwb/pynwb-2.1.0-r1.ebuild
@@ -3,15 +3,13 @@
EAPI=8
+DISTUTILS_USE_PEP517=setuptools
PYTHON_COMPAT=( python3_{8..10} )
inherit distutils-r1
-MY_PV="${PV/_p/.post}.dev5"
-MY_P="${PN}-${MY_PV}"
-
DESCRIPTION="A Python API for working with Neurodata stored in the NWB Format "
HOMEPAGE="https://github.com/NeurodataWithoutBorders/pynwb"
-SRC_URI="https://github.com/NeurodataWithoutBorders/pynwb/releases/download/latest/${MY_P}.tar.gz"
+SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
SLOT="0"
LICENSE="BSD"
@@ -19,7 +17,7 @@ KEYWORDS="~amd64 ~x86"
RDEPEND="
sci-libs/hdf5[ros3(-)]
- dev-python/hdmf[${PYTHON_USEDEP}]
+ >=dev-python/hdmf-3.3.2[${PYTHON_USEDEP}]
dev-python/h5py[${PYTHON_USEDEP}]
dev-python/numpy[${PYTHON_USEDEP}]
dev-python/pandas[${PYTHON_USEDEP}]
@@ -28,14 +26,12 @@ RDEPEND="
BDEPEND=""
PATCHES=(
- "${FILESDIR}/${PN}-2.0.0-versions.patch"
+ "${FILESDIR}/${P}-versions.patch"
)
-S="${WORKDIR}/${MY_P}"
-
EPYTEST_DESELECT=(
- # Reported upsream
- # https://github.com/dandi/dandischema/issues/87
+ # Reported upsream:
+ # https://github.com/NeurodataWithoutBorders/pynwb/issues/1425
tests/validation/test_validate.py::TestValidateScript::test_validate_file_cached
tests/validation/test_validate.py::TestValidateScript::test_validate_file_cached_bad_ns
tests/validation/test_validate.py::TestValidateScript::test_validate_file_cached_hdmf_common
diff --git a/dev-python/pysolar/pysolar-0.8.ebuild b/dev-python/pysolar/pysolar-0.8.ebuild
index 88f0505ef..65027edb9 100644
--- a/dev-python/pysolar/pysolar-0.8.ebuild
+++ b/dev-python/pysolar/pysolar-0.8.ebuild
@@ -1,9 +1,9 @@
# Copyright 1999-2021 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=7
+EAPI=8
-PYTHON_COMPAT=( python3_{7..9} )
+PYTHON_COMPAT=( python3_{8..10} )
AUTHOR=pingswept
@@ -23,6 +23,8 @@ RDEPEND="
dev-python/scipy[${PYTHON_USEDEP}]
"
+distutils_enable_tests nose
+
python_prepare_all() {
sed \
-e "s:'testsolar', ::" \
diff --git a/dev-python/python-gantt/python-gantt-0.6.0_p20200809.ebuild b/dev-python/python-gantt/python-gantt-0.6.0_p20200809.ebuild
index 379816b05..f2d829835 100644
--- a/dev-python/python-gantt/python-gantt-0.6.0_p20200809.ebuild
+++ b/dev-python/python-gantt/python-gantt-0.6.0_p20200809.ebuild
@@ -1,8 +1,8 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=7
-PYTHON_COMPAT=( python3_{7..9} )
+EAPI=8
+PYTHON_COMPAT=( python3_{8..10} )
inherit distutils-r1
@@ -30,7 +30,7 @@ python_prepare() {
-e "s/matplotlib==3.0.3/matplotlib/g"\
-e "s/numpy==1.16.3/numpy/g"\
setup.py || die
- distutils-r1_python_prepare_all
+ python_prepare_all
}
distutils_enable_tests pytest
diff --git a/dev-python/python-igraph/Manifest b/dev-python/python-igraph/Manifest
index bb22f152b..45cb90874 100644
--- a/dev-python/python-igraph/Manifest
+++ b/dev-python/python-igraph/Manifest
@@ -1 +1,2 @@
+DIST igraph-0.9.11.tar.gz 3728842 BLAKE2B 7ddac705757a98c3c9dbbfdc841f078c8766aa9baedf0df693163920c47419da481c4bc54a0b7adc103885e2e75c77832faaa38f954d9596114fa700492a89e2 SHA512 a85e02144d33eb02ce0fe594cf91d5fc852af36d11c6da26d714f1e66bb116a9732945db43939e18f704ac725a9011358b3b89073ba81b0f4bf6440dc727f90e
DIST python-igraph-0.9.0.tar.gz 3366754 BLAKE2B baab83753bea4ee880564fe189b246c2ce0647a74ea1a41299062c3a2e203ec155abe1a3680c228d62a28e7bbf263e60e4529f151094b916ce4a1cae9f360705 SHA512 bd6071fc20c6c8f65034c71be6083e66367eb3047f376eb603e590da3606338fbd9890a2a74b8e0547fba2900c353f952683ea69b4d996f5643e84ee1c450b03
diff --git a/dev-python/python-igraph/python-igraph-0.9.11.ebuild b/dev-python/python-igraph/python-igraph-0.9.11.ebuild
new file mode 100644
index 000000000..4d2a6ee5f
--- /dev/null
+++ b/dev-python/python-igraph/python-igraph-0.9.11.ebuild
@@ -0,0 +1,53 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{8..10} )
+
+inherit distutils-r1
+
+MY_PN="${PN#python-}"
+MY_P="${MY_PN}-${PV}"
+
+DESCRIPTION="Python interface for igraph"
+HOMEPAGE="https://igraph.org"
+SRC_URI="mirror://pypi/${MY_PN:0:1}/${MY_PN}/${MY_P}.tar.gz"
+S="${WORKDIR}/${MY_P}"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+RDEPEND="
+ >=dev-libs/igraph-0.9.0
+ >=dev-python/texttable-1.6.2[${PYTHON_USEDEP}]
+"
+DEPEND="${RDEPEND}"
+BDEPEND="
+ test? (
+ dev-python/cairocffi[${PYTHON_USEDEP}]
+ dev-python/matplotlib[${PYTHON_USEDEP}]
+ dev-python/networkx[${PYTHON_USEDEP}]
+ dev-python/numpy[${PYTHON_USEDEP}]
+ dev-python/pandas[${PYTHON_USEDEP}]
+ dev-python/plotly[${PYTHON_USEDEP}]
+ dev-python/scipy[${PYTHON_USEDEP}]
+ )
+"
+
+distutils_enable_tests pytest
+
+python_prepare_all() {
+ # fix the igraph include path
+ cd src || die
+ find -type f -name "*.h" -exec sed -i -e 's@#include <igraph@#include <igraph/igraph@g' {} + || die
+ find -type f -name "*.c" -exec sed -i -e 's@#include <igraph@#include <igraph/igraph@g' {} + || die
+ cd .. || die
+
+ distutils-r1_python_prepare_all
+}
+
+python_compile() {
+ distutils-r1_python_compile --use-pkg-config
+}
diff --git a/dev-python/traits/traits-6.0.0.ebuild b/dev-python/traits/traits-6.0.0.ebuild
index 732c6247a..0d6ffae85 100644
--- a/dev-python/traits/traits-6.0.0.ebuild
+++ b/dev-python/traits/traits-6.0.0.ebuild
@@ -1,9 +1,9 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=7
+EAPI=8
-PYTHON_COMPAT=( python3_{7,8,9} )
+PYTHON_COMPAT=( python3_{8..10} )
inherit distutils-r1
diff --git a/dev-python/traits/traits-6.1.1.ebuild b/dev-python/traits/traits-6.1.1.ebuild
index e0263e441..677be0b9e 100644
--- a/dev-python/traits/traits-6.1.1.ebuild
+++ b/dev-python/traits/traits-6.1.1.ebuild
@@ -1,9 +1,9 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=7
+EAPI=8
-PYTHON_COMPAT=( python3_{7,8,9} )
+PYTHON_COMPAT=( python3_{8..10} )
inherit distutils-r1
diff --git a/dev-python/visvis/visvis-1.13.0.ebuild b/dev-python/visvis/visvis-1.13.0.ebuild
index 80704b0c3..05eb0e162 100644
--- a/dev-python/visvis/visvis-1.13.0.ebuild
+++ b/dev-python/visvis/visvis-1.13.0.ebuild
@@ -4,7 +4,7 @@
EAPI=8
DISTUTILS_USE_SETUPTOOLS=no
-PYTHON_COMPAT=( python3_{8..9} )
+PYTHON_COMPAT=( python3_{8..10} )
inherit distutils-r1
diff --git a/dev-python/wraps/Manifest b/dev-python/wraps/Manifest
new file mode 100644
index 000000000..84f3a1b37
--- /dev/null
+++ b/dev-python/wraps/Manifest
@@ -0,0 +1 @@
+DIST wraps-0.1.0.tar.gz 11126 BLAKE2B 6db25f60750fedcc44896e7d30f90400994a5c8c8fbb8bcad33696dfa4b3eb53f41c6a4e29a69c11610c6d32084019e9dbbdcdc6d7e462a0fda7f3cc3459c0fc SHA512 597afa975c0cc434ab861699d9de59c3815d240c59364c064346ab267f1f3c1177163db7c3fff20c6e2e68bed9eb9eff7eb068488d1bf427eca84925ba8e2e9f
diff --git a/dev-python/wraps/files/wraps-0.1.0-includes.patch b/dev-python/wraps/files/wraps-0.1.0-includes.patch
new file mode 100644
index 000000000..a5184e52e
--- /dev/null
+++ b/dev-python/wraps/files/wraps-0.1.0-includes.patch
@@ -0,0 +1,16 @@
+--- a/pyproject.toml 2022-06-28 11:08:09.624127900 -0400
++++ b/pyproject.toml 2022-07-11 16:33:14.810411482 -0400
+@@ -20,8 +20,11 @@
+ "Topic :: Utilities",
+ "Typing :: Typed",
+ ]
+-
+-include = ["CHANGELOG.md", "tests"]
++include = [
++ { path = "LICENSE", format = "sdist" },
++ { path = "README.md", format = "sdist" },
++ { path = "CHANGELOG.md", format = "sdist" },
++]
+
+ [tool.poetry.urls]
+ Discord = "https://nekit.dev/discord"
diff --git a/dev-python/wraps/files/wraps-0.1.0-poetry_groups.patch b/dev-python/wraps/files/wraps-0.1.0-poetry_groups.patch
new file mode 100644
index 000000000..8a6de2917
--- /dev/null
+++ b/dev-python/wraps/files/wraps-0.1.0-poetry_groups.patch
@@ -0,0 +1,61 @@
+--- a/pyproject.toml 2022-06-28 11:08:09.624127900 -0400
++++ b/pyproject.toml 2022-07-11 16:33:14.810411482 -0400
+@@ -37,29 +37,6 @@
+
+ typing-extensions = ">= 4.2.0"
+
+-[tool.poetry.group.format]
+-optional = true
+-
+-[tool.poetry.group.format.dependencies]
+-black = "22.6.0"
+-
+-[tool.poetry.group.format.dependencies.isort]
+-version = "5.10.1"
+-python = "^3.7"
+-
+-[tool.poetry.group.check]
+-optional = true
+-
+-[tool.poetry.group.check.dependencies]
+-mypy = "0.961"
+-
+-[tool.poetry.group.test]
+-optional = true
+-
+-[tool.poetry.group.test.dependencies]
+-pytest = "7.1.2"
+-pytest-cov = "3.0.0"
+-
+ [tool.black]
+ line_length = 100
+
+@@ -67,29 +44,6 @@
+ line_length = 100
+ profile = "black"
+
+-[tool.pytest.ini_options]
+-addopts = "--cov wraps"
+-testpaths = ["tests"]
+-
+-[tool.coverage.run]
+-source = ["wraps"]
+-
+-[tool.coverage.report]
+-ignore_errors = true
+-exclude_lines = [
+- "pragma: never",
+- "pragma: no cover",
+- "if TYPE_CHECKING",
+- "@overload",
+- "@abstractmethod",
+- "raise NotImplementedError",
+- "raise AssertionError",
+- "def __repr__",
+-]
+-
+-[tool.coverage.html]
+-directory = "coverage"
+-
+ [tool.mypy]
+ show_column_numbers = true
diff --git a/dev-cpp/castxml/metadata.xml b/dev-python/wraps/metadata.xml
index 3cef409d1..dd3bf5227 100644
--- a/dev-cpp/castxml/metadata.xml
+++ b/dev-python/wraps/metadata.xml
@@ -1,10 +1,7 @@
-<?xml version='1.0' encoding='UTF-8'?>
+<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<maintainer type="person">
- <email>gw.fossdev@gmail.com</email>
- </maintainer>
- <maintainer type="person">
<email>gentoo@chymera.eu</email>
<name>Horea Christian</name>
</maintainer>
@@ -12,4 +9,7 @@
<email>sci@gentoo.org</email>
<name>Gentoo Science Project</name>
</maintainer>
+ <upstream>
+ <remote-id type="github">nekitdev/wraps</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/dev-python/wraps/wraps-0.1.0.ebuild b/dev-python/wraps/wraps-0.1.0.ebuild
new file mode 100644
index 000000000..79df009b5
--- /dev/null
+++ b/dev-python/wraps/wraps-0.1.0.ebuild
@@ -0,0 +1,31 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DISTUTILS_USE_PEP517=poetry
+PYTHON_COMPAT=( python3_{8..11} )
+
+inherit distutils-r1
+
+DESCRIPTION=" Meaningful and safe wrapping types. "
+HOMEPAGE="https://github.com/nekitdev/wraps"
+SRC_URI="https://github.com/nekitdev/wraps/releases/download/v${PV}/${P}.tar.gz"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+RESTRICT="test"
+# package does not have test suite (yet)
+
+RDEPEND="
+ >=dev-python/attrs-21.4.0[${PYTHON_USEDEP}]
+ >=dev-python/typing-extensions-4.2.0[${PYTHON_USEDEP}]
+ "
+
+PATCHES=(
+ "${FILESDIR}/${P}-includes.patch"
+ "${FILESDIR}/${P}-poetry_groups.patch"
+)
+
+distutils_enable_tests pytest
diff --git a/dev-vcs/dandi-cli/Manifest b/dev-vcs/dandi-cli/Manifest
index cce81b9b2..2a70c8348 100644
--- a/dev-vcs/dandi-cli/Manifest
+++ b/dev-vcs/dandi-cli/Manifest
@@ -1,3 +1,3 @@
-DIST dandi-cli-0.37.0.tar.gz 212121 BLAKE2B a38077439edb9975b25eaffd299cba633b538d7c5a93aefeb35e8403e07896f1e93eb6b42790ca84ab20ddfe0ead850a000f857cfd3ef8c6342eb76952b95b62 SHA512 fe96b760bb8526cf2670be4523121b389ede82699a8b13a9b46e4511012ab15390d9aec35b5403fa4d52dd79738a37980bcc83755df738b4039ae56eb6ca0f14
-DIST dandi-cli-0.38.0.tar.gz 322974 BLAKE2B 5451eb922019e0b06de1181161d23fac21ddbd772fb9ff5b23e296eb5ccc54c44b6c6c62d5d8f25bf075e6c93136f1db4d3ab72d372dfa7a28c84fc03008e0f3 SHA512 a77d834dadbd532ce016425fe25324582a5d2c442b52087d5751770d99c84fa9532a08525ee75f40d45ccb5c50ed11b9fbe0c29a24c7d1b24c253d218538e054
-DIST dandi-cli-0.39.4.tar.gz 329268 BLAKE2B c34674570c3474dbc12a2f96c0877a84ca3cddbf8d04cb1bc7cc47e6d03bbf4103cf8f36d4267f59bfb5da2504300e14dc007a3f23a5d807bb92cece506fb7b7 SHA512 8ac4ae25eb9b09530a017ca2812a490c578157caeb0cca2737630f9796ec4559fc2379f150764544e1cd474cf481f87bb08dd255d4bf4dcc7722c8006ae78c4b
+DIST dandi-0.45.1.tar.gz 321362 BLAKE2B d07296be6bd4237fea4aa83c0b087de45234157aa6aa457f8d44f56b514a4deca11226831182b84c19a72b398183b3b181beb3946c7f8cce2d842ac80f0b57e2 SHA512 07d97420651bbd82d8d4146322ff80873489bd49869834ace9986f1ddc1880be5ff6bd1d625d8b4607a90de8007aeba152e8161af05c25a804cb18c7a0c78e29
+DIST dandi-cli-0.38.0.gh.tar.gz 322974 BLAKE2B 5451eb922019e0b06de1181161d23fac21ddbd772fb9ff5b23e296eb5ccc54c44b6c6c62d5d8f25bf075e6c93136f1db4d3ab72d372dfa7a28c84fc03008e0f3 SHA512 a77d834dadbd532ce016425fe25324582a5d2c442b52087d5751770d99c84fa9532a08525ee75f40d45ccb5c50ed11b9fbe0c29a24c7d1b24c253d218538e054
+DIST dandi-cli-0.39.4.gh.tar.gz 329268 BLAKE2B c34674570c3474dbc12a2f96c0877a84ca3cddbf8d04cb1bc7cc47e6d03bbf4103cf8f36d4267f59bfb5da2504300e14dc007a3f23a5d807bb92cece506fb7b7 SHA512 8ac4ae25eb9b09530a017ca2812a490c578157caeb0cca2737630f9796ec4559fc2379f150764544e1cd474cf481f87bb08dd255d4bf4dcc7722c8006ae78c4b
diff --git a/dev-vcs/dandi-cli/dandi-cli-0.38.0.ebuild b/dev-vcs/dandi-cli/dandi-cli-0.38.0.ebuild
index 08d652de9..b5f95e030 100644
--- a/dev-vcs/dandi-cli/dandi-cli-0.38.0.ebuild
+++ b/dev-vcs/dandi-cli/dandi-cli-0.38.0.ebuild
@@ -10,7 +10,7 @@ inherit distutils-r1
DESCRIPTION="DANDI command line client to facilitate common operations"
HOMEPAGE="https://github.com/dandi/dandi-cli"
-SRC_URI="https://github.com/dandi/dandi-cli/archive/refs/tags/${PV}.tar.gz -> ${P}.tar.gz"
+SRC_URI="https://github.com/dandi/dandi-cli/archive/refs/tags/${PV}.tar.gz -> ${P}.gh.tar.gz"
LICENSE="Apache-2.0"
SLOT="0"
@@ -28,7 +28,7 @@ RDEPEND="
dev-python/interleave[${PYTHON_USEDEP}]
dev-python/joblib[${PYTHON_USEDEP}]
dev-python/keyring[${PYTHON_USEDEP}]
- dev-python/keyrings_alt[${PYTHON_USEDEP}]
+ dev-python/keyrings-alt[${PYTHON_USEDEP}]
dev-python/packaging[${PYTHON_USEDEP}]
dev-python/pycryptodome[${PYTHON_USEDEP}]
>=dev-python/pydantic-1.9.0[${PYTHON_USEDEP}]
diff --git a/dev-vcs/dandi-cli/dandi-cli-0.39.4.ebuild b/dev-vcs/dandi-cli/dandi-cli-0.39.4.ebuild
index 11f322912..a12843df7 100644
--- a/dev-vcs/dandi-cli/dandi-cli-0.39.4.ebuild
+++ b/dev-vcs/dandi-cli/dandi-cli-0.39.4.ebuild
@@ -10,7 +10,7 @@ inherit distutils-r1
DESCRIPTION="DANDI command line client to facilitate common operations"
HOMEPAGE="https://github.com/dandi/dandi-cli"
-SRC_URI="https://github.com/dandi/dandi-cli/archive/refs/tags/${PV}.tar.gz -> ${P}.tar.gz"
+SRC_URI="https://github.com/dandi/dandi-cli/archive/refs/tags/${PV}.tar.gz -> ${P}.gh.tar.gz"
LICENSE="Apache-2.0"
SLOT="0"
@@ -28,7 +28,7 @@ RDEPEND="
dev-python/interleave[${PYTHON_USEDEP}]
dev-python/joblib[${PYTHON_USEDEP}]
dev-python/keyring[${PYTHON_USEDEP}]
- dev-python/keyrings_alt[${PYTHON_USEDEP}]
+ dev-python/keyrings-alt[${PYTHON_USEDEP}]
dev-python/nwbinspector[${PYTHON_USEDEP}]
dev-python/packaging[${PYTHON_USEDEP}]
dev-python/pycryptodome[${PYTHON_USEDEP}]
@@ -40,7 +40,6 @@ RDEPEND="
dev-python/ruamel-yaml[${PYTHON_USEDEP}]
dev-python/semantic_version[${PYTHON_USEDEP}]
dev-python/tenacity[${PYTHON_USEDEP}]
- dev-python/versioneer[${PYTHON_USEDEP}]
dev-python/wheel[${PYTHON_USEDEP}]
dev-python/zarr[${PYTHON_USEDEP}]
"
diff --git a/dev-vcs/dandi-cli/dandi-cli-0.37.0.ebuild b/dev-vcs/dandi-cli/dandi-cli-0.45.1.ebuild
index 08d652de9..1dbc002dd 100644
--- a/dev-vcs/dandi-cli/dandi-cli-0.37.0.ebuild
+++ b/dev-vcs/dandi-cli/dandi-cli-0.45.1.ebuild
@@ -8,9 +8,13 @@ PYTHON_COMPAT=( python3_{8..10} )
inherit distutils-r1
+MY_PN="dandi"
+MY_P="${MY_PN}-${PV}"
+
DESCRIPTION="DANDI command line client to facilitate common operations"
HOMEPAGE="https://github.com/dandi/dandi-cli"
-SRC_URI="https://github.com/dandi/dandi-cli/archive/refs/tags/${PV}.tar.gz -> ${P}.tar.gz"
+#SRC_URI="https://github.com/dandi/dandi-cli/archive/refs/tags/${PV}.tar.gz -> ${P}.tar.gz"
+SRC_URI="mirror://pypi/${MY_PN:0:1}/${MY_PN}/${MY_P}.tar.gz"
LICENSE="Apache-2.0"
SLOT="0"
@@ -21,14 +25,15 @@ RDEPEND="
dev-python/appdirs[${PYTHON_USEDEP}]
dev-python/click[${PYTHON_USEDEP}]
dev-python/click-didyoumean[${PYTHON_USEDEP}]
- ~dev-python/dandi-schema-0.6.0[${PYTHON_USEDEP}]
+ =dev-python/dandi-schema-0.7*[${PYTHON_USEDEP}]
dev-python/fasteners[${PYTHON_USEDEP}]
dev-python/fscacher[${PYTHON_USEDEP}]
dev-python/humanize[${PYTHON_USEDEP}]
dev-python/interleave[${PYTHON_USEDEP}]
dev-python/joblib[${PYTHON_USEDEP}]
dev-python/keyring[${PYTHON_USEDEP}]
- dev-python/keyrings_alt[${PYTHON_USEDEP}]
+ dev-python/keyrings-alt[${PYTHON_USEDEP}]
+ dev-python/nwbinspector[${PYTHON_USEDEP}]
dev-python/packaging[${PYTHON_USEDEP}]
dev-python/pycryptodome[${PYTHON_USEDEP}]
>=dev-python/pydantic-1.9.0[${PYTHON_USEDEP}]
@@ -43,7 +48,7 @@ RDEPEND="
dev-python/zarr[${PYTHON_USEDEP}]
"
-DEPEND="
+BDEPEND="
test? (
dev-python/anys[${PYTHON_USEDEP}]
dev-python/responses[${PYTHON_USEDEP}]
@@ -55,22 +60,10 @@ DEPEND="
# Upstream might be amenable to dropping opencv:
# https://github.com/dandi/dandi-cli/issues/944
-# Some tests require deep copy with git history
-# https://github.com/dandi/dandi-cli/issues/878#issuecomment-1021720299
-EPYTEST_DESELECT=(
- "dandi/tests/test_utils.py::test_get_instance_dandi_with_api"
- "dandi/tests/test_utils.py::test_get_instance_url"
- "dandi/tests/test_utils.py::test_get_instance_cli_version_too_old"
- "dandi/tests/test_utils.py::test_get_instance_bad_cli_version"
-)
+S="${WORKDIR}/${MY_P}"
distutils_enable_tests pytest
-PATCHES=(
- "${FILESDIR}/${PN}-0.37.0-pip-versioncheck.patch"
- "${FILESDIR}/${PN}-0.37.0-pep517.patch"
-)
-
src_prepare() {
if use etelemetry; then
default
diff --git a/dev-vcs/datalad/Manifest b/dev-vcs/datalad/Manifest
index c4147a574..5ad5852a2 100644
--- a/dev-vcs/datalad/Manifest
+++ b/dev-vcs/datalad/Manifest
@@ -1,2 +1,5 @@
DIST datalad-0.15.1.tar.gz 1357778 BLAKE2B 7c12c3ff1bd8d260e8e7cfd9e477a1f0798f6fc0fbdbc335229bcf88362ebc7280eeb92bb59c45e0f66677297680e4d8d7bc8f56c7ac171f921bc389c1ceef7c SHA512 d5ae7859486748cbf40bd27f3351fa5620b8342c6a4347b8e3e0cb331de5fa33b9384071adbb899fd7878641a210a11b360a9ea68d0c7437eae709244fa08fd1
DIST datalad-0.15.2.tar.gz 1361038 BLAKE2B c515b374f0781693ed0f1d0d2c260a0bdb1c9e998b782a2232c501b4ab7c022adc38f00a79d0aed04ffde4ade5c696705d53bf16dbaec2378c74ef4ab35a7a15 SHA512 f0206855439c2d376172218ec6bf1ffa3277508256a5a49a2ec65a57bb5720e039481329c16459ed62eb1c9ed0126dc178ca34fa2c3b8dfdf8b8a0706a2b8658
+DIST datalad-0.16.1.tar.gz 1472447 BLAKE2B b62f2fb37d0bc5cdaa8fd36f1bdea1beab4b4c071ba32c45b1ba5f2036788e4dc4767b406b20c0e0ccf3a5e02fbcb77b73ac9d8f254d02d6004ce909a94bffb5 SHA512 7236e635f8c9b9fbc9f82776d325dce1585d9a99d767b66f2877fb935d788c36335562ae8679821dea1b433f5d122f687e0c6b2098d8e388b8f8f6134751cc5b
+DIST datalad-0.17.0.tar.gz 1510529 BLAKE2B 797a4d15139a88d20f03d1b81cf8b19088cf91925852a0a0d2079b3a64debfaa4945c31f21cc701ac507b00c1eabe10eb57653d8cbef1914d2c7babc48324458 SHA512 fea35a574f13b4957149f87553c80eceaebde064921e5fa28960b088e6d8f38a2eb2cbf797c9e031bd696bdca1400c2baa4c3e94c2b78bf8c1349a752928b09c
+DIST datalad-0.17.2.tar.gz 1512123 BLAKE2B 83f1d437f6a2d300c169710fd12c8e126e5ab89aee9f0ccda48325c13c26a7e895fc11d33e61a266d7e4f5ac976244950851080055639b679819f659286c3c57 SHA512 7eceaea6bd0f0e251f194d8c1846e5abfff46174c536a42c1c0f891ca06f9688f8d291dec706f4ca51128d6588ceaf28039d80e63ebc5a15417bca3c74f0d866
diff --git a/dev-vcs/datalad/datalad-0.15.1.ebuild b/dev-vcs/datalad/datalad-0.15.1.ebuild
index 2322ac254..f7d178584 100644
--- a/dev-vcs/datalad/datalad-0.15.1.ebuild
+++ b/dev-vcs/datalad/datalad-0.15.1.ebuild
@@ -1,9 +1,9 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=8
-PYTHON_COMPAT=( python3_{8,9} )
+PYTHON_COMPAT=( python3_{8..10} )
inherit distutils-r1
DESCRIPTION="Keep code, data, containers under control with git and git-annex"
@@ -31,7 +31,7 @@ RDEPEND="
downloaders? (
dev-python/boto[${PYTHON_USEDEP}]
dev-python/keyring[${PYTHON_USEDEP}]
- dev-python/keyrings_alt[${PYTHON_USEDEP}]
+ dev-python/keyrings-alt[${PYTHON_USEDEP}]
dev-python/msgpack[${PYTHON_USEDEP}]
dev-python/requests[${PYTHON_USEDEP}]
)
diff --git a/dev-vcs/datalad/datalad-0.15.2.ebuild b/dev-vcs/datalad/datalad-0.15.2.ebuild
index 2322ac254..f7d178584 100644
--- a/dev-vcs/datalad/datalad-0.15.2.ebuild
+++ b/dev-vcs/datalad/datalad-0.15.2.ebuild
@@ -1,9 +1,9 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=8
-PYTHON_COMPAT=( python3_{8,9} )
+PYTHON_COMPAT=( python3_{8..10} )
inherit distutils-r1
DESCRIPTION="Keep code, data, containers under control with git and git-annex"
@@ -31,7 +31,7 @@ RDEPEND="
downloaders? (
dev-python/boto[${PYTHON_USEDEP}]
dev-python/keyring[${PYTHON_USEDEP}]
- dev-python/keyrings_alt[${PYTHON_USEDEP}]
+ dev-python/keyrings-alt[${PYTHON_USEDEP}]
dev-python/msgpack[${PYTHON_USEDEP}]
dev-python/requests[${PYTHON_USEDEP}]
)
diff --git a/dev-vcs/datalad/datalad-0.16.1.ebuild b/dev-vcs/datalad/datalad-0.16.1.ebuild
new file mode 100644
index 000000000..52b13b5ea
--- /dev/null
+++ b/dev-vcs/datalad/datalad-0.16.1.ebuild
@@ -0,0 +1,72 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{8..10} )
+inherit distutils-r1
+
+DESCRIPTION="Keep code, data, containers under control with git and git-annex"
+HOMEPAGE="https://github.com/datalad/datalad"
+SRC_URI="https://github.com/datalad/datalad/archive/refs/tags/${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64"
+IUSE="test +downloaders +metadata +publish misc"
+RESTRICT="!test? ( test )"
+
+RDEPEND="
+ app-arch/p7zip
+ dev-python/annexremote[${PYTHON_USEDEP}]
+ dev-python/appdirs[${PYTHON_USEDEP}]
+ >=dev-python/chardet-3.0.4[${PYTHON_USEDEP}]
+ dev-python/distro[${PYTHON_USEDEP}]
+ dev-python/iso8601[${PYTHON_USEDEP}]
+ dev-python/humanize[${PYTHON_USEDEP}]
+ dev-python/fasteners[${PYTHON_USEDEP}]
+ app-arch/patool[${PYTHON_USEDEP}]
+ dev-python/tqdm[${PYTHON_USEDEP}]
+ dev-python/wrapt[${PYTHON_USEDEP}]
+ downloaders? (
+ dev-python/boto[${PYTHON_USEDEP}]
+ dev-python/keyring[${PYTHON_USEDEP}]
+ dev-python/keyrings-alt[${PYTHON_USEDEP}]
+ dev-python/msgpack[${PYTHON_USEDEP}]
+ dev-python/requests[${PYTHON_USEDEP}]
+ )
+ metadata? (
+ dev-python/simplejson[${PYTHON_USEDEP}]
+ dev-python/whoosh[${PYTHON_USEDEP}]
+ )
+ misc? (
+ dev-python/argcomplete[${PYTHON_USEDEP}]
+ dev-python/pyperclip[${PYTHON_USEDEP}]
+ dev-python/python-dateutil[${PYTHON_USEDEP}]
+ )
+ publish? (
+ dev-vcs/python-gitlab[${PYTHON_USEDEP}]
+ dev-python/PyGithub[${PYTHON_USEDEP}]
+ )
+"
+DEPEND="
+ dev-python/setuptools[${PYTHON_USEDEP}]
+ test? (
+ dev-python/beautifulsoup4[${PYTHON_USEDEP}]
+ dev-python/httpretty[${PYTHON_USEDEP}]
+ dev-python/vcrpy[${PYTHON_USEDEP}]
+ )
+"
+
+# Noticed by upstream:
+# https://github.com/datalad/datalad/issues/6623
+PATCHES=( "${FILESDIR}/${P}-input.patch" )
+
+distutils_enable_tests nose
+
+python_test() {
+ export DATALAD_TESTS_NONETWORK=1
+ ${EPYTHON} -m nose -s -v -A "not(integration or usecase or slow or network or turtle)" datalad || die
+ # Full test suite takes for ever:
+ # ${EPYTHON} -m nose -s -v datalad || die
+}
diff --git a/dev-vcs/datalad/datalad-0.17.0.ebuild b/dev-vcs/datalad/datalad-0.17.0.ebuild
new file mode 100644
index 000000000..7ad3e0a43
--- /dev/null
+++ b/dev-vcs/datalad/datalad-0.17.0.ebuild
@@ -0,0 +1,75 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DISTUTILS_USE_PEP517=setuptools
+PYTHON_COMPAT=( python3_{8..10} )
+inherit distutils-r1
+
+DESCRIPTION="Keep code, data, containers under control with git and git-annex"
+HOMEPAGE="https://github.com/datalad/datalad"
+SRC_URI="https://github.com/datalad/datalad/archive/refs/tags/${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64"
+IUSE="test +downloaders +metadata +publish misc"
+RESTRICT="!test? ( test )"
+
+RDEPEND="
+ app-arch/p7zip
+ app-arch/patool[${PYTHON_USEDEP}]
+ dev-python/annexremote[${PYTHON_USEDEP}]
+ >=dev-python/chardet-3.0.4[${PYTHON_USEDEP}]
+ dev-python/distro[${PYTHON_USEDEP}]
+ dev-python/fasteners[${PYTHON_USEDEP}]
+ dev-python/humanize[${PYTHON_USEDEP}]
+ dev-python/iso8601[${PYTHON_USEDEP}]
+ dev-python/platformdirs[${PYTHON_USEDEP}]
+ dev-python/tqdm[${PYTHON_USEDEP}]
+ dev-python/wraps[${PYTHON_USEDEP}]
+ downloaders? (
+ dev-python/boto[${PYTHON_USEDEP}]
+ dev-python/keyring[${PYTHON_USEDEP}]
+ dev-python/keyrings-alt[${PYTHON_USEDEP}]
+ dev-python/msgpack[${PYTHON_USEDEP}]
+ dev-python/requests[${PYTHON_USEDEP}]
+ )
+ metadata? (
+ dev-python/simplejson[${PYTHON_USEDEP}]
+ dev-python/whoosh[${PYTHON_USEDEP}]
+ )
+ misc? (
+ dev-python/argcomplete[${PYTHON_USEDEP}]
+ dev-python/pyperclip[${PYTHON_USEDEP}]
+ dev-python/python-dateutil[${PYTHON_USEDEP}]
+ )
+ publish? (
+ dev-vcs/python-gitlab[${PYTHON_USEDEP}]
+ )
+"
+DEPEND="
+ dev-python/setuptools[${PYTHON_USEDEP}]
+ test? (
+ dev-python/beautifulsoup4[${PYTHON_USEDEP}]
+ dev-python/httpretty[${PYTHON_USEDEP}]
+ dev-python/vcrpy[${PYTHON_USEDEP}]
+ )
+"
+
+# Noticed by upstream:
+# https://github.com/datalad/datalad/issues/6623
+PATCHES=( "${FILESDIR}/${PN}-0.17.0-skip.patch" )
+
+distutils_enable_tests pytest
+
+python_test() {
+ local -x DATALAD_TESTS_NONETWORK=1
+ #export DATALAD_TESTS_NONETWORK=1
+ epytest -k "not turtle and not slow and not usecase"
+ #epytest -k "not turtle"
+ #${EPYTHON} -m nose -s -v -A "not(integration or usecase or slow or network or turtle)" datalad || die
+ # Full test suite takes for ever:
+ # ${EPYTHON} -m nose -s -v datalad || die
+}
diff --git a/dev-vcs/datalad/datalad-0.17.2.ebuild b/dev-vcs/datalad/datalad-0.17.2.ebuild
new file mode 100644
index 000000000..86d141996
--- /dev/null
+++ b/dev-vcs/datalad/datalad-0.17.2.ebuild
@@ -0,0 +1,73 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DISTUTILS_USE_PEP517=setuptools
+PYTHON_COMPAT=( python3_{8..10} )
+inherit distutils-r1
+
+DESCRIPTION="Keep code, data, containers under control with git and git-annex"
+HOMEPAGE="https://github.com/datalad/datalad"
+SRC_URI="https://github.com/datalad/datalad/archive/refs/tags/${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64"
+IUSE="test +downloaders +metadata +publish misc"
+RESTRICT="!test? ( test )"
+
+RDEPEND="
+ app-arch/p7zip
+ app-arch/patool[${PYTHON_USEDEP}]
+ dev-python/annexremote[${PYTHON_USEDEP}]
+ >=dev-python/chardet-3.0.4[${PYTHON_USEDEP}]
+ dev-python/distro[${PYTHON_USEDEP}]
+ dev-python/fasteners[${PYTHON_USEDEP}]
+ dev-python/humanize[${PYTHON_USEDEP}]
+ dev-python/iso8601[${PYTHON_USEDEP}]
+ dev-python/platformdirs[${PYTHON_USEDEP}]
+ dev-python/tqdm[${PYTHON_USEDEP}]
+ dev-python/wraps[${PYTHON_USEDEP}]
+ downloaders? (
+ dev-python/boto[${PYTHON_USEDEP}]
+ dev-python/keyring[${PYTHON_USEDEP}]
+ dev-python/keyrings-alt[${PYTHON_USEDEP}]
+ dev-python/msgpack[${PYTHON_USEDEP}]
+ dev-python/requests[${PYTHON_USEDEP}]
+ )
+ metadata? (
+ dev-python/simplejson[${PYTHON_USEDEP}]
+ dev-python/whoosh[${PYTHON_USEDEP}]
+ )
+ misc? (
+ dev-python/argcomplete[${PYTHON_USEDEP}]
+ dev-python/pyperclip[${PYTHON_USEDEP}]
+ dev-python/python-dateutil[${PYTHON_USEDEP}]
+ )
+ publish? (
+ dev-vcs/python-gitlab[${PYTHON_USEDEP}]
+ )
+"
+DEPEND="
+ dev-python/setuptools[${PYTHON_USEDEP}]
+ test? (
+ dev-python/beautifulsoup4[${PYTHON_USEDEP}]
+ dev-python/httpretty[${PYTHON_USEDEP}]
+ dev-python/vcrpy[${PYTHON_USEDEP}]
+ )
+"
+
+EPYTEST_DESELECT=(
+ # Reported upstream: https://github.com/datalad/datalad/issues/6870
+ datalad/distributed/tests/test_ria_basics.py::test_version_check
+ datalad/local/tests/test_gitcredential.py::test_datalad_credential_helper
+)
+
+distutils_enable_tests pytest
+
+python_test() {
+ local -x DATALAD_TESTS_NONETWORK=1
+ # see test groups in "tox.ini"
+ epytest -k "not turtle and not slow and not usecase"
+}
diff --git a/dev-vcs/datalad/files/datalad-0.16.1-input.patch b/dev-vcs/datalad/files/datalad-0.16.1-input.patch
new file mode 100644
index 000000000..beb539b5d
--- /dev/null
+++ b/dev-vcs/datalad/files/datalad-0.16.1-input.patch
@@ -0,0 +1,94 @@
+diff --git a/datalad/local/tests/test_gitcredential.py b/datalad/local/tests/test_gitcredential.py
+index 09387a70d..6dc0e0be4 100644
+--- a/datalad/local/tests/test_gitcredential.py
++++ b/datalad/local/tests/test_gitcredential.py
+@@ -70,89 +70,6 @@ def test_gitcredential_interface(path):
+ assert_false(cred['password'])
+
+
+-@with_tempfile
+-def test_datalad_credential_helper(path):
+-
+- ds = Dataset(path).create()
+-
+- # tell git to use git-credential-datalad
+- ds.config.add('credential.helper', 'datalad', where='local')
+- ds.config.add('datalad.credentials.githelper.noninteractive', 'true',
+- where='global')
+-
+- from datalad.downloaders.providers import Providers
+-
+- url1 = "https://datalad-test.org/some"
+- url2 = "https://datalad-test.org/other"
+- provider_name = "datalad-test.org"
+-
+- # `Providers` code is old and only considers a dataset root based on PWD
+- # for config lookup. contextmanager below can be removed once the
+- # provider/credential system is redesigned.
