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-rw-r--r--README.md32
-rw-r--r--app-arch/libdeflate/Manifest1
-rw-r--r--app-arch/libdeflate/libdeflate-1.11.ebuild28
-rw-r--r--app-arch/libdeflate/libdeflate-1.9.ebuild2
-rw-r--r--app-arch/libdeflate/libdeflate-9999.ebuild4
-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-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/asmjit/Manifest1
-rw-r--r--dev-libs/asmjit/asmjit-1.0_p22092020.ebuild34
-rw-r--r--dev-libs/asmjit/asmjit-9999.ebuild34
-rw-r--r--dev-libs/asmjit/metadata.xml31
-rw-r--r--dev-python/annexremote/Manifest4
-rw-r--r--dev-python/annexremote/annexremote-1.5.0.ebuild9
-rw-r--r--dev-python/annexremote/annexremote-1.6.0.ebuild9
-rw-r--r--dev-python/annexremote/metadata.xml1
-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/cadquery-ocp/Manifest1
-rw-r--r--dev-python/cadquery-ocp/cadquery-ocp-7.5.3.0.ebuild195
-rw-r--r--dev-python/cadquery-pywrap/Manifest1
-rw-r--r--dev-python/cadquery-pywrap/cadquery-pywrap-7.5.3_rc20220113.ebuild63
-rw-r--r--dev-python/cadquery/Manifest1
-rw-r--r--dev-python/cadquery/cadquery-2.2_rc20220506.ebuild58
-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/fiona/Manifest3
-rw-r--r--dev-python/fiona/fiona-1.8.21.ebuild (renamed from dev-python/fiona/fiona-1.8.20.ebuild)8
-rw-r--r--dev-python/fslpy/fslpy-3.8.1.ebuild8
-rw-r--r--dev-python/geopandas/geopandas-0.10.2.ebuild2
-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/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/multimethod/Manifest1
-rw-r--r--dev-python/multimethod/metadata.xml12
-rw-r--r--dev-python/multimethod/multimethod-1.8.ebuild20
-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/nwbinspector-0.3.9.ebuild1
-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/pytorch-lightning/pytorch-lightning-1.5.8.ebuild5
-rw-r--r--dev-python/rasterio/rasterio-1.2.10-r1.ebuild (renamed from dev-python/rasterio/rasterio-1.2.10.ebuild)9
-rw-r--r--dev-python/rasterstats/rasterstats-0.16.0.ebuild2
-rw-r--r--dev-python/snakemake/snakemake-5.32.2.ebuild2
-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/typish/Manifest1
-rw-r--r--dev-python/typish/metadata.xml13
-rw-r--r--dev-python/typish/typish-1.9.3.ebuild29
-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.xml15
-rw-r--r--dev-python/wraps/wraps-0.1.0.ebuild31
-rw-r--r--dev-python/zarr/Manifest2
-rw-r--r--dev-python/zarr/zarr-2.11.1.ebuild5
-rw-r--r--dev-python/zarr/zarr-2.11.3.ebuild5
-rw-r--r--dev-python/zarr/zarr-2.12.0.ebuild (renamed from dev-python/zarr/zarr-2.10.3.ebuild)10
-rw-r--r--dev-vcs/dandi-cli/Manifest1
-rw-r--r--dev-vcs/dandi-cli/dandi-cli-0.39.4.ebuild1
-rw-r--r--dev-vcs/dandi-cli/dandi-cli-0.45.1.ebuild80
-rw-r--r--dev-vcs/datalad/Manifest3
-rw-r--r--dev-vcs/datalad/datalad-0.15.1.ebuild4
-rw-r--r--dev-vcs/datalad/datalad-0.15.2.ebuild4
-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--net-misc/cernbox-client/Manifest2
-rw-r--r--net-misc/cernbox-client/cernbox-client-2.10.1.7389.ebuild (renamed from net-misc/cernbox-client/cernbox-client-2.9.2.6206.ebuild)3
-rw-r--r--profiles/package.mask6
-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/samri/samri-0.5.ebuild6
-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)10
-rw-r--r--sci-libs/arpack/Manifest3
-rw-r--r--sci-libs/arpack/arpack-3.8.0_p20220604.ebuild102
-rw-r--r--sci-libs/arpack/metadata.xml26
-rw-r--r--sci-libs/bids-validator/bids-validator-1.4.4.ebuild6
-rw-r--r--sci-libs/itk/itk-5.0.1.ebuild2
-rw-r--r--sci-libs/itk/itk-5.1.0.ebuild2
-rw-r--r--sci-libs/labbookdb/labbookdb-0.1.ebuild6
-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/pytorch/Manifest38
-rw-r--r--sci-libs/pytorch/files/0002-Don-t-build-libtorch-again-for-PyTorch-1.4.0.patch30
-rw-r--r--sci-libs/pytorch/files/0002-Don-t-build-libtorch-again-for-PyTorch-1.7.1.patch18
-rw-r--r--sci-libs/pytorch/files/0003-Change-path-to-caffe2-build-dir-made-by-libtorch.patch46
-rw-r--r--sci-libs/pytorch/files/0004-Don-t-fill-rpath-of-Caffe2-library-for-system-wide-i.patch104
-rw-r--r--sci-libs/pytorch/files/0005-Change-library-directory-according-to-CMake-build.patch31
-rw-r--r--sci-libs/pytorch/files/0010-Remove-conversion-ambiguity-in-ternary-operators.patch38
-rw-r--r--sci-libs/pytorch/files/get_third_parties20
-rw-r--r--sci-libs/pytorch/files/pytorch-1.10.0-clhpp2.patch52
-rw-r--r--sci-libs/pytorch/files/pytorch-1.10.0-fix-distutils.patch93
-rw-r--r--sci-libs/pytorch/files/pytorch-1.10.0-nonull.patch12
-rw-r--r--sci-libs/pytorch/files/pytorch-1.10.1-nccl-nvccflags.patch37
-rw-r--r--sci-libs/pytorch/files/pytorch-1.2.0-setup.patch24
-rw-r--r--sci-libs/pytorch/files/pytorch-1.4.0-nccl-nvccflags.patch28
-rw-r--r--sci-libs/pytorch/files/pytorch-1.4.0-skip-tests.patch28
-rw-r--r--sci-libs/pytorch/files/pytorch-1.4.0-sleef.patch15
-rw-r--r--sci-libs/pytorch/files/pytorch-1.6.0-global-dlopen.patch15
-rw-r--r--sci-libs/pytorch/files/pytorch-1.6.0-nccl-nvccflags.patch27
-rw-r--r--sci-libs/pytorch/files/pytorch-1.6.0-setup.patch14
-rw-r--r--sci-libs/pytorch/files/pytorch-1.6.0-skip-tests.patch14
-rw-r--r--sci-libs/pytorch/files/pytorch-1.6.0-tensorpipe-unbundle-libuv.patch13
-rw-r--r--sci-libs/pytorch/files/pytorch-1.7.1-no-rpath.patch12
-rw-r--r--sci-libs/pytorch/files/pytorch-1.7.1-setup.patch12
-rw-r--r--sci-libs/pytorch/files/pytorch-1.7.1-tensorpipe-unbundle-libuv.patch12
-rw-r--r--sci-libs/pytorch/files/pytorch-1.7.1-torch_shm_manager.patch13
-rw-r--r--sci-libs/pytorch/files/pytorch-1.9.0-Change-library-directory-according-to-CMake-build.patch32
-rw-r--r--sci-libs/pytorch/files/pytorch-1.9.1-fix-wrong-hipify.patch13
-rw-r--r--sci-libs/pytorch/metadata.xml34
-rw-r--r--sci-libs/pytorch/pytorch-1.10.2.ebuild339
-rw-r--r--sci-libs/simpleitk/simpleitk-1.2.4.ebuild6
-rw-r--r--sci-libs/torchvision/torchvision-0.11.2.ebuild5
-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.ebuild52
-rw-r--r--sci-physics/formcalc/formcalc-9.9.ebuild54
-rw-r--r--sci-physics/formcalc/metadata.xml19
-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
190 files changed, 2366 insertions, 2051 deletions
diff --git a/README.md b/README.md
index 3904770a0..43484c14a 100644
--- a/README.md
+++ b/README.md
@@ -28,25 +28,35 @@
## 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 +65,7 @@ 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 +77,7 @@ 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-arch/libdeflate/Manifest b/app-arch/libdeflate/Manifest
index f2e2fae94..f26d506d5 100644
--- a/app-arch/libdeflate/Manifest
+++ b/app-arch/libdeflate/Manifest
@@ -1,3 +1,4 @@
+DIST libdeflate-1.11.tar.gz 162862 BLAKE2B 70ee15bdbe697083f84eef4bfce069b3bff8499a8daf53037a52fd247a47cd04867c1d93265e1b88232da52919ad15333e90d787dff05f7d8e5abe7a9613a07a SHA512 71badc0d934dde5fa79c0d8661b3a38a45d7189fba6f1c77986b2fb6baa03233b8474f0a83f004242410421c2063d2f98f02ca4f8a7a7a14cc7bcd3a9be4fbbc
DIST libdeflate-1.2.tar.gz 133494 BLAKE2B cd43b691bda16134ee1d2cdeeea8e5bab7bd8b841dec41fcf93ca0b3383f9c465e095fc7c97b743dc34c2bd6a1d340f8bfda4f4448af832cfec0240965957ffa SHA512 181b53ee9aea96b2520e287824573d111eeacaeae2011e093ca4d4fdd77e4e09bd261d741fac567302cf031058779ccc775dce1f603a05810b0c3b7d96b26fdb
DIST libdeflate-1.6.tar.gz 139031 BLAKE2B c9390408322dc71f27d86fb69e0dd47996a725a3f4ddbe1d395e07dcd1b1f2b6fde1a9decfa8d7a0bd841defff67a659b1f2efd2609db7d79626e038cb44e020 SHA512 b7225c7defb3e9b1177c434aa0de80e525de06160894282e9d3e736d6c17d2ee107e321042104a67dfa3649d982a022ee30fe30380259b8aa65ac75d1d02e334
DIST libdeflate-1.7.tar.gz 144143 BLAKE2B 6aa947a4e2489f5a3e5681d56c2272b0a694981ed2607fa4112d90a8b4565ba1066364ffcac2fe8836bacbbad0346bce5efea54b4abae55022a33ee7d983e570 SHA512 82b297af2d3128a244e561893cce1d3664de410469ba6745c3f68fc3a1962c62467c427f3857bb679578e0f704cd0eba1a64b13c30505addd310ff9af1883068
diff --git a/app-arch/libdeflate/libdeflate-1.11.ebuild b/app-arch/libdeflate/libdeflate-1.11.ebuild
new file mode 100644
index 000000000..9e7344b22
--- /dev/null
+++ b/app-arch/libdeflate/libdeflate-1.11.ebuild
@@ -0,0 +1,28 @@
+# Copyright 2019-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DESCRIPTION="Heavily optimized DEFLATE/zlib/gzip (de)compression"
+HOMEPAGE="https://github.com/ebiggers/libdeflate"
+
+if [[ ${PV} == *9999 ]]; then
+ inherit git-r3
+ EGIT_REPO_URI="https://github.com/ebiggers/libdeflate"
+else
+ SRC_URI="https://github.com/ebiggers/libdeflate/archive/v${PV}.tar.gz -> ${P}.tar.gz"
+ KEYWORDS="~amd64 ~x86"
+fi
+
+LICENSE="MIT"
+SLOT="0"
+IUSE="static-libs test"
+RESTRICT="!test? ( test )"
+
+src_install() {
+ emake DESTDIR="${ED}" PREFIX=/usr LIBDIR="/usr/$(get_libdir)" install
+ if ! use static-libs; then
+ find "${ED}" -name '*.a' -delete || die
+ fi
+ dodoc NEWS.md README.md
+}
diff --git a/app-arch/libdeflate/libdeflate-1.9.ebuild b/app-arch/libdeflate/libdeflate-1.9.ebuild
index 9f66534f1..ef7ead774 100644
--- a/app-arch/libdeflate/libdeflate-1.9.ebuild
+++ b/app-arch/libdeflate/libdeflate-1.9.ebuild
@@ -24,5 +24,5 @@ src_install() {
if ! use static-libs; then
find "${ED}" -name '*.a' -delete || die
fi
- dodoc NEWS README.md
+ dodoc NEWS,d README.md
}
diff --git a/app-arch/libdeflate/libdeflate-9999.ebuild b/app-arch/libdeflate/libdeflate-9999.ebuild
index bfafcfecd..35aff28c3 100644
--- a/app-arch/libdeflate/libdeflate-9999.ebuild
+++ b/app-arch/libdeflate/libdeflate-9999.ebuild
@@ -1,7 +1,7 @@
# Copyright 2019-2021 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=7
+EAPI=8
DESCRIPTION="Heavily optimized DEFLATE/zlib/gzip (de)compression"
HOMEPAGE="https://github.com/ebiggers/libdeflate"
@@ -24,5 +24,5 @@ src_install() {
if ! use static-libs; then
find "${ED}" -name '*.a' -delete || die
fi
- dodoc NEWS README.md
+ dodoc NEWS.md README.md
}
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 -> ${P}.tar.gz"
diff --git a/dev-java/jeuclid-core/Manifest b/dev-java/jeuclid-core/Manifest
deleted file mode 100644
index 6df1751b1..000000000
--- a/dev-java/jeuclid-core/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST jeuclid-core-3.1.14.tar.gz 7244186 BLAKE2B 9cada848e516aba942ef87e7b746296f9565d5271a1ce6635e80e6559edcedac3245c4bde28e8d1053cacc5774e6a015079b0281802559e86366a75223b8ea2c SHA512 7b52491d7fac40a13f41176a49f36411681c957aba95c23bb6396f4e1248f5463afcd5394b0bb8e3dfbdd498d3290ac5f787e876636f5f282b703a72799eff4e
diff --git a/dev-java/jeuclid-core/files/jeuclid-core-no-freehep.patch b/dev-java/jeuclid-core/files/jeuclid-core-no-freehep.patch
deleted file mode 100644
index daf123c92..000000000
--- a/dev-java/jeuclid-core/files/jeuclid-core-no-freehep.patch
+++ /dev/null
@@ -1,10 +0,0 @@
---- a/build.xml 2010-01-22 17:46:35.000000000 +0000
-+++ b/build.xml 2010-01-22 17:49:07.000000000 +0000
-@@ -113,6 +113,7 @@
- <src>
- <pathelement location="src/main/java"/>
- </src>
-+ <exclude name="**/FreeHep*" />
- <classpath refid="libs-build-classpath"/>
- </javac>
- <copy todir="${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/asmjit/Manifest b/dev-libs/asmjit/Manifest
deleted file mode 100644
index 8733ba51c..000000000
--- a/dev-libs/asmjit/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST asmjit-1.0_p22092020.tar.gz 601680 BLAKE2B dcbfc7f5385bc12d70e4c0418c89fed4453e3b08e88ccae78775d5b65d0eaada1fc12809732a77fde8b50966aacfa487e213e96754e2b7846836dcd5057a1c0b SHA512 fae457eef331edb8b9ecec23630d109500751e9ff0a7c8081c962d76c67ce68ea5813189185537f916946ce2c9c84c1574799315952f776b703019783632c4cf
diff --git a/dev-libs/asmjit/asmjit-1.0_p22092020.ebuild b/dev-libs/asmjit/asmjit-1.0_p22092020.ebuild
deleted file mode 100644
index 097ccfb7e..000000000
--- a/dev-libs/asmjit/asmjit-1.0_p22092020.ebuild
+++ /dev/null
@@ -1,34 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit cmake
-
-DESCRIPTION="complete x86/x64 JIT-Assembler for C++ language"
-HOMEPAGE="https://asmjit.com/"
-
-if [[ ${PV} == 9999 ]]; then
- inherit git-r3
- EGIT_REPO_URI="https://github.com/asmjit/asmjit"
-else
- COMMIT=b49d685cd9e2e4488f55ce6004306a79bdea056b
- SRC_URI="https://github.com/asmjit/asmjit/archive/${COMMIT}.tar.gz -> ${P}.tar.gz"
- S="${WORKDIR}"/${PN}-${COMMIT}
- KEYWORDS="~amd64"
-fi
-
-SLOT="0"
-LICENSE="BSD"
-IUSE="natvis static-libs test"
-RESTRICT="!test? ( test )"
-
-src_configure() {
- local mycmakeargs=(
- -DASMJIT_EMBED=$(usex static-libs)
- -DASMJIT_BUILD_X86=ON
- -DASMJIT_NO_NATVIS=$(usex natvis)
- -DASMJIT_TEST=$(usex test)
- )
- cmake_src_configure
-}
diff --git a/dev-libs/asmjit/asmjit-9999.ebuild b/dev-libs/asmjit/asmjit-9999.ebuild
deleted file mode 100644
index 097ccfb7e..000000000
--- a/dev-libs/asmjit/asmjit-9999.ebuild
+++ /dev/null
@@ -1,34 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit cmake
-
-DESCRIPTION="complete x86/x64 JIT-Assembler for C++ language"
-HOMEPAGE="https://asmjit.com/"
-
-if [[ ${PV} == 9999 ]]; then
- inherit git-r3
- EGIT_REPO_URI="https://github.com/asmjit/asmjit"
-else
- COMMIT=b49d685cd9e2e4488f55ce6004306a79bdea056b
- SRC_URI="https://github.com/asmjit/asmjit/archive/${COMMIT}.tar.gz -> ${P}.tar.gz"
- S="${WORKDIR}"/${PN}-${COMMIT}
- KEYWORDS="~amd64"
-fi
-
-SLOT="0"
-LICENSE="BSD"
-IUSE="natvis static-libs test"
-RESTRICT="!test? ( test )"
-
-src_configure() {
- local mycmakeargs=(
- -DASMJIT_EMBED=$(usex static-libs)
- -DASMJIT_BUILD_X86=ON
- -DASMJIT_NO_NATVIS=$(usex natvis)
- -DASMJIT_TEST=$(usex test)
- )
- cmake_src_configure
-}
diff --git a/dev-libs/asmjit/metadata.xml b/dev-libs/asmjit/metadata.xml
deleted file mode 100644
index d8cc7be33..000000000
--- a/dev-libs/asmjit/metadata.xml
+++ /dev/null
@@ -1,31 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <maintainer type="person">
- <email>xarthisius@gentoo.org</email>
- <name>Kacper Kowalik</name>
- </maintainer>
- <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">
- AsmJit is complete x86/x64 JIT-Assembler for C++ language. It supports
- 32/64-bit x86 processors including all usable extensions (FPU, MMX,
- 3dNow, SSE, SSE2, SSE3 and SSE4) through type-safe API that mimics Intel
- assembler syntax and eliminates nearly all common mistakes that can be
- done by developers.
-
- AsmJit contains also high-level code generation classes that can be used
- as a portable way to create JIT code that should run on all supported
- architectures. High-level classes can handle various function
- calling-conventions, register allocation and 32/64-bit mode differences.
