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-rw-r--r--README.md4
-rw-r--r--dev-cpp/blitz/blitz-1.0.3_pre20200524.ebuild2
-rw-r--r--dev-cpp/blitz/blitz-9999.ebuild2
-rw-r--r--dev-libs/lief/Manifest1
-rw-r--r--dev-libs/lief/lief-0.11.5.ebuild128
-rw-r--r--dev-libs/lief/metadata.xml14
-rw-r--r--dev-libs/optix/Manifest1
-rw-r--r--dev-libs/optix/optix-7.2.0.ebuild37
-rw-r--r--dev-python/astroquery/astroquery-0.4.1.ebuild2
-rw-r--r--dev-python/av/Manifest1
-rw-r--r--dev-python/av/av-8.0.3.ebuild24
-rw-r--r--dev-python/av/metadata.xml8
-rw-r--r--dev-python/bokeh/bokeh-2.2.1-r1.ebuild4
-rw-r--r--dev-python/bokeh/bokeh-2.2.2-r1.ebuild4
-rw-r--r--dev-python/bokeh/bokeh-2.2.3.ebuild4
-rw-r--r--dev-python/bokeh/bokeh-2.3.0.ebuild2
-rw-r--r--dev-python/bokeh/bokeh-2.3.1.ebuild2
-rw-r--r--dev-python/bokeh/bokeh-2.3.2.ebuild2
-rw-r--r--dev-python/cadquery-ocp/Manifest1
-rw-r--r--dev-python/cadquery-ocp/cadquery-ocp-7.5.2_beta.ebuild195
-rw-r--r--dev-python/cadquery-ocp/metadata.xml (renamed from dev-python/toposort/metadata.xml)3
-rw-r--r--dev-python/cadquery-pywrap/Manifest1
-rw-r--r--dev-python/cadquery-pywrap/cadquery-pywrap-7.5.2_rc20210526.ebuild70
-rw-r--r--dev-python/cadquery-pywrap/metadata.xml12
-rw-r--r--dev-python/cadquery/Manifest1
-rw-r--r--dev-python/cadquery/cadquery-2.2_rc20210804.ebuild56
-rw-r--r--dev-python/cadquery/metadata.xml12
-rw-r--r--dev-python/cymbal/Manifest1
-rw-r--r--dev-python/cymbal/cymbal-1.0.0.ebuild34
-rw-r--r--dev-python/cymbal/metadata.xml13
-rw-r--r--dev-python/datrie/datrie-0.8.2.ebuild4
-rw-r--r--dev-python/ezdxf/Manifest1
-rw-r--r--dev-python/ezdxf/ezdxf-0.16.5.ebuild34
-rw-r--r--dev-python/ezdxf/metadata.xml17
-rw-r--r--dev-python/gffpandas/Manifest1
-rw-r--r--dev-python/gffpandas/gffpandas-1.2.0.ebuild29
-rw-r--r--dev-python/gffpandas/metadata.xml (renamed from sci-biology/rum/metadata.xml)3
-rw-r--r--dev-python/jupyterlab_launcher/Manifest1
-rw-r--r--dev-python/jupyterlab_launcher/jupyterlab_launcher-0.13.1.ebuild26
-rw-r--r--dev-python/jupyterlab_launcher/metadata.xml (renamed from sci-chemistry/talosn/metadata.xml)4
-rw-r--r--dev-python/logzero/Manifest1
-rw-r--r--dev-python/logzero/logzero-1.7.0.ebuild18
-rw-r--r--dev-python/logzero/metadata.xml13
-rw-r--r--dev-python/meshio/Manifest1
-rw-r--r--dev-python/meshio/meshio-4.4.6.ebuild26
-rw-r--r--dev-python/meshio/metadata.xml13
-rw-r--r--dev-python/nptyping/Manifest1
-rw-r--r--dev-python/nptyping/metadata.xml13
-rw-r--r--dev-python/nptyping/nptyping-1.4.3.ebuild27
-rw-r--r--dev-python/numba/Manifest2
-rw-r--r--dev-python/numba/numba-0.54.0.ebuild (renamed from dev-python/numba/numba-0.53.1.ebuild)51
-rw-r--r--dev-python/pynndescent/Manifest2
-rw-r--r--dev-python/pynndescent/pynndescent-0.4.8.ebuild27
-rw-r--r--dev-python/pynndescent/pynndescent-0.5.1.ebuild27
-rw-r--r--dev-python/pynndescent/pynndescent-0.5.2.ebuild8
-rw-r--r--dev-python/pyvista/Manifest1
-rw-r--r--dev-python/pyvista/metadata.xml13
-rw-r--r--dev-python/pyvista/pyvista-0.31.1.ebuild32
-rw-r--r--dev-python/pyzo/Manifest1
-rw-r--r--dev-python/pyzo/metadata.xml8
-rw-r--r--dev-python/pyzo/pyzo-4.11.2.ebuild64
-rw-r--r--dev-python/schema/Manifest1
-rw-r--r--dev-python/schema/metadata.xml13
-rw-r--r--dev-python/schema/schema-0.7.4.ebuild28
-rw-r--r--dev-python/scooby/Manifest1
-rw-r--r--dev-python/scooby/metadata.xml13
-rw-r--r--dev-python/scooby/scooby-0.5.7.ebuild16
-rw-r--r--dev-python/toposort/Manifest1
-rw-r--r--dev-python/toposort/toposort-1.6.ebuild18
-rw-r--r--dev-python/transforms3d/Manifest1
-rw-r--r--dev-python/transforms3d/metadata.xml13
-rw-r--r--dev-python/transforms3d/transforms3d-0.3.1.ebuild23
-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.ebuild21
-rw-r--r--dev-python/visvis/Manifest1
-rw-r--r--dev-python/visvis/metadata.xml8
-rw-r--r--dev-python/visvis/visvis-1.13.0.ebuild25
-rw-r--r--licenses/UPennState7
-rw-r--r--licenses/netCDF31
-rw-r--r--media-libs/libgfx/Manifest1
-rw-r--r--media-libs/libgfx/libgfx-1.1.1.ebuild41
-rw-r--r--profiles/package.mask9
-rw-r--r--sci-biology/MuSeqBox/Manifest2
-rw-r--r--sci-biology/MuSeqBox/MuSeqBox-5.7.2021.ebuild (renamed from sci-biology/MuSeqBox/MuSeqBox-3.4.2020.ebuild)5
-rw-r--r--sci-biology/SEECER/SEECER-0.1.3-r3.ebuild66
-rw-r--r--sci-biology/SEECER/files/SEECER-increase-max-sequence-length.patch44
-rw-r--r--sci-biology/SEECER/files/SEECER-remove-flags.patch30
-rw-r--r--sci-biology/Scaffolder-evaluation/Scaffolder-evaluation-9999.ebuild38
-rw-r--r--sci-biology/Scaffolder-evaluation/metadata.xml15
-rw-r--r--sci-biology/blasr/blasr-9999.ebuild2
-rw-r--r--sci-biology/cg-cat/Manifest1
-rw-r--r--sci-biology/cg-cat/cg-cat-20150130.ebuild59
-rw-r--r--sci-biology/cg-cat/metadata.xml12
-rw-r--r--sci-biology/cgview-bin/Manifest1
-rw-r--r--sci-biology/cgview-bin/cgview-bin-1.0.0.ebuild43
-rw-r--r--sci-biology/cgview-bin/metadata.xml12
-rw-r--r--sci-biology/fsl/Manifest1
-rw-r--r--sci-biology/fsl/files/fsl-6.0.4-cuda_buildsettings.patch12
-rw-r--r--sci-biology/fsl/files/fsl-6.0.4-eddy_cuda.patch21
-rw-r--r--sci-biology/fsl/files/fsl-6.0.4-fdt_cuda.patch14
-rw-r--r--sci-biology/fsl/files/fsl-6.0.4-flameo_std.patch11
-rw-r--r--sci-biology/fsl/files/fsl-6.0.4-fsldir_redux-p1.patch240
-rw-r--r--sci-biology/fsl/files/fsl-6.0.4-fsldir_redux-p2.patch254
-rw-r--r--sci-biology/fsl/files/fsl-6.0.4-gcc10_include.patch11
-rw-r--r--sci-biology/fsl/files/fsl-6.0.4-melodic_std.patch11
-rw-r--r--sci-biology/fsl/files/fsl-6.0.4-remove_fslpy_collisions-p1.patch303
-rw-r--r--sci-biology/fsl/files/fsl-6.0.4-remove_fslpy_collisions-p2.patch348
-rw-r--r--sci-biology/fsl/files/fsl-6.0.4-setup.patch174
-rw-r--r--sci-biology/fsl/fsl-6.0.2-r1.ebuild4
-rw-r--r--sci-biology/fsl/fsl-6.0.2.ebuild6
-rw-r--r--sci-biology/fsl/fsl-6.0.4.ebuild217
-rw-r--r--sci-biology/maker/Manifest1
-rw-r--r--sci-biology/maker/maker-3.01.02_beta.ebuild135
-rw-r--r--sci-biology/maker/metadata.xml12
-rw-r--r--sci-biology/mgblast/Manifest1
-rw-r--r--sci-biology/mgblast/metadata.xml12
-rw-r--r--sci-biology/mgblast/mgblast-0.1.ebuild34
-rw-r--r--sci-biology/ncbi-blast+/ncbi-blast+-2.11.0.ebuild2
-rw-r--r--sci-biology/ncbi-blast+/ncbi-blast+-2.2.30.ebuild2
-rw-r--r--sci-biology/ncbi-blast+/ncbi-blast+-2.2.31.ebuild2
-rw-r--r--sci-biology/ncbi-blast+/ncbi-blast+-2.6.0.ebuild2
-rw-r--r--sci-biology/ncbi-blast+/ncbi-blast+-2.8.1.ebuild2
-rw-r--r--sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild2
-rw-r--r--sci-biology/ncbi-tools++/ncbi-tools++-18.0.0.ebuild2
-rw-r--r--sci-biology/ncbi-tools++/ncbi-tools++-22.0.0.ebuild2
-rw-r--r--sci-biology/nilearn/Manifest2
-rw-r--r--sci-biology/nilearn/metadata.xml3
-rw-r--r--sci-biology/nilearn/nilearn-0.6.2.ebuild61
-rw-r--r--sci-biology/nilearn/nilearn-0.8.0.ebuild42
-rw-r--r--sci-biology/nilearn/nilearn-9999.ebuild56
-rw-r--r--sci-biology/open-ephys-gui/Manifest1
-rw-r--r--sci-biology/open-ephys-gui/files/open-ephys-gui-0.5.5.patch12
-rw-r--r--sci-biology/open-ephys-gui/open-ephys-gui-0.5.2.2.ebuild2
-rw-r--r--sci-biology/open-ephys-gui/open-ephys-gui-0.5.5.ebuild80
-rw-r--r--sci-biology/open-ephys-gui/open-ephys-gui-9999.ebuild40
-rw-r--r--sci-biology/open-ephys-gui/open-ephys-gui-99999999.ebuild40
-rw-r--r--sci-biology/pbcopper/pbcopper-1.9.0.ebuild2
-rw-r--r--sci-biology/primerD/primerD-1.0.0.ebuild2
-rw-r--r--sci-biology/prot4EST/Manifest1
-rw-r--r--sci-biology/prot4EST/metadata.xml12
-rw-r--r--sci-biology/prot4EST/prot4EST-3.1b.ebuild38
-rw-r--r--sci-biology/rum/Manifest1
-rw-r--r--sci-biology/rum/rum-2.0.5.06.ebuild30
-rw-r--r--sci-biology/salmon/salmon-0.10.2.ebuild2
-rw-r--r--sci-biology/salmon/salmon-1.4.0.ebuild2
-rw-r--r--sci-biology/salmon/salmon-9999.ebuild2
-rw-r--r--sci-biology/seqclean/Manifest3
-rw-r--r--sci-biology/seqclean/files/seqclean-110625-build.patch135
-rw-r--r--sci-biology/seqclean/metadata.xml12
-rw-r--r--sci-biology/seqclean/seqclean-110625.ebuild54
-rw-r--r--sci-chemistry/gamess/gamess-20180930.3-r1.ebuild (renamed from sci-chemistry/gamess/gamess-20180930.3.ebuild)8
-rw-r--r--sci-chemistry/gamess/metadata.xml2
-rw-r--r--sci-chemistry/pymol-plugins-psico/pymol-plugins-psico-3.4-r1.ebuild (renamed from sci-chemistry/pymol-plugins-psico/pymol-plugins-psico-3.4.ebuild)13
-rw-r--r--sci-chemistry/talosn/Manifest1
-rw-r--r--sci-chemistry/talosn/talosn-4.12.2015.147.15.40.ebuild68
-rw-r--r--sci-libs/ciftilib/ciftilib-1.6.0.ebuild6
-rw-r--r--sci-libs/ciftilib/files/ciftilib-1.6.0-version.patch27
-rw-r--r--sci-libs/nipype/nipype-1.5.0.ebuild4
-rw-r--r--sci-libs/pytorch/Manifest23
-rw-r--r--sci-libs/pytorch/pytorch-1.9.0.ebuild321
-rw-r--r--sci-libs/rdkit/rdkit-2020.03.6.ebuild2
-rw-r--r--sci-libs/rocBLAS/Manifest1
-rw-r--r--sci-libs/rocBLAS/files/Tensile-4.0.0-locate-commands.patch32
-rw-r--r--sci-libs/rocBLAS/files/rocBLAS-4.0.0-use-system-tensile.patch30
-rw-r--r--sci-libs/rocBLAS/metadata.xml11
-rw-r--r--sci-libs/rocBLAS/rocBLAS-4.0.0-r1.ebuild88
-rw-r--r--sci-libs/rocBLAS/rocBLAS-4.0.0-r2.ebuild76
-rw-r--r--sci-libs/simpleitk/simpleitk-1.2.4.ebuild1
-rw-r--r--sci-libs/superlu_dist/superlu_dist-6.4.0.ebuild2
-rw-r--r--sci-mathematics/acl2/Manifest1
-rw-r--r--sci-mathematics/acl2/acl2-8.3-r1.ebuild86
-rw-r--r--sci-mathematics/acl2/acl2-8.3.ebuild51
-rw-r--r--sci-mathematics/acl2/acl2-8.4.ebuild86
-rw-r--r--sci-mathematics/acl2/files/acl2-use_make_variable.patch13
-rw-r--r--sci-mathematics/acl2/metadata.xml2
-rw-r--r--sci-mathematics/flocq/flocq-3.4.0-r1.ebuild (renamed from sci-mathematics/flocq/flocq-3.4.0.ebuild)6
-rw-r--r--sci-misc/europa-bin/Manifest1
-rw-r--r--sci-misc/europa-bin/europa-bin-1.0.0.ebuild57
-rw-r--r--sci-misc/europa-bin/metadata.xml12
-rw-r--r--sci-misc/irstlm/files/irstlm-6.00.05-doc-obey-docdir.patch22
-rw-r--r--sci-misc/irstlm/files/irstlm-6.00.05-remove-lib-linking.patch18
-rw-r--r--sci-misc/irstlm/irstlm-6.00.05-r1.ebuild38
-rwxr-xr-xscripts/setup-and-run-repoman.sh2
-rw-r--r--sys-kernel/dkms/Manifest1
-rw-r--r--sys-kernel/dkms/dkms-2.8.4.ebuild41
-rw-r--r--sys-kernel/dkms/metadata.xml18
187 files changed, 3924 insertions, 1446 deletions
diff --git a/README.md b/README.md
index 29e518d33..99fcfe316 100644
--- a/README.md
+++ b/README.md
@@ -2,7 +2,7 @@
[![pkgcheck](https://github.com/gentoo/sci/workflows/pkgcheck/badge.svg)](https://github.com/gentoo/sci/actions?query=workflow%3Apkgcheck)
[![repoman](https://github.com/gentoo/sci/workflows/repoman/badge.svg)](https://github.com/gentoo/sci/actions?query=workflow%3Arepoman)
[![contributions welcome](https://img.shields.io/badge/contributions-welcome-brightgreen.svg)](https://github.com/gentoo/sci#guide)
-[![chat on freenode](https://img.shields.io/badge/chat-on%20freenode-brightgreen.svg)](https://webchat.freenode.net/#gentoo-science)
+[![chat on libera](https://img.shields.io/badge/chat-on%20libera-brightgreen.svg)](https://web.libera.chat/#gentoo-science)
<table>
<tr>
@@ -143,5 +143,5 @@ Additionally, please make sure to add the Science Project as an additional maint
## Support
-You can ask for help on [Freenode IRC](https://www.gentoo.org/get-involved/irc-channels/) in [**#gentoo-science**](http://webchat.freenode.net/?channels=gentoo-science).
+You can ask for help on [Libera IRC](https://www.gentoo.org/get-involved/irc-channels/) in [**#gentoo-science**](https://web.libera.chat/#gentoo-science).
Alternatively you can report bugs on the [GitHub issues page](https://github.com/gentoo/sci/issues).
diff --git a/dev-cpp/blitz/blitz-1.0.3_pre20200524.ebuild b/dev-cpp/blitz/blitz-1.0.3_pre20200524.ebuild
index b92ebbcce..3c796ab5f 100644
--- a/dev-cpp/blitz/blitz-1.0.3_pre20200524.ebuild
+++ b/dev-cpp/blitz/blitz-1.0.3_pre20200524.ebuild
@@ -25,7 +25,7 @@ BDEPEND="
doc? ( app-doc/doxygen[dot] )
"
DEPEND="
- boost? ( dev-libs/boost:=[static-libs] )
+ boost? ( dev-libs/boost:=[static-libs(-)] )
"
src_configure() {
diff --git a/dev-cpp/blitz/blitz-9999.ebuild b/dev-cpp/blitz/blitz-9999.ebuild
index 7ac6d5688..cb92e37f0 100644
--- a/dev-cpp/blitz/blitz-9999.ebuild
+++ b/dev-cpp/blitz/blitz-9999.ebuild
@@ -21,7 +21,7 @@ BDEPEND="
doc? ( app-doc/doxygen[dot] )
"
DEPEND="
- boost? ( dev-libs/boost:=[static-libs] )
+ boost? ( dev-libs/boost:=[static-libs(-)] )
"
src_configure() {
diff --git a/dev-libs/lief/Manifest b/dev-libs/lief/Manifest
new file mode 100644
index 000000000..16c730fff
--- /dev/null
+++ b/dev-libs/lief/Manifest
@@ -0,0 +1 @@
+DIST lief-0.11.5.tar.gz 15519537 BLAKE2B 87f16a62df6290652ee1d301b7b067e11882c12066a3abaa4eff750c3a7fd19353001fec6a7d7e70273815064b401707f1afcad9a2006a81c2f1d118fb448d17 SHA512 fa215e6193eadd6be3f8cff92b304ca5a03db24fcb7f48b258318b8f674527fc45f6e3765ca3d6055e7a4e9f2672b2d198df02bbfcc4fa96cb36b9255df7c0c4
diff --git a/dev-libs/lief/lief-0.11.5.ebuild b/dev-libs/lief/lief-0.11.5.ebuild
new file mode 100644
index 000000000..519729525
--- /dev/null
+++ b/dev-libs/lief/lief-0.11.5.ebuild
@@ -0,0 +1,128 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+CMAKE_ECLASS=cmake
+PYTHON_COMPAT=( python3_{8..10} pypy3 )
+
+# Upstream has two alternate approaches to building its Python API:
+# 1. A working "CMakeList.txt" only supporting a single Python target.
+# 2. A non-working "setup.py" supporting multiple Python targets but internally
+# invoking CMake in mostly non-configurable (and thus broken) ways.
+# We choose working.
+#
+# Note that "cmake-multilib" *MUST* be inherited before "python-single-r1".
+inherit cmake-multilib python-single-r1
+
+DESCRIPTION="Library to instrument executable formats"
+HOMEPAGE="https://lief.quarkslab.com"
+SRC_URI="https://github.com/lief-project/LIEF/archive/${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="Apache-2.0"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+# Python is not multilib yet
+IUSE="c examples +python static-libs"
+REQUIRED_USE="python? ( ${PYTHON_REQUIRED_USE} !abi_x86_32 !abi_x86_x32 )"
+
+# See "cmake/LIEFDependencies.cmake" for C and C++ dependencies.
+BDEPEND="
+ python? (
+ $(python_gen_cond_dep '
+ >=dev-python/setuptools-31.0.0[${PYTHON_USEDEP}]
+ ')
+ )
+"
+#FIXME: Add after bumping to the next stable release:
+# >=dev-libs/spdlog-1.8.5[${MULTILIB_USEDEP}]
+RDEPEND="python? ( ${PYTHON_DEPS} )"
+DEPEND="${RDEPEND}"
+
+# LIEF tests are non-trivial (if not infeasible) to run in the general case.
+# For example, "tests/CMakeLists.txt" implies all USE flags must be enabled:
+# if (NOT LIEF_ELF OR NOT LIEF_PE OR NOT LIEF_MACHO)
+# message(FATAL_ERROR "Tests require all LIEF's modules activated" )
+# endif()
+RESTRICT="test"
+
+S="${WORKDIR}/LIEF-${PV}"
+
+pkg_setup() {
+ use python && python-single-r1_pkg_setup
+}
+
+#FIXME: Unvender currently vendored dependencies in "third-party/". Ideally,
+#upstream should add one "LIEF_EXTERNAL_${LIBNAME}" CMake option governing each
+#vendored dependency resembling the existing "LIEF_EXTERNAL_SPDLOG" option.
+#Note that LIEF patches the vendored "Boost leaf" and "utfcpp" dependencies.
+src_prepare() {
+ # Respect "multilib"-based lib dirnames.
+ sed -i -e 's~\bDESTINATION lib\(64\)\{0,1\}\b~DESTINATION ${CMAKE_INSTALL_LIBDIR}~' \
+ CMakeLists.txt || die
+
+ # Respect "python"-based installation of Python bindings. Upstream
+ # currently fails to install these bindings, resulting in Gentoo "RUNPATH"
+ # QA notices at installation time. See also:
+ # https://github.com/lief-project/LIEF/issues/599#issuecomment-889654343
+ cat <<- EOF >> api/python/CMakeLists.txt || die
+ if(LIEF_INSTALL_PYTHON)
+ install(
+ TARGETS pyLIEF
+ DESTINATION "$(python_get_sitedir)"
+ COMPONENT libraries
+ )
+ endif()
+ EOF
+
+ cmake_src_prepare
+}
+
+multilib_src_configure() {
+ # See also:
+ # * "cmake/LIEFDependencies.cmake" for a dependency list.
+ # * "cmake/LIEFOptions.cmake" for option descriptions.
+ local mycmakeargs=(
+ -DLIEF_COVERAGE=OFF
+ -DLIEF_DISABLE_FROZEN=OFF
+ -DLIEF_EXTRA_WARNINGS=OFF
+ -DLIEF_FORCE32=OFF # Defer to "cmake-multilib" for ABI management.
+ -DLIEF_PROFILING=OFF
+ -DLIEF_SUPPORT_CXX14=ON
+ -DLIEF_USE_CCACHE=OFF # Defer to Portage itself for "ccache" support.
+
+ # Disabling LIEF's format options causes build failures. See also:
+ # https://github.com/lief-project/LIEF/issues/599
+ -DLIEF_ELF=ON
+ -DLIEF_PE=ON
+ -DLIEF_MACHO=ON
+ -DLIEF_ART=ON
+ -DLIEF_DEX=ON
+ -DLIEF_OAT=ON
+ -DLIEF_VDEX=ON
+
+ -DBUILD_SHARED_LIBS="$(usex static-libs OFF ON)"
+ -DLIEF_C_API="$(usex c ON OFF)"
+ -DLIEF_EXAMPLES="$(usex examples ON OFF)"
+ -DLIEF_FORCE_API_EXPORTS="$(usex python ON OFF)" # See "setup.py".
+ -DLIEF_PYTHON_API="$(usex python ON OFF)"
+ -DLIEF_INSTALL_PYTHON="$(usex python ON OFF)"
+
+ #FIXME: Add USE flags governing most or all of these options.
+ -DLIEF_ENABLE_JSON=OFF
+ -DLIEF_DOC=OFF
+ -DLIEF_FUZZING=OFF
+ -DLIEF_INSTALL_COMPILED_EXAMPLES=OFF
+ -DLIEF_LOGGING=OFF
+ -DLIEF_LOGGING_DEBUG=OFF
+ -DLIEF_TESTS=OFF
+ -DLIEF_ASAN=OFF
+ -DLIEF_LSAN=OFF
+ -DLIEF_TSAN=OFF
+ -DLIEF_USAN=OFF
+ )
+ use python && mycmakeargs+=( -DPYTHON_EXECUTABLE="${PYTHON}" )
+
+ cmake_src_configure
+}
diff --git a/dev-libs/lief/metadata.xml b/dev-libs/lief/metadata.xml
new file mode 100644
index 000000000..da7baf4c0
--- /dev/null
+++ b/dev-libs/lief/metadata.xml
@@ -0,0 +1,14 @@
+<?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>
+ <upstream>
+ <remote-id type="github">lief-project/LIEF</remote-id>
+ </upstream>
+ <use>
+ <flag name="c">install C API</flag>
+ </use>
+</pkgmetadata>
diff --git a/dev-libs/optix/Manifest b/dev-libs/optix/Manifest
index 99902f6d6..11e08c79f 100644
--- a/dev-libs/optix/Manifest
+++ b/dev-libs/optix/Manifest
@@ -1,3 +1,4 @@
DIST NVIDIA-OptiX-SDK-6.0.0-linux64-25650775.sh 642319364 BLAKE2B 5dc6e23d606ca9f947aff046d20592729e562c66c475d47aa0cda8d3e7361cabbe102b5b0e125744d27e25321d4ac8486a55bc145c54c96c719de6e821744ba9 SHA512 33fbb312c47174a9ddb26bd4b1a1e5089b70eaebdecd80561c91c1926fba2fb8c94ec39b4c2dc8f0ccbb5e27bbd38ad8fb08df1d605ed1ec5b3fd34ecca908b7
DIST NVIDIA-OptiX-SDK-7.0.0-linux64.sh 28930132 BLAKE2B ae09bc862ccd39c25d5cc103d97b5587e21638079905e5811528b3d59deb7fd546034f24f73696c212274c0613f5b1dca7508bff696f5fec535dda7351166d7e SHA512 349baf367af7890afac87a879c8f7360cc9c93e984cf234216062af0a3cedce8fc6f3fd74240897d4b3854622ce1976a78433cbeadf6fa89c8e84d24e26eef89
DIST NVIDIA-OptiX-SDK-7.1.0-linux64-x86_64.sh 45564234 BLAKE2B 374bdbe5045ff36b71da8200ad29189cc3afba9783a38a74515caafeb90176eec5bf7a7d5e2045e47c399aa226a61fd12e6e7dd6c034b8a0f260a5850f775e47 SHA512 808a45e2007d8081de21fe15cad4577ba9fe10fc3612486b1230e03b7f17de91902dc773d1f3fef2b89398f230448d9522a03e19d4e6fa12aa4ffd78f1a4f9dc
+DIST NVIDIA-OptiX-SDK-7.2.0-linux64-x86_64.sh 44573802 BLAKE2B 546f2f02336d7487e2aab3f348290aaf9bdac153a3fe161b48ad8a897f5d14f6126e06d3b8b4c301f8a6df5735d951dcf544795b2668bc42116bd909e032b18d SHA512 c37f36e2c0d5dbf151a03513e9dc82c21c46f1a88b123153647f44f4305367d1021e522236dda97ab9c641db006242507ae323d668cf2186cf04a83a54b5707f
diff --git a/dev-libs/optix/optix-7.2.0.ebuild b/dev-libs/optix/optix-7.2.0.ebuild
new file mode 100644
index 000000000..34dcf66c4
--- /dev/null
+++ b/dev-libs/optix/optix-7.2.0.ebuild
@@ -0,0 +1,37 @@
+# Copyright 2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+DESCRIPTION="NVIDIA Ray Tracing Engine"
+HOMEPAGE="https://developer.nvidia.com/optix"
+SRC_URI="NVIDIA-OptiX-SDK-${PV}-linux64-x86_64.sh"
+S="${WORKDIR}"
+
+SLOT="0/7"
+KEYWORDS="~amd64"
+RESTRICT="fetch mirror"
+LICENSE="NVIDIA-r2"
+
+RDEPEND="
+ dev-util/nvidia-cuda-toolkit:=
+ media-libs/freeglut
+ virtual/opengl
+"
+
+pkg_nofetch() {
+ einfo "Please download ${SRC_URI} from:"
+ einfo " ${HOMEPAGE}"
+ einfo "and move it to your DISTDIR directory."
+ einfo 'DISTDIR value is available from `emerge --info`'
+}
+
+src_unpack() {
+ tail -n +223 "${DISTDIR}"/${A} | tar -zx || die
+}
+
+src_install() {
+ insinto /opt/${PN}
+ dodoc -r doc
+ doins -r include SDK
+}
diff --git a/dev-python/astroquery/astroquery-0.4.1.ebuild b/dev-python/astroquery/astroquery-0.4.1.ebuild
index 370eeb1a2..a7884eb1d 100644
--- a/dev-python/astroquery/astroquery-0.4.1.ebuild
+++ b/dev-python/astroquery/astroquery-0.4.1.ebuild
@@ -26,7 +26,7 @@ RESTRICT="test"
RDEPEND="
>=dev-python/astropy-0.2[${PYTHON_USEDEP}]
- dev-python/beautifulsoup:4[${PYTHON_USEDEP}]
+ dev-python/beautifulsoup4[${PYTHON_USEDEP}]
dev-python/html5lib[${PYTHON_USEDEP}]
dev-python/keyring[${PYTHON_USEDEP}]
dev-python/numpy[${PYTHON_USEDEP}]
diff --git a/dev-python/av/Manifest b/dev-python/av/Manifest
new file mode 100644
index 000000000..535dd5295
--- /dev/null
+++ b/dev-python/av/Manifest
@@ -0,0 +1 @@
+DIST av-8.0.3.tar.gz 2321046 BLAKE2B 546c79ab638ad3587d51fd8c598eb72d56455209f93163660e1e1dccbb325c86639d22a413c1b4cc6abce4c4f96e59ae0eb505d6a6604a6444895d594a652f7f SHA512 ba09286f0d786b6e697b91279d0ed8c2c241ef4579c1d74f33dcf4fd35a53e3a819dbbf9901183defd9f40921e94d261a129f1af660666bcd30868c6e4b6ec99
diff --git a/dev-python/av/av-8.0.3.ebuild b/dev-python/av/av-8.0.3.ebuild
new file mode 100644
index 000000000..57a8bbdfb
--- /dev/null
+++ b/dev-python/av/av-8.0.3.ebuild
@@ -0,0 +1,24 @@
+# Copyright 2020-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{8..10} )
+
+inherit distutils-r1
+
+DESCRIPTION="Pythonic bindings for FFmpeg's libraries."
+HOMEPAGE="https://github.com/mikeboers/PyAV https://pypi.org/project/av/"
+SRC_URI="mirror://pypi/${P:0:1}/${PN}/${P}.tar.gz"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+RESTRICT="test"
+
+DEPEND="media-video/ffmpeg"
+
+distutils_enable_tests setup.py
+# The configuration file (or one of the modules it imports) called sys.exit()
+# distutils_enable_sphinx docs
diff --git a/dev-python/av/metadata.xml b/dev-python/av/metadata.xml
new file mode 100644
index 000000000..325d9cc57
--- /dev/null
+++ b/dev-python/av/metadata.xml
@@ -0,0 +1,8 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <maintainer type="person">
+ <email>jpizarrocallejas@gmail.com</email>
+ <name>Jorge Pizarro Callejas</name>
+ </maintainer>
+</pkgmetadata>
diff --git a/dev-python/bokeh/bokeh-2.2.1-r1.ebuild b/dev-python/bokeh/bokeh-2.2.1-r1.ebuild
index 206e6962e..8381bfbdd 100644
--- a/dev-python/bokeh/bokeh-2.2.1-r1.ebuild
+++ b/dev-python/bokeh/bokeh-2.2.1-r1.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2020 Gentoo Authors
+# Copyright 1999-2021 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=7
@@ -36,7 +36,7 @@ RDEPEND="
"
BDEPEND="
test? (
- dev-python/beautifulsoup:4[${PYTHON_USEDEP}]
+ dev-python/beautifulsoup4[${PYTHON_USEDEP}]
dev-python/flaky[${PYTHON_USEDEP}]
dev-python/ipython_genutils[${PYTHON_USEDEP}]
dev-python/mock[${PYTHON_USEDEP}]
diff --git a/dev-python/bokeh/bokeh-2.2.2-r1.ebuild b/dev-python/bokeh/bokeh-2.2.2-r1.ebuild
index 206e6962e..8381bfbdd 100644
--- a/dev-python/bokeh/bokeh-2.2.2-r1.ebuild
+++ b/dev-python/bokeh/bokeh-2.2.2-r1.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2020 Gentoo Authors
+# Copyright 1999-2021 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=7
@@ -36,7 +36,7 @@ RDEPEND="
"
BDEPEND="
test? (
- dev-python/beautifulsoup:4[${PYTHON_USEDEP}]
+ dev-python/beautifulsoup4[${PYTHON_USEDEP}]
dev-python/flaky[${PYTHON_USEDEP}]
dev-python/ipython_genutils[${PYTHON_USEDEP}]
dev-python/mock[${PYTHON_USEDEP}]
diff --git a/dev-python/bokeh/bokeh-2.2.3.ebuild b/dev-python/bokeh/bokeh-2.2.3.ebuild
index 206e6962e..8381bfbdd 100644
--- a/dev-python/bokeh/bokeh-2.2.3.ebuild
+++ b/dev-python/bokeh/bokeh-2.2.3.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2020 Gentoo Authors
+# Copyright 1999-2021 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=7
@@ -36,7 +36,7 @@ RDEPEND="
"
BDEPEND="
test? (
- dev-python/beautifulsoup:4[${PYTHON_USEDEP}]
+ dev-python/beautifulsoup4[${PYTHON_USEDEP}]
dev-python/flaky[${PYTHON_USEDEP}]
dev-python/ipython_genutils[${PYTHON_USEDEP}]
dev-python/mock[${PYTHON_USEDEP}]
diff --git a/dev-python/bokeh/bokeh-2.3.0.ebuild b/dev-python/bokeh/bokeh-2.3.0.ebuild
index c3f35c24c..8c00f2092 100644
--- a/dev-python/bokeh/bokeh-2.3.0.ebuild
+++ b/dev-python/bokeh/bokeh-2.3.0.ebuild
@@ -35,7 +35,7 @@ RDEPEND="
"
BDEPEND="
test? (
- dev-python/beautifulsoup:4[${PYTHON_USEDEP}]
+ dev-python/beautifulsoup4[${PYTHON_USEDEP}]
dev-python/flaky[${PYTHON_USEDEP}]
dev-python/ipython_genutils[${PYTHON_USEDEP}]
dev-python/mock[${PYTHON_USEDEP}]
diff --git a/dev-python/bokeh/bokeh-2.3.1.ebuild b/dev-python/bokeh/bokeh-2.3.1.ebuild
index c3f35c24c..8c00f2092 100644
--- a/dev-python/bokeh/bokeh-2.3.1.ebuild
+++ b/dev-python/bokeh/bokeh-2.3.1.ebuild
@@ -35,7 +35,7 @@ RDEPEND="
"
BDEPEND="
test? (
- dev-python/beautifulsoup:4[${PYTHON_USEDEP}]
+ dev-python/beautifulsoup4[${PYTHON_USEDEP}]
dev-python/flaky[${PYTHON_USEDEP}]
dev-python/ipython_genutils[${PYTHON_USEDEP}]
dev-python/mock[${PYTHON_USEDEP}]
diff --git a/dev-python/bokeh/bokeh-2.3.2.ebuild b/dev-python/bokeh/bokeh-2.3.2.ebuild
index c3f35c24c..8c00f2092 100644
--- a/dev-python/bokeh/bokeh-2.3.2.ebuild
+++ b/dev-python/bokeh/bokeh-2.3.2.ebuild
@@ -35,7 +35,7 @@ RDEPEND="
"
BDEPEND="
test? (
- dev-python/beautifulsoup:4[${PYTHON_USEDEP}]
+ dev-python/beautifulsoup4[${PYTHON_USEDEP}]
dev-python/flaky[${PYTHON_USEDEP}]
dev-python/ipython_genutils[${PYTHON_USEDEP}]
dev-python/mock[${PYTHON_USEDEP}]
diff --git a/dev-python/cadquery-ocp/Manifest b/dev-python/cadquery-ocp/Manifest
new file mode 100644
index 000000000..2fdce96f0
--- /dev/null
+++ b/dev-python/cadquery-ocp/Manifest
@@ -0,0 +1 @@
+DIST cadquery-ocp-7.5.2_beta.tar.gz 5571554 BLAKE2B 552e44b301b69f1b1b4f6c26c46638bcf94a5f753d4d35e2cbbd6e1d963a23c685d6c05ead56c970c6532a3adbbf7b1f2bd572e72fb482ccd2dac04585764910 SHA512 041d12632678b96f23528f289516e31457a4e0d3251db6f01e3fc2bb2ccc41d2df8b825c94db0cebd7419cf82070c75d20852f25d91f05377502d75adf493fd8
diff --git a/dev-python/cadquery-ocp/cadquery-ocp-7.5.2_beta.ebuild b/dev-python/cadquery-ocp/cadquery-ocp-7.5.2_beta.ebuild
new file mode 100644
index 000000000..1a638a985
--- /dev/null
+++ b/dev-python/cadquery-ocp/cadquery-ocp-7.5.2_beta.ebuild
@@ -0,0 +1,195 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+PYTHON_COMPAT=( python3_{8..9} )
+
+# OCP uses "python-single-r1" only because VTK uses "python-single-r1".
+inherit check-reqs cmake llvm multiprocessing python-single-r1
+
+MY_PN=OCP
+MY_PV="${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="
+ ${PYTHON_DEPS}
+ sci-libs/opencascade:7.5=[json,tbb,vtk,-gles2]
+ >=sci-libs/vtk-9.0.0[python,${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="${EPREFIX}/usr/include/opencascade-${OCCT_PV}"
+ local _OCCT_LIB_DIR="${EPREFIX}/usr/lib64/opencascade-${OCCT_PV}"
+
+ # 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/toposort/metadata.xml b/dev-python/cadquery-ocp/metadata.xml
index 7ef2c3782..a8bf5ee04 100644
--- a/dev-python/toposort/metadata.xml
+++ b/dev-python/cadquery-ocp/metadata.xml
@@ -6,7 +6,6 @@
<name>Gentoo Science Project</name>
</maintainer>
<upstream>
- <remote-id type="gitlab">ericvsmith/toposort</remote-id>
- <remote-id type="pypi">toposort</remote-id>
+ <remote-id type="github">CadQuery/OCP</remote-id>
</upstream>
</pkgmetadata>
diff --git a/dev-python/cadquery-pywrap/Manifest b/dev-python/cadquery-pywrap/Manifest
new file mode 100644
index 000000000..a203693d6
--- /dev/null
+++ b/dev-python/cadquery-pywrap/Manifest
@@ -0,0 +1 @@
+DIST cadquery-pywrap-7.5.2_rc20210526.tar.gz 5584220 BLAKE2B b26fd4092f94e3d3eec191c0791faf29d90da2d85f9aa9a2f1cdf128975564db9f6b6002661eed8bbecddb31988ad2076a3a00ea601a43e38ffaa47e545911ca SHA512 40aa61e0774228c70c8ae41a6078a280d63697d297234dbff51ec84982b4a9f0a09db41c74a834ae91d01881a4d5660b1ebbb701d24141307a5fedcdfb075872
diff --git a/dev-python/cadquery-pywrap/cadquery-pywrap-7.5.2_rc20210526.ebuild b/dev-python/cadquery-pywrap/cadquery-pywrap-7.5.2_rc20210526.ebuild
new file mode 100644
index 000000000..fc97f9db1
--- /dev/null
+++ b/dev-python/cadquery-pywrap/cadquery-pywrap-7.5.2_rc20210526.ebuild
@@ -0,0 +1,70 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+PYTHON_COMPAT=( python3_{8..9} )
+
+inherit llvm toolchain-funcs 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 7.5.2 has yet to be
+# officially released. We instead package a commit known to work as expected.
+MY_COMMIT="f8869e5a47fd3e3e1d31e7ab89b46c158f7487bf"
+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() {
+ # Relax Jinja version requirements. See also upstream pull request:
+ # https://github.com/CadQuery/pywrap/pull/34
+ sed -i -e "s~'jinja2==\\(.*\\)',~'jinja2>=\\1,<4',~" setup.py || die
+ sed -i \
+ -e 's~^\({%- macro super(cls,classes,typedefs\)\() -%}\)$~\1=[]\2~' \
+ bindgen/macros.j2 || die
+
+ #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-pywrap/metadata.xml b/dev-python/cadquery-pywrap/metadata.xml
new file mode 100644
index 000000000..aef989a0c
--- /dev/null
+++ b/dev-python/cadquery-pywrap/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">CadQuery/pywrap</remote-id>
+ </upstream>
+</pkgmetadata>
diff --git a/dev-python/cadquery/Manifest b/dev-python/cadquery/Manifest
new file mode 100644
index 000000000..ae1e31fa3
--- /dev/null
+++ b/dev-python/cadquery/Manifest
@@ -0,0 +1 @@
+DIST cadquery-2.2_rc20210804.tar.gz 2832275 BLAKE2B b1b25130a9eb73e4913c6e9fc8d1fafd689bc9d216adee6d7fcc6fd80805b9351e87839fae3d6bf7e0a1ccf147e5b4a9afe8f6afc0e01c1b3a287e2671870c8d SHA512 0c5b16da24deba2267b204e5f51f707fffab9a238b27af84a500b8a98aa190be24be75d7bc2d1e282c04aea7116eb404ed4520515d53ae5a64aebafc647aa4a3
diff --git a/dev-python/cadquery/cadquery-2.2_rc20210804.ebuild b/dev-python/cadquery/cadquery-2.2_rc20210804.ebuild
new file mode 100644
index 000000000..3eafde559
--- /dev/null
+++ b/dev-python/cadquery/cadquery-2.2_rc20210804.ebuild
@@ -0,0 +1,56 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DISTUTILS_SINGLE_IMPL=1
+PYTHON_COMPAT=( python3_{8..9} )
+
+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="9b657093c30147293034068dd9d58ec2b728e61a"
+
+#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? (
+ $(python_gen_cond_dep '
+ dev-python/pytest[${PYTHON_USEDEP}]
+ 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,${PYTHON_USEDEP}]
+ ')
+"
+DEPEND="${RDEPEND}"
+
+S="${WORKDIR}/${PN}-${MY_COMMIT}"
+
+distutils_enable_tests pytest
+
+#FIXME: Uncomment after packaging "dev-python/sphinx-autodoc-typehints".