+- with chpwd(ds.path):
+-
+- gitcred = GitCredentialInterface(url=url1, repo=ds)
+-
+- # There's nothing set up yet, helper should return empty
+- gitcred.fill()
+- eq_(gitcred['username'], '')
+- eq_(gitcred['password'], '')
+-
+- # store new credentials
+- # Note, that `Providers.enter_new()` currently uses user-level config
+- # files for storage only. TODO: make that an option!
+- # To not mess with existing ones, fail if it already exists:
+-
+- cfg_file = Path(Providers._get_providers_dirs()['user']) \
+- / f"{provider_name}.cfg"
+- assert_false(cfg_file.exists())
+-
+- # Make sure we clean up
+- from datalad.tests import _TEMP_PATHS_GENERATED
+- _TEMP_PATHS_GENERATED.append(str(cfg_file))
+-
+- # Give credentials to git and ask it to store them:
+- gitcred = GitCredentialInterface(url=url1, username="dl-user",
+- password="dl-pwd", repo=ds)
+- gitcred.approve()
+-
+- assert_true(cfg_file.exists())
+- providers = Providers.from_config_files()
+- p1 = providers.get_provider(url=url1, only_nondefault=True)
+- assert_is_instance(p1.credential, UserPassword)
+- eq_(p1.credential.get('user'), 'dl-user')
+- eq_(p1.credential.get('password'), 'dl-pwd')
+-
+- # default regex should be host only, so matching url2, too
+- p2 = providers.get_provider(url=url2, only_nondefault=True)
+- assert_is_instance(p1.credential, UserPassword)
+- eq_(p1.credential.get('user'), 'dl-user')
+- eq_(p1.credential.get('password'), 'dl-pwd')
+-
+- # git, too, should now find it for both URLs
+- gitcred = GitCredentialInterface(url=url1, repo=ds)
+- gitcred.fill()
+- eq_(gitcred['username'], 'dl-user')
+- eq_(gitcred['password'], 'dl-pwd')
+-
+- gitcred = GitCredentialInterface(url=url2, repo=ds)
+- gitcred.fill()
+- eq_(gitcred['username'], 'dl-user')
+- eq_(gitcred['password'], 'dl-pwd')
+-
+- # Rejection must not currently lead to deleting anything, since we would
+- # delete too broadly.
+- gitcred.reject()
+- assert_true(cfg_file.exists())
+- gitcred = GitCredentialInterface(url=url1, repo=ds)
+- gitcred.fill()
+- eq_(gitcred['username'], 'dl-user')
+- eq_(gitcred['password'], 'dl-pwd')
+- dlcred = UserPassword(name=provider_name)
+- eq_(dlcred.get('user'), 'dl-user')
+- eq_(dlcred.get('password'), 'dl-pwd')
+-
+-
+ @with_tempfile
+ def test_credential_cycle(path):
+
diff --git a/dev-vcs/datalad/files/datalad-0.17.0-skip.patch b/dev-vcs/datalad/files/datalad-0.17.0-skip.patch
new file mode 100644
index 000000000..33b2d6f63
--- /dev/null
+++ b/dev-vcs/datalad/files/datalad-0.17.0-skip.patch
@@ -0,0 +1,162 @@
+--- a/datalad/tests/utils_pytest.py 2022-07-08 01:32:06.000000000 -0400
++++ b/datalad/tests/utils_pytest.py 2022-07-21 05:07:09.341386460 -0400
+@@ -209,7 +209,7 @@
+ try:
+ imp = __import__(module)
+ except Exception as exc:
+- pytest.skip("Module %s fails to load" % module)
++ pytest.skip("Module %s fails to load" % module, allow_module_level=True)
+
+
+ def skip_if_scrapy_without_selector():
+@@ -220,7 +220,9 @@
+ except ImportError:
+ pytest.skip(
+ "scrapy misses Selector (too old? version: %s)"
+- % getattr(scrapy, '__version__'))
++ % getattr(scrapy, '__version__'),
++ allow_module_level=True,
++ )
+
+
+ def skip_if_url_is_not_available(url, regex=None):
+@@ -231,9 +233,11 @@
+ try:
+ content = providers.fetch(url)
+ if regex and re.search(regex, content):
+- pytest.skip("%s matched %r -- skipping the test" % (url, regex))
++ pytest.skip("%s matched %r -- skipping the test" % (url, regex),
++ allow_module_level=True,
++ )
+ except DownloadError:
+- pytest.skip("%s failed to download" % url)
++ pytest.skip("%s failed to download" % url, allow_module_level=True)
+
+
+ def check_not_generatorfunction(func):
+@@ -252,7 +256,9 @@
+
+ def check_and_raise():
+ if dl_cfg.get('datalad.tests.nonetwork'):
+- pytest.skip("Skipping since no network settings")
++ pytest.skip("Skipping since no network settings",
++ allow_module_level=True,
++ )
+
+ if func:
+ @wraps(func)
+@@ -273,7 +279,7 @@
+
+ def check_and_raise():
+ if on_windows:
+- pytest.skip("Skipping on Windows")
++ pytest.skip("Skipping on Windows", allow_module_level=True)
+
+ if func:
+ @wraps(func)
+@@ -296,7 +302,9 @@
+
+ def check_and_raise():
+ if hasattr(os, "geteuid") and os.geteuid() == 0:
+- pytest.skip("Skipping: test assumptions fail under root")
++ pytest.skip("Skipping: test assumptions fail under root",
++ allow_module_level=True,
++ )
+
+ if func:
+ @wraps(func)
+@@ -333,7 +341,9 @@
+ def _wrap_skip_if(*args, **kwargs):
+ if cond:
+ if method == 'raise':
+- pytest.skip(msg if msg else "condition was True")
++ pytest.skip(msg if msg else "condition was True",
++ allow_module_level=True,
++ )
+ elif method == 'pass':
+ print(msg if msg else "condition was True")
+ return
+@@ -375,7 +385,7 @@
+ @skip_ssh
+ def _wrap_skip_nomultiplex_ssh(*args, **kwargs):
+ if SSHManager is not MultiplexSSHManager:
+- pytest.skip("SSH without multiplexing is used")
++ pytest.skip("SSH without multiplexing is used", allow_module_level=True)
+ return func(*args, **kwargs)
+ return _wrap_skip_nomultiplex_ssh
+
+@@ -784,7 +794,7 @@
+ port = queue.get(timeout=300)
+ except multiprocessing.queues.Empty as e:
+ if self.use_ssl:
+- pytest.skip('No working SSL support')
++ pytest.skip('No working SSL support', allow_module_level=True)
+ else:
+ raise
+ self.url = 'http{}://{}:{}/'.format(
+@@ -822,7 +832,7 @@
+ #except requests.exceptions.SSLError as e:
+ except Exception as e:
+ self.stop()
+- pytest.skip('No working HTTPS setup')
++ pytest.skip('No working HTTPS setup', allow_module_level=True)
+ # now verify that the stdlib tooling also works
+ # if this fails, check datalad/tests/ca/prov.sh
+ # for info on deploying a datalad-root.crt
+@@ -843,7 +853,7 @@
+ #except URLError as e:
+ except Exception as e:
+ self.stop()
+- pytest.skip('No working HTTPS setup')
++ pytest.skip('No working HTTPS setup', allow_module_level=True)
+
+ def stop(self):
+ """Stop serving `path`.
+@@ -911,7 +921,7 @@
+ @attr('without_http_proxy')
+ def _wrap_without_http_proxy(*args, **kwargs):
+ if on_windows:
+- pytest.skip('Unclear why this is not working on windows')
++ pytest.skip('Unclear why this is not working on windows', allow_module_level=True)
+ # Such tests don't require real network so if http_proxy settings were
+ # provided, we remove them from the env for the duration of this run
+ env = os.environ.copy()
+@@ -1246,7 +1256,9 @@
+ assert(testrepos_uris)
+ else:
+ if not testrepos_uris:
+- pytest.skip("No non-networked repos to test on")
++ pytest.skip("No non-networked repos to test on",
++ allow_module_level=True,
++ )
+
+ fake_dates = dl_cfg.get("datalad.fake-dates")
+ ntested = 0
+@@ -1298,7 +1310,7 @@
+ # https://git-annex.branchable.com/bugs/Recent_hang_with_rsync_remote_with_older_systems___40__Xenial__44___Jessie__41__/
+ if external_versions['cmd:system-ssh'] < '7.4' and \
+ '8.20200522' < external_versions['cmd:annex'] < '8.20200720':
+- pytest.skip("Test known to hang")
++ pytest.skip("Test known to hang", allow_module_level=True)
+
+ sr_path, repo_path = args[-2:]
+ fn_args = args[:-2]
+@@ -2089,7 +2101,7 @@
+ _TESTS_ADJUSTED_TMPDIR = _check()
+
+ if _TESTS_ADJUSTED_TMPDIR:
+- pytest.skip("Test incompatible with adjusted branch default")
++ pytest.skip("Test incompatible with adjusted branch default", allow_module_level=True)
+ return func(*args, **kwargs)
+ return _wrap_skip_if_adjusted_branch
+
+@@ -2134,7 +2146,9 @@
+
+ if port is None:
+ pytest.skip("port for {} could not be determined: {}"
+- .format(host, err))
++ .format(host, err),
++ allow_module_level=True,
++ )
+ return port
+
diff --git a/media-libs/charls/Manifest b/media-libs/charls/Manifest
new file mode 100644
index 000000000..5275ba74f
--- /dev/null
+++ b/media-libs/charls/Manifest
@@ -0,0 +1 @@
+DIST charls-2.3.4.tar.gz 9483782 BLAKE2B 655bbe2f143df1c3b86f2bbb033217c9fa30f39cf9b449cb84ffd56ef2e3eb0ceb7088c8757cc1a59d6d9462363e59e62acee7dabcbe5a16fb68be0d5036b3eb SHA512 3f6e1a054d5f7cfa5309e3d1b280d0dbaaeac7f06b08619cefe15677367631d9f6eb96e54b3e5ec921ac50793a570c39178c3e4b52ce9837b731bbccd6a3d0ad
diff --git a/media-libs/charls/charls-2.3.4.ebuild b/media-libs/charls/charls-2.3.4.ebuild
new file mode 100644
index 000000000..155e910a8
--- /dev/null
+++ b/media-libs/charls/charls-2.3.4.ebuild
@@ -0,0 +1,30 @@
+# Copyright 2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+inherit cmake
+
+DESCRIPTION="C++ JPEG-LS library implementation"
+HOMEPAGE="https://github.com/team-charls/charls"
+SRC_URI="https://github.com/team-charls/charls/archive/refs/tags/${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+DEPEND=""
+RDEPEND="${DEPEND}"
+BDEPEND=""
+
+src_configure() {
+ # It doesn't seem like there is an automated way to run the test programs
+ # The samples option builds them, but do not install the resulting binaries
+ local mycmakeargs=(
+ -DCHARLS_BUILD_TESTS=OFF
+ -DCHARLS_BUILD_FUZZ_TEST=OFF
+ -DCHARLS_BUILD_SAMPLES=OFF
+ -DBUILD_SHARED_LIBS=ON
+ )
+ cmake_src_configure
+}
diff --git a/media-libs/charls/metadata.xml b/media-libs/charls/metadata.xml
new file mode 100644
index 000000000..3eef65eb8
--- /dev/null
+++ b/media-libs/charls/metadata.xml
@@ -0,0 +1,11 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <maintainer type="person">
+ <email>fx.carton91@gmail.com</email>
+ <name>François-Xavier Carton</name>
+ </maintainer>
+ <upstream>
+ <remote-id type="github">team-charls/charls</remote-id>
+ </upstream>
+</pkgmetadata>
diff --git a/net-misc/cernbox-client/Manifest b/net-misc/cernbox-client/Manifest
index ad8668437..af2fbf942 100644
--- a/net-misc/cernbox-client/Manifest
+++ b/net-misc/cernbox-client/Manifest
@@ -1,3 +1,4 @@
DIST cernbox-client-2.7.1-2596.src.rpm 15434250 BLAKE2B 3ef3fcc4010b3f292aee9b6bba7b5f9a72e4fbca1236e1e85e6523cd4e38d980fe4542c5f019647a19040be64628159651630a61ee8894cb7bcf4b69d342ccd0 SHA512 e329b84fc7aa62068f934bf8a9f47432709094adc618274c1b8ddbf7331094cb71b6208d3a777150ee426141301e0279cb219d65b123335f2e198a9b87980e5d
-DIST ownCloud-2.10.0.6519.tar.xz 5791912 BLAKE2B 3cf02ef89a6af249ab8f9d1b0a4cc899fbb11f49bf47ffb0ce042442da984d8dbf49619cf3344cf1837f1f3437e70f6e6d302f4e4c67a7df5f547368be4252ba SHA512 ab1e8aebefa049a73c436325b3b6e1d03e9a74f93ab6e090adbc71ccdd1cf56297898f004b12312ebba82158f5c2e299d9d0b13c14e291b855dcf267bac490f2
+DIST cernbox-client-2.9.2-6339.src.rpm 6243132 BLAKE2B c73c3c338f9d3fb7fa7b22efe9b6ff1380d80f3804e2e732873f5804ed31d98fb04f9dbcdc0f614136c08081bea825d70948f94a6c0c9dddfe20eca66e41c4c1 SHA512 ec0edff177a5b77144eef173e4e3f5d549762faa6682618124f5c64e37f657c3aa00f639723cf2c48b6c4d1049373cd24b41d347cd9bf3c7bb291ab3340d6b2a
DIST ownCloud-2.10.1.7389.tar.xz 5598044 BLAKE2B 8558a8a7b7bd4b8a0685b703f0882d6b5619c4902217d40feb4cf5587555b9a85363c7f61834e4c85a84789142fca8c73910fce66544f491ec5968818c816605 SHA512 2a0893d48786b88f8210966a2b6b48f5bdada82818d4115e68ecc6c0c926ba62bc74df03c4ab35eb271aef2f3a43b36b1a6a115585efe3739fd4a6164f9c45a1
+DIST ownCloud-2.11.1.8438.tar.xz 5655380 BLAKE2B da34adafabfc8c2b0bbfdff99a81b56f2d2639b5168b2165a847a6d5a4efe4e86578984c0f0c20564d0978aab18bb1a62330539bdd137f608a5cfc3ff8d84cf0 SHA512 fe38471f62e7233a7ba04f7fd2c7c7231957e6927c39d0bcf3f6f77fd6cbb1223618bbf6a8cc5fa15de10a35c7f07f2f5df0e49acbc2af5fe9333cda2eb41c92
diff --git a/net-misc/cernbox-client/cernbox-client-2.10.0.6519.ebuild b/net-misc/cernbox-client/cernbox-client-2.11.1.8438.ebuild
index c4eeaa7be..c698f7562 100644
--- a/net-misc/cernbox-client/cernbox-client-2.10.0.6519.ebuild
+++ b/net-misc/cernbox-client/cernbox-client-2.11.1.8438.ebuild
@@ -10,8 +10,8 @@ DESCRIPTION="Synchronize files from CERNBox EOS with your computer"
# Origin is classic owncloud-client, branded for CERN during compilation.
ORIGIN_PN="ownCloud"
BRANDED_P="cernbox"
-BRANDED_PV="2.7.1"
-BRANDED_REL="2596"
+BRANDED_PV="2.9.2"
+BRANDED_REL="6339"
HOMEPAGE="https://cernbox.cern.ch/"
SRC_URI="https://download.owncloud.com/desktop/${ORIGIN_PN}/stable/${PV}/source/${ORIGIN_PN}-${PV}.tar.xz
https://cernbox.cern.ch/cernbox/doc/Linux/repo/CentOS_7/src/${PN}-${BRANDED_PV}-${BRANDED_REL}.src.rpm
@@ -21,8 +21,9 @@ LICENSE="CC-BY-3.0 GPL-2"
SLOT="0"
KEYWORDS="~amd64 ~x86"
IUSE="dolphin gnome-keyring nautilus test"
+RESTRICT="!test? ( test )"
-COMMON_DEPEND=">=dev-db/sqlite-3.4:3
+RDEPEND=">=dev-db/sqlite-3.4:3
dev-libs/qtkeychain[gnome-keyring?,qt5(+)]
dev-qt/qtconcurrent:5
dev-qt/qtcore:5
@@ -39,21 +40,18 @@ COMMON_DEPEND=">=dev-db/sqlite-3.4:3
)
nautilus? ( dev-python/nautilus-python )"
-RDEPEND="${COMMON_DEPEND}"
-DEPEND="${COMMON_DEPEND}
- dev-qt/linguist-tools:5
- kde-frameworks/extra-cmake-modules
+DEPEND="${RDEPEND}
test? (
dev-util/cmocka
dev-qt/qttest:5
)"
-RESTRICT="!test? ( test )"
+BDEPEND="
+ dev-qt/linguist-tools:5
+ kde-frameworks/extra-cmake-modules"
S=${WORKDIR}/${ORIGIN_PN}-${PV}
-PATCHES=( "${FILESDIR}"/cernbox-theme-2.9.1.patch )
-
src_unpack() {
rpm_src_unpack ${PN}-${BRANDED_PV}-${BRANDED_REL}.src.rpm || die "failed to extract branding RPM"
mv ${PN%-*}-${BRANDED_PV}.${BRANDED_REL}/branding "${S}" || die "failed to extract branding"
diff --git a/profiles/package.mask b/profiles/package.mask
index b338c8d20..a21bb9773 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -30,8 +30,10 @@
#--- END OF EXAMPLES ---
-# Andrew Ammerlaan <andrewammerlaan@gentoo.org> (15 May 2022)
-# Requires old and removed batik:1.9::gentoo
-# No updates since 2019
-# Mask for removal in 30 days
-dev-java/jeuclid-core
+# Andrew Ammerlaan <andrewammerlaan@gentoo.org> (2022-08-22)
+# Depends on removed sci-libs/io_lib. removal in 30 days
+sci-biology/caftools
+sci-biology/salmon
+sci-biology/staden
+sci-biology/staden_doc
+sci-biology/roche454ace2caf
diff --git a/profiles/package.use.mask b/profiles/package.use.mask
index 92d1d843a..8aff1df94 100644
--- a/profiles/package.use.mask
+++ b/profiles/package.use.mask
@@ -15,6 +15,10 @@
## =media-video/mplayer-0.90_pre5-r1 foo
#
+# Andrew Ammerlaan <andrewammerlaan@gentoo.org> (23 Aug 2022)
+# vtk<9 no longer available in ::gentoo
+sci-libs/gdcm python
+
# Andrew Savchenko <bircoph@gentoo.org> (02 Jun 2016)
# doesn't link with plotutils-2.6
sci-physics/qcl plotutils
@@ -26,9 +30,3 @@ sci-biology/estscan icc ifc
# Christoph Junghans <ottxor@gentoo.org> (05 Nov 2013)
# gui sandbox error
dev-lang/conceptual gui
-
-# Andrew Ammerlaan <andrewammerlaan@gentoo.org> (15 Jan 2022)
-# dependencies not available
-# https://github.com/gentoo/sci/issues/1085
-# https://github.com/gentoo/sci/issues/1084
-sci-libs/mlpack go R
diff --git a/sci-biology/ants/Manifest b/sci-biology/ants/Manifest
index 867a142eb..c00c77f25 100644
--- a/sci-biology/ants/Manifest
+++ b/sci-biology/ants/Manifest
@@ -1,2 +1 @@
-DIST ants-2.3.4.tar.gz 2455843 BLAKE2B c00a2d3edebc0a121fa3b6618982c64fd986db9ea6aed1a1b2c7ced2f77ab154837a47e5bcb01f432b937160de2248b30a2bb7b526952852946e686858334e12 SHA512 084161505671a19530bec40c8209a67510d7de6e9d5afd151b806755ca703dadbea17c0a8d5c6472c7a81185821e17213ebf1488bc0325bfe858af783e8e6575
-DIST ants_testdata-2.3.4.tar.xz 25056552 BLAKE2B 6478ffe0c98fd3700a6de201f1271339276b45b461b02d4753acdcd1335c83196aa2ed89a89b5b4b0b3df33026f77b231ba1418c9eb7a2380356d4e224f9b310 SHA512 a266fbf2de0003ee689a9369c424c97c92cdf7e4d08ba713623948276d96c9f0f02ab14480c329f462db0059217138680bfe39654f9ec4ac99bf947f51da853d
+DIST ants-2.4.1.tar.gz 2473738 BLAKE2B 9abe2ade15bd8348452a23e15d8c862771ca2c8f971c44f185febfb1ee725b1ceb7e89359c8dfee31bd9c4087f10104831fe56bd1528ea7f5a81d52c1a4a4709 SHA512 533ca8adb934e8fe4e24425b3f8a9a8f0b67999d9593f8c8842e0298087d5bc58f65d1fcbfe78ac7dc17d0e786badc4a65bbde80d82d21c277ee6c1b3af7eae4
diff --git a/sci-biology/ants/ants-2.3.4.ebuild b/sci-biology/ants/ants-2.3.4.ebuild
deleted file mode 100644
index 95eb6355b..000000000
--- a/sci-biology/ants/ants-2.3.4.ebuild
+++ /dev/null
@@ -1,78 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-CMAKE_MAKEFILE_GENERATOR="emake"
-
-inherit cmake
-
-MY_PN="ANTs"
-
-DESCRIPTION="Advanced Normalitazion Tools for neuroimaging"
-HOMEPAGE="http://stnava.github.io/ANTs/"
-SRC_URI="
- https://github.com/ANTsX/ANTs/archive/v${PV}.tar.gz -> ${P}.tar.gz
- test? (
- http://resources.chymera.eu/distfiles/ants_testdata-${PV}.tar.xz
- )
-"
-
-SLOT="0"
-LICENSE="BSD"
-KEYWORDS="~amd64 ~x86"
-IUSE="test vtk"
-RESTRICT="!test? ( test )"
-
-DEPEND="
- vtk? (
- ~sci-libs/itk-5.1.0[vtkglue]
- sci-libs/vtk
- )
- !vtk? ( ~sci-libs/itk-5.1.0 )
-"
-RDEPEND="${DEPEND}"
-
-PATCHES=(
- "${FILESDIR}/${P}-version.patch"
- "${FILESDIR}/${P}-libdir.patch"
-)
-
-S="${WORKDIR}/${MY_PN}-${PV}"
-
-src_unpack() {
- default
- if use test; then
- mkdir -p "${S}/.ExternalData/MD5" || die "Could not create test data directory."
- tar xvf "${DISTDIR}/ants_testdata-${PV}.tar.xz" -C "${S}/.ExternalData/MD5/" > /dev/null || die "Could not unpack test data."
- fi
-}
-
-src_configure() {
- local mycmakeargs=(
- -DUSE_SYSTEM_ITK=ON
- -DITK_DIR="${EPREFIX}/usr/include/ITK-5.1/"
- -DBUILD_TESTING="$(usex test ON OFF)"
- -DUSE_VTK=$(usex vtk ON OFF)
- -DUSE_SYSTEM_VTK=$(usex vtk ON OFF)
- -DANTS_SNAPSHOT_VERSION:STRING=${PV}
- )
- use vtk && mycmakeargs+=(
- -DVTK_DIR="${EPREFIX}/usr/include/vtk-8.1/"
- )
- use test && mycmakeargs+=(
- -DExternalData_OBJECT_STORES="${S}/.ExternalData/MD5"
- )
- cmake_src_configure
-}
-
-src_install() {
- BUILD_DIR="${WORKDIR}/${P}_build/ANTS-build"
- cmake_src_install
- cd "${S}/Scripts" || die "scripts dir not found"
- dobin *.sh
- dodir /usr/$(get_libdir)/ants
- insinto "/usr/$(get_libdir)/ants"
- doins *
- doenvd "${FILESDIR}"/99ants
-}
diff --git a/sci-biology/ants/ants-2.4.1-r1.ebuild b/sci-biology/ants/ants-2.4.1-r1.ebuild
new file mode 100644
index 000000000..70d5d8873
--- /dev/null
+++ b/sci-biology/ants/ants-2.4.1-r1.ebuild
@@ -0,0 +1,60 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+CMAKE_MAKEFILE_GENERATOR="emake"
+inherit cmake
+
+MY_PN="ANTs"
+
+DESCRIPTION="Advanced Normalitazion Tools for neuroimaging"
+HOMEPAGE="https://stnava.github.io/ANTs/"
+SRC_URI="https://github.com/ANTsX/ANTs/archive/v${PV}.tar.gz -> ${P}.tar.gz"
+S="${WORKDIR}/${MY_PN}-${PV}"
+
+SLOT="0"
+LICENSE="BSD"
+KEYWORDS="~amd64 ~x86"
+IUSE="test vtk"
+RESTRICT="test"
+
+DEPEND="
+ !vtk? ( =sci-libs/itk-5.2*[fftw,-vtkglue] )
+ vtk? (
+ =sci-libs/itk-5.2*[fftw,vtkglue]
+ =sci-libs/vtk-9.1*
+ )
+"
+RDEPEND="${DEPEND}"
+
+PATCHES=(
+ "${FILESDIR}/${P}-fix-compile.patch"
+)
+
+src_configure() {
+ local mycmakeargs=(
+ -DBUILD_EXAMPLES=OFF
+ -DUSE_SYSTEM_ITK=ON
+ -DITK_USE_SYSTEM_FFTW=ON
+ -DITK_DIR="${EPREFIX}/usr/include/ITK-5.2/"
+ -DBUILD_TESTING="$(usex test ON OFF)"
+ -DUSE_VTK=$(usex vtk ON OFF)
+ -DUSE_SYSTEM_VTK=$(usex vtk ON OFF)
+ )
+ use vtk && mycmakeargs+=(
+ -DVTK_DIR="${EPREFIX}/usr/include/vtk-9.1/"
+ )
+ cmake_src_configure
+}
+
+src_install() {
+ BUILD_DIR="${WORKDIR}/${MY_PN}-${PV}_build/ANTS-build"
+ cmake_src_install
+ cd "${S}/Scripts" || die "scripts dir not found"
+ dobin *.sh
+ dodir /usr/$(get_libdir)/ants
+ insinto "/usr/$(get_libdir)/ants"
+ doins *
+ doenvd "${FILESDIR}"/99ants
+}
diff --git a/sci-biology/ants/files/ants-2.3.1_p20191013-logic.patch b/sci-biology/ants/files/ants-2.3.1_p20191013-logic.patch
deleted file mode 100644
index 932da9954..000000000
--- a/sci-biology/ants/files/ants-2.3.1_p20191013-logic.patch
+++ /dev/null
@@ -1,37 +0,0 @@
-From b2c828ff8e5ce537d7096af04b086e965fede9e8 Mon Sep 17 00:00:00 2001
-From: "Gabriel A. Devenyi" <gdevenyi@gmail.com>
-Date: Mon, 7 Oct 2019 22:01:51 -0400
-Subject: [PATCH] Fix install logic
-
----
- ANTS.cmake | 3 ++-
- SuperBuild.cmake | 2 ++
- 2 files changed, 4 insertions(+), 1 deletion(-)
-
-diff --git a/ANTS.cmake b/ANTS.cmake
-index a1baf845..95ffdc74 100644
---- a/ANTS.cmake
-+++ b/ANTS.cmake
-@@ -172,7 +172,8 @@ install(PROGRAMS Scripts/ANTSpexec.sh
- COMPONENT SCRIPTS
- )
-
--if(BUILD_SHARED_LIBS AND NOT (USE_SYSTEM_ITK AND USE_SYSTEM_VTK))
-+#Only install ITK/VTK libraries if shared build and superbuild is used
-+if(BUILD_SHARED_LIBS AND ((NOT USE_SYSTEM_ITK) OR ((NOT USE_SYSTEM_VTK) AND USE_VTK)))
- install(DIRECTORY ${CMAKE_BINARY_DIR}/../staging/lib/
- DESTINATION lib)
- endif()
-diff --git a/SuperBuild.cmake b/SuperBuild.cmake
-index f4630e64..32b930c2 100644
---- a/SuperBuild.cmake
-+++ b/SuperBuild.cmake
-@@ -207,6 +207,8 @@ list(APPEND ${CMAKE_PROJECT_NAME}_SUPERBUILD_EP_VARS
- CMAKE_C_COMPILER_LAUNCHER:STRING
- CMAKE_CXX_COMPILER_LAUNCHER:STRING
- CMAKE_CUDA_COMPILER_LAUNCHER:STRING
-+ USE_SYSTEM_ITK:BOOL
-+ USE_SYSTEM_VTK:BOOL
- )
-
- _expand_external_project_vars()
diff --git a/sci-biology/ants/files/ants-2.3.1_p20191013-paths.patch b/sci-biology/ants/files/ants-2.3.1_p20191013-paths.patch
deleted file mode 100644
index aaea92808..000000000
--- a/sci-biology/ants/files/ants-2.3.1_p20191013-paths.patch
+++ /dev/null
@@ -1,40 +0,0 @@
-diff --git a/Examples/CMakeLists.txt b/Examples/CMakeLists.txt
---- a/Examples/CMakeLists.txt
-+++ b/Examples/CMakeLists.txt
-@@ -16,8 +16,9 @@
-+include(GNUInstallDirs)
- install(TARGETS antsUtilities
-- RUNTIME DESTINATION bin
-+ RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR}
- COMPONENT RUNTIME_antsUtilities
-- LIBRARY DESTINATION lib
-+ LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR}
- COMPONENT RUNTIME_antsUtilities
-- ARCHIVE DESTINATION lib
-+ ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR}
- COMPONENT DEVELOPMENT_antsUtilities
- )
-@@ -38,8 +38,8 @@
- install(TARGETS l_${ANTS_FUNCTION_NAME} ${ANTS_FUNCTION_NAME}
-- RUNTIME DESTINATION bin
-+ RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR}
- COMPONENT RUNTIME_${ANTS_FUNCTION_NAME}
-- LIBRARY DESTINATION lib
-+ LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR}
- COMPONENT RUNTIME_${ANTS_FUNCTION_NAME}
-- ARCHIVE DESTINATION lib
-+ ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR}
- COMPONENT DEVELOPMENT_${ANTS_FUNCTION_NAME}
- )
-@@ -61,8 +61,8 @@
- install(TARGETS l_${ANTS_FUNCTION_NAME} ${ANTS_FUNCTION_NAME}
-- RUNTIME DESTINATION bin
-+ RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR}
- COMPONENT RUNTIME_${ANTS_FUNCTION_NAME}
-- LIBRARY DESTINATION lib
-+ LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR}
- COMPONENT RUNTIME_${ANTS_FUNCTION_NAME}
-- ARCHIVE DESTINATION lib
-+ ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR}
- COMPONENT DEVELOPMENT_${ANTS_FUNCTION_NAME}
- )
diff --git a/sci-biology/ants/files/ants-2.3.4-libdir.patch b/sci-biology/ants/files/ants-2.3.4-libdir.patch
deleted file mode 100644
index b593c2778..000000000
--- a/sci-biology/ants/files/ants-2.3.4-libdir.patch
+++ /dev/null
@@ -1,117 +0,0 @@
-From 329a7be631b33294d9cf3d58e8cdeb62e0aa993c Mon Sep 17 00:00:00 2001
-From: Philip A Cook <cookpa@pennmedicine.upenn.edu>
-Date: Fri, 26 Jun 2020 18:23:08 +0000
-Subject: [PATCH] ENH: Use GNUInstallDirs CMake module
-
-Trying to enable installation to the correct lib dir for each platform
----
- Common.cmake | 7 +++++--
- Examples/CMakeLists.txt | 32 ++++++++++++++++----------------
- 2 files changed, 21 insertions(+), 18 deletions(-)
-
-diff --git a/Common.cmake b/Common.cmake
-index 5e52d7f1..1e604113 100644
---- a/Common.cmake
-+++ b/Common.cmake
-@@ -103,8 +103,6 @@ if(PLATFORM_CHECK)
- endif()
- endif()
-
--
--
- #-------------------------------------------------------------------------
- # Augment compiler flags
- #-------------------------------------------------------------------------
-@@ -124,3 +122,8 @@ if(NOT CMAKE_POSITION_INDEPENDENT_CODE)
- set(CMAKE_POSITION_INDEPENDENT_CODE ON)
- endif()
- endif()
-+
-+#-------------------------------------------------------------------------
-+# Define install dirs for different platforms
-+#-------------------------------------------------------------------------
-+include(GNUInstallDirs)
-diff --git a/Examples/CMakeLists.txt b/Examples/CMakeLists.txt
-index 61781f56..cb352748 100644
---- a/Examples/CMakeLists.txt
-+++ b/Examples/CMakeLists.txt
-@@ -1,4 +1,4 @@
--SET(CMAKE_INSTALL_RPATH "${CMAKE_INSTALL_PREFIX}/lib")
-+SET(CMAKE_INSTALL_RPATH "${CMAKE_INSTALL_PREFIX}/${CMAKE_INSTALL_LIBDIR}")
- ## Note that the antsUtilities can always be built static. It will then be linked
- ## Directly into the other libraries.