- </longdescription>
- <use>
- <flag name="natvis">build natvis files</flag>
- </use>
-</pkgmetadata>
diff --git a/dev-python/annexremote/Manifest b/dev-python/annexremote/Manifest
index f60f5eca8..c5eac671a 100644
--- a/dev-python/annexremote/Manifest
+++ b/dev-python/annexremote/Manifest
@@ -1,2 +1,2 @@
-DIST annexremote-1.5.0.tar.gz 65988 BLAKE2B a8ebbe8d4d3bfa7bcdfec3c43ec76788f3b4006804c715c5baf40f7e999a9a28052428ecee9ad865e8216ecf51ebbaf4728f73f622ac6b49edafbf623255419d SHA512 b0d2b3f41046f43ff49ca1d629a34e0d80c200a28bf13a3cf4f138204afa9fb7b04b6d8b9851bb201438fc6ef692d43dbaa96cf129855978fb40fdecf8818b67
-DIST annexremote-1.6.0.tar.gz 66805 BLAKE2B 6663e7ff3e223ac49a2e57ffaab20097bd91f1f8a679e15b7aa0ddd60411f99a602eaa6a7dc2e3f93b57bdff49fc70b3ddfd27f5f48ea89d97c8091fa6f7584b SHA512 657d9f53ebf1f0ad87aae758736ea3e5695e2c0f7ba111bd0810482126e4b38b292abc49fc3c2b55d6e63a42eab90aeaf64c4f287bbfbaa169070aed1356c430
+DIST annexremote-1.5.0.tar.gz 73544 BLAKE2B f5b528faf3d390f9bba6fb97768318ab04224cf05941a2606d49edda7bde30d743bf8e492f277986c0eda62f4000e1446e048d932df436cc2075b1f3e536c7d2 SHA512 7307f5ead82d449eda8b27a83f314b112bfe243a50f556397aed0f563452db6b4ba06b68aacaa27ff722ec9ccd2bdc489a3a8f4f3d849354757bd2fff8ae50d0
+DIST annexremote-1.6.0.tar.gz 74199 BLAKE2B 27956c5ea4789a1bd22bfabe6e0da8a5c8700ba50c3c28610b364d6b358f195124667381094c7786a825fae4464a340b36fd61cd09956477101c7bfd54ba8166 SHA512 1320e06fb3bebe65cce872af6adfb702d9d44cad1671ab8fd432137eb44f22cbd35744b889f11900379da2512fb79da0972c0326fcf3e51c6a404fe497e20ea4
diff --git a/dev-python/annexremote/annexremote-1.5.0.ebuild b/dev-python/annexremote/annexremote-1.5.0.ebuild
index 94549009e..b35e3c274 100644
--- a/dev-python/annexremote/annexremote-1.5.0.ebuild
+++ b/dev-python/annexremote/annexremote-1.5.0.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=8
@@ -6,20 +6,15 @@ EAPI=8
PYTHON_COMPAT=( python3_{8..10} )
inherit distutils-r1
-MY_PN="AnnexRemote"
-MY_P="${MY_PN}-${PV}"
-
DESCRIPTION="Helper module to easily develop git-annex remotes"
HOMEPAGE="https://github.com/Lykos153/AnnexRemote"
-SRC_URI="https://github.com/Lykos153/AnnexRemote/archive/v${PV}.tar.gz -> ${P}.tar.gz"
+SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
LICENSE="GPL-3"
SLOT="0"
KEYWORDS="~amd64 ~x86"
IUSE="examples"
-S="${WORKDIR}/${MY_P}"
-
COMMON_DEPEND="dev-python/future[${PYTHON_USEDEP}]"
RDEPEND="
${COMMON_DEPEND}
diff --git a/dev-python/annexremote/annexremote-1.6.0.ebuild b/dev-python/annexremote/annexremote-1.6.0.ebuild
index 94549009e..b35e3c274 100644
--- a/dev-python/annexremote/annexremote-1.6.0.ebuild
+++ b/dev-python/annexremote/annexremote-1.6.0.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=8
@@ -6,20 +6,15 @@ EAPI=8
PYTHON_COMPAT=( python3_{8..10} )
inherit distutils-r1
-MY_PN="AnnexRemote"
-MY_P="${MY_PN}-${PV}"
-
DESCRIPTION="Helper module to easily develop git-annex remotes"
HOMEPAGE="https://github.com/Lykos153/AnnexRemote"
-SRC_URI="https://github.com/Lykos153/AnnexRemote/archive/v${PV}.tar.gz -> ${P}.tar.gz"
+SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
LICENSE="GPL-3"
SLOT="0"
KEYWORDS="~amd64 ~x86"
IUSE="examples"
-S="${WORKDIR}/${MY_P}"
-
COMMON_DEPEND="dev-python/future[${PYTHON_USEDEP}]"
RDEPEND="
${COMMON_DEPEND}
diff --git a/dev-python/annexremote/metadata.xml b/dev-python/annexremote/metadata.xml
index 0c1ee80ae..a4bcc5d17 100644
--- a/dev-python/annexremote/metadata.xml
+++ b/dev-python/annexremote/metadata.xml
@@ -17,5 +17,6 @@
</longdescription>
<upstream>
<remote-id type="github">Lykos153/AnnexRemote</remote-id>
+ <remote-id type="pypi">annexremote</remote-id>
</upstream>
</pkgmetadata>
diff --git a/dev-python/anys/anys-0.2.0.ebuild b/dev-python/anys/anys-0.2.0.ebuild
index 0d2fec35f..0f1bb884f 100644
--- a/dev-python/anys/anys-0.2.0.ebuild
+++ b/dev-python/anys/anys-0.2.0.ebuild
@@ -4,7 +4,7 @@
EAPI=8
PYTHON_COMPAT=( python3_{8..9} )
-DISTUTILS_USE_SETUPTOOLS=pyproject.toml
+DISTUTILS_USE_PEP517=setuptools
inherit distutils-r1
DESCRIPTION="Matchers for pytest"
diff --git a/dev-python/anys/anys-0.2.1.ebuild b/dev-python/anys/anys-0.2.1.ebuild
index 783fc75ce..d74bb76f9 100644
--- a/dev-python/anys/anys-0.2.1.ebuild
+++ b/dev-python/anys/anys-0.2.1.ebuild
@@ -4,7 +4,7 @@
EAPI=8
PYTHON_COMPAT=( python3_{8..10} )
-DISTUTILS_USE_SETUPTOOLS=pyproject.toml
+DISTUTILS_USE_PEP517=setuptools
inherit distutils-r1
DESCRIPTION="Matchers for pytest"
@@ -18,6 +18,7 @@ IUSE="test"
RESTRICT="!test? ( test )"
RDEPEND="
+ dev-python/deprecated[${PYTHON_USEDEP}]
dev-python/wheel[${PYTHON_USEDEP}]
"
diff --git a/dev-python/cadquery-ocp/Manifest b/dev-python/cadquery-ocp/Manifest
index 2fdce96f0..4818fac84 100644
--- a/dev-python/cadquery-ocp/Manifest
+++ b/dev-python/cadquery-ocp/Manifest
@@ -1 +1,2 @@
DIST cadquery-ocp-7.5.2_beta.tar.gz 5571554 BLAKE2B 552e44b301b69f1b1b4f6c26c46638bcf94a5f753d4d35e2cbbd6e1d963a23c685d6c05ead56c970c6532a3adbbf7b1f2bd572e72fb482ccd2dac04585764910 SHA512 041d12632678b96f23528f289516e31457a4e0d3251db6f01e3fc2bb2ccc41d2df8b825c94db0cebd7419cf82070c75d20852f25d91f05377502d75adf493fd8
+DIST cadquery-ocp-7.5.3.0.tar.gz 5571719 BLAKE2B ba31d7ae2f54e2f4c17f0914cab1299b91254a3fab7d07f18b2d698ce6e47e9ea174e449e18971197b39f08fa755c4d16d8cba24f894372f5bd515ec6686935e SHA512 b89dc91f224ee87e288bd7e3a10cb3b2c6559e2b36c24aac2f675fb05ecda755b723721122a7e58d87ba4253024892795369b1e747fb77684c739d01d516d1a2
diff --git a/dev-python/cadquery-ocp/cadquery-ocp-7.5.3.0.ebuild b/dev-python/cadquery-ocp/cadquery-ocp-7.5.3.0.ebuild
new file mode 100644
index 000000000..064952018
--- /dev/null
+++ b/dev-python/cadquery-ocp/cadquery-ocp-7.5.3.0.ebuild
@@ -0,0 +1,195 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{8..10} )
+
+# OCP uses "python-single-r1" only because VTK uses "python-single-r1".
+inherit check-reqs cmake llvm multiprocessing python-single-r1 toolchain-funcs
+
+MY_PN=OCP
+MY_PV="${PV//_/-}"
+MY_P="${MY_PN}-${MY_PV}"
+OCCT_PV=$(ver_cut 1-3)
+
+DESCRIPTION="Python wrapper for OCCT generated using pywrap"
+HOMEPAGE="https://github.com/CadQuery/OCP"
+SRC_URI="https://github.com/CadQuery/OCP/archive/refs/tags/${MY_PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="Apache-2.0"
+KEYWORDS="~amd64 ~x86"
+SLOT="0"
+REQUIRED_USE="${PYTHON_REQUIRED_USE}"
+
+# CMake and VTK requirements derive from the "OCP/CMakeLists.txt" file
+# generated by the src_prepare() phase. OCP currently requires opencascade
+# (OCCT) to be built with "-DUSE_GLES2=OFF" and thus "-gles2". See also:
+# https://github.com/CadQuery/OCP/issues/46#issuecomment-808920994
+BDEPEND="
+ >=dev-libs/lief-0.11.5[python,${PYTHON_SINGLE_USEDEP}]
+ >=dev-util/cmake-3.16
+"
+RDEPEND="
+ ${PYTHON_DEPS}
+ sci-libs/opencascade:0/7.5[json,tbb,vtk]
+ >=sci-libs/vtk-9.0.0[python,${PYTHON_SINGLE_USEDEP}]
+"
+DEPEND="${RDEPEND}
+ $(python_gen_cond_dep '
+ >=dev-python/cadquery-pywrap-'${OCCT_PV}'_rc0[${PYTHON_USEDEP}]')
+"
+
+S="${WORKDIR}/${MY_P}"
+
+# The source "OCP/CMakeLists.txt" file is output by "bindgen" in src_prepare().
+CMAKE_IN_SOURCE_BUILD=True
+
+# Ensure the path returned by get_llvm_prefix() contains clang.
+llvm_check_deps() {
+ has_version -r "sys-devel/clang:${LLVM_SLOT}"
+}
+
+cadquery-ocp_check_reqs() {
+ CHECKREQS_DISK_BUILD=1300M check-reqs_pkg_${EBUILD_PHASE}
+}
+
+pkg_pretend() {
+ cadquery-ocp_check_reqs
+}
+
+pkg_setup() {
+ cadquery-ocp_check_reqs
+ llvm_pkg_setup
+ python-single-r1_pkg_setup
+}
+
+# OCP currently requires manual configuration, compilation, and installation
+# loosely inspired by the conda-specific "build-bindings-job.yml" file.
+#
+# Note that the cmake_src_prepare() function called below handles user patches.
+src_prepare() {
+ # Most recently installed version of Clang.
+ local _CLANG_VERSION="$(CPP=clang clang-fullversion)"
+
+ # Most recently installed version (excluding trailing patch) of VTK.
+ local _VTK_VERSION="$(best_version -r sci-libs/vtk)"
+ _VTK_VERSION="$(ver_cut 1-2 "${_VTK_VERSION##sci-libs/vtk}")"
+
+ # Absolute dirname of the most recently installed Clang include directory,
+ # mimicing similar logic in the "dev-python/shiboken2" ebuild. See also:
+ # https://bugs.gentoo.org/619490
+ local _CLANG_INCLUDE_DIR="${EPREFIX}/usr/lib/clang/${_CLANG_VERSION}/include"
+
+ # Absolute filename of the most recently installed Clang shared library.
+ local _CLANG_LIB_FILE="$(get_llvm_prefix)/lib64/libclang.so"
+
+ # Absolute dirname of OCCT's include and shared library directories.
+ local _OCCT_INCLUDE_DIR="${EPREFIX}/usr/include/opencascade"
+ local _OCCT_LIB_DIR="${EPREFIX}/usr/lib64/opencascade"
+
+ # Absolute dirname of a temporary directory to store symbol tables for this
+ # OCCT version dumped below by the "dump_symbols.py" script.
+ local _OCCT_DUMP_SYMBOLS_ROOT_DIR="${T}/dump_symbols"
+ local _OCCT_DUMP_SYMBOLS_DIR="${_OCCT_DUMP_SYMBOLS_ROOT_DIR}/lib_linux"
+
+ # Absolute dirname of VTK's include directory,
+ local _VTK_INCLUDE_DIR="${EPREFIX}/usr/include/vtk-${_VTK_VERSION}"
+
+ # Ensure the above paths exist as a crude sanity test.
+ test -d "${_CLANG_INCLUDE_DIR}" || die "${_CLANG_INCLUDE_DIR} not found."
+ test -f "${_CLANG_LIB_FILE}" || die "${_CLANG_LIB_FILE} not found."
+ test -d "${_OCCT_INCLUDE_DIR}" || die "${_OCCT_INCLUDE_DIR} not found."
+ test -d "${_OCCT_LIB_DIR}" || die "${_OCCT_LIB_DIR} not found."
+ test -d "${_VTK_INCLUDE_DIR}" || die "${_VTK_INCLUDE_DIR} not found."
+
+ # "dev-python/clang-python" atom targeting this Clang version.
+ local _CLANG_PYTHON_ATOM="dev-python/clang-python-${_CLANG_VERSION}"
+
+ # Ensure "dev-python/clang-python" targets this Clang version.
+ has_version -r "=${_CLANG_PYTHON_ATOM}" ||
+ die "${_CLANG_PYTHON_ATOM} not installed."
+
+ # Remove all vendored paths.
+ rm -r conda opencascade pywrap *.dat || die
+
+ # Inject a symlink to OCCT's include directory.
+ ln -s "${_OCCT_INCLUDE_DIR}" opencascade || die
+
+ # Inject a symlink from OCCT's shared library directory into this temporary
+ # directory as required by the "dump_symbols.py" script.
+ mkdir -p "${_OCCT_DUMP_SYMBOLS_DIR}" || die
+ ln -s "${_OCCT_LIB_DIR}" "${_OCCT_DUMP_SYMBOLS_DIR}"/. || die
+
+ # Update all hardcoded OCCT shared library versions in "dump_symbols.py".
+ sed -i -e 's~\(\.so\.\)[0-9]\+.[0-9]\+.[0-9]\+~\1'${OCCT_PV}'~' \
+ dump_symbols.py || die
+
+ # Dump (i.e., generate) symbol tables for this OCCT version.
+ einfo 'Dumping OCCT symbol tables...'
+ ${EPYTHON} dump_symbols.py "${_OCCT_DUMP_SYMBOLS_ROOT_DIR}" || die
+
+ # Generate OCCT bindings in the "OCP/" subdirectory.
+ einfo 'Building OCP CMake binary tree...'
+ ${EPYTHON} -m bindgen \
+ --verbose \
+ --njobs $(makeopts_jobs) \
+ --libclang "${_CLANG_LIB_FILE}" \
+ --include "${_CLANG_INCLUDE_DIR}" \
+ --include "${_VTK_INCLUDE_DIR}" \
+ all ocp.toml || die
+
+ # Remove the source "FindOpenCascade.cmake" after generating bindings,
+ # which copied that file to the target "OCP/FindOpenCascade.cmake".
+ rm FindOpenCascade.cmake || die
+
+ #FIXME: Submit an issue recommending upstream replace their
+ #non-working "OCP/FindOpenCascade.cmake" file with a standard top-level
+ #"CMakeLists.txt" file that finds dependency paths: e.g., via @waebbl
+ # find_package(vtk 9 CONFIG REQUIRED)
+ # if(TARGET VTK::VTK)
+ # get_target_property(VTK_INCLUDE_DIRS VTK::VTK INTERFACE_INCLUDE_DIRECTORIES)
+ # endif()
+
+ # Replace all hardcoded paths in "OCP/FindOpenCascade.cmake" with
+ # standard OCCT paths derived above. That file is both fundamentally
+ # broken and useless, as the ${CASROOT} environment variable and
+ # "/usr/lib64/cmake/opencascade-${PV}/OpenCASCADEConfig.cmake" file
+ # already reliably identify all requisite OpenCASCADE paths. Failure to
+ # patch this file results in src_configure() failures resembling:
+ # -- Could NOT find OPENCASCADE (missing: OPENCASCADE_LIBRARIES)
+ sed -i \
+ -e 's~$ENV{CONDA_PREFIX}/include/opencascade\b~'${_OCCT_INCLUDE_DIR}'~' \
+ -e 's~$ENV{CONDA_PREFIX}/lib\b~'${_OCCT_LIB_DIR}'~' \
+ -e 's~$ENV{CONDA_PREFIX}/Library/\(lib\|include/opencascade\)~~' \
+ OCP/FindOpenCascade.cmake || die
+
+ # Patch the "OCP/CMakeLists.txt" file generated by "bindgen" above, passed
+ # as an absolute path both here and below to minimize eclass issues.
+ CMAKE_USE_DIR="${S}/OCP" cmake_src_prepare
+}
+
+src_configure() {
+ local mycmakeargs=(
+ -B "${S}/OCP.build"
+ -DPYTHON_EXECUTABLE="${PYTHON}"
+ -Wno-dev
+ )
+
+ CMAKE_USE_DIR="${S}/OCP" cmake_src_configure
+}
+
+src_compile() {
+ CMAKE_USE_DIR="${S}/OCP.build" cmake_src_compile
+}
+
+# OCP currently ships no test suite, so we synthesize a crude import unit test.
+src_test() {
+ PYTHONPATH="${S}/OCP.build" ${EPYTHON} -c \
+ 'from OCP.gp import gp_Vec, gp_Ax1, gp_Ax3, gp_Pnt, gp_Dir, gp_Trsf, gp_GTrsf, gp, gp_XYZ'
+}
+
+src_install() {
+ python_moduleinto .
+ python_domodule "${S}/OCP.build/"OCP*.so
+}
diff --git a/dev-python/cadquery-pywrap/Manifest b/dev-python/cadquery-pywrap/Manifest
index a203693d6..e5aef7ccf 100644
--- a/dev-python/cadquery-pywrap/Manifest
+++ b/dev-python/cadquery-pywrap/Manifest
@@ -1 +1,2 @@
DIST cadquery-pywrap-7.5.2_rc20210526.tar.gz 5584220 BLAKE2B b26fd4092f94e3d3eec191c0791faf29d90da2d85f9aa9a2f1cdf128975564db9f6b6002661eed8bbecddb31988ad2076a3a00ea601a43e38ffaa47e545911ca SHA512 40aa61e0774228c70c8ae41a6078a280d63697d297234dbff51ec84982b4a9f0a09db41c74a834ae91d01881a4d5660b1ebbb701d24141307a5fedcdfb075872
+DIST cadquery-pywrap-7.5.3_rc20220113.tar.gz 5584755 BLAKE2B d6585d33eddc34c719f9694322d209969698d6e5c67288a95ad841efbc2347d2cb162d8f3443a4e3373d70b97423485d1535c60713e4cb8ace413d114b852083 SHA512 f0d984b6fa6df3151d9cb612560a5266f98d286b9ab283c4647095dda3da1c54fb102babee4d2db574b695604332bc7576740406907995940eb60635afb614b8
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
new file mode 100644
index 000000000..b2213cef7
--- /dev/null
+++ b/dev-python/cadquery-pywrap/cadquery-pywrap-7.5.3_rc20220113.ebuild
@@ -0,0 +1,63 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{8..10} )
+
+inherit llvm distutils-r1
+
+DESCRIPTION="C++ binding generator based on libclang and pybind11"
+HOMEPAGE="https://github.com/CadQuery/pywrap"
+
+#FIXME: Uncomment on bumping to the next stable release.
+# MY_PN=occt
+# MY_PV=$(ver_cut 1-2)
+# MY_P="${MY_PN}${MY_PV}"
+# SRC_URI="https://github.com/CadQuery/pywrap/archive/refs/tags/${MY_P}.tar.gz"
+
+# The official pywrap 7.4.0 tarball is broken, but pywrap 7.5.3 has yet to be
+# officially released. We instead package a commit known to work as expected.
+MY_COMMIT="66e7376d3a27444393fc99acbdbef40bbc7031ae"
+SRC_URI="https://github.com/CadQuery/pywrap/archive/${MY_COMMIT}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="Apache-2.0"
+KEYWORDS="~amd64 ~x86"
+SLOT="0"
+
+# Dependencies are intentionally listed in "setup.py" order.
+RDEPEND="
+ dev-python/click[${PYTHON_USEDEP}]
+ dev-python/logzero[${PYTHON_USEDEP}]
+ dev-python/path-py[${PYTHON_USEDEP}]
+ dev-python/clang-python[${PYTHON_USEDEP}]
+ dev-python/cymbal[${PYTHON_USEDEP}]
+ dev-python/toml[${PYTHON_USEDEP}]
+ dev-python/pandas[${PYTHON_USEDEP}]
+ >=dev-python/joblib-1.0.0[${PYTHON_USEDEP}]
+ dev-python/tqdm[${PYTHON_USEDEP}]
+ dev-python/jinja[${PYTHON_USEDEP}]
+ dev-python/toposort[${PYTHON_USEDEP}]
+ dev-python/pyparsing[${PYTHON_USEDEP}]
+ dev-python/pybind11[${PYTHON_USEDEP}]
+ dev-python/schema[${PYTHON_USEDEP}]
+ sci-libs/vtk
+"
+DEPEND="${RDEPEND}"
+
+S="${WORKDIR}/pywrap-${MY_COMMIT}"
+
+src_prepare() {
+ #FIXME: Submit an upstream issue. This violates PEP 440 standards.
+ # Sanitize the "bindgen" version to avoid Gentoo QA notices.
+ sed -i -e 's~\(version=\)"0.1dev"~\1"'$(ver_rs 3 '')'"~' setup.py || die
+
+ # Replace conda- with Gentoo-specific prefix dirnames.
+ sed -i -e "s~\\bgetenv('CONDA_PREFIX')~'${EPREFIX}/usr'~" bindgen/*.py ||
+ die
+
+ # Reduce all hardcoded header includes to noops.
+ sed -i -e 's~rv\.append(Path(prefix).*~True~' bindgen/utils.py || die
+
+ distutils-r1_src_prepare
+}
diff --git a/dev-python/cadquery/Manifest b/dev-python/cadquery/Manifest
index ae1e31fa3..380c3e6ae 100644
--- a/dev-python/cadquery/Manifest
+++ b/dev-python/cadquery/Manifest
@@ -1 +1,2 @@
DIST cadquery-2.2_rc20210804.tar.gz 2832275 BLAKE2B b1b25130a9eb73e4913c6e9fc8d1fafd689bc9d216adee6d7fcc6fd80805b9351e87839fae3d6bf7e0a1ccf147e5b4a9afe8f6afc0e01c1b3a287e2671870c8d SHA512 0c5b16da24deba2267b204e5f51f707fffab9a238b27af84a500b8a98aa190be24be75d7bc2d1e282c04aea7116eb404ed4520515d53ae5a64aebafc647aa4a3
+DIST cadquery-2.2_rc20220506.tar.gz 2872821 BLAKE2B a48b4279a6e24166842c3f7c43e0ff3552f22f8821fa203fce30b76110423c375019228b1a458b0020ebfd23a052545ae0d90e3246619a2e53dbe8f411449f3d SHA512 65bd62268f920d1fa170921033c4e4f451e1bdf7e4d1cef457bf34c4466a076de57f40d38ed7fb1d8f207b45447d6763a52880d9d49426372b06fefd536e7c17
diff --git a/dev-python/cadquery/cadquery-2.2_rc20220506.ebuild b/dev-python/cadquery/cadquery-2.2_rc20220506.ebuild
new file mode 100644
index 000000000..26aa07b6d
--- /dev/null
+++ b/dev-python/cadquery/cadquery-2.2_rc20220506.ebuild
@@ -0,0 +1,58 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DISTUTILS_USE_PEP517=setuptools
+DISTUTILS_SINGLE_IMPL=1
+PYTHON_COMPAT=( python3_{8..10} )
+
+inherit distutils-r1
+
+DESCRIPTION="Python parametric CAD scripting framework based on OCCT"
+HOMEPAGE="https://cadquery.readthedocs.io"
+
+# The official CadQuery 2.1 tarball requires the obsolete OCCT 7.4.0, but
+# CadQuery 2.2 has yet to be officially released. We instead package a commit
+# known to work as expected with OCCT 7.5.2.
+MY_COMMIT="803a05e78c233fdb537a8604c3f2b56a52179bbe"
+
+#FIXME: Uncomment on bumping to the next stable release.
+# SRC_URI="https://github.com/CadQuery/cadquery/archive/refs/tags/${PV}.tar.gz"
+SRC_URI="https://github.com/CadQuery/cadquery/archive/${MY_COMMIT}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="Apache-2.0"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+# Dependencies are intentionally listed in "conda/meta.yml" order. Due to its
+# Anaconda focus, "setup.py" currently fails to list dependencies.