+# distutils_enable_sphinx docs dev-python/sphinx_rtd_theme dev-python/sphinx-autodoc-typehints
diff --git a/dev-python/cadquery/metadata.xml b/dev-python/cadquery/metadata.xml
new file mode 100644
index 000000000..86166e277
--- /dev/null
+++ b/dev-python/cadquery/metadata.xml
@@ -0,0 +1,12 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <maintainer type="project">
+ <email>sci@gentoo.org</email>
+ <name>Gentoo Science Project</name>
+ </maintainer>
+ <stabilize-allarches/>
+ <upstream>
+ <remote-id type="github">CadQuery/cadquery</remote-id>
+ </upstream>
+</pkgmetadata>
diff --git a/dev-python/cymbal/Manifest b/dev-python/cymbal/Manifest
new file mode 100644
index 000000000..600b61b10
--- /dev/null
+++ b/dev-python/cymbal/Manifest
@@ -0,0 +1 @@
+DIST cymbal-1.0.0.tar.gz 4145 BLAKE2B b6da0ce4e32f19f0a91c7e4d917b13c64f1d0d9b37503962b5d73f6b00a37a54637c5d4ebf95d64952e32df2e7652076bde37a51dc316549775c59ea2ab50bb3 SHA512 0bd6bf5996787c5e24d9f9266654b4a501d5479dd1444d064c6a2241ce3e39ddbc12552f4cf22c03e61ba47f0492dc8a6515bb934bcc3523b5a29cb1a4530348
diff --git a/dev-python/cymbal/cymbal-1.0.0.ebuild b/dev-python/cymbal/cymbal-1.0.0.ebuild
new file mode 100644
index 000000000..a16fcd44c
--- /dev/null
+++ b/dev-python/cymbal/cymbal-1.0.0.ebuild
@@ -0,0 +1,34 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{8..10} )
+
+inherit distutils-r1
+
+DESCRIPTION="Add functionality missing from the python libclang bindings"
+HOMEPAGE="https://pypi.org/project/cymbal"
+SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+DEPEND="dev-python/clang-python[${PYTHON_USEDEP}]"
+RDEPEND="${DEPEND}"
+
+distutils_enable_tests pytest
+
+# Prevent "setup.py" from installing the "tests" package.
+src_prepare() {
+ sed -i -e 's~\(packages = \)find_packages(),~\1["cymbal"],~' \
+ setup.py || die
+
+ default_src_prepare
+}
+
+# Omit "test_class_template_arg", failing due to outdated clang assumptions.
+python_test() {
+ pytest -k 'not test_class_template_arg' || die
+}
diff --git a/dev-python/cymbal/metadata.xml b/dev-python/cymbal/metadata.xml
new file mode 100644
index 000000000..02975a0d9
--- /dev/null
+++ b/dev-python/cymbal/metadata.xml
@@ -0,0 +1,13 @@
+<?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="pypi">cymbal</remote-id>
+ <remote-id type="github">AndrewWalker/cymbal</remote-id>
+ </upstream>
+</pkgmetadata>
diff --git a/dev-python/datrie/datrie-0.8.2.ebuild b/dev-python/datrie/datrie-0.8.2.ebuild
index de547910d..d3046bf8d 100644
--- a/dev-python/datrie/datrie-0.8.2.ebuild
+++ b/dev-python/datrie/datrie-0.8.2.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2020 Gentoo Authors
+# Copyright 1999-2021 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=7
@@ -8,7 +8,7 @@ PYTHON_COMPAT=( python3_{7,8,9} )
inherit distutils-r1
DESCRIPTION="Implements a topological sort algorithm"
-HOMEPAGE="https://gitlab.com/ericvsmith/toposort"
+HOMEPAGE="https://github.com/pytries/datrie"
SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
LICENSE="LGPL-2+"
diff --git a/dev-python/ezdxf/Manifest b/dev-python/ezdxf/Manifest
new file mode 100644
index 000000000..24626a24c
--- /dev/null
+++ b/dev-python/ezdxf/Manifest
@@ -0,0 +1 @@
+DIST ezdxf-0.16.5.zip 1552408 BLAKE2B d52131c776c5560da659db67b87a5403a0a0f44aa21781d9599555cc71a3a91cd4e92574f985079456bfd6c844fb693cdef5d16277e83dbd6ca378013d5423ca SHA512 1e35aea16bf169bc2fe3bc3accf83f42189371a80cea259f46dcee1e9c75b613f9c09e6e300a2f331510722a1eefa1550052b7d58c08c4e3a0868cebdfe7b330
diff --git a/dev-python/ezdxf/ezdxf-0.16.5.ebuild b/dev-python/ezdxf/ezdxf-0.16.5.ebuild
new file mode 100644
index 000000000..43bf7c371
--- /dev/null
+++ b/dev-python/ezdxf/ezdxf-0.16.5.ebuild
@@ -0,0 +1,34 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+#FIXME: Upstream explicitly supports "pypy3", but Gentoo dependencies do not.
+PYTHON_COMPAT=( python3_{8..10} )
+
+inherit distutils-r1
+
+DESCRIPTION="Python interface to DXF"
+HOMEPAGE="https://pypi.org/project/ezdxf"
+SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.zip"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="cython matplotlib qt5"
+
+BDEPEND="
+ cython? ( dev-python/cython[${PYTHON_USEDEP}] )
+ app-arch/unzip
+"
+DEPEND="
+ dev-python/typing-extensions[${PYTHON_USEDEP}]
+ >=dev-python/pyparsing-2.0.1[${PYTHON_USEDEP}]
+"
+RDEPEND="${DEPEND}
+ matplotlib? ( dev-python/matplotlib[${PYTHON_USEDEP}] )
+ qt5? ( dev-python/PyQt5[${PYTHON_USEDEP}] )
+"
+
+#FIXME: Enabling tests requires packaging additional packages (e.g., "geomdl").
+RESTRICT="test"
diff --git a/dev-python/ezdxf/metadata.xml b/dev-python/ezdxf/metadata.xml
new file mode 100644
index 000000000..768dc7877
--- /dev/null
+++ b/dev-python/ezdxf/metadata.xml
@@ -0,0 +1,17 @@
+<?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>
+ <upstream>
+ <remote-id type="pypi">ezdxf</remote-id>
+ <remote-id type="github">mozman/ezdxf</remote-id>
+ </upstream>
+ <use>
+ <flag name="cython">Build Cython-based C extensions</flag>
+ <flag name="matplotlib">Add support for dev-python/matplotlib</flag>
+ <flag name="qt5">Add support for dev-python/PyQt5</flag>
+ </use>
+</pkgmetadata>
diff --git a/dev-python/gffpandas/Manifest b/dev-python/gffpandas/Manifest
new file mode 100644
index 000000000..8d84e74c6
--- /dev/null
+++ b/dev-python/gffpandas/Manifest
@@ -0,0 +1 @@
+DIST gffpandas-1.2.0.tar.gz 32040 BLAKE2B 66f53357876d417997366cdcbacd778f2b17e7df113d21f2a836b082719f549ede5e06a9a6c46e9c5bee2d86946871e68ab1f9b7af0defcaa8a55ae8ef93b274 SHA512 feb67ea93a078547103c1c6b8f32bd6bbd69ab669b93b90aa5f48bc0ebc25ea23e35130976bf1a89ff5e92fdbd054c4df98cc961278c7caaf28b48c202a662d7
diff --git a/dev-python/gffpandas/gffpandas-1.2.0.ebuild b/dev-python/gffpandas/gffpandas-1.2.0.ebuild
new file mode 100644
index 000000000..12ec9927c
--- /dev/null
+++ b/dev-python/gffpandas/gffpandas-1.2.0.ebuild
@@ -0,0 +1,29 @@
+# Copyright 2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+PYTHON_COMPAT=( python3_{8..10} )
+
+inherit distutils-r1
+
+DESCRIPTION="Python library to Filter and sort GFF3 annotations"
+HOMEPAGE="https://github.com/foerstner-lab/gffpandas
+ https://gffpandas.readthedocs.io/en/latest/"
+SRC_URI="https://github.com/foerstner-lab/${PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="ISC"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+RDEPEND="dev-python/pandas[${PYTHON_USEDEP}]"
+
+distutils_enable_tests pytest
+distutils_enable_sphinx docs/source dev-python/sphinx_rtd_theme
+
+python_prepare_all() {
+ # Do not depend on pytest-runner
+ sed -i -e '/pytest-runner/d' setup.py || die
+
+ distutils-r1_python_prepare_all
+}
diff --git a/sci-biology/rum/metadata.xml b/dev-python/gffpandas/metadata.xml
index 032147c48..c3d31ba1d 100644
--- a/sci-biology/rum/metadata.xml
+++ b/dev-python/gffpandas/metadata.xml
@@ -10,6 +10,7 @@
<name>Gentoo Biology Project</name>
</maintainer>
<upstream>
- <remote-id type="github">itmat/rum</remote-id>
+ <remote-id type="github">foerstner-lab/gffpandas</remote-id>
+ <remote-id type="pypi">gffpandas</remote-id>
</upstream>
</pkgmetadata>
diff --git a/dev-python/jupyterlab_launcher/Manifest b/dev-python/jupyterlab_launcher/Manifest
new file mode 100644
index 000000000..c1d49b101
--- /dev/null
+++ b/dev-python/jupyterlab_launcher/Manifest
@@ -0,0 +1 @@
+DIST jupyterlab_launcher-0.13.1.tar.gz 20418 BLAKE2B 1cfe0e357da0926468a7dfb8b6b2d6eb870593b6bb9ac5c798a90f876c76b82c07cca7948bbdfdc0f4e49cefb67c0ba56edc0d7334e969a76cec2407353afd63 SHA512 f7b4267379fd21e80688e565f788277b92aad748971c077e694246ae01c7f56b5a6a50d4fa9d3bfecc561b723d6bcbbb988f019268d2752076ec6293f9960406
diff --git a/dev-python/jupyterlab_launcher/jupyterlab_launcher-0.13.1.ebuild b/dev-python/jupyterlab_launcher/jupyterlab_launcher-0.13.1.ebuild
new file mode 100644
index 000000000..80abd3be5
--- /dev/null
+++ b/dev-python/jupyterlab_launcher/jupyterlab_launcher-0.13.1.ebuild
@@ -0,0 +1,26 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{8..9} )
+
+inherit distutils-r1
+
+DESCRIPTION="Jupyter Launcher"
+HOMEPAGE="https://jupyter.org/"
+SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64"
+
+# TODO: fix this
+RESTRICT="test"
+
+RDEPEND="
+ >=dev-python/jsonschema-2.6.0[${PYTHON_USEDEP}]
+ >=dev-python/notebook-4.2.0[${PYTHON_USEDEP}]
+"
+
+distutils_enable_tests pytest
diff --git a/sci-chemistry/talosn/metadata.xml b/dev-python/jupyterlab_launcher/metadata.xml
index da36ecbfc..ae9640ffb 100644
--- a/sci-chemistry/talosn/metadata.xml
+++ b/dev-python/jupyterlab_launcher/metadata.xml
@@ -2,7 +2,7 @@
<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<maintainer type="project">
- <email>sci-chemistry@gentoo.org</email>
- <name>Gentoo Chemistry Project</name>
+ <email>sci@gentoo.org</email>
+ <name>Gentoo Science Project</name>
</maintainer>
</pkgmetadata>
diff --git a/dev-python/logzero/Manifest b/dev-python/logzero/Manifest
new file mode 100644
index 000000000..73c1e0244
--- /dev/null
+++ b/dev-python/logzero/Manifest
@@ -0,0 +1 @@
+DIST logzero-1.7.0.tar.gz 577803 BLAKE2B d54c16ee55e105bf026695dcac21065f58f04bc1d6a66d0d80f4a8f2a0dddabbca8c901dd596643977010ca1aae29fddaf194ef8f2882fd6660b764ce9070d98 SHA512 6c9647e81f16479a09b11383a9b6e7fb1068e61007cf9884d59469535706850a4ef2893d7393feb68dcdeb0793dcb8c41f8f3865289792de97dd20a5d32224bb
diff --git a/dev-python/logzero/logzero-1.7.0.ebuild b/dev-python/logzero/logzero-1.7.0.ebuild
new file mode 100644
index 000000000..717426899
--- /dev/null
+++ b/dev-python/logzero/logzero-1.7.0.ebuild
@@ -0,0 +1,18 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{8..10} pypy3 )
+
+inherit distutils-r1
+
+DESCRIPTION="Robust and effective logging for Python 2 and 3"
+HOMEPAGE="https://pypi.org/project/logzero"
+SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+distutils_enable_tests pytest
diff --git a/dev-python/logzero/metadata.xml b/dev-python/logzero/metadata.xml
new file mode 100644
index 000000000..3bdc37964
--- /dev/null
+++ b/dev-python/logzero/metadata.xml
@@ -0,0 +1,13 @@
+<?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="pypi">logzero</remote-id>
+ <remote-id type="github">metachris/logzero</remote-id>
+ </upstream>
+</pkgmetadata>
diff --git a/dev-python/meshio/Manifest b/dev-python/meshio/Manifest
new file mode 100644
index 000000000..191a8e4aa
--- /dev/null
+++ b/dev-python/meshio/Manifest
@@ -0,0 +1 @@
+DIST meshio-4.4.6.tar.gz 482071 BLAKE2B f8d410ad7293b5e7f9debbb1e4dc9050304731bee1091b4480aeace006a92bb8f7cec2fc442d0f5b20d492ae859bb76cbb52b6be26f06be2558bc42a27d9cd96 SHA512 624f551b017b6c4e44efc5db0fb6d08a161ceef64d1317264eaf3ba0f36202b93c3fa959ab34ce8212c01083ae570b3db25c7445eee2d51feaf84726984e2770
diff --git a/dev-python/meshio/meshio-4.4.6.ebuild b/dev-python/meshio/meshio-4.4.6.ebuild
new file mode 100644
index 000000000..ec5af300f
--- /dev/null
+++ b/dev-python/meshio/meshio-4.4.6.ebuild
@@ -0,0 +1,26 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+PYTHON_COMPAT=( python3_{8..9} )
+DISTUTILS_USE_SETUPTOOLS=pyproject.toml
+
+inherit distutils-r1
+
+DESCRIPTION="Python input/output for many mesh formats"
+HOMEPAGE="https://pypi.org/project/meshio"
+SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
+
+LICENSE="MIT"
+KEYWORDS="~amd64 ~x86"
+SLOT="0"
+
+BDEPEND="
+ test? (
+ dev-python/h5py[${PYTHON_USEDEP}]
+ dev-python/netcdf4-python[${PYTHON_USEDEP}]
+ )
+"
+
+distutils_enable_tests pytest
diff --git a/dev-python/meshio/metadata.xml b/dev-python/meshio/metadata.xml
new file mode 100644
index 000000000..1bfb9f30f
--- /dev/null
+++ b/dev-python/meshio/metadata.xml
@@ -0,0 +1,13 @@
+<?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="pypi">meshio</remote-id>
+ <remote-id type="github">nschloe/meshio</remote-id>
+ </upstream>
+</pkgmetadata>
diff --git a/dev-python/nptyping/Manifest b/dev-python/nptyping/Manifest
new file mode 100644
index 000000000..585f387a9
--- /dev/null
+++ b/dev-python/nptyping/Manifest
@@ -0,0 +1 @@
+DIST nptyping-1.4.3.tar.gz 47943 BLAKE2B 0e4acfc1bd9cc3cae98c6aebab3c4c1aa47a7547adaacb3835a4cb0150cc11a628ce84e30e3d811ca93a33f0b97f0ebd320b8bd0be2bd2e8651154526a69cdf6 SHA512 1cfec2215965902b9df2b4b440a37fc6241734b6befb76feac509c688073f1dda67f5832673aab3f9d718ce0aebc916b6b3b5218bb74f21118a19722b630a7fe
diff --git a/dev-python/nptyping/metadata.xml b/dev-python/nptyping/metadata.xml
new file mode 100644
index 000000000..7b2aa8131
--- /dev/null
+++ b/dev-python/nptyping/metadata.xml
@@ -0,0 +1,13 @@
+<?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="pypi">nptyping</remote-id>
+ <remote-id type="github">ramonhagenaars/nptyping</remote-id>
+ </upstream>
+</pkgmetadata>
diff --git a/dev-python/nptyping/nptyping-1.4.3.ebuild b/dev-python/nptyping/nptyping-1.4.3.ebuild
new file mode 100644
index 000000000..b2d6ad271
--- /dev/null
+++ b/dev-python/nptyping/nptyping-1.4.3.ebuild
@@ -0,0 +1,27 @@
+# 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
+
+DESCRIPTION="Type hints for NumPy"
+HOMEPAGE="https://pypi.org/project/nptyping"
+
+# Prefer GitHub. Upstream failed to push its source tarball to PyPI.
+SRC_URI="https://github.com/ramonhagenaars/nptyping/archive/refs/tags/v${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+DEPEND="
+ dev-python/numpy[${PYTHON_USEDEP}]
+ >=dev-python/typish-1.7.0[${PYTHON_USEDEP}]
+"
+RDEPEND="${DEPEND}"
+
+#FIXME: Enabling tests requires packaging additional packages (e.g., "xenon").
+RESTRICT="test"
diff --git a/dev-python/numba/Manifest b/dev-python/numba/Manifest
index e9b7bd181..6791f6231 100644
--- a/dev-python/numba/Manifest
+++ b/dev-python/numba/Manifest
@@ -1 +1 @@
-DIST numba-0.53.1.tar.gz 2241224 BLAKE2B cbd018aa15b68ec892259b917f2c1cbac66a35ab39c5a67855f1d2e1d4a2a9c88c4af1c92a64c9394a6acda0ab67b4590547f0d6889b812fc7625f9b7954c374 SHA512 85bee593a6cac7faa5c284881b7ab5a0076c5cc8d5e12d23d03b8c738d5bb8b53dd7a10d45555ecaef0f015e9105a51aef1011592a70a4b3123a58c92305d0ba
+DIST numba-0.54.0.tar.gz 2263308 BLAKE2B 263334786a1bbdec91186e85de5a5a3b003f704be1e925c0c46f5797a0d2c56b1c86760f40e83c2b36fd68a97601fb9ec0df70fac9a5efdc7b2d33a9c19666eb SHA512 c8091e4209ae7005ac04ea8c6f9c0e534b46f38cdfe692db562bb374beff71162c353d597f12a70edcf572792c71e1955e25de60edd69bf4b6a1a0e22b3dff90
diff --git a/dev-python/numba/numba-0.53.1.ebuild b/dev-python/numba/numba-0.54.0.ebuild
index d1ee3f0b7..125b20daf 100644
--- a/dev-python/numba/numba-0.53.1.ebuild
+++ b/dev-python/numba/numba-0.54.0.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..9} )
DISTUTILS_USE_SETUPTOOLS=rdepend
inherit optfeature multiprocessing distutils-r1
@@ -18,27 +18,20 @@ SLOT="0"
KEYWORDS="~amd64 ~arm ~arm64 ~x86"
IUSE="openmp threads"
-# Minimum dependency versions derive from:
-# * For llvmlite, the "min_llvmlite_version" and "max_llvmlite_version" globals
-# in "setup.py".
-# * For NumPy, the "min_numpy_run_version" global in "setup.py".
-# * For TBB, #error pragmas in "numba/np/ufunc/tbbpool.cpp" like:
-# #error "TBB version is too old, 2019 update 5...
-# Lastly, note the "numba -s" subcommand requires "pip" at runtime.
RDEPEND="
- >=dev-python/llvmlite-0.36.0[${PYTHON_USEDEP}]
- <dev-python/llvmlite-0.37.0
- >=dev-python/numpy-1.15.0[${PYTHON_USEDEP}]
- dev-python/pip[${PYTHON_USEDEP}]
- dev-python/scipy[${PYTHON_USEDEP}]
+ >=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 )
"
-DEPEND="${RDEPEND}"
+BDEPEND="
+ dev-python/pip[${PYTHON_USEDEP}]
+ dev-python/versioneer[${PYTHON_USEDEP}]
+"
DISTUTILS_IN_SOURCE_BUILD=1
distutils_enable_tests unittest
-# Only works in a git repository
-#distutils_enable_sphinx docs/source dev-python/numpydoc
+distutils_enable_sphinx docs/source dev-python/numpydoc dev-python/sphinx_rtd_theme
PATCHES=(
"${FILESDIR}/${PN}-0.52.0-skip_tests.patch"
@@ -46,22 +39,34 @@ PATCHES=(
pkg_setup() {
if ! use openmp; then
- export NUMBA_DISABLE_OPENMP=1
+ export NUMBA_DISABLE_OPENMP=1 || die
else
- unset NUMBA_DISABLE_OPENMP
+ unset NUMBA_DISABLE_OPENMP || die
fi
if ! use threads; then
- export NUMBA_DISABLE_TBB=1
+ export NUMBA_DISABLE_TBB=1 || die
else
- unset NUMBA_DISABLE_TBB
- export TBBROOT="${EPREFIX}/usr"
+ 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
+ export MAKEOPTS=-j1 || die
distutils-r1_python_compile
}
diff --git a/dev-python/pynndescent/Manifest b/dev-python/pynndescent/Manifest
index e7ea7da50..d3d33643f 100644
--- a/dev-python/pynndescent/Manifest
+++ b/dev-python/pynndescent/Manifest
@@ -1,3 +1 @@
-DIST pynndescent-0.4.8.tar.gz 1134120 BLAKE2B bb82bf27edee6bb5f92e7ba9c762ffadffd16854450d28c2eda416b98ff0e67127860347748c663a094ddad44027db312b935a49fa60604146a9df1620edffe1 SHA512 e85feed2cc78e9a4364a61ce3c03b029dd0db643b4d9e7efa14dfda90e6e2512ba7a4dc083b440696b070262e2111f50b6dcb41915e26fe8d8332b47837ad9fc
-DIST pynndescent-0.5.1.tar.gz 1138551 BLAKE2B 175fcc284f61f1aa4704587b8dc5fbdf356d75be79b878a7f64ec807e32f241f0c0c94bb689de64f8117e7b593f439564731cba3d2247093a98a4273a05a9e4f SHA512 15694cbed64b86d48aa70a5ccda57b21fe040fca147e367d81bf527a7c329c80b7bd0f46f09612236c470fee0d35c7f48cb42e6476f6fc022ab8612321a7cd95
DIST pynndescent-0.5.2.tar.gz 1148182 BLAKE2B 64cff5fe0d92b2d735564b7e3a1dc62c64bcaec33d8d5bfaffbcf61423ff1cef388dd2335479dff5af7f50848dbe8d9640a22add54b2b90a979cb13d0894b371 SHA512 b38bbf8aab91d4278572a6446e4750022e2b2bc82e7a8f7754b8ec74c0ae1f7795364ef4e22cd6bd39071056ebacaedeb79981620e3143d3c9060a1520c85aae
diff --git a/dev-python/pynndescent/pynndescent-0.4.8.ebuild b/dev-python/pynndescent/pynndescent-0.4.8.ebuild
deleted file mode 100644
index 49c6afa23..000000000
--- a/dev-python/pynndescent/pynndescent-0.4.8.ebuild
+++ /dev/null
@@ -1,27 +0,0 @@
-# Copyright 1999-2020 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-PYTHON_COMPAT=( python3_{6..8} )
-
-inherit distutils-r1
-
-DESCRIPTION="nearest neighbor descent for approximate nearest neighbors"
-HOMEPAGE="https://github.com/lmcinnes/pynndescent"
-SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-
-RDEPEND="${PYTHON_DEPS}
- dev-python/joblib[${PYTHON_USEDEP}]
- >=dev-python/numba-0.51.2[${PYTHON_USEDEP}]
- >=dev-python/llvmlite-0.34[${PYTHON_USEDEP}]
- dev-python/scipy[${PYTHON_USEDEP}]
- <=sci-libs/scikit-learn-0.24.0[${PYTHON_USEDEP}]
-"
-DEPEND="${RDEPEND}"
-
-distutils_enable_tests nose
diff --git a/dev-python/pynndescent/pynndescent-0.5.1.ebuild b/dev-python/pynndescent/pynndescent-0.5.1.ebuild
deleted file mode 100644
index 49c6afa23..000000000
--- a/dev-python/pynndescent/pynndescent-0.5.1.ebuild
+++ /dev/null
@@ -1,27 +0,0 @@
-# Copyright 1999-2020 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-PYTHON_COMPAT=( python3_{6..8} )
-
-inherit distutils-r1
-
-DESCRIPTION="nearest neighbor descent for approximate nearest neighbors"
-HOMEPAGE="https://github.com/lmcinnes/pynndescent"
-SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-
-RDEPEND="${PYTHON_DEPS}
- dev-python/joblib[${PYTHON_USEDEP}]
- >=dev-python/numba-0.51.2[${PYTHON_USEDEP}]
- >=dev-python/llvmlite-0.34[${PYTHON_USEDEP}]
- dev-python/scipy[${PYTHON_USEDEP}]
- <=sci-libs/scikit-learn-0.24.0[${PYTHON_USEDEP}]
-"
-DEPEND="${RDEPEND}"
-
-distutils_enable_tests nose
diff --git a/dev-python/pynndescent/pynndescent-0.5.2.ebuild b/dev-python/pynndescent/pynndescent-0.5.2.ebuild
index 894f3114f..3eeb7ae79 100644
--- a/dev-python/pynndescent/pynndescent-0.5.2.ebuild
+++ b/dev-python/pynndescent/pynndescent-0.5.2.ebuild
@@ -3,7 +3,7 @@
EAPI=7
-PYTHON_COMPAT=( python3_{6..8} )
+PYTHON_COMPAT=( python3_{8..9} )
inherit distutils-r1
@@ -19,9 +19,9 @@ RDEPEND="${PYTHON_DEPS}
dev-python/joblib[${PYTHON_USEDEP}]
>=dev-python/numba-0.51.2[${PYTHON_USEDEP}]
>=dev-python/llvmlite-0.34[${PYTHON_USEDEP}]
- dev-python/scipy[${PYTHON_USEDEP}]
- <=sci-libs/scikit-learn-0.24.0[${PYTHON_USEDEP}]
+ >=dev-python/scipy-1.0[${PYTHON_USEDEP}]
+ >=sci-libs/scikit-learn-0.18.0[${PYTHON_USEDEP}]
"
DEPEND="${RDEPEND}"
-distutils_enable_tests nose
+distutils_enable_tests pytest
diff --git a/dev-python/pyvista/Manifest b/dev-python/pyvista/Manifest
new file mode 100644
index 000000000..b4d7a9196
--- /dev/null
+++ b/dev-python/pyvista/Manifest
@@ -0,0 +1 @@
+DIST pyvista-0.31.1.tar.gz 1249426 BLAKE2B 1f52f5bf5a5bc7bee1197a8b31c8806eae9c6ca03f45b8db601625134f9ce8fd301bc8032923f31ae0e75292c1126fb65076e48a5bc11f6838d6d2b42c75fddf SHA512 f184f667759bf85801831372a91e12617c223c745c2acf778cb7b42f6a1812719714caba322ff3013cb2ed0cb32f72ddcdb279989e93b67fe8a503b85314da71
diff --git a/dev-python/pyvista/metadata.xml b/dev-python/pyvista/metadata.xml
new file mode 100644
index 000000000..0137fea97
--- /dev/null
+++ b/dev-python/pyvista/metadata.xml
@@ -0,0 +1,13 @@
+<?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="pypi">pyvista</remote-id>
+ <remote-id type="github">pyvista/pyvista</remote-id>
+ </upstream>
+</pkgmetadata>
diff --git a/dev-python/pyvista/pyvista-0.31.1.ebuild b/dev-python/pyvista/pyvista-0.31.1.ebuild
new file mode 100644
index 000000000..1ba6d0882
--- /dev/null
+++ b/dev-python/pyvista/pyvista-0.31.1.ebuild
@@ -0,0 +1,32 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+PYTHON_COMPAT=( python3_{8..9} )
+DISTUTILS_SINGLE_IMPL=1 # because "sci-libs/vtk" inherits "python-single-r1"
+
+inherit distutils-r1
+
+DESCRIPTION="Easier Pythonic interface to VTK"
+HOMEPAGE="https://docs.pyvista.org"
+SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
+
+LICENSE="MIT"
+KEYWORDS="~amd64 ~x86"
+SLOT="0"
+
+RDEPEND="
+ sci-libs/vtk[python,imaging,rendering,views,${PYTHON_SINGLE_USEDEP}]
+ $(python_gen_cond_dep '
+ dev-python/appdirs[${PYTHON_USEDEP}]
+ dev-python/imageio[${PYTHON_USEDEP}]
+ dev-python/numpy[${PYTHON_USEDEP}]
+ dev-python/pillow[${PYTHON_USEDEP}]
+ !>=dev-python/meshio-5.0.0[${PYTHON_USEDEP}]
+ >=dev-python/meshio-4.0.3[${PYTHON_USEDEP}]
+ >=dev-python/scooby-0.5.1[${PYTHON_USEDEP}]
+ >=dev-python/transforms3d-0.3.1[${PYTHON_USEDEP}]
+ ')
+"
+DEPEND="${RDEPEND}"
diff --git a/dev-python/pyzo/Manifest b/dev-python/pyzo/Manifest
new file mode 100644
index 000000000..53069b179
--- /dev/null
+++ b/dev-python/pyzo/Manifest
@@ -0,0 +1 @@
+DIST pyzo-4.11.2.tar.gz 5340033 BLAKE2B 0c5c89deac947878ab84e7744dd21ca1092e6a9448573ad85067a20861f7823727623eb45a4c3f598e0bb2056bdf153d6818daed29ec8485313bebe8fccac32f SHA512 f96e4db48b414c5d6c2d9cb723e1bef2c4e0bc461c35710b1d7bf533c935734c5a17824ade59894f273624c80823b6283f131b972cbbe7cef3d0d20ff206f7db
diff --git a/dev-python/pyzo/metadata.xml b/dev-python/pyzo/metadata.xml
new file mode 100644
index 000000000..ae9640ffb
--- /dev/null
+++ b/dev-python/pyzo/metadata.xml
@@ -0,0 +1,8 @@
+<?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>
+</pkgmetadata>
diff --git a/dev-python/pyzo/pyzo-4.11.2.ebuild b/dev-python/pyzo/pyzo-4.11.2.ebuild
new file mode 100644
index 000000000..772793be5
--- /dev/null
+++ b/dev-python/pyzo/pyzo-4.11.2.ebuild
@@ -0,0 +1,64 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{8..9} )
+
+inherit distutils-r1 virtualx desktop xdg
+
+DESCRIPTION="The Python IDE for scientific computing"
+HOMEPAGE="https://pyzo.org/"
+SRC_URI="https://github.com/${PN}/${PN}/archive/refs/tags/v${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="BSD-2"
+SLOT="0"
+KEYWORDS="~amd64"
+
+# For some reason this requires network access
+# Qt: Session management error: Could not open network socket
+RESTRICT="test"
+
+RDEPEND="
+ dev-python/QtPy[${PYTHON_USEDEP}]
+"
+BDEPEND="
+ test? (
+ dev-python/visvis[${PYTHON_USEDEP}]
+ )
+"
+
+distutils_enable_tests pytest
+distutils_enable_sphinx doc
+
+python_prepare_all() {
+ # Use relative path to avoid access violation
+ # Do not install the license file, install other data_files manually
+ sed -i \
+ -e 's:/usr/share/metainfo:share/metainfo:g' \
+ -e '/LICENSE.md/d' \
+ setup.py || die
+
+ distutils-r1_python_prepare_all
+}
+
+src_test() {
+ virtx python_foreach_impl python_test
+}
+
+python_install() {
+ distutils-r1_python_install
+ python_doscript pyzolauncher.py
+}
+
+python_install_all() {
+ insinto /usr/share/metainfo/
+ doins pyzo.appdata.xml
+
+ for size in 16 32 48 64 128; do
+ newicon -s ${size} "${PN}/resources/appicons/pyzologo${size}.png" pyzologo.png
+ done
+ domenu "${PN}/resources/${PN}.desktop"
+
+ distutils-r1_python_install_all
+}
diff --git a/dev-python/schema/Manifest b/dev-python/schema/Manifest
new file mode 100644
index 000000000..e69b4b33b
--- /dev/null
+++ b/dev-python/schema/Manifest
@@ -0,0 +1 @@
+DIST schema-0.7.4.tar.gz 41340 BLAKE2B 3f897e7443da2a227e58e4f8655d75d2dfc9da95faca9f1737488ea7d95eefabf55c0606864164a7146d89fdb22cfb522e7e89bd648b001ac1cfe2e8e8ba4020 SHA512 6dd0ee8348fde4c6a9a39baf2b0fafff851f10ea581b16f438717d5435481f34829176bb4b82ecdd092da26332fd114fab856691b755ecf8e5648fb2233a0daf
diff --git a/dev-python/schema/metadata.xml b/dev-python/schema/metadata.xml
new file mode 100644
index 000000000..440ea4da1
--- /dev/null
+++ b/dev-python/schema/metadata.xml
@@ -0,0 +1,13 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <maintainer type="project">
+ <email>sci@gentoo.org</email>
+ <name>Gentoo Science Project</name>
+ </maintainer>
+ <stabilize-allarches/>
+ <upstream>
+ <remote-id type="pypi">schema</remote-id>
+ <remote-id type="github">keleshev/schema</remote-id>
+ </upstream>
+</pkgmetadata>
diff --git a/dev-python/schema/schema-0.7.4.ebuild b/dev-python/schema/schema-0.7.4.ebuild
new file mode 100644
index 000000000..05e8712bb
--- /dev/null
+++ b/dev-python/schema/schema-0.7.4.ebuild
@@ -0,0 +1,28 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{8..10} pypy3 )
+
+inherit distutils-r1
+
+DESCRIPTION="Schema validation just got Pythonic"
+HOMEPAGE="https://pypi.org/project/schema"
+SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+BDEPEND="test? ( dev-python/mock[${PYTHON_USEDEP}] )"
+
+distutils_enable_tests pytest
+
+src_prepare() {
+ distutils-r1_src_prepare
+
+ # Prevent schema from unconditionally requiring the last-rited contextlib2,
+ # which schema actually conditionally requires only under EOL Python 2.x.
+ sed -i -e '/\binstall_requires=/d' setup.py || die
+}
diff --git a/dev-python/scooby/Manifest b/dev-python/scooby/Manifest
new file mode 100644
index 000000000..0a16de485
--- /dev/null
+++ b/dev-python/scooby/Manifest
@@ -0,0 +1 @@
+DIST scooby-0.5.7.tar.gz 15770 BLAKE2B 08f9cf7c7e35c6c87cb80314b5287d2cbebaf46471e58e574d8f6725eb18fe95488c1043412a0abcd88040cb157713cb2076f425318c28ac02d3ad193df64b54 SHA512 4f8cc4c03c0af707115e11c11d6bbb5fb730d6221ff32598ad56e9592e1bcb2e22f56af189d05ca50fefcefd5262233594dd9b1d0dfd374d66f42700c7553d48
diff --git a/dev-python/scooby/metadata.xml b/dev-python/scooby/metadata.xml
new file mode 100644
index 000000000..c48aae2cf
--- /dev/null
+++ b/dev-python/scooby/metadata.xml
@@ -0,0 +1,13 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <maintainer type="project">
+ <email>sci@gentoo.org</email>
+ <name>Gentoo Science Project</name>
+ </maintainer>
+ <stabilize-allarches/>
+ <upstream>
+ <remote-id type="pypi">scooby</remote-id>
+ <remote-id type="github">banesullivan/scooby</remote-id>
+ </upstream>
+</pkgmetadata>
diff --git a/dev-python/scooby/scooby-0.5.7.ebuild b/dev-python/scooby/scooby-0.5.7.ebuild
new file mode 100644
index 000000000..19d343eca
--- /dev/null
+++ b/dev-python/scooby/scooby-0.5.7.ebuild
@@ -0,0 +1,16 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+PYTHON_COMPAT=( python3_{8..10} )
+
+inherit distutils-r1
+
+DESCRIPTION="Easily report Python package versions and hardware resources"
+HOMEPAGE="https://pypi.org/project/scooby"
+SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
+
+LICENSE="MIT"
+KEYWORDS="~amd64 ~x86"
+SLOT="0"
diff --git a/dev-python/toposort/Manifest b/dev-python/toposort/Manifest
deleted file mode 100644
index 6e30f532e..000000000
--- a/dev-python/toposort/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST toposort-1.6.tar.gz 11690 BLAKE2B a9a57fd182a3324d43112c3f84a20039f032d99bf2c35c6678a6a08c23b123f18610f460529dd39c769b935d98270a25ded2f1a483e4e6f06d3ccc501b340cb8 SHA512 8dc30b5d5a6f476756520236bc93840243690779783ec8f0b5ef0f72c64d774177b25d10d2e024cda968f81352abbc4f89f3069760fc3a86bd5ee387e7951928
diff --git a/dev-python/toposort/toposort-1.6.ebuild b/dev-python/toposort/toposort-1.6.ebuild
deleted file mode 100644
index a9917ed10..000000000
--- a/dev-python/toposort/toposort-1.6.ebuild
+++ /dev/null
@@ -1,18 +0,0 @@
-# Copyright 1999-2020 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-PYTHON_COMPAT=( python3_{7,8,9} )
-
-inherit distutils-r1
-
-DESCRIPTION="Implements a topological sort algorithm"
-HOMEPAGE="https://gitlab.com/ericvsmith/toposort"
-SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
-
-LICENSE="Apache-2.0"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-
-distutils_enable_tests setup.py
diff --git a/dev-python/transforms3d/Manifest b/dev-python/transforms3d/Manifest
new file mode 100644
index 000000000..00bbff4f5
--- /dev/null
+++ b/dev-python/transforms3d/Manifest
@@ -0,0 +1 @@
+DIST transforms3d-0.3.1.tar.gz 62812 BLAKE2B 0f279bfd9cc6bac451ea311d4dc8eb779b391cbbb8a00169271838bbdbe2400a64d8d8f1a7bae91d48de36c2d49ab985f1cc87ea27d0a86b5a5760947e1b6d6d SHA512 bee42558d600f62a01b2ec08049a4680e278cff3b2c47bf9f12bc9f7d67d0b220895187d050678f347443ed02f41be0902ed1b14d976f4034bde7b849ffbc6dd
diff --git a/dev-python/transforms3d/metadata.xml b/dev-python/transforms3d/metadata.xml
new file mode 100644
index 000000000..594eae127
--- /dev/null
+++ b/dev-python/transforms3d/metadata.xml
@@ -0,0 +1,13 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <maintainer type="project">
+ <email>sci@gentoo.org</email>
+ <name>Gentoo Science Project</name>
+ </maintainer>
+ <stabilize-allarches/>
+ <upstream>
+ <remote-id type="pypi">transforms3d</remote-id>
+ <remote-id type="github">matthew-brett/transforms3d</remote-id>
+ </upstream>
+</pkgmetadata>
diff --git a/dev-python/transforms3d/transforms3d-0.3.1.ebuild b/dev-python/transforms3d/transforms3d-0.3.1.ebuild
new file mode 100644
index 000000000..ed719c6a5
--- /dev/null
+++ b/dev-python/transforms3d/transforms3d-0.3.1.ebuild
@@ -0,0 +1,23 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+PYTHON_COMPAT=( python3_{8..10} )
+DISTUTILS_USE_SETUPTOOLS=no
+
+inherit distutils-r1
+
+DESCRIPTION="Functions for 3D coordinate transformations"
+HOMEPAGE="https://matthew-brett.github.io/transforms3d"
+SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
+
+LICENSE="BSD-2"
+KEYWORDS="~amd64 ~x86"
+SLOT="0"
+
+BDEPEND="test? ( dev-python/numpy[${PYTHON_USEDEP}] )"
+RDEPEND=">=dev-python/numpy-1.5.1[${PYTHON_USEDEP}]"
+DEPEND="${RDEPEND}"
+
+distutils_enable_tests nose
diff --git a/dev-python/typish/Manifest b/dev-python/typish/Manifest
new file mode 100644
index 000000000..672b11f96
--- /dev/null
+++ b/dev-python/typish/Manifest
@@ -0,0 +1 @@
+DIST typish-1.9.3.tar.gz 22997 BLAKE2B f399f5d9b3ae8f85f3b719de77d675b142ac45b6535f66d9d0d999411bc5bfc9100523667ea4c1d2be60c15a4bf35ec931ded9e1181a4545bbaa9b96fb27d0dd SHA512 baad9d2229ac289c4eb1d6e64bac0313efd4680f42a95270e0c1141d511392e6a95a5fea767943ddf432f5f0d48d95a05bbf26e06df188079ac177d321e4fa5c
diff --git a/dev-python/typish/metadata.xml b/dev-python/typish/metadata.xml
new file mode 100644
index 000000000..4febcc126
--- /dev/null
+++ b/dev-python/typish/metadata.xml
@@ -0,0 +1,13 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <maintainer type="project">
+ <email>sci@gentoo.org</email>
+ <name>Gentoo Science Project</name>
+ </maintainer>
+ <stabilize-allarches/>
+ <upstream>
+ <remote-id type="pypi">typish</remote-id>
+ <remote-id type="github">ramonhagenaars/typish</remote-id>
+ </upstream>
+</pkgmetadata>
diff --git a/dev-python/typish/typish-1.9.3.ebuild b/dev-python/typish/typish-1.9.3.ebuild
new file mode 100644
index 000000000..f471f6836
--- /dev/null
+++ b/dev-python/typish/typish-1.9.3.ebuild
@@ -0,0 +1,21 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{8..10} pypy3 )
+
+inherit distutils-r1
+
+DESCRIPTION="Python functions for thorough checks on types"
+HOMEPAGE="https://pypi.org/project/typish"
+
+# Prefer GitHub. Upstream failed to push its source tarball to PyPI.