- add_library(antsUtilities antsUtilities.cxx
-@@ -14,11 +14,11 @@ add_library(antsUtilities antsUtilities.cxx
- )
- target_link_libraries(antsUtilities ${ITK_LIBRARIES} )
- install(TARGETS antsUtilities
-- RUNTIME DESTINATION bin
-+ RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR}
- COMPONENT RUNTIME_antsUtilities
-- LIBRARY DESTINATION lib
-+ LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR}
- COMPONENT RUNTIME_antsUtilities
-- ARCHIVE DESTINATION lib
-+ ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR}
- COMPONENT DEVELOPMENT_antsUtilities
- )
-
-@@ -34,22 +34,22 @@ macro(STATIC_ANTS_BUILD ANTS_FUNCTION_NAME EXTRA_LIBS)
-
- if (ANTS_INSTALL_LIBS_ONLY)
- install(TARGETS l_${ANTS_FUNCTION_NAME}
-- # RUNTIME DESTINATION bin
-+ # RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR}
- # COMPONENT RUNTIME_${ANTS_FUNCTION_NAME}
-- LIBRARY DESTINATION lib
-+ LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR}
- COMPONENT RUNTIME_${ANTS_FUNCTION_NAME}
-- ARCHIVE DESTINATION lib
-+ ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR}
- COMPONENT DEVELOPMENT_${ANTS_FUNCTION_NAME}
- )
- else()
- add_executable( ${ANTS_FUNCTION_NAME} cli_${ANTS_FUNCTION_NAME}.cxx )
- target_link_libraries( ${ANTS_FUNCTION_NAME} l_${ANTS_FUNCTION_NAME} )
- install(TARGETS l_${ANTS_FUNCTION_NAME} ${ANTS_FUNCTION_NAME}
-- RUNTIME DESTINATION bin
-+ RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR}
- COMPONENT RUNTIME_${ANTS_FUNCTION_NAME}
-- LIBRARY DESTINATION lib
-+ LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR}
- COMPONENT RUNTIME_${ANTS_FUNCTION_NAME}
-- ARCHIVE DESTINATION lib
-+ ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR}
- COMPONENT DEVELOPMENT_${ANTS_FUNCTION_NAME}
- )
- endif()
-@@ -68,11 +68,11 @@ macro(DYNAMIC_ANTS_BUILD ANTS_FUNCTION_NAME EXTRA_LIBS)
-
- if (ANTS_INSTALL_LIBS_ONLY)
- install(TARGETS l_${ANTS_FUNCTION_NAME}
-- # RUNTIME DESTINATION bin
-+ # RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR}
- # COMPONENT RUNTIME_${ANTS_FUNCTION_NAME}
-- LIBRARY DESTINATION lib
-+ LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR}
- COMPONENT RUNTIME_${ANTS_FUNCTION_NAME}
-- ARCHIVE DESTINATION lib
-+ ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR}
- COMPONENT DEVELOPMENT_${ANTS_FUNCTION_NAME}
- )
- else()
-@@ -80,11 +80,11 @@ macro(DYNAMIC_ANTS_BUILD ANTS_FUNCTION_NAME EXTRA_LIBS)
- target_link_libraries( ${ANTS_FUNCTION_NAME} l_${ANTS_FUNCTION_NAME} )
-
- install(TARGETS l_${ANTS_FUNCTION_NAME} ${ANTS_FUNCTION_NAME}
-- RUNTIME DESTINATION bin
-+ RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR}
- COMPONENT RUNTIME_${ANTS_FUNCTION_NAME}
-- LIBRARY DESTINATION lib
-+ LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR}
- COMPONENT RUNTIME_${ANTS_FUNCTION_NAME}
-- ARCHIVE DESTINATION lib
-+ ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR}
- COMPONENT DEVELOPMENT_${ANTS_FUNCTION_NAME}
- )
- endif()
diff --git a/sci-biology/ants/files/ants-2.3.4-version.patch b/sci-biology/ants/files/ants-2.3.4-version.patch
deleted file mode 100644
index 487151d69..000000000
--- a/sci-biology/ants/files/ants-2.3.4-version.patch
+++ /dev/null
@@ -1,17 +0,0 @@
---- a/ANTS.cmake 2020-06-08 12:11:14.000000000 -0400
-+++ b/ANTS.cmake 2020-08-03 16:44:00.826633506 -0400
-@@ -37,7 +37,6 @@
- set(${PROJECT_NAME}_VERSION_MAJOR 0)
- set(${PROJECT_NAME}_VERSION_MINOR 0)
- set(${PROJECT_NAME}_VERSION_PATCH 0)
-- set(${PROJECT_NAME}_VERSION_TWEAK 0)
- set(${PROJECT_NAME}_VERSION "snapshot-${ANTS_SNAPSHOT_VERSION}")
- endif()
-
-@@ -46,7 +45,6 @@
- set(${PROJECT_NAME}_VERSION_MAJOR 0)
- set(${PROJECT_NAME}_VERSION_MINOR 0)
- set(${PROJECT_NAME}_VERSION_PATCH 0)
-- set(${PROJECT_NAME}_VERSION_TWEAK 0)
- set(${PROJECT_NAME}_VERSION "0.0.0.0")
- endif()
diff --git a/sci-biology/ants/files/ants-2.4.1-fix-compile.patch b/sci-biology/ants/files/ants-2.4.1-fix-compile.patch
new file mode 100644
index 000000000..bd7eecbcf
--- /dev/null
+++ b/sci-biology/ants/files/ants-2.4.1-fix-compile.patch
@@ -0,0 +1,13 @@
+diff --git a/Examples/PrintHeader.cxx b/Examples/PrintHeader.cxx
+index d1e7586..048d934 100644
+--- a/Examples/PrintHeader.cxx
++++ b/Examples/PrintHeader.cxx
+@@ -281,7 +281,7 @@ PrintHeader(int argc, char * argv[])
+ // Get the metadata as a generic object
+ string key = itMeta->first, v_string;
+ itk::SpatialOrientation::ValidCoordinateOrientationFlags v_oflags =
+- itk::SpatialOrientationEnums::ValidCoordinateOrientations::ITK_COORDINATE_ORIENTATION_INVALID;
++ itk::SpatialOrientation::ITK_COORDINATE_ORIENTATION_INVALID;
+
+ if (itk::ExposeMetaData<string>(mdd, key, v_string))
+ {
diff --git a/sci-biology/bidsschematools/Manifest b/sci-biology/bidsschematools/Manifest
new file mode 100644
index 000000000..18637621d
--- /dev/null
+++ b/sci-biology/bidsschematools/Manifest
@@ -0,0 +1,2 @@
+DIST bidsschematools-0.4.0.tar.gz 1158341 BLAKE2B a47ad610936e8bb9f91ade6f234f258535364d5cd3c188544dbb25f2540138596455656a25f167b1b6417cd896e15b4e1baf140999d0dbccdfa01432b2e88783 SHA512 c42dd337a0f2402de2c4794b85382b0e422ffbd9dbc814e943f32bc95cb1d7d2bc31dc40aeef6fd792d14ec09617de289ecdb794c0d22f1154f23e2f04bd5fdd
+DIST bidsschematools-0.5.1.tar.gz 1159308 BLAKE2B a53355b24e87ea7008fa64ca4f7e71c7bf29effc52f4aa3f855af633ce83817d5551eead4224d39f8cd46693dc48a7d9325a7ad8698e159b468e902982c5a940 SHA512 f1d9ab6b37c8fd4fd6a6aa821ef718c1af7f3d453d44c2c76c104f5601d40e5a328b0332255a591d8431e8c0ca3406dccd852c6c1fc8d832657b27a6b0076adc
diff --git a/sci-biology/bidsschematools/bidsschematools-0.4.0.ebuild b/sci-biology/bidsschematools/bidsschematools-0.4.0.ebuild
new file mode 100644
index 000000000..735f130e9
--- /dev/null
+++ b/sci-biology/bidsschematools/bidsschematools-0.4.0.ebuild
@@ -0,0 +1,37 @@
+# Copyright 2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DISTUTILS_USE_PEP517=setuptools
+PYTHON_COMPAT=( python3_{8..10} )
+
+inherit distutils-r1
+
+DESCRIPTION="A Python library for working with the BIDS schema"
+HOMEPAGE="https://github.com/bids-standard/bids-specification"
+SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE="render"
+
+RDEPEND="
+ dev-python/pyyaml[${PYTHON_USEDEP}]
+ render? (
+ dev-python/tabulate[${PYTHON_USEDEP}]
+ dev-python/pandas[${PYTHON_USEDEP}]
+ )
+"
+DEPEND=""
+
+distutils_enable_tests pytest
+
+src_prepare() {
+ if ! use render; then
+ rm "${S}/bidsschematools/render.py"
+ rm "${S}/bidsschematools/tests/test_render.py"
+ fi
+ default
+}
diff --git a/sci-biology/bidsschematools/bidsschematools-0.5.1.ebuild b/sci-biology/bidsschematools/bidsschematools-0.5.1.ebuild
new file mode 100644
index 000000000..735f130e9
--- /dev/null
+++ b/sci-biology/bidsschematools/bidsschematools-0.5.1.ebuild
@@ -0,0 +1,37 @@
+# Copyright 2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DISTUTILS_USE_PEP517=setuptools
+PYTHON_COMPAT=( python3_{8..10} )
+
+inherit distutils-r1
+
+DESCRIPTION="A Python library for working with the BIDS schema"
+HOMEPAGE="https://github.com/bids-standard/bids-specification"
+SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE="render"
+
+RDEPEND="
+ dev-python/pyyaml[${PYTHON_USEDEP}]
+ render? (
+ dev-python/tabulate[${PYTHON_USEDEP}]
+ dev-python/pandas[${PYTHON_USEDEP}]
+ )
+"
+DEPEND=""
+
+distutils_enable_tests pytest
+
+src_prepare() {
+ if ! use render; then
+ rm "${S}/bidsschematools/render.py"
+ rm "${S}/bidsschematools/tests/test_render.py"
+ fi
+ default
+}
diff --git a/sci-biology/bidsschematools/metadata.xml b/sci-biology/bidsschematools/metadata.xml
new file mode 100644
index 000000000..3fac5f14b
--- /dev/null
+++ b/sci-biology/bidsschematools/metadata.xml
@@ -0,0 +1,19 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <maintainer type="person">
+ <email>gentoo@chymera.eu</email>
+ <name>Horea Christian</name>
+ </maintainer>
+ <maintainer type="project">
+ <email>sci@gentoo.org</email>
+ <name>Gentoo Science Project</name>
+ </maintainer>
+ <upstream>
+ <remote-id type="github">bids-standard/bids-specification</remote-id>
+ <remote-id type="pypi">bidsschematools</remote-id>
+ </upstream>
+ <use>
+ <flag name="render">Support for schema table rendering</flag>
+ </use>
+</pkgmetadata>
diff --git a/sci-biology/bruker2nifti/bruker2nifti-1.0.4.ebuild b/sci-biology/bruker2nifti/bruker2nifti-1.0.4.ebuild
index 7a9c238ce..9550415b1 100644
--- a/sci-biology/bruker2nifti/bruker2nifti-1.0.4.ebuild
+++ b/sci-biology/bruker2nifti/bruker2nifti-1.0.4.ebuild
@@ -1,10 +1,10 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=7
+EAPI=8
DISTUTILS_USE_SETUPTOOLS="rdepend"
-PYTHON_COMPAT=( python3_{7,8,9} )
+PYTHON_COMPAT=( python3_{8..10} )
inherit distutils-r1
diff --git a/sci-biology/dcmstack/Manifest b/sci-biology/dcmstack/Manifest
index ca8d74137..c542a92a3 100644
--- a/sci-biology/dcmstack/Manifest
+++ b/sci-biology/dcmstack/Manifest
@@ -1 +1,2 @@
+DIST dcmstack-0.8-pytest.patch 90212 BLAKE2B dd2ddff15b590a19f991ab07a00cdb4facb1d18a9dc3556e85094e95dd8e31a0c49c801a1bc9dca040902d120c3a608c07ebd8f1fab1a350e6ffe0c2f0f52176 SHA512 b02108d77a10fe0e318621cf4e8babdc64b70a210700b286e972c5084a4fbcd44c6d750de77f547881c2d51a844efb10cc7be03e80b48e78d6cbdd99c4abf2f6
DIST dcmstack-0.8.tar.gz 1740289 BLAKE2B d57276c02db3f6a64874635528cb98d874cbc4f64464cfe47aa7217db96caddd46465e9275fced32363a22076b0b75e8c27649aac2fc15133d1354d7dd3b039e SHA512 c6ba0933e173f63426af60fb34fe671c9b49d3cf958628c15920f99925368a14f40c7821c1972c247e7f91c73be3bba288bf8794f334f32fef1feba4c5d5e7c1
diff --git a/sci-biology/dcmstack/dcmstack-0.8.ebuild b/sci-biology/dcmstack/dcmstack-0.8.ebuild
index de4dfde54..0ac8519b7 100644
--- a/sci-biology/dcmstack/dcmstack-0.8.ebuild
+++ b/sci-biology/dcmstack/dcmstack-0.8.ebuild
@@ -1,15 +1,18 @@
-# Copyright 1999-2020 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=7
+EAPI=8
-PYTHON_COMPAT=( python3_{7..9} )
+PYTHON_COMPAT=( python3_{8..10} )
inherit distutils-r1
DESCRIPTION="DICOM to Nifti coversion"
HOMEPAGE="https://dcmstack.readthedocs.org/en/latest/"
-SRC_URI="https://github.com/moloney/dcmstack/archive/v${PV}.tar.gz -> ${P}.tar.gz"
+SRC_URI="
+ https://github.com/moloney/dcmstack/archive/v${PV}.tar.gz -> ${P}.tar.gz
+ https://resources.chymera.eu/patches/dcmstack-0.8-pytest.patch
+"
EGIT_REPO_URI="https://github.com/moloney/dcmstack"
LICENSE="MIT"
@@ -22,4 +25,6 @@ RDEPEND="
sci-libs/pydicom[${PYTHON_USEDEP}]
"
-distutils_enable_tests setup.py
+PATCHES=( "${DISTDIR}/${P}-pytest.patch" )
+
+distutils_enable_tests pytest
diff --git a/sci-biology/dipy/dipy-1.1.1.ebuild b/sci-biology/dipy/dipy-1.1.1.ebuild
index c2c9f724e..15b986afe 100644
--- a/sci-biology/dipy/dipy-1.1.1.ebuild
+++ b/sci-biology/dipy/dipy-1.1.1.ebuild
@@ -1,9 +1,9 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=7
+EAPI=8
-PYTHON_COMPAT=( python3_{7..9} )
+PYTHON_COMPAT=( python3_{8..10} )
inherit distutils-r1
diff --git a/sci-biology/dipy/dipy-9999.ebuild b/sci-biology/dipy/dipy-9999.ebuild
deleted file mode 100644
index a1b162df6..000000000
--- a/sci-biology/dipy/dipy-9999.ebuild
+++ /dev/null
@@ -1,37 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-PYTHON_COMPAT=( python3_{7..9} )
-
-inherit distutils-r1 git-r3
-
-DESCRIPTION="Computational neuroanatomy project focusing on diffusion MRI"
-HOMEPAGE="https://github.com/nipy/dipy"
-SRC_URI=""
-EGIT_REPO_URI="https://github.com/nipy/dipy"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS=""
-IUSE="test"
-RESTRICT="!test? ( test )"
-
-RDEPEND="
- sci-libs/nibabel[${PYTHON_USEDEP}]
- dev-python/numpy[${PYTHON_USEDEP}]
- dev-python/scipy[${PYTHON_USEDEP}]
-"
-DEPEND="
- dev-python/cython[${PYTHON_USEDEP}]
- dev-python/h5py[${PYTHON_USEDEP}]
- dev-python/setuptools[${PYTHON_USEDEP}]
- test? ( dev-python/nose[${PYTHON_USEDEP}] )
-"
-
-python_test() {
- distutils_install_for_testing
- cd "${TEST_DIR}"/lib || die
- nosetests || die
-}
diff --git a/sci-biology/nilearn/nilearn-0.8.1.ebuild b/sci-biology/nilearn/nilearn-0.8.1.ebuild
index c73c9f519..166b45466 100644
--- a/sci-biology/nilearn/nilearn-0.8.1.ebuild
+++ b/sci-biology/nilearn/nilearn-0.8.1.ebuild
@@ -3,7 +3,7 @@
EAPI=8
-PYTHON_COMPAT=( python3_{8..9} )
+PYTHON_COMPAT=( python3_{8..10} )
inherit distutils-r1
diff --git a/sci-biology/nilearn/nilearn-0.9.1.ebuild b/sci-biology/nilearn/nilearn-0.9.1.ebuild
index 7e3716791..14f931258 100644
--- a/sci-biology/nilearn/nilearn-0.9.1.ebuild
+++ b/sci-biology/nilearn/nilearn-0.9.1.ebuild
@@ -3,7 +3,7 @@
EAPI=8
-PYTHON_COMPAT=( python3_{8..9} )
+PYTHON_COMPAT=( python3_{8..10} )
inherit distutils-r1
@@ -40,6 +40,7 @@ EPYTEST_IGNORE=(
# Reported upstream:
# https://github.com/nilearn/nilearn/issues/3232
EPYTEST_DESELECT=(
+ "nilearn/decoding/tests/test_decoder.py::test_decoder_dummy_classifier"
"nilearn/interfaces/fmriprep/tests/test_load_confounds.py::test_nilearn_standardize[False-True-zscore]"
"nilearn/interfaces/fmriprep/tests/test_load_confounds.py::test_nilearn_standardize[False-True-psc]"
"nilearn/interfaces/fmriprep/tests/test_load_confounds.py::test_nilearn_standardize[True-True-zscore]"
diff --git a/sci-biology/open-ephys-gui/Manifest b/sci-biology/open-ephys-gui/Manifest
index a2611bd74..53d2e5925 100644
--- a/sci-biology/open-ephys-gui/Manifest
+++ b/sci-biology/open-ephys-gui/Manifest
@@ -1 +1,2 @@
DIST open-ephys-gui-0.5.5.tar.gz 63347783 BLAKE2B 8f3ab3c20e23dd4f613e2ed47dca1827ddbcc5e95be5ca12dfeefdc84611653d531d629b78049397fd4951d558f63531ea2265d13e629c8da793fc20090d1075 SHA512 b835a7f8bb3eeb08ec77f6d14f988d6278b2f5b1966fbf8bec55d429c9cee36050cf574dd78a2ebad4adc5c681bcec5b64dcfb1ec87e548c55e2bf1bff2eb2dc
+DIST open-ephys-gui-0.6.1.tar.gz 44674639 BLAKE2B 10113418c41ccc62064bd8b993aab5402691259702c53c580e39371bd5034bc3b65babfa0adcaa7e2aadb8a86758e52cc4a86fee83db05614c849ed4c2b76ff4 SHA512 00ef7e5fd1242c84948e8eaf0479337365de21a28cb77252bf2baf806b186b9c8b7a424d756a4b6a883ecac48aefd6d2a532a8cadaa910e295b474d38056547e
diff --git a/sci-biology/open-ephys-gui/files/open-ephys-gui-0.6.1.patch b/sci-biology/open-ephys-gui/files/open-ephys-gui-0.6.1.patch
new file mode 100644
index 000000000..0992f2241
--- /dev/null
+++ b/sci-biology/open-ephys-gui/files/open-ephys-gui-0.6.1.patch
@@ -0,0 +1,15 @@
+# Add 'Gentoo' build type
+
+--- ../CMakeLists.txt 2022-08-24 15:27:32.871426442 -0300
++++ ../CMakeLists.txt 2022-08-24 15:31:03.438087613 -0300
+@@ -171,8 +171,8 @@
+ target_compile_options(open-ephys PRIVATE -O0) #enable optimization for linux debug
+ elseif (${CMAKE_BUILD_TYPE} STREQUAL "Release")
+ target_compile_options(open-ephys PRIVATE -O3) #enable optimization for linux release
+- else()
+- message(FATAL_ERROR "Invalid build type")
++ # else()
++ # message(FATAL_ERROR "Invalid build type")
+ endif()
+ find_package(CURL REQUIRED)
+ find_package(PkgConfig REQUIRED)
diff --git a/sci-biology/open-ephys-gui/files/open-ephys-gui-9999.patch b/sci-biology/open-ephys-gui/files/open-ephys-gui-9999.patch
deleted file mode 100644
index 77e401639..000000000
--- a/sci-biology/open-ephys-gui/files/open-ephys-gui-9999.patch
+++ /dev/null
@@ -1,12 +0,0 @@
-# Add 'Gentoo' build type
-
---- ../CMakeLists.txt 2019-12-02 22:29:24.021065669 -0300
-+++ ../CMakeLists.txt 2019-12-02 22:29:11.251065418 -0300
-@@ -123,6 +123,7 @@
- if(${CMAKE_BUILD_TYPE} STREQUAL "Debug")
-
- elseif (${CMAKE_BUILD_TYPE} STREQUAL "Release")
-+ elseif (${CMAKE_BUILD_TYPE} STREQUAL "Gentoo")
- else()
- message(FATAL_ERROR "Invalid build type")
- endif()
diff --git a/sci-biology/open-ephys-gui/files/open-ephys-gui-99999999.patch b/sci-biology/open-ephys-gui/files/open-ephys-gui-99999999.patch
deleted file mode 100644
index 77e401639..000000000
--- a/sci-biology/open-ephys-gui/files/open-ephys-gui-99999999.patch
+++ /dev/null
@@ -1,12 +0,0 @@
-# Add 'Gentoo' build type
-
---- ../CMakeLists.txt 2019-12-02 22:29:24.021065669 -0300
-+++ ../CMakeLists.txt 2019-12-02 22:29:11.251065418 -0300
-@@ -123,6 +123,7 @@
- if(${CMAKE_BUILD_TYPE} STREQUAL "Debug")
-
- elseif (${CMAKE_BUILD_TYPE} STREQUAL "Release")
-+ elseif (${CMAKE_BUILD_TYPE} STREQUAL "Gentoo")
- else()
- message(FATAL_ERROR "Invalid build type")
- endif()
diff --git a/sci-biology/open-ephys-gui/metadata.xml b/sci-biology/open-ephys-gui/metadata.xml
index ed9bf87e3..2c9af77a9 100644
--- a/sci-biology/open-ephys-gui/metadata.xml
+++ b/sci-biology/open-ephys-gui/metadata.xml
@@ -5,6 +5,10 @@
<email>malfatti@disroot.org</email>
<name>T Malfatti</name>
</maintainer>
+ <maintainer type="project">
+ <email>sci@gentoo.org</email>
+ <name>Gentoo Science Project</name>
+ </maintainer>
<upstream>
<remote-id type="github">open-ephys/plugin-GUI</remote-id>
</upstream>
diff --git a/sci-biology/open-ephys-gui/open-ephys-gui-0.6.1.ebuild b/sci-biology/open-ephys-gui/open-ephys-gui-0.6.1.ebuild
new file mode 100644
index 000000000..fe6791a2d
--- /dev/null
+++ b/sci-biology/open-ephys-gui/open-ephys-gui-0.6.1.ebuild
@@ -0,0 +1,83 @@
+# Copyright 2019-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+inherit cmake udev
+
+DESCRIPTION="Processing, recording, and visualizing multichannel ephys data"
+HOMEPAGE="https://open-ephys.org/gui/"
+LICENSE="GPL-3"
+
+if [[ ${PV} == "9999" ]] ; then
+ inherit git-r3
+ EGIT_REPO_URI="https://github.com/open-ephys/plugin-GUI"
+ EGIT_BRANCH="main"
+ Suffix=${EGIT_BRANCH}
+ SubDir=${P}
+elif [[ ${PV} == "99999999" ]] ; then
+ inherit git-r3
+ EGIT_REPO_URI="https://github.com/open-ephys/plugin-GUI"
+ EGIT_BRANCH="development"
+ Suffix=${EGIT_BRANCH}
+ SubDir=${P}
+else
+ SRC_URI="https://github.com/open-ephys/plugin-GUI/archive/v${PV}.tar.gz -> ${P}.tar.gz"
+ Suffix=${PV}
+ SubDir="plugin-GUI-${PV}"
+ S="${WORKDIR}/${SubDir}"
+ KEYWORDS="~amd64 ~x86"
+fi
+
+SLOT="${PV}"
+IUSE="jack"
+
+DEPEND="
+ dev-libs/openssl
+ media-libs/alsa-lib
+ media-libs/freeglut
+ media-libs/freetype
+ net-libs/webkit-gtk
+ net-misc/curl
+ x11-libs/libXrandr
+ x11-libs/libXcursor
+ x11-libs/libXinerama
+ jack? ( || ( media-sound/jack-audio-connection-kit media-sound/jack2 ) )
+"
+RDEPEND="${DEPEND}"
+
+BUILD_DIR="${S}/Build"
+PATCHES=( "${FILESDIR}"/${P}.patch )
+
+QA_PREBUILT="opt/open-ephys-*/shared/*.so"
+QA_PRESTRIPPED="
+ opt/open-ephys-*/plugins/*.so
+ opt/open-ephys-*/open-ephys
+"
+
+src_prepare() {
+ cmake_src_prepare
+
+ if use jack; then
+ sed -i 's/JUCE_APP_VERSION=/JUCE_JACK=1\n JUCE_APP_VERSION=/' "${WORKDIR}/${SubDir}/CMakeLists.txt" || die "Sed failed!"
+ fi
+}
+
+src_configure() {
+ local mycmakeargs=( -DCMAKE_SKIP_RPATH=ON )
+ cmake_src_configure
+}
+
+src_install() {
+ dodir opt/open-ephys-"${Suffix}"/ lib/udev/rules.d/
+ cp -R "${BUILD_DIR}"/RelWithDebInfo/* "${ED}"/opt/open-ephys-"${Suffix}"/ || die
+ udev_newrules "${WORKDIR}"/"${SubDir}"/Resources/Scripts/40-open-ephys.rules 40-open-ephys-"${Suffix}".rules
+ dosym ../../opt/open-ephys-"${Suffix}"/open-ephys usr/bin/open-ephys-"${Suffix}"
+}
+
+pkg_postinst() {
+ udev_reload
+}
+
+pkg_postrm() {
+ udev_reload
+}
diff --git a/sci-biology/open-ephys-gui/open-ephys-gui-9999.ebuild b/sci-biology/open-ephys-gui/open-ephys-gui-9999.ebuild
index 1c2b20e24..446972aeb 100644
--- a/sci-biology/open-ephys-gui/open-ephys-gui-9999.ebuild
+++ b/sci-biology/open-ephys-gui/open-ephys-gui-9999.ebuild
@@ -1,7 +1,7 @@
-# Copyright 2019-2021 Gentoo Authors
+# Copyright 2019-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=7
+EAPI=8
inherit cmake udev
DESCRIPTION="Processing, recording, and visualizing multichannel ephys data"
@@ -11,7 +11,7 @@ LICENSE="GPL-3"
if [[ ${PV} == "9999" ]] ; then
inherit git-r3
EGIT_REPO_URI="https://github.com/open-ephys/plugin-GUI"
- EGIT_BRANCH="master"
+ EGIT_BRANCH="main"
Suffix=${EGIT_BRANCH}
SubDir=${P}
elif [[ ${PV} == "99999999" ]] ; then
@@ -32,9 +32,12 @@ SLOT="${PV}"
IUSE="jack"
DEPEND="
+ dev-libs/openssl
media-libs/alsa-lib
media-libs/freeglut
media-libs/freetype
+ net-libs/webkit-gtk
+ net-misc/curl
x11-libs/libXrandr
x11-libs/libXcursor
x11-libs/libXinerama
@@ -43,7 +46,7 @@ DEPEND="
RDEPEND="${DEPEND}"
BUILD_DIR="${S}/Build"
-PATCHES=( "${FILESDIR}"/${P}.patch )
+PATCHES=( "${FILESDIR}"/"${PN}"-0.6.1.patch )
QA_PREBUILT="opt/open-ephys-*/shared/*.so"
QA_PRESTRIPPED="
@@ -66,7 +69,7 @@ src_configure() {
src_install() {
dodir opt/open-ephys-"${Suffix}"/ lib/udev/rules.d/
- cp -R "${BUILD_DIR}"/Gentoo/* "${ED}"/opt/open-ephys-"${Suffix}"/
+ cp -R "${BUILD_DIR}"/RelWithDebInfo/* "${ED}"/opt/open-ephys-"${Suffix}"/ || die
udev_newrules "${WORKDIR}"/"${SubDir}"/Resources/Scripts/40-open-ephys.rules 40-open-ephys-"${Suffix}".rules
dosym ../../opt/open-ephys-"${Suffix}"/open-ephys usr/bin/open-ephys-"${Suffix}"
}
diff --git a/sci-biology/open-ephys-gui/open-ephys-gui-99999999.ebuild b/sci-biology/open-ephys-gui/open-ephys-gui-99999999.ebuild
index 1c2b20e24..446972aeb 100644
--- a/sci-biology/open-ephys-gui/open-ephys-gui-99999999.ebuild
+++ b/sci-biology/open-ephys-gui/open-ephys-gui-99999999.ebuild
@@ -1,7 +1,7 @@
-# Copyright 2019-2021 Gentoo Authors
+# Copyright 2019-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=7
+EAPI=8
inherit cmake udev
DESCRIPTION="Processing, recording, and visualizing multichannel ephys data"
@@ -11,7 +11,7 @@ LICENSE="GPL-3"
if [[ ${PV} == "9999" ]] ; then
inherit git-r3
EGIT_REPO_URI="https://github.com/open-ephys/plugin-GUI"
- EGIT_BRANCH="master"
+ EGIT_BRANCH="main"
Suffix=${EGIT_BRANCH}
SubDir=${P}
elif [[ ${PV} == "99999999" ]] ; then
@@ -32,9 +32,12 @@ SLOT="${PV}"
IUSE="jack"
DEPEND="
+ dev-libs/openssl
media-libs/alsa-lib
media-libs/freeglut
media-libs/freetype
+ net-libs/webkit-gtk
+ net-misc/curl
x11-libs/libXrandr
x11-libs/libXcursor
x11-libs/libXinerama
@@ -43,7 +46,7 @@ DEPEND="
RDEPEND="${DEPEND}"
BUILD_DIR="${S}/Build"
-PATCHES=( "${FILESDIR}"/${P}.patch )
+PATCHES=( "${FILESDIR}"/"${PN}"-0.6.1.patch )
QA_PREBUILT="opt/open-ephys-*/shared/*.so"
QA_PRESTRIPPED="
@@ -66,7 +69,7 @@ src_configure() {
src_install() {
dodir opt/open-ephys-"${Suffix}"/ lib/udev/rules.d/
- cp -R "${BUILD_DIR}"/Gentoo/* "${ED}"/opt/open-ephys-"${Suffix}"/
+ cp -R "${BUILD_DIR}"/RelWithDebInfo/* "${ED}"/opt/open-ephys-"${Suffix}"/ || die
udev_newrules "${WORKDIR}"/"${SubDir}"/Resources/Scripts/40-open-ephys.rules 40-open-ephys-"${Suffix}".rules
dosym ../../opt/open-ephys-"${Suffix}"/open-ephys usr/bin/open-ephys-"${Suffix}"
}
diff --git a/sci-biology/samri/samri-0.5.ebuild b/sci-biology/samri/samri-0.5.ebuild
index 4cc90a0ef..aed6061e7 100644
--- a/sci-biology/samri/samri-0.5.ebuild
+++ b/sci-biology/samri/samri-0.5.ebuild
@@ -1,9 +1,9 @@
# Copyright 1999-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=7
+EAPI=8
-PYTHON_COMPAT=( python3_{8..9} )
+PYTHON_COMPAT=( python3_{8..10} )
inherit distutils-r1 prefix
diff --git a/sci-electronics/minipro/Manifest b/sci-electronics/minipro/Manifest
index 38ce85995..d37c88485 100644
--- a/sci-electronics/minipro/Manifest
+++ b/sci-electronics/minipro/Manifest
@@ -1 +1 @@
-DIST minipro-0.4.tar.gz 363052 BLAKE2B e6b07c05c1c2841fa862132d598781f3675df61cb41ac447e8dfb9677913126429f4f547afc757f2d32360ddbfc89850f3b234c13b381920d5f726f5fe163dd7 SHA512 cdbcb1a02b475874a32497b9a683a0b4734a16cc75d2b0336a5c5cd26a30b63ca4c115b3cfbe6448a8bb3be95aeb902c79ac256c45789d45abf9e01cda355eda
+DIST minipro-0.5.tar.gz 388754 BLAKE2B c22110c269405e7b8ff81fd7c649c2b652bc39da84d92cf9a151da71a1c6d4a202baa6ae13a1fb789a04c8e57f3cc9a60403bcef82896320d95e2507c5960f01 SHA512 e2341213bc43ef53b106211d07a488a142083fe4b6dd6ced0f02595164ce2e0e47f6bdc0a6f6c63f19b9b9438c8f5ad173485953d8a29cb39f89272f8e70dc7c
diff --git a/sci-electronics/minipro/files/minipro-0.5-makefile.patch b/sci-electronics/minipro/files/minipro-0.5-makefile.patch
new file mode 100644
index 000000000..221643895
--- /dev/null
+++ b/sci-electronics/minipro/files/minipro-0.5-makefile.patch
@@ -0,0 +1,12 @@
+can't seem to override PREFIX at build time, so patch it
+--- minipro-0.5/Makefile 2020-11-04 21:35:31.000000000 -0800
++++ minipro-0.5/Makefile 2022-07-22 11:42:54.866390621 -0700
+@@ -9,7 +9,7 @@
+
+ # Normally minipro is installed to /usr/local. If you want to put it
+ # somewhere else, define that location here.
+-PREFIX ?= /usr/local
++PREFIX ?= /usr
+ MANDIR ?= $(PREFIX)/share/man
+
+ # Some older releases of MacOS need some extra library flags.
diff --git a/sci-electronics/minipro/metadata.xml b/sci-electronics/minipro/metadata.xml
index 430c9ea1b..438079e92 100644
--- a/sci-electronics/minipro/metadata.xml
+++ b/sci-electronics/minipro/metadata.xml
@@ -5,6 +5,13 @@
<email>sci-electronics@gentoo.org</email>
<name>Gentoo Electronics Project</name>
</maintainer>
+ <maintainer type="person">
+ <email>scott@alfter.us</email>
+ <name>Scott Alfter</name>
+ </maintainer>
+ <longdescription lang="en">
+ an open-source program for controlling the MiniPRO TL866xx series of chip programmers
+ </longdescription>
<upstream>
<remote-id type="github">vdudouyt/minipro</remote-id>
</upstream>
diff --git a/sci-electronics/minipro/minipro-0.4.ebuild b/sci-electronics/minipro/minipro-0.5.ebuild
index ab75d6774..60854d55c 100644
--- a/sci-electronics/minipro/minipro-0.4.ebuild
+++ b/sci-electronics/minipro/minipro-0.5.ebuild
@@ -1,9 +1,9 @@
-# Copyright 1999-2020 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=7
+EAPI=8
-inherit bash-completion-r1 udev
+inherit udev
DESCRIPTION="A free and open TL866XX programmer"
HOMEPAGE="https://gitlab.com/DavidGriffith/minipro"
@@ -16,9 +16,12 @@ KEYWORDS="~amd64"
RDEPEND="virtual/libusb:1"
DEPEND="${RDEPEND}"
-src_install() {
- dobin minipro miniprohex
- doman man/minipro.1
- udev_dorules udev/*.rules
- dobashcomp bash_completion.d/minipro
+PATCHES=( "${FILESDIR}/${P}-makefile.patch" )
+
+pkg_postinst() {
+ udev_reload
+}
+
+pkg_postrm() {
+ udev_reload
}
diff --git a/sci-libs/HDF5Plugin-Zstandard/HDF5Plugin-Zstandard-0_pre20201121.ebuild b/sci-libs/HDF5Plugin-Zstandard/HDF5Plugin-Zstandard-0_pre20201121-r1.ebuild
index a74996b46..d1257f0ee 100644
--- a/sci-libs/HDF5Plugin-Zstandard/HDF5Plugin-Zstandard-0_pre20201121.ebuild
+++ b/sci-libs/HDF5Plugin-Zstandard/HDF5Plugin-Zstandard-0_pre20201121-r1.ebuild
@@ -1,4 +1,4 @@
-# Copyright 2020 Gentoo Authors
+# Copyright 2020-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=7
@@ -14,7 +14,7 @@ LICENSE="Apache-2.0"
SLOT="0"
KEYWORDS="~amd64 ~x86"
-DEPEND="app-arch/zstd >=sci-libs/hdf5-1.12.2-r2"
+DEPEND="app-arch/zstd >=sci-libs/hdf5-1.12.2-r5"
RDEPEND="${DEPEND}"
S=${WORKDIR}/${PN}-${COMMIT}
diff --git a/sci-libs/bids-validator/bids-validator-1.4.4.ebuild b/sci-libs/bids-validator/bids-validator-1.4.4.ebuild
index 00bf81571..c47095d79 100644
--- a/sci-libs/bids-validator/bids-validator-1.4.4.ebuild
+++ b/sci-libs/bids-validator/bids-validator-1.4.4.ebuild
@@ -1,9 +1,9 @@
-# Copyright 1999-2020 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=7
+EAPI=8
-PYTHON_COMPAT=( python3_{7..9} )
+PYTHON_COMPAT=( python3_{8..10} )
inherit distutils-r1
diff --git a/sci-libs/gdcm/Manifest b/sci-libs/gdcm/Manifest
new file mode 100644
index 000000000..64b9caefd
--- /dev/null
+++ b/sci-libs/gdcm/Manifest
@@ -0,0 +1,2 @@
+DIST gdcm-3.0.14.tar.bz2 2992355 BLAKE2B a97209a8bb6896095bfc59ac974b667386c8711f20118252567cf983f15165d259da7858ccfd6bfdfbb25194d7687c98512953b480913acec4bf6d176af7a005 SHA512 9c7d70723d288bf116a8b594c02dd965a4e80476e1c79a7c3cbd09584a229c83ad67f082c9b286305e3bb64150c8267ced06b5fb963adbeeb36e383f76612220
+DIST gdcmData.tar.gz 121157465 BLAKE2B 19b13efc2094d3e373f0f658f1120b1c83ea6da1be73fb392b815433725b4a6db2debb9ab7d9f2caa665637f152f70694cdf226c934850dfda344107050a14a6 SHA512 ddc67a7a0b41b2d6e1e03defb6fb8a06ceeb2e9dd9bb47dfa4f7283d79df7c1e52577b799c00e930719ae6cdda46bded9497a67b8241359f238f5366085ec9ee
diff --git a/sci-libs/gdcm/files/gdcm-3.0.14-include-math-h.patch b/sci-libs/gdcm/files/gdcm-3.0.14-include-math-h.patch
new file mode 100644
index 000000000..ba99c3547
--- /dev/null
+++ b/sci-libs/gdcm/files/gdcm-3.0.14-include-math-h.patch
@@ -0,0 +1,15 @@
+https://cgit.freebsd.org/ports/plain/devel/gdcm/files/patch-Utilities_VTK_vtkImageMapToWindowLevelColors2.cxx?id=8f5541298099b722e34632ca9ed388bda91064e7
+
+- workaround for https://sourceforge.net/p/gdcm/bugs/536/
+
+--- a/Utilities/VTK/vtkImageMapToWindowLevelColors2.cxx 2022-06-26 20:39:45 UTC
++++ b/Utilities/VTK/vtkImageMapToWindowLevelColors2.cxx
+@@ -37,6 +37,8 @@
+ #include "vtkScalarsToColors.h"
+ #include "vtkPointData.h"
+
++#include <math.h>
++
+ //vtkCxxRevisionMacro(vtkImageMapToWindowLevelColors2, "$Revision: 1.3 $")
+ vtkStandardNewMacro(vtkImageMapToWindowLevelColors2)
+
diff --git a/sci-libs/gdcm/files/gdcm_support_vtk9.patch b/sci-libs/gdcm/files/gdcm_support_vtk9.patch
new file mode 100644
index 000000000..3818a82b5
--- /dev/null
+++ b/sci-libs/gdcm/files/gdcm_support_vtk9.patch
@@ -0,0 +1,70 @@
+--- a/Utilities/VTK/CMakeLists.txt
++++ b/Utilities/VTK/CMakeLists.txt
+@@ -26,6 +26,11 @@
+ )
+ endif()
+
++if( ${VTK_MAJOR_VERSION} GREATER_EQUAL 9 )
++ set(VTK_INCLUDE_DIRS "${VTK_PREFIX_PATH}/include/vtk-${VTK_MAJOR_VERSION}.${VTK_MINOR_VERSION}")
++ include_directories(AFTER ${VTK_INCLUDE_DIRS})
++endif()
++
+ include(CheckCXXSourceCompiles)
+ set(CMAKE_REQUIRED_INCLUDES ${VTK_INCLUDE_DIRS})
+ CHECK_CXX_SOURCE_COMPILES(
+@@ -94,6 +99,10 @@
+ endforeach()
+ endif()
+
++if( ${VTK_MAJOR_VERSION} GREATER_EQUAL 9 )
++ string(REGEX REPLACE "vtk([^;]+)" "VTK::\\1" vtkgdcm_LIBS "${vtkgdcm_LIBS}")
++endif()
++
+ # Use wrapping hints for this project.