+BDEPEND="
+ test? (
+ $(python_gen_cond_dep '
+ dev-python/docutils[${PYTHON_USEDEP}]
+ dev-python/path-py[${PYTHON_USEDEP}]
+ ')
+ )
+"
+RDEPEND="
+ >=dev-python/cadquery-ocp-7.5.0[${PYTHON_SINGLE_USEDEP}]
+ $(python_gen_cond_dep '
+ >=dev-python/pyparsing-2.0.0[${PYTHON_USEDEP}]
+ dev-python/ezdxf[${PYTHON_USEDEP}]
+ dev-python/ipython[${PYTHON_USEDEP}]
+ dev-python/typing-extensions[${PYTHON_USEDEP}]
+ dev-python/nptyping[${PYTHON_USEDEP}]
+ sci-libs/nlopt[python,${PYTHON_USEDEP}]
+ dev-python/multimethod[${PYTHON_USEDEP}]
+ dev-python/typish[${PYTHON_USEDEP}]
+ ')
+"
+DEPEND="${RDEPEND}"
+
+S="${WORKDIR}/${PN}-${MY_COMMIT}"
+
+distutils_enable_tests pytest
+
+#FIXME: Uncomment after packaging "dev-python/sphinx-autodoc-typehints".
+# distutils_enable_sphinx docs dev-python/sphinx_rtd_theme dev-python/sphinx-autodoc-typehints
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__ = '${PV}'" >> dandischema/_version.py
+}
+
+distutils_enable_tests pytest
+
+python_test() {
+ export DANDI_TESTS_NONETWORK=1
+ pushd dandischema || die
+ epytest tests
+ popd
+}
diff --git a/dev-python/delegator/delegator-0.1.1.ebuild b/dev-python/delegator/delegator-0.1.1.ebuild
index f56de2340..1ae0a527a 100644
--- a/dev-python/delegator/delegator-0.1.1.ebuild
+++ b/dev-python/delegator/delegator-0.1.1.ebuild
@@ -1,9 +1,9 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=7
+EAPI=8
-PYTHON_COMPAT=( python3_{7..9} )
+PYTHON_COMPAT=( python3_{8..10} )
inherit distutils-r1
diff --git a/dev-python/fiona/Manifest b/dev-python/fiona/Manifest
index 6f48f8721..2140ef1a5 100644
--- a/dev-python/fiona/Manifest
+++ b/dev-python/fiona/Manifest
@@ -1 +1,2 @@
-DIST fiona-1.8.20.tar.gz 269491 BLAKE2B 0778a0824e3ecd70fc7a153a4be4631c04e70dc6218c3c78e7ddffae01db22a081f8f8b7f44cce37f864e32277b88596263d6ac640293c93e6a14ec7a932aa04 SHA512 4864f3c48903b34c6b4d2cf5dcdc5ebb6e155e32e7e138bdf17756a823f36a0985162c211127b283235569235c830e11abd330c229b2bb8de6cee053fe3204d7
+DIST fiona-1.8.21.tar.gz 270166 BLAKE2B 752957f3cc3ed6a35713536e90cdbc542d73de9718e878a449f71c9b9a2150b4ead90ff5d9ce254a6adcfcf7deb61b4483e7cf5bfee12997e581fd0a3ffc767e SHA512 c77cedae67fb7e2b6b6a84aeef39ce5424ccb38b13774f7c2e9bd5934836a6abe6759eeea1d4a8cfc83c5111442f2028d18dd79af209e11618789de2149e7885
+
diff --git a/dev-python/fiona/fiona-1.8.20.ebuild b/dev-python/fiona/fiona-1.8.21.ebuild
index 1127afa70..51ded0d37 100644
--- a/dev-python/fiona/fiona-1.8.20.ebuild
+++ b/dev-python/fiona/fiona-1.8.21.ebuild
@@ -16,7 +16,7 @@ SLOT="0"
KEYWORDS="~amd64 ~x86"
RDEPEND="
- sci-libs/gdal[geos,sqlite,python,${PYTHON_USEDEP}]
+ sci-libs/gdal[geos,sqlite]
dev-python/attrs[${PYTHON_USEDEP}]
dev-python/click-plugins[${PYTHON_USEDEP}]
dev-python/cligj[${PYTHON_USEDEP}]
@@ -24,11 +24,12 @@ RDEPEND="
dev-python/six[${PYTHON_USEDEP}]
dev-python/certifi[${PYTHON_USEDEP}]
"
+
BDEPEND="
dev-python/cython[${PYTHON_USEDEP}]
test? (
dev-python/boto3[${PYTHON_USEDEP}]
- sci-libs/gdal[geos,sqlite,python,${PYTHON_USEDEP}]
+ sci-libs/gdal[geos,sqlite]
)
"
@@ -56,6 +57,9 @@ python_test() {
tests/test_drvsupport.py::test_no_append_driver_cannot_append[PCIDSK]
tests/test_drvsupport.py::test_write_or_driver_error[DGN]
+ # failure in flatgeobuf impl
+ tests/test_drvsupport.py::test_no_append_driver_cannot_append[FlatGeobuf]
+
# geos
#tests/test_collection.py::test_mask_polygon_triangle
#tests/test_collection.py::test_mask_polygon_triangle
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 ${EPYTHON}"
}
diff --git a/dev-python/geopandas/geopandas-0.10.2.ebuild b/dev-python/geopandas/geopandas-0.10.2.ebuild
index 6dde1c23f..e63aaa1bc 100644
--- a/dev-python/geopandas/geopandas-0.10.2.ebuild
+++ b/dev-python/geopandas/geopandas-0.10.2.ebuild
@@ -17,7 +17,7 @@ KEYWORDS="~amd64 ~x86"
RDEPEND="
dev-python/pandas[${PYTHON_USEDEP}]
- sci-libs/shapely[${PYTHON_USEDEP}]
+ dev-python/shapely[${PYTHON_USEDEP}]
dev-python/fiona[${PYTHON_USEDEP}]
dev-python/pyproj[${PYTHON_USEDEP}]"
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/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:${LLVM_MAX_SLOT}
diff --git a/dev-python/multimethod/Manifest b/dev-python/multimethod/Manifest
new file mode 100644
index 000000000..2b7c7d4a6
--- /dev/null
+++ b/dev-python/multimethod/Manifest
@@ -0,0 +1 @@
+DIST multimethod-1.8.gh.tar.gz 15364 BLAKE2B e16a42a9d35387b4a972e0b88299af215df20dd5025ad5a2fa4314410f667ba4cea401c0d050dfa3e45612117774c4a6627f6b84c33bc55ed0e4c4ec42f5fec3 SHA512 433a2c72a6c98129df70aa09d1e640f2f23be6c42236cb88ad4ef9dee89406a9b6a2c01771b2b7e69ffa8d6b6cae05a8e0cd273d77c2eed86c5b8ee0c6887c8c
diff --git a/dev-python/multimethod/metadata.xml b/dev-python/multimethod/metadata.xml
new file mode 100644
index 000000000..cd5b00a2b
--- /dev/null
+++ b/dev-python/multimethod/metadata.xml
@@ -0,0 +1,12 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <maintainer type="project">
+ <email>sci@gentoo.org</email>
+ <name>Gentoo Science Project</name>
+ </maintainer>
+ <stabilize-allarches/>
+ <upstream>
+ <remote-id type="github">coady/multimethod</remote-id>
+ </upstream>
+</pkgmetadata>
diff --git a/dev-python/multimethod/multimethod-1.8.ebuild b/dev-python/multimethod/multimethod-1.8.ebuild
new file mode 100644
index 000000000..4d3c7837c
--- /dev/null
+++ b/dev-python/multimethod/multimethod-1.8.ebuild
@@ -0,0 +1,20 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DISTUTILS_USE_PEP517=setuptools
+PYTHON_COMPAT=( python3_{8..10} )
+
+inherit distutils-r1
+
+DESCRIPTION="Library allowing Python function overloads based on argument types"
+HOMEPAGE="https://github.com/coady/multimethod"
+
+SRC_URI="https://github.com/coady/multimethod/archive/refs/tags/v${PV}.tar.gz -> ${P}.gh.tar.gz"
+
+LICENSE="Apache-2.0"
+KEYWORDS="~amd64 ~x86"
+SLOT="0"
+
+distutils_enable_tests pytest
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/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/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/pytorch-lightning/pytorch-lightning-1.5.8.ebuild b/dev-python/pytorch-lightning/pytorch-lightning-1.5.8.ebuild
index 7b3ad5e3f..cf51f4e9b 100644
--- a/dev-python/pytorch-lightning/pytorch-lightning-1.5.8.ebuild
+++ b/dev-python/pytorch-lightning/pytorch-lightning-1.5.8.ebuild
@@ -4,7 +4,6 @@
EAPI=8
PYTHON_COMPAT=( python3_{8..9} )
-DISTUTILS_SINGLE_IMPL=1
inherit distutils-r1
@@ -17,8 +16,7 @@ SLOT="0"
KEYWORDS="~amd64"
RDEPEND="
- sci-libs/pytorch[python,${PYTHON_SINGLE_USEDEP}]
- $(python_gen_cond_dep '
+ sci-libs/pytorch[${PYTHON_USEDEP}]
dev-python/numpy[${PYTHON_USEDEP}]
dev-python/future[${PYTHON_USEDEP}]
dev-python/tqdm[${PYTHON_USEDEP}]
@@ -28,5 +26,4 @@ RDEPEND="
dev-python/packaging[${PYTHON_USEDEP}]
dev-python/typing-extensions[${PYTHON_USEDEP}]
dev-python/ratelimit[${PYTHON_USEDEP}]
- ')
"
diff --git a/dev-python/rasterio/rasterio-1.2.10.ebuild b/dev-python/rasterio/rasterio-1.2.10-r1.ebuild
index 625e4a7da..7ae9776c7 100644
--- a/dev-python/rasterio/rasterio-1.2.10.ebuild
+++ b/dev-python/rasterio/rasterio-1.2.10-r1.ebuild
@@ -16,7 +16,7 @@ SLOT="0"
KEYWORDS="~amd64 ~x86"
RDEPEND="
- sci-libs/gdal[aux-xml,jpeg,png,threads,python,${PYTHON_USEDEP}]
+ sci-libs/gdal:=[aux-xml(+),jpeg,png,threads(+)]
dev-python/affine[${PYTHON_USEDEP}]
dev-python/attrs[${PYTHON_USEDEP}]
dev-python/certifi[${PYTHON_USEDEP}]
@@ -26,13 +26,15 @@ RDEPEND="
dev-python/click-plugins[${PYTHON_USEDEP}]
dev-python/snuggs[${PYTHON_USEDEP}]
"
+
#DEPEND="${RDEPEND}"
BDEPEND="
dev-python/cython[${PYTHON_USEDEP}]
test? (
dev-python/boto3[${PYTHON_USEDEP}]
dev-python/hypothesis[${PYTHON_USEDEP}]
- sci-libs/gdal[aux-xml,jpeg,png,threads,python,${PYTHON_USEDEP}]
+ dev-python/shapely[${PYTHON_USEDEP}]
+ sci-libs/gdal:=[aux-xml(+),jpeg,png,threads(+)]
)
"
@@ -43,6 +45,9 @@ python_test() {
# disable tests failing for unknown reason
tests/test_env.py::test_rio_env_no_credentials
tests/test_rio_info.py::test_info_azure_unsigned
+
+ tests/test__env.py::test_search_debian_gdal_data
+ tests/test__env.py::test_search_gdal_data_debian
tests/test_warp.py::test_reproject_resampling[Resampling.cubic]
tests/test_warp.py::test_reproject_resampling[Resampling.lanczos]
tests/test_warp.py::test_reproject_resampling_alpha[Resampling.cubic]
diff --git a/dev-python/rasterstats/rasterstats-0.16.0.ebuild b/dev-python/rasterstats/rasterstats-0.16.0.ebuild
index ccaa17351..3567cdb42 100644
--- a/dev-python/rasterstats/rasterstats-0.16.0.ebuild
+++ b/dev-python/rasterstats/rasterstats-0.16.0.ebuild
@@ -17,7 +17,7 @@ KEYWORDS="~amd64 ~x86"
RDEPEND="
dev-python/affine[${PYTHON_USEDEP}]
- sci-libs/shapely[${PYTHON_USEDEP}]
+ dev-python/shapely[${PYTHON_USEDEP}]
dev-python/numpy[${PYTHON_USEDEP}]
dev-python/rasterio[${PYTHON_USEDEP}]
dev-python/cligj[${PYTHON_USEDEP}]
diff --git a/dev-python/snakemake/snakemake-5.32.2.ebuild b/dev-python/snakemake/snakemake-5.32.2.ebuild
index 53874483f..59d2f061a 100644
--- a/dev-python/snakemake/snakemake-5.32.2.ebuild
+++ b/dev-python/snakemake/snakemake-5.32.2.ebuild
@@ -32,7 +32,7 @@ BDEPEND="test? (
RDEPEND="
dev-python/appdirs[${PYTHON_USEDEP}]
- dev-python/configargparse[${PYTHON_USEDEP}]
+ dev-python/ConfigArgParse[${PYTHON_USEDEP}]
dev-python/datrie[${PYTHON_USEDEP}]
dev-python/docutils[${PYTHON_USEDEP}]
dev-python/GitPython[${PYTHON_USEDEP}]
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/typish/Manifest b/dev-python/typish/Manifest
new file mode 100644
index 000000000..809dd7e09
--- /dev/null
+++ b/dev-python/typish/Manifest
@@ -0,0 +1 @@
+DIST typish-1.9.3.gh.tar.gz 22997 BLAKE2B f399f5d9b3ae8f85f3b719de77d675b142ac45b6535f66d9d0d999411bc5bfc9100523667ea4c1d2be60c15a4bf35ec931ded9e1181a4545bbaa9b96fb27d0dd SHA512 baad9d2229ac289c4eb1d6e64bac0313efd4680f42a95270e0c1141d511392e6a95a5fea767943ddf432f5f0d48d95a05bbf26e06df188079ac177d321e4fa5c
diff --git a/dev-python/typish/metadata.xml b/dev-python/typish/metadata.xml
new file mode 100644
index 000000000..603d0691e
--- /dev/null
+++ b/dev-python/typish/metadata.xml
@@ -0,0 +1,13 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <maintainer type="project">
+ <email>sci@gentoo.org</email>
+ <name>Gentoo Science Project</name>
+ </maintainer>
+ <stabilize-allarches/>
+ <upstream>
+ <remote-id type="pypi">typish</remote-id>
+ <remote-id type="github">ramonhagenaars/typish</remote-id>
+ </upstream>
+</pkgmetadata>
diff --git a/dev-python/typish/typish-1.9.3.ebuild b/dev-python/typish/typish-1.9.3.ebuild
new file mode 100644
index 000000000..3c32b1184
--- /dev/null
+++ b/dev-python/typish/typish-1.9.3.ebuild
@@ -0,0 +1,29 @@
+# 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="Functionality for types"
+HOMEPAGE="https://pypi.org/project/typish/
+ https://github.com/ramonhagenaars/typish"
+SRC_URI="
+ https://github.com/ramonhagenaars/typish/archive/v${PV}.tar.gz
+ -> ${P}.gh.tar.gz
+"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~arm ~arm64 ~hppa ~ia64 ~ppc ~ppc64 ~riscv ~s390 ~sparc ~x86"
+
+BDEPEND="
+ test? (
+ dev-python/numpy[${PYTHON_USEDEP}]
+ dev-python/nptyping[${PYTHON_USEDEP}]
+ )
+"
+
+distutils_enable_tests pytest
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-python/wraps/metadata.xml b/dev-python/wraps/metadata.xml
new file mode 100644
index 000000000..dd3bf5227
--- /dev/null
+++ b/dev-python/wraps/metadata.xml
@@ -0,0 +1,15 @@
+<?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">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-python/zarr/Manifest b/dev-python/zarr/Manifest
index 97e66531d..08592fdcc 100644
--- a/dev-python/zarr/Manifest
+++ b/dev-python/zarr/Manifest
@@ -1,3 +1,3 @@
-DIST zarr-2.10.3.tar.gz 3484571 BLAKE2B 2c955e6c55813b417decfcc195fb11292391d341a863ddb769767e7ece25dc1a1776e260d5dfa260fec9b41dc11ba3ad61d7e53f4785bfc4851889a68ff2b5d2 SHA512 949391b65e234d5ae18188c16497145314392d69037b88512626a6e762f920a70badcb36bbb69d66291e9422a5cdacaae318c5c30ebab3d93ab83e37b56d5fca
DIST zarr-2.11.1.tar.gz 3492813 BLAKE2B ff31cc2d11f5f863770f91136694108ab76525c644dd57861a4a57ca03dae0bb8cde5c20a2654f3566ffb69900d581e7592f576b9c0d2746e4fb95ed6991c740 SHA512 e0079a69f65a1bc230049469f50bf52af036d85d84f7c163ecdc2a4a8d7b75b07b59c1fcdecd83f578682914a6463641e9341d2c18f939c57f1e78f298f6b7ea
DIST zarr-2.11.3.tar.gz 3492924 BLAKE2B ca7c5d4b4dd9a3ba4b108fb878e91418fda5b4020a09eb024c774ea8b06b1b329fd7537806632550d60b19ab16b6f6542b6e368cbaef1bbf43a8514b2347c5d6 SHA512 e11e08341769a730a22fcf9a14bbd6d284c4cb051d971dbd3a234ef42224a46e8119cb53360df1aa55580bc4912df61ddde42284c16173f68a3db1d666afbc65
+DIST zarr-2.12.0.tar.gz 3571172 BLAKE2B f8c628d0ff1fdb75fa46dc923de413f4de5f7aeed822a14523c3c2277b2692852f4896c80d160c503c787d510270c25fc813a9556f1a1f54ed2ffa0147f41763 SHA512 300fc20e22def9b444629c5bb7d5ae9d8178100b88f02b5dc4ddeabc2007cc9d19e7fe9b1710f3b69ebf1aa2154f7e03b11b1a78809be9285caf294d4d49c4ee
diff --git a/dev-python/zarr/zarr-2.11.1.ebuild b/dev-python/zarr/zarr-2.11.1.ebuild
index 9822cb161..8cb175408 100644
--- a/dev-python/zarr/zarr-2.11.1.ebuild
+++ b/dev-python/zarr/zarr-2.11.1.ebuild
@@ -51,6 +51,11 @@ EPYTEST_DESELECT=(
zarr/tests/test_sync.py::TestArray::test_object_arrays_vlen_bytes
zarr/tests/test_sync.py::TestArrayWithThreadSynchronizer::test_object_arrays_vlen_bytes
zarr/tests/test_sync.py::TestArrayWithProcessSynchronizer::test_object_arrays_vlen_bytes
+ zarr/tests/test_core.py::TestArrayWithFSStore::test_object_arrays_vlen_bytes
+ zarr/tests/test_core.py::TestArrayWithFSStoreFromFilesystem::test_object_arrays_vlen_bytes
+ zarr/tests/test_core.py::TestArrayWithFSStorePartialRead::test_object_arrays_vlen_bytes
+ zarr/tests/test_core.py::TestArrayWithFSStoreNested::test_object_arrays_vlen_bytes
+ zarr/tests/test_core.py::TestArrayWithFSStoreNestedPartialRead::test_object_arrays_vlen_bytes
)
distutils_enable_tests pytest
diff --git a/dev-python/zarr/zarr-2.11.3.ebuild b/dev-python/zarr/zarr-2.11.3.ebuild
index 50ec85404..1fa4e9af9 100644
--- a/dev-python/zarr/zarr-2.11.3.ebuild
+++ b/dev-python/zarr/zarr-2.11.3.ebuild
@@ -51,6 +51,11 @@ EPYTEST_DESELECT=(
zarr/tests/test_sync.py::TestArray::test_object_arrays_vlen_bytes