+SRC_URI="https://github.com/ramonhagenaars/typish/archive/refs/tags/v${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+#FIXME: Tests require "nptyping" which circularly requires... "typish". *sigh*
+RESTRICT="test"
diff --git a/dev-python/visvis/Manifest b/dev-python/visvis/Manifest
new file mode 100644
index 000000000..10c6f487a
--- /dev/null
+++ b/dev-python/visvis/Manifest
@@ -0,0 +1 @@
+DIST visvis-1.13.0.tar.gz 5095145 BLAKE2B 4c47002902d7ee15f4ccc684b53daec09657422d9e53438a0e91d11ea17b76fd8e413b6caab8fee63752116247b526454bc7830751db1d3bb6d12adab914cc1a SHA512 a2272250060e418c7b78acb51599bf5d440d6d20ffe41d5fbfb3b68f6486b6d9312300dfa94697ff23bdadb2e79a871dc75bf0ba53be3267107d392236693d6a
diff --git a/dev-python/visvis/metadata.xml b/dev-python/visvis/metadata.xml
new file mode 100644
index 000000000..ae9640ffb
--- /dev/null
+++ b/dev-python/visvis/metadata.xml
@@ -0,0 +1,8 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <maintainer type="project">
+ <email>sci@gentoo.org</email>
+ <name>Gentoo Science Project</name>
+ </maintainer>
+</pkgmetadata>
diff --git a/dev-python/visvis/visvis-1.13.0.ebuild b/dev-python/visvis/visvis-1.13.0.ebuild
new file mode 100644
index 000000000..80704b0c3
--- /dev/null
+++ b/dev-python/visvis/visvis-1.13.0.ebuild
@@ -0,0 +1,25 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DISTUTILS_USE_SETUPTOOLS=no
+PYTHON_COMPAT=( python3_{8..9} )
+
+inherit distutils-r1
+
+DESCRIPTION="An object oriented approach to visualization of 1D to 4D data"
+HOMEPAGE="https://github.com/almarklein/visvis"
+SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64"
+
+RDEPEND="
+ dev-python/numpy[${PYTHON_USEDEP}]
+ dev-python/pyopengl[${PYTHON_USEDEP}]
+ dev-python/imageio[${PYTHON_USEDEP}]
+"
+
+distutils_enable_tests pytest
diff --git a/licenses/UPennState b/licenses/UPennState
deleted file mode 100644
index 8d2c6b44f..000000000
--- a/licenses/UPennState
+++ /dev/null
@@ -1,7 +0,0 @@
-Copyright (c) 2012 University of Pennsylvania
-
-Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:
-
-The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
-
-THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
diff --git a/licenses/netCDF b/licenses/netCDF
deleted file mode 100644
index 780ba9ee5..000000000
--- a/licenses/netCDF
+++ /dev/null
@@ -1,31 +0,0 @@
-Copyright 1993-2012 University Corporation for Atmospheric Research/Unidata
-
-Portions of this software were developed by the Unidata Program at the
-University Corporation for Atmospheric Research.
-
-Access and use of this software shall impose the following obligations
-and understandings on the user. The user is granted the right, without
-any fee or cost, to use, copy, modify, alter, enhance and distribute
-this software, and any derivative works thereof, and its supporting
-documentation for any purpose whatsoever, provided that this entire
-notice appears in all copies of the software, derivative works and
-supporting documentation. Further, UCAR requests that the user credit
-UCAR/Unidata in any publications that result from the use of this
-software or in any product that includes this software, although this
-is not an obligation. The names UCAR and/or Unidata, however, may not
-be used in any advertising or publicity to endorse or promote any
-products or commercial entity unless specific written permission is
-obtained from UCAR/Unidata. The user also understands that
-UCAR/Unidata is not obligated to provide the user with any support,
-consulting, training or assistance of any kind with regard to the use,
-operation and performance of this software nor to provide the user
-with any updates, revisions, new versions or "bug fixes."
-
-THIS SOFTWARE IS PROVIDED BY UCAR/UNIDATA "AS IS" AND ANY EXPRESS OR
-IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
-WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
-DISCLAIMED. IN NO EVENT SHALL UCAR/UNIDATA BE LIABLE FOR ANY SPECIAL,
-INDIRECT OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING
-FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT,
-NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION
-WITH THE ACCESS, USE OR PERFORMANCE OF THIS SOFTWARE.
diff --git a/media-libs/libgfx/Manifest b/media-libs/libgfx/Manifest
index c18a5b7eb..68c9b5f8d 100644
--- a/media-libs/libgfx/Manifest
+++ b/media-libs/libgfx/Manifest
@@ -1 +1,2 @@
DIST libgfx-1.1.0.tar.gz 145470 BLAKE2B bbf80adc726f9b4030c22365526af284a3843cf487fb5f606318d651af39d3866cb02d846969735e65aba0c857b715d4c10fcf443f22bb2cb3f65ac642999e29 SHA512 b23744225a63a77f17a78eb49b39e89a5d8c695cac62e1a399516c0e1728074ca80275fccb91cb3a128f20c2a8c66a6756005ba2d2ef9c251be36e3b3ba95d9b
+DIST libgfx-1.1.1.tar.gz 145075 BLAKE2B dab3bf0c4ddde672a3588fa88dc931db5deeef2e5e51ee6adb80ab500796677d200d4cec157828011cde5146c883cad80aae2cd69603e8f68dc67996ef84fc95 SHA512 264288a91ee9a1062bd36fa6ef381f27813e7c87949e8a1e7723f936fc1827d0a63252f2897b393f90ad0c6d47d0d413b5779194b05141efd618fc841b6bb6ff
diff --git a/media-libs/libgfx/libgfx-1.1.1.ebuild b/media-libs/libgfx/libgfx-1.1.1.ebuild
new file mode 100644
index 000000000..6cbedc968
--- /dev/null
+++ b/media-libs/libgfx/libgfx-1.1.1.ebuild
@@ -0,0 +1,41 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DESCRIPTION="Simplify the creation of computer graphics software"
+HOMEPAGE="http://mgarland.org/software/libgfx.html"
+
+COMMIT="f28ca5f0df3044f6399d6214faf66daa36712b91"
+SRC_URI="https://github.com/mjgarland/libgfx/archive/${COMMIT}.tar.gz -> ${P}.tar.gz"
+S="${WORKDIR}/${PN}-${COMMIT}"
+
+LICENSE="LGPL-2.1"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="static-libs"
+
+DEPEND="
+ virtual/opengl
+ x11-libs/fltk
+"
+
+RDEPEND="${DEPEND}"
+
+src_compile() {
+ cd src || die
+ default
+}
+
+src_install() {
+ use static-libs && dolib.a src/*.a
+ doheader include/gfx/gfx.h
+
+ dodoc doc/*
+}
+
+src_test() {
+ cd tests || die
+ sed -i -e 's/t-vec.cxx t-img.cxx t-gui.cxx t-glimg.cxx t-script.cxx t-glext.cxx/t-vec.cxx t-img.cxx t-script.cxx/' Makefile
+ emake
+}
diff --git a/profiles/package.mask b/profiles/package.mask
index 0a67928c5..d39812beb 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -29,12 +29,3 @@
## app-misc/some-package
#--- END OF EXAMPLES ---
-
-# Andrew Ammerlaan <andrewammerlaan@gentoo.org> (24 May 2021)
-# This was originally added for the NationalInstruments/GPIB ebuilds, however
-# due to the number of ebuilds it was decided to maintain these in ::natinst.
-# An ebuild for dkms was also added to ::natinst, so it makes little sense to
-# maintain an ebuild in ::sci as well. Additionally there is also an ebuild
-# for this in ::guru
-# Removal in 30 days
-sys-kernel/dkms
diff --git a/sci-biology/MuSeqBox/Manifest b/sci-biology/MuSeqBox/Manifest
index 584b72cec..e9472a450 100644
--- a/sci-biology/MuSeqBox/Manifest
+++ b/sci-biology/MuSeqBox/Manifest
@@ -1 +1 @@
-DIST MuSeqBox-3-4-2020.tar.gz 86176 BLAKE2B 04ad5a4fda3f4d694dc68c3532fd26cb771393442bdd3e4956bd4eb3dad67c51e15e1a0f948e7b57073b134d5aa59220219ee61b703e37ee5cb3030e1c85273b SHA512 a2237963858ee2e14f56a42e545fce88334f26f402943ec35c8a0df9b6ebfee46ba04695b137d4e8025b15c0e06a3ae71fa69015bcc931865b133ff6ca21d333
+DIST MuSeqBox-5-7-2021.tar.gz 105192 BLAKE2B f9cd38ab403a1b6ff4ae46f4bc07739e38b84f30e48eebeadb7519b9c8954ae83c8ecd4034acd8b80c74327a55b746093aa9652ad0f4ccad83b06f232d1145a5 SHA512 81aaf6c8a9065a944821fb974031c939b8fdf90efddf08303d3c095aebe7a82dc4655b3cd2c682fa67a45a3bd732f44dc2c583c8ad06f1bf403bf56e30c97d6c
diff --git a/sci-biology/MuSeqBox/MuSeqBox-3.4.2020.ebuild b/sci-biology/MuSeqBox/MuSeqBox-5.7.2021.ebuild
index 0d4b5737f..49bd7da9c 100644
--- a/sci-biology/MuSeqBox/MuSeqBox-3.4.2020.ebuild
+++ b/sci-biology/MuSeqBox/MuSeqBox-5.7.2021.ebuild
@@ -1,20 +1,19 @@
# Copyright 1999-2021 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=7
+EAPI=8
inherit toolchain-funcs
DESCRIPTION="Parse and filter BLAST output into tab-delimited file"
HOMEPAGE="http://brendelgroup.org/bioinformatics2go/MuSeqBox.php"
SRC_URI="http://www.brendelgroup.org/bioinformatics2go/Download/MuSeqBox-${PV//./-}.tar.gz"
-# code will move to https://github.com/BrendelGroup
LICENSE="GPL-3"
SLOT="0"
KEYWORDS="~amd64"
-S="${WORKDIR}/MUSEQBOX5.5"
+S="${WORKDIR}/MUSEQBOX$(ver_cut 1-2)"
src_compile(){
cd src || die
diff --git a/sci-biology/SEECER/SEECER-0.1.3-r3.ebuild b/sci-biology/SEECER/SEECER-0.1.3-r3.ebuild
new file mode 100644
index 000000000..e41bbb19d
--- /dev/null
+++ b/sci-biology/SEECER/SEECER-0.1.3-r3.ebuild
@@ -0,0 +1,66 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+inherit autotools toolchain-funcs
+
+DESCRIPTION="SEquence Error Corrector for RNA-Seq reads"
+HOMEPAGE="http://sb.cs.cmu.edu/seecer/"
+SRC_URI="
+ http://sb.cs.cmu.edu/seecer/downloads/"${P}".tar.gz
+ http://sb.cs.cmu.edu/seecer/downloads/manual.pdf -> "${PN}"-manual.pdf"
+
+LICENSE="GPL-3"
+SLOT="0"
+KEYWORDS="~amd64"
+
+# although has bundled jellyfish-1.1.11 copy it just calls the executable during runtime
+# seems jellyfish-2 does not accept same commandline arguments
+DEPEND="
+ sci-libs/gsl:0=
+ sci-biology/seqan:0="
+RDEPEND="${DEPEND}
+ sci-biology/jellyfish:1"
+
+S="${WORKDIR}/${P}/SEECER"
+
+PATCHES=(
+ "${FILESDIR}"/remove-hardcoded-paths.patch
+ "${FILESDIR}"/run_seecer.sh.patch
+ "${FILESDIR}"/run_jellyfish.sh.patch
+ "${FILESDIR}"/${PN}-increase-max-sequence-length.patch
+ "${FILESDIR}"/${PN}-remove-flags.patch
+)
+
+pkg_pretend(){
+ # openmp is a hard requirement due to no gomp switch and source code assuming it is available
+ [[ ${MERGE_TYPE} != "binary" ]] && tc-check-openmp
+}
+
+pkg_setup(){
+ [[ ${MERGE_TYPE} != "binary" ]] && tc-check-openmp
+}
+
+src_prepare(){
+ rm bin/.run*.swp || die
+ rm src/*.o pipeline/*.o || die
+ rm -r seqan-cxx || die
+ default
+ eautoreconf -i
+}
+
+src_configure(){
+ econf \
+ --with-seqan-include-path=/usr/include/seqan \
+ CXXFLAGS="${CXXFLAGS}"
+}
+
+src_install(){
+ dobin bin/seecer bin/random_sub_N bin/replace_ids bin/run_jellyfish.sh bin/run_seecer.sh
+ dodoc README "${DISTDIR}"/"${PN}"-manual.pdf
+}
+
+pkg_postinst(){
+ einfo "Note that the default kmer size 17 is terribly suboptimal, use k=31 instead"
+}
diff --git a/sci-biology/SEECER/files/SEECER-increase-max-sequence-length.patch b/sci-biology/SEECER/files/SEECER-increase-max-sequence-length.patch
new file mode 100644
index 000000000..be6b320a9
--- /dev/null
+++ b/sci-biology/SEECER/files/SEECER-increase-max-sequence-length.patch
@@ -0,0 +1,44 @@
+Increase the max sequence length from 256 to 10000
+Patch created from an updated replace_ids.cc downloaded from an archived upstream email list that is no longer online
+https://web.archive.org/web/20150911132231/http://seecer-rna-read-error-correction-mailing-list.21961.x6.nabble.com/Segmentation-fault-in-step-4-td41.html
+
+--- SEECER-0.1.3/pipeline/replace_ids.cc
++++ SEECER-0.1.3/pipeline/replace_ids.cc
+@@ -5,6 +5,7 @@
+
+ #include <vector>
+ using namespace std;
++#define MAXSEQLENGTH 10000
+
+ char* getread(int& rid, char* annot, char* seq, FILE* f2, FILE* f3) {
+ char a;
+@@ -47,10 +48,10 @@ void closeFiles(vector<FILE*>& files) {
+
+ bool ReadNextLines(FILE* f, char* id, char* seq) {
+ assert(!feof(f));
+- fgets(id, 256, f);
++ fgets(id, MAXSEQLENGTH, f);
+ if (id[0] == '+') {
+- if (!fgets(id, 256, f)) return false;
+- if (!fgets(id, 256, f)) return false;
++ if (!fgets(id, MAXSEQLENGTH, f)) return false;
++ if (!fgets(id, MAXSEQLENGTH, f)) return false;
+ }
+ int i = 0;
+ while (id[i+1] != '\0' && id[i+1] != '\n') {
+@@ -78,11 +79,10 @@ int main(int argc, char* argv[]) {
+ && origs.size() == output.size()) {
+
+ int n = origs.size();
+-
+- char id[256];
+- char seq[256];
+- char seqc[256];
+- char annot[256];
++ char id[MAXSEQLENGTH];
++ char seq[MAXSEQLENGTH];
++ char seqc[MAXSEQLENGTH];
++ char annot[MAXSEQLENGTH];
+ int rid;
+ char a;
+
diff --git a/sci-biology/SEECER/files/SEECER-remove-flags.patch b/sci-biology/SEECER/files/SEECER-remove-flags.patch
new file mode 100644
index 000000000..455ab4a7a
--- /dev/null
+++ b/sci-biology/SEECER/files/SEECER-remove-flags.patch
@@ -0,0 +1,30 @@
+Remove CXXFLAGS, CFLAGS, LDCLAGS set in configure.ac and Makefile.am
+Written and tested by Lucas Mitrak
+
+--- SEECER-0.1.3/Makefile.am
++++ SEECER-0.1.3/Makefile.am
+@@ -1,6 +1,6 @@
+ AM_LDFLAGS = -lgomp
+ AM_CPPFLAGS = -Wno-deprecated -Wall $(SEQAN_CFLAGS) -fopenmp
+-AM_CXXFLAGS = -O3 -g
++AM_CXXFLAGS =
+
+ bin_PROGRAMS = bin/seecer \
+ bin/random_sub_N \
+--- SEECER-0.1.3/configure.ac
++++ SEECER-0.1.3/configure.ac
+@@ -2,10 +2,10 @@ AC_INIT([seecer], [1.0], [hple@cs.cmu.edu,maschulz@cs.cmu.edu])
+ AM_INIT_AUTOMAKE([-Wall subdir-objects foreign])
+ AC_PREREQ(2.62)
+
+-: ${CXXFLAGS=""}
+-CFLAGS="$CFLAGS -I/opt/local/include"
+-CXXFLAGS="$CXXFLAGS -I/opt/local/include"
+-LDFLAGS="$LDFLAGS -L/opt/local/lib"
++#: ${CXXFLAGS=""}
++#CFLAGS="$CFLAGS -I/opt/local/include"
++#CXXFLAGS="$CXXFLAGS -I/opt/local/include"
++#LDFLAGS="$LDFLAGS -L/opt/local/lib"
+ AC_PROG_CXX
+
+ AC_CONFIG_HEADERS([config.h])
diff --git a/sci-biology/Scaffolder-evaluation/Scaffolder-evaluation-9999.ebuild b/sci-biology/Scaffolder-evaluation/Scaffolder-evaluation-9999.ebuild
deleted file mode 100644
index 4e291ece2..000000000
--- a/sci-biology/Scaffolder-evaluation/Scaffolder-evaluation-9999.ebuild
+++ /dev/null
@@ -1,38 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-PYTHON_COMPAT=( python3_{7,8,9} )
-
-inherit python-r1 perl-functions git-r3
-
-DESCRIPTION="Scripts to run genome assembly scaffolding tools and analyse output for accuracy"
-HOMEPAGE="https://github.com/martinghunt/Scaffolder-evaluation
- https://genomebiology.biomedcentral.com/articles/10.1186/gb-2014-15-3-r42"
-EGIT_REPO_URI="https://github.com/martinghunt/Scaffolder-evaluation.git"
-
-LICENSE="GPL-3"
-SLOT="0"
-KEYWORDS=""
-
-REQUIRED_USE="${PYTHON_REQUIRED_USE}"
-
-DEPEND="${PYTHON_DEPS}"
-RDEPEND="${DEPEND}
- dev-lang/perl
- dev-lang/R
- media-gfx/graphviz
- sci-biology/mummer
- sci-biology/bowtie
- sci-biology/samtools
- sci-biology/ncbi-tools
- sci-biology/Fastaq[${PYTHON_USEDEP}]
-"
-
-src_install(){
- python_foreach_impl python_doscript Analysis-scripts/*.py
- dobin Analysis-scripts/*.sh
- perl_domodule Wrapper-scripts/*
- dodoc README.md
-}
diff --git a/sci-biology/Scaffolder-evaluation/metadata.xml b/sci-biology/Scaffolder-evaluation/metadata.xml
deleted file mode 100644
index 337db209e..000000000
--- a/sci-biology/Scaffolder-evaluation/metadata.xml
+++ /dev/null
@@ -1,15 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <maintainer type="person">
- <email>mmokrejs@fold.natur.cuni.cz</email>
- <name>Martin Mokrejs</name>
- </maintainer>
- <maintainer type="project">
- <email>sci-biology@gentoo.org</email>
- <name>Gentoo Biology Project</name>
- </maintainer>
- <upstream>
- <remote-id type="github">martinghunt/Scaffolder-evaluation</remote-id>
- </upstream>
-</pkgmetadata>
diff --git a/sci-biology/blasr/blasr-9999.ebuild b/sci-biology/blasr/blasr-9999.ebuild
index 6f5d10b16..cbd012727 100644
--- a/sci-biology/blasr/blasr-9999.ebuild
+++ b/sci-biology/blasr/blasr-9999.ebuild
@@ -21,6 +21,6 @@ BDEPEND="
DEPEND="
sci-biology/pbbam
sci-biology/libblasr
- dev-libs/boost:=[threads]
+ dev-libs/boost:=[threads(-)]
"
RDEPEND="${DEPEND}"
diff --git a/sci-biology/cg-cat/Manifest b/sci-biology/cg-cat/Manifest
deleted file mode 100644
index 2125e4476..000000000
--- a/sci-biology/cg-cat/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST r2cat.tar.gz 409067 BLAKE2B 18cffbc3ecf9655b3155a85495ee5be6f87735ebc9311588ee92b6e1c4130152c3f08d974854ceffe58201b9a232f70ae01fadcb388da20d222e156ce76f5bc5 SHA512 a837d216664fede82e147204e8f1ba07b2d5ad92ee3db6f3a1285ff4acc4fb5b70715ac272d727304901548d68cb4865c051ef24690226692c4c4d693c7988f1
diff --git a/sci-biology/cg-cat/cg-cat-20150130.ebuild b/sci-biology/cg-cat/cg-cat-20150130.ebuild
deleted file mode 100644
index 0c48ecbc5..000000000
--- a/sci-biology/cg-cat/cg-cat-20150130.ebuild
+++ /dev/null
@@ -1,59 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit java-pkg-2 java-ant-2
-
-DESCRIPTION="r2cat and treecat, scaffolding tools for ordering and orienting contigs"
-HOMEPAGE="http://bibiserv.techfak.uni-bielefeld.de/cgcat"
-SRC_URI="http://bibiserv.techfak.uni-bielefeld.de/applications/cgcat/resources/downloads/r2cat.tar.gz"
-# SRC_URI="http://bibiserv.techfak.uni-bielefeld.de/applications/cgcat/resources/downloads/r2cat.jar"
-
-LICENSE="GPL-3"
-SLOT="0"
-KEYWORDS="~amd64"
-
-RDEPEND="${DEPEND}
- >=virtual/jre-1.6:*
- dev-lang/perl
- sci-biology/ncbi-tools"
-DEPEND="${RDEPEND}
- >=virtual/jdk-1.6:*
- dev-java/ant-core"
-
-S="${WORKDIR}"/r2cat
-
-src_prepare(){
- default
- sed -e "s#/vol/bioapps#"${D}"/usr#" -e "s#/vol/bibidev/r2cat#"${D}"/usr#" -i Makefile || die
- sed -e "s#/vol/gnu#/usr#" -i de/bielefeld/uni/cebitec/r2cat/blast_to_r2cat.pl || die
-}
-
-src_compile(){
- emake r2cat.jar
-}
-
-src_install(){
- # emake install dies with:
- # jarsigner -tsa https://timestamp.geotrust.com/tsa -keystore /homes/phuseman/.gnupg/jarsigner_keystore_cg-cat cg-cat.jar cgcat
- # Enter Passphrase for keystore: jarsigner: you must enter key password
- # Makefile:44: recipe for target 'cg-cat.jar' failed
- mkdir -p "${D}"/usr/share/r2cat
- # emake install_cebitec
- # emake install_bibiserv
- # the blast_to_r2cat.pl script needs bioperl
- dobin de/bielefeld/uni/cebitec/r2cat/blast_to_r2cat.pl
- java-pkg_dojar r2cat.jar || die
- dodoc README.md ReadmeLicenses.txt
- docinto html
- dodoc de/bielefeld/uni/cebitec/r2cat/help/*
-}
-
-# to start r2cat:
-# java -Xmx10240M -jar r2cat.jar de.bielefeld.uni.cebitec.r2cat.R2cat
-
-# to start treecat:
-# java -Xmx10240M -cp r2cat.jar de.bielefeld.uni.cebitec.treecat.Treecat -Xmx -d64
-
-# add -d64 on the java commandline if you need more than 4GB of memory and your system can handle it
diff --git a/sci-biology/cg-cat/metadata.xml b/sci-biology/cg-cat/metadata.xml
deleted file mode 100644
index 138cb7705..000000000
--- a/sci-biology/cg-cat/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <maintainer type="person">
- <email>mmokrejs@fold.natur.cuni.cz</email>
- <name>Martin Mokrejs</name>
- </maintainer>
- <maintainer type="project">
- <email>sci-biology@gentoo.org</email>
- <name>Gentoo Biology Project</name>
- </maintainer>
-</pkgmetadata>
diff --git a/sci-biology/cgview-bin/Manifest b/sci-biology/cgview-bin/Manifest
deleted file mode 100644
index afa77ff40..000000000
--- a/sci-biology/cgview-bin/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST cgview-bin-1.0.0.tar.gz 689045496 BLAKE2B c6a8ab568c7fa4e168ee9c6457b860f32e5f6554186ea8532a812997e8aebb675be1e8ea02a0c3a89d83e2d2ead34287403d7a502be23fd12b73ea14986132c4 SHA512 9fe19997d8e204c6ebdece551e9e3ce3f5eb3ec0bfbb0e2839e8be6053d566d58894380a0c625f695b67c44399d88d892b03cd6ddff7b4cc1f28598ac549d3fb
diff --git a/sci-biology/cgview-bin/cgview-bin-1.0.0.ebuild b/sci-biology/cgview-bin/cgview-bin-1.0.0.ebuild
deleted file mode 100644
index 5135e04ab..000000000
--- a/sci-biology/cgview-bin/cgview-bin-1.0.0.ebuild
+++ /dev/null
@@ -1,43 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit java-pkg-2 perl-module eutils toolchain-funcs
-
-DESCRIPTION="CGView Comparison Tool to compare genome sequences graphically (aka CCT)"
-HOMEPAGE="https://paulstothard.github.io/cgview_comparison_tool/"
-SRC_URI="https://github.com/paulstothard/cgview_comparison_tool/archive/v${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~amd64"
-
-DEPEND="
- >=dev-lang/perl-5.8.8
- >=sci-biology/ncbi-tools-2.2.15
- >=virtual/jre-1.4.2:*
- dev-java/xerces:2
- dev-java/batik
- dev-java/commons-lang:2.1
- >=media-gfx/imagemagick-6
- >=sci-biology/bioperl-1.4.0"
-RDEPEND="${DEPEND}"
-
-S="${WORKDIR}/cgview_comparison_tool-${PV}"
-
-src_install() {
- insinto /usr/share/${PN}/scripts
- chmod a+x scripts/* # BUG: this does not work
- doins -r scripts/*
- insinto /usr/share/${PN}/lib/scripts
- doins -r lib/scripts/*
- echo 'CCT_HOME='${EPREFIX}'/usr/share/cgview' > "${S}/99cgview"
- echo 'PATH="$PATH":"'${CCT_HOME}'/scripts"' >> "${S}/99cgview"
- doenvd "${S}/99cgview"
- perl_set_version
- perl_domodule lib/perl_modules/Util/*.pm
- #
- # Exception in thread "main" java.lang.NoClassDefFoundError: org/apache/batik/svggen/SVGGraphics2DIOException
- java-pkg_dojar bin/cgview/cgview.jar
-}
diff --git a/sci-biology/cgview-bin/metadata.xml b/sci-biology/cgview-bin/metadata.xml
deleted file mode 100644
index 138cb7705..000000000
--- a/sci-biology/cgview-bin/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <maintainer type="person">
- <email>mmokrejs@fold.natur.cuni.cz</email>
- <name>Martin Mokrejs</name>
- </maintainer>
- <maintainer type="project">
- <email>sci-biology@gentoo.org</email>
- <name>Gentoo Biology Project</name>
- </maintainer>
-</pkgmetadata>
diff --git a/sci-biology/fsl/Manifest b/sci-biology/fsl/Manifest
index ce2b4be84..868861b84 100644
--- a/sci-biology/fsl/Manifest
+++ b/sci-biology/fsl/Manifest
@@ -1 +1,2 @@
DIST fsl-6.0.2.tar.gz 2505331864 BLAKE2B 0fbc23c788e0960e41a895f8eddd346e8facfae448c637eca18d39b142f8aabd9531427ce4ff97c634fdc5d16a74163947c7bade219a8900722815321144b41e SHA512 fe308393076c51c50b086f9bf7ff5ddebcf8b1284128e734b9d9e501019917ceba7c0ee5cd5aa1ed44452bcd042ad72653c1a8693f94eab9b83a80fe508a56ca
+DIST fsl-6.0.4.tar.gz 2507673220 BLAKE2B 21e7437f8a3fde03ec6711b8022ee203ae159c07b5a3b998f37db768205d3335ffe9b28ad05b859e6bde4916933ea58e4e188012f147648f00fd6e6253ce1a12 SHA512 c65edcf5728920752e6dceea440dc2b528d007b7e4f56390a3d7eed91b1014457544563f699cae77f62c44cdfbdfcc5031265a5fd619fe0ecb99cad5653080d3
diff --git a/sci-biology/fsl/files/fsl-6.0.4-cuda_buildsettings.patch b/sci-biology/fsl/files/fsl-6.0.4-cuda_buildsettings.patch
new file mode 100644
index 000000000..749e80623
--- /dev/null
+++ b/sci-biology/fsl/files/fsl-6.0.4-cuda_buildsettings.patch
@@ -0,0 +1,12 @@
+diff -Naur fsl.orig/config/buildSettings.mk fsl/config/buildSettings.mk
+--- fsl.orig/config/buildSettings.mk 2020-12-02 16:22:57.999912865 -0500
++++ fsl/config/buildSettings.mk 2020-12-02 16:24:15.332915270 -0500
+@@ -144,7 +144,7 @@
+ # CUDA development environment
+ CUDAVER := $(or $(CUDAVER),9.1)
+ #$(info $$CUDAVER is [${CUDAVER}])
+-CUDA_INSTALLATION = /opt/cuda-${CUDAVER}
++CUDA_INSTALLATION = /opt/cuda
+ ifdef SINGULARITY_NAME
+ CUDA_INSTALLATION = /usr/local/cuda-${CUDAVER}
+ endif
diff --git a/sci-biology/fsl/files/fsl-6.0.4-eddy_cuda.patch b/sci-biology/fsl/files/fsl-6.0.4-eddy_cuda.patch
new file mode 100644
index 000000000..ad118c39a
--- /dev/null
+++ b/sci-biology/fsl/files/fsl-6.0.4-eddy_cuda.patch
@@ -0,0 +1,21 @@
+diff -Naur fsl.orig/src/eddy/Makefile fsl/src/eddy/Makefile
+--- fsl.orig/src/eddy/Makefile 2020-12-02 16:07:47.327884548 -0500
++++ fsl/src/eddy/Makefile 2020-12-02 16:11:21.149891196 -0500
+@@ -29,6 +29,8 @@
+ TMPCXXFLAGS_2=
+ TMPNAME_1=
+ TMPNAME_2=
++cuda=1
++cpu=1
+ TOPUP_DIR=../topup
+
+ ifndef cuda
+@@ -74,7 +75,7 @@
+ ifdef NVCC11
+ NVCC=${NVCC11}
+ endif
+-NVCCFLAGS=-c -DCOMPILE_GPU -O3 -m 64 -std=c++11
++NVCCFLAGS=-c -DCOMPILE_GPU -O3 -m 64 -std=c++11 @@GENTOO_NVCC_FLAGS@@
+ ifeq ($(CLOBBER_CLANG),1)
+ NVCCFLAGS+= -DCLOBBER_CLANG
+ endif
diff --git a/sci-biology/fsl/files/fsl-6.0.4-fdt_cuda.patch b/sci-biology/fsl/files/fsl-6.0.4-fdt_cuda.patch
new file mode 100644
index 000000000..7f322027b
--- /dev/null
+++ b/sci-biology/fsl/files/fsl-6.0.4-fdt_cuda.patch
@@ -0,0 +1,14 @@
+diff -Naur fsl.orig/src/fdt/Makefile fsl/src/fdt/Makefile
+--- fsl.orig/src/fdt/Makefile 2020-12-02 19:06:55.826218772 -0500
++++ fsl/src/fdt/Makefile 2020-12-02 19:08:02.883220858 -0500
+@@ -6,7 +6,9 @@
+ $(eval $($(PROJNAME)_MASTERBUILD))
+ endif
+
+-ifeq ($(COMPILE_GPU), 1)
++# disable CUDA support for fdt
++#ifeq ($(COMPILE_GPU), 1)
++ifeq (0, 1)
+ COMPILE_WITH_GPU=libbedpostx_cuda.so merge_parts_gpu xfibres_gpu CUDA/split_parts_gpu
+ SCRIPTS_GPU=CUDA/bedpostx_gpu CUDA/bedpostx_postproc_gpu.sh
+ endif
diff --git a/sci-biology/fsl/files/fsl-6.0.4-flameo_std.patch b/sci-biology/fsl/files/fsl-6.0.4-flameo_std.patch
new file mode 100644
index 000000000..a991f1ed3
--- /dev/null
+++ b/sci-biology/fsl/files/fsl-6.0.4-flameo_std.patch
@@ -0,0 +1,11 @@
+diff -Naur fsl.orig/src/flameo/Makefile fsl/src/flameo/Makefile
+--- fsl.orig/src/flameo/Makefile 2021-01-06 14:04:35.728274475 -0500
++++ fsl/src/flameo/Makefile 2021-01-06 14:08:18.204269285 -0500
+@@ -4,6 +4,7 @@
+
+ USRINCFLAGS = -I${INC_NEWMAT} -I${INC_PROB} -I${INC_ZLIB} -DCIFTILIB_USE_XMLPP -I${FSLEXTINC} -I${INC_XML2} -I${INC_XML++} -I${INC_XML++CONF} -I${INC_BOOST} -I${FSLDIR}/include/ciftiio
+ USRLDFLAGS = -L${LIB_NEWMAT} -L${LIB_PROB} -L${LIB_ZLIB}
++USRCXXFLAGS = -std=c++11
+
+ UNAME := $(shell uname)
+ ifeq (${UNAME},Darwin)
diff --git a/sci-biology/fsl/files/fsl-6.0.4-fsldir_redux-p1.patch b/sci-biology/fsl/files/fsl-6.0.4-fsldir_redux-p1.patch
new file mode 100644
index 000000000..ca3945442
--- /dev/null
+++ b/sci-biology/fsl/files/fsl-6.0.4-fsldir_redux-p1.patch
@@ -0,0 +1,240 @@
+From 2bc4be1f55b27a733e1e624b34bc570187ba95e1 Mon Sep 17 00:00:00 2001
+From: François Bissey <frp.bissey@gmail.com>
+Date: Mon, 20 Jan 2020 11:40:53 +1300
+Subject: [PATCH] Making sure fsl code and executable can find other executable
+ and data in standard location.