+ #set(VTK_WRAP_HINTS "${PROJECT_SOURCE_DIR}/hints")
+
+--- a/Utilities/VTK/Applications/CMakeLists.txt
++++ b/Utilities/VTK/Applications/CMakeLists.txt
+@@ -25,6 +25,11 @@
+ )
+ endif()
+
++set(vtk_ioxml vtkIOXML)
++if( ${VTK_MAJOR_VERSION} GREATER_EQUAL 9 )
++ set(vtk_ioxml VTK::IOXML)
++endif()
++
+ foreach(app ${GDCM_VTK_APPS})
+ add_executable(${app} ${app}.cxx)
+ if(GDCM_EXECUTABLE_PROPERTIES)
+@@ -42,7 +47,7 @@
+ endif()
+ else()
+ # >= 6.0
+- target_link_libraries(${app} ${VTK_LIBRARIES} vtkIOXML)
++ target_link_libraries(${app} ${VTK_LIBRARIES} ${vtk_ioxml})
+ endif()
+ if(WIN32 AND NOT CYGWIN)
+ target_link_libraries(${app} gdcmgetopt)
+--- a/Utilities/VTK/vtkGDCMPolyDataWriter.cxx
++++ b/Utilities/VTK/vtkGDCMPolyDataWriter.cxx
+@@ -496,6 +496,9 @@
+ sqi = new SequenceOfItems;
+
+ vtkIdType npts = 0;
++#if VTK_MAJOR_VERSION >= 9
++ const
++#endif
+ vtkIdType *indx = 0;
+ double v[3];
+ unsigned int cellnum = 0;
+@@ -759,6 +762,9 @@
+ vtkPoints *pts;
+ vtkCellArray *polys;
+ vtkIdType npts = 0;
++#if VTK_MAJOR_VERSION >= 9
++ const
++#endif
+ vtkIdType *indx = 0;
+ pts = theData->GetPoints();
+ polys = theData->GetPolys();
diff --git a/sci-libs/gdcm/gdcm-3.0.14.ebuild b/sci-libs/gdcm/gdcm-3.0.14.ebuild
new file mode 100644
index 000000000..5249e81b7
--- /dev/null
+++ b/sci-libs/gdcm/gdcm-3.0.14.ebuild
@@ -0,0 +1,121 @@
+# Copyright 2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{9..10} )
+
+inherit cmake python-single-r1
+
+DESCRIPTION="Cross-platform DICOM implementation"
+HOMEPAGE="http://gdcm.sourceforge.net/"
+SRC_URI="mirror://sourceforge/gdcm/${P}.tar.bz2
+ test? ( mirror://sourceforge/gdcm/gdcmData.tar.gz )" # 3.0.14: .bz2 is broken, should be checked in next release
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="doc python test vtk"
+RESTRICT="!test? ( test )"
+
+DEPEND="
+ app-text/poppler:0=[cxx]
+ dev-libs/expat:0=
+ dev-libs/json-c:0=
+ dev-libs/libxml2:2=
+ dev-libs/openssl:0=
+ >=media-libs/charls-2.0.0:0=
+ >=media-libs/openjpeg-2.0.0:2=
+ sys-apps/util-linux:0=
+ sys-libs/zlib:0=
+ python? ( ${PYTHON_DEPS} )
+ vtk? (
+ sci-libs/vtk[rendering]
+ python? (
+ sci-libs/vtk[python,${PYTHON_SINGLE_USEDEP}]
+ )
+ )
+"
+RDEPEND="${DEPEND}"
+BDEPEND="
+ dev-libs/libxslt
+ app-text/docbook-xsl-ns-stylesheets
+ doc? ( app-doc/doxygen[dot] )
+ python? (
+ ${PYTHON_DEPS}
+ >=dev-lang/swig-3.0.7
+ )"
+
+REQUIRED_USE="python? ( ${PYTHON_REQUIRED_USE} )"
+
+PATCHES=(
+ "${FILESDIR}/gdcm_support_vtk9.patch"
+ "${FILESDIR}/gdcm-3.0.14-include-math-h.patch"
+)
+
+pkg_setup() {
+ use python && python-single-r1_pkg_setup
+}
+
+src_prepare() {
+ # drop unbundled libs
+ local -a DROPS=( gdcmcharls gdcmexpat gdcmopenjpeg gdcmuuid gdcmzlib getopt pvrg KWStyle Release )
+ local x
+ for x in "${DROPS[@]}"; do
+ ebegin "Dropping bundled ${x#gdcm}"
+ rm -r "Utilities/${x}" || die
+ sed -i "s,^[ \t]*APPEND_COPYRIGHT(\\\${CMAKE_CURRENT_SOURCE_DIR}/${x}/,#&," "Utilities/CMakeLists.txt" || die
+ eend $?
+ done
+ find Utilities -mindepth 1 -maxdepth 1 '!' -name doxygen '!' -name VTK -type d \
+ -exec ewarn "Using bundled" {} ';' || die
+
+ # fix charls include case
+ sed -i 's:CharLS/charls\.h:charls/charls.h:' CMake/FindCharLS.cmake Utilities/gdcm_charls.h || die
+ sed -i 's:NAMES CharLS:NAMES charls:' CMake/FindCharLS.cmake || die
+
+ # Use prefixed socket++ (to avoid potential conflicts)
+ sed -i '/target_link_libraries(/s/socketxx/gdcm&/' \
+ Source/MessageExchangeDefinition/CMakeLists.txt \
+ Applications/Cxx/CMakeLists.txt \
+ || die
+
+ cmake_src_prepare
+}
+
+src_configure() {
+ local mycmakeargs=(
+ -DCMAKE_SKIP_RPATH=ON
+ -DGDCM_BUILD_SHARED_LIBS=ON
+ -DGDCM_DATA_ROOT="${WORKDIR}/gdcmData"
+ -DGDCM_INSTALL_LIB_DIR="$(get_libdir)"
+ -DGDCM_INSTALL_DOC_DIR="share/doc/${P}"
+ -DGDCM_INSTALL_PYTHONMODULE_DIR="lib/${EPYTHON}/site-packages"
+ -DGDCM_USE_SYSTEM_ZLIB=ON
+ -DGDCM_USE_SYSTEM_OPENSSL=ON
+ -DGDCM_USE_SYSTEM_UUID=ON
+ -DGDCM_USE_SYSTEM_EXPAT=ON
+ -DGDCM_USE_SYSTEM_JSON=ON
+ -DGDCM_USE_SYSTEM_PAPYRUS3=OFF
+ -DGDCM_USE_SYSTEM_SOCKETXX=OFF
+ -DSOCKETXX_NAMESPACE=GDCMSOCKETXX
+ -DGDCM_USE_SYSTEM_LJPEG=OFF
+ -DGDCM_USE_SYSTEM_OPENJPEG=ON
+ -DGDCM_USE_SYSTEM_CHARLS=ON
+ -DGDCM_USE_SYSTEM_POPPLER=ON
+ -DGDCM_USE_SYSTEM_LIBXML2=ON
+ -DGDCM_BUILD_TESTING=$(usex test)
+ -DGDCM_WRAP_PYTHON=$(usex python)
+ $(usex python "-DGDCM_DEFAULT_PYTHON_VERSION=${EPYTHON#python}" "")
+ -DGDCM_WRAP_PERL=OFF
+ -DGDCM_WRAP_PHP=OFF
+ -DGDCM_WRAP_JAVA=OFF
+ -DGDCM_WRAP_CSHARP=OFF
+ -DGDCM_DOCUMENTATION=$(usex doc)
+ $(usex doc "-DGDCM_PDF_DOCUMENTATION=OFF" "")
+ -DGDCM_BUILD_EXAMPLES=OFF
+ -DGDCM_BUILD_APPLICATIONS=ON
+ -DGDCM_USE_VTK=$(usex vtk)
+ )
+ cmake_src_configure
+}
diff --git a/sci-libs/gdcm/metadata.xml b/sci-libs/gdcm/metadata.xml
new file mode 100644
index 000000000..1845bf1bd
--- /dev/null
+++ b/sci-libs/gdcm/metadata.xml
@@ -0,0 +1,14 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <maintainer type="person">
+ <email>fx.carton91@gmail.com</email>
+ <name>François-Xavier Carton</name>
+ </maintainer>
+ <use>
+ <flag name="vtk">Build <pkg>sci-libs/vtk</pkg> bridge</flag>
+ </use>
+ <upstream>
+ <remote-id type="sourceforge">gdcm</remote-id>
+ </upstream>
+</pkgmetadata>
diff --git a/sci-libs/itk/Manifest b/sci-libs/itk/Manifest
index 31310f8b1..b346829c9 100644
--- a/sci-libs/itk/Manifest
+++ b/sci-libs/itk/Manifest
@@ -1,10 +1,7 @@
-DIST ITKGenericLabelInterpolator-5.0.1.tar.gz 136432 BLAKE2B c367d5f29b3b3250f73d3b03b80b50a99607d895ebb83c3613b40ed665bce87b2731b2ecf471a5b77983db1f8894e486404662bb5787056f23de24c8ee897704 SHA512 6044aab4893d6c68c6190c5d81f460ea0dfc4683d33a03a5d56a8a0ae3b767edde530cdc8976e6777237cb1d172f66df044afe11c4cfc9148e5712cf9f3a11fc
-DIST ITKGenericLabelInterpolator-5.1.0.tar.gz 140286 BLAKE2B 1c8efa033586368931d78fe4620ddd1449fcd15153b1585c716bce580df74a6fc990b3714677a81cdcedcd0e4626e4f155c522f6e7306e5be399d521213891b4 SHA512 7bf6310e8b0ea2356ae8ce0ddd0bc3a1516aa6bb5e3e8df9ed0114f1bb2b299d2edd046f27dbae364082afc63e225a3691c794c93d347ee564db617ea3fbf489
-DIST ITKGenericLabelInterpolator_test-5.0.1.zip 430662 BLAKE2B f46683bd1b3479ae6fc9ae63752810a1dda7940c67d4be8524edcb8b40ed384b331ac785ab752c3ed1570cce8d79af7de873820fdb76a11f2e4241ad7fd2d2c2 SHA512 435200a70ee8de30cc02b30d805697ebc61fb2792e6e7d8f5da923d2773ccd6adfdcec2ab953a6a043d624ebb01b9f7f30e2aad83a6442272f28104d357a7bde
-DIST InsightData-5.0.1.tar.gz 290801718 BLAKE2B dcb7657cb1f8555365b2ec94e7f95c4feab13ba4d585fd70ec240e63e7a55cf48aadf091a63ba2263f1f8c10ce3935812655449bea275af3d2eeff3f2689ef46 SHA512 eb766c115049949937d6527937f1f49ef84304a71dc4924581a53173f45c4e5a0c5a0e180550e75ecd840314609580b9d1fe9b2358c5a87c82a2c6aff8e9f50e
-DIST InsightData-5.1.0.tar.gz 292322103 BLAKE2B e55eddf06d72e87e68e7654c634f545923202467b710c75aa929cd040f37a9caa48ee262ca6465631961816af1cd854b9a046ff7e7ffed7731e428e092bc6020 SHA512 458c2959ba5e0745eee23e16ff7178230a7bae94d7dff065b3b38136e238becff96554693e3b2149d2307949c23a6c695c92676f8d44e6f7305dbb8bed48c9fa
-DIST InsightToolkit-5.0.1.tar.gz 20627889 BLAKE2B 2bd53f64f18746a7d0226d4d97bc02529a1dd2c05fc2294b0c2a5adb3783a8e766b1d20e051a17f20b4e5855e7c5b4a18d5f177f239113bc64f1a0400ce6f04b SHA512 f36613ff72c513ded3d32504f71308a94fe75555cf9fd22b77485d1375601f6e1f1539cc5ac82a9e1e229bcf514a88ccb55122a7dfc74a6ae1b6604aa70bd814
-DIST InsightToolkit-5.1.0.tar.gz 20694338 BLAKE2B 6a14e2e00f6d68a1420cdeebabdef254d23c6ba6610828bb860cf4e27a87f0e1448cd222bf3bc02f6d32b4eb262d7ba032f4459ed05f59f8c95d80907e03571c SHA512 413b6ef549b59d8f507038130446ccb704794c6d0980d8ab631d1b1051cb91f399e77c26b69fab6a1e9b9bb4cc233d49996c3ee735cd4de065993d4379b4ed4c
-DIST itk-5.1.0-test-a5e11ea71164ff78c65fcf259db01ea5db981a9d868e60045ff2bffca92984df1174bf984a1076e450f0d5d69b4f0191ed1a61465c220e2c91a893b5df150c0a 1017 BLAKE2B e6a3b734c3f4a23238dbb921c46297b491436e6c4b0b6d8992fe8fa3c813374f354495ca575d5d371ef49b7bcdc8b63d89a5e8d1ae608bce50fea0efc95ec60d SHA512 e69c77894cab5b295ec5edbecdf693525ec9a4673810b87cbc28646ea40888b7792b5707840069e277905c8b0014bd84ecea036836f87c3b16f388f544e34341
-DIST itk-5.1.0-test-bcdbb347f3704262d1f00be7179d6a0a6e68aed56c0653e8072ee5a94985c713bd229c935b1226a658af84fb7f1fffc2458c98364fc35303a2303b12f9f7ce2f 1018 BLAKE2B 50cad64ac0b674fe4dce36c732f8fababe13ec2893e22caa0b22274320fb4f6d70aec1e8b4f6ee5878ebc20b02c7300c877db911b77f82ac0cf2d6e3284f4ffa SHA512 27952af5d6243aa31c187280ea9ba82c434db3614b3db3b406fe8e5c7e4b7e333bc179d5d9956d5a17aa670a7aa7cfce037d37c4225125e703602e322d8ec68b
-DIST itk-5.1.0-testingdata.tar.gz 2409232372 BLAKE2B 7eb1c3ca21558603d3aa915c2a17e9bb656867331dc48e7b514ece50a7eac3d24bdf01c8b0acc703566b598959780d6736b27d1516d932f949e3a5cfe6acd9e0 SHA512 8b451608cb3f75d3ba6a78fd23e79495948c2792a98d831e0f0c93745595df84d3c2a8d76389976f67ac7e7e1f5a44a18d201e51d2ee659cdb708ae28536df8f
+DIST ITKAdaptiveDenoising-5.2.1.tar.gz 757851 BLAKE2B 3d94e1db6d2524adf7491e6e24308618b7b69e54184cbfe29a7084b55b8a337228a308233e0f0ab2cef04df9c8f42010a758e0071efdfd4905c28ca6399bfdfd SHA512 7e9c5a6681cd9777b33f11d1a1a5f6d8b1b6f7d2ec2d4d829398c78045b53b247bddea99e4a5450ba8d6666a31b5216ef6e07a2c874c5723af072e0d3c8cf9f4
+DIST ITKGenericLabelInterpolator-5.2.1.tar.gz 140427 BLAKE2B b19703872926516d9d07acd4078d343e02f00a162d2cb8b6787d6210223be375a059e767cf9c32dd234e77ff51d1af5e08d9a9844c34e23a531938c7d3ded4a9 SHA512 69e53b281cd3f7c136ad9e7ded2c362e0d9e22dc2bd595f42abcefe2cf9ec4fa0f44192efc3d328290be4adaee1ebd74be3035b18147081cc8b8479a333cdea6
+DIST InsightData-5.2.1.tar.gz 293448802 BLAKE2B fd2bb012c0d96243d3543993a87e73c43be0626b0478959e36633f22c7e8d48a46d0f4d18fa3a8d952d4a705ca20594d92c07044000b8e1bc65390ce981af3e7 SHA512 93eae6bdf62ce29ea6dfb1dddedffe4046400a86074dd4d47e3ddcd7ff9ab10031363275cb7f9741add7c02343f1f3e6a41b0ec6533531f4a3a42607c51aa704
+DIST InsightToolkit-5.2.1.tar.gz 20702482 BLAKE2B 06dc73a80b4999baff3fc75e225c8720d00927fd268bd0398bb0eea44679777b777836f307f02a2df3641a300e17c9c2ee9f77d2a87539bf8a6ed49ce341bf23 SHA512 6786e39cdf3d0c3a31abd1e23481e30f6dc9dac189ffe372dde3db688f2f57686a8beb321778327e1ff683ed844d41f1dee937b0ba542b2365e2195dfca398c7
+DIST itk-5.2.1-testingdata.tar.gz 2411475710 BLAKE2B edb8ba9bea8bf890749aa46ab3fb29f7d3e25e0f8bb7da7d7cca8c6524f75778b823232536602ade763c025b8e0fe134a555e6fcf652b8d42cc08f08cbd0c29b SHA512 89b160dc5f7781e148aad065f539b80b9accb9ec384e424398287e62b42a88cff610afcf41622a6d3e4e12c1938e7403b3dae65fa13bfb40c29a6b2f90a02398
+DIST itk-test-a5e11ea71164ff78c65fcf259db01ea5db981a9d868e60045ff2bffca92984df1174bf984a1076e450f0d5d69b4f0191ed1a61465c220e2c91a893b5df150c0a 214819 BLAKE2B cd65212e72cb80eff54ee3f22d05b55036470684c582334fe94826a2d4ed49c840c50a214996f64f2bcd710e5973c2d46201ef31732fe847a43504379df62e25 SHA512 a5e11ea71164ff78c65fcf259db01ea5db981a9d868e60045ff2bffca92984df1174bf984a1076e450f0d5d69b4f0191ed1a61465c220e2c91a893b5df150c0a
+DIST itk-test-bcdbb347f3704262d1f00be7179d6a0a6e68aed56c0653e8072ee5a94985c713bd229c935b1226a658af84fb7f1fffc2458c98364fc35303a2303b12f9f7ce2f 215417 BLAKE2B 318a6c55ba259a5af1e3e19cf859267caa0a612b05abfd9a83d9943902fd7edc25ec002707ed4ec85f7aebd4c5a82411942b5cfe2dc713c905a5bb5d1aa5ef23 SHA512 bcdbb347f3704262d1f00be7179d6a0a6e68aed56c0653e8072ee5a94985c713bd229c935b1226a658af84fb7f1fffc2458c98364fc35303a2303b12f9f7ce2f
diff --git a/sci-libs/itk/files/0001-BUG-Wrap-TransformFileReader-TransformFileWriter.patch b/sci-libs/itk/files/0001-BUG-Wrap-TransformFileReader-TransformFileWriter.patch
deleted file mode 100644
index 094ee3229..000000000
--- a/sci-libs/itk/files/0001-BUG-Wrap-TransformFileReader-TransformFileWriter.patch
+++ /dev/null
@@ -1,50 +0,0 @@
-From d069b7b94287dae15fcaf707775f5dd2bbebcc38 Mon Sep 17 00:00:00 2001
-From: Matt McCormick <matt.mccormick@kitware.com>
-Date: Wed, 5 Feb 2014 15:52:34 -0500
-Subject: [PATCH 1/3] BUG: Wrap TransformFileReader, TransformFileWriter.
-
-Missing CMakeLists.txt in the wrapping directory. Need to explicitly include
-the headers after "Template" was appended to the class name.
-
-Suggested-by: Sami Koho <sami.koho@gmail.com>
-
-Change-Id: I6f994bb18f37d5adf1d0f0311fa73506c41239a7
----
- Modules/IO/TransformBase/wrapping/CMakeLists.txt | 3 +++
- Modules/IO/TransformBase/wrapping/itkTransformFileReader.wrap | 2 ++
- Modules/IO/TransformBase/wrapping/itkTransformFileWriter.wrap | 2 ++
- 3 files changed, 7 insertions(+)
- create mode 100644 Modules/IO/TransformBase/wrapping/CMakeLists.txt
-
-diff --git a/Modules/IO/TransformBase/wrapping/CMakeLists.txt b/Modules/IO/TransformBase/wrapping/CMakeLists.txt
-new file mode 100644
-index 0000000..6072567
---- /dev/null
-+++ b/Modules/IO/TransformBase/wrapping/CMakeLists.txt
-@@ -0,0 +1,3 @@
-+itk_wrap_module(ITKIOTransformBase)
-+itk_auto_load_submodules()
-+itk_end_wrap_module()
-diff --git a/Modules/IO/TransformBase/wrapping/itkTransformFileReader.wrap b/Modules/IO/TransformBase/wrapping/itkTransformFileReader.wrap
-index 9b52fbc..662df9e 100644
---- a/Modules/IO/TransformBase/wrapping/itkTransformFileReader.wrap
-+++ b/Modules/IO/TransformBase/wrapping/itkTransformFileReader.wrap
-@@ -1,3 +1,5 @@
-+set(WRAPPER_AUTO_INCLUDE_HEADERS OFF)
-+itk_wrap_include("itkTransformFileReader.h")
- itk_wrap_class("itk::TransformFileReaderTemplate" POINTER)
- foreach(t ${WRAP_ITK_REAL})
- itk_wrap_template("${ITKM_${t}}" "${ITKT_${t}}")
-diff --git a/Modules/IO/TransformBase/wrapping/itkTransformFileWriter.wrap b/Modules/IO/TransformBase/wrapping/itkTransformFileWriter.wrap
-index 4f1ac4a..356aaf3 100644
---- a/Modules/IO/TransformBase/wrapping/itkTransformFileWriter.wrap
-+++ b/Modules/IO/TransformBase/wrapping/itkTransformFileWriter.wrap
-@@ -1,3 +1,5 @@
-+set(WRAPPER_AUTO_INCLUDE_HEADERS OFF)
-+itk_wrap_include("itkTransformFileWriter.h")
- itk_wrap_class("itk::TransformFileWriterTemplate" POINTER)
- foreach(t ${WRAP_ITK_REAL})
- itk_wrap_template("${ITKM_${t}}" "${ITKT_${t}}")
---
-1.8.5.3
-
diff --git a/sci-libs/itk/files/0002-COMP-Fixed-itkQuasiNewtonOptimizerv4-wrapping-warnin.patch b/sci-libs/itk/files/0002-COMP-Fixed-itkQuasiNewtonOptimizerv4-wrapping-warnin.patch
deleted file mode 100644
index 4c74d5451..000000000
--- a/sci-libs/itk/files/0002-COMP-Fixed-itkQuasiNewtonOptimizerv4-wrapping-warnin.patch
+++ /dev/null
@@ -1,28 +0,0 @@
-From 66d2955fbe5528d9df216c639277d1d2686447e5 Mon Sep 17 00:00:00 2001
-From: Michka Popoff <michkapopoff@gmail.com>
-Date: Fri, 7 Feb 2014 19:24:49 +0100
-Subject: [PATCH 2/3] COMP: Fixed itkQuasiNewtonOptimizerv4 wrapping warnings
-
-The warning :
-/scratch/dashboards/Linux-x86_64-gcc4.4-WrapITK/ITK-build/Wrapping/Modules/ITKOptimizersv4/itkQuasiNewtonOptimizerv4.xml: warning(5): Unknown type type: itk::QuasiNewtonOptimizerv4 [typedef]
-/scratch/dashboards/Linux-x86_64-gcc4.4-WrapITK/ITK-build/Wrapping/Modules/ITKOptimizersv4/itkQuasiNewtonOptimizerv4.xml: warning(4): ITK type not wrapped, or currently not known: itk::QuasiNewtonOptimizerv4Template< double >
----
- .../Numerics/Optimizersv4/wrapping/itkQuasiNewtonOptimizerv4.wrap | 8 +++++++-
- 1 file changed, 7 insertions(+), 1 deletion(-)
-
-diff --git a/Modules/Numerics/Optimizersv4/wrapping/itkQuasiNewtonOptimizerv4.wrap b/Modules/Numerics/Optimizersv4/wrapping/itkQuasiNewtonOptimizerv4.wrap
-index 4a43dd4..7eed11c 100644
---- a/Modules/Numerics/Optimizersv4/wrapping/itkQuasiNewtonOptimizerv4.wrap
-+++ b/Modules/Numerics/Optimizersv4/wrapping/itkQuasiNewtonOptimizerv4.wrap
-@@ -1 +1,7 @@
--itk_wrap_simple_class("itk::QuasiNewtonOptimizerv4" POINTER)
-+set(WRAPPER_AUTO_INCLUDE_HEADERS OFF)
-+itk_wrap_include("itkQuasiNewtonOptimizerv4.h")
-+itk_wrap_class("itk::QuasiNewtonOptimizerv4Template" POINTER)
-+ foreach(t ${WRAP_ITK_REAL})
-+ itk_wrap_template("${ITKM_${t}}" "${ITKT_${t}}")
-+ endforeach(t)
-+itk_end_wrap_class()
---
-1.8.5.3
-
diff --git a/sci-libs/itk/files/0003-COMP-Fixed-itkGradientDescentOptimizerv4-wrapping-wa.patch b/sci-libs/itk/files/0003-COMP-Fixed-itkGradientDescentOptimizerv4-wrapping-wa.patch
deleted file mode 100644
index d77345edf..000000000
--- a/sci-libs/itk/files/0003-COMP-Fixed-itkGradientDescentOptimizerv4-wrapping-wa.patch
+++ /dev/null
@@ -1,73 +0,0 @@
-From fced46ce8769b4edc7971ea0928045390b5c3f84 Mon Sep 17 00:00:00 2001
-From: Michka Popoff <michkapopoff@gmail.com>
-Date: Mon, 10 Feb 2014 09:41:42 +0100
-Subject: [PATCH 3/3] COMP: Fixed itkGradientDescentOptimizerv4 wrapping
- warnings
-
-I splitted the 3 wrapping calls in 3 separate files and fixed the wrapping.
-
-The warnings :
-/home/kevin/kitware/ITK_Build/Wrapping/Modules/ITKOptimizersv4/itkGradientDescentOptimizerv4.xml: warning(5): Unknown type type: itk::GradientDescentOptimizerBasev4 [typedef]
-/home/kevin/kitware/ITK_Build/Wrapping/Modules/ITKOptimizersv4/itkGradientDescentOptimizerv4.xml: warning(5): Unknown type type: itk::GradientDescentOptimizerv4 [typedef]
-/home/kevin/kitware/ITK_Build/Wrapping/Modules/ITKOptimizersv4/itkGradientDescentOptimizerv4.xml: warning(5): Unknown type type: itk::ObjectToObjectOptimizerBase [typedef]
-/home/kevin/kitware/ITK_Build/Wrapping/Modules/ITKOptimizersv4/itkGradientDescentOptimizerv4.xml: warning(4): ITK type not wrapped, or currently not known: itk::GradientDescentOptimizerBasev4Template< double >
-/home/kevin/kitware/ITK_Build/Wrapping/Modules/ITKOptimizersv4/itkGradientDescentOptimizerv4.xml: warning(4): ITK type not wrapped, or currently not known: itk::GradientDescentOptimizerv4Template< double >
-/home/kevin/kitware/ITK_Build/Wrapping/Modules/ITKOptimizersv4/itkGradientDescentOptimizerv4.xml: warning(4): ITK type not wrapped, or currently not known: itk::ObjectToObjectOptimizerBaseTemplate< double >
-
-Should also hopefully fix the new error on the dashboard I introduced by fixing the itkQuasiNewtonOptimizerv4 warnings (http://review.source.kitware.com/#/c/14317/)
-/home/kevin/kitware/ITK_Build/Wrapping/Typedefs/itkQuasiNewtonOptimizerv4.i:87: Warning 401: Nothing known about base class 'itk::GradientDescentOptimizerv4Template< float >'. Ignored.
-/home/kevin/kitware/ITK_Build/Wrapping/Typedefs/itkQuasiNewtonOptimizerv4.i:87: Warning 401: Maybe you forgot to instantiate 'itk::GradientDescentOptimizerv4Template< float >' using %template.
-
-Change-Id: I15b6af11690ed6efeaced68f73af5212ab5dc364
----
- .../wrapping/itkGradientDescentOptimizerBasev4.wrap | 7 +++++++
- .../Optimizersv4/wrapping/itkGradientDescentOptimizerv4.wrap | 10 +++++++---
- .../Optimizersv4/wrapping/itkObjectToObjectOptimizerBase.wrap | 7 +++++++
- 3 files changed, 21 insertions(+), 3 deletions(-)
- create mode 100644 Modules/Numerics/Optimizersv4/wrapping/itkGradientDescentOptimizerBasev4.wrap
- create mode 100644 Modules/Numerics/Optimizersv4/wrapping/itkObjectToObjectOptimizerBase.wrap
-
-diff --git a/Modules/Numerics/Optimizersv4/wrapping/itkGradientDescentOptimizerBasev4.wrap b/Modules/Numerics/Optimizersv4/wrapping/itkGradientDescentOptimizerBasev4.wrap
-new file mode 100644
-index 0000000..74f5a6c
---- /dev/null
-+++ b/Modules/Numerics/Optimizersv4/wrapping/itkGradientDescentOptimizerBasev4.wrap
-@@ -0,0 +1,7 @@
-+set(WRAPPER_AUTO_INCLUDE_HEADERS OFF)
-+itk_wrap_include("itkGradientDescentOptimizerBasev4.h")
-+itk_wrap_class("itk::GradientDescentOptimizerBasev4Template" POINTER)
-+ foreach(t ${WRAP_ITK_REAL})
-+ itk_wrap_template("${ITKM_${t}}" "${ITKT_${t}}")
-+ endforeach(t)
-+itk_end_wrap_class()
-diff --git a/Modules/Numerics/Optimizersv4/wrapping/itkGradientDescentOptimizerv4.wrap b/Modules/Numerics/Optimizersv4/wrapping/itkGradientDescentOptimizerv4.wrap
-index d53a176..3236448 100644
---- a/Modules/Numerics/Optimizersv4/wrapping/itkGradientDescentOptimizerv4.wrap
-+++ b/Modules/Numerics/Optimizersv4/wrapping/itkGradientDescentOptimizerv4.wrap
-@@ -1,3 +1,7 @@
--itk_wrap_simple_class("itk::ObjectToObjectOptimizerBase" POINTER)
--itk_wrap_simple_class("itk::GradientDescentOptimizerBasev4" POINTER)
--itk_wrap_simple_class("itk::GradientDescentOptimizerv4" POINTER)
-+set(WRAPPER_AUTO_INCLUDE_HEADERS OFF)
-+itk_wrap_include("itkGradientDescentOptimizerv4.h")
-+itk_wrap_class("itk::GradientDescentOptimizerv4Template" POINTER)
-+ foreach(t ${WRAP_ITK_REAL})
-+ itk_wrap_template("${ITKM_${t}}" "${ITKT_${t}}")
-+ endforeach(t)
-+itk_end_wrap_class()
-diff --git a/Modules/Numerics/Optimizersv4/wrapping/itkObjectToObjectOptimizerBase.wrap b/Modules/Numerics/Optimizersv4/wrapping/itkObjectToObjectOptimizerBase.wrap
-new file mode 100644
-index 0000000..61b2c44
---- /dev/null
-+++ b/Modules/Numerics/Optimizersv4/wrapping/itkObjectToObjectOptimizerBase.wrap
-@@ -0,0 +1,7 @@
-+set(WRAPPER_AUTO_INCLUDE_HEADERS OFF)
-+itk_wrap_include("itkObjectToObjectOptimizerBase.h")
-+itk_wrap_class("itk::ObjectToObjectOptimizerBaseTemplate" POINTER)
-+ foreach(t ${WRAP_ITK_REAL})
-+ itk_wrap_template("${ITKM_${t}}" "${ITKT_${t}}")
-+ endforeach(t)
-+itk_end_wrap_class()
---
-1.8.5.3
-
diff --git a/sci-libs/itk/files/0004-COMP-Warp-OptimizerParameterScalesEstimatorTemplate.patch b/sci-libs/itk/files/0004-COMP-Warp-OptimizerParameterScalesEstimatorTemplate.patch
deleted file mode 100644
index 83b395626..000000000
--- a/sci-libs/itk/files/0004-COMP-Warp-OptimizerParameterScalesEstimatorTemplate.patch
+++ /dev/null
@@ -1,30 +0,0 @@
-Author: Matt McCormick <matt.mccormick@kitware.com>
-Date: Thu Feb 6 10:26:49 2014 -0500
-
- COMP: Wrap OptimizerParameterScalesEstimatorTemplate.
-
- The class name changed and it became templated. Fixes:
-
- /playpen/blowekamp/MacOSX-WrapITK/ITK-build/Wrapping/Modules/ITKOptimizersv4/itkOptimizerParameterScalesEstimator.xml:
- warning(5): Unknown type type: itk::OptimizerParameterScalesEstimator
- [typedef]
- /playpen/blowekamp/MacOSX-WrapITK/ITK-build/Wrapping/Modules/ITKOptimizersv4/itkOptimizerParameterScalesEstimator.xml:
- warning(4): ITK type not wrapped, or currently not known:
- itk::OptimizerParameterScalesEstimatorTemplate< double >
-
- Change-Id: Ic6b4d6fba10d5d6c7b58de8d842bad6511e1ae7b
-
-diff --git a/Modules/Numerics/Optimizersv4/wrapping/itkOptimizerParameterScalesEstimator.wrap b/Modules/Numerics/Optimizersv4/wrapping/itkOptim
-index efd6a8c..a647ee4 100644
---- a/Modules/Numerics/Optimizersv4/wrapping/itkOptimizerParameterScalesEstimator.wrap
-+++ b/Modules/Numerics/Optimizersv4/wrapping/itkOptimizerParameterScalesEstimator.wrap
-@@ -1 +1,7 @@
--itk_wrap_simple_class("itk::OptimizerParameterScalesEstimator" POINTER)
-+set(WRAPPER_AUTO_INCLUDE_HEADERS OFF)
-+itk_wrap_include("itkOptimizerParameterScalesEstimator.h")
-+itk_wrap_class("itk::OptimizerParameterScalesEstimatorTemplate" POINTER)
-+ foreach(t ${WRAP_ITK_REAL})
-+ itk_wrap_template("${ITKM_${t}}" "${ITKT_${t}}")
-+ endforeach(t)
-+itk_end_wrap_class()
-
diff --git a/sci-libs/itk/files/0005-make-gdcm-helper-library-static.patch b/sci-libs/itk/files/0005-make-gdcm-helper-library-static.patch
deleted file mode 100644
index d760ac7ba..000000000
--- a/sci-libs/itk/files/0005-make-gdcm-helper-library-static.patch
+++ /dev/null
@@ -1,11 +0,0 @@
-diff --git a/Modules/ThirdParty/GDCM/src/CMakeLists.txt b/Modules/ThirdParty/GDCM/src/CMakeLists.txt
-index e98077c..70f4286 100644
---- a/Modules/ThirdParty/GDCM/src/CMakeLists.txt
-+++ b/Modules/ThirdParty/GDCM/src/CMakeLists.txt
-@@ -1,5 +1,5 @@
- if(ITK_USE_SYSTEM_GDCM)
-- add_library(ITKGDCM ITK-GDCM.cxx)
-+ add_library(ITKGDCM STATIC ITK-GDCM.cxx)
- target_link_libraries(ITKGDCM gdcmDICT gdcmMSFF)
- itk_module_target(ITKGDCM)
- return()
diff --git a/sci-libs/itk/files/ITKModuleRemote.patch b/sci-libs/itk/files/ITKModuleRemote.patch
deleted file mode 100644
index eb130159a..000000000
--- a/sci-libs/itk/files/ITKModuleRemote.patch
+++ /dev/null
@@ -1,45 +0,0 @@
-Disable automatic git clone attempt for modules:
-https://github.com/InsightSoftwareConsortium/ITK/issues/1157
-
---- a/CMake/ITKModuleRemote.cmake 2019-08-13 18:10:33.385472767 +0200
-+++ b/CMake/ITKModuleRemote.cmake 2019-08-13 18:12:04.020198966 +0200
-@@ -165,39 +165,4 @@
- set(Module_${_name} ON CACHE FORCE "${_description}")
- endif()
-
-- if(Module_${_name})
-- itk_download_attempt_check(Module_${_name})
-- include(CMakeParseArguments)
-- cmake_parse_arguments(_fetch_options "" "GIT_REPOSITORY;GIT_TAG" "" ${ARGN})
-- find_package(Git)
-- if(NOT GIT_EXECUTABLE)
-- message(FATAL_ERROR "error: could not find git for clone of ${_name}")
-- endif()
-- execute_process(
-- COMMAND "${GIT_EXECUTABLE}" --version
-- OUTPUT_VARIABLE ov
-- OUTPUT_STRIP_TRAILING_WHITESPACE
-- )
-- string(REGEX REPLACE "^git version (.+)$" "\\1" _version "${ov}")
-- if("${_version}" VERSION_LESS 1.6.6)
-- message(FATAL_ERROR "Git version 1.6.6 or later is required.")