zarr/tests/test_sync.py::TestArrayWithThreadSynchronizer::test_object_arrays_vlen_bytes
zarr/tests/test_sync.py::TestArrayWithProcessSynchronizer::test_object_arrays_vlen_bytes
+ zarr/tests/test_core.py::TestArrayWithFSStore::test_object_arrays_vlen_bytes
+ zarr/tests/test_core.py::TestArrayWithFSStoreFromFilesystem::test_object_arrays_vlen_bytes
+ zarr/tests/test_core.py::TestArrayWithFSStorePartialRead::test_object_arrays_vlen_bytes
+ zarr/tests/test_core.py::TestArrayWithFSStoreNested::test_object_arrays_vlen_bytes
+ zarr/tests/test_core.py::TestArrayWithFSStoreNestedPartialRead::test_object_arrays_vlen_bytes
)
distutils_enable_tests pytest
diff --git a/dev-python/zarr/zarr-2.10.3.ebuild b/dev-python/zarr/zarr-2.12.0.ebuild
index 9822cb161..1fa4e9af9 100644
--- a/dev-python/zarr/zarr-2.10.3.ebuild
+++ b/dev-python/zarr/zarr-2.12.0.ebuild
@@ -21,8 +21,8 @@ RESTRICT="!test? ( test )"
RDEPEND="
dev-python/asciitree[${PYTHON_USEDEP}]
dev-python/fasteners[${PYTHON_USEDEP}]
- dev-python/numcodecs[${PYTHON_USEDEP}]
- dev-python/numpy[${PYTHON_USEDEP}]
+ >=dev-python/numcodecs-0.6.4[${PYTHON_USEDEP}]
+ >=dev-python/numpy-1.7[${PYTHON_USEDEP}]
"
DEPEND="
@@ -51,6 +51,12 @@ EPYTEST_DESELECT=(
zarr/tests/test_sync.py::TestArray::test_object_arrays_vlen_bytes
zarr/tests/test_sync.py::TestArrayWithThreadSynchronizer::test_object_arrays_vlen_bytes
zarr/tests/test_sync.py::TestArrayWithProcessSynchronizer::test_object_arrays_vlen_bytes
+ zarr/tests/test_core.py::TestArrayWithFSStore::test_object_arrays_vlen_bytes
+ zarr/tests/test_core.py::TestArrayWithFSStoreFromFilesystem::test_object_arrays_vlen_bytes
+ zarr/tests/test_core.py::TestArrayWithFSStorePartialRead::test_object_arrays_vlen_bytes
+ zarr/tests/test_core.py::TestArrayWithFSStoreNested::test_object_arrays_vlen_bytes
+ zarr/tests/test_core.py::TestArrayWithFSStoreNestedPartialRead::test_object_arrays_vlen_bytes
)
distutils_enable_tests pytest
+distutils_enable_sphinx docs dev-python/numpydoc dev-python/sphinx-issues dev-python/sphinx_rtd_theme
diff --git a/dev-vcs/dandi-cli/Manifest b/dev-vcs/dandi-cli/Manifest
index cce81b9b2..9cc6d0a63 100644
--- a/dev-vcs/dandi-cli/Manifest
+++ b/dev-vcs/dandi-cli/Manifest
@@ -1,3 +1,4 @@
+DIST dandi-0.45.1.tar.gz 321362 BLAKE2B d07296be6bd4237fea4aa83c0b087de45234157aa6aa457f8d44f56b514a4deca11226831182b84c19a72b398183b3b181beb3946c7f8cce2d842ac80f0b57e2 SHA512 07d97420651bbd82d8d4146322ff80873489bd49869834ace9986f1ddc1880be5ff6bd1d625d8b4607a90de8007aeba152e8161af05c25a804cb18c7a0c78e29
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
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..0c8ba225e 100644
--- a/dev-vcs/dandi-cli/dandi-cli-0.39.4.ebuild
+++ b/dev-vcs/dandi-cli/dandi-cli-0.39.4.ebuild
@@ -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[${PYTHON_USEDEP}]
"
diff --git a/dev-vcs/dandi-cli/dandi-cli-0.45.1.ebuild b/dev-vcs/dandi-cli/dandi-cli-0.45.1.ebuild
new file mode 100644
index 000000000..dcdb13e85
--- /dev/null
+++ b/dev-vcs/dandi-cli/dandi-cli-0.45.1.ebuild
@@ -0,0 +1,80 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DISTUTILS_USE_PEP517=setuptools
+PYTHON_COMPAT=( python3_{8..10} )
+
+inherit distutils-r1
+
+MY_PN="dandi"
+MY_P="${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 -> ${P}.tar.gz"
+SRC_URI="mirror://pypi/${MY_PN:0:1}/${MY_PN}/${MY_P}.tar.gz"
+
+LICENSE="Apache-2.0"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="test etelemetry"
+
+RDEPEND="
+ dev-python/appdirs[${PYTHON_USEDEP}]
+ dev-python/click[${PYTHON_USEDEP}]
+ dev-python/click-didyoumean[${PYTHON_USEDEP}]
+ =dev-python/dandi-schema-0.7*[${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[${PYTHON_USEDEP}]
+ dev-python/nwbinspector[${PYTHON_USEDEP}]
+ dev-python/packaging[${PYTHON_USEDEP}]
+ dev-python/pycryptodome[${PYTHON_USEDEP}]
+ >=dev-python/pydantic-1.9.0[${PYTHON_USEDEP}]
+ dev-python/pynwb[${PYTHON_USEDEP}]
+ dev-python/pyout[${PYTHON_USEDEP}]
+ dev-python/python-dateutil[${PYTHON_USEDEP}]
+ dev-python/requests[${PYTHON_USEDEP}]
+ dev-python/ruamel-yaml[${PYTHON_USEDEP}]
+ dev-python/semantic_version[${PYTHON_USEDEP}]
+ dev-python/tenacity[${PYTHON_USEDEP}]
+ dev-python/wheel[${PYTHON_USEDEP}]
+ dev-python/zarr[${PYTHON_USEDEP}]
+"
+
+BDEPEND="
+ test? (
+ dev-python/anys[${PYTHON_USEDEP}]
+ dev-python/responses[${PYTHON_USEDEP}]
+ dev-python/pyfakefs[${PYTHON_USEDEP}]
+ dev-python/pytest-mock[${PYTHON_USEDEP}]
+ media-libs/opencv[ffmpeg,${PYTHON_USEDEP}]
+ )
+"
+# Upstream might be amenable to dropping opencv:
+# https://github.com/dandi/dandi-cli/issues/944
+
+S="${WORKDIR}/${MY_P}"
+
+distutils_enable_tests pytest
+
+src_prepare() {
+ if use etelemetry; then
+ default
+ else
+ eapply "${FILESDIR}/${PN}-0.28.0-no-etelemetry.patch"
+ default
+ sed -i "/etelemetry/d" setup.cfg
+ fi
+}
+
+python_test() {
+ export DANDI_TESTS_NONETWORK=1
+ epytest
+}
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..1142cad18 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"
diff --git a/dev-vcs/datalad/datalad-0.15.2.ebuild b/dev-vcs/datalad/datalad-0.15.2.ebuild
index 2322ac254..1142cad18 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"
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..50e29f19d
--- /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:
+ # ${EPYTHON} -m nose -s -v datalad || die
+}
diff --git a/dev-vcs/datalad/datalad-0.17.0.ebuild b/dev-vcs/datalad/datalad-0.17.0.ebuild
new file mode 100644
index 000000000..4fb1d3de1
--- /dev/null
+++ b/dev-vcs/datalad/datalad-0.17.0.ebuild
@@ -0,0 +1,75 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DISTUTILS_USE_PEP517=setuptools
+PYTHON_COMPAT=( python3_{8..10} )
+inherit distutils-r1
+
+DESCRIPTION="Keep code, data, containers under control with git and git-annex"
+HOMEPAGE="https://github.com/datalad/datalad"
+SRC_URI="https://github.com/datalad/datalad/archive/refs/tags/${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:
+ # ${EPYTHON} -m nose -s -v datalad || die
+}
diff --git a/dev-vcs/datalad/datalad-0.17.2.ebuild b/dev-vcs/datalad/datalad-0.17.2.ebuild
new file mode 100644
index 000000000..753985ef6
--- /dev/null
+++ b/dev-vcs/datalad/datalad-0.17.2.ebuild
@@ -0,0 +1,73 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DISTUTILS_USE_PEP517=setuptools
+PYTHON_COMPAT=( python3_{8..10} )
+inherit distutils-r1
+
+DESCRIPTION="Keep code, data, containers under control with git and git-annex"
+HOMEPAGE="https://github.com/datalad/datalad"
+SRC_URI="https://github.com/datalad/datalad/archive/refs/tags/${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/net-misc/cernbox-client/Manifest b/net-misc/cernbox-client/Manifest
index 05ff69f80..ad8668437 100644
--- a/net-misc/cernbox-client/Manifest
+++ b/net-misc/cernbox-client/Manifest
@@ -1,3 +1,3 @@
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 ownCloud-2.9.2.6206.tar.xz 5759996 BLAKE2B c328ea261a4fddecf93837dbcac01aab0971542d8dfb3f5b0a32a8432ca0e0904c3f4fc81c5c7811da8b3af64b58e929c055e7cec0649f00049e037372948eec SHA512 d075a11ee92aa9771c631a766feddfa1a70907d7d341b58043e1ba96ac52786a6a750b15c2f9b7a0992fe02a45586cc3445755dc9df4cd267e72f070d2222f0f
+DIST ownCloud-2.10.1.7389.tar.xz 5598044 BLAKE2B 8558a8a7b7bd4b8a0685b703f0882d6b5619c4902217d40feb4cf5587555b9a85363c7f61834e4c85a84789142fca8c73910fce66544f491ec5968818c816605 SHA512 2a0893d48786b88f8210966a2b6b48f5bdada82818d4115e68ecc6c0c926ba62bc74df03c4ab35eb271aef2f3a43b36b1a6a115585efe3739fd4a6164f9c45a1
diff --git a/net-misc/cernbox-client/cernbox-client-2.9.2.6206.ebuild b/net-misc/cernbox-client/cernbox-client-2.10.1.7389.ebuild
index 27080cd72..c4eeaa7be 100644
--- a/net-misc/cernbox-client/cernbox-client-2.9.2.6206.ebuild
+++ b/net-misc/cernbox-client/cernbox-client-2.10.1.7389.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=8
@@ -73,7 +73,6 @@ src_prepare() {
src_configure() {
local mycmakeargs=(
- -DSYSCONF_INSTALL_DIR="${EPREFIX}"/etc
-DCMAKE_INSTALL_DOCDIR=/usr/share/doc/${PF}
-DBUILD_SHELL_INTEGRATION_DOLPHIN=$(usex dolphin)
-DBUILD_TESTING=$(usex test)
diff --git a/profiles/package.mask b/profiles/package.mask
index b338c8d20..d39812beb 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -29,9 +29,3 @@
## app-misc/some-package
#--- 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
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/samri/samri-0.5.ebuild b/sci-biology/samri/samri-0.5.ebuild
index 7966ad16b..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
@@ -41,7 +41,7 @@ RDEPEND="
sci-libs/nibabel[${PYTHON_USEDEP}]
>=sci-libs/nipy-0.4.1[${PYTHON_USEDEP}]
>=sci-libs/nipype-1.0.0[${PYTHON_USEDEP}]
- sci-libs/pybids[${PYTHON_USEDEP}]
+ <sci-libs/pybids-0.10.2[${PYTHON_USEDEP}]
sci-libs/scikit-image[${PYTHON_USEDEP}]
sci-biology/ants
sci-biology/afni
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 ab1a155c3..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"
+DEPEND="app-arch/zstd >=sci-libs/hdf5-1.12.2-r5"
RDEPEND="${DEPEND}"
S=${WORKDIR}/${PN}-${COMMIT}
@@ -25,9 +25,3 @@ src_configure() {
)
cmake_src_configure
}
-
-src_install() {
- echo "HDF5_PLUGIN_PATH=${EPREFIX}/usr/$(get_libdir)/hdf5/plugin" >> 99h5zstd || die
- doenvd 99h5zstd
- cmake_src_install
-}
diff --git a/sci-libs/arpack/Manifest b/sci-libs/arpack/Manifest
new file mode 100644
index 000000000..730cdcfdd
--- /dev/null
+++ b/sci-libs/arpack/Manifest
@@ -0,0 +1,3 @@
+DIST arpack-3.8.0_p20220604.gh.tar.gz 1012341 BLAKE2B 30f71c334f3ce8b24bce309cdfa5869fa4781baa1935dbd7772936f1f135e4d6a3b576f9fece8ba9ff48f053bac1d1328c4f5f5545cacaa568e1ea5695013e2f SHA512 f31c7bd45a82a8a64e1d041ca18eac9c50dac0ebecf845ad5e57c70d1c12ab36ab0630db224897bfe6181c0fff9152f1dea7b3a6a2eb53bfda2f2a590ca8a37b
+DIST arpack-tutorial.ps.gz 105599 BLAKE2B 99570e6a0cc1c020b9c271e8ce1cc224f69ff5333cc818c10b063dc8ffbaf66a9f5c6ede99541b4212286d422146b1c4e332eba7e1635c99efa0e4c2620f0630 SHA512 a7b8fefd1a572ed477ae208d49094c1c65c9368990d12de9b3528e33fed546c947659f74e54a810d04154b4a1b0f9a94bcba4db0cf59d379e20786a261066aa4
+DIST arpack-ug.ps.gz 248543 BLAKE2B ac010aef470060636fa00360636ba093f0d24d219fa927c79fb1726b798160eda74fa8b4be6c7dff94f5759efcf30afa99ad310e7959115e028738beb8aa125d SHA512 3349117fb10b07207ffbab2ffa31b406d026855ea4c16e8649b14c7d70bc94e11b5730672e34acd654817799136d4bd76569ac50ec78d787df5582d18ed61328
diff --git a/sci-libs/arpack/arpack-3.8.0_p20220604.ebuild b/sci-libs/arpack/arpack-3.8.0_p20220604.ebuild
new file mode 100644
index 000000000..b7a989641
--- /dev/null
+++ b/sci-libs/arpack/arpack-3.8.0_p20220604.ebuild
@@ -0,0 +1,102 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+COMMIT="5eafea4328f1631eab28b1a20e757d1f0e21f8a6"
+PYTHON_COMPAT=( python3_{8..10} )
+
+inherit cmake flag-o-matic fortran-2 python-single-r1
+
+DESCRIPTION="Arnoldi package library to solve large scale eigenvalue problems"
+HOMEPAGE="
+ https://www.caam.rice.edu/software/ARPACK/
+ https://github.com/opencollab/arpack-ng
+"
+SRC_URI="
+ https://github.com/opencollab/${PN}-ng/archive/${COMMIT}.tar.gz -> ${PF}.gh.tar.gz
+ doc? (
+ http://www.caam.rice.edu/software/ARPACK/SRC/ug.ps.gz -> ${PN}-ug.ps.gz
+ http://www.caam.rice.edu/software/ARPACK/DOCS/tutorial.ps.gz -> ${PN}-tutorial.ps.gz
+ )
+"
+S="${WORKDIR}/${PN}-ng-${COMMIT}"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64 ~arm ~arm64 ~hppa ~ia64 ~ppc ~ppc64 ~riscv ~sparc ~x86 ~amd64-linux ~x86-linux ~ppc-macos"
+IUSE="doc examples icb icbexmm int64 mpi python"
+
+RDEPEND="
+ virtual/blas
+ virtual/lapack
+
+ icbexmm? ( dev-cpp/eigen )
+ mpi? ( virtual/mpi[fortran] )
+ icb? ( virtual/mpi[cxx] )
+ python? (
+ ${PYTHON_DEPS}
+ $(python_gen_cond_dep 'dev-libs/boost:=[numpy,python,${PYTHON_USEDEP}]')
+ )
+"
+DEPEND="${RDEPEND}"
+BDEPEND="virtual/pkgconfig"
+
+REQUIRED_USE="
+ icb? ( mpi )
+ python? (
+ ${PYTHON_REQUIRED_USE}
+ icbexmm
+ )
+"
+
+src_configure() {
+ append-fflags '-fallow-argument-mismatch'
+
+ local mycmakeargs=(
+ -DBUILD_SHARED_LIBS=ON
+ -DEXAMPLES=$(usex examples)
+ -DICB=$(usex icb)
+ -DICBEXMM=$(usex icbexmm)
+ -DINTERFACE64=$(usex int64)
+ -DMPI=$(usex mpi)
+ -DPYTHON3=$(usex python)
+ )
+ cmake_src_configure
+}
+
+src_install() {
+ cmake_src_install
+
+ dodoc DOCUMENTS/*.doc
+ newdoc DOCUMENTS/README README.doc
+ use doc && dodoc "${WORKDIR}"/*.ps
+ if use examples; then
+ for i in BAND COMPLEX NONSYM SIMPLE SVD SYM ; do
+ exeinto "/usr/libexec/${PN}/examples/${i}"
+ doexe "${BUILD_DIR}/EXAMPLES/${i}"/*
+ done
+
+ if use mpi; then
+ exeinto "/usr/libexec/${PN}/examples/MPI"
+ doexe "${BUILD_DIR}"/PARPACK/EXAMPLES/MPI/*
+ fi
+
+ if use python; then
+ docinto examples/pyarpack
+ dodoc "${BUILD_DIR}"/*.py
+ fi
+ docompress -x "/usr/share/doc/${PF}/examples"
+ fi
+ if use icbexmm; then
+ exeinto "/usr/libexec/${PN}/examples/MATRIX_MARKET"
+ doexe "${BUILD_DIR}/EXAMPLES/MATRIX_MARKET/arpackmm"
+ rm "${BUILD_DIR}/EXAMPLES/MATRIX_MARKET/arpackmm" || die
+ docinto examples
+ dodoc -r "${BUILD_DIR}/EXAMPLES/MATRIX_MARKET"
+ fi
+ if use python; then
+ python_domodule "${ED}/usr/$(get_libdir)/pyarpack"
+ rm -r "${ED}/usr/$(get_libdir)/pyarpack" || die
+ fi
+}
diff --git a/sci-libs/arpack/metadata.xml b/sci-libs/arpack/metadata.xml
new file mode 100644
index 000000000..9cd539912
--- /dev/null
+++ b/sci-libs/arpack/metadata.xml
@@ -0,0 +1,26 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <maintainer type="project">
+ <email>sci@gentoo.org</email>
+ <name>Gentoo Science Project</name>
+ </maintainer>
+ <longdescription lang="en">
+ The ARnoldi PACKage is a library of routines capable of solving large scale symmetric,
+ nonsymmetric, and generalized eigenproblems. The software is designed to compute a few
+ eigenvalues with user specified features such as those of largest real
+ part or largest magnitude. Storage requirements are on the order of
+ n*k locations. No auxiliary storage is required. A set of Schur basis
+ vectors for the desired k-dimensional eigen-space is computed which is
+ numerically orthogonal to working precision. Numerically accurate
+ eigenvectors are available on request.