+
+---
+ src/fast4/fast_two.cc | 8 ++++----
+ src/feat5/feat_model.cc | 8 +++-----
+ src/feat5/tsplot.cc | 7 +++----
+ src/first/first_utils.cc | 4 ++--
+ src/fnirt/fnirtfns.cpp | 11 ++++-------
+ src/fslsurface/fslsurface_first.cc | 6 ++----
+ src/fslsurface/fslsurfacemaths.cpp | 12 ------------
+ src/libvis/miscpic.h | 7 +------
+ src/melodic/meldata.cc | 4 ++--
+ src/melodic/meloptions.cc | 8 --------
+ src/melodic/meloptions.h | 1 -
+ src/melodic/melreport.cc | 12 ++++++------
+ src/melodic/melreport.h | 20 ++++++++++----------
+ src/mm/mixture_model.cc | 4 ++--
+ src/siena/siena_diff.cc | 28 +++++++++++++---------------
+ src/topup/topupfns.cpp | 3 +--
+ 16 files changed, 53 insertions(+), 90 deletions(-)
+
+diff --git a/src/fast4/fast_two.cc b/src/fast4/fast_two.cc
+index 592b5df..b525444 100644
+--- a/src/fast4/fast_two.cc
++++ b/src/fast4/fast_two.cc
+@@ -166,7 +166,7 @@ int prior_registration(string inname, string main_prior_vol, NEWIMAGE::volume<fl
+ string csfPriorName, grayPriorName, whitePriorName;
+ if(alternatePriors.unset())
+ {
+- string priorRootName=string(getenv("FSLDIR")) + "/data/standard/tissuepriors/avg152T1_";
++ string priorRootName="@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/data/standard/tissuepriors/avg152T1_";
+ csfPriorName = priorRootName+"csf";
+ grayPriorName = priorRootName+"gray";
+ whitePriorName = priorRootName+"white";
+@@ -215,15 +215,15 @@ string csfPriorName, grayPriorName, whitePriorName;
+ if(bapused>0)
+ {
+ char reg[1024];
+- sprintf(reg, "%s/bin/flirt -ref %s -in %s -out %s -applyxfm -init %s", getenv("FSLDIR"), inname.c_str(), csfPriorName.c_str(), (main_prior_vol+"_csf_stdspace").c_str(), bapriori.value().c_str());
++ sprintf(reg, "flirt -ref %s -in %s -out %s -applyxfm -init %s", inname.c_str(), csfPriorName.c_str(), (main_prior_vol+"_csf_stdspace").c_str(), bapriori.value().c_str());
+ if(verbose.value())
+ cout<<reg<<endl;
+ system(reg);
+- sprintf(reg, "%s/bin/flirt -ref %s -in %s -out %s -applyxfm -init %s", getenv("FSLDIR"), inname.c_str(), grayPriorName.c_str(), (main_prior_vol+"_gm_stdspace").c_str(), bapriori.value().c_str());
++ sprintf(reg, "flirt -ref %s -in %s -out %s -applyxfm -init %s", inname.c_str(), grayPriorName.c_str(), (main_prior_vol+"_gm_stdspace").c_str(), bapriori.value().c_str());
+ if(verbose.value())
+ cout<<reg<<endl;
+ system(reg);
+- sprintf(reg, "%s/bin/flirt -ref %s -in %s -out %s -applyxfm -init %s", getenv("FSLDIR"), inname.c_str(), whitePriorName.c_str(), (main_prior_vol+"_wm_stdspace").c_str(), bapriori.value().c_str());
++ sprintf(reg, "flirt -ref %s -in %s -out %s -applyxfm -init %s", inname.c_str(), whitePriorName.c_str(), (main_prior_vol+"_wm_stdspace").c_str(), bapriori.value().c_str());
+ if(verbose.value())
+ cout << reg << endl;
+ system(reg);
+diff --git a/src/feat5/feat_model.cc b/src/feat5/feat_model.cc
+index 399a13e..e15e43c 100644
+--- a/src/feat5/feat_model.cc
++++ b/src/feat5/feat_model.cc
+@@ -744,7 +744,7 @@ int main(int argc, char **argv)
+ vector<int> G;
+ vector<string> titles;
+ float tr, mult, trmult, nltffwhm=0, maxconvwin=0;
+- char fl[10000], *FSLDIR;
++ char fl[10000];
+ string fn, filename;
+ FONT_DATA *font_data = new FONT_DATA[1];
+
+@@ -763,8 +763,6 @@ int main(int argc, char **argv)
+ if (argc==3)
+ motionparams=remmean(read_ascii_matrix(argv[2]));
+
+- FSLDIR=getenv("FSLDIR");
+-
+ fn = string(argv[1])+".fsf";
+
+ level = atoi(find_line(fn, "fmri(level)", fl));
+@@ -1510,7 +1508,7 @@ int main(int argc, char **argv)
+ writeCovarianceImage(string(argv[1])+"_cov.ppm", contrasts, F, nftests, realDesign, level, evs.eigenvals, font_data, contrasts.RE);
+ writeImagePreview(string(argv[1])+".ppm", contrasts, F, nftests, realDesign, level, evs, font_data, titles, tr, nltffwhm, nTimepoints, G);
+
+- filename=string(getenv("FSLDIR"))+"/bin/wpng -q -overwrite "+string(argv[1])+".ppm ";
++ filename="wpng -q -overwrite "+string(argv[1])+".ppm ";
+ system(filename.c_str());
+
+ return(0);
+@@ -2161,6 +2159,6 @@ char the_string[10000];
+
+ fclose(outputfile);
+
+- filename=string(getenv("FSLDIR")) + "/bin/wpng -q -overwrite " + filename;
++ filename="wpng -q -overwrite " + filename;
+ system(filename.c_str());
+ }
+diff --git a/src/feat5/tsplot.cc b/src/feat5/tsplot.cc
+index ae191fd..3a02b55 100644
+--- a/src/feat5/tsplot.cc
++++ b/src/feat5/tsplot.cc
+@@ -293,7 +293,7 @@ int main(int argc, char **argv)
+ ofstream outputFile;
+ int numEVs, npts, numContrasts=1, nftests=0, GRPHSIZE(600), PSSIZE(600);
+ vector<double> normalisedContrasts, model, triggers;
+- string fmriFileName, fslPath, featdir, vType, indexText;
++ string fmriFileName, featdir, vType, indexText;
+ ColumnVector NewimageVoxCoord(4),NiftiVoxCoord(4);
+ bool outputText(true), useCoordinate(false), prewhiten(false), useTriggers(false), customMask(false), modelFree(false), isHigherLevel(false), outputDataOnly(false);
+ bool zWeightClusters(true);
+@@ -307,7 +307,6 @@ volume<float> immask;
+ if (argc<2) usage("");
+ featdir=string(argv[1]);
+ fmriFileName=featdir+"/filtered_func_data";
+- fslPath=string(getenv("FSLDIR"));
+
+ string outputName(featdir);
+
+@@ -753,7 +752,7 @@ volume4D<float> acs;
+ cerr << "Can't open output report file " << outputName << endl;
+ exit(1);
+ }
+- outputFile << "<HTML>\n<TITLE>"<< statType << num2str(i) <<"</TITLE>\n<BODY BACKGROUND=\"file:"<< fslPath <<"/doc/images/fsl-bg.jpg\">\n<hr><CENTER>\n<H1>FEAT Time Series Report - "<< statType << num2str(i) <<"</H1>\n</CENTER>\n<hr><b>Full plots</b><p>\n"<< graphText;
++ outputFile << "<HTML>\n<TITLE>"<< statType << num2str(i) <<"</TITLE>\n<BODY BACKGROUND=\"file:"<< "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/images/fsl-bg.jpg\">\n<hr><CENTER>\n<H1>FEAT Time Series Report - "<< statType << num2str(i) <<"</H1>\n</CENTER>\n<hr><b>Full plots</b><p>\n"<< graphText;
+ if (useTriggers) outputFile << "\n<hr><b>Peristimulus plots</b><p>\n"<< peristimulusText <<"\n<HR></BODY></HTML>\n\n";
+ else outputFile << "\n</BODY></HTML>\n\n";
+ outputFile.close();
+@@ -768,7 +767,7 @@ volume4D<float> acs;
+ cerr << "Can't open output report file " << outputName << endl;
+ exit(1);
+ }
+- outputFile << "<HTML>\n<TITLE>FEAT Time Series Report</TITLE>\n<BODY BACKGROUND=\"file:" << fslPath << "/doc/images/fsl-bg.jpg\">\n<hr><CENTER>\n<H1>FEAT Time Series Report</H1>\n</CENTER>\n<hr>" << indexText << "<HR></BODY></HTML>" << endl << endl;
++ outputFile << "<HTML>\n<TITLE>FEAT Time Series Report</TITLE>\n<BODY BACKGROUND=\"file:" << "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/images/fsl-bg.jpg\">\n<hr><CENTER>\n<H1>FEAT Time Series Report</H1>\n</CENTER>\n<hr>" << indexText << "<HR></BODY></HTML>" << endl << endl;
+ outputFile.close();
+
+ /* now output same thing without start and end, for inclusion in feat report */
+diff --git a/src/first/first_utils.cc b/src/first/first_utils.cc
+index 68be44b..85960f4 100644
+--- a/src/first/first_utils.cc
++++ b/src/first/first_utils.cc
+@@ -1954,8 +1954,8 @@ void do_work_bvars(){
+ if (!surfaceVAout.value()) {
+ // do not output on the surface, instead do the new default of outputting a volume with the scalar normal dot product values (for use with randomise)
+ volume<float> refim;
+- if (useReconMNI.value()) { read_volume(refim,string(getenv("FSLDIR")) + "/data/standard/MNI152_T1_1mm"); }
+- else { read_volume(refim,string(getenv("FSLDIR")) + "/data/standard/MNI152_T1_1mm"); }
++ if (useReconMNI.value()) { read_volume(refim,"@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/data/standard/MNI152_T1_1mm"); }
++ else { read_volume(refim,"@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/data/standard/MNI152_T1_1mm"); }
+ volume<float> maskvol(refim);
+ maskvol=0.0f;
+ volume4D<float> volnormals;
+diff --git a/src/fnirt/fnirtfns.cpp b/src/fnirt/fnirtfns.cpp
+index 24e26fd..77899e7 100644
+--- a/src/fnirt/fnirtfns.cpp
++++ b/src/fnirt/fnirtfns.cpp
+@@ -1203,8 +1203,7 @@ string existing_ref_fname(const string& ref_fname)
+ return(string(ref_fname));
+ }
+ else {
+- const char *fsldir_ptr = getenv("FSLDIR");
+- string eref_fname = string(fsldir_ptr) + string("/data/standard/") + ref_fname;
++ string eref_fname = string("@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/data/standard/") + ref_fname;
+ if (NEWIMAGE::FslFileExists(eref_fname)) return(eref_fname);
+ else return(string(""));
+ }
+@@ -1230,9 +1229,8 @@ string existing_ref_fname(const string& ref_fname)
+ NEWIMAGE::read_volume_hdr_only(vref,ref_fname); // Throws if file dont exist
+ eref_fname = ref_fname;
+ }
+- catch(...) { // Didn't exist in current directory, try in ${FSLDIR}/data/standard
+- const char *fsldir_ptr = getenv("FSLDIR");
+- eref_fname = string(fsldir_ptr) + string("/data/standard/") + ref_fname;
++ catch(...) { // Didn't exist in current directory, try in .../data/standard
++ eref_fname = string("@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/data/standard/") + ref_fname;
+ try {
+ cout << "Could not find " << ref_fname << ", now checking " << eref_fname << endl;
+ NEWIMAGE::read_volume_hdr_only(vref,eref_fname); // Throws if file dont exist
+@@ -1267,8 +1265,7 @@ string existing_conf_file(const string& cfname)
+ if (check_exist(ecfname)) return(ecfname);
+ }
+ if (!FNIRT::path(cfname).length()) { // If no path explicitly given
+- const char *fsldir_ptr = getenv("FSLDIR");
+- ecfname = string(fsldir_ptr) + string("/etc/flirtsch/") + cfname;
++ ecfname = string("@GENTOO_PORTAGE_EPREFIX@/etc/flirtsch/") + cfname;
+ if (check_exist(ecfname)) return(ecfname);
+ else if (!FNIRT::extension(ecfname).length()) { // If no path _and_ no extension given
+ ecfname += string(".cnf");
+diff --git a/src/fslsurface/fslsurface_first.cc b/src/fslsurface/fslsurface_first.cc
+index faec642..b2ef794 100644
+--- a/src/fslsurface/fslsurface_first.cc
++++ b/src/fslsurface/fslsurface_first.cc
+@@ -500,8 +500,7 @@ namespace fslsurface_name {
+
+ volume<float>* immni = new volume<float>();
+
+- char* fsldir = getenv("FSLDIR");
+- read_volume_hdr_only(*immni, string(fsldir) + "/data/standard/MNI152_T1_1mm");
++ read_volume_hdr_only(*immni, "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/data/standard/MNI152_T1_1mm");
+
+ //read_volume_hdr_only(*immni, template_name);
+
+@@ -699,8 +698,7 @@ namespace fslsurface_name {
+
+ volume<float>* immni = new volume<float>();
+
+- char* fsldir = getenv("FSLDIR");
+- read_volume_hdr_only(*immni, string(fsldir) + "/data/standard/MNI152_T1_1mm");
++ read_volume_hdr_only(*immni, "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/data/standard/MNI152_T1_1mm");
+
+ //read_volume_hdr_only(*immni, template_name);
+
+diff --git a/src/fslsurface/fslsurfacemaths.cpp b/src/fslsurface/fslsurfacemaths.cpp
+index eaf55eb..3dc184d 100644
+--- a/src/fslsurface/fslsurfacemaths.cpp
++++ b/src/fslsurface/fslsurfacemaths.cpp
+@@ -598,12 +598,6 @@ int main (int argc, char * argv[])
+
+ }else if (command == "-reconFromBvars"){
+ cout<<"do recon "<<endl;
+- char* fsldir = getenv("FSLDIR");
+- if (fsldir == NULL)
+- {
+- cerr<<"FSLDIR has not been set. "<<endl;
+- exit(EXIT_FAILURE);
+- }
+ //file.bvars,mni_template.nii.gz
+ // string mni = string(fsldir)+"/data/standard/MNI152_T1_1mm";
+ reconSurface_from_bvars( surf, string(argv[i_arg+1]));
+@@ -612,12 +606,6 @@ int main (int argc, char * argv[])
+
+ }else if (command == "-reconAllFromBvarsAndSave"){
+ cout<<"do recon+save "<<argc<<" "<<i_arg<<endl;
+- char* fsldir = getenv("FSLDIR");
+- if (fsldir == NULL)
+- {
+- cerr<<"FSLDIR has not been set. "<<endl;
+- exit(EXIT_FAILURE);
+- }
+ //file.bvars,mni_template.nii.gz
+ // string mni = string(fsldir)+"/data/standard/MNI152_T1_1mm";
+ cout<<"recon "<< string(argv[i_arg+1])<<endl;
diff --git a/sci-biology/fsl/files/fsl-6.0.4-fsldir_redux-p2.patch b/sci-biology/fsl/files/fsl-6.0.4-fsldir_redux-p2.patch
new file mode 100644
index 000000000..af498b400
--- /dev/null
+++ b/sci-biology/fsl/files/fsl-6.0.4-fsldir_redux-p2.patch
@@ -0,0 +1,254 @@
+diff --git a/src/libvis/miscpic.h b/src/libvis/miscpic.h
+index a2f3855..5f440f2 100644
+--- a/src/libvis/miscpic.h
++++ b/src/libvis/miscpic.h
+@@ -90,12 +90,7 @@ namespace MISCPIC{
+ markRight=false;
+ trans= -10;
+ edgethresh = 0.0;
+- if(getenv("FSLDIR")!=0){
+- lutbase = string(getenv("FSLDIR")) + "/etc/luts/";
+- }
+- else{
+- lutbase = string("/");
+- }
++ lutbase = "@GENTOO_PORTAGE_EPREFIX@/etc/luts/";
+ title = string("");
+ cbartype = string("");
+ cbarptr = NULL;
+diff --git a/src/melodic/meldata.cc b/src/melodic/meldata.cc
+index 1749a45..c4ad234 100644
+--- a/src/melodic/meldata.cc
++++ b/src/melodic/meldata.cc
+@@ -992,7 +992,7 @@ namespace Melodic{
+ void MelodicData::est_smoothness()
+ {
+ if(Resels == 0){
+- string SM_path = opts.binpath + "smoothest";
++ string SM_path = "smoothest";
+ string Mask_fname = logger.appendDir("mask");
+
+ if(opts.segment.value().length()>0){
+@@ -1157,7 +1157,7 @@ namespace Melodic{
+ // set up all strings
+ string BET_outputfname = string(Mean_fname)+"_brain";
+
+- string BET_path = opts.binpath + "bet";
++ string BET_path = "bet";
+ string BET_optarg = "-m -f 0.4"; // see man bet
+ string Mask_fname = BET_outputfname+"_mask";
+
+diff --git a/src/melodic/meloptions.cc b/src/melodic/meloptions.cc
+index 08170c7..252e72b 100644
+--- a/src/melodic/meloptions.cc
++++ b/src/melodic/meloptions.cc
+@@ -93,14 +93,6 @@ MelodicOptions* MelodicOptions::gopt = NULL;
+ explicitnums = false;
+ logfname = string("log.txt");
+
+- // work out the path to the $FSLDIR/bin directory
+- if(getenv("FSLDIR")!=0){
+- binpath = (string) getenv("FSLDIR") + "/bin/";
+- } else{
+- binpath = argv[0];
+- binpath = binpath.substr(0,binpath.length()-7);
+- }
+-
+ // parse once to establish log directory name
+ for(int a = options.parse_command_line(argc, argv); a < argc; a++);
+
+diff --git a/src/melodic/meloptions.h b/src/melodic/meloptions.h
+index f546125..b964b7d 100644
+--- a/src/melodic/meloptions.h
++++ b/src/melodic/meloptions.h
+@@ -93,7 +93,6 @@ class MelodicOptions {
+ ~MelodicOptions() { delete gopt; }
+
+ string version;
+- string binpath;
+ string logfname;
+ bool filtermode;
+ bool explicitnums;
+diff --git a/src/melodic/melreport.cc b/src/melodic/melreport.cc
+index 141b6c2..2625059 100644
+--- a/src/melodic/melreport.cc
++++ b/src/melodic/melreport.cc
+@@ -84,8 +84,8 @@ namespace Melodic{
+ IChtml.setDir(report.getDir(),mmodel.get_prefix()+".html");
+
+ {//start IC page
+- IChtml << "<HTML><HEAD><link REL=stylesheet TYPE=text/css href=file:" +
+- (string) getenv("FSLDIR") +"/doc/fsl.css>" << endl
++ IChtml << "<HTML><HEAD><link REL=stylesheet TYPE=text/css href=file:"
++ << "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/fsl.css>" << endl
+ << "<style type=\"text/css\">OBJECT { width: 100% }</style>"
+ << "<TITLE>FSL</TITLE></HEAD>" << endl
+ << "<IFRAME height=" << int(melodat.get_numfiles()/30 + 1)*50
+@@ -486,8 +486,8 @@ namespace Melodic{
+
+ {//start IC2 page
+ IChtml2.setDir(report.getDir(),mmodel.get_prefix()+"_MM.html");
+- IChtml2 << "<HTML><HEAD><link REL=stylesheet TYPE=text/css href=file:" +
+- (string) getenv("FSLDIR") +"/doc/fsl.css>" << endl
++ IChtml2 << "<HTML><HEAD><link REL=stylesheet TYPE=text/css href=file:"
++ << "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/fsl.css>" << endl
+ << "<style type=\"text/css\">OBJECT { width: 100% }</style>"
+ << "<TITLE>FSL</TITLE></HEAD>" << endl
+ << "<IFRAME height="<< int(melodat.get_numfiles()/30 + 1)*50
+@@ -665,8 +665,8 @@ namespace Melodic{
+ IChtml << "<HTML> " << endl
+ << "<TITLE>MELODIC Component " << num2str(cnum)
+ << "</TITLE>" << endl
+- << "<BODY BACKGROUND=\"file:" << getenv("FSLDIR")
+- << "/doc/images/fsl-bg.jpg\">" << endl
++ << "<BODY BACKGROUND=\"file:"
++ << "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/images/fsl-bg.jpg\">" << endl
+ << "<hr><CENTER><H1>MELODIC Component " << num2str(cnum)
+ << "</H1>"<< endl;
+
+diff --git a/src/melodic/melreport.h b/src/melodic/melreport.h
+index 574fc4c..e444681 100644
+--- a/src/melodic/melreport.h
++++ b/src/melodic/melreport.h
+@@ -104,21 +104,21 @@ namespace Melodic{
+ const time_t tmptime = time(NULL);
+ system(("mkdir "+ logger.appendDir("report") + " 2>/dev/null").c_str());
+ report.setDir(logger.appendDir("report"),"00index.html",true,false,ios::out);
+- report << "<HTML><HEAD><link REL=stylesheet TYPE=text/css href=file:" +
+- (string) getenv("FSLDIR") +"/doc/fsl.css>"
++ report << "<HTML><HEAD><link REL=stylesheet TYPE=text/css href=file:"
++ << "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/fsl.css>"
+ << "<TITLE>MELODIC report</TITLE></HEAD><BODY>"
+ << endl <<endl;
+ loghtml.setDir(report.getDir(),"log.html");
+- loghtml << "<HTML><HEAD><link REL=stylesheet TYPE=text/css href=file:" +
+- (string) getenv("FSLDIR") +"/doc/fsl.css>"
++ loghtml << "<HTML><HEAD><link REL=stylesheet TYPE=text/css href=file:"
++ << "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/fsl.css>"
+ << "<TITLE>MELODIC report</TITLE></HEAD><BODY>"
+ << endl <<endl;
+ navigator.setDir(report.getDir(),"nav.html");
+ head.setDir(report.getDir(),"head.html");
+- navigator << "<link REL=stylesheet TYPE=text/css href=file:"+
+- (string) getenv("FSLDIR") +"/doc/fsl.css>" << endl;
+- head << "<link REL=stylesheet TYPE=text/css href=file:"+
+- (string) getenv("FSLDIR") +"/doc/fsl.css>" << endl;
++ navigator << "<link REL=stylesheet TYPE=text/css href=file:"
++ << "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/fsl.css>" << endl;
++ head << "<link REL=stylesheet TYPE=text/css href=file:"
++ << "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/fsl.css>" << endl;
+ head <<"<TABLE BORDER=0><TR>" << endl
+ <<" <TD ALIGN=CENTER WIDTH=100%>"<< endl
+ <<"<TABLE BORDER=0>"<< endl
+@@ -130,8 +130,8 @@ namespace Melodic{
+ << "</tr></table>" << endl
+ << "<TD ALIGN=RIGHT>" << endl
+ << "<a href=http://www.fmrib.ox.ac.uk/fsl target=_top>" << endl
+- << "<IMG BORDER=0 SRC=file:"<< getenv("FSLDIR")
+- << "/doc/images/fsl-logo-big.jpg WIDTH=165></a>" << endl
++ << "<IMG BORDER=0 SRC=file:"
++ << "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/images/fsl-logo-big.jpg WIDTH=165></a>" << endl
+ << "</TD>"<<endl<<"</TR></TABLE> <hr>"<<endl;
+ if(opts.guireport.value()==""){
+ report <<"<OBJECT data=head.html></OBJECT>" << endl;
+diff --git a/src/mm/mixture_model.cc b/src/mm/mixture_model.cc
+index b8e6167..5f00693 100644
+--- a/src/mm/mixture_model.cc
++++ b/src/mm/mixture_model.cc
+@@ -2224,8 +2224,8 @@ namespace Mm {
+
+ htmllog << "<HTML> " << endl
+ << "<TITLE>Mixture Model fit for" << data_name << "</TITLE>" << endl
+- << "<BODY BACKGROUND=\"file:" << getenv("FSLDIR")
+- << "/doc/images/fsl-bg.jpg\">" << endl
++ << "<BODY BACKGROUND=\"file:"
++ << "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/images/fsl-bg.jpg\">" << endl
+ << "<hr><CENTER><H1>Mixture Model fit for<br>" << data_name << " </H1>"<< endl;
+
+ htmllog << "<hr><p>" << endl;
+diff -Naur fsl.orig/src/siena/siena_diff.cc fsl/src/siena/siena_diff.cc
+--- fsl.orig/src/siena/siena_diff.cc 2020-12-02 15:52:50.359856656 -0500
++++ fsl/src/siena/siena_diff.cc 2020-12-02 16:03:25.699876412 -0500
+@@ -107,7 +107,7 @@
+ {
+ // {{{ vars
+
+-char thestring[10000], segoptions[10000], fsldir[10000];
++char thestring[10000], segoptions[10000];
+ int x_size, y_size, z_size, size, x, y, z, i, count,
+ seg2=0, ignore_z=0, ignore_top_slices=0, //erode_mask=0,
+ ignore_bottom_slices=0, debug=0, flow_output=1, edge_masking=0;
+@@ -124,8 +124,6 @@
+
+ string argv1(argv[1]), argv2(argv[2]);
+
+-sprintf(fsldir,"%s",getenv("FSLDIR"));
+-
+ for (i = 3; i < argc; i++)
+ {
+ if (!strcmp(argv[i], "-i"))
+@@ -206,26 +204,26 @@
+ // }}}
+ // {{{ transform images and masks
+
+-sprintf(thestring,"%s/bin/flirt -o %s_halfwayto_%s -applyisoxfm 1 -paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s",
+- fsldir,argv[1],argv[2],argv[1],argv[2],argv[1],argv[1]);
++sprintf(thestring,"flirt -o %s_halfwayto_%s -applyisoxfm 1 -paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s",
++ argv[1],argv[2],argv[1],argv[2],argv[1],argv[1]);
+ printf("%s\n",thestring); system(thestring);
+
+-sprintf(thestring,"%s/bin/flirt -o %s_halfwayto_%s -applyisoxfm 1 -paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s",
+- fsldir,argv[2],argv[1],argv[2],argv[1],argv[1],argv[2]);
++sprintf(thestring,"flirt -o %s_halfwayto_%s -applyisoxfm 1 -paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s",
++ argv[2],argv[1],argv[2],argv[1],argv[1],argv[2]);
+ printf("%s\n",thestring); system(thestring);
+
+-sprintf(thestring,"%s/bin/flirt -o %s_halfwayto_%s_mask -applyisoxfm 1 -paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s_brain_mask",
+- fsldir,argv[1],argv[2],argv[1],argv[2],argv[1],argv[1]);
++sprintf(thestring,"flirt -o %s_halfwayto_%s_mask -applyisoxfm 1 -paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s_brain_mask",
++ argv[1],argv[2],argv[1],argv[2],argv[1],argv[1]);
+ printf("%s\n",thestring); system(thestring);
+
+-sprintf(thestring,"%s/bin/flirt -o %s_halfwayto_%s_mask -applyisoxfm 1 -paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s_brain_mask",
+- fsldir,argv[2],argv[1],argv[2],argv[1],argv[1],argv[2]);
++sprintf(thestring,"flirt -o %s_halfwayto_%s_mask -applyisoxfm 1 -paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s_brain_mask",
++ argv[2],argv[1],argv[2],argv[1],argv[1],argv[2]);
+ printf("%s\n",thestring); system(thestring);
+
+ if (edge_masking)
+ {
+- sprintf(thestring,"%s/bin/flirt -o %s_halfwayto_%s_valid_mask -applyisoxfm 1 -paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s_valid_mask_with_%s",
+- fsldir,argv[1],argv[2],argv[1],argv[2],argv[1],argv[1],argv[2]);
++ sprintf(thestring,"flirt -o %s_halfwayto_%s_valid_mask -applyisoxfm 1 -paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s_valid_mask_with_%s",
++ argv[1],argv[2],argv[1],argv[2],argv[1],argv[1],argv[2]);
+ printf("%s\n",thestring); system(thestring);
+ }
+
+@@ -284,8 +282,8 @@
+ cout << "saving image 1 to disk prior to segmentation" << endl;
+ save_volume(in1,argv1+"_halfwayto_"+argv2+"_brain");
+ in1.destroy();
+- sprintf(thestring,"%s/bin/fast %s %s %s_halfwayto_%s_brain > %s_halfwayto_%s_brain.vol 2>&1",
+- fsldir,segtype,segoptions,argv[1],argv[2],argv[1],argv[2]);
++ sprintf(thestring,"fast %s %s %s_halfwayto_%s_brain > %s_halfwayto_%s_brain.vol 2>&1",
++ segtype,segoptions,argv[1],argv[2],argv[1],argv[2]);
+ cout << thestring << endl;
+ system(thestring);
+ }
+diff --git a/src/topup/topupfns.cpp b/src/topup/topupfns.cpp
+index 6873758..9e8b956 100644
+--- a/src/topup/topupfns.cpp
++++ b/src/topup/topupfns.cpp
+@@ -463,8 +463,7 @@ string existing_conf_file(const string& cfname)
+ if (TOPUP::check_exist(ecfname)) return(ecfname);
+ }
+ if (!TOPUP::path(cfname).length()) { // If no path explicitly given
+- const char *fsldir_ptr = getenv("FSLDIR");
+- ecfname = string(fsldir_ptr) + string("/etc/flirtsch/") + cfname;
++ ecfname = string("@GENTOO_PORTAGE_EPREFIX@/etc/flirtsch/") + cfname;
+ if (TOPUP::check_exist(ecfname)) return(ecfname);
+ else if (!TOPUP::extension(ecfname).length()) { // If no path _and_ no extension given
+ ecfname += string(".cnf");
+--
+2.24.1
+
diff --git a/sci-biology/fsl/files/fsl-6.0.4-gcc10_include.patch b/sci-biology/fsl/files/fsl-6.0.4-gcc10_include.patch
new file mode 100644
index 000000000..ae836c065
--- /dev/null
+++ b/sci-biology/fsl/files/fsl-6.0.4-gcc10_include.patch
@@ -0,0 +1,11 @@
+diff -Naur fsl.orig/src/newimage/newimageio.h fsl/src/newimage/newimageio.h
+--- fsl.orig/src/newimage/newimageio.h 2020-12-02 15:15:27.012786899 -0500
++++ fsl/src/newimage/newimageio.h 2020-12-02 15:19:51.046795110 -0500
+@@ -75,6 +75,7 @@
+ #include <iostream>
+ #include <fstream>
+ #include <sstream>
++#include <stdexcept>
+ #include "NewNifti/NewNifti.h"
+ #include "newmatio.h"
+ #include "newimage.h"
diff --git a/sci-biology/fsl/files/fsl-6.0.4-melodic_std.patch b/sci-biology/fsl/files/fsl-6.0.4-melodic_std.patch
new file mode 100644
index 000000000..83b5b9932
--- /dev/null
+++ b/sci-biology/fsl/files/fsl-6.0.4-melodic_std.patch
@@ -0,0 +1,11 @@
+diff -Naur fsl.orig/src/melodic/Makefile fsl/src/melodic/Makefile
+--- fsl.orig/src/melodic/Makefile 2021-01-06 14:04:35.743274475 -0500
++++ fsl/src/melodic/Makefile 2021-01-06 14:11:27.924264859 -0500
+@@ -9,6 +9,7 @@
+
+ USRINCFLAGS = -I${INC_NEWMAT} -I${INC_PROB} -I${INC_GD} -I${INC_GDC} -I${INC_PNG} -I${INC_ZLIB} -DCIFTILIB_USE_XMLPP -I${FSLEXTINC} -I${INC_XML2} -I${INC_XML++} -I${INC_XML++CONF} -I${INC_BOOST} -I${FSLDIR}/include/ciftiio
+ USRLDFLAGS = -L${LIB_NEWMAT} -L${LIB_PROB} -L${LIB_GD} -L${LIB_GDC} -L${LIB_PNG} -L${LIB_ZLIB}
++USRCXXFLAGS = -std=c++11
+
+ UNAME := $(shell uname)
+ ifeq (${UNAME},Darwin)
diff --git a/sci-biology/fsl/files/fsl-6.0.4-remove_fslpy_collisions-p1.patch b/sci-biology/fsl/files/fsl-6.0.4-remove_fslpy_collisions-p1.patch
new file mode 100644
index 000000000..434dc9cf6
--- /dev/null
+++ b/sci-biology/fsl/files/fsl-6.0.4-remove_fslpy_collisions-p1.patch
@@ -0,0 +1,303 @@
+diff -Naur fsl.orig/src/fslio/imln fsl/src/fslio/imln
+--- fsl.orig/src/fslio/imln 2021-02-01 15:29:34.842752994 -0500
++++ fsl/src/fslio/imln 1969-12-31 19:00:00.000000000 -0500
+@@ -1,90 +0,0 @@
+-#!/bin/sh
+-
+-# imln - make symbolic link(s) to image file(s)
+-#
+-# Stephen Smith and Mark Jenkinson, FMRIB Image Analysis Group
+-#
+-# Copyright (C) 1999-2004 University of Oxford
+-#
+-# Part of FSL - FMRIB's Software Library
+-# http://www.fmrib.ox.ac.uk/fsl
+-# fsl@fmrib.ox.ac.uk
+-#
+-# Developed at FMRIB (Oxford Centre for Functional Magnetic Resonance
+-# Imaging of the Brain), Department of Clinical Neurology, Oxford
+-# University, Oxford, UK
+-#
+-#
+-# LICENCE
+-#
+-# FMRIB Software Library, Release 6.0 (c) 2018, The University of
+-# Oxford (the "Software")
+-#
+-# The Software remains the property of the Oxford University Innovation
+-# ("the University").
+-#
+-# The Software is distributed "AS IS" under this Licence solely for
+-# non-commercial use in the hope that it will be useful, but in order
+-# that the University as a charitable foundation protects its assets for
+-# the benefit of its educational and research purposes, the University
+-# makes clear that no condition is made or to be implied, nor is any
+-# warranty given or to be implied, as to the accuracy of the Software,
+-# or that it will be suitable for any particular purpose or for use
+-# under any specific conditions. Furthermore, the University disclaims
+-# all responsibility for the use which is made of the Software. It
+-# further disclaims any liability for the outcomes arising from using
+-# the Software.
+-#
+-# The Licensee agrees to indemnify the University and hold the
+-# University harmless from and against any and all claims, damages and
+-# liabilities asserted by third parties (including claims for
+-# negligence) which arise directly or indirectly from the use of the
+-# Software or the sale of any products based on the Software.
+-#
+-# No part of the Software may be reproduced, modified, transmitted or
+-# transferred in any form or by any means, electronic or mechanical,
+-# without the express permission of the University. The permission of
+-# the University is not required if the said reproduction, modification,
+-# transmission or transference is done without financial return, the
+-# conditions of this Licence are imposed upon the receiver of the
+-# product, and all original and amended source code is included in any
+-# transmitted product. You may be held legally responsible for any
+-# copyright infringement that is caused or encouraged by your failure to
+-# abide by these terms and conditions.
+-#
+-# You are not permitted under this Licence to use this Software
+-# commercially. Use for which any financial return is received shall be
+-# defined as commercial use, and includes (1) integration of all or part
+-# of the source code or the Software into a product for sale or license
+-# by or on behalf of Licensee to third parties or (2) use of the
+-# Software or any derivative of it for research with the final aim of
+-# developing software products for sale or license to a third party or
+-# (3) use of the Software or any derivative of it for research with the
+-# final aim of developing non-software products for sale or license to a
+-# third party, or (4) use of the Software to provide any service to an
+-# external organisation for which payment is received. If you are
+-# interested in using the Software commercially, please contact Oxford
+-# University Innovation ("OUI"), the technology transfer company of the
+-# University, to negotiate a licence. Contact details are:
+-# fsl@innovation.ox.ac.uk quoting Reference Project 9564, FSL.
+-export LC_ALL=C
+-
+-if [ $# -lt 2 ] ; then
+- echo "Usage: $0 <file1> <file2>"
+- echo " Makes a link (called file2) to file1"
+- echo " NB: filenames can be basenames or include an extension"
+- exit 1;
+-fi
+-
+-f1=`${FSLDIR}/bin/remove_ext $1`;
+-f2=`${FSLDIR}/bin/remove_ext $2`;
+-
+-if [ -f ${f1}.hdr ] ; then ln -fs ${f1}.hdr ${f2}.hdr ; fi
+-if [ -f ${f1}.hdr.gz ] ; then ln -fs ${f1}.hdr.gz ${f2}.hdr.gz ; fi
+-if [ -f ${f1}.img ] ; then ln -fs ${f1}.img ${f2}.img ; fi
+-if [ -f ${f1}.img.gz ] ; then ln -fs ${f1}.img.gz ${f2}.img.gz ; fi
+-if [ -f ${f1}.nii ] ; then ln -fs ${f1}.nii ${f2}.nii ; fi
+-if [ -f ${f1}.nii.gz ] ; then ln -fs ${f1}.nii.gz ${f2}.nii.gz ; fi
+-if [ -f ${f1}.mnc ] ; then ln -fs ${f1}.mnc ${f2}.mnc ; fi
+-if [ -f ${f1}.mnc.gz ] ; then ln -fs ${f1}.mnc.gz ${f2}.mnc.gz ; fi
+-
+diff -Naur fsl.orig/src/fslio/imrm fsl/src/fslio/imrm
+--- fsl.orig/src/fslio/imrm 2021-02-01 15:29:34.842752994 -0500
++++ fsl/src/fslio/imrm 1969-12-31 19:00:00.000000000 -0500
+@@ -1,83 +0,0 @@
+-#!/bin/sh
+-
+-# imrm - remove image files
+-#
+-# Stephen Smith and Mark Jenkinson, FMRIB Image Analysis Group
+-#
+-# Copyright (C) 1999-2004 University of Oxford
+-#
+-# Part of FSL - FMRIB's Software Library
+-# http://www.fmrib.ox.ac.uk/fsl
+-# fsl@fmrib.ox.ac.uk
+-#
+-# Developed at FMRIB (Oxford Centre for Functional Magnetic Resonance
+-# Imaging of the Brain), Department of Clinical Neurology, Oxford
+-# University, Oxford, UK
+-#
+-#
+-# LICENCE
+-#
+-# FMRIB Software Library, Release 6.0 (c) 2018, The University of
+-# Oxford (the "Software")
+-#
+-# The Software remains the property of the Oxford University Innovation
+-# ("the University").
+-#
+-# The Software is distributed "AS IS" under this Licence solely for
+-# non-commercial use in the hope that it will be useful, but in order
+-# that the University as a charitable foundation protects its assets for
+-# the benefit of its educational and research purposes, the University
+-# makes clear that no condition is made or to be implied, nor is any
+-# warranty given or to be implied, as to the accuracy of the Software,
+-# or that it will be suitable for any particular purpose or for use
+-# under any specific conditions. Furthermore, the University disclaims
+-# all responsibility for the use which is made of the Software. It
+-# further disclaims any liability for the outcomes arising from using
+-# the Software.
+-#
+-# The Licensee agrees to indemnify the University and hold the
+-# University harmless from and against any and all claims, damages and
+-# liabilities asserted by third parties (including claims for
+-# negligence) which arise directly or indirectly from the use of the
+-# Software or the sale of any products based on the Software.
+-#
+-# No part of the Software may be reproduced, modified, transmitted or
+-# transferred in any form or by any means, electronic or mechanical,
+-# without the express permission of the University. The permission of
+-# the University is not required if the said reproduction, modification,
+-# transmission or transference is done without financial return, the
+-# conditions of this Licence are imposed upon the receiver of the
+-# product, and all original and amended source code is included in any
+-# transmitted product. You may be held legally responsible for any
+-# copyright infringement that is caused or encouraged by your failure to
+-# abide by these terms and conditions.
+-#
+-# You are not permitted under this Licence to use this Software
+-# commercially. Use for which any financial return is received shall be
+-# defined as commercial use, and includes (1) integration of all or part
+-# of the source code or the Software into a product for sale or license
+-# by or on behalf of Licensee to third parties or (2) use of the
+-# Software or any derivative of it for research with the final aim of
+-# developing software products for sale or license to a third party or
+-# (3) use of the Software or any derivative of it for research with the
+-# final aim of developing non-software products for sale or license to a
+-# third party, or (4) use of the Software to provide any service to an
+-# external organisation for which payment is received. If you are
+-# interested in using the Software commercially, please contact Oxford
+-# University Innovation ("OUI"), the technology transfer company of the
+-# University, to negotiate a licence. Contact details are:
+-# fsl@innovation.ox.ac.uk quoting Reference Project 9564, FSL.
+-export LC_ALL=C
+-
+-if [ $# -lt 1 ] ; then
+- echo "Usage: $0 <list of image names to remove>"
+- echo "NB: filenames can be basenames or not"
+- exit 1;
+-fi
+-
+-for f in $@ ; do
+- fn=`${FSLDIR}/bin/remove_ext $f`;
+- # do the rm silently
+- /bin/rm -f ${fn}.img ${fn}.hdr ${fn}.hdr.gz ${fn}.img.gz ${fn}.nii ${fn}.nii.gz ${fn}.mnc ${fn}.mnc.gz
+-done
+-
+diff -Naur fsl.orig/src/fslio/imtest fsl/src/fslio/imtest
+--- fsl.orig/src/fslio/imtest 2021-02-01 15:29:34.842752994 -0500
++++ fsl/src/fslio/imtest 1969-12-31 19:00:00.000000000 -0500
+@@ -1,118 +0,0 @@
+-#!/bin/sh
+-
+-# imtest - test to see if a valid image file exists with this name (root)
+-#
+-# Stephen Smith and Mark Jenkinson, FMRIB Image Analysis Group
+-#
+-# Copyright (C) 1999-2004 University of Oxford
+-#
+-# Part of FSL - FMRIB's Software Library
+-# http://www.fmrib.ox.ac.uk/fsl
+-# fsl@fmrib.ox.ac.uk
+-#
+-# Developed at FMRIB (Oxford Centre for Functional Magnetic Resonance
+-# Imaging of the Brain), Department of Clinical Neurology, Oxford
+-# University, Oxford, UK
+-#
+-#
+-# LICENCE
+-#
+-# FMRIB Software Library, Release 6.0 (c) 2018, The University of
+-# Oxford (the "Software")
+-#
+-# The Software remains the property of the Oxford University Innovation
+-# ("the University").
+-#
+-# The Software is distributed "AS IS" under this Licence solely for
+-# non-commercial use in the hope that it will be useful, but in order
+-# that the University as a charitable foundation protects its assets for
+-# the benefit of its educational and research purposes, the University
+-# makes clear that no condition is made or to be implied, nor is any
+-# warranty given or to be implied, as to the accuracy of the Software,
+-# or that it will be suitable for any particular purpose or for use
+-# under any specific conditions. Furthermore, the University disclaims
+-# all responsibility for the use which is made of the Software. It
+-# further disclaims any liability for the outcomes arising from using
+-# the Software.
+-#
+-# The Licensee agrees to indemnify the University and hold the
+-# University harmless from and against any and all claims, damages and
+-# liabilities asserted by third parties (including claims for
+-# negligence) which arise directly or indirectly from the use of the
+-# Software or the sale of any products based on the Software.
+-#
+-# No part of the Software may be reproduced, modified, transmitted or
+-# transferred in any form or by any means, electronic or mechanical,
+-# without the express permission of the University. The permission of
+-# the University is not required if the said reproduction, modification,
+-# transmission or transference is done without financial return, the
+-# conditions of this Licence are imposed upon the receiver of the
+-# product, and all original and amended source code is included in any
+-# transmitted product. You may be held legally responsible for any
+-# copyright infringement that is caused or encouraged by your failure to
+-# abide by these terms and conditions.
+-#
+-# You are not permitted under this Licence to use this Software
+-# commercially. Use for which any financial return is received shall be
+-# defined as commercial use, and includes (1) integration of all or part
+-# of the source code or the Software into a product for sale or license
+-# by or on behalf of Licensee to third parties or (2) use of the
+-# Software or any derivative of it for research with the final aim of
+-# developing software products for sale or license to a third party or
+-# (3) use of the Software or any derivative of it for research with the
+-# final aim of developing non-software products for sale or license to a
+-# third party, or (4) use of the Software to provide any service to an
+-# external organisation for which payment is received. If you are
+-# interested in using the Software commercially, please contact Oxford
+-# University Innovation ("OUI"), the technology transfer company of the
+-# University, to negotiate a licence. Contact details are:
+-# fsl@innovation.ox.ac.uk quoting Reference Project 9564, FSL.
+-export LC_ALL=C
+-
+-# return 0 if no image exists or 1 if the image exists
+-
+-if [ $# -lt 1 ] ; then
+- echo "0";
+- exit;
+-fi
+-
+-inputfile=$1
+-
+-
+-
+-for i in 1 2 3 4 5 6 7 8 9 10 11 12
+-do
+-if [ -h $inputfile ] ; then
+-inputfile=`readlink $inputfile`;
+-fi
+-done
+-
+-filename=`${FSLDIR}/bin/remove_ext $inputfile`;
+-
+-if [ -r ${filename}.nii ] || [ -r ${filename}.nii.gz ] ; then
+- echo "1";
+- exit;
+-fi
+-
+-if [ -r ${filename}.mnc ] || [ -r ${filename}.mnc.gz ] ; then
+- echo "1";
+- exit;
+-fi
+-
+-if [ ! -r ${filename}.hdr ] && [ ! -r ${filename}.hdr.gz ] ; then
+- # return 0 here as no header exists and no single image means no image!
+- echo "0";
+- exit;
+-fi
+-
+-if [ ! -r ${filename}.img ] && [ ! -r ${filename}.img.gz ] ; then
+- # return 0 here as no img file exists and no single image means no image!
+- echo "0";
+- exit;
+-fi
+-
+-# only gets to here if there was a hdr and an img file
+-
+-echo "1";
+-exit;
+-
diff --git a/sci-biology/fsl/files/fsl-6.0.4-remove_fslpy_collisions-p2.patch b/sci-biology/fsl/files/fsl-6.0.4-remove_fslpy_collisions-p2.patch
new file mode 100644
index 000000000..ddb7cfb67
--- /dev/null
+++ b/sci-biology/fsl/files/fsl-6.0.4-remove_fslpy_collisions-p2.patch
@@ -0,0 +1,348 @@
+diff -Naur fsl.orig/src/fslio/Makefile fsl/src/fslio/Makefile
+--- fsl.orig/src/fslio/Makefile 2021-02-01 15:29:34.842752994 -0500
++++ fsl/src/fslio/Makefile 2021-02-01 15:32:19.723761859 -0500
+@@ -6,7 +6,7 @@
+
+ OBJS=fslio.o
+
+-SCRIPTS = remove_ext fsloutputtype imtest imglob imcp imln imrm immv
++SCRIPTS = fsloutputtype imglob imcp immv
+
+ all:
+
+diff -Naur fsl.orig/src/fslio/remove_ext fsl/src/fslio/remove_ext
+--- fsl.orig/src/fslio/remove_ext 2021-02-01 15:29:34.842752994 -0500
++++ fsl/src/fslio/remove_ext 1969-12-31 19:00:00.000000000 -0500
+@@ -1,87 +0,0 @@
+-#!/bin/sh
+-
+-# remove_ext - remove extension from image filename
+-#
+-# Stephen Smith and Mark Jenkinson, FMRIB Image Analysis Group
+-#
+-# Copyright (C) 1999-2004 University of Oxford
+-#
+-# Part of FSL - FMRIB's Software Library
+-# http://www.fmrib.ox.ac.uk/fsl
+-# fsl@fmrib.ox.ac.uk
+-#
+-# Developed at FMRIB (Oxford Centre for Functional Magnetic Resonance
+-# Imaging of the Brain), Department of Clinical Neurology, Oxford
+-# University, Oxford, UK
+-#
+-#
+-# LICENCE
+-#
+-# FMRIB Software Library, Release 6.0 (c) 2018, The University of
+-# Oxford (the "Software")
+-#
+-# The Software remains the property of the Oxford University Innovation
+-# ("the University").
+-#
+-# The Software is distributed "AS IS" under this Licence solely for
+-# non-commercial use in the hope that it will be useful, but in order
+-# that the University as a charitable foundation protects its assets for
+-# the benefit of its educational and research purposes, the University
+-# makes clear that no condition is made or to be implied, nor is any
+-# warranty given or to be implied, as to the accuracy of the Software,
+-# or that it will be suitable for any particular purpose or for use
+-# under any specific conditions. Furthermore, the University disclaims
+-# all responsibility for the use which is made of the Software. It
+-# further disclaims any liability for the outcomes arising from using
+-# the Software.
+-#
+-# The Licensee agrees to indemnify the University and hold the
+-# University harmless from and against any and all claims, damages and
+-# liabilities asserted by third parties (including claims for
+-# negligence) which arise directly or indirectly from the use of the
+-# Software or the sale of any products based on the Software.
+-#
+-# No part of the Software may be reproduced, modified, transmitted or
+-# transferred in any form or by any means, electronic or mechanical,
+-# without the express permission of the University. The permission of
+-# the University is not required if the said reproduction, modification,
+-# transmission or transference is done without financial return, the
+-# conditions of this Licence are imposed upon the receiver of the
+-# product, and all original and amended source code is included in any
+-# transmitted product. You may be held legally responsible for any
+-# copyright infringement that is caused or encouraged by your failure to
+-# abide by these terms and conditions.
+-#
+-# You are not permitted under this Licence to use this Software
+-# commercially. Use for which any financial return is received shall be
+-# defined as commercial use, and includes (1) integration of all or part
+-# of the source code or the Software into a product for sale or license
+-# by or on behalf of Licensee to third parties or (2) use of the
+-# Software or any derivative of it for research with the final aim of
+-# developing software products for sale or license to a third party or
+-# (3) use of the Software or any derivative of it for research with the
+-# final aim of developing non-software products for sale or license to a
+-# third party, or (4) use of the Software to provide any service to an
+-# external organisation for which payment is received. If you are
+-# interested in using the Software commercially, please contact Oxford
+-# University Innovation ("OUI"), the technology transfer company of the
+-# University, to negotiate a licence. Contact details are:
+-# fsl@innovation.ox.ac.uk quoting Reference Project 9564, FSL.
+-export LC_ALL=C
+-
+-
+-if [ $# -lt 1 ] ; then
+- exit 1
+-fi
+-
+-lst="";
+-for fn in $@ ; do
+- # for the ones at the end of the line
+- f=`echo "$fn" | sed 's/\.hdr\.gz$//' | sed 's/\.img\.gz$//' | sed 's/\.hdr$//' | sed 's/\.img$//' | sed 's/\.nii.gz$//' | sed 's/\.nii$//' | sed 's/\.mnc.gz$//' | sed 's/\.mnc$//' | sed 's/\.$//'`;
+- # for the ones in the middle of the line
+- f=`echo "$f" | sed 's/\.hdr\.gz[ ]/ /g' | sed 's/\.img\.gz[ ]/ /g' | sed 's/\.hdr[ ]/ /g' | sed 's/\.img[ ]/ /g' | sed 's/\.nii\.gz[ ]/ /g' | sed 's/\.nii[ ]/ /g' | sed 's/\.mnc\.gz[ ]/ /g' | sed 's/\.mnc[ ]/ /g' |sed 's/\.[ ]/ /g'`;
+- lst="$lst $f";
+-done
+-echo $lst;
+-
+-
+diff -Naur fsl.orig/src/misc_scripts/fsl_abspath fsl/src/misc_scripts/fsl_abspath
+--- fsl.orig/src/misc_scripts/fsl_abspath 2021-02-01 15:29:34.828752994 -0500
++++ fsl/src/misc_scripts/fsl_abspath 1969-12-31 19:00:00.000000000 -0500
+@@ -1,71 +0,0 @@
+-#!/usr/bin/env fslpython
+-# fsl_abspath - return true file path
+-# Matthew Webster FMRIB Image Analysis Group
+-# Copyright (C) 2009 University of Oxford
+-# Part of FSL - FMRIB's Software Library
+-# http://www.fmrib.ox.ac.uk/fsl
+-# fsl@fmrib.ox.ac.uk
+-#
+-# Developed at FMRIB (Oxford Centre for Functional Magnetic Resonance
+-# Imaging of the Brain), Department of Clinical Neurology, Oxford
+-# University, Oxford, UK
+-#
+-#
+-# LICENCE
+-#
+-# FMRIB Software Library, Release 6.0 (c) 2018, The University of
+-# Oxford (the "Software")
+-#
+-# The Software remains the property of the Oxford University Innovation
+-# ("the University").