-- endif()
--
-- set(REMOTE_GIT_TAG "${_fetch_options_GIT_TAG}")
--
-- if( DEFINED REMOTE_GIT_TAG_${_name} AND NOT "${REMOTE_GIT_TAG_${_name}}" STREQUAL "${_fetch_options_GIT_TAG}")
-- set(REMOTE_GIT_TAG "${REMOTE_GIT_TAG_${_name}}")
-- message(STATUS "NOTE: Using override 'REMOTE_GIT_TAG_${_name}=${REMOTE_GIT_TAG}'\n"
-- " instead of value 'GIT_TAG=${_fetch_options_GIT_TAG}'\n"
-- " specified in file ${ITK_SOURCE_DIR}/Modules/Remote/${_name}.remote.cmake'")
-- endif()
-- set(REMOTE_GIT_TAG_${_name} "${REMOTE_GIT_TAG}" CACHE STRING "Override default GIT_TAG value for remote module ${_name}")
-- mark_as_advanced(REMOTE_GIT_TAG_${_name})
--
-- _fetch_with_git("${GIT_EXECUTABLE}"
-- "${_fetch_options_GIT_REPOSITORY}"
-- "${REMOTE_GIT_TAG}"
-- "${ITK_SOURCE_DIR}/Modules/Remote/${_name}"
-- )
-- endif()
- endfunction()
diff --git a/sci-libs/itk/files/itk-5.1.0-downloads.patch b/sci-libs/itk/files/itk-5.1.0-downloads.patch
deleted file mode 100644
index 34fdb76d1..000000000
--- a/sci-libs/itk/files/itk-5.1.0-downloads.patch
+++ /dev/null
@@ -1,20 +0,0 @@
---- a/CMake/ITKDownloadSetup.cmake 2020-07-30 19:03:10.330325423 -0400
-+++ b/CMake/ITKDownloadSetup.cmake 2020-07-30 19:03:10.330325423 -0400
-@@ -11,7 +11,7 @@
-
- macro(itk_download_attempt_check _name)
- if(ITK_FORBID_DOWNLOADS)
-- message(SEND_ERROR "Attempted to download ${_name} when ITK_FORBID_DOWNLOADS is ON")
-+ message(WARNING "Attempted to download ${_name} when ITK_FORBID_DOWNLOADS is ON")
- endif()
- endmacro()
-
---- a/Modules/Remote/GenericLabelInterpolator.remote.cmake 2020-04-25 14:30:53.000000000 -0400
-+++ b/Modules/Remote/GenericLabelInterpolator.remote.cmake 2020-04-25 14:30:53.000000000 -0400
-@@ -44,6 +44,4 @@
- itk_fetch_module(GenericLabelInterpolator
- "A generic interpolator for multi-label images."
- MODULE_COMPLIANCE_LEVEL 2
-- GIT_REPOSITORY ${git_protocol}://github.com/InsightSoftwareConsortium/ITKGenericLabelInterpolator.git
-- GIT_TAG b95fe46c7f4fe8002af67c67e6fe4e1f087bf6b7
- )
diff --git a/sci-libs/itk/files/itk-5.1.0-include_limits.patch b/sci-libs/itk/files/itk-5.1.0-include_limits.patch
deleted file mode 100644
index 9a8fae820..000000000
--- a/sci-libs/itk/files/itk-5.1.0-include_limits.patch
+++ /dev/null
@@ -1,10 +0,0 @@
---- a/Modules/ThirdParty/GDCM/src/gdcm/Source/MediaStorageAndFileFormat/gdcmImageChangePhotometricInterpretation.h
-+++ a/Modules/ThirdParty/GDCM/src/gdcm/Source/MediaStorageAndFileFormat/gdcmImageChangePhotometricInterpretation.h
-@@ -16,6 +16,7 @@
-
- #include "gdcmImageToImageFilter.h"
- #include "gdcmPhotometricInterpretation.h"
-+#include <limits>
-
- namespace gdcm
- {
diff --git a/sci-libs/itk/files/itk-5.2.1-fix-castxml-clang-attr-malloc.patch b/sci-libs/itk/files/itk-5.2.1-fix-castxml-clang-attr-malloc.patch
new file mode 100644
index 000000000..05c9d5635
--- /dev/null
+++ b/sci-libs/itk/files/itk-5.2.1-fix-castxml-clang-attr-malloc.patch
@@ -0,0 +1,25 @@
+From: François-Xavier Carton <fx.carton91@gmail.com>
+Date: Thu, 9 Jun 2022 14:56:22 +0200
+Subject: [PATCH] fix attr malloc error with recent glibc/gcc
+
+Recent GCC has support for __attribute__((__malloc__)) with arguments, but clang
+does not. castxml uses clang internally. And recent glibc/gcc uses the attribute
+with arguments. Mix all this, and you get:
+
+error: '__malloc__' attribute takes no arguments
+
+when compiling itk with python wrapping.
+
+To fix this, we add a define to castxml flags to remove the extra arguments.
+
+--- a/Wrapping/Generators/CastXML/CMakeLists.txt 2022-06-09 14:53:15.582352715 +0200
++++ b/Wrapping/Generators/CastXML/CMakeLists.txt 2022-06-09 14:54:38.182351433 +0200
+@@ -237,7 +237,7 @@
+ set(_castxml_cc ${_castxml_cc} "-D_HAS_TR1=0")
+ endif()
+ else()
+- set(_castxml_cc --castxml-cc-gnu ( "${CMAKE_CXX_COMPILER}" ${_castxml_cc_flags} ))
++ set(_castxml_cc --castxml-cc-gnu ( "${CMAKE_CXX_COMPILER}" ${_castxml_cc_flags} -D__malloc__\(a,b\)=__malloc__ ))
+ endif()
+ set(_target)
+ if(CMAKE_CROSSCOMPILING)
diff --git a/sci-libs/itk/files/itk-5.2.1-system-openjpeg.patch b/sci-libs/itk/files/itk-5.2.1-system-openjpeg.patch
new file mode 100644
index 000000000..ad717f677
--- /dev/null
+++ b/sci-libs/itk/files/itk-5.2.1-system-openjpeg.patch
@@ -0,0 +1,558 @@
+--- a/Modules/ThirdParty/OpenJPEG/CMakeLists.txt
++++ b/Modules/ThirdParty/OpenJPEG/CMakeLists.txt
+@@ -1,16 +1,32 @@
+ project(ITKOpenJPEG)
+ set(ITKOpenJPEG_THIRD_PARTY 1)
+
+-set(ITKOpenJPEG_INCLUDE_DIRS
+- ${ITKOpenJPEG_BINARY_DIR}/src/openjpeg
+- ${ITKOpenJPEG_SOURCE_DIR}/src/openjpeg
+- )
+-set(ITKOpenJPEG_LIBRARIES itkopenjpeg)
++option(ITK_USE_SYSTEM_OPENJPEG "Use system-installed openjpeg" ${ITK_USE_SYSTEM_LIBRARIES})
++mark_as_advanced(ITK_USE_SYSTEM_OPENJPEG)
++
++if(ITK_USE_SYSTEM_OPENJPEG)
++ find_package(OpenJPEG REQUIRED)
++ set(ITKOpenJPEG_INCLUDE_DIRS
++ ${ITKOpenJPEG_BINARY_DIR}/src
++ )
++ set(ITKOpenJPEG_SYSTEM_INCLUDE_DIRS
++ ${OPENJPEG_INCLUDE_DIRS}
++ )
++ set(ITKOpenJPEG_LIBRARIES "${OPENJPEG_LIBRARIES}")
++ set(ITKOpenJPEG_NO_SRC 1)
++else()
++ set(ITKOpenJPEG_INCLUDE_DIRS
++ ${ITKOpenJPEG_BINARY_DIR}/src/openjpeg
++ ${ITKOpenJPEG_SOURCE_DIR}/src/openjpeg
++ )
++ set(ITKOpenJPEG_LIBRARIES itkopenjpeg)
++endif()
++
++configure_file(src/itk_openjpeg.h.in src/itk_openjpeg.h)
+ set(ITK_LIBRARY_PROPERTIES WINDOWS_EXPORT_ALL_SYMBOLS FALSE)
+-
+ itk_module_impl()
+
+-install(FILES ${ITKOpenJPEG_SOURCE_DIR}/src/itk_openjpeg.h
++install(FILES ${ITKOpenJPEG_BINARY_DIR}/src/itk_openjpeg.h
+ DESTINATION ${ITKOpenJPEG_INSTALL_INCLUDE_DIR}
+ COMPONENT Development
+ )
+diff --git a/Modules/ThirdParty/OpenJPEG/src/itk_openjpeg.h b/Modules/ThirdParty/OpenJPEG/src/itk_openjpeg.h.in
+rename from Modules/ThirdParty/OpenJPEG/src/itk_openjpeg.h
+rename to Modules/ThirdParty/OpenJPEG/src/itk_openjpeg.h.in
+--- a/Modules/ThirdParty/OpenJPEG/src/itk_openjpeg.h
++++ b/Modules/ThirdParty/OpenJPEG/src/itk_openjpeg.h.in
+@@ -25,6 +25,12 @@
+ #ifndef itk_openjpeg_h
+ #define itk_openjpeg_h
+
+-#include <itkopenjpeg/openjpeg.h>
++/* Use the openjpeg library configured for ITK. */
++#cmakedefine ITK_USE_SYSTEM_OPENJPEG
++#ifdef ITK_USE_SYSTEM_OPENJPEG
++# include <openjpeg.h>
++#else
++# include <itkopenjpeg/openjpeg.h>
++#endif
+
+ #endif
+--- a/Modules/IO/JPEG2000/src/itkJPEG2000ImageIO.cxx
++++ b/Modules/IO/JPEG2000/src/itkJPEG2000ImageIO.cxx
+@@ -27,8 +27,6 @@
+ extern "C"
+ {
+ #include "openjpeg.h"
+-#include "j2k.h"
+-#include "jp2.h"
+ }
+
+
+@@ -139,11 +137,11 @@
+ {
+ itkDebugMacro(<< "ReadImageInformation()");
+
+- FILE * l_file = fopen(this->m_FileName.c_str(), "rb");
+-
+- /* decompression parameters */
++ /* set decoding parameters to default values */
++ opj_set_default_decoder_parameters(&(this->m_Internal->m_DecompressionParameters));
+
+- if (!l_file)
++ opj_stream_t * cio = opj_stream_create_default_file_stream(this->m_FileName.c_str(), true);
++ if (!cio)
+ {
+ itkExceptionMacro("JPEG2000ImageIO failed to open file for reading: " << this->GetFileName() << std::endl
+ << "Reason: "
+@@ -151,10 +149,5 @@
+ }
+
+- /* set decoding parameters to default values */
+- opj_set_default_decoder_parameters(&(this->m_Internal->m_DecompressionParameters));
+-
+- opj_stream_t * cio = opj_stream_create_default_file_stream(l_file, true);
+-
+ this->m_Internal->m_Dinfo = nullptr; /* handle to a decompressor */
+
+ opj_image_t * l_image = nullptr;
+@@ -188,9 +181,8 @@
+
+ /* get a decoder handle */
+- this->m_Internal->m_Dinfo = opj_create_decompress(CODEC_J2K);
++ this->m_Internal->m_Dinfo = opj_create_decompress(OPJ_CODEC_J2K);
+ if (!this->m_Internal->m_Dinfo)
+ {
+ opj_stream_destroy(cio);
+- fclose(l_file);
+ itkExceptionMacro("JPEG2000ImageIO failed to read file: "
+ << this->GetFileName() << std::endl
+@@ -202,10 +194,9 @@
+ {
+ /* JPEG 2000 compressed image data */
+ /* get a decoder handle */
+- this->m_Internal->m_Dinfo = opj_create_decompress(CODEC_JP2);
++ this->m_Internal->m_Dinfo = opj_create_decompress(OPJ_CODEC_JP2);
+ if (!this->m_Internal->m_Dinfo)
+ {
+ opj_stream_destroy(cio);
+- fclose(l_file);
+ itkExceptionMacro("JPEG2000ImageIO failed to read file: "
+ << this->GetFileName() << std::endl
+@@ -217,10 +208,9 @@
+ {
+ /* JPEG 2000, JPIP */
+ /* get a decoder handle */
+- this->m_Internal->m_Dinfo = opj_create_decompress(CODEC_JPT);
++ this->m_Internal->m_Dinfo = opj_create_decompress(OPJ_CODEC_JPT);
+ if (!this->m_Internal->m_Dinfo)
+ {
+ opj_stream_destroy(cio);
+- fclose(l_file);
+ itkExceptionMacro("JPEG2000ImageIO failed to read file: "
+ << this->GetFileName() << std::endl
+@@ -230,7 +220,6 @@
+ }
+ default:
+ opj_stream_destroy(cio);
+- fclose(l_file);
+ itkExceptionMacro("JPEG2000ImageIO failed to read file: "
+ << this->GetFileName() << std::endl
+ << "Reason: "
+@@ -248,26 +237,8 @@
+ }
+
+- // Image parameters - first tile
+- OPJ_INT32 l_tile_x0;
+- OPJ_INT32 l_tile_y0;
+-
+- // Image parameters - tile width, height and number of tiles
+- OPJ_UINT32 l_tile_width;
+- OPJ_UINT32 l_tile_height;
+- OPJ_UINT32 l_nb_tiles_x;
+- OPJ_UINT32 l_nb_tiles_y;
+-
+ itkDebugMacro(<< "Trying to read header now...");
+
+- bResult = opj_read_header(this->m_Internal->m_Dinfo,
+- &l_image,
+- &l_tile_x0,
+- &l_tile_y0,
+- &l_tile_width,
+- &l_tile_height,
+- &l_nb_tiles_x,
+- &l_nb_tiles_y,
+- cio);
++ bResult = opj_read_header(cio, this->m_Internal->m_Dinfo, &l_image);
+
+ if (!bResult)
+ {
+@@ -284,13 +255,21 @@
+ }
+
+- this->m_Internal->m_TileStartX = l_tile_x0;
+- this->m_Internal->m_TileStartY = l_tile_y0;
++ opj_codestream_info_v2_t* cp = opj_get_cstr_info(this->m_Internal->m_Dinfo);
++ if (!cp)
++ {
++ opj_stream_destroy(cio);
++ opj_image_destroy(l_image);
++ itkExceptionMacro("JPEG2000ImageIO failed to read file: " << this->GetFileName() << std::endl
++ << "Reason: Error while reading image header");
++ }
++ this->m_Internal->m_TileStartX = cp->tx0;
++ this->m_Internal->m_TileStartY = cp->ty0;
+
+- this->m_Internal->m_TileWidth = l_tile_width;
+- this->m_Internal->m_TileHeight = l_tile_height;
++ this->m_Internal->m_TileWidth = cp->tdx;
++ this->m_Internal->m_TileHeight = cp->tdy;
+
+- this->m_Internal->m_NumberOfTilesInX = l_nb_tiles_x;
+- this->m_Internal->m_NumberOfTilesInY = l_nb_tiles_y;
++ this->m_Internal->m_NumberOfTilesInX = cp->tw;
++ this->m_Internal->m_NumberOfTilesInY = cp->th;
+
+
+ itkDebugMacro(<< "Number of Components = " << l_image->numcomps);
+@@ -307,6 +286,7 @@
+ else
+ {
+ opj_stream_destroy(cio);
++ opj_image_destroy(l_image);
+ itkExceptionMacro("JPEG2000ImageIO failed to read file: " << this->GetFileName() << std::endl
+ << "Reason: "
+ << "Unknown precision in file: "
+@@ -320,6 +300,6 @@
+ break;
+ case 3:
+- if (l_image->color_space != CLRSPC_SRGB)
++ if (l_image->color_space != OPJ_CLRSPC_SRGB)
+ {
+ itkWarningMacro(<< "file does not specify color space, assuming sRGB");
+ }
+@@ -349,7 +329,6 @@
+
+ /* close the byte stream */
+ opj_stream_destroy(cio);
+- fclose(l_file);
+
+ if (this->m_Internal->m_Dinfo)
+ {
+@@ -368,16 +347,7 @@
+ {
+ itkDebugMacro(<< "JPEG2000ImageIO::Read() Begin");
+
+- FILE * l_file = fopen(this->m_FileName.c_str(), "rb");
+-
+- if (!l_file)
+- {
+- itkExceptionMacro("JPEG2000ImageIO failed to open file for reading: " << this->GetFileName() << std::endl
+- << "Reason: "
+- << itksys::SystemTools::GetLastSystemError());
+- }
+-
+- opj_stream_t * l_stream = opj_stream_create_default_file_stream(l_file, true);
++ opj_stream_t * l_stream = opj_stream_create_default_file_stream(this->m_FileName.c_str(), true);
+ if (!l_stream)
+ {
+ itkExceptionMacro("JPEG2000ImageIO failed to read file: "
+@@ -397,9 +367,10 @@
+ {
+ /* JPEG-2000 codestream */
+ /* get a decoder handle */
+- this->m_Internal->m_Dinfo = opj_create_decompress(CODEC_J2K);
++ this->m_Internal->m_Dinfo = opj_create_decompress(OPJ_CODEC_J2K);
+ if (!this->m_Internal->m_Dinfo)
+ {
++ opj_stream_destroy(l_stream);
+ itkExceptionMacro("JPEG2000ImageIO failed to read file: "
+ << this->GetFileName() << std::endl
+ << "Reason: opj_create_decompress(CODEC_J2K) returns nullptr");
+@@ -410,9 +381,10 @@
+ {
+ /* JPEG 2000 compressed image data */
+ /* get a decoder handle */
+- this->m_Internal->m_Dinfo = opj_create_decompress(CODEC_JP2);
++ this->m_Internal->m_Dinfo = opj_create_decompress(OPJ_CODEC_JP2);
+ if (!this->m_Internal->m_Dinfo)
+ {
++ opj_stream_destroy(l_stream);
+ itkExceptionMacro("JPEG2000ImageIO failed to read file: "
+ << this->GetFileName() << std::endl
+ << "Reason: opj_create_decompress(CODEC_JP2) returns nullptr");
+@@ -423,9 +395,10 @@
+ {
+ /* JPEG 2000, JPIP */
+ /* get a decoder handle */
+- this->m_Internal->m_Dinfo = opj_create_decompress(CODEC_JPT);
++ this->m_Internal->m_Dinfo = opj_create_decompress(OPJ_CODEC_JPT);
+ if (!this->m_Internal->m_Dinfo)
+ {
++ opj_stream_destroy(l_stream);
+ itkExceptionMacro("JPEG2000ImageIO failed to read file: "
+ << this->GetFileName() << std::endl
+ << "Reason: opj_create_decompress(CODEC_JPT) returns nullptr");
+@@ -433,7 +406,7 @@
+ break;
+ }
+ default:
+- fclose(l_file);
++ opj_stream_destroy(l_stream);
+ itkExceptionMacro("JPEG2000ImageIO failed to read file: "
+ << this->GetFileName() << std::endl
+ << "Reason: "
+@@ -445,32 +418,17 @@
+ if (!opj_setup_decoder(this->m_Internal->m_Dinfo, &(this->m_Internal->m_DecompressionParameters)))
+ {
++ opj_stream_destroy(l_stream);
+ itkExceptionMacro("JPEG2000ImageIO failed to read file: " << this->GetFileName() << std::endl
+ << "Reason: opj_setup_decoder returns false");
+ }
+
+- OPJ_INT32 l_tile_x0, l_tile_y0;
+-
+- OPJ_UINT32 l_tile_width;
+- OPJ_UINT32 l_tile_height;
+- OPJ_UINT32 l_nb_tiles_x;
+- OPJ_UINT32 l_nb_tiles_y;
+-
+- bool bResult = opj_read_header(this->m_Internal->m_Dinfo,
+- &l_image,
+- &l_tile_x0,
+- &l_tile_y0,
+- &l_tile_width,
+- &l_tile_height,
+- &l_nb_tiles_x,
+- &l_nb_tiles_y,
+- l_stream);
++ bool bResult = opj_read_header(l_stream, this->m_Internal->m_Dinfo, &l_image);
+
+ if (!bResult)
+ {
+ opj_destroy_codec(this->m_Internal->m_Dinfo);
+ this->m_Internal->m_Dinfo = nullptr;
+ opj_stream_destroy(l_stream);
+- fclose(l_file);
+ itkExceptionMacro("JPEG2000ImageIO failed to read file: " << this->GetFileName() << std::endl
+ << "Reason: opj_read_header returns false");
+ }
+@@ -499,7 +457,7 @@
+ itkDebugMacro(<< "p_end_x = " << p_end_x);
+ itkDebugMacro(<< "p_end_y = " << p_end_y);
+
+- bResult = opj_set_decode_area(this->m_Internal->m_Dinfo, p_start_x, p_start_y, p_end_x, p_end_y);
++ bResult = opj_set_decode_area(this->m_Internal->m_Dinfo, l_image, p_start_x, p_start_y, p_end_x, p_end_y);
+
+ itkDebugMacro(<< "opj_set_decode_area() after");
+
+@@ -509,6 +467,5 @@
+ this->m_Internal->m_Dinfo = nullptr;
+ opj_stream_destroy(l_stream);
+- fclose(l_file);
+ itkExceptionMacro("JPEG2000ImageIO failed to read file: " << this->GetFileName() << std::endl
+ << "Reason: opj_set_decode_area returns false");
+ }
+@@ -525,13 +482,14 @@
+
+ OPJ_UINT32 l_max_data_size = 1000;
+
+- bool l_go_on = true;
++ OPJ_BOOL l_go_on = true;
+
+ auto * l_data = (OPJ_BYTE *)malloc(1000);
+
+ while (l_go_on)
+ {
+ bool tileHeaderRead = opj_read_tile_header(this->m_Internal->m_Dinfo,
++ l_stream,
+ &l_tile_index,
+ &l_data_size,
+ &l_current_tile_x0,
+@@ -540,13 +498,11 @@
+ &l_current_tile_y1,
+ &l_nb_comps,
+- &l_go_on,
+- l_stream);
++ &l_go_on);
+
+ if (!tileHeaderRead)
+ {
+ free(l_data);
+ opj_stream_destroy(l_stream);
+- fclose(l_file);
+ opj_destroy_codec(this->m_Internal->m_Dinfo);
+ opj_image_destroy(l_image);
+ itkExceptionMacro("JPEG2000ImageIO failed to read file: " << this->GetFileName() << std::endl
+@@ -571,7 +527,6 @@
+ if (!l_data)
+ {
+ opj_stream_destroy(l_stream);
+- fclose(l_file);
+ opj_destroy_codec(this->m_Internal->m_Dinfo);
+ opj_image_destroy(l_image);
+ itkExceptionMacro("JPEG2000ImageIO failed to read file: " << this->GetFileName() << std::endl
+@@ -590,7 +545,6 @@
+ {
+ free(l_data);
+ opj_stream_destroy(l_stream);
+- fclose(l_file);
+ opj_destroy_codec(this->m_Internal->m_Dinfo);
+ opj_image_destroy(l_image);
+ itkExceptionMacro("JPEG2000ImageIO failed to read file: " << this->GetFileName() << std::endl
+@@ -654,7 +608,6 @@
+ {
+ free(l_data);
+ opj_stream_destroy(l_stream);
+- fclose(l_file);
+ opj_destroy_codec(this->m_Internal->m_Dinfo);
+ opj_image_destroy(l_image);
+ itkExceptionMacro("JPEG2000ImageIO failed to read file: " << this->GetFileName() << std::endl
+@@ -667,13 +620,11 @@
+ this->m_Internal->m_Dinfo = nullptr;
+ opj_stream_destroy(l_stream);
+- fclose(l_file);
+ itkExceptionMacro("JPEG2000ImageIO failed to read file: " << this->GetFileName() << std::endl
+ << "Reason: error whle reading image");
+ }
+
+ /* close the byte stream */
+ opj_stream_destroy(l_stream);
+- fclose(l_file);
+
+ if (this->m_Internal->m_Dinfo)
+ {
+@@ -775,6 +726,6 @@
+ }
+
+- for (int i = 0; i < parameters.numpocs; i++)
++ for (OPJ_UINT32 i = 0; i < parameters.numpocs; i++)
+ {
+ if (parameters.POC[i].prg == -1)
+ {
+@@ -840,13 +791,13 @@
+
+ parameters.numresolution = numberOfResolutions;
+
+- OPJ_COLOR_SPACE color_space = CLRSPC_GRAY;
++ OPJ_COLOR_SPACE color_space = OPJ_CLRSPC_GRAY;
+ opj_image_cmptparm_t cmptparms[3];
+
+ if (this->GetNumberOfComponents() == 3)
+ {
+
+- color_space = (this->GetPixelType() == IOPixelEnum::RGB) ? CLRSPC_SRGB : CLRSPC_UNSPECIFIED;
++ color_space = (this->GetPixelType() == IOPixelEnum::RGB) ? OPJ_CLRSPC_SRGB : OPJ_CLRSPC_UNSPECIFIED;
+
+ /* initialize image components */
+ memset(&cmptparms[0], 0, 3 * sizeof(opj_image_cmptparm_t));
+@@ -864,7 +815,7 @@
+
+ if (this->GetNumberOfComponents() == 1)
+ {
+- color_space = CLRSPC_GRAY;
++ color_space = OPJ_CLRSPC_GRAY;
+
+ /* initialize image components */
+ memset(&cmptparms[0], 0, sizeof(opj_image_cmptparm_t));
+@@ -941,8 +892,9 @@
+ if (extension == ".j2k")
+ {
+- cinfo = opj_create_compress(CODEC_J2K);
++ cinfo = opj_create_compress(OPJ_CODEC_J2K);
+ if (!cinfo)
+ {
++ opj_image_destroy(l_image);
+ itkExceptionMacro("JPEG2000ImageIO failed to write file: "
+ << this->GetFileName() << std::endl
+ << "Reason: opj_create_compress(CODEC_J2K) returns nullptr");
+@@ -950,9 +902,10 @@
+ }
+ else if (extension == ".jp2")
+ {
+- cinfo = opj_create_compress(CODEC_JP2);
++ cinfo = opj_create_compress(OPJ_CODEC_JP2);
+ if (!cinfo)
+ {
++ opj_image_destroy(l_image);
+ itkExceptionMacro("JPEG2000ImageIO failed to write file: "
+ << this->GetFileName() << std::endl
+ << "Reason: opj_create_compress(CODEC_JP2) returns nullptr");
+@@ -960,9 +913,10 @@
+ }
+ else if (extension == ".jpt")
+ {
+- cinfo = opj_create_compress(CODEC_JPT);
++ cinfo = opj_create_compress(OPJ_CODEC_JPT);
+ if (!cinfo)
+ {
++ opj_image_destroy(l_image);
+ itkExceptionMacro("JPEG2000ImageIO failed to write file: "
+ << this->GetFileName() << std::endl
+ << "Reason: opj_create_compress(CODEC_JPT) returns nullptr");
+@@ -970,6 +924,7 @@
+ }
+ else
+ {
++ opj_image_destroy(l_image);
+ itkExceptionMacro("JPEG2000ImageIO failed to write file: " << this->GetFileName() << std::endl
+ << "Reason: unknown encode format: " << extension);
+ }
+@@ -985,23 +940,19 @@
+
+ if (!opj_setup_encoder(cinfo, &parameters, l_image))
+ {
++ opj_destroy_codec(cinfo);
++ opj_image_destroy(l_image);
+ itkExceptionMacro("JPEG2000ImageIO failed to write file: " << this->GetFileName() << std::endl
+ << "Reason: opj_setup_encoder returns false");
+ }
+
+- FILE * l_file = fopen(parameters.outfile, "wb");
+- if (!l_file)
+- {
+- itkExceptionMacro("JPEG2000ImageIO failed to open file for writing: " << this->GetFileName() << std::endl
+- << "Reason: "
+- << itksys::SystemTools::GetLastSystemError());
+- }
+-
+ /* open a byte stream for writing */
+ /* allocate memory for all tiles */
+- opj_stream_t * cio = opj_stream_create_default_file_stream(l_file, false);
++ opj_stream_t * cio = opj_stream_create_default_file_stream(parameters.outfile, false);
+ if (!cio)
+ {
++ opj_destroy_codec(cinfo);
++ opj_image_destroy(l_image);
+ itkExceptionMacro("JPEG2000ImageIO failed to write file: "
+ << this->GetFileName() << std::endl
+ << "Reason: "
+@@ -1017,7 +968,8 @@
+ if (!bSuccess)
+ {
+ opj_stream_destroy(cio);
+- fclose(l_file);
++ opj_destroy_codec(cinfo);
++ opj_image_destroy(l_image);
+ itkExceptionMacro("JPEG2000ImageIO failed to write file: " << this->GetFileName() << std::endl
+ << "Reason: opj_start_compress returns false");
+ }
+@@ -1026,7 +978,8 @@
+ if (!bSuccess)
+ {
+ opj_stream_destroy(cio);
+- fclose(l_file);
++ opj_destroy_codec(cinfo);
++ opj_image_destroy(l_image);
+ itkExceptionMacro("JPEG2000ImageIO failed to write file: " << this->GetFileName() << std::endl
+ << "Reason: opj_encode returns false");
+ }
+@@ -1035,14 +988,14 @@
+ if (!bSuccess)
+ {
+ opj_stream_destroy(cio);
+- fclose(l_file);
++ opj_destroy_codec(cinfo);
++ opj_image_destroy(l_image);
+ itkExceptionMacro("JPEG2000ImageIO failed to write file: " << this->GetFileName() << std::endl
+ << "Reason: opj_end_compress returns false");
+ }
+
+ /* close and free the byte stream */
+ opj_stream_destroy(cio);
+- fclose(l_file);
+
+ /* free remaining compression structures */
+ opj_destroy_codec(cinfo);
+--- a/Modules/Nonunit/Review/src/CMakeLists.txt
++++ b/Modules/Nonunit/Review/src/CMakeLists.txt
+@@ -5,7 +5,7 @@
+
+ add_library(ITKReview ${ITKReview_SRC})
+ itk_module_link_dependencies()
+-target_link_libraries(ITKReview LINK_PUBLIC ${ITKTestKernel_LIBRARIES} ${ITKIOLSM_LIBRARIES} itkopenjpeg)
++target_link_libraries(ITKReview LINK_PUBLIC ${ITKTestKernel_LIBRARIES} ${ITKIOLSM_LIBRARIES} ${ITKOpenJPEG_LIBRARIES})
+ itk_module_target(ITKReview)
+
+
diff --git a/sci-libs/itk/files/itk-5.2.1-system-tiff-has-64.patch b/sci-libs/itk/files/itk-5.2.1-system-tiff-has-64.patch
new file mode 100644
index 000000000..25c44db2c
--- /dev/null
+++ b/sci-libs/itk/files/itk-5.2.1-system-tiff-has-64.patch
@@ -0,0 +1,18 @@
+From: François-Xavier Carton <fx.carton91@gmail.com>
+Date: Wed, 8 Jun 2022 19:36:48 +0200
+Subject: [PATCH] system libtiff has INT64
+
+Enabling this, otherwise using system libtiff leads to errors. In particular
+tests fail because there is some IFD8 data but the itkTIFFDataSize function
+returns 0 instead of 8, resulting in invalid mem access.
+
+--- a/Modules/ThirdParty/TIFF/src/itk_tiff.h.in.orig 2022-06-08 19:34:04.412431969 +0200
++++ b/Modules/ThirdParty/TIFF/src/itk_tiff.h.in 2022-06-08 19:34:26.240431631 +0200
+@@ -34,6 +34,7 @@
+ #cmakedefine ITK_TIFF_HAS_TIFFFieldReadCount
+ #cmakedefine ITK_TIFF_HAS_TIFFField
+ #ifdef ITK_USE_SYSTEM_TIFF
++# define TIFF_INT64_T int64_t
+ # include <tiffio.h>
+ #else
+ # include "itktiff/tiffio.h"
diff --git a/sci-libs/itk/files/itk-5.2.1-upstream-fixes.patch b/sci-libs/itk/files/itk-5.2.1-upstream-fixes.patch
new file mode 100644
index 000000000..2af8c4998
--- /dev/null
+++ b/sci-libs/itk/files/itk-5.2.1-upstream-fixes.patch
@@ -0,0 +1,309 @@
+https://github.com/InsightSoftwareConsortium/ITK/commit/2a7f5ed199926999b67f61a97c2c9a2595a11558.patch
+https://github.com/InsightSoftwareConsortium/ITK/commit/0c31aa688e82a34e5430873bc6176740fd09ad75.patch
+https://github.com/InsightSoftwareConsortium/ITK/commit/28325d921a9b8793e6aaefd612f53989f951d19c.patch
+https://github.com/InsightSoftwareConsortium/ITK/commit/aafd1f9631d0fad60e1b6f53e049e95a50c48bd1.patch
+
+From 2a7f5ed199926999b67f61a97c2c9a2595a11558 Mon Sep 17 00:00:00 2001
+From: Niels Dekker <N.Dekker@lumc.nl>
+Date: Thu, 24 Jun 2021 18:00:01 +0200
+Subject: [PATCH] COMP: Add missing `#include <iostream>` to Deprecated module
+ test
+
+Fixed a Visual C++ 2019 error, saying:
+
+> Deprecated\test\itkSimpleFastMutexLockTest.cxx(48,12): error C2039: 'cout': is not a member of 'std'
+---
+ .../Deprecated/test/itkSimpleFastMutexLockTest.cxx | 2 ++
+ 1 file changed, 2 insertions(+)
+
+diff --git a/Modules/Compatibility/Deprecated/test/itkSimpleFastMutexLockTest.cxx b/Modules/Compatibility/Deprecated/test/itkSimpleFastMutexLockTest.cxx
+index 11ad0c52700..60aa1c065b4 100644
+--- a/Modules/Compatibility/Deprecated/test/itkSimpleFastMutexLockTest.cxx
++++ b/Modules/Compatibility/Deprecated/test/itkSimpleFastMutexLockTest.cxx
+@@ -19,6 +19,8 @@
+
+ #include "itkSimpleFastMutexLock.h"
+
++#include <iostream> // For cout.
++
+
+ int
+ itkSimpleFastMutexLockTest(int, char *[])
+From 0c31aa688e82a34e5430873bc6176740fd09ad75 Mon Sep 17 00:00:00 2001
+From: Pablo Hernandez-Cerdan <pablo.hernandez.cerdan@outlook.com>
+Date: Tue, 20 Apr 2021 17:21:21 +0200
+Subject: [PATCH] COMP: CastXML, ITKVtkGlue, include only when property exists
+
+Some targets (VTK libraries) didn't have the property INTERFACE_INCLUDE_DIRECTORIES
+
+```bash
+CMake Error in Modules/Bridge/VtkGlue/wrapping/CMakeLists.txt:
+ Found relative path while evaluating include directories of
+ "ITKVtkGluePython":
+
+ "_vtk_lib_include_dirs-NOTFOUND"
+```
+
+Triggered when compiling Slicer with `Slicer_BUILD_ITKPython:BOOL=ON`
+aka `ITK_WRAP_PYTHON:BOOL=ON`.
+
+Full error log with extra printing:
+
+```bash
+
+CMake Warning at Modules/Bridge/VtkGlue/wrapping/CMakeLists.txt:3 (message):
+ ITKVtkGlue_VTK_LIBRARIES:
+ VTK::IOImage;VTK::ImagingSources;VTK::WrappingPythonCore;VTK::CommonCore;VTK::CommonDataModel;VTK::kwiml;VTK::CommonExecutionModel;VTK::RenderingOpenGL2;VTK::RenderingFreeType;VTK::InteractionStyle;VTK::InteractionWidgets
+
+CMake Warning at Modules/Bridge/VtkGlue/wrapping/CMakeLists.txt:6 (message):
+ _vtk_lib_include_dirs: _vtk_lib_include_dirs-NOTFOUND
+
+CMake Warning at Modules/Bridge/VtkGlue/wrapping/CMakeLists.txt:6 (message):
+ _vtk_lib_include_dirs: _vtk_lib_include_dirs-NOTFOUND
+
+CMake Warning at Modules/Bridge/VtkGlue/wrapping/CMakeLists.txt:6 (message):
+ _vtk_lib_include_dirs:
+ build/VTK-build/Wrapping/PythonCore;build/VTK/Wrapping/PythonCore
+
+CMake Warning at Modules/Bridge/VtkGlue/wrapping/CMakeLists.txt:6 (message):
+ _vtk_lib_include_dirs: _vtk_lib_include_dirs-NOTFOUND
+
+CMake Warning at Modules/Bridge/VtkGlue/wrapping/CMakeLists.txt:6 (message):
+ _vtk_lib_include_dirs: _vtk_lib_include_dirs-NOTFOUND
+
+CMake Warning at Modules/Bridge/VtkGlue/wrapping/CMakeLists.txt:6 (message):
+ _vtk_lib_include_dirs:
+ build/VTK-build/Utilities/KWIML;build/VTK/Utilities/KWIML
+
+CMake Warning at Modules/Bridge/VtkGlue/wrapping/CMakeLists.txt:6 (message):
+ _vtk_lib_include_dirs: _vtk_lib_include_dirs-NOTFOUND
+
+CMake Warning at Modules/Bridge/VtkGlue/wrapping/CMakeLists.txt:6 (message):
+ _vtk_lib_include_dirs: _vtk_lib_include_dirs-NOTFOUND
+
+CMake Warning at Modules/Bridge/VtkGlue/wrapping/CMakeLists.txt:6 (message):
+ _vtk_lib_include_dirs: _vtk_lib_include_dirs-NOTFOUND
+
+CMake Warning at Modules/Bridge/VtkGlue/wrapping/CMakeLists.txt:6 (message):
+ _vtk_lib_include_dirs: _vtk_lib_include_dirs-NOTFOUND
+
+CMake Warning at Modules/Bridge/VtkGlue/wrapping/CMakeLists.txt:6 (message):
+ _vtk_lib_include_dirs: _vtk_lib_include_dirs-NOTFOUND
+
+-- ITKVtkGlue: Creating module.
+-- ITKVtkGlue: Creating itkImageToVTKImageFilter submodule.
+-- ITKVtkGlue: Creating itkVTKImageToImageFilter submodule.