+ </longdescription>
+ <upstream>
+ <remote-id type="github">opencollab/arpack-ng</remote-id>
+ </upstream>
+ <use>
+ <flag name="icb">Enable support for *[ae]upd_c with ISO_C_BINDING</flag>
+ <flag name="icbexmm">Enable support for matrix market example based on ICB</flag>
+ <flag name="int64">Use the 64-bit integer interface (ILP64)</flag>
+ </use>
+</pkgmetadata>
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/itk/itk-5.0.1.ebuild b/sci-libs/itk/itk-5.0.1.ebuild
index bf9f0f021..4580c659a 100644
--- a/sci-libs/itk/itk-5.0.1.ebuild
+++ b/sci-libs/itk/itk-5.0.1.ebuild
@@ -3,7 +3,7 @@
EAPI=7
-PYTHON_COMPAT=( python3_{7,8,9} )
+PYTHON_COMPAT=( python3_{8..10} )
inherit cmake python-single-r1
diff --git a/sci-libs/itk/itk-5.1.0.ebuild b/sci-libs/itk/itk-5.1.0.ebuild
index 3f6c759ec..e6e0b25f9 100644
--- a/sci-libs/itk/itk-5.1.0.ebuild
+++ b/sci-libs/itk/itk-5.1.0.ebuild
@@ -3,7 +3,7 @@
EAPI=7
-PYTHON_COMPAT=( python3_{7,8,9} )
+PYTHON_COMPAT=( python3_{8..10} )
inherit cmake python-single-r1
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/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/pytorch/Manifest b/sci-libs/pytorch/Manifest
deleted file mode 100644
index 1df2744f2..000000000
--- a/sci-libs/pytorch/Manifest
+++ /dev/null
@@ -1,38 +0,0 @@
-DIST FP16-4dfe081cf6bcd15db339cf2680b9281b8451eeb3.tar.gz 71301 BLAKE2B f6a2115a82ca9acd7ccb1bf94c59f68e6ffea4b0e20aa5152349a10119b45d8ba45f5673899b6f18ee044289a51141944e41d7b0972889afc1d93db88d88ed7c SHA512 e79a1f6f8d4aeca85982158d5b070923d31d4f2062ed84cfa6f26c47a34f2e8ac49e0f330b7d49f5732d5e1eec6e7afccdac43645070060fb7827e2ce261dd3e
-DIST FXdiv-b408327ac2a15ec3e43352421954f5b1967701d1.tar.gz 9652 BLAKE2B ce2082f9e0ec55ab43cfee57e29cfc8f1957bdde70c1bbeadc599ac34ed8ade9d1334e68583a0fb14b4405357cc1039579b09fff4b39a5190bdae304c4ea3de3 SHA512 d46d7c1437eccf8dc5ab5e51b0641d190839451ab059c8a24a220a9cf05a84a66b5d08c3ff730622efe491152a8378a2c726fd9abad19a3df98db40d6a13e4b9
-DIST NNPACK-c07e3a0400713d546e0dea2d5466dd22ea389c73.tar.gz 219318 BLAKE2B 6b6619c8a706ef9630f20fda1e276314b2ef7f6c9aed26836a48bdaa0ae198a86383e68b04c651f37c07d34e400bc54b5daa75b06fc18cdb0a9c55e2cb33bbe1 SHA512 f0b261e8698b412d12dd739e5d0cf71c284965ae28da735ae22814a004358ba3ecaea6cd26fa17b594c0245966b7dd2561c1e05c6cbf0592fd7b85ea0f21eb37
-DIST PeachPy-07d8fde8ac45d7705129475c0f94ed8925b93473.tar.gz 401648 BLAKE2B c563cd77a9e2eda34bbec6a34f94111a6db9500b7cda9a18e791984b789c29dde7199ed21696f10cdfb088b05e18163b02a8ca8c9e48a91b9e4a757020f096b0 SHA512 8d6cc91c8c4d56b86ef93f0acd6768a1830ecd078524b21d1a3b9ecb015f06607070148de3e634d9c5ce63ed523a8e34aa388d490e7eee061200098f39126afa
-DIST QNNPACK-7d2a4e9931a82adc3814275b6219a03e24e36b4c.tar.gz 205600 BLAKE2B f174051cba9e3307633f0b12326a37d8fde23562d47e09d3c078350146439094ca6cb2f032cf3aa4af40e5968ee16b8847241f787f7c84ea501124e0528fb82d SHA512 437a835acfedae851a9a8572fa6eea9854dcb8bcca499bc4a2582314e44f5f199778e857932da4aecf943bea7cb2eb5b1c41d4b4ca6075bddbe0f18b2c7b9127
-DIST XNNPACK-79cd5f9e18ad0925ac9a050b00ea5a36230072db.tar.gz 3955905 BLAKE2B d787d4a965c53c8d65887f3b111da950f3b5558cd28ce468764c5bf8efbaddeea567803cfcd89a1aab4a0bc781816871dcca2901e762257aaf96a1d8f868ffd2 SHA512 72c3e53b00d77cfd94db93c60276ca7fd419554dadddf74286e85e0500dbdad0bf65694e451e832de89ea17e7731a9ec9e9f1d831b03c1b81946e0dacb96197d
-DIST asmjit-d0d14ac774977d0060a351f66e35cb57ba0bf59c.tar.gz 717277 BLAKE2B 1e743a3293f780aadd413efe896d75851dfde03a60604f09f2230a6bb3923e57a12a5b124531dddb8ca3d226b4abf7c3906c007da47e9326250a5864d5241f9d SHA512 2822763fcb3c18f6699119c1773404667d81f8afb86f8f2e8dbe627526a2877b049d16505557e680e4e310f0e0667263dc4ac442f682e95f2568bf0bf8b61b4b
-DIST benchmark-5b7683f4.tar.gz 102332 BLAKE2B a7210a2c7a173a9df8bf03b83fc9712d5b52ded13c932e4d13a93004b93ad816895b722acc941b1d94c6b403e4ccb846141f5a38f42baafc5fb3cb108c039559 SHA512 a4e69ee8ec824e418abd713cb3597175cd40ecee9bc539e2d3592f9ec0f8ee54e7466984874f410b78beee82b4c396a7f2824880f808c4217704cf9970411ebf
-DIST benchmark-e776aa02.tar.gz 126890 BLAKE2B 389a4fc0bfedc20227de31d4b1447b8370300a8e3cbea8a8d4b1c82ee90757c2a035ea0324e762217f5a6279a4277f431b7e511d8a9a3bcf226fe31c0022b83c SHA512 d9f70c617af75683dfcf5a0d7ff14b3374258bcf869e3b69b23e85c980366cc4f9859fef3d3dd84a2a92933729053eb02663eaf4bbe0a020a2e001f42b85230d
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-DIST onnx-a82c6a70.tar.gz 4874549 BLAKE2B 055f89d63c03304264b7dd64d5eb6c892a4a280693001ca932f0d352379630870d96dadd6e734b1ec1044cfd92856cd9bb362021a6424ef79e6a408a9c17bc3c SHA512 1ead6644cd28198a428ebcd0f127343c6cbcfdbf39a0832c62ee5ee320a06c655448f508406637702e2da33057c92f76da12302b403ac339a5cad8ea4b5ebab2
-DIST onnx-tensorrt-c153211418a7c57ce071d9ce2a41f8d1c85a878f.tar.gz 72464 BLAKE2B 45301706ca5c91c39e24db84e1dc4e968a8540b760d7b16df08f3a76c407dfceb38962520d822b84618be088fc3d69431f738a8bc7b0f578c84f35234061e99a SHA512 9e814b5dfc3a65ddba229bbddada4c686afab233463329a02cea176b6b1994643f9835ce44a84a9ac1a49e12a7fe2325fd6cd9d2d99a422284089df0202a69a5
-DIST psimd-072586a71b55b7f8c584153d223e95687148a90.tar.gz 6825 BLAKE2B db255d2a62ffa320b1e190a7a9ac923d812e918a72ce8ecfeeb926709ece92d05497430196b0fc833d910b9d24bf0140d20bcce1de695e1c39211158440608db SHA512 a18faea093423dd9fe19ece8b228e011dccce0a2a22222f777ea19b023a13173966d4a8aea01147e8fc58de5d39cffcedeb2221a1572ae52bd5aba1295f86a94
-DIST pthreadpool-a134dd5d4cee80cce15db81a72e7f929d71dd413.tar.gz 49011 BLAKE2B 7bfbca81321243e64aa53c668dfe380ce4f7b88477a1c794a4dea9062c9b0969ca745dbfe0abbb95fffbf44080763506609c387ed085d89f6c612be6804b5cc2 SHA512 5f5a1275bbcef13cea88e381010bf2654c9646d30c5fb061f1d6e9e9a0ae6398e137c5e4f7da69f7d8d8b58fb5a7e79f7a4c0c1c3bbaad8f3d0c896d21bc7691
-DIST pytorch-1.10.2.tar.gz 18475199 BLAKE2B 56fc3f7e052637853f31190f604323ec66d25e4966c102d1adeafa560ac5613d357a8e9115402456f26d5d0350839f645dd7ec226c353d06f484c4e297a13f33 SHA512 fb3722f0c0760419cb197aedf4e23726bd8e8eb498e1ebe39f8f244f95f1fd40334ef8bc95a3e0f5c45beb95abc8683b73cf4fed107e21e7f5690b1d15661699
-DIST sleef-e0a003ee838b75d11763aa9c3ef17bf71a725bff.tar.gz 1642070 BLAKE2B 366fa96e35f429199e8462c63bc9cfbd1888aa65170d3203a5b0391fb855c29241eb225f847e416650e6ed5544f17a745c5a43a622a2847416ad7bd207572840 SHA512 13ea28745e796f8b77a40c99f679e0955e213128fb05d17b61cdcef102b7a758cbda04def3544767a81ddf170b7800f168d25fb1b55093614c7126456765cbea
-DIST tensorpipe-d2aa3485e8229c98891dfd604b514a39d45a5c99.tar.gz 259599 BLAKE2B 89a948430a4a662a475417b60c8a962e5f89eadabe72f303275d113bcd768ad4d86308cceb902c9c65b1c6f23eeef6fe0e5e5329d270d37ae87632ca34406de8 SHA512 fbefc18792458ac2234045df8e3cce8dbb17a5e719258f020c2c1d388092358bd2562e53a0377ca18f40bcfbeae4367c277a74c31c5e45296b891453a962e460
diff --git a/sci-libs/pytorch/files/0002-Don-t-build-libtorch-again-for-PyTorch-1.4.0.patch b/sci-libs/pytorch/files/0002-Don-t-build-libtorch-again-for-PyTorch-1.4.0.patch
deleted file mode 100644
index de9fe9a0d..000000000
--- a/sci-libs/pytorch/files/0002-Don-t-build-libtorch-again-for-PyTorch-1.4.0.patch
+++ /dev/null
@@ -1,30 +0,0 @@
-From e5003b88ad3a504eb04c0ba66c2f439149de2ee3 Mon Sep 17 00:00:00 2001
-From: Alexey Chernov <4ernov@gmail.com>
-Date: Tue, 5 Nov 2019 00:58:17 +0300
-Subject: [PATCH 2/7] Don't build `libtorch` again for PyTorch
-
-If starting with building of `libtorch` using CMake,
-don't build it again for the sake of running `setup.py`
-to build Python version (PyTorch).
----
- setup.py | 7 -------
- 1 file changed, 7 deletions(-)
-
-Index: pytorch-1.4.0_p0/setup.py
-===================================================================
---- pytorch-1.4.0_p0.orig/setup.py
-+++ pytorch-1.4.0_p0/setup.py
-@@ -303,13 +303,6 @@ def build_deps():
- check_pydep('yaml', 'pyyaml')
- check_pydep('typing', 'typing')
-
-- build_caffe2(version=version,
-- cmake_python_library=cmake_python_library,
-- build_python=True,
-- rerun_cmake=RERUN_CMAKE,
-- cmake_only=CMAKE_ONLY,
-- cmake=cmake)
--
- version_path = os.path.join(cwd, 'torch', 'version.py')
- with open(version_path, 'w') as f:
- f.write("__version__ = '{}'\n".format(version))
diff --git a/sci-libs/pytorch/files/0002-Don-t-build-libtorch-again-for-PyTorch-1.7.1.patch b/sci-libs/pytorch/files/0002-Don-t-build-libtorch-again-for-PyTorch-1.7.1.patch
deleted file mode 100644
index 16d2c1f2e..000000000
--- a/sci-libs/pytorch/files/0002-Don-t-build-libtorch-again-for-PyTorch-1.7.1.patch
+++ /dev/null
@@ -1,18 +0,0 @@
-diff --git a/setup.py b/setup.py
-index 2db381644c..2241a33015 100644
---- a/setup.py
-+++ b/setup.py
-@@ -307,13 +307,6 @@ def build_deps():
- check_pydep('yaml', 'pyyaml')
- check_pydep('typing', 'typing')
-
-- build_caffe2(version=version,
-- cmake_python_library=cmake_python_library,
-- build_python=True,
-- rerun_cmake=RERUN_CMAKE,
-- cmake_only=CMAKE_ONLY,
-- cmake=cmake)
--
- if CMAKE_ONLY:
- report('Finished running cmake. Run "ccmake build" or '
- '"cmake-gui build" to adjust build options and '
diff --git a/sci-libs/pytorch/files/0003-Change-path-to-caffe2-build-dir-made-by-libtorch.patch b/sci-libs/pytorch/files/0003-Change-path-to-caffe2-build-dir-made-by-libtorch.patch
deleted file mode 100644
index f71ba17bc..000000000
--- a/sci-libs/pytorch/files/0003-Change-path-to-caffe2-build-dir-made-by-libtorch.patch
+++ /dev/null
@@ -1,46 +0,0 @@
-From dbb0bac77986016217cdfe779499a2ccd0e10570 Mon Sep 17 00:00:00 2001
-From: Alexey Chernov <4ernov@gmail.com>
-Date: Wed, 6 Nov 2019 00:16:24 +0300
-Subject: [PATCH 3/4] Change path to `caffe2` build dir made by `libtorch`
-
-Setup and use properly `caffe2` build dir made while
-`libtorch` building with CMake, so that it was used
-by the Python installation.
----
- setup.py | 6 +++---
- 1 file changed, 3 insertions(+), 3 deletions(-)
-
-diff --git a/setup.py b/setup.py
-index f4bfdc99cd..60502b6add 100644
---- a/setup.py
-+++ b/setup.py
-@@ -236,7 +236,7 @@ else:
- cwd = os.path.dirname(os.path.abspath(__file__))
- lib_path = os.path.join(cwd, "torch", "lib")
- third_party_path = os.path.join(cwd, "third_party")
--caffe2_build_dir = os.path.join(cwd, "build")
-+caffe2_build_dir = os.environ.get("CMAKE_BUILD_DIR", os.path.join(cwd, "build"))
- # lib/pythonx.x/site-packages
- rel_site_packages = distutils.sysconfig.get_python_lib(prefix='')
- # full absolute path to the dir above
-@@ -279,7 +279,7 @@ elif sha != 'Unknown':
- version += '+' + sha[:7]
- report("Building wheel {}-{}".format(package_name, version))
-
--cmake = CMake()
-+cmake = CMake(caffe2_build_dir)
-
- # all the work we need to do _before_ setup runs
- def build_deps():
-@@ -445,7 +445,7 @@ class build_ext(setuptools.command.build_ext.build_ext):
- filename = self.get_ext_filename(fullname)
- report("\nCopying extension {}".format(ext.name))
-
-- src = os.path.join("torch", rel_site_packages, filename)
-+ src = os.path.join(caffe2_build_dir, filename)
- if not os.path.exists(src):
- report("{} does not exist".format(src))
- del self.extensions[i]
---
-2.23.0
-
diff --git a/sci-libs/pytorch/files/0004-Don-t-fill-rpath-of-Caffe2-library-for-system-wide-i.patch b/sci-libs/pytorch/files/0004-Don-t-fill-rpath-of-Caffe2-library-for-system-wide-i.patch
deleted file mode 100644
index c8f57d9e6..000000000
--- a/sci-libs/pytorch/files/0004-Don-t-fill-rpath-of-Caffe2-library-for-system-wide-i.patch
+++ /dev/null
@@ -1,104 +0,0 @@
-From a0ace7295b6895954d2a0f8d6fe311a34a7c4e85 Mon Sep 17 00:00:00 2001
-From: Alexey Chernov <4ernov@gmail.com>
-Date: Tue, 12 Nov 2019 02:01:36 +0300
-Subject: [PATCH 4/4] Don't fill rpath of Caffe2 library for system-wide
- install
-
-Don't fill in runtime path of Caffe2 library for the case of
-building for system-wide installation.
----
- CMakeLists.txt | 3 +++
- caffe2/CMakeLists.txt | 18 +++++++++++++++---
- cmake/Dependencies.cmake | 19 +++++++++++--------
- 3 files changed, 29 insertions(+), 11 deletions(-)
-
-diff --git a/CMakeLists.txt b/CMakeLists.txt
-index 20923c0544..45a882ae0e 100644
---- a/CMakeLists.txt
-+++ b/CMakeLists.txt
-@@ -193,6 +193,9 @@ option(USE_TBB "Use TBB" OFF)
- # Used when building Caffe2 through setup.py
- option(BUILDING_WITH_TORCH_LIBS "Tell cmake if Caffe2 is being built alongside torch libs" ON)
-
-+# Used when building Caffe2 for further system-wide installation
-+option(BUILDING_SYSTEM_WIDE "Tell cmake if Caffe2 is being built for system-wide installation" OFF)
-+
- # /Z7 override option
- # When generating debug symbols, CMake default to use the flag /Zi.
- # However, it is not compatible with sccache. So we rewrite it off.
-diff --git a/caffe2/CMakeLists.txt b/caffe2/CMakeLists.txt
-index 1f7d037243..30d5615cdb 100644
---- a/caffe2/CMakeLists.txt
-+++ b/caffe2/CMakeLists.txt
-@@ -1235,7 +1235,11 @@ if (BUILD_PYTHON)
- if (MSVC AND BUILD_SHARED_LIBS)
- install(FILES $<TARGET_PDB_FILE:caffe2_pybind11_state> DESTINATION "${PYTHON_LIB_REL_PATH}/caffe2/python" OPTIONAL)
- endif()
-- set_target_properties(caffe2_pybind11_state PROPERTIES INSTALL_RPATH "${caffe2_pybind11_rpath}")
-+ if (NOT BUILDING_SYSTEM_WIDE)
-+ set_target_properties(caffe2_pybind11_state PROPERTIES INSTALL_RPATH "${caffe2_pybind11_rpath}")
-+else()
-+ set_target_properties(caffe2_pybind11_state PROPERTIES SKIP_BUILD_RPATH ON)
-+ endif()
-
- if(USE_CUDA)
- add_library(caffe2_pybind11_state_gpu MODULE ${Caffe2_GPU_PYTHON_SRCS})
-@@ -1261,7 +1265,11 @@ if (BUILD_PYTHON)
- if (MSVC AND BUILD_SHARED_LIBS)
- install(FILES $<TARGET_PDB_FILE:caffe2_pybind11_state_gpu> DESTINATION "${PYTHON_LIB_REL_PATH}/caffe2/python" OPTIONAL)
- endif()
-- set_target_properties(caffe2_pybind11_state_gpu PROPERTIES INSTALL_RPATH "${caffe2_pybind11_rpath}")
-+ if (NOT BUILDING_SYSTEM_WIDE)
-+ set_target_properties(caffe2_pybind11_state_gpu PROPERTIES INSTALL_RPATH "${caffe2_pybind11_rpath}")
-+ else()
-+ set_target_properties(caffe2_pybind11_state_gpu PROPERTIES SKIP_BUILD_RPATH ON)
-+ endif()
- endif()
-
- if(USE_ROCM)
-@@ -1284,7 +1292,11 @@ if (BUILD_PYTHON)
- caffe2_pybind11_state_hip PROPERTIES LIBRARY_OUTPUT_DIRECTORY
- ${CMAKE_BINARY_DIR}/caffe2/python)
- install(TARGETS caffe2_pybind11_state_hip DESTINATION "${PYTHON_LIB_REL_PATH}/caffe2/python")
-- set_target_properties(caffe2_pybind11_state_hip PROPERTIES INSTALL_RPATH "${caffe2_pybind11_rpath}")
-+ if (NOT BUILDING_SYSTEM_WIDE)
-+ set_target_properties(caffe2_pybind11_state_hip PROPERTIES INSTALL_RPATH "${caffe2_pybind11_rpath}")
-+ else()
-+ set_target_properties(caffe2_pybind11_state_hip PROPERTIES SKIP_BUILD_RPATH ON)
-+ endif()
- endif()
-
- if (MSVC AND CMAKE_GENERATOR MATCHES "Visual Studio")
-diff --git a/cmake/Dependencies.cmake b/cmake/Dependencies.cmake
-index a8e9769536..6ef9d7b0e2 100644
---- a/cmake/Dependencies.cmake
-+++ b/cmake/Dependencies.cmake
-@@ -6,14 +6,17 @@ if (APPLE)
- else()
- set(_rpath_portable_origin $ORIGIN)
- endif(APPLE)
--# Use separate rpaths during build and install phases
--set(CMAKE_SKIP_BUILD_RPATH FALSE)
--# Don't use the install-rpath during the build phase
--set(CMAKE_BUILD_WITH_INSTALL_RPATH FALSE)
--set(CMAKE_INSTALL_RPATH "${_rpath_portable_origin}")
--# Automatically add all linked folders that are NOT in the build directory to
--# the rpath (per library?)
--set(CMAKE_INSTALL_RPATH_USE_LINK_PATH TRUE)
-+
-+if (NOT BUILDING_SYSTEM_WIDE)
-+ # Use separate rpaths during build and install phases
-+ set(CMAKE_SKIP_BUILD_RPATH FALSE)
-+ # Don't use the install-rpath during the build phase
-+ set(CMAKE_BUILD_WITH_INSTALL_RPATH FALSE)
-+ set(CMAKE_INSTALL_RPATH "${_rpath_portable_origin}")
-+ # Automatically add all linked folders that are NOT in the build directory to
-+ # the rpath (per library?)
-+ set(CMAKE_INSTALL_RPATH_USE_LINK_PATH TRUE)
-+endif()
-
- # UBSAN triggers when compiling protobuf, so we need to disable it.
- set(UBSAN_FLAG "-fsanitize=undefined")
---
-2.23.0
-
diff --git a/sci-libs/pytorch/files/0005-Change-library-directory-according-to-CMake-build.patch b/sci-libs/pytorch/files/0005-Change-library-directory-according-to-CMake-build.patch
deleted file mode 100644
index 324b8f682..000000000
--- a/sci-libs/pytorch/files/0005-Change-library-directory-according-to-CMake-build.patch
+++ /dev/null
@@ -1,31 +0,0 @@
-From 52019a3f395e5fa97b26d424152d91f73b400f8e Mon Sep 17 00:00:00 2001
-From: Alexey Chernov <4ernov@gmail.com>
-Date: Wed, 13 Nov 2019 23:44:12 +0300
-Subject: [PATCH 5/5] Change library directory according to CMake build
-
-Change `lib_path` in favour of out-of-tree CMake build
-directory, so that all the C++ libraries be found.
----
- setup.py | 5 +++--
- 1 file changed, 3 insertions(+), 2 deletions(-)
-
-diff --git a/setup.py b/setup.py
-index 60502b6add..cbced52192 100644
---- a/setup.py
-+++ b/setup.py
-@@ -234,9 +234,10 @@ else:
-
- # Constant known variables used throughout this file
- cwd = os.path.dirname(os.path.abspath(__file__))
--lib_path = os.path.join(cwd, "torch", "lib")
-+cmake_build_dir = os.environ.get("CMAKE_BUILD_DIR", os.path.join(cwd, "build"))
-+lib_path = os.path.join(cmake_build_dir, "lib")
- third_party_path = os.path.join(cwd, "third_party")
--caffe2_build_dir = os.environ.get("CMAKE_BUILD_DIR", os.path.join(cwd, "build"))
-+caffe2_build_dir = cmake_build_dir
- # lib/pythonx.x/site-packages
- rel_site_packages = distutils.sysconfig.get_python_lib(prefix='')
- # full absolute path to the dir above
---
-2.23.0
-
diff --git a/sci-libs/pytorch/files/0010-Remove-conversion-ambiguity-in-ternary-operators.patch b/sci-libs/pytorch/files/0010-Remove-conversion-ambiguity-in-ternary-operators.patch
deleted file mode 100644
index 49835d201..000000000
--- a/sci-libs/pytorch/files/0010-Remove-conversion-ambiguity-in-ternary-operators.patch
+++ /dev/null
@@ -1,38 +0,0 @@
-From 0f3a0d9a948fdd8481a5f7751a255ecd9ed4d37a Mon Sep 17 00:00:00 2001
-From: Alexey Chernov <4ernov@gmail.com>
-Date: Mon, 20 Jan 2020 01:21:22 +0300
-Subject: [PATCH 3/3] Remove conversion ambiguity in ternary operators
-
-It fails to compile with recent versions of Clang
-(namely, version 10 used behind HCC compiler when
-being built with ROCm support) with the
-`conditional expression is ambiguous` error.