+-#
+-# The Software is distributed "AS IS" under this Licence solely for
+-# non-commercial use in the hope that it will be useful, but in order
+-# that the University as a charitable foundation protects its assets for
+-# the benefit of its educational and research purposes, the University
+-# makes clear that no condition is made or to be implied, nor is any
+-# warranty given or to be implied, as to the accuracy of the Software,
+-# or that it will be suitable for any particular purpose or for use
+-# under any specific conditions. Furthermore, the University disclaims
+-# all responsibility for the use which is made of the Software. It
+-# further disclaims any liability for the outcomes arising from using
+-# the Software.
+-#
+-# The Licensee agrees to indemnify the University and hold the
+-# University harmless from and against any and all claims, damages and
+-# liabilities asserted by third parties (including claims for
+-# negligence) which arise directly or indirectly from the use of the
+-# Software or the sale of any products based on the Software.
+-#
+-# No part of the Software may be reproduced, modified, transmitted or
+-# transferred in any form or by any means, electronic or mechanical,
+-# without the express permission of the University. The permission of
+-# the University is not required if the said reproduction, modification,
+-# transmission or transference is done without financial return, the
+-# conditions of this Licence are imposed upon the receiver of the
+-# product, and all original and amended source code is included in any
+-# transmitted product. You may be held legally responsible for any
+-# copyright infringement that is caused or encouraged by your failure to
+-# abide by these terms and conditions.
+-#
+-# You are not permitted under this Licence to use this Software
+-# commercially. Use for which any financial return is received shall be
+-# defined as commercial use, and includes (1) integration of all or part
+-# of the source code or the Software into a product for sale or license
+-# by or on behalf of Licensee to third parties or (2) use of the
+-# Software or any derivative of it for research with the final aim of
+-# developing software products for sale or license to a third party or
+-# (3) use of the Software or any derivative of it for research with the
+-# final aim of developing non-software products for sale or license to a
+-# third party, or (4) use of the Software to provide any service to an
+-# external organisation for which payment is received. If you are
+-# interested in using the Software commercially, please contact Oxford
+-# University Innovation ("OUI"), the technology transfer company of the
+-# University, to negotiate a licence. Contact details are:
+-# fsl@innovation.ox.ac.uk quoting Reference Project 9564, FSL.
+-from __future__ import print_function
+-import sys
+-import os
+-
+-print (os.path.realpath(sys.argv[1]))
+-sys.exit(0)
+diff -Naur fsl.orig/src/misc_scripts/Makefile fsl/src/misc_scripts/Makefile
+--- fsl.orig/src/misc_scripts/Makefile 2021-02-01 15:29:34.828752994 -0500
++++ fsl/src/misc_scripts/Makefile 2021-02-01 15:32:56.027763811 -0500
+@@ -2,6 +2,6 @@
+
+ PROJNAME = misc_scripts
+
+-SCRIPTS = fslecho regscript remove_vols replace_and_average_fmrib linkbedpost ocmr_preproc correct_and_average eddy_correct Text2Vest Vest2Text AnatomicalAverage fsl_abspath fsl_anat fslFixText
++SCRIPTS = fslecho regscript remove_vols replace_and_average_fmrib linkbedpost ocmr_preproc correct_and_average eddy_correct AnatomicalAverage fsl_anat fslFixText
+
+ all:
+diff -Naur fsl.orig/src/misc_scripts/Text2Vest fsl/src/misc_scripts/Text2Vest
+--- fsl.orig/src/misc_scripts/Text2Vest 2021-02-01 15:29:34.828752994 -0500
++++ fsl/src/misc_scripts/Text2Vest 1969-12-31 19:00:00.000000000 -0500
+@@ -1,80 +0,0 @@
+-#!/bin/sh
+-# Copyright (C) 2012 University of Oxford
+-#
+-# Part of FSL - FMRIB's Software Library
+-# http://www.fmrib.ox.ac.uk/fsl
+-# fsl@fmrib.ox.ac.uk
+-#
+-# Developed at FMRIB (Oxford Centre for Functional Magnetic Resonance
+-# Imaging of the Brain), Department of Clinical Neurology, Oxford
+-# University, Oxford, UK
+-#
+-#
+-# LICENCE
+-#
+-# FMRIB Software Library, Release 6.0 (c) 2018, The University of
+-# Oxford (the "Software")
+-#
+-# The Software remains the property of the Oxford University Innovation
+-# ("the University").
+-#
+-# The Software is distributed "AS IS" under this Licence solely for
+-# non-commercial use in the hope that it will be useful, but in order
+-# that the University as a charitable foundation protects its assets for
+-# the benefit of its educational and research purposes, the University
+-# makes clear that no condition is made or to be implied, nor is any
+-# warranty given or to be implied, as to the accuracy of the Software,
+-# or that it will be suitable for any particular purpose or for use
+-# under any specific conditions. Furthermore, the University disclaims
+-# all responsibility for the use which is made of the Software. It
+-# further disclaims any liability for the outcomes arising from using
+-# the Software.
+-#
+-# The Licensee agrees to indemnify the University and hold the
+-# University harmless from and against any and all claims, damages and
+-# liabilities asserted by third parties (including claims for
+-# negligence) which arise directly or indirectly from the use of the
+-# Software or the sale of any products based on the Software.
+-#
+-# No part of the Software may be reproduced, modified, transmitted or
+-# transferred in any form or by any means, electronic or mechanical,
+-# without the express permission of the University. The permission of
+-# the University is not required if the said reproduction, modification,
+-# transmission or transference is done without financial return, the
+-# conditions of this Licence are imposed upon the receiver of the
+-# product, and all original and amended source code is included in any
+-# transmitted product. You may be held legally responsible for any
+-# copyright infringement that is caused or encouraged by your failure to
+-# abide by these terms and conditions.
+-#
+-# You are not permitted under this Licence to use this Software
+-# commercially. Use for which any financial return is received shall be
+-# defined as commercial use, and includes (1) integration of all or part
+-# of the source code or the Software into a product for sale or license
+-# by or on behalf of Licensee to third parties or (2) use of the
+-# Software or any derivative of it for research with the final aim of
+-# developing software products for sale or license to a third party or
+-# (3) use of the Software or any derivative of it for research with the
+-# final aim of developing non-software products for sale or license to a
+-# third party, or (4) use of the Software to provide any service to an
+-# external organisation for which payment is received. If you are
+-# interested in using the Software commercially, please contact Oxford
+-# University Innovation ("OUI"), the technology transfer company of the
+-# University, to negotiate a licence. Contact details are:
+-# fsl@innovation.ox.ac.uk quoting Reference Project 9564, FSL.
+-export LC_ALL=C
+-if [ $# -lt 2 ] ; then
+- echo "`basename $0` <text file> <vest file>"
+- exit 0
+-fi
+-
+-NumPoints=`grep -cve '^\s*$' $1`
+-NumWaves=`wc $1 | awk '{ print $2 }'`
+-NumWaves=`expr $NumWaves / $NumPoints`
+-
+-echo /NumWaves $NumWaves > $2
+-echo /NumPoints $NumPoints >> $2
+-echo /Matrix >> $2
+-
+-cat $1 >> $2
+-
+diff -Naur fsl.orig/src/misc_scripts/Vest2Text fsl/src/misc_scripts/Vest2Text
+--- fsl.orig/src/misc_scripts/Vest2Text 2021-02-01 15:29:34.828752994 -0500
++++ fsl/src/misc_scripts/Vest2Text 1969-12-31 19:00:00.000000000 -0500
+@@ -1,71 +0,0 @@
+-#!/bin/sh
+-# Copyright (C) 2012 University of Oxford
+-#
+-# Part of FSL - FMRIB's Software Library
+-# http://www.fmrib.ox.ac.uk/fsl
+-# fsl@fmrib.ox.ac.uk
+-#
+-# Developed at FMRIB (Oxford Centre for Functional Magnetic Resonance
+-# Imaging of the Brain), Department of Clinical Neurology, Oxford
+-# University, Oxford, UK
+-#
+-#
+-# LICENCE
+-#
+-# FMRIB Software Library, Release 6.0 (c) 2018, The University of
+-# Oxford (the "Software")
+-#
+-# The Software remains the property of the Oxford University Innovation
+-# ("the University").
+-#
+-# The Software is distributed "AS IS" under this Licence solely for
+-# non-commercial use in the hope that it will be useful, but in order
+-# that the University as a charitable foundation protects its assets for
+-# the benefit of its educational and research purposes, the University
+-# makes clear that no condition is made or to be implied, nor is any
+-# warranty given or to be implied, as to the accuracy of the Software,
+-# or that it will be suitable for any particular purpose or for use
+-# under any specific conditions. Furthermore, the University disclaims
+-# all responsibility for the use which is made of the Software. It
+-# further disclaims any liability for the outcomes arising from using
+-# the Software.
+-#
+-# The Licensee agrees to indemnify the University and hold the
+-# University harmless from and against any and all claims, damages and
+-# liabilities asserted by third parties (including claims for
+-# negligence) which arise directly or indirectly from the use of the
+-# Software or the sale of any products based on the Software.
+-#
+-# No part of the Software may be reproduced, modified, transmitted or
+-# transferred in any form or by any means, electronic or mechanical,
+-# without the express permission of the University. The permission of
+-# the University is not required if the said reproduction, modification,
+-# transmission or transference is done without financial return, the
+-# conditions of this Licence are imposed upon the receiver of the
+-# product, and all original and amended source code is included in any
+-# transmitted product. You may be held legally responsible for any
+-# copyright infringement that is caused or encouraged by your failure to
+-# abide by these terms and conditions.
+-#
+-# You are not permitted under this Licence to use this Software
+-# commercially. Use for which any financial return is received shall be
+-# defined as commercial use, and includes (1) integration of all or part
+-# of the source code or the Software into a product for sale or license
+-# by or on behalf of Licensee to third parties or (2) use of the
+-# Software or any derivative of it for research with the final aim of
+-# developing software products for sale or license to a third party or
+-# (3) use of the Software or any derivative of it for research with the
+-# final aim of developing non-software products for sale or license to a
+-# third party, or (4) use of the Software to provide any service to an
+-# external organisation for which payment is received. If you are
+-# interested in using the Software commercially, please contact Oxford
+-# University Innovation ("OUI"), the technology transfer company of the
+-# University, to negotiate a licence. Contact details are:
+-# fsl@innovation.ox.ac.uk quoting Reference Project 9564, FSL.
+-export LC_ALL=C
+-if [ $# -lt 2 ] ; then
+- echo "`basename $0` <vest file> <text file>"
+- exit 0
+-fi
+-sed -e "/\//d" $1 | sed '/^$/d' > $2
+-
diff --git a/sci-biology/fsl/files/fsl-6.0.4-setup.patch b/sci-biology/fsl/files/fsl-6.0.4-setup.patch
new file mode 100644
index 000000000..061e1a22a
--- /dev/null
+++ b/sci-biology/fsl/files/fsl-6.0.4-setup.patch
@@ -0,0 +1,174 @@
+diff -Naur fsl.orig/build fsl/build
+--- fsl.orig/build 2020-12-02 15:29:12.180812558 -0500
++++ fsl/build 2020-12-02 15:34:03.854821628 -0500
+@@ -28,7 +28,6 @@
+ # The build order for MASTERLIBS is very important, and should not be modified unless you know what
+ # you are doing.
+ MASTERLIBS="
+- CiftiLib-master \
+ utils \
+ znzlib \
+ NewNifti \
+@@ -157,8 +156,8 @@
+ done #project (MASTERPROJECTS)
+ fi #full build
+
+-echo "Building projects - see build.log file for progress..."
+-./config/common/buildproj $PROJECTS > ./build.log 2>&1
++echo "Building projects"
++./config/common/buildproj $PROJECTS
+ finalStatus=$?
+ if [ $finalStatus -eq 0 ]; then
+ echo "Build completed successfully.";
+diff -Naur fsl.orig/config/buildSettings.mk fsl/config/buildSettings.mk
+--- fsl.orig/config/buildSettings.mk 2020-12-02 15:29:11.993812552 -0500
++++ fsl/config/buildSettings.mk 2020-12-02 15:39:37.269831995 -0500
+@@ -18,7 +18,7 @@
+ CHMOD = /bin/chmod
+ MKDIR = /bin/mkdir
+ INSTALL = install -p
+-TCLSH = ${FSLDIR}/bin/fsltclsh
++TCLSH = tclsh
+ DEPENDFLAGS = -MM
+ MACHDBGFLAGS = -g
+ #####################################################################
+@@ -127,19 +127,19 @@
+ #####################################################################
+ ifeq ($(SYSTYPE), Linux)
+ ############### System Vars #####################################
+-CC = gcc
+-CXX = c++
+-CXX11 = c++
++CC = @@GENTOO_CC@@
++CXX = @@GENTOO_CXX@@
++CXX11 = @@GENTOO_CXX@@
+ CSTATICFLAGS = -static
+ CXXSTATICFLAGS = -static
+-ARCHFLAGS = -m64
+-ARCHLDFLAGS = -Wl,-rpath,'$$ORIGIN/../lib'
++ARCHFLAGS =
++ARCHLDFLAGS =
+ PARALLELFLAGS = -fopenmp
+-OPTFLAGS = -g -O3 -fexpensive-optimizations ${ARCHFLAGS}
++OPTFLAGS =
+ GNU_ANSI_FLAGS = -Wall -ansi -pedantic -Wno-long-long
+ SGI_ANSI_FLAGS = -ansi -fullwarn
+ ANSI_FLAGS = ${GNU_ANSI_FLAGS}
+-RANLIB = echo
++RANLIB = @@GENTOO_RANLIB@@
+ FSLML = ${FSLDIR}/bin/fslml
+ # CUDA development environment
+ CUDAVER := $(or $(CUDAVER),9.1)
+@@ -158,8 +158,8 @@
+ NVCC = ${CUDA_INSTALLATION}/bin/nvcc
+ ############### External Libs #####################################
+ # ZLIB library
+-LIB_ZLIB = ${FSLEXTLIB}
+-INC_ZLIB = ${FSLEXTINC}
++#LIB_ZLIB = ${FSLEXTLIB}
++#INC_ZLIB = ${FSLEXTINC}
+ # QT library
+ QTDIR = /usr/lib/qt3
+ LIB_QT = ${QTDIR}/lib
+diff -Naur fsl.orig/config/common/buildproj fsl/config/common/buildproj
+--- fsl.orig/config/common/buildproj 2020-12-02 15:29:11.993812552 -0500
++++ fsl/config/common/buildproj 2020-12-02 15:41:25.579835363 -0500
+@@ -11,10 +11,10 @@
+ fi
+ PROJECTS="$@" ; export PROJECTS ;
+
+-FSLDIR=`pwd`
++#FSLDIR=`pwd`
+ FSLDEVDIR=${FSLDIR}
+ FSLCONFDIR=${FSLDIR}/config
+-FSLMACHTYPE=`${FSLDIR}/etc/fslconf/fslmachtype.sh`
++#FSLMACHTYPE=`${FSLDIR}/etc/fslconf/fslmachtype.sh`
+ FSLMASTERBUILD=1
+ export FSLDIR FSLDEVDIR FSLCONFDIR FSLMACHTYPE FSLMASTERBUILD
+
+@@ -67,7 +67,7 @@
+ if [ -x ./fslconfig ] ; then
+ . ./fslconfig ;
+ fi
+- if ${MAKE} -k ${MAKEOPTIONS} ; then
++ if ${MAKE} ${MAKEOPTIONS} ; then
+ if ${MAKE} ${MAKEOPTIONS} install ; then
+ installok=true;
+ # Clean up after ourselves
+@@ -82,6 +82,7 @@
+ if [ $installok = false ] ; then
+ echo " "
+ echo "ERROR::Could not install $projname successfully" ;
++ exit 1
+ fi
+ else
+ echo " "
+@@ -90,6 +91,7 @@
+ echo " "
+ echo " "
+ errorprojs="$errorprojs $projname" ; export errorprojs ;
++ exit 1
+ fi
+ fi
+ done
+diff -Naur fsl.orig/config/common/vars.mk fsl/config/common/vars.mk
+--- fsl.orig/config/common/vars.mk 2020-12-02 15:29:11.993812552 -0500
++++ fsl/config/common/vars.mk 2020-12-02 15:43:00.602838318 -0500
+@@ -24,15 +24,15 @@
+ USRCFLAGS =
+ USRCXXFLAGS =
+
+-LDFLAGS = ${ARCHLDFLAGS} ${USRLDFLAGS} -L. -L${DEVLIBDIR} -L${LIBDIR}
++LDFLAGS = ${ARCHLDFLAGS} ${USRLDFLAGS} -L. -L${DEVLIBDIR} -L${LIBDIR} ${USERLDFLAGS}
+
+-AccumulatedIncFlags = -I${INC_BOOST} ${USRINCFLAGS} -I. -I${DEVINCDIR} -I${INCDIR}
++AccumulatedIncFlags = ${USRINCFLAGS} -I. -I${DEVINCDIR} -I${INCDIR} ${CPPFLAGS}
+
+ CFLAGS = ${ANSI_FLAGS} ${ANSI_CFLAGS} ${DBGFLAGS} ${USEDCSTATICFLAGS} ${USRCFLAGS} ${ARCHFLAGS} ${OPTFLAGS} \
+- ${AccumulatedIncFlags}
++ ${AccumulatedIncFlags} ${USERCFLAGS}
+
+-CXXFLAGS = ${ANSI_FLAGS} ${ANSI_CXXFLAGS} ${DBGFLAGS} ${USEDCXXSTATICFLAGS} ${USRCXXFLAGS} ${ARCHFLAGS} ${OPTFLAGS} \
+- ${AccumulatedIncFlags}
++CXXFLAGS = ${ANSI_CXXFLAGS} ${DBGFLAGS} ${USEDCXXSTATICFLAGS} ${USRCXXFLAGS} ${ARCHFLAGS} ${OPTFLAGS} \
++ ${AccumulatedIncFlags} ${USERCXXFLAGS}
+
+ HFILES = *.h
+ AFILES = *.a
+diff -Naur fsl.orig/extras/build fsl/extras/build
+--- fsl.orig/extras/build 2020-12-02 15:29:12.404812565 -0500
++++ fsl/extras/build 2020-12-02 15:44:06.906840380 -0500
+@@ -96,16 +96,16 @@
+ BUILDICONV=1
+ fi
+ fi
+-PROJECTS="tcl tk"
++#PROJECTS="tcl tk"
+ if [ ${BUILDZLIB} -eq 1 ]; then
+ PROJECTS="${PROJECTS} zlib"
+ fi
+-PROJECTS="${PROJECTS} libpng"
++#PROJECTS="${PROJECTS} libpng"
+ if [ ${BUILDICONV} -eq 1 ]; then
+ PROJECTS="${PROJECTS} libiconv"
+ fi
+-PROJECTS="${PROJECTS} libgd libgdc libprob libcprob newmat cprob newran fftw"
+-PROJECTS="${PROJECTS} boost libxml2-2.9.2 libxmlpp libsqlite libnlopt ../include/armawrap/dummy_newmat"
++PROJECTS="${PROJECTS} libgdc libprob libcprob newmat cprob newran"
++PROJECTS="${PROJECTS} ../include/armawrap/dummy_newmat"
+ for projname in $PROJECTS; do
+ if [ -d $FSLESRCDIR/$projname ] ; then
+ buildIt $FSLESRCDIR $projname 1
+diff -Naur fsl.orig/src/mist/Makefile fsl/src/mist/Makefile
+--- fsl.orig/src/mist/Makefile 2020-12-02 15:29:12.875812580 -0500
++++ fsl/src/mist/Makefile 2020-12-02 15:45:09.805842335 -0500
+@@ -52,6 +52,8 @@
+ cp -r python/* ${DESTDIR}/python/mist
+
+ clean:
+- rm -f ${OBJS} mist/mist.o mist/mist
++ rm -f ${OBJS} mist/mist.o mist/mist || echo "CLEAN could not locate some files scheduled for deletion."
++
++
+
+ .PHONY: all clean installdata
diff --git a/sci-biology/fsl/fsl-6.0.2-r1.ebuild b/sci-biology/fsl/fsl-6.0.2-r1.ebuild
index 71314a8f8..ae12098ec 100644
--- a/sci-biology/fsl/fsl-6.0.2-r1.ebuild
+++ b/sci-biology/fsl/fsl-6.0.2-r1.ebuild
@@ -6,7 +6,7 @@ EAPI=7
inherit cuda flag-o-matic toolchain-funcs prefix
DESCRIPTION="Analysis of functional, structural, and diffusion MRI brain imaging data"
-HOMEPAGE="http://www.fmrib.ox.ac.uk/fsl"
+HOMEPAGE="https://www.fmrib.ox.ac.uk/fsl"
SRC_URI="https://fsl.fmrib.ox.ac.uk/fsldownloads/${P}-sources.tar.gz -> ${P}.tar.gz"
LICENSE="FSL BSD-2 newmat"
@@ -16,7 +16,7 @@ IUSE="cuda"
DEPEND="
dev-libs/boost
- dev-python/fslpy
+ <dev-python/fslpy-3
media-gfx/graphviz
media-libs/gd
media-libs/glu
diff --git a/sci-biology/fsl/fsl-6.0.2.ebuild b/sci-biology/fsl/fsl-6.0.2.ebuild
index 8a7e0eebb..f490b6e7c 100644
--- a/sci-biology/fsl/fsl-6.0.2.ebuild
+++ b/sci-biology/fsl/fsl-6.0.2.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2020 Gentoo Authors
+# Copyright 1999-2021 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=7
@@ -6,7 +6,7 @@ EAPI=7
inherit flag-o-matic toolchain-funcs prefix
DESCRIPTION="Analysis of functional, structural, and diffusion MRI brain imaging data"
-HOMEPAGE="http://www.fmrib.ox.ac.uk/fsl"
+HOMEPAGE="https://www.fmrib.ox.ac.uk/fsl"
SRC_URI="https://fsl.fmrib.ox.ac.uk/fsldownloads/${P}-sources.tar.gz -> ${P}.tar.gz"
LICENSE="FSL BSD-2 newmat"
@@ -16,7 +16,7 @@ IUSE=""
DEPEND="
dev-libs/boost
- dev-python/fslpy
+ <dev-python/fslpy-3
media-gfx/graphviz
media-libs/gd
media-libs/glu
diff --git a/sci-biology/fsl/fsl-6.0.4.ebuild b/sci-biology/fsl/fsl-6.0.4.ebuild
new file mode 100644
index 000000000..e0feb82d9
--- /dev/null
+++ b/sci-biology/fsl/fsl-6.0.4.ebuild
@@ -0,0 +1,217 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+inherit cuda flag-o-matic toolchain-funcs prefix
+
+DESCRIPTION="Analysis of functional, structural, and diffusion MRI brain imaging data"
+HOMEPAGE="https://www.fmrib.ox.ac.uk/fsl"
+SRC_URI="https://fsl.fmrib.ox.ac.uk/fsldownloads/${P}-sources.tar.gz -> ${P}.tar.gz"
+
+LICENSE="FSL BSD-2 newmat"
+SLOT="0"
+KEYWORDS="~amd64"
+IUSE="cuda"
+
+DEPEND="
+ dev-libs/boost
+ >=dev-python/fslpy-3
+ media-gfx/graphviz
+ media-libs/gd
+ media-libs/glu
+ media-libs/libpng:0=
+ sci-libs/ciftilib
+ sci-libs/nlopt
+ sys-libs/zlib
+ dev-lang/tcl:0=
+ dev-lang/tk:0=
+ >=virtual/lapack-3.8
+ >=virtual/blas-3.8
+
+ cuda? (
+ || (
+ ( =dev-util/nvidia-cuda-toolkit-10* =sys-devel/gcc-8*:* )
+ ( =dev-util/nvidia-cuda-toolkit-11* =sys-devel/gcc-9*:* )
+ )
+ )
+ "
+RDEPEND="${DEPEND}"
+
+S=${WORKDIR}/${PN}
+UPSTREAM_FSLDIR="/usr/share/fsl"
+
+PATCHES=(
+ "${FILESDIR}/${P}"-gcc10_include.patch
+ "${FILESDIR}/${P}"-setup.patch
+ "${FILESDIR}/${PN}"-6.0.2-template.patch
+ "${FILESDIR}/${PN}"-6.0.2-no_xmlpp.patch
+ "${FILESDIR}/${PN}"-5.0.11-niftiio_var_fix.patch
+ "${FILESDIR}/${PN}"-5.0.11-ifstream_use.patch
+ "${FILESDIR}/${PN}"-5.0.11-fslsurface_parallel_make.patch
+ "${FILESDIR}/${PN}"-6.0.2-qstring_compat.patch
+ "${FILESDIR}/${PN}"-5.0.9-headers.patch
+ "${FILESDIR}/${P}"-fsldir_redux-p1.patch
+ "${FILESDIR}/${P}"-fsldir_redux-p2.patch
+ "${FILESDIR}/${P}"-flameo_std.patch
+ "${FILESDIR}/${P}"-melodic_std.patch
+ "${FILESDIR}/${P}"-remove_fslpy_collisions-p1.patch
+ "${FILESDIR}/${P}"-remove_fslpy_collisions-p2.patch
+ "${FILESDIR}/${P}"-fdt_cuda.patch
+)
+
+src_prepare() {
+ default
+
+ sed -i \
+ -e "s:@@GENTOO_RANLIB@@:$(tc-getRANLIB):" \
+ -e "s:@@GENTOO_CC@@:$(tc-getCC):" \
+ -e "s:@@GENTOO_CXX@@:$(tc-getCXX):" \
+ config/buildSettings.mk || die
+
+ eprefixify $(grep -rl GENTOO_PORTAGE_EPREFIX src/*) \
+ etc/js/label-div.html
+
+ # Disable mist the hard way for now.
+ rm -r src/mist || die
+
+ # Disable ptx2 for now
+ rm -r src/ptx2 || die
+
+ makefilelist=$(find src/ -name Makefile)
+
+ sed -i \
+ -e "s:-I\${INC_BOOST}::" \
+ -e "s:-I\${INC_ZLIB}::" \
+ -e "s:-I\${INC_GD}::" \
+ -e "s:-I\${INC_PNG}::" \
+ -e "s:-L\${LIB_GD}::" \
+ -e "s:-L\${LIB_PNG}::" \
+ -e "s:-L\${LIB_ZLIB}::" \
+ ${makefilelist} || die
+
+ sed -e "s:\${FSLDIR}/bin/::g" \
+ -e "s:\$FSLDIR/bin/::g" \
+ -i $(grep -rl "\${FSLDIR}/bin" src/*) \
+ -i $(grep -rl "\$FSLDIR/bin" src/*) \
+ $(grep -rl "\${FSLDIR}/bin" etc/matlab/*)\
+ $(grep -rl "\$FSLDIR/bin" etc/matlab/*) || die
+
+ sed -e "s:\$FSLDIR/data:${EPREFIX}/usr/share/fsl/data:g" \
+ -e "s:\${FSLDIR}/data:${EPREFIX}/usr/share/fsl/data:g" \
+ -i $(grep -rl "\$FSLDIR/data" src/*) \
+ $(grep -rl "\${FSLDIR}/data" src/*) || die
+
+ sed -e "s:\$FSLDIR/doc:${EPREFIX}/usr/share/fsl/doc:g" \
+ -e "s:\${FSLDIR}/doc:${EPREFIX}/usr/share/fsl/doc:g" \
+ -i $(grep -rl "\$FSLDIR/doc" src/*) \
+ $(grep -rl "\${FSLDIR}/doc" src/*) || die
+
+ sed -e "s:/usr/share/fsl/doc:${EPREFIX}/usr/share/fsl/doc:g" \
+ -i $(grep -rl "/usr/share/fsl/doc" src/*) || die
+
+ sed -e "s:\$FSLDIR/etc:${EPREFIX}/etc:g" \
+ -e "s:\${FSLDIR}/etc:${EPREFIX}/etc:g" \
+ -i $(grep -rlI "\$FSLDIR/etc" *) \
+ -i $(grep -rlI "\${FSLDIR}/etc" *) || die
+
+ # Use generic blas/lapack rather than openblas
+ sed -e "s:-lopenblas:-llapack -lblas:g" \
+ -i $(grep -rlI lopenblas *) || die
+
+ # script wanting to have access to fslversion at buildtime
+ sed -e "s:/etc/fslversion:${S}/etc/fslversion:g" \
+ -i ${makefilelist} || die
+
+ if use cuda; then
+ einfo
+
+ gcc_ver=`gcc-fullversion`
+ einfo "GCC version: ${gcc_ver}"
+
+ cuda_gcc=`cuda_gccdir`
+ cuda_NVCC_flags=`cuda_gccdir -f`
+ einfo "CUDA GCC path: ${cuda_gcc}"
+ einfo " ${cuda_NVCC_flags}"
+
+ CUDA_INSTALLATION="/opt/cuda"
+ CUDAVER=`cuda_toolkit_version`
+
+ eapply "${FILESDIR}/${P}-eddy_cuda.patch"
+ eapply "${FILESDIR}/${P}-cuda_buildsettings.patch"
+
+ sed -i \
+ -e "s:@@GENTOO_NVCC_FLAGS@@:${cuda_NVCC_flags}:" \
+ src/eddy/Makefile || die
+
+ cuda_sanitize
+ fi
+}
+
+src_compile() {
+ export FSLDIR=${WORKDIR}/${PN}
+ export FSLCONDIR=${WORKDIR}/${PN}/config
+ export FSLMACHTYPE=generic
+
+ # define the default build system to match upstream official standard
+ # -> individual projects may overwrite the '-std=' flag
+ export ANSI_CFLAGS="-std=c99"
+ export ANSI_CXXFLAGS="-std=c++98"
+
+ export USERLDFLAGS="${LDFLAGS}"
+ export USERCFLAGS="${CFLAGS}"
+ export USERCPPFLAGS="${CPPFLAGS}"
+ export USERCXXFLAGS="${CXXFLAGS}"
+
+ export CIFTICFLAGS="$($(tc-getPKG_CONFIG) --cflags CiftiLib)"
+ export CIFTILIBS="$($(tc-getPKG_CONFIG) --libs-only-l CiftiLib)"
+
+ if use cuda; then
+ einfo "CUDA_INSTALLATION: ${CUDA_INSTALLATION}"
+ einfo "CUDAVER: ${CUDAVER}"
+ fi
+
+ ./build || die
+}
+
+src_install() {
+ sed -i "s:\${FSLDIR}/tcl:/usr/libexec/fsl:g" \
+ $(grep -lI "\${FSLDIR}/tcl" bin/*) \
+ $(grep -l "\${FSLDIR}/tcl" tcl/*) || die
+ sed -i "s:\$FSLDIR/tcl:/usr/libexec/fsl:g" \
+ $(grep -l "\$FSLDIR/tcl" tcl/*) || die
+
+ dobin bin/*
+
+ insinto /usr/share/${PN}
+ doins -r data
+ dodoc -r doc/. refdoc
+
+ insinto /usr/libexec/fsl
+ doins -r tcl/*
+
+ insinto /etc/fslconf
+ doins etc/fslconf/fsl.sh
+
+ insinto /etc
+ doins etc/fslversion
+ doins -r etc/default_flobs.flobs etc/flirtsch etc/js etc/luts
+
+ #the following is needed for FSL and depending programs to be able
+ #to find its files, since FSL uses an uncommon installation path:
+ #https://github.com/gentoo-science/sci/pull/612#r60289295
+ dosym ../../../etc ${UPSTREAM_FSLDIR}/etc
+ dosym ../doc/${PF} ${UPSTREAM_FSLDIR}/doc
+ dosym ../../bin ${UPSTREAM_FSLDIR}/bin
+
+ doenvd "$(prefixify_ro "${FILESDIR}"/99fsl)"
+ mv "${ED}"/usr/bin/{,fsl_}cluster || die
+}
+
+pkg_postinst() {
+ echo
+ einfo "Please run the following commands if you"
+ einfo "intend to use fsl from an existing shell:"
+ einfo "env-update && source /etc/profile"
+ echo
+}
diff --git a/sci-biology/maker/Manifest b/sci-biology/maker/Manifest
deleted file mode 100644
index 7ac1c24b6..000000000
--- a/sci-biology/maker/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST maker-3.01.02_beta.tgz 13646218 BLAKE2B d2767ddd160e98ed843652c4a4259ad8997ec5ee58dcda277dcebc531e3195ff823f6b00eeb0114099f70d412a17fcf7bd784c67eab445a2e6989c3a3c0d23e8 SHA512 69d9b8e03a3094ca0ad1db40d02391a100a360c0917ea6f850dae7bc8c345a12cdb9935473fd388b508e9c5b2fc7f9fbfb5c3f64df9821c1df652803fb469e0e
diff --git a/sci-biology/maker/maker-3.01.02_beta.ebuild b/sci-biology/maker/maker-3.01.02_beta.ebuild
deleted file mode 100644
index 975a83c14..000000000
--- a/sci-biology/maker/maker-3.01.02_beta.ebuild
+++ /dev/null
@@ -1,135 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit perl-functions
-
-DESCRIPTION="A genome annotation viewer and pipeline for small eukaryota and prokaryota"
-HOMEPAGE="http://www.yandell-lab.org/software/maker.html"
-SRC_URI="maker-"${PV}".tgz"
-
-RESTRICT="fetch"
-
-# for academia: GPL-v2 or Artistic-2
-# for commercial: ask
-LICENSE="|| ( GPL-2 Artistic-2 )"
-SLOT="0"
-KEYWORDS=""
-IUSE="mpi"
-
-# http://search.cpan.org/~rybskej/forks-0.36/lib/forks.pm # bug #566360
-# http://search.cpan.org/~rybskej/forks-0.36/lib/forks/shared.pm
-#
-# MAKER does not work with MVAPICH2.
-# It can work with Intel MPI and OpenMPI with some command line modification.
-# It always works with MPICH, but MPICH may not be able to scale to more than ~100 CPUs.
-DEPEND="
- mpi? ( sys-cluster/mpich2 || ( sys-cluster/openmpi ) )
- dev-perl/DBI
- dev-perl/DBD-SQLite
- dev-perl/File-Which
- dev-perl/Bit-Vector
- dev-perl/Inline-C
- dev-perl/IO-All
- dev-perl/libwww-perl
- dev-perl/DBD-Pg
- dev-perl/Module-Build
- dev-perl/Want
- dev-perl/IO-Prompt
- dev-perl/Perl-Unsafe-Signals
- dev-perl/forks
- >=sci-biology/GAL-0.2.1
- >=sci-biology/bioperl-1.6
- sci-biology/ncbi-tools || ( sci-biology/ncbi-tools++ )
- sci-biology/snap
- sci-biology/exonerate
- >=sci-biology/augustus-2.0
- sci-biology/repeatmasker"
- #sci-biology/GeneMark_ES-bin
- #sci-biology/GeneMark_S-bin
- #>=sci-biology/FGENESH-bin-2.4 (not in gentoo yet)
-RDEPEND="${DEPEND}"
-# dev-perl/forks-shared ?
-
-# ==============================================================================
-# STATUS MAKER v2.31.8
-# ==============================================================================
-# PERL Dependencies: MISSING
-# ! Perl::Unsafe::Signals
-# ! Want
-# ! forks
-# ! forks::shared
-#
-# External Programs: MISSING
-# ! RepeatMasker
-#
-# External C Libraries: VERIFIED
-# MPI SUPPORT: DISABLED
-# MWAS Web Interface: DISABLED
-# MAKER PACKAGE: MISSING PREREQUISITES
-#
-#
-# Important Commands:
-# ./Build installdeps #installs missing PERL dependencies
-# ./Build installexes #installs all missing external programs
-# ./Build install #installs MAKER
-# ./Build status #Shows this status menu
-#
-# Other Commands:
-# ./Build repeatmasker #installs RepeatMasker (asks for RepBase)
-# ./Build blast #installs BLAST (NCBI BLAST+)
-# ./Build exonerate #installs Exonerate (v2 on UNIX / v1 on Mac OSX)
-# ./Build snap #installs SNAP
-# ./Build augustus #installs Augustus
-# ./Build apollo #installs Apollo
-# ./Build gbrowse #installs GBrowse (must be root)
-# ./Build jbrowse #installs JBrowse (MAKER copy, not web accecible)
-# ./Build webapollo #installs WebApollo (use maker2wap to create DBs)
-# ./Build mpich2 #installs MPICH2 (but manual install recommended)
-# Building MAKER
-#
-# * MISSING MAKER PREREQUISITES - CANNOT CONTINUE!!
-
-S="${WORKDIR}"/maker/src
-
-pkg_nofetch() {
- einfo "Please visit ${HOMEPAGE} and obtain the file"
- einfo "maker-"${PV}".tgz and place it into your DISTDIR folder"
- einfo "If it is '-beta' rename it to '_beta'"
- einfo "You must also install sci-biology/repeatmasker otherwise"
- einfo "MAKER install process will stop."
- einfo "That in turn requires you to register at http://www.girinst.org/server/RepBase"
- einfo "to obtain sci-biology/repeatmasker-libraries data file"
- einfo "For execution through openmpi or mpich please read INSTALL file"
- einfo "Customization typically go into maker_opts.ctl file"
-}
-
-src_compile(){
- perl Build.PL || die
- ./Build install || die
-}
-
-# If you move it, then the executables won't able to locate dependencies
-# in the /maker/data, /maker/lib, /maker/perl directories. You should
-# really either add the location of /maker/bin to you PATH environmental
-# variable or at most soft link the executables somewhere
-# else using the 'ln -s' command.
-src_install(){
- cd "${WORKDIR}"/maker || die
- rm -f bin/fasta_tool # is part of sci-biology/GAL
- mv bin/compare bin/compare_gff3_to_chado # rename as agreed by upstream, will be in maker-3 as well
- dobin bin/*
- perl_set_version
- perl_domodule perl/lib/MAKER/*.pm
- doman perl/man/*.3pm
- perl_domodule perl/lib/Parallel/Application/*.pm
- insinto /usr/share/"${PN}"/data
- doins data/*
- # FIXME: find equivalent perl packages for lib/* contents, for example lib/GI.pm
- dodoc README INSTALL
- insinto /usr/share/"${PN}"/GMOD/Apollo
- doins GMOD/Apollo/gff3.tiers
- insinto /usr/share/"${PN}"/GMOD/JBrowse
- doins GMOD/JBrowse/maker.css
-}
diff --git a/sci-biology/maker/metadata.xml b/sci-biology/maker/metadata.xml
deleted file mode 100644
index 138cb7705..000000000
--- a/sci-biology/maker/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <maintainer type="person">
- <email>mmokrejs@fold.natur.cuni.cz</email>
- <name>Martin Mokrejs</name>
- </maintainer>
- <maintainer type="project">
- <email>sci-biology@gentoo.org</email>
- <name>Gentoo Biology Project</name>
- </maintainer>
-</pkgmetadata>
diff --git a/sci-biology/mgblast/Manifest b/sci-biology/mgblast/Manifest
deleted file mode 100644
index 4cef2f7f2..000000000
--- a/sci-biology/mgblast/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST mgblast-0.1.tar.gz 22904 BLAKE2B b56d16ef878e32ffb2673889c55c658156620f89753205fb013578b04caea175d67c41fba830c3cb8bce6ac90cafa4de13c7229d5f47972946060b3e3f247261 SHA512 64e36e7bcfd013c85d7b7a79a0728dc2e3aee476772550147680ea2bdd2d3255d4ee9e20a26f886e459e34b42f47082fc34581a60112d99774d291664f45819f
diff --git a/sci-biology/mgblast/metadata.xml b/sci-biology/mgblast/metadata.xml
deleted file mode 100644
index 138cb7705..000000000
--- a/sci-biology/mgblast/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <maintainer type="person">
- <email>mmokrejs@fold.natur.cuni.cz</email>
- <name>Martin Mokrejs</name>
- </maintainer>
- <maintainer type="project">
- <email>sci-biology@gentoo.org</email>
- <name>Gentoo Biology Project</name>
- </maintainer>
-</pkgmetadata>
diff --git a/sci-biology/mgblast/mgblast-0.1.ebuild b/sci-biology/mgblast/mgblast-0.1.ebuild
deleted file mode 100644
index 9eb877c27..000000000
--- a/sci-biology/mgblast/mgblast-0.1.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
-
-DESCRIPTION="Customized version of megablast from TIGR Gene Indices project"
-HOMEPAGE="https://web.archive.org/web/20140726030702/http://compbio.dfci.harvard.edu/tgi/software/"
-SRC_URI="ftp://occams.dfci.harvard.edu/pub/bio/tgi/software/tgicl/mgblast.tar.gz -> ${P}.tar.gz"
-
-LICENSE="Artistic"
-SLOT="0"
-KEYWORDS=""
-
-DEPEND="sci-biology/ncbi-tools"
-RDEPEND="${DEPEND}"
-
-S="${WORKDIR}/${PN}"
-
-# mgblast needs old version of ncbi-tools unpacked and compiled during its own compilation
-# from newer tools you need to include blfmtutl.h but the next error is no go for me:
-# mgblast.c:2205: error: too few arguments to function ‘BXMLBuildOneQueryIteration’
-
-# Quoting from mgblast/README: the present package was built and tested only with the release 20060507
-
-src_prepare(){
- # mgblast cannot be compiled against newer ncbi-tools but let's try
- mv makefile Makefile 2>/dev/null || true
- sed -i -e 's#/usr/local/projects/tgi/ncbitoolkit/ncbi#/usr#' \
- -e's#NCBIDIR = /mylocal/src/ncbi#NCBIDIR = /usr#' \
- -e's#NCBI_INCDIR = .*#NCBI_INCDIR = /usr/include/ncbi#' \
- -e 's#NCBI_LIBDIR = .*#NCBI_LIBDIR = /usr/lib#' \
- -e "s#-I-#-iquote#" Makefile || die # a PATH to NCBI-TOOLKIT (/usr/lib) while NOT /usr/lib/ncbi-tools++ !