+-- ITKVtkGlue: Creating itkViewImage submodule.
+-- MGHIO: Creating module.
+-- MGHIO: Creating itkMGHImageIO submodule.
+-- MorphologicalContourInterpolation: Creating module.
+-- MorphologicalContourInterpolation: Creating itkMorphologicalContourInterpolator submodule.
+-- ITKPyUtils: Creating module.
+-- ITKPyUtils: Creating itkPyCommand submodule.
+-- ITKPyUtils: Creating itkPyImageFilter submodule.
+-- Configuring done
+CMake Error: The following variables are used in this project, but they are set to NOTFOUND.
+Please set them or make sure they are set and tested correctly in the CMake files:
+_vtk_lib_include_dirs
+ used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+ used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+ used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+ used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+ used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+ used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+ used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+ used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+ used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+ used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+ used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+ used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+ used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+ used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+ used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+ used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+ used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+ used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+ used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+ used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+ used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+ used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+ used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+ used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+ used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+ used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+ used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+ used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+ used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+ used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+ used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+ used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+ used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+ used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+ used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+ used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+ used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+ used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+ used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+ used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+ used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+ used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+ used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+ used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+ used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+ used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+ used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+ used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+ used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+ used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+ used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+ used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+ used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+ used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+ used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+ used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+ used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+ used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+ used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+ used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+ used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+ used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+ used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+ used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+ used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+ used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+ used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+ used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+ used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+ used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+ used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+ used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+ used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+ used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+ used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+ used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+ used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+ used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+ used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+ used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+ used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+ used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+ used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+ used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+ used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+ used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+ used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+ used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+ used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+ used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+ used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+ used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+ used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+ used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+ used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+ used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+ used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+ used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+ used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping
+
+CMake Error in Modules/Bridge/VtkGlue/wrapping/CMakeLists.txt:
+ Found relative path while evaluating include directories of
+ "ITKVtkGluePython":
+
+ "_vtk_lib_include_dirs-NOTFOUND"
+
+```
+---
+ Modules/Bridge/VtkGlue/wrapping/CMakeLists.txt | 4 +++-
+ 1 file changed, 3 insertions(+), 1 deletion(-)
+
+diff --git a/Modules/Bridge/VtkGlue/wrapping/CMakeLists.txt b/Modules/Bridge/VtkGlue/wrapping/CMakeLists.txt
+index 3f3322957e1..2fd6a5af8f6 100644
+--- a/Modules/Bridge/VtkGlue/wrapping/CMakeLists.txt
++++ b/Modules/Bridge/VtkGlue/wrapping/CMakeLists.txt
+@@ -2,7 +2,9 @@
+ if(NOT VTK_RENDERING_BACKEND STREQUAL "None")
+ foreach(_vtk_lib IN LISTS ITKVtkGlue_VTK_LIBRARIES)
+ get_target_property(_vtk_lib_include_dirs ${_vtk_lib} INTERFACE_INCLUDE_DIRECTORIES)
+- include_directories(${_vtk_lib_include_dirs})
++ if(_vtk_lib_include_dirs)
++ include_directories(${_vtk_lib_include_dirs})
++ endif()
+ endforeach()
+ endif()
+
+From 28325d921a9b8793e6aaefd612f53989f951d19c Mon Sep 17 00:00:00 2001
+From: Butui Hu <hot123tea123@gmail.com>
+Date: Mon, 1 Aug 2022 14:26:39 +0800
+Subject: [PATCH] COMP: use sysconfig.get_path as PEP 632 deprecate distutils
+ module
+
+---
+ Wrapping/Generators/Python/CMakeLists.txt | 2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+diff --git a/Wrapping/Generators/Python/CMakeLists.txt b/Wrapping/Generators/Python/CMakeLists.txt
+index fca3d999b87..3b7a1d37334 100644
+--- a/Wrapping/Generators/Python/CMakeLists.txt
++++ b/Wrapping/Generators/Python/CMakeLists.txt
+@@ -36,7 +36,7 @@ file(MAKE_DIRECTORY ${WRAPPER_MASTER_INDEX_OUTPUT_DIR}/python)
+ ###############################################################################
+ # Configure Python wrapping installation
+ if(Python3_EXECUTABLE AND NOT PY_SITE_PACKAGES_PATH)
+- set(python_check "try:\n import distutils.sysconfig\n print(distutils.sysconfig.get_python_lib(plat_specific=1, prefix=''))\nexcept:\n pass")
++ set(python_check "try:\n import sysconfig\n print(sysconfig.get_path('platlib'))\nexcept:\n pass")
+ file(WRITE ${CMAKE_CURRENT_BINARY_DIR}/detect_site_package_path.py ${python_check})
+ execute_process(COMMAND "${Python3_EXECUTABLE}" "${CMAKE_CURRENT_BINARY_DIR}/detect_site_package_path.py"
+ OUTPUT_VARIABLE py_spp
+From aafd1f9631d0fad60e1b6f53e049e95a50c48bd1 Mon Sep 17 00:00:00 2001
+From: Hans Johnson <hans-johnson@uiowa.edu>
+Date: Wed, 15 Dec 2021 08:10:58 -0600
+Subject: [PATCH] COMP: Remove inclusion of .hxx files as headers
+
+The ability to include either .h or .hxx files as
+header files required recursively reading the
+.h files twice. The added complexity is
+unnecessary, costly, and can confuse static
+analysis tools that monitor header guardes (due
+to reaching the maximum depth of recursion
+limits for nested #ifdefs in checking).
+
+Co-authored-by: Simon Rit <simon.rit@creatis.insa-lyon.fr>
+---
+ CMake/ITKModuleHeaderTest.cmake | 3 +--
+ Utilities/Maintenance/BuildHeaderTest.py | 4 ----
+ 2 files changed, 1 insertion(+), 6 deletions(-)
+
+diff --git a/CMake/ITKModuleHeaderTest.cmake b/CMake/ITKModuleHeaderTest.cmake
+index eb809d7e93d..82ad192a6f8 100644
+--- a/CMake/ITKModuleHeaderTest.cmake
++++ b/CMake/ITKModuleHeaderTest.cmake
+@@ -36,8 +36,7 @@ macro( itk_module_headertest _name )
+ # effected.
+ set( _include ${${_name}_SOURCE_DIR}/include )
+ file( GLOB _h_files ${_include}/*.h )
+- file( GLOB _hxx_files ${_include}/*.hxx )
+- set( _header_files ${_h_files} ${_hxx_files} )
++ set( _header_files ${_h_files} )
+ list( LENGTH _h_files _num_headers )
+ set( _outputs ${${_name}_BINARY_DIR}/test/${_name}HeaderTest1.cxx )
+ set( _test_num 1 )
+diff --git a/Utilities/Maintenance/BuildHeaderTest.py b/Utilities/Maintenance/BuildHeaderTest.py
+index 26a4b6ccb3f..f8ed9f7901e 100755
+--- a/Utilities/Maintenance/BuildHeaderTest.py
++++ b/Utilities/Maintenance/BuildHeaderTest.py
+@@ -130,15 +130,11 @@ def main():
+ else:
+ max_idx = added_header_idx + maximum_number_of_headers
+ for i in range(added_header_idx, max_idx):
+- # Use the .hxx if possible.
+- hxx_file = h_files[i][:-1] + "hxx"
+ # Files that include VTK headers need to link to VTK.
+ if h_files[i] in BANNED_HEADERS or h_files[i].lower().find("vtk") != -1:
+ to_include = (
+ '// #include "' + h_files[i] + '" // Banned in BuildHeaderTest.py\n'
+ )
+- elif os.path.exists(os.path.join(module_source_path, "include", hxx_file)):
+- to_include = '#include "' + hxx_file + '"\n'
+ else:
+ to_include = '#include "' + h_files[i] + '"\n'
+
diff --git a/sci-libs/itk/files/nrrdio-linking.patch b/sci-libs/itk/files/nrrdio-linking.patch
deleted file mode 100644
index a549650d2..000000000
--- a/sci-libs/itk/files/nrrdio-linking.patch
+++ /dev/null
@@ -1,15 +0,0 @@
-Description: Link libITKNrrdIO with -lm (needed for sqrt)
-Author: Steve Robbins <smr@debian.org>
-Forwarded: no
-
---- insighttoolkit4-4.5.0.orig/Modules/ThirdParty/NrrdIO/src/NrrdIO/CMakeLists.txt
-+++ insighttoolkit4-4.5.0/Modules/ThirdParty/NrrdIO/src/NrrdIO/CMakeLists.txt
-@@ -64,7 +64,7 @@
- ADD_DEFINITIONS(-DTEEM_ZLIB=1)
-
- ADD_LIBRARY(ITKNrrdIO ${nrrdio_SRCS} )
--TARGET_LINK_LIBRARIES(ITKNrrdIO ${ITKZLIB_LIBRARIES})
-+TARGET_LINK_LIBRARIES(ITKNrrdIO ${ITKZLIB_LIBRARIES} -lm)
-
- IF(ITK_LIBRARY_PROPERTIES)
- SET_TARGET_PROPERTIES(ITKNrrdIO PROPERTIES ${ITK_LIBRARY_PROPERTIES})
diff --git a/sci-libs/itk/files/tests.patch b/sci-libs/itk/files/tests.patch
deleted file mode 100644
index c24714e4d..000000000
--- a/sci-libs/itk/files/tests.patch
+++ /dev/null
@@ -1,41 +0,0 @@
-Known to fail by upstream:
-https://github.com/InsightSoftwareConsortium/ITK/issues/1212#issuecomment-527998115
-
---- a/Modules/Bridge/VtkGlue/test/CMakeLists.txt 2019-09-09 00:45:14.736032139 +0200
-+++ b/Modules/Bridge/VtkGlue/test/CMakeLists.txt 2019-09-09 00:49:42.183935497 +0200
-@@ -7,8 +7,6 @@
- if(NOT VTK_RENDERING_BACKEND STREQUAL "None")
- list(APPEND ITKVtkGlueTests
- itkVtkMedianFilterTest.cxx
-- itkVtkConnectedComponentImageFilterTest.cxx
-- QuickViewTest.cxx
- # ### runViewImage ###
- # No test generated. Use it for view images (2D or 3D) with:
- # ITKVtkGlueTestDriver runViewImage image_file
-@@ -40,26 +38,3 @@
- NAME itkVTKImageToImageFilterTest
- COMMAND ITKVtkGlueTestDriver
- itkVTKImageToImageFilterTest)
--
--if(NOT VTK_RENDERING_BACKEND STREQUAL "None")
-- itk_add_test(
-- NAME itkVtkMedianImageFilterTest
-- COMMAND ITKVtkGlueTestDriver
-- itkVtkMedianFilterTest DATA{${ITK_DATA_ROOT}/Input/cthead1.png} 2)
-- set_property(TEST itkVtkMedianImageFilterTest APPEND PROPERTY LABELS REQUIRES_DISPLAY)
--
-- itk_add_test(
-- NAME QuickViewTest
-- COMMAND ITKVtkGlueTestDriver
-- --compare DATA{Baseline/QuickViewTest.png,:}
-- ${ITK_TEST_OUTPUT_DIR}/QuickViewTest0.png
-- --compareNumberOfPixelsTolerance 1500
-- QuickViewTest DATA{${ITK_DATA_ROOT}/Input/peppers.png} ${ITK_TEST_OUTPUT_DIR})
-- set_property(TEST QuickViewTest APPEND PROPERTY LABELS REQUIRES_DISPLAY)
--
-- itk_add_test(
-- NAME itkVtkConnectedComponentImageFilterTest
-- COMMAND ITKVtkGlueTestDriver
-- itkVtkConnectedComponentImageFilterTest DATA{${ITK_DATA_ROOT}/Input/cthead1.png})
-- set_property(TEST itkVtkConnectedComponentImageFilterTest APPEND PROPERTY LABELS REQUIRES_DISPLAY)
--endif()
diff --git a/sci-libs/itk/itk-5.0.1.ebuild b/sci-libs/itk/itk-5.0.1.ebuild
deleted file mode 100644
index bf9f0f021..000000000
--- a/sci-libs/itk/itk-5.0.1.ebuild
+++ /dev/null
@@ -1,178 +0,0 @@
-# Copyright 1999-2022 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-PYTHON_COMPAT=( python3_{7,8,9} )
-
-inherit cmake python-single-r1
-
-MY_PN="InsightToolkit"
-MY_P="${MY_PN}-${PV}"
-GLI_HASH="187ab99b7d42718c99e5017f0acd3900d7469bd1"
-GLI_TEST_HASH="57b5d5de8d777f10f269445a"
-
-DESCRIPTION="NLM Insight Segmentation and Registration Toolkit"
-HOMEPAGE="http://www.itk.org"
-SRC_URI="
- https://github.com/InsightSoftwareConsortium/ITK/releases/download/v${PV}/${MY_P}.tar.gz
- https://github.com/InsightSoftwareConsortium/ITKGenericLabelInterpolator/archive/${GLI_HASH}.tar.gz -> ITKGenericLabelInterpolator-${PV}.tar.gz
- test? (
- https://data.kitware.com/api/v1/folder/${GLI_TEST_HASH}/download -> ITKGenericLabelInterpolator_test-${PV}.zip
- https://github.com/InsightSoftwareConsortium/ITK/releases/download/v${PV}/InsightData-${PV}.tar.gz
- )
- "
-
-LICENSE="Apache-2.0"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="debug doc examples fftw python review test vtkglue"
-RESTRICT="!test? ( test )"
-# python will not work, this is a know issue upstream:
-# https://github.com/InsightSoftwareConsortium/ITK/issues/1229
-# https://github.com/InsightSoftwareConsortium/ITKGenericLabelInterpolator/issues/10
-
-RDEPEND="
- dev-libs/double-conversion:0=
- media-libs/openjpeg:2
- media-libs/libpng:0=
- media-libs/tiff:0=
- sci-libs/dcmtk:0=
- sci-libs/hdf5:0=[cxx]
- sys-libs/zlib:0=
- media-libs/libjpeg-turbo:0=
- fftw? ( sci-libs/fftw:3.0= )
- vtkglue? ( sci-libs/vtk:0=[rendering,python?] )
- python? ( ${PYTHON_DEPS} )
-"
-DEPEND="${RDEPEND}
- sys-apps/coreutils
- python? (
- >=dev-lang/swig-2.0:0
- dev-cpp/castxml
- )
- doc? ( app-doc/doxygen )
-"
-BDEPEND="app-arch/unzip"
-
-REQUIRED_USE="python? ( ${PYTHON_REQUIRED_USE} )"
-
-S="${WORKDIR}/${MY_P}"
-
-PATCHES=(
- "${FILESDIR}"/ITKModuleRemote.patch
- "${FILESDIR}"/tests.patch
-)
-
-pkg_pretend() {
- if [[ -z ${ITK_COMPUTER_MEMORY_SIZE} ]]; then
- elog "To tune ITK to make the best use of working memory you can set"
- elog " ITK_COMPUTER_MEMORY_SIZE=XX"
- elog "in make.conf, default is 1 (unit is GB)"
- fi
- if use python && [[ -z ${ITK_WRAP_DIMS} ]]; then
- elog "For Python language bindings, you can define the dimensions"
- elog "you want to create bindings for by setting"
- elog " ITK_WRAP_DIMS=X;Y;Z..."
- elog "in make.conf, default is 2;3 for 2D and 3D data"
- fi
-}
-
-src_prepare() {
- sed -i -e "s/find_package(OpenJPEG 2.0.0/find_package(OpenJPEG/g"\
- Modules/ThirdParty/GDCM/src/gdcm/CMakeLists.txt
- ln -sr ../ITKGenericLabelInterpolator-* Modules/Remote/ITKGenericLabelInterpolator || die
- if use test; then
- for filename in ../GenericLabelInterpolator/test/*/*mha; do
- MD5=$(md5sum $filename) || die
- MD5=${MD5% *} || die
- cp "$filename" ".ExternalData/MD5/${MD5}" || die
- done
- fi
- cmake_src_prepare
-}
-
-src_configure() {
- local mycmakeargs=(
- -DBUILD_SHARED_LIBS=ON
- -DGDCM_USE_SYSTEM_OPENJPEG=ON
- -DITK_FORBID_DOWNLOADS:BOOL=OFF
- -DITK_USE_SYSTEM_DCMTK=ON
- -DITK_USE_SYSTEM_DOUBLECONVERSION=ON
- -DITK_USE_SYSTEM_CASTXML=ON
- -DITK_USE_SYSTEM_HDF5=ON
- -DITK_USE_SYSTEM_JPEG=ON
- -DITK_USE_SYSTEM_PNG=ON
- -DITK_USE_SYSTEM_SWIG=ON
- -DITK_USE_SYSTEM_TIFF=ON
- -DITK_USE_SYSTEM_ZLIB=ON
- -DITK_USE_KWSTYLE=OFF
- -DITK_BUILD_DEFAULT_MODULES=ON
- -DITK_COMPUTER_MEMORY_SIZE="${ITK_COMPUTER_MEMORY_SIZE:-1}"
- -DWRAP_ITK_JAVA=OFF
- -DWRAP_ITK_TCL=OFF
- -Ddouble-conversion_INCLUDE_DIRS="${EPREFIX}/usr/include/double-conversion"
- -DExternalData_OBJECT_STORES="${WORKDIR}/InsightToolkit-${PV}/.ExternalData"
- -DModule_GenericLabelInterpolator:BOOL=ON
- -DModule_ITKReview:BOOL=ON
- -DBUILD_TESTING="$(usex test ON OFF)"
- -DBUILD_EXAMPLES="$(usex examples ON OFF)"
- -DITK_USE_REVIEW="$(usex review ON OFF)"
- -DITK_BUILD_DOCUMENTATION="$(usex doc ON OFF)"
- -DITK_INSTALL_LIBRARY_DIR=$(get_libdir)
- )
- if use fftw; then
- mycmakeargs+=(
- -DUSE_FFTWD=ON
- -DUSE_FFTWF=ON
- -DUSE_SYSTEM_FFTW=ON
- -DITK_WRAP_double=ON
- -DITK_WRAP_vector_double=ON
- -DITK_WRAP_covariant_vector_double=ON
- -DITK_WRAP_complex_double=ON
- )
- fi
- if use vtkglue; then
- mycmakeargs+=(
- -DModule_ITKVtkGlue=ON
- )
- fi
- if use python; then
- mycmakeargs+=(
- -DITK_WRAP_PYTHON=ON
- -DITK_WRAP_DIMS="${ITK_WRAP_DIMS:-2;3}"
- )
- else
- mycmakeargs+=(
- -DITK_WRAP_PYTHON=OFF
- )
- fi
- cmake_src_configure
-}
-
-src_install() {
- cmake_src_install
-
- if use examples; then
- docinto examples
- docompress -x /usr/share/doc/${PF}/examples
- dodoc -r "${S}"/Examples/*
- fi
-
- echo "ITK_DATA_ROOT=${EPREFIX}/usr/share/${PN}/data" > ${T}/40${PN}
- local ldpath="${EPREFIX}/usr/$(get_libdir)/InsightToolkit"
- if use python; then
- echo "PYTHONPATH=${EPREFIX}/usr/$(get_libdir)/InsightToolkit/WrapITK/Python" >> "${T}"/40${PN}
- ldpath="${ldpath}:${EPREFIX}/usr/$(get_libdir)/InsightToolkit/WrapITK/lib"
- fi
- echo "LDPATH=${ldpath}" >> "${T}"/40${PN}
- doenvd "${T}"/40${PN}
-
- if use doc; then
- cd "${WORKDIR}"/html || die
- rm *.md5 || die "Failed to remove superfluous hashes"
- einfo "Installing API docs. This may take some time."
- docinto api-docs
- dodoc -r *
- fi
-}
diff --git a/sci-libs/itk/itk-5.1.0.ebuild b/sci-libs/itk/itk-5.2.1-r2.ebuild
index 3f6c759ec..98e39935e 100644
--- a/sci-libs/itk/itk-5.1.0.ebuild
+++ b/sci-libs/itk/itk-5.2.1-r2.ebuild
@@ -1,16 +1,18 @@
# Copyright 1999-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=7
+EAPI=8
-PYTHON_COMPAT=( python3_{7,8,9} )
+PYTHON_COMPAT=( python3_{9..10} )
+VIRTUALX_REQUIRED="manual"
-inherit cmake python-single-r1
+inherit cmake python-single-r1 virtualx
MY_PN="InsightToolkit"
MY_P="${MY_PN}-${PV}"
-GLI_HASH="a02cbeaf28cb3d28ac66b9ac651073530eb6ab78"
-TEST_HASH="0eb202e23ae81be123b1b26cf31a9ba743824700"
+GLI_HASH="89da9305f5750d3990ca9fd35ecc5ce0b39c71a6"
+IAD_HASH="24825c8d246e941334f47968553f0ae388851f0c"
+TEST_HASH="7ab9d41ad5b42ccbe8adcaf0b24416d439a264d0"
declare -a GLI_TEST_HASHES=(
"a5e11ea71164ff78c65fcf259db01ea5db981a9d868e60045ff2bffca92984df1174bf984a1076e450f0d5d69b4f0191ed1a61465c220e2c91a893b5df150c0a"
"bcdbb347f3704262d1f00be7179d6a0a6e68aed56c0653e8072ee5a94985c713bd229c935b1226a658af84fb7f1fffc2458c98364fc35303a2303b12f9f7ce2f"
@@ -18,14 +20,15 @@ declare -a GLI_TEST_HASHES=(
GLI_TEST_SRC=""
for i in "${GLI_TEST_HASHES[@]}"; do
- GLI_TEST_SRC+="https://data.kitware.com/api/v1/file/hashsum/sha512/${i} -> ${P}-test-${i} "
+ GLI_TEST_SRC+="https://data.kitware.com/api/v1/file/hashsum/sha512/${i}/download -> ${PN}-test-${i} "
done
DESCRIPTION="NLM Insight Segmentation and Registration Toolkit"
-HOMEPAGE="http://www.itk.org"
+HOMEPAGE="https://itk.org"
SRC_URI="
https://github.com/InsightSoftwareConsortium/ITK/releases/download/v${PV}/${MY_P}.tar.gz
https://github.com/InsightSoftwareConsortium/ITKGenericLabelInterpolator/archive/${GLI_HASH}.tar.gz -> ITKGenericLabelInterpolator-${PV}.tar.gz
+ https://github.com/ntustison/ITKAdaptiveDenoising/archive/${IAD_HASH}.tar.gz -> ITKAdaptiveDenoising-${PV}.tar.gz
test? (
https://github.com/InsightSoftwareConsortium/ITK/releases/download/v${PV}/InsightData-${PV}.tar.gz
https://github.com/InsightSoftwareConsortium/ITKTestingData/archive/${TEST_HASH}.tar.gz -> ${P}-testingdata.tar.gz
@@ -37,42 +40,55 @@ LICENSE="Apache-2.0"
SLOT="0"
KEYWORDS="~amd64 ~x86"
IUSE="debug doc examples fftw itkv4-compat python review test vtkglue"
+REQUIRED_USE="python? ( ${PYTHON_REQUIRED_USE} )"
+
RESTRICT="!test? ( test )"
-# python will not work, this is a know issue upstream:
-# https://github.com/InsightSoftwareConsortium/ITK/issues/2005
-# https://github.com/InsightSoftwareConsortium/ITK/issues/1229
-# https://github.com/InsightSoftwareConsortium/ITKGenericLabelInterpolator/issues/10
RDEPEND="
+ dev-cpp/eigen:3
dev-libs/double-conversion:0=
+ dev-libs/expat:0=
media-libs/openjpeg:2
media-libs/libpng:0=
media-libs/tiff:0=[jpeg]
sci-libs/dcmtk:0=
sci-libs/hdf5:0=[cxx]
+ sci-libs/gdcm:0=
sys-libs/zlib:0=
media-libs/libjpeg-turbo:0=
fftw? ( sci-libs/fftw:3.0= )
- vtkglue? ( sci-libs/vtk:0=[rendering,python?] )
+ vtkglue? (
+ sci-libs/vtk:0=[rendering]
+ python? (
+ sci-libs/vtk:0=[python,${PYTHON_SINGLE_USEDEP}]
+ )
+ )
python? ( ${PYTHON_DEPS} )
"
DEPEND="${RDEPEND}
sys-apps/coreutils
python? (
>=dev-lang/swig-2.0:0
- dev-cpp/castxml
+ dev-libs/castxml
)
doc? ( app-doc/doxygen )
"
-
-REQUIRED_USE="python? ( ${PYTHON_REQUIRED_USE} )"
+BDEPEND="
+ test? (
+ vtkglue? ( ${VIRTUALX_DEPEND} )
+ python? (
+ $(python_gen_cond_dep 'dev-python/numpy[${PYTHON_USEDEP}]')
+ )
+ )
+"
S="${WORKDIR}/${MY_P}"
PATCHES=(
- "${FILESDIR}"/tests.patch
- "${FILESDIR}"/${P}-downloads.patch
- "${FILESDIR}"/${P}-include_limits.patch
+ "${FILESDIR}/${P}-upstream-fixes.patch"
+ "${FILESDIR}/${P}-system-tiff-has-64.patch"
+ "${FILESDIR}/${P}-fix-castxml-clang-attr-malloc.patch"
+ "${FILESDIR}/${P}-system-openjpeg.patch"
)
pkg_pretend() {
@@ -90,16 +106,42 @@ pkg_pretend() {
}
src_prepare() {
- sed -i -e "s/find_package(OpenJPEG 2.0.0/find_package(OpenJPEG/g"\
- Modules/ThirdParty/GDCM/src/gdcm/CMakeLists.txt
- ln -sr ../ITKGenericLabelInterpolator-* Modules/External/ITKGenericLabelInterpolator || die
+ # drop bundled libs
+ local -a DROPS=(
+ DoubleConversion/src/double-conversion
+ Eigen3/src/itkeigen
+ Expat/src/expat
+ GDCM/src/gdcm
+ JPEG/src/itkjpeg
+ HDF5/src/itkhdf5
+ OpenJPEG/src/openjpeg
+ PNG/src/itkpng
+ TIFF/src/itktiff
+ ZLIB/src/itkzlib
+ )
+ local x
+ for x in "${DROPS[@]}"; do
+ ebegin "Dropping bundled ${x%%/*}"
+ rm -r "Modules/ThirdParty/${x}" || die
+ eend $?
+ done
+ {
+ find Modules/ThirdParty -mindepth 2 -maxdepth 2 -type d -name src -printf '%P\n'
+ printf '%s\n' "${DROPS[@]}" | sed 's,/[^/]*$,,'
+ } | sort | uniq -u | xargs -n 1 ewarn "Using bundled" || die
+
+ # Remote modules
+ ln -sr "../ITKGenericLabelInterpolator-${GLI_HASH}" Modules/External/ITKGenericLabelInterpolator || die
+ ln -sr "../ITKAdaptiveDenoising-${IAD_HASH}" Modules/External/ITKAdaptiveDenoising || die
+
cmake_src_prepare
+
if use test; then
cp -rf "../ITKTestingData-${TEST_HASH}/"* ".ExternalData/" || die
mv "../ITKTestingData-${TEST_HASH}" "${BUILD_DIR}/.ExternalData" || die
for i in "${GLI_TEST_HASHES[@]}"; do
- cp "${DISTDIR}/${i}" ".ExternalData/SHA512/" || die
- cp "${DISTDIR}/${i}" "${BUILD_DIR}/.ExternalData/SHA512/" || die
+ cp "${DISTDIR}/${PN}-test-${i}" ".ExternalData/SHA512/${i}" || die
+ cp "${DISTDIR}/${PN}-test-${i}" "${BUILD_DIR}/.ExternalData/SHA512/${i}" || die
done
fi
}
@@ -107,6 +149,7 @@ src_prepare() {
src_configure() {
local mycmakeargs=(
-DITK_BUILD_DOCUMENTATION="$(usex doc ON OFF)"
+ -DITK_INSTALL_DOC_DIR="share/doc/${P}"
-DBUILD_EXAMPLES="$(usex examples ON OFF)"
-DBUILD_SHARED_LIBS=ON
-DBUILD_TESTING="$(usex test ON OFF)"
@@ -119,8 +162,12 @@ src_configure() {
-DITK_USE_SYSTEM_DCMTK=ON
-DITK_USE_SYSTEM_DOUBLECONVERSION=ON
-DITK_USE_SYSTEM_CASTXML=ON
+ -DITK_USE_SYSTEM_EIGEN=ON
+ -DITK_USE_SYSTEM_EXPAT=ON
+ -DITK_USE_SYSTEM_GDCM=ON
-DITK_USE_SYSTEM_HDF5=ON
-DITK_USE_SYSTEM_JPEG=ON
+ -DITK_USE_SYSTEM_OPENJPEG=ON
-DITK_USE_SYSTEM_PNG=ON
-DITK_USE_SYSTEM_SWIG=ON
-DITK_USE_SYSTEM_TIFF=ON
@@ -128,6 +175,7 @@ src_configure() {
-DITK_USE_KWSTYLE=OFF
-DITK_BUILD_DEFAULT_MODULES=ON
-DITK_COMPUTER_MEMORY_SIZE="${ITK_COMPUTER_MEMORY_SIZE:-1}"
+ -DModule_AdaptiveDenoising:BOOL=ON
-DModule_GenericLabelInterpolator:BOOL=ON
-DModule_ITKReview:BOOL=ON
-DWRAP_ITK_JAVA=OFF
@@ -153,6 +201,7 @@ src_configure() {
if use python; then
mycmakeargs+=(
-DITK_WRAP_PYTHON=ON
+ -DPython3_EXECUTABLE="${PYTHON}"
-DITK_WRAP_DIMS="${ITK_WRAP_DIMS:-2;3}"
)
else
@@ -172,13 +221,13 @@ src_install() {
dodoc -r "${S}"/Examples/*
fi
- echo "ITK_DATA_ROOT=${EPREFIX}/usr/share/${PN}/data" > ${T}/40${PN}
+ echo "ITK_DATA_ROOT=${EPREFIX}/usr/share/${PN}/data" > ${T}/40${PN} || die
local ldpath="${EPREFIX}/usr/$(get_libdir)/InsightToolkit"
if use python; then
- echo "PYTHONPATH=${EPREFIX}/usr/$(get_libdir)/InsightToolkit/WrapITK/Python" >> "${T}"/40${PN}
+ echo "PYTHONPATH=${EPREFIX}/usr/$(get_libdir)/InsightToolkit/WrapITK/Python" >> "${T}"/40${PN} || die
ldpath="${ldpath}:${EPREFIX}/usr/$(get_libdir)/InsightToolkit/WrapITK/lib"
fi
- echo "LDPATH=${ldpath}" >> "${T}"/40${PN}
+ echo "LDPATH=${ldpath}" >> "${T}"/40${PN} || die
doenvd "${T}"/40${PN}
if use doc; then
@@ -188,4 +237,14 @@ src_install() {
docinto api-docs
dodoc -r *
fi
+
+ use python && python_optimize
+}
+
+src_test() {
+ if use vtkglue; then
+ virtx cmake_src_test
+ else
+ cmake_src_test
+ fi
}
diff --git a/sci-libs/labbookdb/labbookdb-0.1.ebuild b/sci-libs/labbookdb/labbookdb-0.1.ebuild
index 4da4106a2..8f148746d 100644
--- a/sci-libs/labbookdb/labbookdb-0.1.ebuild
+++ b/sci-libs/labbookdb/labbookdb-0.1.ebuild
@@ -1,9 +1,9 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=7
+EAPI=8
-PYTHON_COMPAT=( python3_{7..9} )
+PYTHON_COMPAT=( python3_{8..10} )
inherit distutils-r1
diff --git a/sci-libs/mlpack/Manifest b/sci-libs/mlpack/Manifest
deleted file mode 100644
index 827319a78..000000000
--- a/sci-libs/mlpack/Manifest
+++ /dev/null
@@ -1,2 +0,0 @@
-DIST mlpack-3.4.1.tar.gz 5782241 BLAKE2B d5a1050489c61a934330a0f3d1142e7949f7fdd9c31f679d7963208fc8aaea8fd8c0eb7e45920c3799712cb059808c75098e31b913557ec3c2af2f1d32e561f0 SHA512 53de83c2ca36829a0ae952357b25bee44bf85d01c2414848fe2c5f09ebe4732bd0a1d3c72de202646345fa66964fbc3247ddeb6a327e87459c036a215fe55fc2
-DIST mlpack-3.4.2.tar.gz 5782921 BLAKE2B d775124462357b489f91f6ef75f5f908d9a9234082c48223f19a728ab9e41cb6576fca9b4b59415d3096471f4ab2d2970296387954977652169a447b8e036263 SHA512 05a66b73cba8d83f630b0999023913e7a4a3214632930ff3c598d964d52bcae4eab113018eecf385130c0e7e9c16c25380b31dd62a2e0ecf419b4bf3856b34b0
diff --git a/sci-libs/mlpack/metadata.xml b/sci-libs/mlpack/metadata.xml
deleted file mode 100644
index f587c48a7..000000000
--- a/sci-libs/mlpack/metadata.xml
+++ /dev/null
@@ -1,27 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <maintainer type="person">
- <email>gentoo@aisha.cc</email>
- <name>Aisha Tammy</name>
- </maintainer>
- <maintainer type="project">
- <email>sci@gentoo.org</email>
- <name>Gentoo Science Project</name>
- </maintainer>
- <longdescription lang="en">
- mlpack is a C++ machine learning library with emphasis on
- scalability, speed, and ease-of-use. Its aim is to make machine
- learning possible for novice users by means of a simple, consistent
- API, while simultaneously exploiting C++ language features to
- provide maximum performance and maximum flexibility for expert
- users.
- </longdescription>
- <use>
- <flag name="arma-debug">build with armadillo dbug symbols</flag>
- <flag name="go">build go bindings</flag>
- <flag name="julia">build julia bindings</flag>
- <flag name="matlab">build matlab bindings</flag>
- <flag name="R">build R bindings</flag>
- </use>
-</pkgmetadata>
diff --git a/sci-libs/mlpack/mlpack-3.4.1.ebuild b/sci-libs/mlpack/mlpack-3.4.1.ebuild
deleted file mode 100644
index d03dd9ab1..000000000
--- a/sci-libs/mlpack/mlpack-3.4.1.ebuild
+++ /dev/null
@@ -1,112 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-PYTHON_COMPAT=( python3_{7..9} )
-
-inherit cmake python-single-r1
-
-DESCRIPTION="scalable C++ machine learning library"
-HOMEPAGE="https://www.mlpack.org/"
-SRC_URI="https://www.mlpack.org/files/${P}.tar.gz"
-
-LICENSE="LGPL-3"
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE+="arma-debug debug doc go julia matlab openmp profile R test"
-REQUIRED_USE="${PYTHON_REQUIRED_USE} arma-debug? ( debug )"
-RESTRICT="!test? ( test )"
-
-CDEPEND="
- ${PYTHON_DEPS}
- julia? ( || (
- dev-lang/julia
- dev-lang/julia-bin:*
- )
- )
- go? ( dev-lang/go )
- R? ( dev-lang/R )
-"
-
-RDEPEND="
- ${CDEPEND}
- $(python_gen_cond_dep '
- dev-libs/boost[${PYTHON_USEDEP}]
- dev-libs/libxml2[${PYTHON_USEDEP}]
- ')
- dev-python/pandas
- dev-python/cython
- dev-python/numpy
- dev-libs/stb
- >=sci-libs/armadillo-8.4.0[arpack,blas,lapack]
- sci-libs/ensmallen
-"
-DEPEND="${RDEPEND}"
-BDEPEND="
- ${CDEPEND}
- app-text/txt2man
- virtual/pkgconfig
- doc? (
- app-doc/doxygen
- dev-libs/mathjax
- )
- test? ( $( python_gen_cond_dep '
- dev-python/pytest[${PYTHON_USEDEP}]
- ')
- )
-"
-
-pkg_setup() {
- elog "If you want to build matlab bindings then you"
- elog "need to make sure that matlab has been installed"
- elog "prior to building this package and it is available"
- elog "in the standard locations to be found by"
- elog "CMake, library finders, header includes and other"
- elog "trinkets that are used while compiling."