----
- caffe2/operators/relu_op.cu | 4 ++--
- 1 file changed, 2 insertions(+), 2 deletions(-)
-
-diff --git a/caffe2/operators/relu_op.cu b/caffe2/operators/relu_op.cu
-index f6edf7105e..ab49540fc9 100644
---- a/caffe2/operators/relu_op.cu
-+++ b/caffe2/operators/relu_op.cu
-@@ -51,7 +51,7 @@ __global__ void ReluCUDAKernel<half2>(const int N, const half2* X, half2* Y) {
- #else
- const float2 xx = __half22float2(X[i]);
- Y[i] =
-- __floats2half2_rn(xx.x > 0.0f ? xx.x : 0.0f, xx.y > 0.0f ? xx.y : 0.0f);
-+ __floats2half2_rn(xx.x > 0.0f ? float(xx.x) : 0.0f, xx.y > 0.0f ? float(xx.y) : 0.0f);
- #endif
- }
- }
-@@ -101,7 +101,7 @@ __global__ void ReluGradientCUDAKernel<half2>(
- const float2 dy = __half22float2(dY[i]);
- const float2 yy = __half22float2(Y[i]);
- dX[i] =
-- __floats2half2_rn(yy.x > 0.0f ? dy.x : 0.0f, yy.y > 0.0f ? dy.y : 0.0f);
-+ __floats2half2_rn(yy.x > 0.0f ? float(dy.x) : 0.0f, yy.y > 0.0f ? float(dy.y) : 0.0f);
- #endif
- }
- }
---
-2.24.1
-
diff --git a/sci-libs/pytorch/files/get_third_parties b/sci-libs/pytorch/files/get_third_parties
deleted file mode 100644
index 8c38a9b73..000000000
--- a/sci-libs/pytorch/files/get_third_parties
+++ /dev/null
@@ -1,20 +0,0 @@
-#!/bin/bash
-
-path_url() {
- local dir=$(dirname $1)/
- git config --file $1 --get-regexp '(path|url)' | sed -r -e "N;s,[^ ]* ([^ ]*)\n[^ ]* ([^ ]*),${dir#./}\1 \2,"
-}
-
-join \
- <(for gm in $(find . -name '.gitmodules' | sort -r); do path_url $gm; done | sort -u) \
- <(git submodule status --recursive | awk '{print $2 " " $1}' | sort -u) | \
-while read path url hash; do
- [[ ${path} =~ (eigen|six|ios|neon2sse|protobuf|pybind11|python-enum|tbb|zstd|fbjni) ]] && continue
- u=${url%.git}
- hfull=${hash#-}
- h=${hfull:0:8}
- p=$(basename $u)
- echo "${u}/archive/${h}.tar.gz -> ${p}-${h}.tar.gz" >> SRC_URI
- [[ $p = fbgemm ]] && p=${p^^}
- echo "rmdir ${path} && ln -sv \"\${WORKDIR}\"/${p}-${hfull} ${path}" >> src_prepare
-done
diff --git a/sci-libs/pytorch/files/pytorch-1.10.0-clhpp2.patch b/sci-libs/pytorch/files/pytorch-1.10.0-clhpp2.patch
deleted file mode 100644
index 9c267dc6e..000000000
--- a/sci-libs/pytorch/files/pytorch-1.10.0-clhpp2.patch
+++ /dev/null
@@ -1,52 +0,0 @@
-diff --git a/caffe2/contrib/opencl/OpenCL/cl.hpp b/caffe2/contrib/opencl/OpenCL/cl.hpp
-index 87cc4a1..7c27e33 100644
---- a/caffe2/contrib/opencl/OpenCL/cl.hpp
-+++ b/caffe2/contrib/opencl/OpenCL/cl.hpp
-@@ -76,7 +76,7 @@
- * #if defined(__APPLE__) || defined(__MACOSX)
- * #include <OpenCL/cl.hpp>
- * #else
-- * #include <CL/cl.hpp>
-+ * #include <CL/cl2.hpp>
- * #endif
- * #include <cstdio>
- * #include <cstdlib>
-diff --git a/caffe2/contrib/opencl/context.h b/caffe2/contrib/opencl/context.h
-index b1e61c2..968d3c7 100644
---- a/caffe2/contrib/opencl/context.h
-+++ b/caffe2/contrib/opencl/context.h
-@@ -11,7 +11,7 @@
- #if defined(__APPLE__) || defined(__MACOSX)
- #include <OpenCL/cl.hpp>
- #else
--#include <CL/cl.hpp>
-+#include <CL/cl2.hpp>
- #endif
-
- #define OPENCL_CHECK(expr) (void)expr
-diff --git a/caffe2/mobile/contrib/libopencl-stub/include/CL/cl.hpp b/caffe2/mobile/contrib/libopencl-stub/include/CL/cl.hpp
-index f3badf7..928c9f0 100644
---- a/caffe2/mobile/contrib/libopencl-stub/include/CL/cl.hpp
-+++ b/caffe2/mobile/contrib/libopencl-stub/include/CL/cl.hpp
-@@ -76,7 +76,7 @@
- * #if defined(__APPLE__) || defined(__MACOSX)
- * #include <OpenCL/cl.hpp>
- * #else
-- * #include <CL/cl.hpp>
-+ * #include <CL/cl2.hpp>
- * #endif
- * #include <cstdio>
- * #include <cstdlib>
-diff --git a/third_party/tensorflow_cuda_bazel_build/cuda/BUILD b/third_party/tensorflow_cuda_bazel_build/cuda/BUILD
-index f7271af..334f4ec 100755
---- a/third_party/tensorflow_cuda_bazel_build/cuda/BUILD
-+++ b/third_party/tensorflow_cuda_bazel_build/cuda/BUILD
-@@ -188,7 +188,7 @@ CUDA_INCLUDES_FILES = [
- "include/CL/cl_gl_ext.h",
- "include/CL/cl_gl.h",
- "include/CL/cl.h",
-- "include/CL/cl.hpp",
-+ "include/CL/cl2.hpp",
- "include/CL/cl_platform.h",
- "include/CL/opencl.h",
- "include/common_functions.h",
diff --git a/sci-libs/pytorch/files/pytorch-1.10.0-fix-distutils.patch b/sci-libs/pytorch/files/pytorch-1.10.0-fix-distutils.patch
deleted file mode 100644
index 334bcda6f..000000000
--- a/sci-libs/pytorch/files/pytorch-1.10.0-fix-distutils.patch
+++ /dev/null
@@ -1,93 +0,0 @@
-This fix distutils-r1_src_install failure with setuptools-59
-
-From 9af2edb158b3603c44eff6e12896f1d215e8b898 Mon Sep 17 00:00:00 2001
-From: Nikita Shulga <nshulga@fb.com>
-Date: Tue, 14 Dec 2021 07:15:34 -0800
-Subject: [PATCH] Properly import LooseVersion
-
-This fixes regression introduced by https://github.com/pytorch/pytorch/pull/57040
-
-Somehow importing `distutils` from `setuptool` caused import of
-`distutils.versions`, which is not a documented dependency and got
-change with the release of
-[setuptools-59.6.0](https://github.com/pypa/setuptools/tree/v59.6.0)
-We should not rely on that, as
-`import distutils` never re-imports `distutils.version`, which one can
-see by observing
-https://github.com/python/cpython/blob/3.9/Lib/distutils/__init__.py
-or by running:
-```
-% python3 -c "import distutils;print(distutils.__version__, dir(distutils))"
-3.7.5 ['__builtins__', '__cached__', '__doc__', '__file__', '__loader__', '__name__', '__package__', '__path__', '__spec__', '__version__', 'sys']
-% python3 -c "from setuptools import distutils;print(distutils.__version__, dir(distutils))"
-3.7.5 ['__builtins__', '__cached__', '__doc__', '__file__', '__loader__', '__name__', '__package__', '__path__', '__spec__', '__version__', 'archive_util', 'ccompiler', 'cmd', 'config', 'core', 'debug', 'dep_util', 'dir_util', 'dist', 'errors', 'extension', 'fancy_getopt', 'file_util', 'filelist', 'log', 'spawn', 'sys', 'sysconfig', 'util', 'version']
-```
----
- test/run_test.py | 4 ++--
- tools/setup_helpers/cmake.py | 8 ++++----
- torch/testing/_internal/common_methods_invocations.py | 8 ++++----
- 3 files changed, 10 insertions(+), 10 deletions(-)
-
-diff --git a/tools/setup_helpers/cmake.py b/tools/setup_helpers/cmake.py
-index 01e87b4bca879..686b5c4a34f4c 100644
---- a/tools/setup_helpers/cmake.py
-+++ b/tools/setup_helpers/cmake.py
-@@ -8,7 +8,7 @@
- from subprocess import check_call, check_output, CalledProcessError
- import sys
- import sysconfig
--from setuptools import distutils # type: ignore[import]
-+from distutils.version import LooseVersion
- from typing import IO, Any, Dict, List, Optional, Union, cast
-
- from . import which
-@@ -120,10 +120,10 @@ def _get_cmake_command() -> str:
- return cmake_command
- cmake3 = which('cmake3')
- cmake = which('cmake')
-- if cmake3 is not None and CMake._get_version(cmake3) >= distutils.version.LooseVersion("3.10.0"):
-+ if cmake3 is not None and CMake._get_version(cmake3) >= LooseVersion("3.10.0"):
- cmake_command = 'cmake3'
- return cmake_command
-- elif cmake is not None and CMake._get_version(cmake) >= distutils.version.LooseVersion("3.10.0"):
-+ elif cmake is not None and CMake._get_version(cmake) >= LooseVersion("3.10.0"):
- return cmake_command
- else:
- raise RuntimeError('no cmake or cmake3 with version >= 3.10.0 found')
-@@ -134,7 +134,7 @@ def _get_version(cmd: str) -> Any:
-
- for line in check_output([cmd, '--version']).decode('utf-8').split('\n'):
- if 'version' in line:
-- return distutils.version.LooseVersion(line.strip().split(' ')[2])
-+ return LooseVersion(line.strip().split(' ')[2])
- raise RuntimeError('no version found')
-
- def run(self, args: List[str], env: Dict[str, str]) -> None:
-diff --git a/torch/testing/_internal/common_methods_invocations.py b/torch/testing/_internal/common_methods_invocations.py
-index b66e6470b590c..6ec77c2b0ce2e 100644
---- a/torch/testing/_internal/common_methods_invocations.py
-+++ b/torch/testing/_internal/common_methods_invocations.py
-@@ -40,7 +40,7 @@
- freeze_rng_state)
- import torch.testing._internal.opinfo_helper as opinfo_helper
-
--from setuptools import distutils
-+from distutils.version import LooseVersion
-
- has_scipy_fft = False
- if TEST_SCIPY:
-@@ -14008,11 +14008,11 @@ def ref_pairwise_distance(input1, input2):
- skips=(
- # Reference: https://github.com/pytorch/pytorch/pull/49155#issuecomment-742664611
- DecorateInfo(unittest.skip("Skipped!"), 'TestUnaryUfuncs', 'test_reference_numerics_extremal',
-- active_if=TEST_SCIPY and distutils.version.LooseVersion(scipy.__version__) < "1.4.0"),
-+ active_if=TEST_SCIPY and LooseVersion(scipy.__version__) < "1.4.0"),
- DecorateInfo(unittest.skip("Skipped!"), 'TestUnaryUfuncs', 'test_reference_numerics_hard',
-- active_if=TEST_SCIPY and distutils.version.LooseVersion(scipy.__version__) < "1.4.0"),
-+ active_if=TEST_SCIPY and LooseVersion(scipy.__version__) < "1.4.0"),
- DecorateInfo(unittest.skip("Skipped!"), 'TestUnaryUfuncs', 'test_reference_numerics_normal',
-- active_if=TEST_SCIPY and distutils.version.LooseVersion(scipy.__version__) < "1.4.0"),
-+ active_if=TEST_SCIPY and LooseVersion(scipy.__version__) < "1.4.0"),
- )),
- UnaryUfuncInfo('lgamma',
- ref=reference_lgamma if TEST_SCIPY else _NOTHING,
diff --git a/sci-libs/pytorch/files/pytorch-1.10.0-nonull.patch b/sci-libs/pytorch/files/pytorch-1.10.0-nonull.patch
deleted file mode 100644
index adc258556..000000000
--- a/sci-libs/pytorch/files/pytorch-1.10.0-nonull.patch
+++ /dev/null
@@ -1,12 +0,0 @@
---- a/torch/csrc/jit/frontend/ir_emitter.cpp 2021-10-15 05:35:23.000000000 +0400
-+++ b/torch/csrc/jit/frontend/ir_emitter.cpp 2021-10-15 05:35:23.000000000 +0400
-@@ -1678,7 +1678,7 @@
- << "Union type annotation `" << type_hint->repr_str()
- << "` can hold " << vector_repr.str() << ", but none of "
- << "those list types can hold the types of the given dict"
-- << " elements, which were unified to " << candidate->repr_str();
-+ << " elements, which were unified";
- } else {
- refined_type_hint = candidate;
- }
-
diff --git a/sci-libs/pytorch/files/pytorch-1.10.1-nccl-nvccflags.patch b/sci-libs/pytorch/files/pytorch-1.10.1-nccl-nvccflags.patch
deleted file mode 100644
index 0ac12a1e7..000000000
--- a/sci-libs/pytorch/files/pytorch-1.10.1-nccl-nvccflags.patch
+++ /dev/null
@@ -1,37 +0,0 @@
-From 7b04cd503fa1a6265893e0320ee246bcc0bd98cf Mon Sep 17 00:00:00 2001
-From: Miezhiko <Miezhiko@gmail.com>
-Date: Mon, 27 Dec 2021 14:48:12 +0400
-Subject: [PATCH] neutral flags
-
----
- makefiles/common.mk | 10 +---------
- 1 file changed, 1 insertion(+), 9 deletions(-)
-
-diff --git a/makefiles/common.mk b/makefiles/common.mk
-index 64f8d2dc6..7a979c90f 100644
---- a/makefiles/common.mk
-+++ b/makefiles/common.mk
-@@ -55,7 +55,7 @@ CXXFLAGS := -DCUDA_MAJOR=$(CUDA_MAJOR) -DCUDA_MINOR=$(CUDA_MINOR) -fPIC -fvisi
- # Maxrregcount needs to be set accordingly to NCCL_MAX_NTHREADS (otherwise it will cause kernel launch errors)
- # 512 : 120, 640 : 96, 768 : 80, 1024 : 60
- # We would not have to set this if we used __launch_bounds__, but this only works on kernels, not on functions.
--NVCUFLAGS := -ccbin $(CXX) $(NVCC_GENCODE) -std=c++11 --expt-extended-lambda -Xptxas -maxrregcount=96 -Xfatbin -compress-all
-+NVCUFLAGS := $(NVCCFLAGS) $(NVCC_GENCODE) -std=c++11 --expt-extended-lambda -Xptxas -maxrregcount=96 -Xfatbin -compress-all
- # Use addprefix so that we can specify more than one path
- NVLDFLAGS := -L${CUDA_LIB} -lcudart -lrt
-
-@@ -69,14 +69,6 @@ NVLDFLAGS += ${GCOV_FLAGS:%=-Xcompiler %}
- # $(warning GCOV_FLAGS=${GCOV_FLAGS})
- ########## GCOV ##########
-
--ifeq ($(DEBUG), 0)
--NVCUFLAGS += -O3
--CXXFLAGS += -O3 -g
--else
--NVCUFLAGS += -O0 -G -g
--CXXFLAGS += -O0 -g -ggdb3
--endif
--
- ifneq ($(VERBOSE), 0)
- NVCUFLAGS += -Xptxas -v -Xcompiler -Wall,-Wextra,-Wno-unused-parameter
- CXXFLAGS += -Wall -Wextra
diff --git a/sci-libs/pytorch/files/pytorch-1.2.0-setup.patch b/sci-libs/pytorch/files/pytorch-1.2.0-setup.patch
deleted file mode 100644
index 85e796a60..000000000
--- a/sci-libs/pytorch/files/pytorch-1.2.0-setup.patch
+++ /dev/null
@@ -1,24 +0,0 @@
-Index: pytorch-1.4.0_p0/setup.py
-===================================================================
---- pytorch-1.4.0_p0.orig/setup.py
-+++ pytorch-1.4.0_p0/setup.py
-@@ -288,9 +288,7 @@ def build_deps():
- sys.exit(1)
-
- check_file(os.path.join(third_party_path, "gloo", "CMakeLists.txt"))
-- check_file(os.path.join(third_party_path, "pybind11", "CMakeLists.txt"))
- check_file(os.path.join(third_party_path, 'cpuinfo', 'CMakeLists.txt'))
-- check_file(os.path.join(third_party_path, 'tbb', 'Makefile'))
- check_file(os.path.join(third_party_path, 'onnx', 'CMakeLists.txt'))
- check_file(os.path.join(third_party_path, 'foxi', 'CMakeLists.txt'))
- check_file(os.path.join(third_party_path, 'QNNPACK', 'CMakeLists.txt'))
-@@ -341,9 +339,6 @@ def build_deps():
- if not same:
- shutil.copyfile(orig_file, sym_file)
-
-- dir_util.copy_tree('third_party/pybind11/include/pybind11/',
-- 'torch/include/pybind11')
--
- ################################################################################
- # Building dependent libraries
- ################################################################################
diff --git a/sci-libs/pytorch/files/pytorch-1.4.0-nccl-nvccflags.patch b/sci-libs/pytorch/files/pytorch-1.4.0-nccl-nvccflags.patch
deleted file mode 100644
index 165e79dd4..000000000
--- a/sci-libs/pytorch/files/pytorch-1.4.0-nccl-nvccflags.patch
+++ /dev/null
@@ -1,28 +0,0 @@
-Index: nccl-7c72dee660e4d055b81721dd6b03e4e1c0a983cf/makefiles/common.mk
-===================================================================
---- nccl-7c72dee660e4d055b81721dd6b03e4e1c0a983cf.orig/makefiles/common.mk
-+++ nccl-7c72dee660e4d055b81721dd6b03e4e1c0a983cf/makefiles/common.mk
-@@ -46,7 +46,7 @@ endif
- CXXFLAGS := -DCUDA_MAJOR=$(CUDA_MAJOR) -DCUDA_MINOR=$(CUDA_MINOR) -fPIC -fvisibility=hidden
- CXXFLAGS += -Wall -Wno-unused-function -Wno-sign-compare -std=c++11 -Wvla
- CXXFLAGS += -I $(CUDA_INC)
--NVCUFLAGS := -ccbin $(CXX) $(NVCC_GENCODE) -lineinfo -std=c++11 -Xptxas -maxrregcount=96 -Xfatbin -compress-all
-+NVCUFLAGS := $(NVCCFLAGS) $(NVCC_GENCODE) -lineinfo -std=c++11 -Xptxas -maxrregcount=96 -Xfatbin -compress-all
- # Use addprefix so that we can specify more than one path
- NVLDFLAGS := -L${CUDA_LIB} -lcudart -lrt
-
-@@ -60,14 +60,6 @@ NVLDFLAGS += ${GCOV_FLAGS:%=-Xcompiler
- # $(warning GCOV_FLAGS=${GCOV_FLAGS})
- ########## GCOV ##########
-
--ifeq ($(DEBUG), 0)
--NVCUFLAGS += -O3
--CXXFLAGS += -O3 -g
--else
--NVCUFLAGS += -O0 -G -g
--CXXFLAGS += -O0 -g -ggdb3
--endif
--
- ifneq ($(VERBOSE), 0)
- NVCUFLAGS += -Xptxas -v -Xcompiler -Wall,-Wextra,-Wno-unused-parameter
- CXXFLAGS += -Wall -Wextra
diff --git a/sci-libs/pytorch/files/pytorch-1.4.0-skip-tests.patch b/sci-libs/pytorch/files/pytorch-1.4.0-skip-tests.patch
deleted file mode 100644
index 3682469d7..000000000
--- a/sci-libs/pytorch/files/pytorch-1.4.0-skip-tests.patch
+++ /dev/null
@@ -1,28 +0,0 @@
-Disable expected test failures.
-
-TCPStoreTest is too slow to run.
-
-Reference: https://github.com/pytorch/pytorch/issues/13746
-Reference: https://github.com/pytorch/pytorch/issues/21873
-
-Index: pytorch-1.4.0_p0/torch/lib/c10d/test/CMakeLists.txt
-===================================================================
---- pytorch-1.4.0_p0.orig/torch/lib/c10d/test/CMakeLists.txt
-+++ pytorch-1.4.0_p0/torch/lib/c10d/test/CMakeLists.txt
-@@ -14,7 +14,6 @@ function(c10d_add_test test_src)
- endfunction()
-
- c10d_add_test(FileStoreTest.cpp c10d)
--c10d_add_test(TCPStoreTest.cpp c10d)
-
- if(USE_CUDA)
- if(USE_C10D_GLOO)
-Index: pytorch-1.4.0_p0/caffe2/share/contrib/depthwise/CMakeLists.txt
-===================================================================
---- pytorch-1.4.0_p0.orig/caffe2/share/contrib/depthwise/CMakeLists.txt
-+++ pytorch-1.4.0_p0/caffe2/share/contrib/depthwise/CMakeLists.txt
-@@ -6,4 +6,3 @@ set(Caffe2_CONTRIB_DEPTHWISE3x3_TEST_CPU
- )
-
- set(Caffe2_CPU_SRCS ${Caffe2_CPU_SRCS} ${Caffe2_CONTRIB_DEPTHWISE3x3_CPU_SRC} PARENT_SCOPE)
--set(Caffe2_CPU_TEST_SRCS ${Caffe2_CPU_TEST_SRCS} ${Caffe2_CONTRIB_DEPTHWISE3x3_TEST_CPU_SRC} PARENT_SCOPE)
diff --git a/sci-libs/pytorch/files/pytorch-1.4.0-sleef.patch b/sci-libs/pytorch/files/pytorch-1.4.0-sleef.patch
deleted file mode 100644
index 222a0f73e..000000000
--- a/sci-libs/pytorch/files/pytorch-1.4.0-sleef.patch
+++ /dev/null
@@ -1,15 +0,0 @@
-Give the location of sleef.h.
-
-Reference: https://github.com/pytorch/pytorch/issues/26555
-Index: pytorch-1.4.0/caffe2/CMakeLists.txt
-===================================================================
---- pytorch-1.4.0.orig/caffe2/CMakeLists.txt
-+++ pytorch-1.4.0/caffe2/CMakeLists.txt
-@@ -1062,6 +1062,7 @@ if (BUILD_TEST)
- add_executable(${test_name} "${test_src}")
- target_link_libraries(${test_name} ${Caffe2_MAIN_LIBS} gtest_main)
- target_include_directories(${test_name} PRIVATE $<INSTALL_INTERFACE:include>)
-+ target_include_directories(${test_name} PRIVATE $<BUILD_INTERFACE:${CMAKE_BINARY_DIR}/include>)
- target_include_directories(${test_name} PRIVATE ${Caffe2_CPU_INCLUDE})
- add_test(NAME ${test_name} COMMAND $<TARGET_FILE:${test_name}>)
- if (INSTALL_TEST)
diff --git a/sci-libs/pytorch/files/pytorch-1.6.0-global-dlopen.patch b/sci-libs/pytorch/files/pytorch-1.6.0-global-dlopen.patch
deleted file mode 100644
index 1e9388ff1..000000000
--- a/sci-libs/pytorch/files/pytorch-1.6.0-global-dlopen.patch
+++ /dev/null
@@ -1,15 +0,0 @@
-Don't hardcode the library path. Leave it to the dynamic loader.