- default
-}
diff --git a/sci-biology/ncbi-blast+/ncbi-blast+-2.11.0.ebuild b/sci-biology/ncbi-blast+/ncbi-blast+-2.11.0.ebuild
index 40f338bc3..94c273172 100644
--- a/sci-biology/ncbi-blast+/ncbi-blast+-2.11.0.ebuild
+++ b/sci-biology/ncbi-blast+/ncbi-blast+-2.11.0.ebuild
@@ -38,7 +38,7 @@ DEPEND="
<sys-devel/gcc-10:=
!sci-biology/ncbi-tools++
!sci-biology/sra_sdk
- berkdb? ( sys-libs/db:4.3[cxx] )
+ berkdb? ( sys-libs/db:=[cxx(-)] )
boost? ( dev-libs/boost )
curl? ( net-misc/curl )
sqlite? ( dev-db/sqlite:3 )
diff --git a/sci-biology/ncbi-blast+/ncbi-blast+-2.2.30.ebuild b/sci-biology/ncbi-blast+/ncbi-blast+-2.2.30.ebuild
index 08103e703..783f3a266 100644
--- a/sci-biology/ncbi-blast+/ncbi-blast+-2.2.30.ebuild
+++ b/sci-biology/ncbi-blast+/ncbi-blast+-2.2.30.ebuild
@@ -33,7 +33,7 @@ DEPEND="
<sys-devel/gcc-10:=
!sci-biology/ncbi-tools++
!sci-biology/sra_sdk
- berkdb? ( sys-libs/db:4.3[cxx] )
+ berkdb? ( sys-libs/db:=[cxx(-)] )
boost? ( dev-libs/boost )
curl? ( net-misc/curl )
sqlite? ( dev-db/sqlite:3 )
diff --git a/sci-biology/ncbi-blast+/ncbi-blast+-2.2.31.ebuild b/sci-biology/ncbi-blast+/ncbi-blast+-2.2.31.ebuild
index fbd1a9d4c..7874c2295 100644
--- a/sci-biology/ncbi-blast+/ncbi-blast+-2.2.31.ebuild
+++ b/sci-biology/ncbi-blast+/ncbi-blast+-2.2.31.ebuild
@@ -33,7 +33,7 @@ DEPEND="
<sys-devel/gcc-10:=
!sci-biology/ncbi-tools++
!sci-biology/sra_sdk
- berkdb? ( sys-libs/db:4.3[cxx] )
+ berkdb? ( sys-libs/db:=[cxx(-)] )
boost? ( dev-libs/boost )
curl? ( net-misc/curl )
sqlite? ( dev-db/sqlite:3 )
diff --git a/sci-biology/ncbi-blast+/ncbi-blast+-2.6.0.ebuild b/sci-biology/ncbi-blast+/ncbi-blast+-2.6.0.ebuild
index ec3426cfb..c04fb4cae 100644
--- a/sci-biology/ncbi-blast+/ncbi-blast+-2.6.0.ebuild
+++ b/sci-biology/ncbi-blast+/ncbi-blast+-2.6.0.ebuild
@@ -34,7 +34,7 @@ DEPEND="
<sys-devel/gcc-10:=
!sci-biology/ncbi-tools++
!sci-biology/sra_sdk
- berkdb? ( sys-libs/db:4.3[cxx] )
+ berkdb? ( sys-libs/db:=[cxx(-)] )
boost? ( dev-libs/boost )
curl? ( net-misc/curl )
sqlite? ( dev-db/sqlite:3 )
diff --git a/sci-biology/ncbi-blast+/ncbi-blast+-2.8.1.ebuild b/sci-biology/ncbi-blast+/ncbi-blast+-2.8.1.ebuild
index 40f338bc3..94c273172 100644
--- a/sci-biology/ncbi-blast+/ncbi-blast+-2.8.1.ebuild
+++ b/sci-biology/ncbi-blast+/ncbi-blast+-2.8.1.ebuild
@@ -38,7 +38,7 @@ DEPEND="
<sys-devel/gcc-10:=
!sci-biology/ncbi-tools++
!sci-biology/sra_sdk
- berkdb? ( sys-libs/db:4.3[cxx] )
+ berkdb? ( sys-libs/db:=[cxx(-)] )
boost? ( dev-libs/boost )
curl? ( net-misc/curl )
sqlite? ( dev-db/sqlite:3 )
diff --git a/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild b/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild
index fa1caf715..e646cd099 100644
--- a/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild
+++ b/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild
@@ -38,7 +38,7 @@ DEPEND="
<sys-devel/gcc-10:=
!sci-biology/sra_sdk
app-arch/cpio
- berkdb? ( sys-libs/db:4.3[cxx] )
+ berkdb? ( sys-libs/db:=[cxx(-)] )
boost? ( dev-libs/boost[tools] )
curl? ( net-misc/curl )
sqlite? ( dev-db/sqlite:3 )
diff --git a/sci-biology/ncbi-tools++/ncbi-tools++-18.0.0.ebuild b/sci-biology/ncbi-tools++/ncbi-tools++-18.0.0.ebuild
index 5c0b619df..e6f233bc7 100644
--- a/sci-biology/ncbi-tools++/ncbi-tools++-18.0.0.ebuild
+++ b/sci-biology/ncbi-tools++/ncbi-tools++-18.0.0.ebuild
@@ -41,7 +41,7 @@ DEPEND="
<sys-devel/gcc-10:=
!sci-biology/sra_sdk
app-arch/cpio
- berkdb? ( sys-libs/db:4.3[cxx] )
+ berkdb? ( sys-libs/db:=[cxx(-)] )
boost? ( dev-libs/boost[tools] )
curl? ( net-misc/curl )
sqlite? ( dev-db/sqlite:3 )
diff --git a/sci-biology/ncbi-tools++/ncbi-tools++-22.0.0.ebuild b/sci-biology/ncbi-tools++/ncbi-tools++-22.0.0.ebuild
index 004cc7086..f98fd4282 100644
--- a/sci-biology/ncbi-tools++/ncbi-tools++-22.0.0.ebuild
+++ b/sci-biology/ncbi-tools++/ncbi-tools++-22.0.0.ebuild
@@ -41,7 +41,7 @@ DEPEND="
<sys-devel/gcc-10:=
!sci-biology/sra_sdk
app-arch/cpio
- berkdb? ( sys-libs/db:4.3[cxx] )
+ berkdb? ( sys-libs/db:=[cxx(-)] )
boost? ( dev-libs/boost[tools] )
curl? ( net-misc/curl )
sqlite? ( >=dev-db/sqlite-3.6.6:3 )
diff --git a/sci-biology/nilearn/Manifest b/sci-biology/nilearn/Manifest
index 186997114..580b087b0 100644
--- a/sci-biology/nilearn/Manifest
+++ b/sci-biology/nilearn/Manifest
@@ -1 +1 @@
-DIST nilearn-0.6.2.tar.gz 5890630 BLAKE2B 54bf4f52ea287a98ac29f2aaa9af90bed8f8a61e5d4cc3b9e9e5ca533d69537d0d1779d88faf823712bb3eee384e7d618b78cdae4cbd3c3bdfadeea24429f147 SHA512 98ff82f66aa29a4cadab00ac6cd6f3497822a63c2120f40458a491f4a93365b03e8e63dd9b42b53a45adf9287bd3466ade38cf18dec275aeb69b404ef7e64412
+DIST nilearn-0.8.0.tar.gz 6603264 BLAKE2B f96621b68255722f89ac18cfc8b44e2dc5fc6d4bda2d867d5f83ba669f1c3369318e8458360071245398362122b501c70849741068f7bfa567e49a7f8cdeefa1 SHA512 6e7da3963cd29282ab77bbf1dbb5c1879897dae3d3296a8e0c57edc11a272d9e386914fc3af81d13b57199d64880f534806dca6851b5d8ddecae9083ec5df18e
diff --git a/sci-biology/nilearn/metadata.xml b/sci-biology/nilearn/metadata.xml
index 8ccfeac5c..9da61e484 100644
--- a/sci-biology/nilearn/metadata.xml
+++ b/sci-biology/nilearn/metadata.xml
@@ -14,9 +14,6 @@ Nilearn is a Python module for fast and easy statistical learning on NeuroImagin
It leverages the scikit-learn Python toolbox for multivariate statistics with applications
such as predictive modelling, classification, decoding, or connectivity analysis.
</longdescription>
- <use>
- <flag name="plot">Adds optional dependency needed for plotting function subset.</flag>
- </use>
<upstream>
<remote-id type="github">nilearn/nilearn</remote-id>
<remote-id type="pypi">nilearn</remote-id>
diff --git a/sci-biology/nilearn/nilearn-0.6.2.ebuild b/sci-biology/nilearn/nilearn-0.6.2.ebuild
deleted file mode 100644
index acea71fb2..000000000
--- a/sci-biology/nilearn/nilearn-0.6.2.ebuild
+++ /dev/null
@@ -1,61 +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="Fast and easy statistical learning on NeuroImaging data"
-HOMEPAGE="http://nilearn.github.io/"
-SRC_URI="https://github.com/nilearn/nilearn/archive/${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="+plot test"
-
-# Tests attempt to download external data.
-RESTRICT="test"
-
-DEPEND="
- test? (
- ${RDEPEND}
- dev-python/nose[${PYTHON_USEDEP}]
- )
- dev-python/setuptools[${PYTHON_USEDEP}]
- "
-RDEPEND="
- dev-python/joblib[${PYTHON_USEDEP}]
- dev-python/numpy[${PYTHON_USEDEP}]
- sci-libs/scikit-learn[${PYTHON_USEDEP}]
- dev-python/scipy[${PYTHON_USEDEP}]
- sci-libs/nibabel[${PYTHON_USEDEP}]
- plot? ( <dev-python/matplotlib-3.4.0[${PYTHON_USEDEP}] )"
-
-# (Temporarily) commented out, since Gentoo sci-libs/scikit-learn decided it
-# is a mess to maintain system joblib usage
-#PATCHES=( "${FILESDIR}/0.4.1-bundled_joblib_test.patch" )
-
-python_prepare_all() {
- # upstream is reluctant to *not* depend on bundled scikit-learn:
- # https://github.com/nilearn/nilearn/pull/1398
- # (Temporarily) commented out, since Gentoo sci-libs/scikit-learn decided it
- # is a mess to maintain system joblib usage
- #local f
- #for f in nilearn/{*/*/,*/,}*.py; do
- # sed -r \
- # -e '/^from/s/(sklearn|\.|)\.externals\.joblib/joblib/' \
- # -e 's/from (sklearn|\.|)\.externals import/import/' \
- # -i $f || die
- #done
-
- distutils-r1_python_prepare_all
-}
-
-python_test() {
- echo "backend: Agg" > matplotlibrc
- #MPLCONFIGDIR=. nosetests -v || die
- MPLCONFIGDIR=. pytest -vv || die
-}
diff --git a/sci-biology/nilearn/nilearn-0.8.0.ebuild b/sci-biology/nilearn/nilearn-0.8.0.ebuild
new file mode 100644
index 000000000..a70e8d0fc
--- /dev/null
+++ b/sci-biology/nilearn/nilearn-0.8.0.ebuild
@@ -0,0 +1,42 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{8..9} )
+
+inherit distutils-r1
+
+DESCRIPTION="Fast and easy statistical learning on NeuroImaging data"
+HOMEPAGE="http://nilearn.github.io/"
+SRC_URI="https://github.com/nilearn/nilearn/archive/${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+# Tests attempt to download external data.
+RESTRICT="test"
+
+BDEPEND="
+ test? (
+ dev-python/matplotlib[${PYTHON_USEDEP}]
+ )
+"
+
+RDEPEND="
+ >=dev-python/joblib-0.12[${PYTHON_USEDEP}]
+ >=dev-python/numpy-1.16[${PYTHON_USEDEP}]
+ >=sci-libs/scikit-learn-0.21[${PYTHON_USEDEP}]
+ >=dev-python/scipy-1.2[${PYTHON_USEDEP}]
+ >=sci-libs/nibabel-2.5[${PYTHON_USEDEP}]
+ >=dev-python/pandas-0.24.0[${PYTHON_USEDEP}]
+ >=dev-python/requests-2[${PYTHON_USEDEP}]
+"
+
+distutils_enable_tests pytest
+
+python_test() {
+ echo "backend: Agg" > matplotlibrc
+ MPLCONFIGDIR=. pytest -vv || die
+}
diff --git a/sci-biology/nilearn/nilearn-9999.ebuild b/sci-biology/nilearn/nilearn-9999.ebuild
index 7aca41bd5..a9478fc8e 100644
--- a/sci-biology/nilearn/nilearn-9999.ebuild
+++ b/sci-biology/nilearn/nilearn-9999.ebuild
@@ -1,62 +1,42 @@
# 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..9} )
inherit distutils-r1 git-r3
DESCRIPTION="Fast and easy statistical learning on NeuroImaging data"
HOMEPAGE="http://nilearn.github.io/"
-SRC_URI=""
EGIT_REPO_URI="https://github.com/nilearn/nilearn"
LICENSE="BSD"
SLOT="0"
-KEYWORDS=""
-IUSE="+plot test"
+KEYWORDS="~amd64 ~x86"
# Tests attempt to download external data.
RESTRICT="test"
-DEPEND="
+BDEPEND="
test? (
- ${RDEPEND}
- dev-python/nose[${PYTHON_USEDEP}]
- )
- dev-python/setuptools[${PYTHON_USEDEP}]
- "
+ dev-python/matplotlib[${PYTHON_USEDEP}]
+ )
+"
+
RDEPEND="
- dev-python/joblib[${PYTHON_USEDEP}]
- dev-python/numpy[${PYTHON_USEDEP}]
- sci-libs/scikit-learn[${PYTHON_USEDEP}]
- dev-python/scipy[${PYTHON_USEDEP}]
- sci-libs/nibabel[${PYTHON_USEDEP}]
- plot? ( dev-python/matplotlib[${PYTHON_USEDEP}] )"
-
-# (Temporarily) commented out, since Gentoo sci-libs/scikit-learn decided it
-# is a mess to maintain system joblib usage
-#PATCHES=( "${FILESDIR}/0.4.1-bundled_joblib_test.patch" )
-
-python_prepare_all() {
- # upstream is reluctant to *not* depend on bundled scikit-learn:
- # https://github.com/nilearn/nilearn/pull/1398
- # (Temporarily) commented out, since Gentoo sci-libs/scikit-learn decided it
- # is a mess to maintain system joblib usage
- #local f
- #for f in nilearn/{*/*/,*/,}*.py; do
- # sed -r \
- # -e '/^from/s/(sklearn|\.|)\.externals\.joblib/joblib/' \
- # -e 's/from (sklearn|\.|)\.externals import/import/' \
- # -i $f || die
- #done
-
- distutils-r1_python_prepare_all
-}
+ >=dev-python/joblib-0.12[${PYTHON_USEDEP}]
+ >=dev-python/numpy-1.16[${PYTHON_USEDEP}]
+ >=sci-libs/scikit-learn-0.21[${PYTHON_USEDEP}]
+ >=dev-python/scipy-1.2[${PYTHON_USEDEP}]
+ >=sci-libs/nibabel-2.5[${PYTHON_USEDEP}]
+ >=dev-python/pandas-0.24.0[${PYTHON_USEDEP}]
+ >=dev-python/requests-2[${PYTHON_USEDEP}]
+"
+
+distutils_enable_tests pytest
python_test() {
echo "backend: Agg" > matplotlibrc
- #MPLCONFIGDIR=. nosetests -v || die
MPLCONFIGDIR=. pytest -vv || die
}
diff --git a/sci-biology/open-ephys-gui/Manifest b/sci-biology/open-ephys-gui/Manifest
index f4b770e24..9f8d8eeac 100644
--- a/sci-biology/open-ephys-gui/Manifest
+++ b/sci-biology/open-ephys-gui/Manifest
@@ -1 +1,2 @@
DIST open-ephys-gui-0.5.2.2.tar.gz 64533170 BLAKE2B dc70c3eca6a8fbc7c4f6e84580fa6d5b31b837fedbdff20f532e3c01c764cbc3c51637e4fd678d048c78b6f79b4b4a5cd4d437125beeaf712f6f322e82579c85 SHA512 b6369bb0abd8ca18ff225cffab04a24915865647ee1ab5b6d83d5d6fbda3bc64d1b7db04c23deb8d29b8ff378e703b88cfa9d409f4cde62a3af34a7984427219
+DIST open-ephys-gui-0.5.5.tar.gz 63347783 BLAKE2B 8f3ab3c20e23dd4f613e2ed47dca1827ddbcc5e95be5ca12dfeefdc84611653d531d629b78049397fd4951d558f63531ea2265d13e629c8da793fc20090d1075 SHA512 b835a7f8bb3eeb08ec77f6d14f988d6278b2f5b1966fbf8bec55d429c9cee36050cf574dd78a2ebad4adc5c681bcec5b64dcfb1ec87e548c55e2bf1bff2eb2dc
diff --git a/sci-biology/open-ephys-gui/files/open-ephys-gui-0.5.5.patch b/sci-biology/open-ephys-gui/files/open-ephys-gui-0.5.5.patch
new file mode 100644
index 000000000..77e401639
--- /dev/null
+++ b/sci-biology/open-ephys-gui/files/open-ephys-gui-0.5.5.patch
@@ -0,0 +1,12 @@
+# Add 'Gentoo' build type
+
+--- ../CMakeLists.txt 2019-12-02 22:29:24.021065669 -0300
++++ ../CMakeLists.txt 2019-12-02 22:29:11.251065418 -0300
+@@ -123,6 +123,7 @@
+ if(${CMAKE_BUILD_TYPE} STREQUAL "Debug")
+
+ elseif (${CMAKE_BUILD_TYPE} STREQUAL "Release")
++ elseif (${CMAKE_BUILD_TYPE} STREQUAL "Gentoo")
+ else()
+ message(FATAL_ERROR "Invalid build type")
+ endif()
diff --git a/sci-biology/open-ephys-gui/open-ephys-gui-0.5.2.2.ebuild b/sci-biology/open-ephys-gui/open-ephys-gui-0.5.2.2.ebuild
index b0266e0ac..b4cbc6d8f 100644
--- a/sci-biology/open-ephys-gui/open-ephys-gui-0.5.2.2.ebuild
+++ b/sci-biology/open-ephys-gui/open-ephys-gui-0.5.2.2.ebuild
@@ -5,7 +5,7 @@ EAPI=7
inherit cmake
DESCRIPTION="Processing, recording, and visualizing multichannel ephys data"
-HOMEPAGE="http://www.open-ephys.org/gui/"
+HOMEPAGE="https://open-ephys.org/gui/"
LICENSE="GPL-3"
if [[ ${PV} == "9999" ]] ; then
diff --git a/sci-biology/open-ephys-gui/open-ephys-gui-0.5.5.ebuild b/sci-biology/open-ephys-gui/open-ephys-gui-0.5.5.ebuild
new file mode 100644
index 000000000..1c2b20e24
--- /dev/null
+++ b/sci-biology/open-ephys-gui/open-ephys-gui-0.5.5.ebuild
@@ -0,0 +1,80 @@
+# Copyright 2019-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+inherit cmake udev
+
+DESCRIPTION="Processing, recording, and visualizing multichannel ephys data"
+HOMEPAGE="https://open-ephys.org/gui/"
+LICENSE="GPL-3"
+
+if [[ ${PV} == "9999" ]] ; then
+ inherit git-r3
+ EGIT_REPO_URI="https://github.com/open-ephys/plugin-GUI"
+ EGIT_BRANCH="master"
+ Suffix=${EGIT_BRANCH}
+ SubDir=${P}
+elif [[ ${PV} == "99999999" ]] ; then
+ inherit git-r3
+ EGIT_REPO_URI="https://github.com/open-ephys/plugin-GUI"
+ EGIT_BRANCH="development"
+ Suffix=${EGIT_BRANCH}
+ SubDir=${P}
+else
+ SRC_URI="https://github.com/open-ephys/plugin-GUI/archive/v${PV}.tar.gz -> ${P}.tar.gz"
+ Suffix=${PV}
+ SubDir="plugin-GUI-${PV}"
+ S="${WORKDIR}/${SubDir}"
+ KEYWORDS="~amd64 ~x86"
+fi
+
+SLOT="${PV}"
+IUSE="jack"
+
+DEPEND="
+ media-libs/alsa-lib
+ media-libs/freeglut
+ media-libs/freetype
+ x11-libs/libXrandr
+ x11-libs/libXcursor
+ x11-libs/libXinerama
+ jack? ( || ( media-sound/jack-audio-connection-kit media-sound/jack2 ) )
+"
+RDEPEND="${DEPEND}"
+
+BUILD_DIR="${S}/Build"
+PATCHES=( "${FILESDIR}"/${P}.patch )
+
+QA_PREBUILT="opt/open-ephys-*/shared/*.so"
+QA_PRESTRIPPED="
+ opt/open-ephys-*/plugins/*.so
+ opt/open-ephys-*/open-ephys
+"
+
+src_prepare() {
+ cmake_src_prepare
+
+ if use jack; then
+ sed -i 's/JUCE_APP_VERSION=/JUCE_JACK=1\n JUCE_APP_VERSION=/' "${WORKDIR}/${SubDir}/CMakeLists.txt" || die "Sed failed!"
+ fi
+}
+
+src_configure() {
+ local mycmakeargs=( -DCMAKE_SKIP_RPATH=ON )
+ cmake_src_configure
+}
+
+src_install() {
+ dodir opt/open-ephys-"${Suffix}"/ lib/udev/rules.d/
+ cp -R "${BUILD_DIR}"/Gentoo/* "${ED}"/opt/open-ephys-"${Suffix}"/
+ udev_newrules "${WORKDIR}"/"${SubDir}"/Resources/Scripts/40-open-ephys.rules 40-open-ephys-"${Suffix}".rules
+ dosym ../../opt/open-ephys-"${Suffix}"/open-ephys usr/bin/open-ephys-"${Suffix}"
+}
+
+pkg_postinst() {
+ udev_reload
+}
+
+pkg_postrm() {
+ udev_reload
+}
diff --git a/sci-biology/open-ephys-gui/open-ephys-gui-9999.ebuild b/sci-biology/open-ephys-gui/open-ephys-gui-9999.ebuild
index b0266e0ac..1c2b20e24 100644
--- a/sci-biology/open-ephys-gui/open-ephys-gui-9999.ebuild
+++ b/sci-biology/open-ephys-gui/open-ephys-gui-9999.ebuild
@@ -2,38 +2,35 @@
# Distributed under the terms of the GNU General Public License v2
EAPI=7
-inherit cmake
+inherit cmake udev
DESCRIPTION="Processing, recording, and visualizing multichannel ephys data"
-HOMEPAGE="http://www.open-ephys.org/gui/"
+HOMEPAGE="https://open-ephys.org/gui/"
LICENSE="GPL-3"
if [[ ${PV} == "9999" ]] ; then
inherit git-r3
EGIT_REPO_URI="https://github.com/open-ephys/plugin-GUI"
EGIT_BRANCH="master"
- Suffix=$EGIT_BRANCH
+ Suffix=${EGIT_BRANCH}
SubDir=${P}
elif [[ ${PV} == "99999999" ]] ; then
inherit git-r3
EGIT_REPO_URI="https://github.com/open-ephys/plugin-GUI"
EGIT_BRANCH="development"
- Suffix=$EGIT_BRANCH
+ Suffix=${EGIT_BRANCH}
SubDir=${P}
else
SRC_URI="https://github.com/open-ephys/plugin-GUI/archive/v${PV}.tar.gz -> ${P}.tar.gz"
Suffix=${PV}
SubDir="plugin-GUI-${PV}"
- S="${WORKDIR}/$SubDir"
+ S="${WORKDIR}/${SubDir}"
KEYWORDS="~amd64 ~x86"
fi
SLOT="${PV}"
IUSE="jack"
-BDEPEND="
- <sys-devel/gcc-9
-"
DEPEND="
media-libs/alsa-lib
media-libs/freeglut
@@ -41,17 +38,17 @@ DEPEND="
x11-libs/libXrandr
x11-libs/libXcursor
x11-libs/libXinerama
- jack? ( media-sound/jack-audio-connection-kit )
+ jack? ( || ( media-sound/jack-audio-connection-kit media-sound/jack2 ) )
"
RDEPEND="${DEPEND}"
-BUILD_DIR="$S/Build"
+BUILD_DIR="${S}/Build"
PATCHES=( "${FILESDIR}"/${P}.patch )
-QA_PREBUILT="opt/open-ephys-0.5.2.2/shared/*.so"
+QA_PREBUILT="opt/open-ephys-*/shared/*.so"
QA_PRESTRIPPED="
- opt/open-ephys-0.5.2.2/plugins/*.so
- opt/open-ephys-0.5.2.2/open-ephys
+ opt/open-ephys-*/plugins/*.so
+ opt/open-ephys-*/open-ephys
"
src_prepare() {
@@ -68,15 +65,16 @@ src_configure() {
}
src_install() {
- dodir opt/open-ephys-"$Suffix"/ lib/udev/rules.d/
- cp -R "${BUILD_DIR}"/Gentoo/* "${ED}"/opt/open-ephys-"$Suffix"/
- cp -R "${WORKDIR}"/"${SubDir}"/Resources/Scripts/40-open-ephys.rules "${ED}"/lib/udev/rules.d/
- dosym ../../opt/open-ephys-"$Suffix"/open-ephys usr/bin/open-ephys-"$Suffix"
+ dodir opt/open-ephys-"${Suffix}"/ lib/udev/rules.d/
+ cp -R "${BUILD_DIR}"/Gentoo/* "${ED}"/opt/open-ephys-"${Suffix}"/
+ udev_newrules "${WORKDIR}"/"${SubDir}"/Resources/Scripts/40-open-ephys.rules 40-open-ephys-"${Suffix}".rules
+ dosym ../../opt/open-ephys-"${Suffix}"/open-ephys usr/bin/open-ephys-"${Suffix}"
}
pkg_postinst() {
- ewarn " "
- ewarn "You must restart the udev service in order to allow your computer to"
- ewarn "communicate with the Open Ephys acquisition board."
- ewarn " "
+ udev_reload
+}
+
+pkg_postrm() {
+ udev_reload
}
diff --git a/sci-biology/open-ephys-gui/open-ephys-gui-99999999.ebuild b/sci-biology/open-ephys-gui/open-ephys-gui-99999999.ebuild
index b0266e0ac..1c2b20e24 100644
--- a/sci-biology/open-ephys-gui/open-ephys-gui-99999999.ebuild
+++ b/sci-biology/open-ephys-gui/open-ephys-gui-99999999.ebuild
@@ -2,38 +2,35 @@
# Distributed under the terms of the GNU General Public License v2
EAPI=7
-inherit cmake
+inherit cmake udev
DESCRIPTION="Processing, recording, and visualizing multichannel ephys data"
-HOMEPAGE="http://www.open-ephys.org/gui/"
+HOMEPAGE="https://open-ephys.org/gui/"
LICENSE="GPL-3"
if [[ ${PV} == "9999" ]] ; then
inherit git-r3
EGIT_REPO_URI="https://github.com/open-ephys/plugin-GUI"
EGIT_BRANCH="master"
- Suffix=$EGIT_BRANCH
+ Suffix=${EGIT_BRANCH}
SubDir=${P}
elif [[ ${PV} == "99999999" ]] ; then
inherit git-r3
EGIT_REPO_URI="https://github.com/open-ephys/plugin-GUI"
EGIT_BRANCH="development"
- Suffix=$EGIT_BRANCH
+ Suffix=${EGIT_BRANCH}
SubDir=${P}
else
SRC_URI="https://github.com/open-ephys/plugin-GUI/archive/v${PV}.tar.gz -> ${P}.tar.gz"
Suffix=${PV}
SubDir="plugin-GUI-${PV}"
- S="${WORKDIR}/$SubDir"
+ S="${WORKDIR}/${SubDir}"
KEYWORDS="~amd64 ~x86"
fi
SLOT="${PV}"
IUSE="jack"
-BDEPEND="
- <sys-devel/gcc-9
-"
DEPEND="
media-libs/alsa-lib
media-libs/freeglut
@@ -41,17 +38,17 @@ DEPEND="
x11-libs/libXrandr
x11-libs/libXcursor
x11-libs/libXinerama
- jack? ( media-sound/jack-audio-connection-kit )
+ jack? ( || ( media-sound/jack-audio-connection-kit media-sound/jack2 ) )
"
RDEPEND="${DEPEND}"
-BUILD_DIR="$S/Build"
+BUILD_DIR="${S}/Build"
PATCHES=( "${FILESDIR}"/${P}.patch )
-QA_PREBUILT="opt/open-ephys-0.5.2.2/shared/*.so"
+QA_PREBUILT="opt/open-ephys-*/shared/*.so"
QA_PRESTRIPPED="
- opt/open-ephys-0.5.2.2/plugins/*.so
- opt/open-ephys-0.5.2.2/open-ephys
+ opt/open-ephys-*/plugins/*.so
+ opt/open-ephys-*/open-ephys
"
src_prepare() {
@@ -68,15 +65,16 @@ src_configure() {
}
src_install() {
- dodir opt/open-ephys-"$Suffix"/ lib/udev/rules.d/
- cp -R "${BUILD_DIR}"/Gentoo/* "${ED}"/opt/open-ephys-"$Suffix"/
- cp -R "${WORKDIR}"/"${SubDir}"/Resources/Scripts/40-open-ephys.rules "${ED}"/lib/udev/rules.d/
- dosym ../../opt/open-ephys-"$Suffix"/open-ephys usr/bin/open-ephys-"$Suffix"
+ dodir opt/open-ephys-"${Suffix}"/ lib/udev/rules.d/
+ cp -R "${BUILD_DIR}"/Gentoo/* "${ED}"/opt/open-ephys-"${Suffix}"/
+ udev_newrules "${WORKDIR}"/"${SubDir}"/Resources/Scripts/40-open-ephys.rules 40-open-ephys-"${Suffix}".rules
+ dosym ../../opt/open-ephys-"${Suffix}"/open-ephys usr/bin/open-ephys-"${Suffix}"
}
pkg_postinst() {
- ewarn " "
- ewarn "You must restart the udev service in order to allow your computer to"
- ewarn "communicate with the Open Ephys acquisition board."
- ewarn " "
+ udev_reload
+}
+
+pkg_postrm() {
+ udev_reload
}
diff --git a/sci-biology/pbcopper/pbcopper-1.9.0.ebuild b/sci-biology/pbcopper/pbcopper-1.9.0.ebuild
index 52d7611d4..972b98d65 100644
--- a/sci-biology/pbcopper/pbcopper-1.9.0.ebuild
+++ b/sci-biology/pbcopper/pbcopper-1.9.0.ebuild
@@ -21,6 +21,6 @@ BDEPEND="
DEPEND="
>=sci-libs/htslib-1.3.1:=
- >=dev-libs/boost-1.55:=[threads]
+ >=dev-libs/boost-1.55:=[threads(-)]
"
RDEPEND="${DEPEND}"
diff --git a/sci-biology/primerD/primerD-1.0.0.ebuild b/sci-biology/primerD/primerD-1.0.0.ebuild
index b5365336a..6d46832a9 100644
--- a/sci-biology/primerD/primerD-1.0.0.ebuild
+++ b/sci-biology/primerD/primerD-1.0.0.ebuild
@@ -7,12 +7,12 @@ inherit toolchain-funcs
DESCRIPTION="Design degenerate primers"
HOMEPAGE="https://mblab.wustl.edu/software.html"
+SRC_URI="primerD.tar.gz"
#SRC_URI="https://mblab.wustl.edu/software/download/primerD.tar.gz -> primerD-1.0.tar.gz"
# ERROR: cannot verify mblab.wustl.edu's certificate, issued by ‘CN=InCommon RSA Server CA,OU=InCommon,O=Internet2,L=Ann Arbor,ST=MI,C=US’:
# Unable to locally verify the issuer's authority.
# To connect to mblab.wustl.edu insecurely, use `--no-check-certificate'.
RESTRICT="fetch"
-SRC_URI="primerD.tar.gz"
LICENSE="LGPL-2.1"
SLOT="0"
diff --git a/sci-biology/prot4EST/Manifest b/sci-biology/prot4EST/Manifest
deleted file mode 100644
index b010efd0e..000000000
--- a/sci-biology/prot4EST/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST prot4EST_rl3.1b.tgz 21869514 BLAKE2B eeafdd97482ff397c54d85195069471756b7dca685c9e066038aa78fbd76a84a907e2b0b16b4912c445644aedf2bea7117eb4ebd857a644c337154bdbfb8bf98 SHA512 0768d36066c9d0f88ce53100ffaf71cdb27bb75ab2e36cc0f5950ac5995292bb31c3226033b17acbaf43f002474df4ddafed7bc2cf4e454bcd3282e85656ff78
diff --git a/sci-biology/prot4EST/metadata.xml b/sci-biology/prot4EST/metadata.xml
deleted file mode 100644
index 138cb7705..000000000
--- a/sci-biology/prot4EST/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <maintainer type="person">
- <email>mmokrejs@fold.natur.cuni.cz</email>
- <name>Martin Mokrejs</name>
- </maintainer>
- <maintainer type="project">
- <email>sci-biology@gentoo.org</email>
- <name>Gentoo Biology Project</name>
- </maintainer>
-</pkgmetadata>
diff --git a/sci-biology/prot4EST/prot4EST-3.1b.ebuild b/sci-biology/prot4EST/prot4EST-3.1b.ebuild
deleted file mode 100644
index 9f8fb4302..000000000
--- a/sci-biology/prot4EST/prot4EST-3.1b.ebuild
+++ /dev/null
@@ -1,38 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit perl-module
-
-DESCRIPTION="Predict proteins from EST sequences overcoming frameshifts"
-HOMEPAGE="http://www.compsysbio.org/
- http://www.biomedcentral.com/1471-2105/5/187"
-SRC_URI="http://www.compsysbio.org/lab/james/prot4EST_rl3.1b.tgz"
-
-LICENSE="GPL-1"
-SLOT="0"
-KEYWORDS="~amd64"
-
-DEPEND="
- sci-biology/emboss
- sci-biology/estscan
- sci-biology/bioperl
- sci-biology/ncbi-tools
- virtual/perl-File-Path
- virtual/perl-Getopt-Long
- dev-perl/Statistics-Descriptive
- dev-perl/Tie-IxHash
- dev-perl/Algorithm-Loops"
- # sci-biology/DECODER
-RDEPEND="${DEPEND}"
-
-S="${WORKDIR}/p4e3.1b"
-
-src_install(){
- mydoc="README INSTALL"
- perl-module_src_install
- mv bin/prot4EST*.pl bin/prot4EST.pl
- dobin bin/*.pl
- dodoc doc/*
-}
diff --git a/sci-biology/rum/Manifest b/sci-biology/rum/Manifest
deleted file mode 100644
index 84b0619e4..000000000
--- a/sci-biology/rum/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST rum-2.0.5.06.tar.gz 5420681 BLAKE2B f9c6c34b8ebc939754686633e449ab69484bfb7f66108e44a25095bde85e35cf2b91936641d00d5d78ca921b05026c3d9721638e00d87603095494dab4801408 SHA512 98e316cbdb0860a6449ed39e20d96e6b0926d3eaf7fd0e0a1dcfb1ef41a5c3d681ccc74b241452d896e5d235c77b79bad89aebaf2d2050ab6c72c8dc2383d3c3
diff --git a/sci-biology/rum/rum-2.0.5.06.ebuild b/sci-biology/rum/rum-2.0.5.06.ebuild
deleted file mode 100644
index 7234c72e7..000000000
--- a/sci-biology/rum/rum-2.0.5.06.ebuild
+++ /dev/null
@@ -1,30 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit perl-module
-
-DESCRIPTION="RNA-Seq Unified Mapper (digital normalization)"
-HOMEPAGE="https://github.com/itmat/rum/wiki"
-SRC_URI="https://github.com/itmat/rum/archive/v$(ver_rs 3-4 _).tar.gz -> ${P}.tar.gz"
-
-LICENSE="UPennState"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-
-DEPEND="
- dev-perl/Log-Log4perl
- virtual/perl-autodie"
-RDEPEND="${DEPEND}
- sci-biology/seqclean
- sci-biology/blat
- sci-biology/bowtie
- sci-biology/seqclean"
-
-S="${WORKDIR}/${PN}-$(ver_rs 3-4 _)"
-
-src_install(){
- default
- rm "${ED}"/usr/lib64/perl5/vendor_perl/*/RUM/{bowtie,blat,mdust} ]] || die
-}
diff --git a/sci-biology/salmon/salmon-0.10.2.ebuild b/sci-biology/salmon/salmon-0.10.2.ebuild
index 671309ed0..b5bd8bdfe 100644
--- a/sci-biology/salmon/salmon-0.10.2.ebuild
+++ b/sci-biology/salmon/salmon-0.10.2.ebuild
@@ -48,7 +48,7 @@ DEPEND="
sys-libs/zlib
app-arch/bzip2
app-arch/xz-utils
- dev-libs/boost:0[threads]
+ dev-libs/boost:0[threads(-)]
dev-libs/libdivsufsort
sci-biology/bwa
>=dev-libs/jemalloc-5.0.1
diff --git a/sci-biology/salmon/salmon-1.4.0.ebuild b/sci-biology/salmon/salmon-1.4.0.ebuild
index 0338e5ebe..420cb2ae2 100644
--- a/sci-biology/salmon/salmon-1.4.0.ebuild
+++ b/sci-biology/salmon/salmon-1.4.0.ebuild
@@ -14,7 +14,7 @@ SLOT="0"
KEYWORDS=""
RDEPEND="
- dev-libs/boost:=[threads]
+ dev-libs/boost:=[threads(-)]
sys-libs/zlib
"
diff --git a/sci-biology/salmon/salmon-9999.ebuild b/sci-biology/salmon/salmon-9999.ebuild
index da5a220c8..89ca690c6 100644
--- a/sci-biology/salmon/salmon-9999.ebuild
+++ b/sci-biology/salmon/salmon-9999.ebuild
@@ -13,7 +13,7 @@ LICENSE="GPL-3"
SLOT="0"
RDEPEND="
- dev-libs/boost:=[threads]
+ dev-libs/boost:=[threads(-)]
sys-libs/zlib
"
diff --git a/sci-biology/seqclean/Manifest b/sci-biology/seqclean/Manifest
deleted file mode 100644
index 5a742c218..000000000
--- a/sci-biology/seqclean/Manifest
+++ /dev/null
@@ -1,3 +0,0 @@
-DIST mdust-110625.tar.gz 7526 BLAKE2B 9d2f91025d6cfccb8c75b8f2d6c9f3df9b76469ef7b77a74c3bbd3e37c2d2ba0ce737eaca518200246e1c302d7862af4929bad4bffb6c53692fbfaa586dbf4d7 SHA512 349446115d3b778d28a184eb118ada112476b2c51a058dd7467ff539678f7550dab675a731c452f9aa002fda9a54f13576db02302df935946d034eb9e0d4566e
-DIST seqcl_scripts-110625.tar.gz 14840 BLAKE2B 107ac1d966870f976c5b8f2bd74beb95f49cc1d57975c686e730ad4f519378c3435a626c086244f04e3e075d9f63d1f6541a9bf8dbae1c141ccc3bbd8c613fb5 SHA512 84cca02165856f51614b05e3fb416765695ca3442a8f9d47ee341946a375b6fc9ec6b77e5f18b58d21d5a6e93e21010a866efd2940dc60771f9e6e97722d5a96
-DIST trimpoly-110625.tar.gz 12747 BLAKE2B e395c19549e376b373028c9ca22197021dcf7a7465f2528e1b9051d5e9bbd27c8180103a0a849c3aa8de98eef0edeb71db18b457a62bd3a07e6fe68e083d4062 SHA512 74e7ed6169cbe5f9e9bdcaaffed8ceb74c4ea1ccce912fc656dc29f5ddf8bbeee2975814c97691a8b5eb419c202e332ba79634feb11ffac9a3ab3341db61076f
diff --git a/sci-biology/seqclean/files/seqclean-110625-build.patch b/sci-biology/seqclean/files/seqclean-110625-build.patch
deleted file mode 100644
index b5797618f..000000000
--- a/sci-biology/seqclean/files/seqclean-110625-build.patch
+++ /dev/null
@@ -1,135 +0,0 @@
- mdust/Makefile | 18 +++++++++---------
- mdust/fastafile.c | 3 ++-
- mdust/mdust.c | 1 +
- trimpoly/Makefile | 16 ++++++++--------
- 4 files changed, 20 insertions(+), 18 deletions(-)
-
-diff --git a/mdust/Makefile b/mdust/Makefile
-index 81bf4e9..0c75e69 100644
---- a/mdust/Makefile
-+++ b/mdust/Makefile
-@@ -1,40 +1,40 @@
- # Useful directories
-
- # Directories to search for header files
--SEARCHDIRS := -I. -I-
-+SEARCHDIRS := -I. -iquote
-
-
- #SYSTYPE := $(shell uname)
-
--CC := gcc
--CFLAGS = -O2 -Wall ${SEARCHDIRS} -D_REENTRANT
-+CC ?= gcc
-+CFLAGS += ${SEARCHDIRS} -D_REENTRANT
-+CXXFLAGS += ${SEARCHDIRS} -D_REENTRANT
-
- %.o : %.c
- ${CC} ${CFLAGS} -c $< -o $@
-
- %.o : %.cc
-- ${CC} ${CFLAGS} -c $< -o $@
-+ ${CXX} ${CXXFLAGS} -c $< -o $@
-
- %.o : %.C
-- ${CC} ${CFLAGS} -c $< -o $@
-+ ${CXX} ${CXXFLAGS} -c $< -o $@
-
- %.o : %.cpp
-- ${CC} ${CFLAGS} -c $< -o $@
-+ ${CXX} ${CXXFLAGS} -c $< -o $@
-
- %.o : %.cxx
-- ${CC} ${CFLAGS} -c $< -o $@
-+ ${CXX} ${CXXFLAGS} -c $< -o $@
-
- # C/C++ linker
-
- LINKER := gcc
--LDFLAGS =
- LOADLIBES :=
-
- .PHONY : all
- all: mdust
-
- mdust: ./mdust.o ./dust.o ./fastafile.o
-- ${LINKER} ${LDFLAGS} -o $@ ${filter-out %.a %.so, $^} ${LOADLIBES}
-+ ${CXX} ${LDFLAGS} -o $@ ${filter-out %.a %.so, $^} ${LOADLIBES}
-
- # target for removing all object files
-
-diff --git a/mdust/fastafile.c b/mdust/fastafile.c
-index 6c14b99..5f70f14 100644
---- a/mdust/fastafile.c
-+++ b/mdust/fastafile.c
-@@ -1,7 +1,8 @@
- #include <stdio.h>
- #include <ctype.h>
- #include <malloc.h>
--
-+#include <string.h>
-+#include <stdlib.h>
- #include "fastafile.h"
-
-
-diff --git a/mdust/mdust.c b/mdust/mdust.c
-index f2bae99..c3ee686 100644
---- a/mdust/mdust.c
-+++ b/mdust/mdust.c
-@@ -1,6 +1,7 @@
- #include <stdlib.h>
- #include <stdio.h>
- #include <ctype.h>
-+#include <string.h>
- #include "dust.h"
- #include "fastafile.h"
-
-diff --git a/trimpoly/Makefile b/trimpoly/Makefile
-index 84db22d..71145c2 100644
---- a/trimpoly/Makefile
-+++ b/trimpoly/Makefile
-@@ -3,28 +3,28 @@
- # Directories to search for header files
- SEARCHDIRS := -I.