- elog "Matlab will not be entertained as a first class"
- elog "citizen until we have enough personnel"
-
- python-single-r1_pkg_setup
-}
-
-src_prepare() {
- sed -i \
- -e "s:share/doc/mlpack:share/doc/${PF}:" \
- -e 's/-O3//g' \
- CMakeLists.txt || die
- cmake_src_prepare
-}
-
-src_configure() {
- local mycmakeargs=(
- -DDISABLE_DOWNLOADS=ON
- -DDOWNLOAD_ENSMALLEN=OFF
- -DDOWNLOAD_STB_IMAGE=OFF
- -DBUILD_WITH_COVERAGE=OFF
- -DBUILD_PYTHON_BINDINGS=ON
- -DBUILD_SHARED_LIBS=ON
- -DBUILD_CLI_EXECUTABLES=ON
- -DTEST_VERBOSE=$(usex test)
- -DBUILD_TESTS=$(usex test)
- -DDEBUG=$(usex debug)
- -DPROFILE=$(usex profile)
- -DARMA_EXTRA_DEBUG=$(usex arma-debug)
- -DUSE_OPENMP=$(usex openmp)
- -DMATLAB_BINDINGS=$(usex matlab)
- -DBUILD_GO_SHLIB=$(usex go)
- -DBUILD_JULIA_BINDINGS=$(usex julia)
- -DBUILD_GO_BINDINGS=$(usex go)
- -DBUILD_R_BINDINGS=$(usex R)
- -DBUILD_MARKDOWN_BINDINGS=$(usex doc)
- -DMATHJAX=$(usex doc)
- ${EXTRA_ECONF[@]}
- )
- cmake_src_configure
-}
-
-src_install() {
- cmake_src_install
-
- python_optimize
-}
diff --git a/sci-libs/mlpack/mlpack-3.4.2.ebuild b/sci-libs/mlpack/mlpack-3.4.2.ebuild
deleted file mode 100644
index bfc7231e1..000000000
--- a/sci-libs/mlpack/mlpack-3.4.2.ebuild
+++ /dev/null
@@ -1,118 +0,0 @@
-# Copyright 1999-2022 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-PYTHON_COMPAT=( python3_{7..9} )
-
-inherit cmake python-single-r1
-
-DESCRIPTION="scalable C++ machine learning library"
-HOMEPAGE="https://www.mlpack.org/"
-SRC_URI="https://www.mlpack.org/files/${P}.tar.gz"
-
-LICENSE="LGPL-3"
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE+="arma-debug debug doc go julia matlab openmp profile R test"
-REQUIRED_USE="${PYTHON_REQUIRED_USE} arma-debug? ( debug )"
-RESTRICT="!test? ( test )"
-
-CDEPEND="
- ${PYTHON_DEPS}
- julia? ( || (
- dev-lang/julia
- dev-lang/julia-bin:*
- )
- )
- go? ( dev-lang/go )
- R? ( dev-lang/R )
-"
-
-RDEPEND="
- ${CDEPEND}
- $(python_gen_cond_dep '
- dev-libs/boost[${PYTHON_USEDEP}]
- dev-libs/libxml2[${PYTHON_USEDEP}]
- dev-python/pandas[${PYTHON_USEDEP}]
- dev-python/numpy[${PYTHON_USEDEP}]
- dev-python/cython[${PYTHON_USEDEP}]
- ')
- dev-libs/stb
- >=sci-libs/armadillo-8.4.0[arpack,blas,lapack]
- sci-libs/ensmallen
-"
-DEPEND="${RDEPEND}"
-BDEPEND="
- ${CDEPEND}
- app-text/txt2man
- virtual/pkgconfig
- doc? (
- app-doc/doxygen
- dev-libs/mathjax
- )
- $(python_gen_cond_dep '
- dev-python/cython[${PYTHON_USEDEP}]
- ')
- test? ( $( python_gen_cond_dep '
- dev-python/pytest[${PYTHON_USEDEP}]
- ')
- )
-"
-
-pkg_setup() {
- elog "If you want to build matlab bindings then you"
- elog "need to make sure that matlab has been installed"
- elog "prior to building this package and it is available"
- elog "in the standard locations to be found by"
- elog "CMake, library finders, header includes and other"
- elog "trinkets that are used while compiling."
- elog "Matlab will not be entertained as a first class"
- elog "citizen until we have enough personnel"
-
- python-single-r1_pkg_setup
-}
-
-src_prepare() {
- sed -i \
- -e "s:share/doc/mlpack:share/doc/${PF}:" \
- -e 's/-O3//g' \
- CMakeLists.txt || die
- # drop dep on pytest-runner
- sed -i -e "/setup_requires/d" \
- src/mlpack/bindings/python/setup.py.in || die
- cmake_src_prepare
-}
-
-src_configure() {
- local mycmakeargs=(
- -DDISABLE_DOWNLOADS=ON
- -DDOWNLOAD_ENSMALLEN=OFF
- -DDOWNLOAD_STB_IMAGE=OFF
- -DBUILD_WITH_COVERAGE=OFF
- -DBUILD_PYTHON_BINDINGS=ON
- -DBUILD_SHARED_LIBS=ON
- -DBUILD_CLI_EXECUTABLES=ON
- -DTEST_VERBOSE=$(usex test)
- -DBUILD_TESTS=$(usex test)
- -DDEBUG=$(usex debug)
- -DPROFILE=$(usex profile)
- -DARMA_EXTRA_DEBUG=$(usex arma-debug)
- -DUSE_OPENMP=$(usex openmp)
- -DMATLAB_BINDINGS=$(usex matlab)
- -DBUILD_GO_SHLIB=$(usex go)
- -DBUILD_JULIA_BINDINGS=$(usex julia)
- -DBUILD_GO_BINDINGS=$(usex go)
- -DBUILD_R_BINDINGS=$(usex R)
- -DBUILD_MARKDOWN_BINDINGS=$(usex doc)
- -DMATHJAX=$(usex doc)
- ${EXTRA_ECONF[@]}
- )
- cmake_src_configure
-}
-
-src_install() {
- cmake_src_install
-
- python_optimize
-}
diff --git a/sci-libs/nibabel/Manifest b/sci-libs/nibabel/Manifest
index 31eb1f65e..ea228479f 100644
--- a/sci-libs/nibabel/Manifest
+++ b/sci-libs/nibabel/Manifest
@@ -1,3 +1,2 @@
-DIST nibabel-2.5.1.tar.gz 4281663 BLAKE2B 361f1118d850a76fb8d2aa3ac6ebf0da711cf8df93aa6e2689201f3e713f35e028442ef00f69ce7a4a96d3c376b4966d0b76a087005123101f743b4d6074d3b2 SHA512 49de1a42113e64a56336e02f3143588b574c7b063b10b892ee125048451be701955e505bd1d51183327e2ee221f8364005fdd9fa7d256343113ab6ca1994820d
DIST nibabel-3.0.2.tar.gz 4336181 BLAKE2B b95ea57f28265eab627caea71f65c8ad1b0f868d40d80efb68f2dbb1e81f7d4f10b2da21d33f803abcd9441f3afe2c861f96828f8701f3981e4b7a4b2f97308e SHA512 51a10a72ade0382e43a006a0b9453b0c00f962a1c0d32c7a9da6ce3b9c95db05cd3bd672389d514107768b688a8315cba2e34d52bc845db3ca3e7912a1a0a8ac
DIST nibabel-3.2.1.tar.gz 4442534 BLAKE2B 5a76275c0c3746bbe094789350f4f6d9dc17e332915c9f567660138c44ba50672415272d21d7b0834c77f4f9660950bda8c684f7664d58f0e5784b782384cb2f SHA512 5c5d95313f4b22462ba67c23d52dd34ed5d690c72a3137b21ac0bdbc4d20aa4f0c1d87d23c675f8c2f6e4335dc51fb9ab788ac8c63be56eec8ab8657ed95a6d7
diff --git a/sci-libs/nibabel/nibabel-2.5.1.ebuild b/sci-libs/nibabel/nibabel-2.5.1.ebuild
deleted file mode 100644
index 3316b84d5..000000000
--- a/sci-libs/nibabel/nibabel-2.5.1.ebuild
+++ /dev/null
@@ -1,42 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-PYTHON_COMPAT=( python3_{7..9} )
-
-inherit distutils-r1
-
-DESCRIPTION="Access a cacophony of neuro-imaging file formats"
-HOMEPAGE="https://nipy.org/nibabel/"
-SRC_URI="https://github.com/nipy/nibabel/archive/${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="dicom doc test"
-RESTRICT="!test? ( test )"
-
-RDEPEND="
- dev-python/numpy[${PYTHON_USEDEP}]
- dev-python/scipy[${PYTHON_USEDEP}]
- dev-python/mock[${PYTHON_USEDEP}]
- dicom? (
- sci-libs/pydicom
- dev-python/pillow[${PYTHON_USEDEP}]
- )
-"
-DEPEND="
- dev-python/setuptools[${PYTHON_USEDEP}]
- test? (
- ${RDEPEND}
- dev-python/nose[${PYTHON_USEDEP}]
- )
- doc? ( dev-python/sphinx[${PYTHON_USEDEP}] )
-"
-
-python_test() {
- cd "${BUILD_DIR}" || die
- echo "backend: Agg" > matplotlibrc
- MPLCONFIGDIR=. nosetests || die
-}
diff --git a/sci-libs/nibabel/nibabel-3.0.2.ebuild b/sci-libs/nibabel/nibabel-3.0.2.ebuild
index 3316b84d5..f0759b51a 100644
--- a/sci-libs/nibabel/nibabel-3.0.2.ebuild
+++ b/sci-libs/nibabel/nibabel-3.0.2.ebuild
@@ -1,9 +1,9 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=7
+EAPI=8
-PYTHON_COMPAT=( python3_{7..9} )
+PYTHON_COMPAT=( python3_{8..10} )
inherit distutils-r1
diff --git a/sci-libs/nibabel/nibabel-3.2.1.ebuild b/sci-libs/nibabel/nibabel-3.2.1.ebuild
index d469867f9..c3b45a93b 100644
--- a/sci-libs/nibabel/nibabel-3.2.1.ebuild
+++ b/sci-libs/nibabel/nibabel-3.2.1.ebuild
@@ -1,9 +1,9 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=7
+EAPI=8
-PYTHON_COMPAT=( python3_{7..9} )
+PYTHON_COMPAT=( python3_{8..10} )
DISTUTILS_USE_SETUPTOOLS=rdepend
inherit distutils-r1
@@ -23,14 +23,19 @@ RDEPEND="
dev-python/scipy[${PYTHON_USEDEP}]
dev-python/mock[${PYTHON_USEDEP}]
dicom? (
- sci-libs/pydicom
dev-python/pillow[${PYTHON_USEDEP}]
- )
+ sci-libs/pydicom
+ )
"
BDEPEND="test? (
dev-python/pytest-doctestplus[${PYTHON_USEDEP}]
)"
+EPYTEST_DESELECT=(
+ # Re-evaluate after 3.2.1
+ nibabel/gifti/tests/test_parse_gifti_fast.py::test_parse_dataarrays
+)
+
distutils_enable_sphinx doc/source dev-python/texext dev-python/numpydoc dev-python/matplotlib
distutils_enable_tests pytest
diff --git a/sci-libs/nibabel/nibabel-9999.ebuild b/sci-libs/nibabel/nibabel-9999.ebuild
deleted file mode 100644
index 283ad8804..000000000
--- a/sci-libs/nibabel/nibabel-9999.ebuild
+++ /dev/null
@@ -1,37 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-PYTHON_COMPAT=( python3_{7..9} )
-DISTUTILS_USE_SETUPTOOLS=rdepend
-
-inherit distutils-r1 git-r3
-
-DESCRIPTION="Access a cacophony of neuro-imaging file formats"
-HOMEPAGE="https://nipy.org/nibabel/"
-SRC_URI=""
-EGIT_REPO_URI="https://github.com/nipy/nibabel.git"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS=""
-IUSE="dicom"
-
-RDEPEND="
- dev-python/numpy[${PYTHON_USEDEP}]
- dev-python/packaging[${PYTHON_USEDEP}]
- dev-python/scipy[${PYTHON_USEDEP}]
- dev-python/mock[${PYTHON_USEDEP}]
- dicom? (
- sci-libs/pydicom
- dev-python/pillow[${PYTHON_USEDEP}]
- )
-"
-
-BDEPEND="test? (
- dev-python/pytest-doctestplus[${PYTHON_USEDEP}]
-)"
-
-distutils_enable_sphinx doc/source dev-python/texext dev-python/numpydoc dev-python/matplotlib
-distutils_enable_tests pytest
diff --git a/sci-libs/nipy/Manifest b/sci-libs/nipy/Manifest
index d9bac81b5..bbe6e4b5d 100644
--- a/sci-libs/nipy/Manifest
+++ b/sci-libs/nipy/Manifest
@@ -1 +1,2 @@
-DIST nipy-0.4.2.tar.gz 2403688 BLAKE2B 883377356787652450bb5a8090be48708144c9d11473232248d48e8bc36eb292cdd672ae30b337de6fb8c5e593a772489908c9575c2f97a8dbd82a8e4d6ad0df SHA512 730654e422c9fd15c0abf7ce0e0cb5e9569788527a35e9cc6deb71e2384b0ed2dbbf82f9eafe9cd739647bb1dc3a3d43606d0244fae5accd0896f1fc5bb3a8cc
+DIST nipy-0.4.2.tar.gz 2403690 BLAKE2B bd75e6b76095b825494ec9f78dd126d089c9c0b660d808f5510fab3449ae6c3e71ed59866203d6c2e3f5cfe5bc342b9edc96c6c2b8dab97e532d99705c80410c SHA512 a1a590f35833a4238be87a01fa4e0609a1c18243d626cb8e54a5904fa8702247292b030671bb628ee075cf9346ee4040a9222e60e36dde0d4153d3bef33bcf89
+DIST nipy-0.5.0.tar.gz 2404225 BLAKE2B d57a2a29cb8d9538731631e2f73520082905c4944b7d99682e0453a6f05173ffb6f27fc2f29fe172d94790e3d904471ebd2d5a3de55cdf39608b605d7d9a5344 SHA512 ec91f8b7b555e2baeadc9d6d2f83d5ad77080e0505579bcc72cae051869e9f8c1ffdfa679afc7380173a6454f45ec457a3657fd9b9396a28a5e273701ecaf0a5
diff --git a/sci-libs/nipy/nipy-0.4.2.ebuild b/sci-libs/nipy/nipy-0.4.2.ebuild
index c20d904f5..3b483638f 100644
--- a/sci-libs/nipy/nipy-0.4.2.ebuild
+++ b/sci-libs/nipy/nipy-0.4.2.ebuild
@@ -1,11 +1,11 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=7
+EAPI=8
-PYTHON_COMPAT=( python3_{7..9} )
+PYTHON_COMPAT=( python3_{8..10} )
-inherit distutils-r1 flag-o-matic
+inherit distutils-r1
DESCRIPTION="Neuroimaging tools for Python"
HOMEPAGE="https://nipy.org/"
@@ -15,6 +15,8 @@ LICENSE="BSD"
SLOT="0"
KEYWORDS="~amd64 ~x86"
IUSE=""
+RESTRICT="test"
+# reported upstream: https://github.com/nipy/nipy/issues/493
RDEPEND="
dev-python/prov[${PYTHON_USEDEP}]
diff --git a/sci-libs/nipy/nipy-0.5.0.ebuild b/sci-libs/nipy/nipy-0.5.0.ebuild
new file mode 100644
index 000000000..81a462c96
--- /dev/null
+++ b/sci-libs/nipy/nipy-0.5.0.ebuild
@@ -0,0 +1,52 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{8..10} )
+
+inherit distutils-r1
+
+DESCRIPTION="Neuroimaging tools for Python"
+HOMEPAGE="https://nipy.org/"
+SRC_URI="https://github.com/${PN}/${PN}/archive/${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE=""
+RESTRICT="test"
+# reported upstream: https://github.com/nipy/nipy/issues/493
+
+RDEPEND="
+ dev-python/scipy[${PYTHON_USEDEP}]
+ dev-python/sympy[${PYTHON_USEDEP}]
+ >=sci-libs/nibabel-1.2[${PYTHON_USEDEP}]
+ dev-python/numpy[${PYTHON_USEDEP}]
+ "
+DEPEND=""
+
+distutils_enable_tests nose
+
+python_prepare_all() {
+ distutils-r1_python_prepare_all
+ # bug #397605
+ [[ ${CHOST} == *-darwin* ]] \
+ && append-ldflags -bundle "-undefined dynamic_lookup" \
+ || append-ldflags -shared
+
+ # nipy uses the horrible numpy.distutils automagic
+}
+
+#python_test() {
+# distutils-r1_install_for_testing
+# cp nipy/testing/*.nii.gz "${BUILD_DIR}/lib/nipy/testing/"
+# cp nipy/modalities/fmri/tests/*.{mat,npz,txt} "${BUILD_DIR}/lib/nipy/modalities/fmri/tests/"
+# cp nipy/algorithms/statistics/models/tests/test_data.bin "${BUILD_DIR}/lib/nipy/algorithms/statistics/models/tests"
+# cp nipy/labs/spatial_models/tests/some_blobs.nii "${BUILD_DIR}/lib/nipy/labs/spatial_models/tests/some_blobs.nii"
+# mkdir "${BUILD_DIR}/lib/nipy/algorithms/diagnostics/tests/data/"
+# cp nipy/algorithms/diagnostics/tests/data/tsdiff_results.mat "${BUILD_DIR}/lib/nipy/algorithms/diagnostics/tests/data/"
+# cd "${BUILD_DIR}" || die
+# echo "backend : agg" > matplotlibrc
+# nosetests || die
+#}
diff --git a/sci-libs/nipy/nipy-9999.ebuild b/sci-libs/nipy/nipy-9999.ebuild
deleted file mode 100644
index 7acc9a234..000000000
--- a/sci-libs/nipy/nipy-9999.ebuild
+++ /dev/null
@@ -1,54 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-PYTHON_COMPAT=( python3_{7..9} )
-
-inherit distutils-r1 flag-o-matic git-r3
-
-DESCRIPTION="Neuroimaging tools for Python"
-HOMEPAGE="https://nipy.org/"
-SRC_URI=""
-EGIT_REPO_URI="https://github.com/nipy/nipy"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS=""
-IUSE=""
-
-RDEPEND="
- dev-python/prov[${PYTHON_USEDEP}]
- dev-python/scipy[${PYTHON_USEDEP}]
- dev-python/sympy[${PYTHON_USEDEP}]
- >=sci-libs/nibabel-1.2[${PYTHON_USEDEP}]
- dev-python/numpy[${PYTHON_USEDEP}]
- "
-
-DEPEND="
- ${RDEPEND}
- dev-python/setuptools[${PYTHON_USEDEP}]
- "
-
-python_prepare_all() {
- distutils-r1_python_prepare_all
- # bug #397605
- [[ ${CHOST} == *-darwin* ]] \
- && append-ldflags -bundle "-undefined dynamic_lookup" \
- || append-ldflags -shared
-
- # nipy uses the horrible numpy.distutils automagic
-}
-
-python_test() {
- distutils-r1_install_for_testing
- cp nipy/testing/*.nii.gz "${BUILD_DIR}/lib/nipy/testing/"
- cp nipy/modalities/fmri/tests/*.{mat,npz,txt} "${BUILD_DIR}/lib/nipy/modalities/fmri/tests/"
- cp nipy/algorithms/statistics/models/tests/test_data.bin "${BUILD_DIR}/lib/nipy/algorithms/statistics/models/tests"
- cp nipy/labs/spatial_models/tests/some_blobs.nii "${BUILD_DIR}/lib/nipy/labs/spatial_models/tests/some_blobs.nii"
- mkdir "${BUILD_DIR}/lib/nipy/algorithms/diagnostics/tests/data/"
- cp nipy/algorithms/diagnostics/tests/data/tsdiff_results.mat "${BUILD_DIR}/lib/nipy/algorithms/diagnostics/tests/data/"
- cd "${BUILD_DIR}" || die
- echo "backend : agg" > matplotlibrc
- nosetests || die
-}
diff --git a/sci-libs/nipype/files/nipype-1.5.0-collections.patch b/sci-libs/nipype/files/nipype-1.5.0-collections.patch
new file mode 100644
index 000000000..e784ba48b
--- /dev/null
+++ b/sci-libs/nipype/files/nipype-1.5.0-collections.patch
@@ -0,0 +1,28 @@
+--- a/nipype/interfaces/base/traits_extension.py 2020-06-03 11:08:30.000000000 -0400
++++ b/nipype/interfaces/base/traits_extension.py 2022-07-11 14:09:31.847784312 -0400
+@@ -19,7 +19,10 @@
+ (usually by Robert Kern).
+
+ """
+-from collections import Sequence
++try:
++ from collections import Sequence
++except ImportError:
++ from collections.abc import Sequence
+
+ # perform all external trait imports here
+ from traits import __version__ as traits_version
+--- a/nipype/utils/misc.py 2020-06-03 11:08:30.000000000 -0400
++++ b/nipype/utils/misc.py 2020-06-03 14:08:57.951408897 -0400
+@@ -6,7 +6,10 @@
+ import os
+ import sys
+ import re
+-from collections import Iterator
++try:
++ from collections import Iterator
++except ImportError:
++ from collections.abc import Iterator
+ from warnings import warn
+
+ from distutils.version import LooseVersion
diff --git a/sci-libs/nipype/nipype-1.5.0.ebuild b/sci-libs/nipype/nipype-1.5.0.ebuild
index 35792adbc..f2a0815dc 100644
--- a/sci-libs/nipype/nipype-1.5.0.ebuild
+++ b/sci-libs/nipype/nipype-1.5.0.ebuild
@@ -1,9 +1,9 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=7
+EAPI=8
-PYTHON_COMPAT=( python3_{7..9} )
+PYTHON_COMPAT=( python3_{8..10} )
PYTHON_REQ_USE="threads(+),sqlite"
inherit distutils-r1
@@ -47,11 +47,12 @@ RDEPEND="
PATCHES=(
"${FILESDIR}/${P}"-version_check.patch
+ "${FILESDIR}/${P}"-collections.patch
)
src_prepare() {
# Remove etelemetry
- sed -i '/"etelemetry/d' nipype/info.py || die
+ sed -i '/"etelemetry/d' nipype/info.py requirements.txt || die
# Mark failing tests
sed -i \
@@ -68,11 +69,18 @@ python_install_all() {
doenvd "${FILESDIR}/98nipype"
}
+EPYTEST_DESELECT=(
+ nipype/algorithms/tests/test_CompCor.py::TestCompCor::test_compcor
+ nipype/algorithms/tests/test_CompCor.py::TestCompCor::test_compcor_variance_threshold_and_metadata
+ nipype/algorithms/tests/test_CompCor.py::TestCompCor::test_tcompcor
+ nipype/interfaces/tests/test_io.py::test_s3datagrabber_communication
+ nipype/utils/tests/test_cmd.py::TestNipypeCMD::test_main_returns_0_on_help
+)
+
python_test() {
# Setting environment variable to disable etelemetry version check:
# https://github.com/nipy/nipype/issues/3196#issuecomment-605980044
- NIPYPE_NO_ET=1 pytest -vv\
- || die
+ NIPYPE_NO_ET=1 epytest
# Upstream test configuration fails
#-c nipype/pytest.ini\
#--doctest-modules nipype\
diff --git a/sci-libs/pybids/Manifest b/sci-libs/pybids/Manifest
index 28c1b4626..fc1863ad9 100644
--- a/sci-libs/pybids/Manifest
+++ b/sci-libs/pybids/Manifest
@@ -1,4 +1,3 @@
DIST pybids-0.10.2.tar.gz 3013772 BLAKE2B 70255fbca7a7d5a51efa454ee20d30a9527703d6028a965b51da883aa10f8b63d180f72fd127e12b27249c3f388825a9bb2ba4604680c57f3a512ec7093c01c4 SHA512 c90b7e471d73b070e86452ca5d03639d0263e74c3c79386b52ed2c5fc49576f985bc923f2327882ee56bc4691631105c831ebe40f78aade5b9943be83909ba16
-DIST pybids-0.11.1.tar.gz 3026079 BLAKE2B 9ca7d1299a074f4b7ae51e7d6ff29a55664b6c32c85511913fb69459bd66a0c09b63dddfef2c433c5cccf47c4e358720cbd101f85e7794e22a9935bd6a36ac65 SHA512 bcc1cc3a06b6921e8336990e83e820439c217cfdce6aee3b4b93f2c1ee04acf0bf9009fa2fc80fd50cd59bd9b1a2a3ceb934589b5fd590612de386e91e4f7340
DIST pybids-0.12.4.tar.gz 3031862 BLAKE2B de9d1ba0a0eb400da1de44189f4920a8d1f003dba1c47b18e339d593c68b5a80c340a9acc5267dbfbf730a59aad004035568a1f8b0de30dbab9c211b11790fbd SHA512 1f2f3a784a1e3f0e74919c6ada2ae0365ab89315d724f0a6b6b38a0416c1e6f7e938966b2dda80f090ef2bbf84ce0bcf0bb214a652743432b1d193d9569eb7b1
DIST pybids-0.6.5.tar.gz 2915557 BLAKE2B d7765b872917bbffcd2706488d7c789976be5bbb1eb5d112cb0b7bcedb483236643f8bf7c177f4a64a44a4d50787a4df1d39fbec8e826bfffd2e2e6f891b3ef3 SHA512 9eef42f00440dddf0147d91f90e07db81f9f95a650f0e47c04304771173ca8691cdb366bd0df1d752c0444f102a4aa010c2343ba75df96528cceb9a98f9d8a0e
diff --git a/sci-libs/pybids/pybids-0.10.2.ebuild b/sci-libs/pybids/pybids-0.10.2.ebuild
index 062cad939..1143655d7 100644
--- a/sci-libs/pybids/pybids-0.10.2.ebuild
+++ b/sci-libs/pybids/pybids-0.10.2.ebuild
@@ -1,9 +1,9 @@
-# Copyright 1999-2020 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=7
+EAPI=8
-PYTHON_COMPAT=( python3_{7..9} )
+PYTHON_COMPAT=( python3_{8..10} )
inherit distutils-r1
@@ -29,12 +29,4 @@ RDEPEND="
dev-python/scipy[${PYTHON_USEDEP}]
"
-#RESTRICT="test"
-# Fails because fixtures are called directly
-# https://github.com/bids-standard/pybids/issues/289#issuecomment-476853673
-
-python_test() {
- #rm bids/tests/test_config.py || die
- distutils_install_for_testing
- pytest -vv || die
-}
+distutils_enable_tests pytest
diff --git a/sci-libs/pybids/pybids-0.11.1.ebuild b/sci-libs/pybids/pybids-0.11.1.ebuild
deleted file mode 100644
index 062cad939..000000000
--- a/sci-libs/pybids/pybids-0.11.1.ebuild
+++ /dev/null
@@ -1,40 +0,0 @@
-# Copyright 1999-2020 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-PYTHON_COMPAT=( python3_{7..9} )
-
-inherit distutils-r1
-
-DESCRIPTION="Python package to access BIDS datasets"
-HOMEPAGE="https://github.com/INCF/pybids"
-SRC_URI="https://github.com/INCF/pybids/archive/${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE="test"
-RESTRICT="!test? ( test )"
-
-DEPEND=""
-RDEPEND="
- dev-python/num2words[${PYTHON_USEDEP}]
- dev-python/numpy[${PYTHON_USEDEP}]
- dev-python/pandas[${PYTHON_USEDEP}]
- dev-python/patsy[${PYTHON_USEDEP}]
- dev-python/sqlalchemy[${PYTHON_USEDEP}]
- sci-libs/bids-validator[${PYTHON_USEDEP}]
- sci-libs/nibabel[${PYTHON_USEDEP}]
- dev-python/scipy[${PYTHON_USEDEP}]
- "
-
-#RESTRICT="test"
-# Fails because fixtures are called directly
-# https://github.com/bids-standard/pybids/issues/289#issuecomment-476853673
-
-python_test() {
- #rm bids/tests/test_config.py || die
- distutils_install_for_testing
- pytest -vv || die
-}
diff --git a/sci-libs/pybids/pybids-0.12.4.ebuild b/sci-libs/pybids/pybids-0.12.4.ebuild
index 40a8adc17..ace1712ce 100644
--- a/sci-libs/pybids/pybids-0.12.4.ebuild
+++ b/sci-libs/pybids/pybids-0.12.4.ebuild
@@ -1,9 +1,9 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=7
+EAPI=8
-PYTHON_COMPAT=( python3_{7..9} )
+PYTHON_COMPAT=( python3_{8..10} )
DISTUTILS_USE_SETUPTOOLS=rdepend
inherit distutils-r1
@@ -16,9 +16,7 @@ LICENSE="MIT"
SLOT="0"
KEYWORDS="~amd64"
-BDEPEND="dev-python/versioneer[${PYTHON_USEDEP}]
- test? ( dev-python/mock[${PYTHON_USEDEP}] )
-"
+BDEPEND="test? ( dev-python/mock[${PYTHON_USEDEP}] )"
RDEPEND="
dev-python/click[${PYTHON_USEDEP}]
@@ -32,4 +30,4 @@ RDEPEND="
dev-python/scipy[${PYTHON_USEDEP}]
"
-distutils_enable_tests --install pytest
+distutils_enable_tests pytest
diff --git a/sci-libs/pybids/pybids-0.6.5.ebuild b/sci-libs/pybids/pybids-0.6.5.ebuild
index 521ef9947..ceb6784d1 100644
--- a/sci-libs/pybids/pybids-0.6.5.ebuild
+++ b/sci-libs/pybids/pybids-0.6.5.ebuild
@@ -1,9 +1,9 @@
-# Copyright 1999-2020 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=7
+EAPI=8
-PYTHON_COMPAT=( python3_{7..9} )
+PYTHON_COMPAT=( python3_{8..10} )
inherit distutils-r1
diff --git a/sci-libs/simpleitk/simpleitk-1.2.4.ebuild b/sci-libs/simpleitk/simpleitk-1.2.4.ebuild
index 8a3bf5f5a..fa9a721e3 100644
--- a/sci-libs/simpleitk/simpleitk-1.2.4.ebuild
+++ b/sci-libs/simpleitk/simpleitk-1.2.4.ebuild
@@ -1,9 +1,9 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=7
+EAPI=8
-PYTHON_COMPAT=( python3_{7..9} )
+PYTHON_COMPAT=( python3_{8..10} )
LUA_COMPAT=( lua5-{1..3} )
inherit lua-single cmake python-single-r1
diff --git a/sci-libs/torchvision/torchvision-0.11.2.ebuild b/sci-libs/torchvision/torchvision-0.11.2.ebuild
index 6df2cbc01..b17ac9007 100644
--- a/sci-libs/torchvision/torchvision-0.11.2.ebuild
+++ b/sci-libs/torchvision/torchvision-0.11.2.ebuild
@@ -23,7 +23,7 @@ RDEPEND="
dev-python/six[${PYTHON_USEDEP}]
dev-python/tqdm[${PYTHON_USEDEP}]
dev-python/scipy[${PYTHON_USEDEP}]
- sci-libs/pytorch[${PYTHON_USEDEP}]
+ sci-libs/pytorch[cuda(-)?,${PYTHON_USEDEP}]
media-video/ffmpeg
dev-qt/qtcore:5
"
diff --git a/sci-misc/elmer-fem/elmer-fem-9.0-r1.ebuild b/sci-misc/elmer-fem/elmer-fem-9.0-r2.ebuild
index 6d810ed14..82e1c796f 100644
--- a/sci-misc/elmer-fem/elmer-fem-9.0-r1.ebuild
+++ b/sci-misc/elmer-fem/elmer-fem-9.0-r2.ebuild
@@ -40,6 +40,8 @@ DEPEND="${RDEPEND}"
PATCHES=(
"${FILESDIR}/${PN}-DCRComplexSolve-compile-error.patch"
"${FILESDIR}/${PN}-ElmerIce-compile.patch"
+ "${FILESDIR}/${PN}-rpath.patch"
+ "${FILESDIR}/${P}-qwt-6.2.patch"
)
S="${WORKDIR}/elmerfem-release-${PV}"
diff --git a/sci-misc/elmer-fem/files/elmer-fem-9.0-qwt-6.2.patch b/sci-misc/elmer-fem/files/elmer-fem-9.0-qwt-6.2.patch
new file mode 100644
index 000000000..13eaf1c5f
--- /dev/null
+++ b/sci-misc/elmer-fem/files/elmer-fem-9.0-qwt-6.2.patch
@@ -0,0 +1,35 @@
+From 48e9430ccb858ca5bda28b967a0c84b51e2404b2 Mon Sep 17 00:00:00 2001
+From: "E. Albiter" <ealbiter@gmail.com>
+Date: Fri, 15 Oct 2021 13:12:48 -0500
+Subject: [PATCH] Compatibility with Qwt 6.2. Fix for #293
+
+---
+ ElmerGUI/Application/src/convergenceview.h | 8 ++++----
+ 1 file changed, 4 insertions(+), 4 deletions(-)
+
+diff --git a/ElmerGUI/Application/src/convergenceview.h b/ElmerGUI/Application/src/convergenceview.h
+index 377b644b99..4259eb730e 100755
+--- a/ElmerGUI/Application/src/convergenceview.h
++++ b/ElmerGUI/Application/src/convergenceview.h
+@@ -51,8 +51,8 @@
+ #include <qwt_plot_curve.h>
+ #include <qwt_plot_grid.h>
+ #include <qwt_legend.h>
+-/*#include <qwt_data.h> <-- deprecated in Qwt6, using qwt_compat.h instead*/
+-#include <qwt_compat.h>
++/*#include <qwt_data.h> <-- deprecated in Qwt6, using qwt_compat.h instead
++#include <qwt_compat.h> <-- Removed in Qwt 6.2 */
+ #include <qwt_text.h>
+ #include <qwt_scale_engine.h>
+
+@@ -76,8 +76,8 @@ class CurveData
+
+ private:
+ int d_count;
+- QwtArray<double> d_x;
+- QwtArray<double> d_y;
++ QVector<double> d_x;
++ QVector<double> d_y;
+ };
+
+ class Curve
diff --git a/sci-misc/elmer-fem/files/elmer-fem-rpath.patch b/sci-misc/elmer-fem/files/elmer-fem-rpath.patch
new file mode 100644
index 000000000..27249fef9
--- /dev/null
+++ b/sci-misc/elmer-fem/files/elmer-fem-rpath.patch
@@ -0,0 +1,11 @@
+--- a/CMakeLists.txt.orig 2022-08-24 21:50:59.940905698 -0500
++++ b/CMakeLists.txt 2022-08-24 21:51:08.610804464 -0500
+@@ -479,7 +479,7 @@
+
+ # Set up rpaths to point ELMER_INSTALL_LIB_DIR
+ IF(${CMAKE_SYSTEM_NAME} MATCHES "Linux")
+- SET(ELMERSOLVER_RPATH_STRING "\$ORIGIN/../${ELMER_INSTALL_LIB_DIR}")
++ SET(ELMERSOLVER_RPATH_STRING "${ELMER_INSTALL_LIB_DIR}")
+ SET(ELMERLIB_RPATH_STRING "\$ORIGIN/")
+ ELSEIF(APPLE)
+ SET(ELMERSOLVER_RPATH_STRING "@loader_path/../${ELMER_INSTALL_LIB_DIR}")
diff --git a/sci-physics/feynarts/Manifest b/sci-physics/feynarts/Manifest
new file mode 100644
index 000000000..d66304b21
--- /dev/null
+++ b/sci-physics/feynarts/Manifest
@@ -0,0 +1 @@
+DIST FeynArts-3.11.tar.gz 3146405 BLAKE2B d22a19faecaa3a87ebf48b035736a04a6ae9b28e47300240edac541cb86438781092bf0a16d84808fb0256cf7547ba9d04024934007fa017cab08811d6b2b41b SHA512 2032172c86316b1703c0ff0c9cc511db0b97d6268bde30b6948ea98c5f2b39996071675d25aba4ed65af99f0c6535bce4e5eca8ca942be3591f922937c4aa79b
diff --git a/sci-physics/feynarts/feynarts-3.11.ebuild b/sci-physics/feynarts/feynarts-3.11.ebuild
new file mode 100644
index 000000000..0851757d3
--- /dev/null
+++ b/sci-physics/feynarts/feynarts-3.11.ebuild
@@ -0,0 +1,29 @@
+# Copyright 2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+MY_PN=FeynArts
+MY_P=${MY_PN}-${PV}
+
+DESCRIPTION="FeynArts renders Feynman diagrams and generates their topologies."
+HOMEPAGE="http://feynarts.de"
+SRC_URI="http://feynarts.de/${MY_P}.tar.gz"
+S="${WORKDIR}/${MY_P}"
+
+LICENSE="LGPL-3+"
+SLOT="0"
+KEYWORDS="~amd64"
+
+RDEPEND="
+ sci-mathematics/mathematica
+ "
+DEPEND="${RDEPEND}"
+
+src_install() {
+ MMADIR=/usr/share/Mathematica/Applications
+ dosym "${MY_P}" "${MMADIR}/${MY_PN}"
+ dodir "${MMADIR}/${MY_P}"
+ insinto ${MMADIR}
+ doins -r "${S}"
+}
diff --git a/sci-physics/feynarts/metadata.xml b/sci-physics/feynarts/metadata.xml
new file mode 100644
index 000000000..14606c162
--- /dev/null
+++ b/sci-physics/feynarts/metadata.xml
@@ -0,0 +1,19 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <maintainer type="project">
+ <email>sci@gentoo.org</email>
+ <name>Gentoo Science Project</name>
+ </maintainer>
+ <maintainer type="project">
+ <email>sci-physics@gentoo.org</email>
+ <name>Gentoo Physics Project</name>
+ </maintainer>
+ <maintainer type="person">
+ <email>alexander@neuwirth-informatik.de</email>
+ <name>Alexander Puck Neuwirth</name>
+ </maintainer>
+ <longdescription lang="en">
+ FeynArts is a Mathematica package for the generation and visualization of Feynman diagrams and amplitudes.
+ </longdescription>
+</pkgmetadata>
diff --git a/sci-physics/feyncalc/Manifest b/sci-physics/feyncalc/Manifest
new file mode 100644
index 000000000..9514cfd33
--- /dev/null
+++ b/sci-physics/feyncalc/Manifest
@@ -0,0 +1,2 @@
+DIST FeynCalc-9.3.1.tar.gz 4296784 BLAKE2B bb9e2e17ee8c51ec9417f900982af494e44a19cad651065d769820756056d6accfa8955da1c03dcc054e32c8ca5a5b1974594e77f95cc0a8e7100919783d20ad SHA512 3e7f4e87920e26712008754498f2d7e3a5873f6adf3e7dbea1e98f7f0f9ff20e1e08941b959e18143d3f602aa3f0c1ac4c574f450bcd6d2e8ad68e775e95aeee
+DIST FeynCalc-9999.tar.gz 4298804 BLAKE2B a4b404aed41d510f32ddf5a242d0c6129174ace1eeb92a19c2cf6f9620f82b37f3b01709d063619567590d38d4506431b5d9af6fbf3fe1184c07c683c1f2d3b4 SHA512 30ef3f0249b9dd639e0d83767d1aaea272c6ce3083d0a36a96ced11c68bd4d9c499efcd95abb209d56cd8ae3142b925c6b723c541821c7856e4ac787c2c52e34
diff --git a/sci-physics/feyncalc/feyncalc-9.3.1.ebuild b/sci-physics/feyncalc/feyncalc-9.3.1.ebuild
new file mode 100644
index 000000000..2f54f878b
--- /dev/null
+++ b/sci-physics/feyncalc/feyncalc-9.3.1.ebuild
@@ -0,0 +1,43 @@
+# Copyright 2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+MY_PV=$(ver_rs 1-3 '_')
+MY_PN=FeynCalc
+
+DESCRIPTION="FeynCalc is a Mathematica package for computing Feynman diagrams."