-
-Index: pytorch-1.6.0/torch/__init__.py
-===================================================================
---- pytorch-1.6.0.orig/torch/__init__.py
-+++ pytorch-1.6.0/torch/__init__.py
-@@ -138,7 +138,7 @@ def _load_global_deps():
- here = os.path.abspath(__file__)
- lib_path = os.path.join(os.path.dirname(here), 'lib', lib_name)
-
-- ctypes.CDLL(lib_path, mode=ctypes.RTLD_GLOBAL)
-+ ctypes.CDLL(lib_name, mode=ctypes.RTLD_GLOBAL)
-
-
- if (USE_RTLD_GLOBAL_WITH_LIBTORCH or os.getenv('TORCH_USE_RTLD_GLOBAL')) and \
diff --git a/sci-libs/pytorch/files/pytorch-1.6.0-nccl-nvccflags.patch b/sci-libs/pytorch/files/pytorch-1.6.0-nccl-nvccflags.patch
deleted file mode 100644
index 052474ee4..000000000
--- a/sci-libs/pytorch/files/pytorch-1.6.0-nccl-nvccflags.patch
+++ /dev/null
@@ -1,27 +0,0 @@
-diff -uprN nccl-5949d96f36d050e59d05872f8bbffd2549318e95/makefiles/common.mk nccl-patched/makefiles/common.mk
---- nccl-5949d96f36d050e59d05872f8bbffd2549318e95/makefiles/common.mk 2020-06-09 00:31:44.000000000 +0800
-+++ nccl-patched/makefiles/common.mk 2020-08-06 21:25:57.784279738 +0800
-@@ -54,7 +54,7 @@ CXXFLAGS := -DCUDA_MAJOR=$(CUDA_MAJOR)
- # Maxrregcount needs to be set accordingly to NCCL_MAX_NTHREADS (otherwise it will cause kernel launch errors)
- # 512 : 120, 640 : 96, 768 : 80, 1024 : 60
- # We would not have to set this if we used __launch_bounds__, but this only works on kernels, not on functions.
--NVCUFLAGS := -ccbin $(CXX) $(NVCC_GENCODE) -std=c++11 -Xptxas -maxrregcount=96 -Xfatbin -compress-all
-+NVCUFLAGS := $(NVCCFLAGS) $(NVCC_GENCODE) -std=c++11 -Xptxas -maxrregcount=96 -Xfatbin -compress-all
- # Use addprefix so that we can specify more than one path
- NVLDFLAGS := -L${CUDA_LIB} -lcudart -lrt
-
-@@ -68,14 +68,6 @@ NVLDFLAGS += ${GCOV_FLAGS:%=-Xcompiler
- # $(warning GCOV_FLAGS=${GCOV_FLAGS})
- ########## GCOV ##########
-
--ifeq ($(DEBUG), 0)
--NVCUFLAGS += -O3
--CXXFLAGS += -O3 -g
--else
--NVCUFLAGS += -O0 -G -g
--CXXFLAGS += -O0 -g -ggdb3
--endif
--
- ifneq ($(VERBOSE), 0)
- NVCUFLAGS += -Xptxas -v -Xcompiler -Wall,-Wextra,-Wno-unused-parameter
- CXXFLAGS += -Wall -Wextra
diff --git a/sci-libs/pytorch/files/pytorch-1.6.0-setup.patch b/sci-libs/pytorch/files/pytorch-1.6.0-setup.patch
deleted file mode 100644
index 6a197a907..000000000
--- a/sci-libs/pytorch/files/pytorch-1.6.0-setup.patch
+++ /dev/null
@@ -1,14 +0,0 @@
-Index: pytorch-1.4.0_p0/setup.py
-===================================================================
---- pytorch-1.4.0_p0.orig/setup.py
-+++ pytorch-1.4.0_p0/setup.py
-@@ -288,9 +288,7 @@ def build_deps():
- sys.exit(1)
-
- check_file(os.path.join(third_party_path, "gloo", "CMakeLists.txt"))
-- check_file(os.path.join(third_party_path, "pybind11", "CMakeLists.txt"))
- check_file(os.path.join(third_party_path, 'cpuinfo', 'CMakeLists.txt'))
-- check_file(os.path.join(third_party_path, 'tbb', 'Makefile'))
- check_file(os.path.join(third_party_path, 'onnx', 'CMakeLists.txt'))
- check_file(os.path.join(third_party_path, 'foxi', 'CMakeLists.txt'))
- check_file(os.path.join(third_party_path, 'QNNPACK', 'CMakeLists.txt'))
diff --git a/sci-libs/pytorch/files/pytorch-1.6.0-skip-tests.patch b/sci-libs/pytorch/files/pytorch-1.6.0-skip-tests.patch
deleted file mode 100644
index 3ef2c533f..000000000
--- a/sci-libs/pytorch/files/pytorch-1.6.0-skip-tests.patch
+++ /dev/null
@@ -1,14 +0,0 @@
-Disable expected test failures.
-
-Reference: https://github.com/pytorch/pytorch/issues/13746
-Reference: https://github.com/pytorch/pytorch/issues/21873
-
-Index: pytorch-1.4.0_p0/caffe2/share/contrib/depthwise/CMakeLists.txt
-===================================================================
---- pytorch-1.4.0_p0.orig/caffe2/share/contrib/depthwise/CMakeLists.txt
-+++ pytorch-1.4.0_p0/caffe2/share/contrib/depthwise/CMakeLists.txt
-@@ -6,4 +6,3 @@ set(Caffe2_CONTRIB_DEPTHWISE3x3_TEST_CPU
- )
-
- set(Caffe2_CPU_SRCS ${Caffe2_CPU_SRCS} ${Caffe2_CONTRIB_DEPTHWISE3x3_CPU_SRC} PARENT_SCOPE)
--set(Caffe2_CPU_TEST_SRCS ${Caffe2_CPU_TEST_SRCS} ${Caffe2_CONTRIB_DEPTHWISE3x3_TEST_CPU_SRC} PARENT_SCOPE)
diff --git a/sci-libs/pytorch/files/pytorch-1.6.0-tensorpipe-unbundle-libuv.patch b/sci-libs/pytorch/files/pytorch-1.6.0-tensorpipe-unbundle-libuv.patch
deleted file mode 100644
index a4ba38322..000000000
--- a/sci-libs/pytorch/files/pytorch-1.6.0-tensorpipe-unbundle-libuv.patch
+++ /dev/null
@@ -1,13 +0,0 @@
-Index: tensorpipe/cmake/pytorch.cmake
-===================================================================
---- tensorpipe.orig/cmake/pytorch.cmake
-+++ tensorpipe/cmake/pytorch.cmake
-@@ -138,7 +138,7 @@ endif()
-
- add_library(tensorpipe ${TENSORPIPE_SRC})
-
--set(TP_BUILD_LIBUV ON)
-+set(TP_BUILD_LIBUV OFF)
- find_package(uv REQUIRED)
- target_link_libraries(tensorpipe PRIVATE uv::uv)
-
diff --git a/sci-libs/pytorch/files/pytorch-1.7.1-no-rpath.patch b/sci-libs/pytorch/files/pytorch-1.7.1-no-rpath.patch
deleted file mode 100644
index eabda092e..000000000
--- a/sci-libs/pytorch/files/pytorch-1.7.1-no-rpath.patch
+++ /dev/null
@@ -1,12 +0,0 @@
-diff --git a/cmake/Dependencies.cmake b/cmake/Dependencies.cmake
-index b3a892cf88..2c8622870c 100644
---- a/cmake/Dependencies.cmake
-+++ b/cmake/Dependencies.cmake
-@@ -4,7 +4,6 @@ if(APPLE)
- set(CMAKE_MACOSX_RPATH ON)
- set(_rpath_portable_origin "@loader_path")
- else()
-- set(_rpath_portable_origin $ORIGIN)
- endif(APPLE)
- # Use separate rpaths during build and install phases
- set(CMAKE_SKIP_BUILD_RPATH FALSE)
diff --git a/sci-libs/pytorch/files/pytorch-1.7.1-setup.patch b/sci-libs/pytorch/files/pytorch-1.7.1-setup.patch
deleted file mode 100644
index 28db5692c..000000000
--- a/sci-libs/pytorch/files/pytorch-1.7.1-setup.patch
+++ /dev/null
@@ -1,12 +0,0 @@
-diff --git a/setup.py b/setup.py
-index 2db381644c..01a2e57aea 100644
---- a/setup.py
-+++ b/setup.py
-@@ -294,7 +294,6 @@ def build_deps():
-
- check_file(os.path.join(third_party_path, "gloo", "CMakeLists.txt"))
- check_file(os.path.join(third_party_path, 'cpuinfo', 'CMakeLists.txt'))
-- check_file(os.path.join(third_party_path, 'tbb', 'Makefile'))
- check_file(os.path.join(third_party_path, 'onnx', 'CMakeLists.txt'))
- check_file(os.path.join(third_party_path, 'foxi', 'CMakeLists.txt'))
- check_file(os.path.join(third_party_path, 'QNNPACK', 'CMakeLists.txt'))
diff --git a/sci-libs/pytorch/files/pytorch-1.7.1-tensorpipe-unbundle-libuv.patch b/sci-libs/pytorch/files/pytorch-1.7.1-tensorpipe-unbundle-libuv.patch
deleted file mode 100644
index 960ae3618..000000000
--- a/sci-libs/pytorch/files/pytorch-1.7.1-tensorpipe-unbundle-libuv.patch
+++ /dev/null
@@ -1,12 +0,0 @@
-diff --git a/cmake/Dependencies.cmake b/cmake/Dependencies.cmake
-index d1e4bdaed6..85821a78df 100644
---- a/cmake/Dependencies.cmake
-+++ b/cmake/Dependencies.cmake
-@@ -1308,7 +1308,6 @@ if(USE_DISTRIBUTED AND USE_TENSORPIPE)
- if(MSVC)
- message(WARNING "Tensorpipe cannot be used on Windows.")
- else()
-- set(TP_BUILD_LIBUV ON CACHE BOOL "" FORCE)
- set(TP_ENABLE_SHM OFF CACHE BOOL "" FORCE)
- set(TP_ENABLE_CMA OFF CACHE BOOL "" FORCE)
- set(TP_STATIC_OR_SHARED STATIC CACHE STRING "" FORCE)
diff --git a/sci-libs/pytorch/files/pytorch-1.7.1-torch_shm_manager.patch b/sci-libs/pytorch/files/pytorch-1.7.1-torch_shm_manager.patch
deleted file mode 100644
index 44b27cac3..000000000
--- a/sci-libs/pytorch/files/pytorch-1.7.1-torch_shm_manager.patch
+++ /dev/null
@@ -1,13 +0,0 @@
-diff --git a/torch/__init__.py b/torch/__init__.py
-index 03f6eca622..297fb169a4 100644
---- a/torch/__init__.py
-+++ b/torch/__init__.py
-@@ -412,7 +412,7 @@ def manager_path():
-
-
- # Shared memory manager needs to know the exact location of manager executable
--_C._initExtension(manager_path())
-+_C._initExtension(b"@GENTOO_PORTAGE_EPREFIX@/usr/bin/torch_shm_manager")
- del manager_path
-
- # Appease the type checker: it can't deal with direct setting of globals().
diff --git a/sci-libs/pytorch/files/pytorch-1.9.0-Change-library-directory-according-to-CMake-build.patch b/sci-libs/pytorch/files/pytorch-1.9.0-Change-library-directory-according-to-CMake-build.patch
deleted file mode 100644
index 214267487..000000000
--- a/sci-libs/pytorch/files/pytorch-1.9.0-Change-library-directory-according-to-CMake-build.patch
+++ /dev/null
@@ -1,32 +0,0 @@
-From 52019a3f395e5fa97b26d424152d91f73b400f8e Mon Sep 17 00:00:00 2001
-From: Alexey Chernov <4ernov@gmail.com>
-Date: Wed, 13 Nov 2019 23:44:12 +0300
-Subject: [PATCH 5/5] Change library directory according to CMake build
-Modified: Tue, 03 Aug 2021, fit for pytorch-1.9.0
-
-Change `lib_path` in favour of out-of-tree CMake build
-directory, so that all the C++ libraries be found.
----
- setup.py | 5 +++--
- 1 file changed, 3 insertions(+), 2 deletions(-)
-
-diff --git a/setup.py b/setup.py
-index 60502b6add..cbced52192 100644
---- a/setup.py
-+++ b/setup.py
-@@ -268,9 +268,10 @@ else:
-
- # Constant known variables used throughout this file
- cwd = os.path.dirname(os.path.abspath(__file__))
--lib_path = os.path.join(cwd, "torch", "lib")
-+cmake_build_dir = os.environ.get("CMAKE_BUILD_DIR", os.path.join(cwd, "build"))
-+lib_path = os.path.join(cmake_build_dir, "lib")
- third_party_path = os.path.join(cwd, "third_party")
--caffe2_build_dir = os.path.join(cwd, "build")
-+caffe2_build_dir = cmake_build_dir
-
- # CMAKE: full path to python library
- if IS_WINDOWS:
---
-2.23.0
-
diff --git a/sci-libs/pytorch/files/pytorch-1.9.1-fix-wrong-hipify.patch b/sci-libs/pytorch/files/pytorch-1.9.1-fix-wrong-hipify.patch
deleted file mode 100644
index 4e37acd3f..000000000
--- a/sci-libs/pytorch/files/pytorch-1.9.1-fix-wrong-hipify.patch
+++ /dev/null
@@ -1,13 +0,0 @@
-The hipify misadd a ) and causes compilation error
-
---- orig/aten/src/ATen/native/sparse/hip/SparseHIPTensor.hip
-+++ pytorch-1.9.1/aten/src/ATen/native/sparse/hip/SparseHIPTensor.hip
-@@ -282,7 +282,7 @@ Tensor sparse_mask_helper_cuda(
- mask_indices_ti,
- t_indices_pos_ti,
- t_values_ti,
-- r_values_ti);
-+ r_values_ti;
- C10_HIP_KERNEL_LAUNCH_CHECK();
- });
- }
diff --git a/sci-libs/pytorch/metadata.xml b/sci-libs/pytorch/metadata.xml
deleted file mode 100644
index df07ea4be..000000000
--- a/sci-libs/pytorch/metadata.xml
+++ /dev/null
@@ -1,34 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <maintainer type="person">
- <email>4ernov@gmail.com</email>
- <name>Alexey Chernov</name>
- </maintainer>
- <maintainer type="person">
- <email>heroxbd@gentoo.org</email>
- <name>Benda Xu</name>
- </maintainer>
- <use>
- <flag name="asan">Build with address sanitizer (ASAN)</flag>
- <flag name="cuda">Enable support for nVidia CUDA</flag>
- <flag name="fbgemm">Enable FBGEMM (Facebook GEneral Matrix Multiplication) support</flag>
- <flag name="gflags">Build with gflags</flag>
- <flag name="glog">Build with glog support</flag>
- <flag name="gloo">Build gloo distributed communication backend support</flag>
- <flag name="leveldb">Enable support for LevelDB</flag>
- <flag name="lmdb">Enable support for LMDB</flag>
- <flag name="mkldnn">Build with Intel MKL-DNN support</flag>
- <flag name="namedtensor">Enable support for named tensors</flag>
- <flag name="nnpack">Enable NNPACK support</flag>
- <flag name="numa">Enable support for NUMA</flag>
- <flag name="observers">Build observers</flag>
- <flag name="opencv">Enable support for OpenCV</flag>
- <flag name="opencl">Enable support for OpenCL</flag>
- <flag name="qnnpack">Enable QNNPACK support</flag>
- <flag name="redis">Enable support for Redis</flag>
- <flag name="rocm">Enable AMD ROCm</flag>
- <flag name="tools">Build binary tools</flag>
- <flag name="zeromq">Enable support for ZeroMQ</flag>
- </use>
-</pkgmetadata>
diff --git a/sci-libs/pytorch/pytorch-1.10.2.ebuild b/sci-libs/pytorch/pytorch-1.10.2.ebuild
deleted file mode 100644
index 8ba76f1bd..000000000
--- a/sci-libs/pytorch/pytorch-1.10.2.ebuild
+++ /dev/null
@@ -1,339 +0,0 @@
-# Copyright 1999-2022 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-DISTUTILS_USE_SETUPTOOLS=manual
-DISTUTILS_SINGLE_IMPL=1
-PYTHON_COMPAT=( python3_{8..10} )
-
-inherit cmake cuda distutils-r1 prefix
-
-DESCRIPTION="Tensors and Dynamic neural networks in Python with strong GPU acceleration"
-HOMEPAGE="https://pytorch.org/"
-SRC_URI="https://github.com/pytorch/${PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz
-https://github.com/google/benchmark/archive/e991355c02b93fe17713efe04cbc2e278e00fdbd.tar.gz -> benchmark-e991355c02b93fe17713efe04cbc2e278e00fdbd.tar.gz
-https://github.com/pytorch/cpuinfo/archive/63b25457.tar.gz -> cpuinfo-63b25457.tar.gz
-https://github.com/NVlabs/cub/archive/d106ddb991a56c3df1b6d51b2409e36ba8181ce4.tar.gz -> cub-d106ddb991a56c3df1b6d51b2409e36ba8181ce4.tar.gz
-https://github.com/pytorch/fbgemm/archive/7588d9d804826b428fc0e4fd418e9cc3f7a72e52.tar.gz -> fbgemm-7588d9d804826b428fc0e4fd418e9cc3f7a72e52.tar.gz
-https://github.com/asmjit/asmjit/archive/d0d14ac774977d0060a351f66e35cb57ba0bf59c.tar.gz -> asmjit-d0d14ac774977d0060a351f66e35cb57ba0bf59c.tar.gz
-https://github.com/pytorch/cpuinfo/archive/5916273f79a21551890fd3d56fc5375a78d1598d.tar.gz -> cpuinfo-5916273f79a21551890fd3d56fc5375a78d1598d.tar.gz
-https://github.com/google/googletest/archive/0fc5466d.tar.gz -> googletest-0fc5466d.tar.gz
-https://github.com/fmtlib/fmt/archive/cd4af11efc9c622896a3e4cb599fa28668ca3d05.tar.gz -> fmt-cd4af11efc9c622896a3e4cb599fa28668ca3d05.tar.gz
-https://github.com/houseroad/foxi/archive/c278588e34e535f0bb8f00df3880d26928038cad.tar.gz -> foxi-c278588e34e535f0bb8f00df3880d26928038cad.tar.gz
-https://github.com/Maratyszcza/FP16/archive/4dfe081cf6bcd15db339cf2680b9281b8451eeb3.tar.gz -> FP16-4dfe081cf6bcd15db339cf2680b9281b8451eeb3.tar.gz
-https://github.com/Maratyszcza/FXdiv/archive/b408327ac2a15ec3e43352421954f5b1967701d1.tar.gz -> FXdiv-b408327ac2a15ec3e43352421954f5b1967701d1.tar.gz
-https://github.com/google/gemmlowp/archive/3fb5c176.tar.gz -> gemmlowp-3fb5c176.tar.gz
-https://github.com/facebookincubator/gloo/archive/c22a5cfba94edf8ea4f53a174d38aa0c629d070f.tar.gz -> gloo-c22a5cfba94edf8ea4f53a174d38aa0c629d070f.tar.gz
-https://github.com/google/googletest/archive/e2239ee6043f73722e7aa812a459f54a28552929.tar.gz -> googletest-e2239ee6043f73722e7aa812a459f54a28552929.tar.gz
-https://github.com/intel/ideep/archive/9ca27bbfd88fa1469cbf0467bd6f14cd1738fa40.tar.gz -> ideep-9ca27bbfd88fa1469cbf0467bd6f14cd1738fa40.tar.gz
-https://github.com/intel/mkl-dnn/archive/5ef631a0.tar.gz -> mkl-dnn-5ef631a0.tar.gz
-cuda? ( https://github.com/NVIDIA/nccl/archive/c5790b36722d5b41ee2a9b2bad69e364180ffd22.tar.gz -> nccl-c5790b36722d5b41ee2a9b2bad69e364180ffd22.tar.gz )
-https://github.com/Maratyszcza/NNPACK/archive/c07e3a0400713d546e0dea2d5466dd22ea389c73.tar.gz -> NNPACK-c07e3a0400713d546e0dea2d5466dd22ea389c73.tar.gz
-https://github.com/onnx/onnx/archive/a82c6a70.tar.gz -> onnx-a82c6a70.tar.gz
-https://github.com/onnx/onnx-tensorrt/archive/c153211418a7c57ce071d9ce2a41f8d1c85a878f.tar.gz -> onnx-tensorrt-c153211418a7c57ce071d9ce2a41f8d1c85a878f.tar.gz
-https://github.com/onnx/onnx/archive/29e7aa7048809784465d06e897f043a4600642b2.tar.gz -> onnx-29e7aa7048809784465d06e897f043a4600642b2.tar.gz
-https://github.com/google/benchmark/archive/e776aa02.tar.gz -> benchmark-e776aa02.tar.gz
-https://github.com/google/benchmark/archive/5b7683f4.tar.gz -> benchmark-5b7683f4.tar.gz
-https://github.com/google/googletest/archive/5ec7f0c4.tar.gz -> googletest-5ec7f0c4.tar.gz
-https://github.com/Maratyszcza/psimd/archive/072586a71b55b7f8c584153d223e95687148a90.tar.gz -> psimd-072586a71b55b7f8c584153d223e95687148a90.tar.gz
-https://github.com/Maratyszcza/pthreadpool/archive/a134dd5d4cee80cce15db81a72e7f929d71dd413.tar.gz -> pthreadpool-a134dd5d4cee80cce15db81a72e7f929d71dd413.tar.gz
-https://github.com/Maratyszcza/PeachPy/archive/07d8fde8ac45d7705129475c0f94ed8925b93473.tar.gz -> PeachPy-07d8fde8ac45d7705129475c0f94ed8925b93473.tar.gz