-
--CC := gcc
--CFLAGS = -O2 -Wall ${SEARCHDIRS} -D_REENTRANT
-+CC ?= gcc
-+CFLAGS += ${SEARCHDIRS} -D_REENTRANT
-+CXXFLAGS += ${SEARCHDIRS} -D_REENTRANT
-
- %.o : %.c
- ${CC} ${CFLAGS} -c $< -o $@
-
- %.o : %.cc
-- ${CC} ${CFLAGS} -c $< -o $@
-+ ${CXX} ${CXXFLAGS} -c $< -o $@
-
- %.o : %.C
-- ${CC} ${CFLAGS} -c $< -o $@
-+ ${CXX} ${CXXFLAGS} -c $< -o $@
-
- %.o : %.cpp
-- ${CC} ${CFLAGS} -c $< -o $@
-+ ${CXX} ${CXXFLAGS} -c $< -o $@
-
- %.o : %.cxx
-- ${CC} ${CFLAGS} -c $< -o $@
-+ ${CXX} ${CXXFLAGS} -c $< -o $@
-
- # C/C++ linker
-
- LINKER := gcc
--LDFLAGS =
- LOADLIBES =
- SYSTYPE := $(shell uname)
- #ifeq ($(SYSTYPE), Linux)
-@@ -37,7 +37,7 @@ SYSTYPE := $(shell uname)
- all: trimpoly
-
- trimpoly: ./trimpoly.o color_c.o
-- ${LINKER} ${LDFLAGS} -o $@ ${filter-out %.a %.so, $^} ${LOADLIBES}
-+ ${CXX} ${LDFLAGS} -o $@ ${filter-out %.a %.so, $^} ${LOADLIBES}
-
- # target for removing all object files
-
diff --git a/sci-biology/seqclean/metadata.xml b/sci-biology/seqclean/metadata.xml
deleted file mode 100644
index 138cb7705..000000000
--- a/sci-biology/seqclean/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <maintainer type="person">
- <email>mmokrejs@fold.natur.cuni.cz</email>
- <name>Martin Mokrejs</name>
- </maintainer>
- <maintainer type="project">
- <email>sci-biology@gentoo.org</email>
- <name>Gentoo Biology Project</name>
- </maintainer>
-</pkgmetadata>
diff --git a/sci-biology/seqclean/seqclean-110625.ebuild b/sci-biology/seqclean/seqclean-110625.ebuild
deleted file mode 100644
index f98fdf3b8..000000000
--- a/sci-biology/seqclean/seqclean-110625.ebuild
+++ /dev/null
@@ -1,54 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit toolchain-funcs
-
-DESCRIPTION="Trimpoly and mdust for trimming and validation of ESTs/DNA sequences"
-HOMEPAGE="https://web.archive.org/web/20140726030702/http://compbio.dfci.harvard.edu/tgi/software/"
-for i in seqcl_scripts mdust trimpoly; do
- SRC_URI="${SRC_URI} ftp://occams.dfci.harvard.edu/pub/bio/tgi/software/seqclean/${i}.tar.gz -> ${i}-${PV}.tar.gz"
-done
-
-LICENSE="Artistic"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-
-DEPEND="
- dev-lang/perl
- sci-biology/ncbi-tools"
-RDEPEND="${DEPEND}"
-
-S=${WORKDIR}
-
-PATCHES=(
- "${FILESDIR}"/${P}-build.patch
-)
-
-src_prepare() {
- default
- # disable the necessity to install Mailer.pm with this tool
- einfo "Disabling mailer feature within seqclean"
- sed -i 's/use Mailer;/#use Mailer;/' "${S}"/"${PN}"/"${PN}" || die
- tc-export CC CXX
-}
-
-src_compile() {
- for i in mdust trimpoly; do
- LDLFAGS="${LDFLAGS}" \
- emake -C "${S}"/${i}
- done
-}
-
-src_install() {
- dobin seqclean/{seqclean,cln2qual,bin/seqclean.psx}
- newdoc seqclean/README README.seqclean
- for i in mdust trimpoly; do
- dobin ${i}/${i}
- done
-
- einfo "Optionally, you may want to download UniVec from NCBI if you do not have your own"
- einfo "fasta file with vector sequences you want to remove from sequencing"
- einfo "reads. See http://www.ncbi.nlm.nih.gov/VecScreen/UniVec.html"
-}
diff --git a/sci-chemistry/gamess/gamess-20180930.3.ebuild b/sci-chemistry/gamess/gamess-20180930.3-r1.ebuild
index 77b60edca..17fe76f76 100644
--- a/sci-chemistry/gamess/gamess-20180930.3.ebuild
+++ b/sci-chemistry/gamess/gamess-20180930.3-r1.ebuild
@@ -19,7 +19,7 @@ LICENSE="gamess"
# new version comes out the stable version will be useless since
# users can not get at the tarball any more.
KEYWORDS="~amd64 ~x86"
-IUSE="mpi msucc neo openmp pax_kernel qmmm-tinker vb2000"
+IUSE="mpi msucc neo openmp pax-kernel qmmm-tinker vb2000"
CDEPEND="
app-shells/tcsh
@@ -136,7 +136,7 @@ src_prepare() {
# for hardened-gcc let't turn off ssp, since it breakes
# a few routines
- if use pax_kernel && [[ ${FCOMP} == g77 ]]; then
+ if use pax-kernel && [[ ${FCOMP} == g77 ]]; then
FFLAGS="${FFLAGS} -fno-stack-protector-all"
fi
@@ -263,7 +263,7 @@ src_compile() {
# for hardened (PAX) users and ifc we need to turn
# MPROTECT off
- if [[ ${FCOMP} == "ifort" ]] && use pax_kernel; then
+ if [[ ${FCOMP} == "ifort" ]] && use pax-kernel; then
pax-mark -PemRxS actvte.x
fi
@@ -281,7 +281,7 @@ src_compile() {
# for hardened (PAX) users and ifc we need to turn
# MPROTECT off
- if [[ ${FCOMP} == "ifort" ]] && use pax_kernel; then
+ if [[ ${FCOMP} == "ifort" ]] && use pax-kernel; then
pax-mark -PemRxS ${PN}.00.x
fi
}
diff --git a/sci-chemistry/gamess/metadata.xml b/sci-chemistry/gamess/metadata.xml
index 7f7e33d86..5d367dd16 100644
--- a/sci-chemistry/gamess/metadata.xml
+++ b/sci-chemistry/gamess/metadata.xml
@@ -13,7 +13,7 @@
<flag name="msucc">Build Michigan State University CCT3 and CCSD3A methods.
This will increase build time and memory requirements by ~10 times</flag>
<flag name="neo">Enable NEO for nuclear basis support</flag>
- <flag name="pax_kernel">Make this package work on PAX kernels</flag>
+ <flag name="pax-kernel">Make this package work on PAX kernels</flag>
<flag name="qmmm-tinker">Enable tinker qmmm code</flag>
<flag name="vb2000">Enable Valence Bond method using VB2000 code</flag>
</use>
diff --git a/sci-chemistry/pymol-plugins-psico/pymol-plugins-psico-3.4.ebuild b/sci-chemistry/pymol-plugins-psico/pymol-plugins-psico-3.4-r1.ebuild
index df141a739..471e85be8 100644
--- a/sci-chemistry/pymol-plugins-psico/pymol-plugins-psico-3.4.ebuild
+++ b/sci-chemistry/pymol-plugins-psico/pymol-plugins-psico-3.4-r1.ebuild
@@ -15,23 +15,12 @@ SRC_URI="https://github.com/speleo3/pymol-psico/archive/${PV}.tar.gz -> ${P}.tar
SLOT="0"
KEYWORDS="~amd64 ~x86"
LICENSE="BSD-2"
-IUSE="minimal"
S="${WORKDIR}/pymol-psico-${PV}"
RDEPEND="
sci-chemistry/pymol[${PYTHON_USEDEP}]
- !minimal? (
- media-libs/qhull
- media-video/mplayer
- sci-biology/stride
- sci-chemistry/dssp
- sci-chemistry/mm-align
- sci-chemistry/pdbmat
- sci-chemistry/theseus
- sci-chemistry/tm-align
- sci-mathematics/diagrtb
- )"
+"
pkg_post_inst() {
optfeature sci-libs/mmtk "Normal modes via mmtk"
diff --git a/sci-chemistry/talosn/Manifest b/sci-chemistry/talosn/Manifest
deleted file mode 100644
index fbfff5dbd..000000000
--- a/sci-chemistry/talosn/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST talosn-4.12.2015.147.15.40.tgz 137074857 BLAKE2B 950ed21334b4e2b97164ba90b9a60f4f7ad738da955d763c0388bbad3029dd8d49e0e443309e0faaa0028375fb3a0e28291f805075cadffe96c985cc9618f296 SHA512 2d4150434687e394303cabb5153b39037f427dd7137650beeaac1f161fdb1c77c43a37fe61df3182b9a4425d88ef531f4a855a88bd5e9ed19ed662640b347df9
diff --git a/sci-chemistry/talosn/talosn-4.12.2015.147.15.40.ebuild b/sci-chemistry/talosn/talosn-4.12.2015.147.15.40.ebuild
deleted file mode 100644
index 1fbcea875..000000000
--- a/sci-chemistry/talosn/talosn-4.12.2015.147.15.40.ebuild
+++ /dev/null
@@ -1,68 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit java-pkg-opt-2
-
-DESCRIPTION="Prediction of Protein bb and sc Torsion Angles from NMR Chemical Shifts"
-HOMEPAGE="https://spin.niddk.nih.gov/bax/software/TALOS-N/"
-SRC_URI="https://spin.niddk.nih.gov/bax/software/TALOS-N/talosn.tZ -> ${P}.tgz"
-
-SLOT="0"
-LICENSE="all-rights-reserved"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="examples"
-
-DEPEND=">=virtual/jre-1.5:*"
-RDEPEND="${DEPEND}
- app-shells/tcsh
- sci-biology/ncbi-tools"
-
-S="${WORKDIR}"
-
-QA_PREBUILT="/opt/.*"
-
-src_prepare() {
- default
- local s64
- use amd64 || s64="_x64"
- rm -f bin/TALOSN.{linux,mac,static.*,winxp,linux9${s64}} || die
-
- sed \
- -e '/setenv TALOSN_DIR/d' \
- -e "/set BLAST/s:=.*:= \"${EPREFIX}/usr/bin/blastpgp\":g" \
- -e '/set NR_DBNAME/s:=.*:= ${BLASTDB}:g' \
- -i talosn_ss || die
-}
-
-src_install() {
- local TALOSN="/opt/${PN}"
- exeinto ${TALOSN}/bin
- doexe bin/*
-
- exeinto ${TALOSN}/com
- doexe com/*
-
- exeinto /opt/bin
- doexe talosn{,_ss}
-
- insinto ${TALOSN}
- doins -r tab
-
- java-pkg_jarinto ${TALOSN}
- java-pkg_dojar rama.jar
-
- java-pkg_dolauncher jrama --jar rama.jar -into /opt/
-
- if use examples; then
- insinto /usr/share/${PN}
- doins -r demo
- fi
-
- cat >> "${T}"/40talosn <<- EOF
- TALOSN_DIR="${EPREFIX}/${TALOSN}"
- #BLASTDB=
- EOF
- doenvd "${T}"/40talosn
-}
diff --git a/sci-libs/ciftilib/ciftilib-1.6.0.ebuild b/sci-libs/ciftilib/ciftilib-1.6.0.ebuild
index 062fa44ef..fffd4f9c1 100644
--- a/sci-libs/ciftilib/ciftilib-1.6.0.ebuild
+++ b/sci-libs/ciftilib/ciftilib-1.6.0.ebuild
@@ -24,6 +24,12 @@ RDEPEND="${DEPEND}"
S="${WORKDIR}/CiftiLib-${PV}"
+# fix submitted upstream
+# https://github.com/Washington-University/CiftiLib/pull/23
+PATCHES=(
+ "${FILESDIR}/${P}-version.patch"
+)
+
#TODO: Enable doc building and installation
src_prepare(){
diff --git a/sci-libs/ciftilib/files/ciftilib-1.6.0-version.patch b/sci-libs/ciftilib/files/ciftilib-1.6.0-version.patch
new file mode 100644
index 000000000..e64a55f2f
--- /dev/null
+++ b/sci-libs/ciftilib/files/ciftilib-1.6.0-version.patch
@@ -0,0 +1,27 @@
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -83,18 +83,18 @@ ENDIF (NOT QT_FOUND)
+ INCLUDE_DIRECTORIES(${Boost_INCLUDE_DIRS})
+ SET(LIBS ${LIBS} ${Boost_LIBRARIES})
+ #boost quirks
+-IF (Boost_VERSION LESS 104400)
++IF (Boost_VERSION VERSION_LESS 1.44.00)
+ #absolute() was added in 1.44.0, with filesystem v3
+ ADD_DEFINITIONS(-DCIFTILIB_BOOST_NO_FSV3)
+-ENDIF (Boost_VERSION LESS 104400)
+-IF (Boost_VERSION LESS 104800)
++ENDIF (Boost_VERSION VERSION_LESS 1.44.00)
++IF (Boost_VERSION VERSION_LESS 1.48.00)
+ #canonical() was added in 1.48.0
+ ADD_DEFINITIONS(-DCIFTILIB_BOOST_NO_CANONICAL)
+-ENDIF (Boost_VERSION LESS 104800)
+-IF (Boost_VERSION LESS 105600)
++ENDIF (Boost_VERSION VERSION_LESS 1.48.00)
++IF (Boost_VERSION VERSION_LESS 1.56.00)
+ #try_lexical_cast was added in 1.56.0
+ ADD_DEFINITIONS(-DCIFTILIB_BOOST_NO_TRY_LEXICAL)
+-ENDIF (Boost_VERSION LESS 105600)
++ENDIF (Boost_VERSION VERSION_LESS 1.56.00)
+
+ #zlib, useful for volume reading
+ FIND_PACKAGE(ZLIB)
diff --git a/sci-libs/nipype/nipype-1.5.0.ebuild b/sci-libs/nipype/nipype-1.5.0.ebuild
index 87975149e..35792adbc 100644
--- a/sci-libs/nipype/nipype-1.5.0.ebuild
+++ b/sci-libs/nipype/nipype-1.5.0.ebuild
@@ -1,9 +1,9 @@
-# Copyright 1999-2020 Gentoo Authors
+# Copyright 1999-2021 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=7
-PYTHON_COMPAT=( python3_{7..8} )
+PYTHON_COMPAT=( python3_{7..9} )
PYTHON_REQ_USE="threads(+),sqlite"
inherit distutils-r1
diff --git a/sci-libs/pytorch/Manifest b/sci-libs/pytorch/Manifest
index feaaba61d..65e5fc7a8 100644
--- a/sci-libs/pytorch/Manifest
+++ b/sci-libs/pytorch/Manifest
@@ -1,58 +1,81 @@
DIST FP16-4dfe081c.tar.gz 71301 BLAKE2B f6a2115a82ca9acd7ccb1bf94c59f68e6ffea4b0e20aa5152349a10119b45d8ba45f5673899b6f18ee044289a51141944e41d7b0972889afc1d93db88d88ed7c SHA512 e79a1f6f8d4aeca85982158d5b070923d31d4f2062ed84cfa6f26c47a34f2e8ac49e0f330b7d49f5732d5e1eec6e7afccdac43645070060fb7827e2ce261dd3e
DIST FP16-4dfe081cf.tar.gz 71301 BLAKE2B f6a2115a82ca9acd7ccb1bf94c59f68e6ffea4b0e20aa5152349a10119b45d8ba45f5673899b6f18ee044289a51141944e41d7b0972889afc1d93db88d88ed7c SHA512 e79a1f6f8d4aeca85982158d5b070923d31d4f2062ed84cfa6f26c47a34f2e8ac49e0f330b7d49f5732d5e1eec6e7afccdac43645070060fb7827e2ce261dd3e
+DIST FP16-4dfe081cf6bcd15db339cf2680b9281b8451eeb3.tar.gz 71301 BLAKE2B f6a2115a82ca9acd7ccb1bf94c59f68e6ffea4b0e20aa5152349a10119b45d8ba45f5673899b6f18ee044289a51141944e41d7b0972889afc1d93db88d88ed7c SHA512 e79a1f6f8d4aeca85982158d5b070923d31d4f2062ed84cfa6f26c47a34f2e8ac49e0f330b7d49f5732d5e1eec6e7afccdac43645070060fb7827e2ce261dd3e
DIST FXdiv-b408327a.tar.gz 9652 BLAKE2B ce2082f9e0ec55ab43cfee57e29cfc8f1957bdde70c1bbeadc599ac34ed8ade9d1334e68583a0fb14b4405357cc1039579b09fff4b39a5190bdae304c4ea3de3 SHA512 d46d7c1437eccf8dc5ab5e51b0641d190839451ab059c8a24a220a9cf05a84a66b5d08c3ff730622efe491152a8378a2c726fd9abad19a3df98db40d6a13e4b9
DIST FXdiv-b408327ac.tar.gz 9652 BLAKE2B ce2082f9e0ec55ab43cfee57e29cfc8f1957bdde70c1bbeadc599ac34ed8ade9d1334e68583a0fb14b4405357cc1039579b09fff4b39a5190bdae304c4ea3de3 SHA512 d46d7c1437eccf8dc5ab5e51b0641d190839451ab059c8a24a220a9cf05a84a66b5d08c3ff730622efe491152a8378a2c726fd9abad19a3df98db40d6a13e4b9
+DIST FXdiv-b408327ac2a15ec3e43352421954f5b1967701d1.tar.gz 9652 BLAKE2B ce2082f9e0ec55ab43cfee57e29cfc8f1957bdde70c1bbeadc599ac34ed8ade9d1334e68583a0fb14b4405357cc1039579b09fff4b39a5190bdae304c4ea3de3 SHA512 d46d7c1437eccf8dc5ab5e51b0641d190839451ab059c8a24a220a9cf05a84a66b5d08c3ff730622efe491152a8378a2c726fd9abad19a3df98db40d6a13e4b9
DIST NNPACK-24b55303.tar.gz 219131 BLAKE2B 7fbc786d59352270d7b3664c46ab9401a0199aa8973cdbe8385840354f576eb945faa93be7070dafc9e453a415af227f5f64ffc21a33fd28e4c7a9ec94ca00b3 SHA512 43d6c69f19f9604809a2cc9cd9f8f027ff1f3dc2bac106429df1a0cf65f3f8b8fc3ec4c6b76a29decf3584440ad4c83f800ae2f8bfdc9b73df903a076cd97a18
DIST NNPACK-24b55303f.tar.gz 219131 BLAKE2B 7fbc786d59352270d7b3664c46ab9401a0199aa8973cdbe8385840354f576eb945faa93be7070dafc9e453a415af227f5f64ffc21a33fd28e4c7a9ec94ca00b3 SHA512 43d6c69f19f9604809a2cc9cd9f8f027ff1f3dc2bac106429df1a0cf65f3f8b8fc3ec4c6b76a29decf3584440ad4c83f800ae2f8bfdc9b73df903a076cd97a18
+DIST NNPACK-c07e3a0400713d546e0dea2d5466dd22ea389c73.tar.gz 219318 BLAKE2B 6b6619c8a706ef9630f20fda1e276314b2ef7f6c9aed26836a48bdaa0ae198a86383e68b04c651f37c07d34e400bc54b5daa75b06fc18cdb0a9c55e2cb33bbe1 SHA512 f0b261e8698b412d12dd739e5d0cf71c284965ae28da735ae22814a004358ba3ecaea6cd26fa17b594c0245966b7dd2561c1e05c6cbf0592fd7b85ea0f21eb37
DIST PeachPy-07d8fde8.tar.gz 401648 BLAKE2B c563cd77a9e2eda34bbec6a34f94111a6db9500b7cda9a18e791984b789c29dde7199ed21696f10cdfb088b05e18163b02a8ca8c9e48a91b9e4a757020f096b0 SHA512 8d6cc91c8c4d56b86ef93f0acd6768a1830ecd078524b21d1a3b9ecb015f06607070148de3e634d9c5ce63ed523a8e34aa388d490e7eee061200098f39126afa
DIST PeachPy-07d8fde8a.tar.gz 401648 BLAKE2B c563cd77a9e2eda34bbec6a34f94111a6db9500b7cda9a18e791984b789c29dde7199ed21696f10cdfb088b05e18163b02a8ca8c9e48a91b9e4a757020f096b0 SHA512 8d6cc91c8c4d56b86ef93f0acd6768a1830ecd078524b21d1a3b9ecb015f06607070148de3e634d9c5ce63ed523a8e34aa388d490e7eee061200098f39126afa
+DIST PeachPy-07d8fde8ac45d7705129475c0f94ed8925b93473.tar.gz 401648 BLAKE2B c563cd77a9e2eda34bbec6a34f94111a6db9500b7cda9a18e791984b789c29dde7199ed21696f10cdfb088b05e18163b02a8ca8c9e48a91b9e4a757020f096b0 SHA512 8d6cc91c8c4d56b86ef93f0acd6768a1830ecd078524b21d1a3b9ecb015f06607070148de3e634d9c5ce63ed523a8e34aa388d490e7eee061200098f39126afa
DIST QNNPACK-7d2a4e99.tar.gz 205600 BLAKE2B f174051cba9e3307633f0b12326a37d8fde23562d47e09d3c078350146439094ca6cb2f032cf3aa4af40e5968ee16b8847241f787f7c84ea501124e0528fb82d SHA512 437a835acfedae851a9a8572fa6eea9854dcb8bcca499bc4a2582314e44f5f199778e857932da4aecf943bea7cb2eb5b1c41d4b4ca6075bddbe0f18b2c7b9127
DIST QNNPACK-7d2a4e993.tar.gz 205600 BLAKE2B f174051cba9e3307633f0b12326a37d8fde23562d47e09d3c078350146439094ca6cb2f032cf3aa4af40e5968ee16b8847241f787f7c84ea501124e0528fb82d SHA512 437a835acfedae851a9a8572fa6eea9854dcb8bcca499bc4a2582314e44f5f199778e857932da4aecf943bea7cb2eb5b1c41d4b4ca6075bddbe0f18b2c7b9127
+DIST QNNPACK-7d2a4e9931a82adc3814275b6219a03e24e36b4c.tar.gz 205600 BLAKE2B f174051cba9e3307633f0b12326a37d8fde23562d47e09d3c078350146439094ca6cb2f032cf3aa4af40e5968ee16b8847241f787f7c84ea501124e0528fb82d SHA512 437a835acfedae851a9a8572fa6eea9854dcb8bcca499bc4a2582314e44f5f199778e857932da4aecf943bea7cb2eb5b1c41d4b4ca6075bddbe0f18b2c7b9127
DIST XNNPACK-1b354636.tar.gz 1353346 BLAKE2B ce286e1a1f14aa195baffa48ef8c21c4ae0ec85ae89169a429fc06077e34f28302930e081cf464dbe78252bb065a247b65b61d8aa3872375043176d150f97651 SHA512 9e7528334a8e3df18a54fce44a122fb6d989a946bb456b01f81772f160bd6532fad460e787c976bbdd76ebaa78cd1c64329ffeb498c5d27e1cd53195bb8a9db4
DIST XNNPACK-1b354636b.tar.gz 1353346 BLAKE2B ce286e1a1f14aa195baffa48ef8c21c4ae0ec85ae89169a429fc06077e34f28302930e081cf464dbe78252bb065a247b65b61d8aa3872375043176d150f97651 SHA512 9e7528334a8e3df18a54fce44a122fb6d989a946bb456b01f81772f160bd6532fad460e787c976bbdd76ebaa78cd1c64329ffeb498c5d27e1cd53195bb8a9db4
+DIST XNNPACK-79cd5f9e18ad0925ac9a050b00ea5a36230072db.tar.gz 3955905 BLAKE2B d787d4a965c53c8d65887f3b111da950f3b5558cd28ce468764c5bf8efbaddeea567803cfcd89a1aab4a0bc781816871dcca2901e762257aaf96a1d8f868ffd2 SHA512 72c3e53b00d77cfd94db93c60276ca7fd419554dadddf74286e85e0500dbdad0bf65694e451e832de89ea17e7731a9ec9e9f1d831b03c1b81946e0dacb96197d
DIST asmjit-9057aa30.tar.gz 534633 BLAKE2B faec98981c67110294e4135a9cb7f47b038d44a02483728a4c79c7094da62b8a6a1c805eba69f1258a99b24b699823f02516c50d166a96eb5ff65227406f402e SHA512 678e5ce4a8d96961be4c10aac67d43aa8949ff022dce855a92cf6d626738be8667668c48953d43b6ef21ad7c5f913d07f7f692ad719870700aa97deb80662baf
DIST benchmark-505be96a.tar.gz 129647 BLAKE2B d9f435f464fa1db18b86258947b8c5077b8b20b9c26ca00aeeca79da604f299f776673c374b7d0db10a5d40cbc84774642b29e756a83f02cda5d085280387346 SHA512 2ec79b66c31d4741b214c04f7865cf0139b4c0b14a8fb2a70bf332cf90e73821282b510719689bc2fe59542ee51c87e9f9b49a47b6a67cad897f7f906f0b05e9
DIST benchmark-505be96ab.tar.gz 129647 BLAKE2B d9f435f464fa1db18b86258947b8c5077b8b20b9c26ca00aeeca79da604f299f776673c374b7d0db10a5d40cbc84774642b29e756a83f02cda5d085280387346 SHA512 2ec79b66c31d4741b214c04f7865cf0139b4c0b14a8fb2a70bf332cf90e73821282b510719689bc2fe59542ee51c87e9f9b49a47b6a67cad897f7f906f0b05e9
DIST benchmark-5b7683f4.tar.gz 102332 BLAKE2B a7210a2c7a173a9df8bf03b83fc9712d5b52ded13c932e4d13a93004b93ad816895b722acc941b1d94c6b403e4ccb846141f5a38f42baafc5fb3cb108c039559 SHA512 a4e69ee8ec824e418abd713cb3597175cd40ecee9bc539e2d3592f9ec0f8ee54e7466984874f410b78beee82b4c396a7f2824880f808c4217704cf9970411ebf
DIST benchmark-e776aa02.tar.gz 126890 BLAKE2B 389a4fc0bfedc20227de31d4b1447b8370300a8e3cbea8a8d4b1c82ee90757c2a035ea0324e762217f5a6279a4277f431b7e511d8a9a3bcf226fe31c0022b83c SHA512 d9f70c617af75683dfcf5a0d7ff14b3374258bcf869e3b69b23e85c980366cc4f9859fef3d3dd84a2a92933729053eb02663eaf4bbe0a020a2e001f42b85230d
+DIST benchmark-e991355c02b93fe17713efe04cbc2e278e00fdbd.tar.gz 176771 BLAKE2B 22280c0777635d57574852e6e3ad276683d582eed9b17ef93f09f6a5560dc3d06bbabdead9cfc72f5059570436515855a841118c47f23c3793e1b83e368cc75b SHA512 aa4455fa0f8546ec5762f14065e0be6667b5874e6991ca6dd21dc7b29e38c7c74cfddb2c99c7a1ed2f7636aa7bdec8fc0fc1523967b179f5642c2dc2e968089c
+DIST cpuinfo-5916273f79a21551890fd3d56fc5375a78d1598d.tar.gz 3496223 BLAKE2B 4da452faf12138fbc1abd266d8ae6e0a0192f48a84faccb55fd05c3ac85d0bea2ecbd80b5eda69bb51c6704a223f90dd83d1f0fc79d56d35dd21cae5c5b8fab5 SHA512 50e537b61d991e8579577fb1ecf8d9ceb2171dbad96dfe159a062eadfdc0b2372b94988fc6f223c20e327453c7f55042ee06779f5b5fe0922f4470f746c9686b
DIST cpuinfo-63b25457.tar.gz 3495405 BLAKE2B bb7cefa2bfe6e44134c52b8ba8048a84f0063623e566e89dd92ed6ff5e383a150c554a45b66ee5c4ba6d1544de948ac978ab6e53101399d4768bace20110b4e6 SHA512 44f4a55eea9c0d707818dedfec26f007c2bc2271c7bf9375e6e30171384fb0fa2e1d5731cb946570c717e6d88e6b1496d498e6e55dbf37d66174a4c675a3a006
DIST cpuinfo-63b254577.tar.gz 3495405 BLAKE2B bb7cefa2bfe6e44134c52b8ba8048a84f0063623e566e89dd92ed6ff5e383a150c554a45b66ee5c4ba6d1544de948ac978ab6e53101399d4768bace20110b4e6 SHA512 44f4a55eea9c0d707818dedfec26f007c2bc2271c7bf9375e6e30171384fb0fa2e1d5731cb946570c717e6d88e6b1496d498e6e55dbf37d66174a4c675a3a006
DIST cpuinfo-d5e37adf.tar.gz 3489028 BLAKE2B aa6b7719eb9871b6cc71318cb4a9c2e2397e665662b7978daecd9e8380304691a78b95118eba5cbbb738c4b490352a847f6ce6b5c4ae29de0543b95ecc557cbb SHA512 ecd2115340fa82a67db7889ce286c3070d5ab9c30b02372b08aac893e90ccebc65c6b3e66aa02a9ae9c57892d2d8c3b77cb836e5fc3b88df2c75d33e574d90d2
DIST cub-d106ddb9.tar.gz 398104 BLAKE2B 287f020189be877c7a9e667bdfb591da14046199b7336074040c3301d69110c8408d89a72cdcd74d8519deb200ec61823a6d2160d4ecbd00002338651dbf312e SHA512 8d65c0407448125378495190ee2a2c0e3b27a3577efbd6bb5aa8ad76f5bf2bf17becdc6ef931672a4d16b033fd7c0a199bb60e62b0b2b311e5f59c4136f55835
DIST cub-d106ddb99.tar.gz 398104 BLAKE2B 287f020189be877c7a9e667bdfb591da14046199b7336074040c3301d69110c8408d89a72cdcd74d8519deb200ec61823a6d2160d4ecbd00002338651dbf312e SHA512 8d65c0407448125378495190ee2a2c0e3b27a3577efbd6bb5aa8ad76f5bf2bf17becdc6ef931672a4d16b033fd7c0a199bb60e62b0b2b311e5f59c4136f55835
+DIST cub-d106ddb991a56c3df1b6d51b2409e36ba8181ce4.tar.gz 398104 BLAKE2B 287f020189be877c7a9e667bdfb591da14046199b7336074040c3301d69110c8408d89a72cdcd74d8519deb200ec61823a6d2160d4ecbd00002338651dbf312e SHA512 8d65c0407448125378495190ee2a2c0e3b27a3577efbd6bb5aa8ad76f5bf2bf17becdc6ef931672a4d16b033fd7c0a199bb60e62b0b2b311e5f59c4136f55835
DIST fbgemm-1d710393.tar.gz 259645 BLAKE2B 7b159c67ee66679985758f59b001aea02f141e2a36af2dd12731bd260ba5a5834a2a5eefd9b8b43454a0d4c75df929fa302e7ba0e5210ee67c150b405d3b4cac SHA512 19bbc9ed274bced7b8453d9ec4f43bb998725764aeeee72782abff36fc77e9ef918396f5c462da7b448e9a3bb7a834f143cfdf6777ef0cdddada63bc2bf98761
+DIST fbgemm-7495417ad31c38a06b1b13db66b355b6f23cd96d.tar.gz 444575 BLAKE2B 97c0672119eee2e0a770445fbc7d3fad8d91d86d7a860f75e20b0a9b8dabae555b324f12d63092463eb1882ccb9d587e73cbb34013acaa3a76f015f093792e9f SHA512 b4cb8964e84dbe4065d7b9292c5877305a43b7dc21e896e3d20d3082c208eca2afe2348face8ce2236256e436c611d6adf9c9f729ef07b2ae9f939e25ec21e00
DIST fbgemm-87c378172.tar.gz 244850 BLAKE2B 322d892cc34921c9ffd7b9faf67804f3cfc3a427281e12afeeca4af3df37a8aa47198695e28e33feb836605d29925f566a4a290206ce6209478af87883561564 SHA512 42e678560dc774694ed6e2eb7d62a0284532be9c206aa1e056810e00bb7c06d557541e0ce56446735e163d480b504854e45cce9d7f23368974c500ecfe6e9961
DIST fmt-9bdd1596c.tar.gz 733867 BLAKE2B b5c62ea43bfd99268dd120d5a09eb5f80bc29411268367e63bdf7034aeb98c9aed00da019ad6e259922adbb849b4484353142e9d3449a256909e72f4a50ddee4 SHA512 3639b4984a88fc5495c6cb1a0a09bb0a13f5dc05286f5a2b15e60dfda780bcc1fe213497006cc27247c3c358be27d8af4dd995db2b3de0f6a5a1288dc1058585
DIST fmt-cd4af11e.tar.gz 740467 BLAKE2B da998415363b8205cb3be5c677ff8c3ea4aa5636741a5cfe45d7b6e54c1f6d0a36696158e2e21f37978323a11150e01efb2793de6a42af4ed19aac52381e0afc SHA512 24b42288be97849533dc82282fc08833d74642ad2afeb511e65c6389d88c709cf25345dec5b550c18af3705f4c0847fa0d4066308b51cd41ccfdda1a2c3babd0
+DIST fmt-cd4af11efc9c622896a3e4cb599fa28668ca3d05.tar.gz 740467 BLAKE2B da998415363b8205cb3be5c677ff8c3ea4aa5636741a5cfe45d7b6e54c1f6d0a36696158e2e21f37978323a11150e01efb2793de6a42af4ed19aac52381e0afc SHA512 24b42288be97849533dc82282fc08833d74642ad2afeb511e65c6389d88c709cf25345dec5b550c18af3705f4c0847fa0d4066308b51cd41ccfdda1a2c3babd0
DIST foxi-4aba696e.tar.gz 28740 BLAKE2B 54b2eb9610f402b89ed64b0f487326a58c8ecf9a195d0081329e4b55cc531bca45065f10176ba29ff7cc18b29c89ba7f0aa5046c35a78c562986e8dab40451e8 SHA512 6aec53e9489f87fab6ef70ddef20854f551ccc54368800f7c465c73858f13fd6db8f031fb6db43c9e26c1fd13d65389501d1db97148afc518277f4f95a5367d6
DIST foxi-8015abb72.tar.gz 28571 BLAKE2B d64b00bb81e43a9b1f55f640ab6e6845d33e01520daf7e1b56cd6ef3f82b38c5c8d6cb5c54d55302524f46a6ca2fbc43ef1aa3ee0fba563a8de502a8c4720175 SHA512 94c8c25d90273941161e04bedee521d3f7bbb296c125083e1d3c1421210b18758917d95c95bbd213c8eb19ad36f4e088c943816505e7fc462aecf12e00ebd2f6
+DIST foxi-c278588e34e535f0bb8f00df3880d26928038cad.tar.gz 28960 BLAKE2B 06c960f829b090eec4fe9e8c981e119578f358724e0b63991173bb7e318d23654261b901d1e15efeb6240bba75cc05fd45ab32fb30bbdf48369e139cf152f398 SHA512 ad42cfd70e40ba0f0a9187b34ae9e3bd361c8c0038669f4c1591c4f7421d12ad93f76f42b33c2575eea1a3ddb3ff781da2895cdc636df5b60422598f450203c7
DIST gemmlowp-3fb5c176.tar.gz 826382 BLAKE2B c5e68cb78429fe8ce96c752270e747382287937d0a0c1af26b444eda495a78438193c54900cd7906b34b369e170d582c5599f541d23d1280e38f972d6daea1ea SHA512 1c97bba41931c7fddf0e7c01312892cfa3d87abe2a4cdaf4cd20d846a102c5ad3d85329ccdb386f7047f2f037e92639cbcf91b317c2bf38bee11c12e71584afc
DIST gemmlowp-3fb5c176c.tar.gz 826382 BLAKE2B c5e68cb78429fe8ce96c752270e747382287937d0a0c1af26b444eda495a78438193c54900cd7906b34b369e170d582c5599f541d23d1280e38f972d6daea1ea SHA512 1c97bba41931c7fddf0e7c01312892cfa3d87abe2a4cdaf4cd20d846a102c5ad3d85329ccdb386f7047f2f037e92639cbcf91b317c2bf38bee11c12e71584afc
DIST gloo-3d08580f9.tar.gz 227739 BLAKE2B 3b011cc8ae08da36a917860dd58b87bc5b08c7189926b2f5bfaf839a9d53c5e7dee881e836f659e90269149eba6d80807e3a8e450b31f71220ba442ab59a389a SHA512 3dee533b350862cabce410f054fd943b4524b60394da1e92b9c73830e143b9abd30e5a493fe0c064d6fee8c15bd09b12620f0b528122170df329548c57116bd1
DIST gloo-3dc0328f.tar.gz 231048 BLAKE2B aa06ea3ca8c522652a405c0b56662bc5bd0eba5ef38770aaa2a078a8fd19fd1eeaa2e1007e537e584c5b07a84abe991c810f2a9c73e5b8df820dacde703bb81a SHA512 a6401f4b5e91130a7880a6742c075fdeb94026c3a04a57ce59b6dabc78b44d2f5e93803b3a7289e0c116bde4366536bb55f6dfd91a9a0d8af9640a81e3e4fe7b
+DIST gloo-c22a5cfba94edf8ea4f53a174d38aa0c629d070f.tar.gz 247789 BLAKE2B a8b72ee81c47d6b52559a5a7dc7a74dec56747c2fa46437fc9b3be9535b2ac577031a235c1a2cc7029c840a1ad28e58d2e91d7db820af3c0ce474e2a3ebea8a8 SHA512 1aa7bd5511a55ecb7a318cafa6ae1bde94d7cbc4d1483727e3b07c86a4c6e32864aa740d5a58a452d7cb7f37d84a928fa740f1fdb73e3309061d88b018083c56
DIST googletest-0fc5466d.tar.gz 993626 BLAKE2B f80e5d7e92c665a964add6370b6420ac00b0309768d21d52ce74e87b548293e05271456c63d171eb36389c601febc3514ea81d991145b1921e27f38e5fc0e084 SHA512 ac57b52454c027d4c14b0ca339ff4b5d36b66da38c7420164c44c11c214b617c79cf690b74b6f2f233b5df5dff200d97afa40c9b814f8b6117cd3d9e382a20c5
DIST googletest-2fe3bd99.tar.gz 993527 BLAKE2B fa631eadc310607dbe19cec6d66d8fb1c5e99e2dfc5031fff26f8c12c951d7798ad2062edf21589020cafc821bfe4b5e89310ee4e85f45d7d7fcd435ddd5eef9 SHA512 130182d2c1067bcd263fb27999c164d240f5d06d837475e71e7cadbf65c7211de00154dc1e15deae0b6ec2963799e55c0c21ee971e1c588064c5063e69a2bf1e
DIST googletest-2fe3bd994.tar.gz 993527 BLAKE2B fa631eadc310607dbe19cec6d66d8fb1c5e99e2dfc5031fff26f8c12c951d7798ad2062edf21589020cafc821bfe4b5e89310ee4e85f45d7d7fcd435ddd5eef9 SHA512 130182d2c1067bcd263fb27999c164d240f5d06d837475e71e7cadbf65c7211de00154dc1e15deae0b6ec2963799e55c0c21ee971e1c588064c5063e69a2bf1e
DIST googletest-5ec7f0c4.tar.gz 961649 BLAKE2B 2c518a4006e7a9decff3d4b81c30a910c01f6bf2a71593da25f6e74d5117cbf56de486078a3caf6be255df473fc1c2a04de5317cf882396114be0625d67d041b SHA512 623b077b3334958fafcbc34aa85891883277994af33be530efd903f47738a3e3562001cbf3b6da1a5e7d03803c5bd51bcc1fab81490db85d5a4f2b15e7de1495
+DIST googletest-e2239ee6043f73722e7aa812a459f54a28552929.tar.gz 887296 BLAKE2B 8f29b7028a6dd8190a113cd93398705b23b61d88bee38beaf9dcc0dfc8a463aed7fcd3719f6f1b131d4363aa57231629aaeffa108f6558efb58416cfface6d6e SHA512 cf9e7f3fd3e31ce6677eac355fb8bfe19c5b56a8ec3af8b9417d0904cdf5da92f99f7411a08131cc9fa4fc7d38e6a71fcfac993648e47b269a74a27de7607f7a
DIST ideep-938cc6889.tar.gz 27315 BLAKE2B 967bff56175d6f6b6e9895ef8e7ecf22f2bcbc4aa33074654b8c527165beb280e70c1b39da37ae2cd432eaa8d0ec600b83282d86faac05e17319dbd647f22107 SHA512 24a3f0b35756e3892af99658f7de7d17dff369601ffa7d39a6e2c3609c9c667f341cc66b6664fb69c4d938a1f7b3454e7106b8e27ec9995be5ad2d541927e2e1
+DIST ideep-9ca27bbfd88fa1469cbf0467bd6f14cd1738fa40.tar.gz 30949 BLAKE2B 07028f6544e5e088c01b111e89defd02eed022663536c4b1fe582e3b8da65a383aeb75e191f433e4cf497236630dcc531fa16a2758cd9be6db504c6b04f2a9b0 SHA512 0b51c41124ed033fd608b1ae7a6de3ebbb5c8b96c53cea594966178b5e0bd38d8b1b2773c4ba5e8f7b2f4af6d6ce1aef8fcb84bbe05780822976644d0e79b20f
DIST ideep-ba885200.tar.gz 27307 BLAKE2B 710dde31a8784315c88df9869e50c3940416263958ab653bce9876d60786906565b12f36c2d716a8a1f6009bc9e532e06733ddfac0d4079dba13ea153b8acbd9 SHA512 0c1bca04adbe797e5767f8b86fb3b247a2a287ffa2b3b19a918f976312175b459a6488166d12cf55e68c9aced84038fcda0d1d1c51a5034c83f844f51d462727
+DIST kineto-dbfa0ead96612f7ca265c63a35fdf0488395179b.tar.gz 7245955 BLAKE2B 09e6b1b1e15c485bbcc20713d07dab42fcc1b075557b6f202089696944b379d9fb3a860f68c16946b6f3eb76b12cf52a7fbc99a14af1baa40fb09b3f6d295c4e SHA512 6c479c3a14887c0703843416a961b6c92169caada029683a1d6d8463b4001a5bf8606dcd480df509c0f1fe53206001ab7428c9352fa638acc581523f55687e2b
DIST libnop-aa95422e.tar.gz 124202 BLAKE2B 5a74ecbf473dba09db1a11172a4aa432d81b14adb3826bef9aa8bae1bf1e2d0d5a7bf775fd4343fa9d7b235b17cafe949e47c903e92fd5eae9cc0717a552ea45 SHA512 62b21be874d2117294925c2497394d166da43d534776764c9c124699b5799d99790a2c6420804f8e143e1a18a536106852082f3a9d0052a726abc624fc19f937
DIST libuv-02a9e1be.tar.gz 1250418 BLAKE2B 49d7c6161614218bf856f7e23cd3e483bf1ac682bdc78b9624b9b5b52edde31aae005638bbc01e89f01421097e0bd4e07893db464326741ca6d1abaf45e633fe SHA512 de6d5d014b61804884a3945f2992f4aecf642fdd330927aa9a3bc17b76c29c51f6615d3d04542b24bb9ccdfd5207155e282f2fcd3aac14233d5bde4b1bc30284
DIST mkl-dnn-5ef631a0.tar.gz 5799312 BLAKE2B ea2aafcf45adadb0546781b00b44a0e9712c28e4937ef4daeef8b910e76bbb152e5434e45bec2aae0f6cb86fd7b5098e61842d7e99258db6fa846a79996d2e23 SHA512 66df9ea574010616df46d85ef25d23bd9ed31f9719cdbec4c727de58728fe095cd412d7663c2d456dba2f26848e45c1d67e34bffe4e25beeef9c1d40f187e8d6