+HOMEPAGE="https://feyncalc.github.io/"
+SLOT="0"
+SRC_URI="https://github.com/FeynCalc/feyncalc/archive/refs/tags/Release-${MY_PV}.tar.gz -> ${MY_PN}-${PV}.tar.gz"
+S="${WORKDIR}/feyncalc-Release-${MY_PV}"
+
+LICENSE="GPL-3+"
+KEYWORDS="~amd64"
+IUSE="+FCtraditionalFormOutput"
+
+RDEPEND="
+ sci-mathematics/mathematica
+ "
+DEPEND="${RDEPEND}"
+
+src_configure() {
+ mv "${MY_PN}/DocOutput" "${MY_PN}/Documentation" || die
+ if use FCtraditionalFormOutput; then
+ echo '$FCTraditionalFormOutput=True;' > "${MY_PN}/FCConfig.m" || die
+ fi
+}
+
+src_install() {
+ MMADIR=/usr/share/Mathematica/Applications
+ dodir "${MMADIR}/${MY_PN}"
+ insinto "${MMADIR}/"
+ doins -r "${S}/${MY_PN}"
+ # copy permissions
+ for f in $(find "${MY_PN}/*" ! -type l); do
+ fperms --reference="${S}/$f" "${MMADIR}/$f"
+ done
+ # documentation are notebook(.nb) files
+ dodoc -r ${MY_PN}/Documentation/English/*
+ docompress -x /usr/share/doc/${PF}/
+}
diff --git a/sci-physics/feyncalc/feyncalc-9999.ebuild b/sci-physics/feyncalc/feyncalc-9999.ebuild
new file mode 100644
index 000000000..1c26d976e
--- /dev/null
+++ b/sci-physics/feyncalc/feyncalc-9999.ebuild
@@ -0,0 +1,47 @@
+# Copyright 2020 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+# Copyright 1999-2020 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+MY_PV=$(ver_rs 1-3 '_')
+MY_PN=FeynCalc
+
+DESCRIPTION="FeynCalc is a Mathematica package for computing Feynman diagrams."
+HOMEPAGE="https://feyncalc.github.io/"
+SLOT="0"
+SRC_URI="https://github.com/FeynCalc/feyncalc/archive/hotfix-stable.tar.gz -> ${MY_PN}-${PV}.tar.gz"
+S="${WORKDIR}/feyncalc-hotfix-stable"
+
+LICENSE="GPL-3+"
+IUSE="+FCtraditionalFormOutput"
+REQUIRED_USE=""
+PROPERTIES+=" live"
+
+RDEPEND="
+ sci-mathematics/mathematica
+ "
+DEPEND="${RDEPEND}"
+
+src_configure() {
+ mv "${MY_PN}/DocOutput" "${MY_PN}/Documentation" || die
+ if use FCtraditionalFormOutput; then
+ echo '$FCTraditionalFormOutput=True;' > "${MY_PN}/FCConfig.m" || die
+ fi
+}
+
+src_install() {
+ MMADIR=/usr/share/Mathematica/Applications
+ dodir "${MMADIR}/${MY_PN}"
+ insinto "${MMADIR}/"
+ doins -r "${S}/${MY_PN}"
+ # copy permissions
+ for f in $(find "${MY_PN}/*" ! -type l); do
+ fperms --reference="${S}/$f" "${MMADIR}/$f"
+ done
+ # documentation are notebook(.nb) files
+ dodoc -r ${MY_PN}/Documentation/English/*
+ docompress -x /usr/share/doc/${PF}/
+}
diff --git a/sci-physics/feyncalc/metadata.xml b/sci-physics/feyncalc/metadata.xml
new file mode 100644
index 000000000..9e87f772e
--- /dev/null
+++ b/sci-physics/feyncalc/metadata.xml
@@ -0,0 +1,22 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <maintainer type="project">
+ <email>sci@gentoo.org</email>
+ <name>Gentoo Science Project</name>
+ </maintainer>
+ <maintainer type="project">
+ <email>sci-physics@gentoo.org</email>
+ <name>Gentoo Physics Project</name>
+ </maintainer>
+ <maintainer type="person">
+ <email>alexander@neuwirth-informatik.de</email>
+ <name>Alexander Puck Neuwirth</name>
+ </maintainer>
+ <longdescription lang="en">
+ FeynCalc is a Mathematica package for symbolic evaluation of Feynman diagrams and algebraic calculations in quantum field theory and elementary particle physics.
+ </longdescription>
+ <use>
+ <flag name="FCtraditionalFormOutput">Use TraditionalForm typesetting.</flag>
+ </use>
+</pkgmetadata>
diff --git a/sci-physics/formcalc/Manifest b/sci-physics/formcalc/Manifest
new file mode 100644
index 000000000..6ac4c74b1
--- /dev/null
+++ b/sci-physics/formcalc/Manifest
@@ -0,0 +1,2 @@
+DIST FormCalc-9.10.tar.gz 32070519 BLAKE2B e789d7eea0cc92f27033373fd6516e94ec66d1780ae7bb1254537fa508640436a4595dbf09594a2cad8b4178d1e950806089ae4584bff0f2848674325a734212 SHA512 30519fcd6a9e616f6bfa23825056afdc27111605ca66e35f6baebac5bcb7ff43e07c7d40ed90157c584be82392fc85a32b769e637a793817377a8ffc5601af6d
+DIST FormCalc-9.9.tar.gz 32059045 BLAKE2B 69e3d063bf746d86d02f63d3a1fdce314582b190bafc66d063a6f25575476fcb6b60121b9133f850ffd5d173e437b160a2661072051083b3f4affc48fcb4bda7 SHA512 9661a07fac13348de13ec09dc8f043df02ef9a5391be64217d432e04d4d82ad3dea94f43951f839fbe8947338bc0ab721a9a9ebdc0900979e16ea89d857c87c7
diff --git a/sci-physics/formcalc/files/formcalc-9.9-compile.patch b/sci-physics/formcalc/files/formcalc-9.9-compile.patch
new file mode 100644
index 000000000..48be7f06e
--- /dev/null
+++ b/sci-physics/formcalc/files/formcalc-9.9-compile.patch
@@ -0,0 +1,50 @@
+--- a/compile 2022-07-20 14:51:59.605328833 +0200
++++ b/compile 2022-07-20 15:37:09.122446647 +0200
+@@ -96,7 +96,7 @@
+
+ mcc="REALCC=\"$CC\" CC=\"$t/fcc\" \
+ REALCXX=\"$CXX\" CXX=\"$t/f++\" \
+-PATH=\""'$$PATH'":$t\" $MCC -st $MCFLAGS $CFLAGS"
++PATH=\""'$$PATH'":$t\" $MCC -st -g $MCFLAGS $CFLAGS"
+
+ # Mma 5.1's mcc needs -lpthread for static linking
+ mclibs="-lpthread"
+@@ -104,37 +104,28 @@
+ cc="$CC $CFLAGS"
+
+ make -f - << _EOF_ || exit 1
+-all: $DEST/tform$exe \
++all: \
+ $DEST/ReadForm$exe $DEST/ToForm$exe \
+ $DEST/ToFortran$exe $DEST/ToC$exe \
+ $DEST/ReadData$exe $DEST/reorder$exe
+
+-$DEST/tform$exe: $SRC/bin/$BIN/tform$exe
+- cp -p $SRC/bin/$BIN/* $DEST/
+-
+ $DEST/ReadForm$exe: $SRC/FormCalc/ReadForm.tm
+ $mcc -o $DEST/ReadForm$exe $SRC/FormCalc/ReadForm.tm $mclibs
+- -strip $DEST/ReadForm$exe
+
+ $DEST/ToForm$exe: $SRC/FormCalc/ToForm.c
+ $cc -o $DEST/ToForm$exe $SRC/FormCalc/ToForm.c
+- -strip $DEST/ToForm$exe
+
+ $DEST/ToFortran$exe: $SRC/FormCalc/ToFortran.c
+ $cc -o $DEST/ToFortran$exe $SRC/FormCalc/ToFortran.c
+- -strip $DEST/ToFortran$exe
+
+ $DEST/ToC$exe: $SRC/FormCalc/ToC.c
+ $cc -o $DEST/ToC$exe $SRC/FormCalc/ToC.c
+- -strip $DEST/ToC$exe
+
+ $DEST/ReadData$exe: $SRC/tools/ReadData.tm
+ $mcc -o $DEST/ReadData$exe $SRC/tools/ReadData.tm $mclibs
+- -strip $DEST/ReadData$exe
+
+ $DEST/reorder$exe: $SRC/tools/reorder.c
+ $cc -o $DEST/reorder$exe $SRC/tools/reorder.c
+- -strip $DEST/reorder$exe
+ _EOF_
+
+
diff --git a/sci-physics/formcalc/formcalc-9.10-r1.ebuild b/sci-physics/formcalc/formcalc-9.10-r1.ebuild
new file mode 100644
index 000000000..9a3734d2a
--- /dev/null
+++ b/sci-physics/formcalc/formcalc-9.10-r1.ebuild
@@ -0,0 +1,52 @@
+# Copyright 2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+MY_PN=FormCalc
+MY_P=${MY_PN}-${PV}
+
+DESCRIPTION="FormCalc can be used for automatic Feynman diagram computation."
+HOMEPAGE="http://feynarts.de/formcalc"
+SRC_URI="http://feynarts.de/formcalc/${MY_P}.tar.gz"
+S="${WORKDIR}/${MY_P}"
+
+LICENSE="LGPL-3+"
+SLOT="0"
+KEYWORDS="~amd64"
+
+RDEPEND="
+ sci-mathematics/mathematica
+ sci-mathematics/form[threads]
+ "
+DEPEND="${RDEPEND}"
+BDEPEND="
+ sci-mathematics/mathematica
+ sci-mathematics/form
+ "
+PATCHES=( "${FILESDIR}"/${PN}-9.9-compile.patch )
+
+src_compile() {
+ # remove shipped binaries
+ rm bin/Linux-x86-64/* || die
+ rm bin/Linux-x86-64-kernel2.6/* || die
+ export DEST=Linux-x86-64
+ ./compile ${LDFLAGS} || die
+}
+
+src_install() {
+ MMADIR=/usr/share/Mathematica/Applications
+ dosym ${MY_P} ${MMADIR}/${MY_PN}
+ dodir ${MMADIR}/${MY_P}
+ insinto ${MMADIR}
+ doins -r "${S}"
+ # Copy executable, etc. permissions
+ for f in $(find * ! -type l); do
+ fperms --reference="${S}/$f" ${MMADIR}/${MY_P}/$f
+ done
+ # switch to system form
+ dosym `command -v form` ${MMADIR}/${MY_P}/Linux-x86-64/form
+ dosym `command -v tform` ${MMADIR}/${MY_P}/Linux-x86-64/tform
+
+ dodoc manual/*.pdf
+}
diff --git a/sci-physics/formcalc/formcalc-9.9-r1.ebuild b/sci-physics/formcalc/formcalc-9.9-r1.ebuild
new file mode 100644
index 000000000..c73a3e804
--- /dev/null
+++ b/sci-physics/formcalc/formcalc-9.9-r1.ebuild
@@ -0,0 +1,54 @@
+# Copyright 2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+MY_PN=FormCalc
+MY_P=${MY_PN}-${PV}
+
+DESCRIPTION="FormCalc can be used for automatic Feynman diagram computation."
+HOMEPAGE="http://feynarts.de/formcalc"
+SRC_URI="http://feynarts.de/formcalc/${MY_P}.tar.gz"
+S="${WORKDIR}/${MY_P}"
+
+LICENSE="LGPL-3+"
+SLOT="0"
+KEYWORDS="~amd64"
+
+RDEPEND="
+ sci-mathematics/mathematica
+ sci-mathematics/form[threads]
+ "
+DEPEND="${RDEPEND}"
+BDEPEND="
+ sci-mathematics/mathematica
+ sci-mathematics/form
+ "
+
+PATCHES=( "${FILESDIR}"/${P}-compile.patch )
+
+src_compile() {
+ # remove shipped binaries
+ rm bin/Linux-x86-64/* || die
+ rm bin/Linux-x86-64-old/* || die
+
+ export DEST=Linux-x86-64
+ ./compile ${LDFLAGS} || die
+}
+
+src_install() {
+ MMADIR=/usr/share/Mathematica/Applications
+ dosym ${MY_P} ${MMADIR}/${MY_PN}
+ dodir ${MMADIR}/${MY_P}
+ insinto ${MMADIR}
+ doins -r "${S}"
+ # Copy executable, etc. permissions
+ for f in $(find * ! -type l); do
+ fperms --reference="${S}/$f" ${MMADIR}/${MY_P}/$f
+ done
+ # switch to system form
+ dosym `command -v form` ${MMADIR}/${MY_P}/Linux-x86-64/form
+ dosym `command -v tform` ${MMADIR}/${MY_P}/Linux-x86-64/tform
+
+ dodoc manual/*.pdf
+}
diff --git a/sci-physics/formcalc/metadata.xml b/sci-physics/formcalc/metadata.xml
new file mode 100644
index 000000000..b103d8f63
--- /dev/null
+++ b/sci-physics/formcalc/metadata.xml
@@ -0,0 +1,19 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <maintainer type="project">
+ <email>sci@gentoo.org</email>
+ <name>Gentoo Science Project</name>
+ </maintainer>
+ <maintainer type="project">
+ <email>sci-physics@gentoo.org</email>
+ <name>Gentoo Physics Project</name>
+ </maintainer>
+ <maintainer type="person">
+ <email>alexander@neuwirth-informatik.de</email>
+ <name>Alexander Puck Neuwirth</name>
+ </maintainer>
+ <longdescription lang="en">
+ FormCalc is a Mathematica package for the calculation of tree-level and one-loop Feynman diagrams. It makes extensive use of the form tool.
+ </longdescription>
+</pkgmetadata>
diff --git a/sci-physics/rivet/Manifest b/sci-physics/rivet/Manifest
new file mode 100644
index 000000000..5950a9997
--- /dev/null
+++ b/sci-physics/rivet/Manifest
@@ -0,0 +1,2 @@
+DIST Rivet-3.1.5.tar.gz 30576082 BLAKE2B 2fcf0f03219832d48546235f25d844837c37aa20e3972c35184741d1e14d70224bd7db597cd01e946dde4768b941ce9cf1dee3b3c385cb8a81e7b291c7edb1d3 SHA512 8dea32ef1ec7596904f1209a89343ed767e57b67e5fb85a230fd52a05231c901ea9f4663e6cea145e72d5d1beaf94dd642afaa1d5814843672b33073bb359c3f
+DIST Rivet-3.1.6.tar.gz 28804847 BLAKE2B b4e5a35285a4abdedaefbeaa06e5a703e5bf3b1ef4721db3d664dac5197b63845d228ab0dc0370b7b5095dccc3c9b5f3456ef59aabdcfb6c2f65cfbccd322635 SHA512 dd57d40db15fd55bae06a0faffbea80a15558763caf1f6f1defdde69d3abda709bdf806a1d9703f5e5796743af0482643c577332f69892de858aa5802e26279e
diff --git a/sci-physics/rivet/files/rivet-3.1.5-doc.patch b/sci-physics/rivet/files/rivet-3.1.5-doc.patch
new file mode 100644
index 000000000..ae01b1812
--- /dev/null
+++ b/sci-physics/rivet/files/rivet-3.1.5-doc.patch
@@ -0,0 +1,38 @@
+--- a/doc/Makefile.am
++++ b/doc/Makefile.am
+@@ -11,7 +11,7 @@
+ $(mkdir_p) analists && cd analists && \
+ LD_LIBRARY_PATH=$(abs_top_builddir)/src/.libs:$(FASTJETLIBPATH):$(FJCONTRIBLIBPATH):$(HEPMCLIBPATH):$(HEPMC3LIBPATH):$(YODALIBPATH):$(LD_LIBRARY_PATH) \
+ DYLD_LIBRARY_PATH=$(abs_top_builddir)/src/.libs:$(FASTJETLIBPATH):$(FJCONTRIBLIBPATH):$(HEPMCLIBPATH):$(HEPMC3LIBPATH):$(YODALIBPATH):$(DYLD_LIBRARY_PATH) \
+- PYTHONPATH=$(YODA_PYTHONPATH):$(RIVET_PYTHONPATH):$(PYTHONPATH) \
++ PYTHONPATH=$(shell realpath $(abs_top_builddir)/pyext/build/lib*):$(YODA_PYTHONPATH):$(RIVET_PYTHONPATH):$(PYTHONPATH) \
+ RIVET_ANALYSIS_PATH=$(abs_top_builddir)/analyses:: \
+ $(PYTHON) $(abs_srcdir)/analists/mk-analysis-html || true
+
+@@ -21,7 +21,7 @@
+ $(mkdir_p) analists && cd analists && \
+ LD_LIBRARY_PATH=$(abs_top_builddir)/src/.libs:$(FASTJETLIBPATH):$(FJCONTRIBLIBPATH):$(HEPMCLIBPATH):$(HEPMC3LIBPATH):$(YODALIBPATH):$(LD_LIBRARY_PATH) \
+ DYLD_LIBRARY_PATH=$(abs_top_builddir)/src/.libs:$(FASTJETLIBPATH):$(FJCONTRIBLIBPATH):$(HEPMCLIBPATH):$(HEPMC3LIBPATH):$(YODALIBPATH):$(DYLD_LIBRARY_PATH) \
+- PYTHONPATH=$(YODA_PYTHONPATH):$(RIVET_PYTHONPATH):$(PYTHONPATH) \
++ PYTHONPATH=$(shell realpath $(abs_top_builddir)/pyext/build/lib*):$(YODA_PYTHONPATH):$(RIVET_PYTHONPATH):$(PYTHONPATH) \
+ RIVET_ANALYSIS_PATH=$(abs_top_builddir)/analyses:: \
+ $(PYTHON) $(abs_srcdir)/analists/mk-analysis-json || true
+
+@@ -31,7 +31,7 @@
+ $(mkdir_p) analists && cd analists && \
+ LD_LIBRARY_PATH=$(abs_top_builddir)/src/.libs:$(FASTJETLIBPATH):$(FJCONTRIBLIBPATH):$(HEPMCLIBPATH):$(HEPMC3LIBPATH):$(YODALIBPATH):$(LD_LIBRARY_PATH) \
+ DYLD_LIBRARY_PATH=$(abs_top_builddir)/src/.libs:$(FASTJETLIBPATH):$(FJCONTRIBLIBPATH):$(HEPMCLIBPATH):$(HEPMC3LIBPATH):$(YODALIBPATH):$(DYLD_LIBRARY_PATH) \
+- PYTHONPATH=$(YODA_PYTHONPATH):$(RIVET_PYTHONPATH):$(PYTHONPATH) \
++ PYTHONPATH=$(shell realpath $(abs_top_builddir)/pyext/build/lib*):$(YODA_PYTHONPATH):$(RIVET_PYTHONPATH):$(PYTHONPATH) \
+ RIVET_ANALYSIS_PATH=$(abs_top_builddir)/analyses:: \
+ $(PYTHON) $(abs_srcdir)/analists/mk-analysis-txt || true
+
+@@ -46,7 +46,7 @@
+ $(mkdir_p) coverage && cd coverage && \
+ LD_LIBRARY_PATH=$(abs_top_builddir)/src/.libs:$(FASTJETLIBPATH):$(FJCONTRIBLIBPATH):$(LD_LIBRARY_PATH):$(LD_LIBRARY_PATH) \
+ DYLD_LIBRARY_PATH=$(abs_top_builddir)/src/.libs:$(FASTJETLIBPATH):$(FJCONTRIBLIBPATH):$(DYLD_LIBRARY_PATH):$(DYLD_LIBRARY_PATH) \
+- PYTHONPATH=$(YODA_PYTHONPATH):$(RIVET_PYTHONPATH):$(PYTHONPATH) \
++ PYTHONPATH=$(shell realpath $(abs_top_builddir)/pyext/build/lib*):$(YODA_PYTHONPATH):$(RIVET_PYTHONPATH):$(PYTHONPATH) \
+ RIVET_ANALYSIS_PATH=$(abs_top_builddir)/analyses:: \
+ $(abs_srcdir)/coverage/mk-coverage-htmls || true
+
diff --git a/sci-physics/rivet/files/rivet-3.1.5-test.patch b/sci-physics/rivet/files/rivet-3.1.5-test.patch
new file mode 100644
index 000000000..915473eb1
--- /dev/null
+++ b/sci-physics/rivet/files/rivet-3.1.5-test.patch
@@ -0,0 +1,11 @@
+--- a/test/Makefile.am
++++ b/test/Makefile.am
+@@ -26,7 +26,7 @@
+ LIBLOCATION=$(top_builddir)/src/.libs \
+ LD_LIBRARY_PATH=$(top_builddir)/src/.libs:$(HEPMCLIBPATH):$(HEPMC3LIBPATH):$(YODALIBPATH) \
+ DYLD_LIBRARY_PATH=$(top_builddir)/src/.libs:$(HEPMCLIBPATH):$(HEPMC3LIBPATH):$(YODALIBPATH) \
+- PYTHONPATH=$(top_builddir)/pyext/build/$(RIVET_SETUP_PY_PATH):$(PYTHONPATH) \
++ PYTHONPATH=$(shell realpath $(top_builddir)/pyext/build/lib*):$(top_builddir)/pyext/build/$(RIVET_SETUP_PY_PATH):$(PYTHONPATH) \
+ PATH=$(top_builddir)/bin:$(top_srcdir)/bin:$(PATH) \
+ PYTHON=$(PYTHON) \
+ RIVET_TESTS_SRC=$(srcdir)
diff --git a/sci-physics/rivet/files/rivet-3.1.6-binreloc.patch b/sci-physics/rivet/files/rivet-3.1.6-binreloc.patch
new file mode 100644
index 000000000..68fd4436c
--- /dev/null
+++ b/sci-physics/rivet/files/rivet-3.1.6-binreloc.patch
@@ -0,0 +1,12 @@
+diff -Naru Rivet-3.1.6.orig/src/Tools/binreloc.c Rivet-3.1.6/src/Tools/binreloc.c
+--- Rivet-3.1.6.orig/src/Tools/binreloc.c 2022-06-26 23:23:44.359890803 +0200
++++ Rivet-3.1.6/src/Tools/binreloc.c 2022-06-26 23:24:36.962045655 +0200
+@@ -215,7 +215,7 @@
+ break;
+
+ /* Sanity check. */
+- if (strchr (line, '/') == NULL)
++ if (strstr (line, " r-xp ") == NULL || strchr (line, '/') == NULL)
+ /* With binutils > 2.30 (const void *) "" is placed in "r--p" area of memory
+ In general, for the mechanism of detection it doesn't really matter where your symbol is,
+ therefore, check for strstr (line, " r-xp ") == NULL is removed */
diff --git a/sci-physics/rivet/metadata.xml b/sci-physics/rivet/metadata.xml
new file mode 100644
index 000000000..7f9434874
--- /dev/null
+++ b/sci-physics/rivet/metadata.xml
@@ -0,0 +1,20 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <maintainer type="person">
+ <email>alexander@neuwirth-informatik.de</email>
+ <name>Alexander Puck Neuwirth</name>
+ </maintainer>
+ <maintainer type="project">
+ <email>sci-physics@gentoo.org</email>
+ <name>Gentoo Physics Project</name>
+ </maintainer>
+ <longdescription lang="en">
+ Rivet is a system for preservation of particle-collider analysis logic, analysis reinterpretation via MC simulations, and the validation and improvement of Monte Carlo event generator codes.
+ It covers all aspects of collider physics, from unfolded precision measurements to reconstruction-level searches, and physics from the Standard Model to BSM theories, and from perturbative jet, boson and top-quarks to hadron decays, inclusive QCD, and Heavy Ion physics.
+ </longdescription>
+ <use>
+ <flag name="hepmc3">Build with HepMC3</flag>
+ <flag name="hepmc2">Build with HepMC2</flag>
+ </use>
+</pkgmetadata>
diff --git a/sci-physics/rivet/rivet-3.1.5.ebuild b/sci-physics/rivet/rivet-3.1.5.ebuild
new file mode 100644
index 000000000..4cc7c6018
--- /dev/null
+++ b/sci-physics/rivet/rivet-3.1.5.ebuild
@@ -0,0 +1,75 @@
+# Copyright 2020 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{8..10} )
+
+inherit python-single-r1 flag-o-matic autotools
+
+MY_PN="Rivet"
+MY_PF=${MY_PN}-${PV}
+
+DESCRIPTION="Rivet toolkit (Robust Independent Validation of Experiment and Theory)"
+HOMEPAGE="https://gitlab.com/hepcedar/rivet"
+SRC_URI="https://www.hepforge.org/archive/rivet/${MY_PF}.tar.gz"
+S=${WORKDIR}/${MY_PF}
+
+LICENSE="GPL-3+"
+SLOT="3"
+KEYWORDS="~amd64"
+IUSE="+hepmc3 hepmc2"
+REQUIRED_USE="
+ ^^ ( hepmc3 hepmc2 )
+ ${PYTHON_REQUIRED_USE}
+"
+
+RDEPEND="
+ >=sci-physics/yoda-1.9.4[python(-),${PYTHON_SINGLE_USEDEP}]
+ >=sci-physics/fastjet-3.4.0[plugins]
+ >=sci-physics/fastjet-contrib-1.046
+ hepmc2? ( sci-physics/hepmc:2=[-cm(-),gev(+)] )
+ hepmc3? ( sci-physics/hepmc:3=[-cm(-),gev(+)] )
+
+ sci-libs/gsl
+
+ virtual/latex-base
+ media-gfx/imagemagick
+ app-text/ghostscript-gpl
+
+ ${PYTHON_DEPS}
+"
+DEPEND="${RDEPEND}"
+BDEPEND="
+ virtual/fortran
+ >=dev-python/cython-0.29.24
+"
+
+PATCHES=(
+ "${FILESDIR}"/${P}-doc.patch
+ "${FILESDIR}"/${P}-test.patch
+)
+
+src_prepare() {
+ default
+ eautoreconf
+}
+
+src_configure() {
+ # Eigen complains about alignment (see https://gitlab.com/libeigen/eigen/-/issues/2523).
+ # does this affect more cpus?
+ replace-cpu-flags znver1 x86-64
+ PREFIX_YODA=$(yoda-config --prefix) || die
+ PREFIX_FJ=$(fastjet-config --prefix) || die
+ econf \
+ $(usex hepmc2 "--with-hepmc=${ESYSROOT}/usr" "") \
+ $(usex hepmc3 "--with-hepmc3=${ESYSROOT}/usr" "") \
+ --with-yoda=${PREFIX_YODA} \
+ --with-fastjet=${PREFIX_FJ}
+}
+
+src_install() {
+ default
+ python_optimize
+ find "${ED}" -name '*.la' -delete || die
+}
diff --git a/sci-physics/rivet/rivet-3.1.6.ebuild b/sci-physics/rivet/rivet-3.1.6.ebuild
new file mode 100644
index 000000000..3a83f7136
--- /dev/null
+++ b/sci-physics/rivet/rivet-3.1.6.ebuild
@@ -0,0 +1,75 @@
+# Copyright 2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{8..10} )
+
+inherit python-single-r1 flag-o-matic autotools
+
+MY_PN="Rivet"
+MY_PF=${MY_PN}-${PV}
+
+DESCRIPTION="Rivet toolkit (Robust Independent Validation of Experiment and Theory)"
+HOMEPAGE="https://gitlab.com/hepcedar/rivet"
+SRC_URI="https://www.hepforge.org/archive/rivet/${MY_PF}.tar.gz"
+S=${WORKDIR}/${MY_PF}
+
+LICENSE="GPL-3+"
+SLOT="3"
+KEYWORDS="~amd64"
+IUSE="+hepmc3 hepmc2"
+REQUIRED_USE="
+ ^^ ( hepmc3 hepmc2 )
+ ${PYTHON_REQUIRED_USE}
+"
+
+RDEPEND="
+ >=sci-physics/yoda-1.9.5[python(-),${PYTHON_SINGLE_USEDEP}]
+ >=sci-physics/fastjet-3.4.0[plugins]
+ >=sci-physics/fastjet-contrib-1.048
+ hepmc2? ( sci-physics/hepmc:2=[-cm(-),gev(+)] )
+ hepmc3? ( sci-physics/hepmc:3=[-cm(-),gev(+)] )
+
+ sci-libs/gsl
+
+ virtual/latex-base
+ media-gfx/imagemagick
+ app-text/ghostscript-gpl
+
+ ${PYTHON_DEPS}
+"
+DEPEND="${RDEPEND}"
+BDEPEND="
+ virtual/fortran
+ >=dev-python/cython-0.29.24
+"
+
+PATCHES=(
+ "${FILESDIR}"/${P}-binreloc.patch
+ "${FILESDIR}"/${PN}-3.1.5-test.patch
+)
+
+src_prepare() {
+ default
+ eautoreconf
+}
+
+src_configure() {
+ # Eigen complains about alignment (see https://gitlab.com/libeigen/eigen/-/issues/2523).
+ # does this affect more cpus?
+ replace-cpu-flags znver1 x86-64
+ PREFIX_YODA=$(yoda-config --prefix) || die
+ PREFIX_FJ=$(fastjet-config --prefix) || die
+ econf \
+ $(usex hepmc2 "--with-hepmc=${ESYSROOT}/usr" "") \
+ $(usex hepmc3 "--with-hepmc3=${ESYSROOT}/usr" "") \
+ --with-yoda=${PREFIX_YODA} \
+ --with-fastjet=${PREFIX_FJ}
+}
+
+src_install() {
+ default
+ python_optimize
+ find "${ED}" -name '*.la' -delete || die
+}
diff --git a/sci-physics/spheno/Manifest b/sci-physics/spheno/Manifest
new file mode 100644
index 000000000..afe87bb28
--- /dev/null
+++ b/sci-physics/spheno/Manifest
@@ -0,0 +1 @@
+DIST ?f=SPheno-3.3.8.tar.gz 1415645 BLAKE2B 830cdbcd8f213f0de0cd0b72455d5919e390069f097bca5a0cabdbfb77ec21549c9455139ff960a0cdbd425368805c1f2d11384c240a8e82f66e33864f4fce7b SHA512 e6c923586eae198f62121e0410f9f1f87e7badfd58d90e3b5f600e8364ea054dfb8b58c1c39d74ec6067112fa6cad727797230bce6cfc6040e2bf4c6d01b0eae
diff --git a/sci-physics/spheno/files/spheno-3.3.8-gfortran.patch b/sci-physics/spheno/files/spheno-3.3.8-gfortran.patch
new file mode 100644
index 000000000..8f6fa7e19
--- /dev/null
+++ b/sci-physics/spheno/files/spheno-3.3.8-gfortran.patch
@@ -0,0 +1,32 @@
+--- a/src/Makefile 2022-07-20 11:47:44.078639381 +0200
++++ b/src/Makefile 2022-07-24 02:16:38.972041809 +0200
+@@ -9,10 +9,11 @@
+ # options for various compilers
+ #
+
+-# Intels ifort, default in optimized mode
+-F90 = ifort
+-comp = -c -O -module ${Mdir} -I${InDir}
+-LFlagsB = -O
++
++# gentoo toolchain
++F90 = ${F90}
++comp = -c -O -J${Mdir} -I${InDir} ${FFLAGS} ${FCFLAGS} ${CFLAGS}
++LFlagsB = -O ${LDFLAGS}
+
+ # Intels ifort, debug modus
+ ifeq (${F90},ifortg)
+@@ -70,11 +71,11 @@
+ #
+ .f90.a:
+ ${F90} ${comp} $<
+- ar -ruc $@ $*.o
++ $(AR) -ruc $@ $*.o
+ rm -f $*.o
+ .F90.a:
+ ${F90} ${comp} ${PreDef} $<
+- ar -ruc $@ $*.o
++ $(AR) -ruc $@ $*.o
+ rm -f $*.o
+ .f90.o:
+ ${F90} ${comp} $<
diff --git a/sci-physics/spheno/metadata.xml b/sci-physics/spheno/metadata.xml
new file mode 100644
index 000000000..277841e1a
--- /dev/null
+++ b/sci-physics/spheno/metadata.xml
@@ -0,0 +1,19 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <maintainer type="project">
+ <email>sci@gentoo.org</email>
+ <name>Gentoo Science Project</name>
+ </maintainer>
+ <maintainer type="project">
+ <email>sci-physics@gentoo.org</email>
+ <name>Gentoo Physics Project</name>
+ </maintainer>
+ <maintainer type="person">
+ <email>alexander@neuwirth-informatik.de</email>
+ <name>Alexander Puck Neuwirth</name>
+ </maintainer>
+ <longdescription lang="en">
+The code calculates the SUSY spectrum using low energy data and a user supplied high scale model as input. The spectrum is used to calculate two- and three body decay modes of supersymmetric particle as well as of Higgs bosons. In addition the production cross sections for supersymmetric particle and Higgs bosons in e^+ e^- annihilation is calculated. Moreover, the branching of the decay $b \to s \gamma$, the SUSY contribution to anomalous magnetic moment of the muon as well as the SUSY contributions to the rho parameter due to sfermions are calculated. The code is written in F90 with an emphasis on easy generalisability. The structure is set such that complex phases as well as the extension to include the flavour structure can be done in a straight forward way. The 2-loop renormalization group equations as well as the one-loop finite corrections a la Bagger, Matchev, Pierce and Zhang are included. In addition the two-loop corrections to the neutral Higgs boson masses (a la Brignole, Degrassi, Slavich and Zwirner) and to the mu-parameter (a la Dedes and Slavich) are included. Starting with version 2.2.2 the SUSY Les Houches Accord is supported as well as the SPA conventions (for details see hep-ph/0511344).
+ </longdescription>
+</pkgmetadata>
diff --git a/sci-physics/spheno/spheno-3.3.8.ebuild b/sci-physics/spheno/spheno-3.3.8.ebuild
new file mode 100644
index 000000000..9a740b89e
--- /dev/null
+++ b/sci-physics/spheno/spheno-3.3.8.ebuild
@@ -0,0 +1,43 @@
+# Copyright 2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+inherit toolchain-funcs
+
+MY_PN=SPheno
+MY_P=${MY_PN}-${PV}
+
+DESCRIPTION="SPheno stands for S(upersymmetric) Pheno(menology)"
+HOMEPAGE="https://spheno.hepforge.org/"
+SRC_URI="https://spheno.hepforge.org/downloads/?f=${MY_P}.tar.gz"
+S="${WORKDIR}/${MY_P}"
+
+LICENSE="all-rights-reserved"
+RESTRICT="bindist mirror"
+SLOT="0"
+KEYWORDS="~amd64"
+
+DEPEND="virtual/fortran"
+RDEPEND="${DEPEND}"
+
+PATCHES=( "${FILESDIR}"/${P}-gfortran.patch )
+
+src_compile() {
+ # single thread force needed since fortan mods depend on each other
+ export MAKEOPTS=-j1
+ tc-export FC AR
+ emake AR="${AR}" F90="${FC}"
+}
+
+src_install() {
+ dobin bin/${MY_PN}
+ # convenience symlink since the package is lowercase but the default produced binary is uppercase
+ dosym ${MY_PN} /usr/bin/${PN}
+ dolib.a lib/lib${MY_PN}.a
+ doheader include/*
+ dodoc doc/*
+ docinto examples
+ dodoc input/*
+ docompress -x /usr/share/doc/${PF}/examples
+}
diff --git a/sci-visualization/fsleyes-props/fsleyes-props-1.7.3.ebuild b/sci-visualization/fsleyes-props/fsleyes-props-1.7.3.ebuild
index b3440c6ba..3fd2a3e01 100644
--- a/sci-visualization/fsleyes-props/fsleyes-props-1.7.3.ebuild
+++ b/sci-visualization/fsleyes-props/fsleyes-props-1.7.3.ebuild
@@ -3,7 +3,7 @@
EAPI=8
-PYTHON_COMPAT=( python3_{8..9} )
+PYTHON_COMPAT=( python3_{8..10} )
inherit distutils-r1 virtualx
@@ -36,6 +36,10 @@ python_prepare_all() {
distutils-r1_python_prepare_all
}
+src_test() {
+ virtx distutils-r1_src_test
+}
+
python_test() {
- virtx epytest
+ epytest || die "Tests failed with ${EPYTHON}"
}
diff --git a/sci-visualization/fsleyes-widgets/fsleyes-widgets-0.12.2.ebuild b/sci-visualization/fsleyes-widgets/fsleyes-widgets-0.12.2.ebuild
index 82a1e587c..4153ca1b8 100644
--- a/sci-visualization/fsleyes-widgets/fsleyes-widgets-0.12.2.ebuild
+++ b/sci-visualization/fsleyes-widgets/fsleyes-widgets-0.12.2.ebuild
@@ -3,7 +3,7 @@
EAPI=8
-PYTHON_COMPAT=( python3_{8..9} )
+PYTHON_COMPAT=( python3_{8..10} )
inherit distutils-r1 virtualx
@@ -49,9 +49,13 @@ python_prepare_all() {
distutils-r1_python_prepare_all
}
+src_test() {
+ virtx distutils-r1_src_test
+}
+
python_test() {
# If this could be set for the eclass, it might fix some of the tests:
# https://github.com/pauldmccarthy/fsleyes-widgets/issues/1#issuecomment-575387724
#xvfbargs="-screen 0 1920x1200x24 +extension RANDR"
- virtx epytest
+ epytest || die "Tests failed with ${EPYTHON}"
}