-https://github.com/pytorch/QNNPACK/archive/7d2a4e9931a82adc3814275b6219a03e24e36b4c.tar.gz -> QNNPACK-7d2a4e9931a82adc3814275b6219a03e24e36b4c.tar.gz
-https://github.com/shibatch/sleef/archive/e0a003ee838b75d11763aa9c3ef17bf71a725bff.tar.gz -> sleef-e0a003ee838b75d11763aa9c3ef17bf71a725bff.tar.gz
-https://github.com/pytorch/tensorpipe/archive/d2aa3485e8229c98891dfd604b514a39d45a5c99.tar.gz -> tensorpipe-d2aa3485e8229c98891dfd604b514a39d45a5c99.tar.gz
-https://github.com/google/googletest/archive/2fe3bd99.tar.gz -> googletest-2fe3bd99.tar.gz
-https://github.com/google/libnop/archive/aa95422e.tar.gz -> libnop-aa95422e.tar.gz
-https://github.com/libuv/libuv/archive/48e04275332f5753427d21a52f17ec6206451f2c.tar.gz -> libuv-48e04275332f5753427d21a52f17ec6206451f2c.tar.gz
-https://github.com/google/XNNPACK/archive/79cd5f9e18ad0925ac9a050b00ea5a36230072db.tar.gz -> XNNPACK-79cd5f9e18ad0925ac9a050b00ea5a36230072db.tar.gz
-https://github.com/pytorch/kineto/archive/879a203d9bf554e95541679ddad6e0326f272dc1.tar.gz -> kineto-879a203d9bf554e95541679ddad6e0326f272dc1.tar.gz
-https://github.com/driazati/breakpad/archive/edbb99f95c75be27d038fffb1d969cdacf705db2.tar.gz -> breakpad-edbb99f95c75be27d038fffb1d969cdacf705db2.tar.gz
-https://github.com/mikey/linux-syscall-support/archive/e1e7b0ad8ee99a875b272c8e33e308472e897660.tar.gz -> lss-e1e7b0ad8ee99a875b272c8e33e308472e897660.tar.gz
-"
-
-# git clone git@github.com:pytorch/pytorch.git && cd pytorch
-# git submodules update --init --recursive
-# ${FILESDIR}/get_third_paries
-# cat SRC_URI src_prepare
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS="~amd64"
-
-IUSE="asan blas cuda +fbgemm ffmpeg gflags glog +gloo leveldb lmdb mkldnn mpi namedtensor +nnpack numa +observers opencl opencv +openmp +python +qnnpack redis rocm static tools zeromq"
-REQUIRED_USE=" ?? ( cuda rocm )"
-
-RDEPEND="
- $(python_gen_cond_dep '
- dev-python/pyyaml[${PYTHON_USEDEP}]
- ')
- blas? ( virtual/blas )
- cuda? ( dev-libs/cudnn
- dev-cpp/eigen[cuda] )
- rocm? ( >=dev-util/hip-4.3
- >=dev-libs/rccl-4.3
- >=sci-libs/rocThrust-4.3
- >=sci-libs/hipCUB-4.3
- >=sci-libs/rocPRIM-4.3
- >=sci-libs/miopen-4.3
- >=sci-libs/rocBLAS-4.3
- >=sci-libs/rocRAND-4.3
- >=sci-libs/hipSPARSE-4.3
- >=sci-libs/rocFFT-4.3
- >=dev-util/roctracer-4.3 )
- ffmpeg? ( media-video/ffmpeg )
- gflags? ( dev-cpp/gflags )
- glog? ( dev-cpp/glog[gflags] )
- leveldb? ( dev-libs/leveldb )
- lmdb? ( dev-db/lmdb )
- mpi? ( virtual/mpi )
- opencl? ( dev-libs/clhpp )
- opencv? ( media-libs/opencv )
- python? ( ${PYTHON_DEPS}
- $(python_gen_cond_dep '
- dev-python/setuptools[${PYTHON_USEDEP}]
- dev-python/pybind11[${PYTHON_USEDEP}]
- dev-python/numpy[${PYTHON_USEDEP}]
- dev-python/protobuf-python:=[${PYTHON_USEDEP}]
- ')
- )
- redis? ( dev-db/redis )
- zeromq? ( net-libs/zeromq )
- dev-cpp/eigen
- dev-libs/protobuf:=
- dev-libs/libuv
-"
-
-#ATen code generation
-BDEPEND="dev-python/pyyaml"
-
-DEPEND="${RDEPEND}
- dev-cpp/tbb
- app-arch/zstd
- $(python_gen_cond_dep '
- dev-python/pybind11[${PYTHON_USEDEP}]
- dev-python/typing-extensions[${PYTHON_USEDEP}]
- ')
- sys-cluster/rdma-core
- sys-process/numactl
-"
-
-PATCHES=(
- "${FILESDIR}"/${PN}-1.9.0-Change-library-directory-according-to-CMake-build.patch
- "${FILESDIR}"/${PN}-1.6.0-global-dlopen.patch
- "${FILESDIR}"/0002-Don-t-build-libtorch-again-for-PyTorch-1.7.1.patch
- "${FILESDIR}"/${PN}-1.7.1-no-rpath.patch
- "${FILESDIR}"/${PN}-1.7.1-torch_shm_manager.patch
- "${FILESDIR}"/${PN}-1.10.0-nonull.patch
- "${FILESDIR}"/${PN}-1.10.0-fix-distutils.patch
- "${FILESDIR}"/${PN}-1.10.0-clhpp2.patch
-)
-
-distutils_enable_tests --install pytest
-
-src_prepare() {
- cmake_src_prepare
- eprefixify torch/__init__.py
-
- rmdir third_party/benchmark || die
- ln -sv "${WORKDIR}"/benchmark-e991355c02b93fe17713efe04cbc2e278e00fdbd third_party/benchmark || die
- rmdir third_party/cpuinfo || die
- ln -sv "${WORKDIR}"/cpuinfo-5916273f79a21551890fd3d56fc5375a78d1598d third_party/cpuinfo || die
- rmdir third_party/cub || die
- ln -sv "${WORKDIR}"/cub-d106ddb991a56c3df1b6d51b2409e36ba8181ce4 third_party/cub || die
- rmdir third_party/fbgemm || die
- ln -sv "${WORKDIR}"/FBGEMM-7588d9d804826b428fc0e4fd418e9cc3f7a72e52 third_party/fbgemm || die
- rmdir third_party/fbgemm/third_party/asmjit || die
- ln -sv "${WORKDIR}"/asmjit-d0d14ac774977d0060a351f66e35cb57ba0bf59c third_party/fbgemm/third_party/asmjit || die
- rmdir third_party/fbgemm/third_party/cpuinfo || die
- ln -sv "${WORKDIR}"/cpuinfo-d5e37adf1406cf899d7d9ec1d317c47506ccb970 third_party/fbgemm/third_party/cpuinfo || die
- rmdir third_party/fbgemm/third_party/googletest || die
- ln -sv "${WORKDIR}"/googletest-0fc5466dbb9e623029b1ada539717d10bd45e99e third_party/fbgemm/third_party/googletest || die
- rmdir third_party/fmt || die
- ln -sv "${WORKDIR}"/fmt-cd4af11efc9c622896a3e4cb599fa28668ca3d05 third_party/fmt || die
- rmdir third_party/foxi || die
- ln -sv "${WORKDIR}"/foxi-c278588e34e535f0bb8f00df3880d26928038cad third_party/foxi || die
- rmdir third_party/FP16 || die
- ln -sv "${WORKDIR}"/FP16-4dfe081cf6bcd15db339cf2680b9281b8451eeb3 third_party/FP16 || die
- rmdir third_party/FXdiv
- ln -sv "${WORKDIR}"/FXdiv-b408327ac2a15ec3e43352421954f5b1967701d1 third_party/FXdiv || die
- rmdir third_party/gemmlowp/gemmlowp || die
- ln -sv "${WORKDIR}"/gemmlowp-3fb5c176c17c765a3492cd2f0321b0dab712f350 third_party/gemmlowp/gemmlowp || die
- rmdir third_party/gloo || die
- ln -sv "${WORKDIR}"/gloo-c22a5cfba94edf8ea4f53a174d38aa0c629d070f third_party/gloo || die
- rmdir third_party/googletest || die
- ln -sv "${WORKDIR}"/googletest-e2239ee6043f73722e7aa812a459f54a28552929 third_party/googletest || die
- rmdir third_party/ideep || die
- ln -sv "${WORKDIR}"/ideep-9ca27bbfd88fa1469cbf0467bd6f14cd1738fa40 third_party/ideep || die
- rmdir third_party/ideep/mkl-dnn || die
- ln -sv "${WORKDIR}"/mkl-dnn-5ef631a030a6f73131c77892041042805a06064f third_party/ideep/mkl-dnn || die
- rmdir third_party/nccl/nccl || die
- ln -sv "${WORKDIR}"/nccl-c5790b36722d5b41ee2a9b2bad69e364180ffd22 third_party/nccl/nccl || die
- rmdir third_party/NNPACK || die
- ln -sv "${WORKDIR}"/NNPACK-c07e3a0400713d546e0dea2d5466dd22ea389c73 third_party/NNPACK || die
- rmdir third_party/onnx || die
- ln -sv "${WORKDIR}"/onnx-29e7aa7048809784465d06e897f043a4600642b2 third_party/onnx || die
- rmdir third_party/onnx-tensorrt || die
- ln -sv "${WORKDIR}"/onnx-tensorrt-c153211418a7c57ce071d9ce2a41f8d1c85a878f third_party/onnx-tensorrt || die
- rmdir third_party/onnx-tensorrt/third_party/onnx || die
- ln -sv "${WORKDIR}"/onnx-765f5ee823a67a866f4bd28a9860e81f3c811ce8 third_party/onnx-tensorrt/third_party/onnx || die
- rmdir third_party/onnx/third_party/benchmark || die
- ln -sv "${WORKDIR}"/benchmark-e776aa0275e293707b6a0901e0e8d8a8a3679508 third_party/onnx/third_party/benchmark || die
- rmdir third_party/psimd || die
- ln -sv "${WORKDIR}"/psimd-072586a71b55b7f8c584153d223e95687148a900 third_party/psimd || die
- rmdir third_party/pthreadpool || die
- ln -sv "${WORKDIR}"/pthreadpool-a134dd5d4cee80cce15db81a72e7f929d71dd413 third_party/pthreadpool || die
- rmdir third_party/python-peachpy || die
- ln -sv "${WORKDIR}"/PeachPy-07d8fde8ac45d7705129475c0f94ed8925b93473 third_party/python-peachpy || die
- rmdir third_party/QNNPACK || die
- ln -sv "${WORKDIR}"/QNNPACK-7d2a4e9931a82adc3814275b6219a03e24e36b4c third_party/QNNPACK || die
- rmdir third_party/sleef || die
- ln -sv "${WORKDIR}"/sleef-e0a003ee838b75d11763aa9c3ef17bf71a725bff third_party/sleef || die
- rmdir third_party/tensorpipe || die
- ln -sv "${WORKDIR}"/tensorpipe-d2aa3485e8229c98891dfd604b514a39d45a5c99 third_party/tensorpipe || die
- rmdir third_party/tensorpipe/third_party/googletest || die
- ln -sv "${WORKDIR}"/googletest-2fe3bd994b3189899d93f1d5a881e725e046fdc2 third_party/tensorpipe/third_party/googletest || die
- rmdir third_party/tensorpipe/third_party/libnop || die
- ln -sv "${WORKDIR}"/libnop-aa95422ea8c409e3f078d2ee7708a5f59a8b9fa2 third_party/tensorpipe/third_party/libnop || die
- rmdir third_party/tensorpipe/third_party/libuv || die
- ln -sv "${WORKDIR}"/libuv-48e04275332f5753427d21a52f17ec6206451f2c third_party/tensorpipe/third_party/libuv || die
- rmdir third_party/XNNPACK || die
- ln -sv "${WORKDIR}"/XNNPACK-79cd5f9e18ad0925ac9a050b00ea5a36230072db third_party/XNNPACK || die
- rmdir third_party/kineto || die
- ln -sv "${WORKDIR}"/kineto-879a203d9bf554e95541679ddad6e0326f272dc1 third_party/kineto || die
- rmdir third_party/breakpad || die
- ln -sv "${WORKDIR}"/breakpad-edbb99f95c75be27d038fffb1d969cdacf705db2 third_party/breakpad || die
- rmdir third_party/breakpad/src/third_party/lss || die
- ln -sv "${WORKDIR}"/linux-syscall-support-e1e7b0ad8ee99a875b272c8e33e308472e897660 third_party/breakpad/src/third_party/lss || die
-
- if use cuda; then
- cd third_party/nccl/nccl || die
- eapply "${FILESDIR}"/${PN}-1.10.1-nccl-nvccflags.patch
- cuda_src_prepare
- export CUDAHOSTCXX=$(cuda_gccdir)/g++
- cd "${S}"
- fi
-
- if use rocm; then
- #Allow escaping sandbox
- addread /dev/kfd
- addread /dev/dri
- addpredict /dev/kfd
- addpredict /dev/dri
-
- ebegin "HIPifying cuda sources"
- ${EPYTHON} tools/amd_build/build_amd.py || die
- eapply "${FILESDIR}"/${PN}-1.9.1-fix-wrong-hipify.patch
- eend $?
-
- local ROCM_VERSION="$(hipconfig -v)-"
- export PYTORCH_ROCM_ARCH="${AMDGPU_TARGETS}"
- sed -e "/set(roctracer_INCLUDE_DIRS/s,\${ROCTRACER_PATH}/include,${EPREFIX}/usr/include/roctracer," \
- -e "/PYTORCH_HIP_HCC_LIBRARIES/s,\${HIP_PATH}/lib,${EPREFIX}/usr/lib/hip/lib," \
- -e "/set(roctracer_INCLUDE_DIRS/a\ set(thrust_INCLUDE_DIRS ${EPREFIX}/usr/include/rocthrust)" \
- -e "s,\${ROCTRACER_PATH}/lib,${EPREFIX}/usr/lib64/roctracer," \
- -e "/READ.*\.info\/version-dev/c\ set(ROCM_VERSION_DEV_RAW ${ROCM_VERSION})" \
- -i cmake/public/LoadHIP.cmake || die
- sed -r -e '/^if\(USE_ROCM/{:a;N;/\nendif/!ba; s,\{([^\{]*)_PATH\}(/include)?,\{\L\1_\UINCLUDE_DIRS\},g}' -i cmake/Dependencies.cmake || die
- fi
-
- # Set build dir for pytorch's setup
- sed -e "/BUILD_DIR/s,build,${BUILD_DIR}," -i tools/setup_helpers/env.py || die
-}
-
-src_configure() {
- local mycmakeargs=(
- -DWERROR=OFF
- -DTORCH_BUILD_VERSION=${PV}
- -DTORCH_INSTALL_LIB_DIR=$(get_libdir)
- -DBUILD_BINARY=$(usex tools ON OFF)
- -DBUILD_CUSTOM_PROTOBUF=OFF
- -DBUILD_PYTHON=$(usex python ON OFF)
- -DBUILD_SHARED_LIBS=$(usex static OFF ON)
- -DBUILD_TEST=$(usex test ON OFF)
- -DUSE_ASAN=$(usex asan ON OFF)
- -DUSE_CUDA=$(usex cuda ON OFF)
- -DUSE_NCCL=$(usex cuda ON OFF)
- -DUSE_SYSTEM_NCCL=OFF
- -DUSE_ROCM=$(usex rocm ON OFF)
- -DUSE_FBGEMM=$(usex fbgemm ON OFF)
- -DUSE_FFMPEG=$(usex ffmpeg ON OFF)
- -DUSE_GFLAGS=$(usex gflags ON OFF)
- -DUSE_GLOG=$(usex glog ON OFF)
- -DUSE_LEVELDB=$(usex leveldb ON OFF)
- -DUSE_LITE_PROTO=OFF
- -DUSE_LMDB=$(usex lmdb ON OFF)
- -DUSE_MKLDNN=$(usex mkldnn ON OFF)
- -DUSE_MKLDNN_CBLAS=OFF
- -DUSE_NNPACK=$(usex nnpack ON OFF)
- -DUSE_NUMPY=$(usex python ON OFF)
- -DUSE_NUMA=$(usex numa ON OFF)
- -DUSE_OBSERVERS=$(usex observers ON OFF)
- -DUSE_OPENCL=$(usex opencl ON OFF)
- -DUSE_OPENCV=$(usex opencv ON OFF)
- -DUSE_OPENMP=$(usex openmp ON OFF)
- -DUSE_TBB=OFF
- -DUSE_PROF=OFF
- -DUSE_QNNPACK=$(usex qnnpack ON OFF)
- -DUSE_REDIS=$(usex redis ON OFF)
- -DUSE_ROCKSDB=OFF
- -DUSE_ZMQ=$(usex zeromq ON OFF)
- -DUSE_MPI=$(usex mpi ON OFF)
- -DUSE_GLOO=$(usex gloo ON OFF)
- -DUSE_SYSTEM_EIGEN_INSTALL=ON
- -DUSE_SYSTEM_PYBIND11=ON
- -DBLAS=$(usex blas Generic Eigen)
- -DTP_BUILD_LIBUV=OFF
- -Wno-dev
- )
-
- HIP_PATH="${EPREFIX}/usr/lib/hip" cmake_src_configure
-
- if use python; then
- CMAKE_BUILD_DIR="${BUILD_DIR}" distutils-r1_src_configure
- fi
-
- # do not rerun cmake and the build process in src_install
- sed '/RERUN/,+1d' -i "${BUILD_DIR}"/build.ninja || die
-}
-
-src_compile() {
- cmake_src_compile
-
- if use python; then
- USE_SYSTEM_LIBS=ON CMAKE_BUILD_DIR=${BUILD_DIR} distutils-r1_src_compile
- fi
-}
-
-src_install() {
- cmake_src_install
-
- local LIB=$(get_libdir)
- if [[ ${LIB} != lib ]]; then
- mv -fv "${ED}"/usr/lib/*.so "${ED}"/usr/${LIB}/ || die
- fi
-
- rm -r "${ED}/usr/lib" || die
-
- rm -r "${ED}/usr/include/asmjit" || die
- rm -r "${ED}/usr/include/c10d" || die
- rm -r "${ED}/usr/include/fbgemm" || die
- rm -r "${ED}/usr/include/fp16" || die
- rm -r "${ED}/usr/include/gloo" || die
-
- if use python; then
- scanelf -r --fix "${BUILD_DIR}/caffe2/python" || die
- USE_SYSTEM_LIBS=ON CMAKE_BUILD_DIR=${BUILD_DIR} distutils-r1_src_install
-
- python_optimize
- fi
-
- find "${ED}/usr/${LIB}" -name "*.a" -exec rm -fv {} \; || die
-
- if use test; then
- rm -r "${ED}/usr/test" "${ED}"/usr/bin/test_{api,jit} || die
- fi
-
- # Remove the empty directories by CMake Python:
- find "${ED}" -type d -empty -delete || die
-}
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 e0ecf971e..b17ac9007 100644
--- a/sci-libs/torchvision/torchvision-0.11.2.ebuild
+++ b/sci-libs/torchvision/torchvision-0.11.2.ebuild
@@ -3,7 +3,6 @@
EAPI=8
-DISTUTILS_SINGLE_IMPL=1
PYTHON_COMPAT=( python3_{8..10} )
inherit distutils-r1
@@ -18,15 +17,13 @@ KEYWORDS="~amd64"
IUSE="cuda"
RDEPEND="
- $(python_gen_cond_dep '
dev-python/av[${PYTHON_USEDEP}]
dev-python/numpy[${PYTHON_USEDEP}]
dev-python/pillow[${PYTHON_USEDEP}]
dev-python/six[${PYTHON_USEDEP}]
dev-python/tqdm[${PYTHON_USEDEP}]
dev-python/scipy[${PYTHON_USEDEP}]
- ')
- sci-libs/pytorch[cuda?,python,${PYTHON_SINGLE_USEDEP}]
+ sci-libs/pytorch[cuda(-)?,${PYTHON_USEDEP}]
media-video/ffmpeg
dev-qt/qtcore:5
"
diff --git a/sci-physics/feynarts/Manifest b/sci-physics/feynarts/Manifest
new file mode 100644
index 000000000..d66304b21
--- /dev/null
+++ b/sci-physics/feynarts/Manifest
@@ -0,0 +1 @@
+DIST FeynArts-3.11.tar.gz 3146405 BLAKE2B d22a19faecaa3a87ebf48b035736a04a6ae9b28e47300240edac541cb86438781092bf0a16d84808fb0256cf7547ba9d04024934007fa017cab08811d6b2b41b SHA512 2032172c86316b1703c0ff0c9cc511db0b97d6268bde30b6948ea98c5f2b39996071675d25aba4ed65af99f0c6535bce4e5eca8ca942be3591f922937c4aa79b
diff --git a/sci-physics/feynarts/feynarts-3.11.ebuild b/sci-physics/feynarts/feynarts-3.11.ebuild
new file mode 100644
index 000000000..0851757d3
--- /dev/null
+++ b/sci-physics/feynarts/feynarts-3.11.ebuild
@@ -0,0 +1,29 @@
+# Copyright 2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+MY_PN=FeynArts
+MY_P=${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..de9e1e708
--- /dev/null
+++ b/sci-physics/formcalc/Manifest
@@ -0,0 +1,2 @@
+DIST FormCalc-9.10.tar.gz 32069351 BLAKE2B e46b9cbce5c797b8d4f09d03f617668df799edcdfec8f55631e6a626c4f06bf317f5d3b546b7e335babf734e5919d7c5900e1959a6f46f1343e758b7bdec045b SHA512 4a8c620fecbe07ce0fbdef459645a44b4f2abfe2d92085d7891e980ee162bf559556ba8dfea68cdc9bf71e36223f88683fb7f76bbf1f1969fdbc761e68ba2c42
+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.ebuild b/sci-physics/formcalc/formcalc-9.10.ebuild
new file mode 100644
index 000000000..81f69f294
--- /dev/null
+++ b/sci-physics/formcalc/formcalc-9.10.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}/${MY_P}"
+
+LICENSE="LGPL-3+"
+SLOT="0"
+KEYWORDS="~amd64"
+
+RDEPEND="
+ sci-mathematics/mathematica
+ sci-mathematics/form
+ "
+DEPEND="${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 form` ${MMADIR}/${MY_P}/Linux-x86-64/tform
+
+ dodoc manual/*.pdf
+}
diff --git a/sci-physics/formcalc/formcalc-9.9.ebuild b/sci-physics/formcalc/formcalc-9.9.ebuild
new file mode 100644
index 000000000..6e031ef5c
--- /dev/null
+++ b/sci-physics/formcalc/formcalc-9.9.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}/${MY_P}"
+
+LICENSE="LGPL-3+"
+SLOT="0"
+KEYWORDS="~amd64"
+
+RDEPEND="
+ sci-mathematics/mathematica
+ sci-mathematics/form
+ "
+DEPEND="${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 form` ${MMADIR}/${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/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}"
}