DIST nccl-033d7995.tar.gz 146624 BLAKE2B b6f15d5d4690a5cbcf882c10826def400a14c58ff5f5af276b5b9a615a567de36ca907120cc681cdf2f2eb207f22bc87ee87d145a365097a64fb3d9de82432fb SHA512 3b3e087cb729b10e3251dfef52196bddd33e3e777df289c5fc537e99473e78f8720255fbd3e14ae2d2a6126d1e9d59aa6d57d7c7958d919e65834fef92c1c835
DIST nccl-5949d96f3.tar.gz 147548 BLAKE2B f3d3dd222ae90ac9ac1457a9695f112a21f5652a5b40e10ac049da910f07707b1c3910f59734fbe5e2c6523c1e83f3801f809efa77d122a57e859828c74ba8c2 SHA512 d9ea83caf7940fb47134293236fcb7478c0d4e40365d3b0a29427758e2e2dbb980c5e8c05fc9fc3956ed5e21a82ec0efaa31d973fe9c73fa3f50465f76756131
+DIST onnx-29e7aa7048809784465d06e897f043a4600642b2.tar.gz 9332964 BLAKE2B 20858ed93a7e2064624f13bb345ad7ad699ddc8c5e9ce9af27ae49d14bd7db9a0d9ff463919dd0c840595916ac7a720344608c586e87b522d5e2b78fde42eb6a SHA512 bcc1edbc4ce29b1c3c9f1ac4854f13d547d9efa6b712ddb5afb3d84637687aba1dbb2224ac4278a2b2e677ee485397c432554e7f02d51333c57a1ed7e0909d32
DIST onnx-765f5ee8.tar.gz 2379139 BLAKE2B 3e3299e2f3c1184937820b137d5fb492abe216ae3a054f4a17c6cb037168f4a77d8c90db0ba657ba9c9f7af2099f71ae0b8658a573c9f2f6d29fbc9d5f0f1b8a SHA512 7e10717546d1ed0bab780768e907f957294bfda47748b4c7576b75a761f5e006fdd21f0b014ce6d761a0ac6ae59dd8bc71592785b67167a6b3692d1a56dbbda9
DIST onnx-a82c6a70.tar.gz 4874549 BLAKE2B 055f89d63c03304264b7dd64d5eb6c892a4a280693001ca932f0d352379630870d96dadd6e734b1ec1044cfd92856cd9bb362021a6424ef79e6a408a9c17bc3c SHA512 1ead6644cd28198a428ebcd0f127343c6cbcfdbf39a0832c62ee5ee320a06c655448f508406637702e2da33057c92f76da12302b403ac339a5cad8ea4b5ebab2
DIST onnx-a82c6a701.tar.gz 4874549 BLAKE2B 055f89d63c03304264b7dd64d5eb6c892a4a280693001ca932f0d352379630870d96dadd6e734b1ec1044cfd92856cd9bb362021a6424ef79e6a408a9c17bc3c SHA512 1ead6644cd28198a428ebcd0f127343c6cbcfdbf39a0832c62ee5ee320a06c655448f508406637702e2da33057c92f76da12302b403ac339a5cad8ea4b5ebab2
DIST onnx-tensorrt-c1532114.tar.gz 72464 BLAKE2B 45301706ca5c91c39e24db84e1dc4e968a8540b760d7b16df08f3a76c407dfceb38962520d822b84618be088fc3d69431f738a8bc7b0f578c84f35234061e99a SHA512 9e814b5dfc3a65ddba229bbddada4c686afab233463329a02cea176b6b1994643f9835ce44a84a9ac1a49e12a7fe2325fd6cd9d2d99a422284089df0202a69a5
DIST onnx-tensorrt-c15321141.tar.gz 72464 BLAKE2B 45301706ca5c91c39e24db84e1dc4e968a8540b760d7b16df08f3a76c407dfceb38962520d822b84618be088fc3d69431f738a8bc7b0f578c84f35234061e99a SHA512 9e814b5dfc3a65ddba229bbddada4c686afab233463329a02cea176b6b1994643f9835ce44a84a9ac1a49e12a7fe2325fd6cd9d2d99a422284089df0202a69a5
+DIST onnx-tensorrt-c153211418a7c57ce071d9ce2a41f8d1c85a878f.tar.gz 72464 BLAKE2B 45301706ca5c91c39e24db84e1dc4e968a8540b760d7b16df08f3a76c407dfceb38962520d822b84618be088fc3d69431f738a8bc7b0f578c84f35234061e99a SHA512 9e814b5dfc3a65ddba229bbddada4c686afab233463329a02cea176b6b1994643f9835ce44a84a9ac1a49e12a7fe2325fd6cd9d2d99a422284089df0202a69a5
DIST psimd-072586a7.tar.gz 6825 BLAKE2B db255d2a62ffa320b1e190a7a9ac923d812e918a72ce8ecfeeb926709ece92d05497430196b0fc833d910b9d24bf0140d20bcce1de695e1c39211158440608db SHA512 a18faea093423dd9fe19ece8b228e011dccce0a2a22222f777ea19b023a13173966d4a8aea01147e8fc58de5d39cffcedeb2221a1572ae52bd5aba1295f86a94
DIST psimd-072586a71.tar.gz 6825 BLAKE2B db255d2a62ffa320b1e190a7a9ac923d812e918a72ce8ecfeeb926709ece92d05497430196b0fc833d910b9d24bf0140d20bcce1de695e1c39211158440608db SHA512 a18faea093423dd9fe19ece8b228e011dccce0a2a22222f777ea19b023a13173966d4a8aea01147e8fc58de5d39cffcedeb2221a1572ae52bd5aba1295f86a94
+DIST psimd-072586a71b55b7f8c584153d223e95687148a90.tar.gz 6825 BLAKE2B db255d2a62ffa320b1e190a7a9ac923d812e918a72ce8ecfeeb926709ece92d05497430196b0fc833d910b9d24bf0140d20bcce1de695e1c39211158440608db SHA512 a18faea093423dd9fe19ece8b228e011dccce0a2a22222f777ea19b023a13173966d4a8aea01147e8fc58de5d39cffcedeb2221a1572ae52bd5aba1295f86a94
DIST pthreadpool-029c8862.tar.gz 45970 BLAKE2B 09bd7d258f45fbe703238826b7435d8a5d013700cd734282b646420ba0854c0a386712f6bc3ed44e7496d51471b1e0a965f01ebdb09786e2020d979ecddb767a SHA512 b51099fa9d62065883cc43dcd5f9717a17be5ee2e87fc861667172a09acb3a62929c8bbc8a5c0c00885a638af0ec2ae4149adde2ba85bf3c80834f9b973c2d5b
DIST pthreadpool-029c88620.tar.gz 45970 BLAKE2B 09bd7d258f45fbe703238826b7435d8a5d013700cd734282b646420ba0854c0a386712f6bc3ed44e7496d51471b1e0a965f01ebdb09786e2020d979ecddb767a SHA512 b51099fa9d62065883cc43dcd5f9717a17be5ee2e87fc861667172a09acb3a62929c8bbc8a5c0c00885a638af0ec2ae4149adde2ba85bf3c80834f9b973c2d5b
+DIST pthreadpool-a134dd5d4cee80cce15db81a72e7f929d71dd413.tar.gz 49011 BLAKE2B 7bfbca81321243e64aa53c668dfe380ce4f7b88477a1c794a4dea9062c9b0969ca745dbfe0abbb95fffbf44080763506609c387ed085d89f6c612be6804b5cc2 SHA512 5f5a1275bbcef13cea88e381010bf2654c9646d30c5fb061f1d6e9e9a0ae6398e137c5e4f7da69f7d8d8b58fb5a7e79f7a4c0c1c3bbaad8f3d0c896d21bc7691
DIST pytorch-1.6.0.tar.gz 11376568 BLAKE2B 30aac34e14837ed6942ef7577aea77752cd9c809cb751fa837693b2b60eeda9a371421c4b4678fe94763a47e434b65ea60afc56aec7863887ba12bf362b96f0a SHA512 117ff1588ed1ebd0df15fbed066c65ea026893fe9a40d14aa1f73d848fab114b1b11bd7ed083815030f7fdf13a824480521cb40865f48a24c7028f4d195f2127
DIST pytorch-1.7.1.tar.gz 13012087 BLAKE2B ff498814178281ca59ae80bfe51dde3ffb0cde1eaa762bd9b36c2ff7f07d4b5ae4d68e10c76158e5e9e4250fcb01265a3755575b761495e20cf677e9a9825454 SHA512 359e271093e7afd374202f48e40356d195f644f78377a0b88f38627ad7aeabb9201a18c12ff35fb4aaf0d731168e511504445d8b4c08e92eed50264e23d81bae
+DIST pytorch-1.9.0.tar.gz 16772380 BLAKE2B 16f369cf2752082ab07fa0e497aaff7b90daf94cf39cce533c4a8b06a9237710089af0c137e29fbc79b4cf72d8d47681408e9ada1692431b573d90a07c373f1e SHA512 389ff114367a4337ab6e68178184f04751e4641fac685923afa019093951fa3a446f5265f6661f3aaad99c733c0107391431896c6e876796b8837f5ae75edd99
DIST sleef-7f523de6.tar.gz 1174007 BLAKE2B 58ebdddea912c841a4d917111d81051860631e93abbed43fb9899eff9370181f9227419e87872799a650e6a50cf174d0bf3b90c699a0e0763e903976baf95c9c SHA512 d83b24c34e83b36314344d5b31f1c3b673e38b44bc2d2bbbfdaf2019c3f0e73a83f2d13c6d745ca99d1532c1a3e0fcb4a71bd212e423bec03d610af5dd49e3f3
DIST sleef-7f523de65.tar.gz 1174007 BLAKE2B 58ebdddea912c841a4d917111d81051860631e93abbed43fb9899eff9370181f9227419e87872799a650e6a50cf174d0bf3b90c699a0e0763e903976baf95c9c SHA512 d83b24c34e83b36314344d5b31f1c3b673e38b44bc2d2bbbfdaf2019c3f0e73a83f2d13c6d745ca99d1532c1a3e0fcb4a71bd212e423bec03d610af5dd49e3f3
+DIST sleef-e0a003ee838b75d11763aa9c3ef17bf71a725bff.tar.gz 1642070 BLAKE2B 366fa96e35f429199e8462c63bc9cfbd1888aa65170d3203a5b0391fb855c29241eb225f847e416650e6ed5544f17a745c5a43a622a2847416ad7bd207572840 SHA512 13ea28745e796f8b77a40c99f679e0955e213128fb05d17b61cdcef102b7a758cbda04def3544767a81ddf170b7800f168d25fb1b55093614c7126456765cbea
DIST tensorpipe-3b8089c9c.tar.gz 141980 BLAKE2B 6c2a1e630412e9f8e039d5c44aaed4623f51516d59ee4237b9ec95d5b30970dbf4961aca0d84f1fee621ab8b8f668f0e8dbfbe558614d5651a00d9be21259a88 SHA512 1e9473532b11c23ec7dd9fdb148c0440263ae41f42a7826a4f7e098ed2a7e0c99d5e9df344b310e17098c3d70749a38d20d8af992c4820bebdbd5078d1a20dcc
DIST tensorpipe-95ff9319.tar.gz 155511 BLAKE2B bc074efe7501fd29fbff177c2782d4be1d514c8f2f5c9fe0fcdcbd0ca3a33bb91cab8fc95e8e5dac1bc4f65d904d0beef3d30f001eab9884b0506edbbee774fd SHA512 5ef38f10c65c49b3feea964c45564196005ebf47b365ed0cf60916215bac4fa04525ec9de007342fe520206b8e8663c0264fd838e89073a752d308418a2b1dd6
+DIST tensorpipe-c0e7623adb05f36311c7cde6dac8fc4c290419d9.tar.gz 253518 BLAKE2B fcef24208f97c1a96a3b0d30a76c3956de4383823c908982bcf1ef7fdacd14f6ada6fa3b797d3b6c9bd3dea3d1dd4bfc6f7b2136057a385ab42b2909cd1beee3 SHA512 734e919df485b590ff3bc022b53bbe8aeda1c2178ab8c6938e9fb6d977b48d4fa9a395f65f3727f602d0b25d0a7d419ad9ea96566b644b83073291ae40c54856
diff --git a/sci-libs/pytorch/pytorch-1.9.0.ebuild b/sci-libs/pytorch/pytorch-1.9.0.ebuild
new file mode 100644
index 000000000..c997f8da8
--- /dev/null
+++ b/sci-libs/pytorch/pytorch-1.9.0.ebuild
@@ -0,0 +1,321 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+PYTHON_COMPAT=( python3_{7,8,9} )
+
+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/7495417ad31c38a06b1b13db66b355b6f23cd96d.tar.gz -> fbgemm-7495417ad31c38a06b1b13db66b355b6f23cd96d.tar.gz
+https://github.com/asmjit/asmjit/archive/9057aa30.tar.gz -> asmjit-9057aa30.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/033d7995.tar.gz -> nccl-033d7995.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/c0e7623adb05f36311c7cde6dac8fc4c290419d9.tar.gz -> tensorpipe-c0e7623adb05f36311c7cde6dac8fc4c290419d9.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/02a9e1be.tar.gz -> libuv-02a9e1be.tar.gz
+https://github.com/google/XNNPACK/archive/79cd5f9e18ad0925ac9a050b00ea5a36230072db.tar.gz -> XNNPACK-79cd5f9e18ad0925ac9a050b00ea5a36230072db.tar.gz
+https://github.com/pytorch/kineto/archive/dbfa0ead96612f7ca265c63a35fdf0488395179b.tar.gz -> kineto-dbfa0ead96612f7ca265c63a35fdf0488395179b.tar.gz
+"
+
+# git clone git@github.com:pytorch/pytorch.git && cd pytorch
+# git submodules update --init --recursive
+# ${FILESDIR}/get_third_paries
+# cat SRC_URI src_prepare
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS=""
+
+IUSE="asan blas cuda +fbgemm ffmpeg gflags glog +gloo leveldb lmdb mkldnn mpi namedtensor +nnpack numa +observers opencl opencv +openmp +python +qnnpack redis rocm static test tools zeromq"
+RESTRICT="!test? ( test )"
+REQUIRED_USE="
+ ?? ( cuda rocm )
+"
+
+RDEPEND="
+ dev-python/pyyaml[${PYTHON_USEDEP}]
+ blas? ( virtual/blas )
+ cuda? ( dev-libs/cudnn
+ dev-cpp/eigen[cuda] )
+ rocm? ( >=dev-util/hip-4.0.0-r1
+ >=dev-libs/rccl-4
+ >=sci-libs/rocThrust-4
+ >=sci-libs/hipCUB-4
+ >=sci-libs/rocPRIM-4
+ >=sci-libs/miopen-4
+ >=sci-libs/rocBLAS-4
+ >=sci-libs/rocRAND-4
+ >=sci-libs/hipSPARSE-4
+ >=sci-libs/rocFFT-4
+ >=dev-util/roctracer-4 )
+ ffmpeg? ( media-video/ffmpeg )
+ gflags? ( dev-cpp/gflags )
+ glog? ( dev-cpp/glog )
+ leveldb? ( dev-libs/leveldb )
+ lmdb? ( dev-db/lmdb )
+ mpi? ( virtual/mpi )
+ opencl? ( dev-libs/clhpp virtual/opencl )
+ opencv? ( media-libs/opencv )
+ python? ( ${PYTHON_DEPS}
+ dev-python/pybind11[${PYTHON_USEDEP}]
+ dev-python/numpy[${PYTHON_USEDEP}]
+ dev-python/protobuf-python:0/22
+ )
+ redis? ( dev-db/redis )
+ zeromq? ( net-libs/zeromq )
+ dev-cpp/eigen
+ dev-libs/protobuf:0/22
+ dev-libs/libuv
+"
+
+#ATen code generation
+BDEPEND="dev-python/pyyaml"
+
+DEPEND="${RDEPEND}
+ test? ( dev-python/pytest[${PYTHON_USEDEP}] )
+ dev-cpp/tbb
+ app-arch/zstd
+ dev-python/pybind11[${PYTHON_USEDEP}]
+ dev-python/typing-extensions[${PYTHON_USEDEP}]
+ sys-fabric/libibverbs
+ sys-process/numactl
+"
+
+PATCHES=(
+ "${FILESDIR}"/${PN}-1.6.0-skip-tests.patch
+ "${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
+)
+
+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-7495417ad31c38a06b1b13db66b355b6f23cd96d third_party/fbgemm || die
+ rmdir third_party/fbgemm/third_party/asmjit || die
+ ln -sv "${WORKDIR}"/asmjit-9057aa30b620f0662ff51e2230c126a345063064 third_party/fbgemm/third_party/asmjit || die
+ rmdir third_party/fbgemm/third_party/cpuinfo || die
+ ln -sv "${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 "${WORKDIR}"/nccl-033d799524fb97629af5ac2f609de367472b2696 third_party/nccl/nccl || die
+ rmdir third_party/NNPACK || die
+ ln -sv "${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-c0e7623adb05f36311c7cde6dac8fc4c290419d9 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 "${WORKDIR}"/libuv-02a9e1be252b623ee032a3137c0b0c94afbe6809 third_party/tensorpipe/third_party/libuv || die
+ rmdir third_party/XNNPACK || die
+ ln -sv "${WORKDIR}"/XNNPACK-79cd5f9e18ad0925ac9a050b00ea5a36230072db third_party/XNNPACK || die
+ rmdir third_party/kineto || die
+ ln -sv "${WORKDIR}"/kineto-dbfa0ead96612f7ca265c63a35fdf0488395179b third_party/kineto || die
+
+ if use cuda; then
+ cd third_party/nccl/nccl || die
+ eapply "${FILESDIR}"/${PN}-1.6.0-nccl-nvccflags.patch
+
+# addpredict /dev/nvidiactl
+ cuda_src_prepare
+ export CUDAHOSTCXX=$(cuda_gccdir)/g++
+ fi
+
+ if use rocm; then
+ #Allow escaping sandbox
+ addread /dev/kfd
+ addread /dev/dri
+ addwrite /dev/kfd
+ addwrite /dev/dri
+
+ ebegin "HIPifying cuda sources"
+ tools/amd_build/build_amd.py
+ eend $?
+
+ export PYTORCH_ROCM_ARCH=$(rocminfo | egrep -o "gfx[0-9]+" | uniq | awk -vORS=';' "{print $1}" | sed 's/;$/\n/') || die
+ sed -e "/set(roctracer_INCLUDE_DIRS/s,\${ROCTRACER_PATH}/include,${EPREFIX}/usr/include/roctracer," \
+ -i cmake/public/LoadHIP.cmake || die
+ fi
+}
+
+src_configure() {
+ local mycmakeargs=(
+ -DTORCH_BUILD_VERSION=${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
+ -DBUILD_NAMEDTENSOR=$(usex namedtensor ON OFF)
+ -DBLAS=$(usex blas Generic Eigen)
+ -DTP_BUILD_LIBUV=OFF
+ -Wno-dev
+ )
+
+ 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
+ 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 -rfv "${ED}/torch"
+ rm -rfv "${ED}/var"
+ rm -rfv "${ED}/usr/lib"
+
+ rm -fv "${ED}/usr/include/*.{h,hpp}"
+ rm -rfv "${ED}/usr/include/asmjit"
+ rm -rfv "${ED}/usr/include/c10d"
+ rm -rfv "${ED}/usr/include/fbgemm"
+ rm -rfv "${ED}/usr/include/fp16"
+ rm -rfv "${ED}/usr/include/gloo"
+ rm -rfv "${ED}/usr/include/include"
+ rm -rfv "${ED}/usr/include/var"
+
+ cp -rv "${WORKDIR}/${P}/third_party/pybind11/include/pybind11" "${ED}/usr/include/"
+
+ rm -fv "${ED}/usr/${LIB}/libtbb.so"
+ rm -rfv "${ED}/usr/${LIB}/cmake"
+
+ if use python; then
+ scanelf -r --fix "${BUILD_DIR}/caffe2/python"
+ CMAKE_BUILD_DIR=${BUILD_DIR} distutils-r1_src_install
+
+ python_foreach_impl python_optimize
+ fi
+
+ find "${ED}/usr/${LIB}" -name "*.a" -exec rm -fv {} \;
+
+ use test && rm -rfv "${ED}/usr/test" "${ED}"/usr/bin/test_{api,jit}
+
+ # Remove the empty directories by CMake Python:
+ find "${ED}" -type d -empty -delete || die
+}
diff --git a/sci-libs/rdkit/rdkit-2020.03.6.ebuild b/sci-libs/rdkit/rdkit-2020.03.6.ebuild
index c38bac753..b73817270 100644
--- a/sci-libs/rdkit/rdkit-2020.03.6.ebuild
+++ b/sci-libs/rdkit/rdkit-2020.03.6.ebuild
@@ -22,7 +22,7 @@ LICENSE="BSD"
SLOT="0"
KEYWORDS=""
# build configuration issues https://github.com/rdkit/rdkit/issues/3444
-IUSE="+python -static-libs"
+IUSE="+python static-libs"
REQUIRED_USE="python? ( ${PYTHON_REQUIRED_USE} )"
RDEPEND="dev-libs/boost
diff --git a/sci-libs/rocBLAS/Manifest b/sci-libs/rocBLAS/Manifest
deleted file mode 100644
index d45adc2a4..000000000
--- a/sci-libs/rocBLAS/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST rocm-rocBLAS-4.0.0.tar.gz 6815197 BLAKE2B 32de8d14fe2a41090fdb4903ed4069aa95441962caa38f5c14294e79be50f426c2b076408a7f6fdd9e9a498acd6cc85700ccbf2989c0e645e9d5b43cad0c1710 SHA512 87b2b029ce3c1845cc0726c44b6270028504de2d6a9b82798082d45a672804a11250b85ed526c5bd4dd5305ba66ed7caa2076193d623a7448b8bdc0886b3e33c
diff --git a/sci-libs/rocBLAS/files/Tensile-4.0.0-locate-commands.patch b/sci-libs/rocBLAS/files/Tensile-4.0.0-locate-commands.patch
deleted file mode 100644
index 461a736a2..000000000
--- a/sci-libs/rocBLAS/files/Tensile-4.0.0-locate-commands.patch
+++ /dev/null
@@ -1,32 +0,0 @@
-Index: Tensile-rocm-4.0.0/Tensile/Common.py
-===================================================================
---- Tensile-rocm-4.0.0.orig/Tensile/Common.py
-+++ Tensile-rocm-4.0.0/Tensile/Common.py
-@@ -1521,14 +1521,14 @@ def assignGlobalParameters( config ):
- print2(" %24s: %8s (unspecified)" % (key, defaultValue))
-
- # ROCm Agent Enumerator Path
-- globalParameters["ROCmAgentEnumeratorPath"] = locateExe("/opt/rocm/bin", "rocm_agent_enumerator")
-+ globalParameters["ROCmAgentEnumeratorPath"] = locateExe("", "rocm_agent_enumerator")
- if "CxxCompiler" in config:
- globalParameters["CxxCompiler"] = config["CxxCompiler"]
-
- if "TENSILE_ROCM_ASSEMBLER_PATH" in os.environ:
- globalParameters["AssemblerPath"] = os.environ.get("TENSILE_ROCM_ASSEMBLER_PATH")
- elif globalParameters["AssemblerPath"] is None and globalParameters["CxxCompiler"] == "hipcc":
-- globalParameters["AssemblerPath"] = locateExe("/opt/rocm/llvm/bin", "clang++")
-+ globalParameters["AssemblerPath"] = locateExe("", "clang++")
- elif globalParameters["AssemblerPath"] is None and globalParameters["CxxCompiler"] == "hcc":
- globalParameters["AssemblerPath"] = locateExe("/opt/rocm/bin", "hcc")
-
-@@ -1536,8 +1536,8 @@ def assignGlobalParameters( config ):
- if globalParameters["CxxCompiler"] == "hcc":
- globalParameters["ExtractKernelPath"] = locateExe("/opt/rocm/bin", "extractkernel")
- else:
-- globalParameters["ExtractKernelPath"] = locateExe("/opt/rocm/hip/bin", "extractkernel")
-- globalParameters["ClangOffloadBundlerPath"] = locateExe("/opt/rocm/llvm/bin", "clang-offload-bundler")
-+ globalParameters["ExtractKernelPath"] = locateExe("", "extractkernel")
-+ globalParameters["ClangOffloadBundlerPath"] = locateExe("", "clang-offload-bundler")
-
- if "ROCmAgentEnumeratorPath" in config:
- globalParameters["ROCmAgentEnumeratorPath"] = config["ROCmAgentEnumeratorPath"]
diff --git a/sci-libs/rocBLAS/files/rocBLAS-4.0.0-use-system-tensile.patch b/sci-libs/rocBLAS/files/rocBLAS-4.0.0-use-system-tensile.patch
deleted file mode 100644
index 3b8e44a99..000000000
--- a/sci-libs/rocBLAS/files/rocBLAS-4.0.0-use-system-tensile.patch
+++ /dev/null
@@ -1,30 +0,0 @@
-diff --color -uprN rocBLAS-rocm-4.0.0/CMakeLists.txt new/CMakeLists.txt
---- rocBLAS-rocm-4.0.0/CMakeLists.txt 2020-11-11 00:56:04.000000000 +0800
-+++ new/CMakeLists.txt 2021-01-20 15:23:09.570222990 +0800
-@@ -208,25 +208,7 @@ if( BUILD_WITH_TENSILE )
- option(TENSILE_USE_MSGPACK "Use msgpack for parsing config files." ON)
- endif()
-
-- include(virtualenv)
-- if (Tensile_TEST_LOCAL_PATH)
-- virtualenv_install(${Tensile_TEST_LOCAL_PATH})
-- message (STATUS "using local Tensile from ${Tensile_TEST_LOCAL_PATH}, copied to ${Tensile_ROOT}")
-- else()
-- # Use the virtual-env setup and download package from specified repot:
-- set( tensile_fork "ROCmSoftwarePlatform" CACHE STRING "Tensile fork to use" )
-- file (STRINGS "tensile_tag.txt" read_tensile_tag)
-- set( tensile_tag ${read_tensile_tag} CACHE STRING "Tensile tag to download" )
-- virtualenv_install("git+https://github.com/${tensile_fork}/Tensile.git@${tensile_tag}")
-- message (STATUS "using GIT Tensile fork=${tensile_fork} from branch=${tensile_tag}")
-- endif()
-- message(STATUS "Adding ${VIRTUALENV_HOME_DIR} to CMAKE_PREFIX_PATH")
-- list(APPEND CMAKE_PREFIX_PATH ${VIRTUALENV_HOME_DIR})
-- if (TENSILE_VERSION)
-- find_package(Tensile ${TENSILE_VERSION} EXACT REQUIRED HIP LLVM OpenMP PATHS "${INSTALLED_TENSILE_PATH}")
-- else()
-- find_package(Tensile 4.24.0 EXACT REQUIRED HIP LLVM OpenMP PATHS "${INSTALLED_TENSILE_PATH}")
-- endif()
-+ find_package(Tensile 4.24.0 EXACT REQUIRED HIP LLVM OpenMP)
- endif()
-
- # Find HCC/HIP dependencies
diff --git a/sci-libs/rocBLAS/metadata.xml b/sci-libs/rocBLAS/metadata.xml
deleted file mode 100644
index 336bdb639..000000000
--- a/sci-libs/rocBLAS/metadata.xml
+++ /dev/null
@@ -1,11 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM 'http://www.gentoo.org/dtd/metadata.dtd'>
-<pkgmetadata>
- <maintainer type="project">
- <email>sci@gentoo.org</email>
- </maintainer>
- <maintainer type="person">
- <email>gentoo@holzke.net</email>
- <name>Wilfried Holzke</name>
- </maintainer>
-</pkgmetadata>
diff --git a/sci-libs/rocBLAS/rocBLAS-4.0.0-r1.ebuild b/sci-libs/rocBLAS/rocBLAS-4.0.0-r1.ebuild
deleted file mode 100644
index ca0fcfd8c..000000000
--- a/sci-libs/rocBLAS/rocBLAS-4.0.0-r1.ebuild
+++ /dev/null
@@ -1,88 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit cmake
-
-DESCRIPTION="AMD's library for BLAS on ROCm."
-HOMEPAGE="https://github.com/ROCmSoftwarePlatform/rocBLAS"
-SRC_URI="https://github.com/ROCmSoftwarePlatform/rocBLAS/archive/rocm-${PV}.tar.gz -> rocm-rocBLAS-${PV}.tar.gz"
-
-LICENSE="MIT"
-KEYWORDS="~amd64"
-SLOT="0"
-
-IUSE="debug"
-
-RDEPEND="=dev-util/hip-$(ver_cut 1-2)*"
-DEPEND="${RDEPEND}
- dev-util/cmake
- dev-util/rocm-cmake
- dev-libs/msgpack
- dev-perl/File-Which"
-
-# stripped library is not working
-RESTRICT="strip"
-
-S="${WORKDIR}/rocBLAS-rocm-${PV}"
-
-rocBLAS_V="0.1"
-
-PATCHES="${FILESDIR}/${PN}-4.0.0-use-system-tensile.patch"
-
-src_prepare() {
- eapply_user
-
- sed -e "/PREFIX rocblas/d" \
- -e "/<INSTALL_INTERFACE/s:include:include/rocblas:" \
- -e "s:rocblas/include:include/rocblas:" \
- -e "s:\\\\\${CPACK_PACKAGING_INSTALL_PREFIX}rocblas/lib:${EPREFIX}/usr/$(get_libdir)/rocblas:" \
- -e "/rocm_install_symlink_subdir( rocblas )/d" -i library/src/CMakeLists.txt || die
-
- cmake_src_prepare
-}
-
-src_configure() {
- # allow acces to hardware
- addwrite /dev/kfd
- addpredict /dev/dri/
-
- # Compiler to use
- export CXX="hipcc"
-
- if use debug; then
- buildtype="Debug"
- else
- buildtype="Release"
- fi
-
- local mycmakeargs=(
- -DTensile_LOGIC="asm_full"
- -DTensile_COMPILER="hipcc"
- -DTensile_ARCHITECTURE="all"
- -DTensile_LIBRARY_FORMAT="msgpack"
- -DTensile_CODE_OBJECT_VERSION="V3"
- -DTensile_TEST_LOCAL_PATH="${WORKDIR}/Tensile-rocm-${PV}"
- -DBUILD_WITH_TENSILE=ON
- -DBUILD_WITH_TENSILE_HOST=ON
- -DCMAKE_BUILD_TYPE="${buildtype}"
- -DCMAKE_CXX_FLAGS="--rocm-path=${EPREFIX}/usr"
- -DCMAKE_INSTALL_PREFIX="${EPREFIX}/usr"
- -DCMAKE_INSTALL_INCLUDEDIR="include/rocblas"
- -DBUILD_TESTING=OFF
- -DBUILD_CLIENTS_SAMPLES=OFF
- -DBUILD_CLIENTS_TESTS=OFF
- -DBUILD_CLIENTS_BENCHMARKS=OFF
- )
-
- cmake_src_configure
-
- # do not rerun cmake and the build process in src_install
- sed -e '/RERUN/,+1d' -i "${BUILD_DIR}"/build.ninja || die
-}
-
-src_install() {
- cmake_src_install
- chrpath --delete "${ED}/usr/lib64/librocblas.so.${rocBLAS_V}"
-}
diff --git a/sci-libs/rocBLAS/rocBLAS-4.0.0-r2.ebuild b/sci-libs/rocBLAS/rocBLAS-4.0.0-r2.ebuild
deleted file mode 100644
index bb44363d3..000000000
--- a/sci-libs/rocBLAS/rocBLAS-4.0.0-r2.ebuild
+++ /dev/null
@@ -1,76 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit cmake
-
-DESCRIPTION="AMD's library for BLAS on ROCm."
-HOMEPAGE="https://github.com/ROCmSoftwarePlatform/rocBLAS"
-SRC_URI="https://github.com/ROCmSoftwarePlatform/rocBLAS/archive/rocm-${PV}.tar.gz -> rocm-${PN}-${PV}.tar.gz"
-
-LICENSE="MIT"
-KEYWORDS="~amd64"
-SLOT="0"
-
-RDEPEND="=dev-util/hip-$(ver_cut 1-2)*"
-DEPEND="${RDEPEND}
- dev-perl/File-Which
- dev-libs/msgpack
- dev-util/cmake
- dev-util/rocm-cmake
- >=dev-util/Tensile-4.0.0-r1
- >=sys-devel/llvm-roc-4.0.0-r2
- "
-
-# stripped library is not working
-RESTRICT="strip"
-
-S="${WORKDIR}"/${PN}-rocm-${PV}
-
-rocBLAS_V="0.1"
-
-PATCHES=( "${FILESDIR}"/${PN}-4.0.0-use-system-tensile.patch )
-
-src_prepare() {
- eapply_user
-
- sed -e "/PREFIX rocblas/d" \
- -e "/<INSTALL_INTERFACE/s:include:include/rocblas:" \
- -e "s:rocblas/include:include/rocblas:" \
- -e "s:\\\\\${CPACK_PACKAGING_INSTALL_PREFIX}rocblas/lib:${EPREFIX}/usr/$(get_libdir)/rocblas:" \
- -e "/rocm_install_symlink_subdir( rocblas )/d" -i library/src/CMakeLists.txt || die
-
- cmake_src_prepare
-}
-
-src_configure() {
- # allow acces to hardware
- addwrite /dev/kfd
- addwrite /dev/dri/
- addwrite /dev/random
-
- export PATH="${EPREFIX}/usr/lib/llvm/roc/bin:${PATH}"
-
- local mycmakeargs=(
- -DTensile_LOGIC="asm_full"
- -DTensile_COMPILER="hipcc"
- -DTensile_ARCHITECTURE="all"
- -DTensile_LIBRARY_FORMAT="msgpack"
- -DTensile_CODE_OBJECT_VERSION="V3"
- -DTensile_TEST_LOCAL_PATH="${WORKDIR}/Tensile-rocm-${PV}"
- -DBUILD_WITH_TENSILE=ON
- -DBUILD_WITH_TENSILE_HOST=ON
- -DCMAKE_INSTALL_PREFIX="${EPREFIX}/usr"
- -DCMAKE_INSTALL_INCLUDEDIR="include/rocblas"
- -DBUILD_TESTING=OFF
- -DBUILD_CLIENTS_SAMPLES=OFF
- -DBUILD_CLIENTS_TESTS=OFF
- -DBUILD_CLIENTS_BENCHMARKS=OFF
- )
-
- CXX="hipcc" cmake_src_configure
-
- # do not rerun cmake and the build process in src_install
- sed -e '/RERUN/,+1d' -i "${BUILD_DIR}"/build.ninja || die
-}
diff --git a/sci-libs/simpleitk/simpleitk-1.2.4.ebuild b/sci-libs/simpleitk/simpleitk-1.2.4.ebuild
index d8324a014..afc114669 100644
--- a/sci-libs/simpleitk/simpleitk-1.2.4.ebuild
+++ b/sci-libs/simpleitk/simpleitk-1.2.4.ebuild
@@ -16,7 +16,6 @@ SRC_URI="
https://github.com/SimpleITK/SimpleITK/releases/download/v${PV}/SimpleITK-${PV}.tar.gz
https://github.com/SimpleITK/SimpleITK/releases/download/v${PV}/SimpleITKData-${PV}.tar.gz
"
-RESTRICT="primaryuri"
LICENSE="Apache-2.0"
SLOT="0"
diff --git a/sci-libs/superlu_dist/superlu_dist-6.4.0.ebuild b/sci-libs/superlu_dist/superlu_dist-6.4.0.ebuild
index fbe477498..8c0b87423 100644
--- a/sci-libs/superlu_dist/superlu_dist-6.4.0.ebuild
+++ b/sci-libs/superlu_dist/superlu_dist-6.4.0.ebuild
@@ -21,7 +21,7 @@ IUSE="examples test"
RESTRICT="!test? ( test )"
RDEPEND="
- sci-libs/parmetis[mpi]
+ sci-libs/parmetis[mpi(-)]
virtual/mpi"
DEPEND="${RDEPEND}"
BDEPEND="virtual/pkgconfig"
diff --git a/sci-mathematics/acl2/Manifest b/sci-mathematics/acl2/Manifest
index a03fdbdd6..b824d2c10 100644
--- a/sci-mathematics/acl2/Manifest
+++ b/sci-mathematics/acl2/Manifest
@@ -1 +1,2 @@
DIST acl2-8.3.tar.gz 116808616 BLAKE2B 77bba8c91231c2ae6ebae34ceeec9939101862156bfda4be2a0e3389f51cfdc183004d9cb3b27511a7494a9ead8ced5016f648a1712ab468c781dd8f8feca822 SHA512 92b59d1b31ce8d980bf043d02d4ee6ae36c69b3c2cc7be106e4d8f46e660a813e42f6e41a0903159ce65e9332dccb770cbd69472602889724f8ba724bfa301e2
+DIST acl2-8.4.tar.gz 202242463 BLAKE2B 887273910c7913d08455e5053a4c4d065743e0ba247f94f994a3400f27c97f8fce07debb145dbf26287c8b72e9335d995fcbc49f7085e17384b38035d260c8b8 SHA512 5a38271ffa9f9aad79d2aaf575144a58cf1b926b9ba3f9fb34af927862c95f6f683e870c9b453b2527abe8bdcd5603c6b5ad4c50b70c407606db78e0a79545bb
diff --git a/sci-mathematics/acl2/acl2-8.3-r1.ebuild b/sci-mathematics/acl2/acl2-8.3-r1.ebuild
new file mode 100644
index 000000000..d0bb4eade
--- /dev/null
+++ b/sci-mathematics/acl2/acl2-8.3-r1.ebuild
@@ -0,0 +1,86 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+inherit elisp-common
+
+DESCRIPTION="Industrial strength theorem prover"
+HOMEPAGE="https://www.cs.utexas.edu/users/moore/acl2/"
+SRC_URI="https://github.com/acl2/acl2/archive/${PV}/${P}.tar.gz"
+
+SLOT="0"
+LICENSE="BSD"
+KEYWORDS="~amd64 ~x86"
+IUSE="books doc emacs"
+
+BDEPEND="
+ dev-lisp/sbcl
+ emacs? ( >=app-editors/emacs-23.1:* )
+"
+DEPEND="
+ dev-lisp/sbcl:=
+ books? ( dev-lang/perl )
+ doc? ( dev-lang/perl )
+"
+RDEPEND="${DEPEND}"
+
+PATCHES=( "${FILESDIR}"/${PN}-use_make_variable.patch )
+
+src_prepare() {
+ find . -type f -name "*.bak" -delete
+ find . -type f -name "*.orig" -delete
+ # Remove sparc binary inadvertently included in upstream
+ rm books/workshops/2003/schmaltz-al-sammane-et-al/support/acl2link || die
+ default
+}
+
+src_compile() {
+ emake LISP="sbcl --noinform --noprint \
+ --no-sysinit --no-userinit --disable-debugger"
+
+ if use books; then
+ emake "ACL2=${S}/saved_acl2" basic
+ fi
+
+ if use doc; then
+ emake "ACL2=${S}/saved_acl2" DOC
+ fi
+
+ if use emacs; then
+ elisp-compile emacs/*.el
+ fi
+}
+
+src_install() {
+ local SAVED_NAME=saved_acl2
+ sed -e "s:${S}:/usr/share/acl2:g" -i ${SAVED_NAME} || die
+ dobin ${SAVED_NAME}
+
+ insinto /usr/share/acl2
+ doins ${SAVED_NAME}.core
+ if use books; then
+ sed -e "/5/a export ACL2_SYSTEM_BOOKS=/usr/share/acl2/books/" \
+ -i ${SAVED_NAME} || die
+ doins -r books
+ fi
+
+ DOCS=( books/README.md )
+ if use doc; then
+ HTML_DOCS=( doc/HTML/. )
+ fi
+ einstalldocs
+
+ if use emacs; then
+ elisp-install ${PN} emacs/*{.el,elc}
+ doins TAGS
+ fi
+}
+
+pkg_postinst() {
+ use emacs && elisp-site-regen
+}
+
+pkg_postrm() {
+ use emacs && elisp-site-regen
+}
diff --git a/sci-mathematics/acl2/acl2-8.3.ebuild b/sci-mathematics/acl2/acl2-8.3.ebuild
deleted file mode 100644
index 63326e257..000000000
--- a/sci-mathematics/acl2/acl2-8.3.ebuild
+++ /dev/null
@@ -1,51 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit eutils
-
-DESCRIPTION="Industrial strength theorem prover"
-HOMEPAGE="https://www.cs.utexas.edu/users/moore/acl2/"
-MY_PN=${PN}-devel
-SRC_URI="https://github.com/${MY_PN}/${MY_PN}/releases/download/${PV}/${P}.tar.gz"
-
-SLOT="0"
-LICENSE="BSD"
-KEYWORDS="~amd64 ~x86"
-IUSE="books"
-
-BDEPEND="dev-lisp/sbcl"
-DEPEND="
- dev-lisp/sbcl:=
- books? ( dev-lang/perl )
-"
-RDEPEND="${DEPEND}"
-
-src_compile() {
- emake LISP="sbcl --noinform --noprint \
- --no-sysinit --no-userinit --disable-debugger"
-
- if use books; then
- echo
- einfo "Building certificates ..."
- einfo "(this may take hours to finish)"
- emake certify-books
- fi
-}
-
-src_install() {
- SAVED_NAME=saved_acl2
- sed -e "s:${S}:/usr/share/acl2:g" -i ${SAVED_NAME} || die
- if use books; then
- sed -e "/5/a export ACL2_SYSTEM_BOOKS=/usr/share/acl2/books/" \
- -i ${SAVED_NAME} || die
- fi
- dobin ${SAVED_NAME}
-
- insinto /usr/share/acl2
- doins TAGS ${SAVED_NAME}.core
- if use books; then
- doins -r books
- fi
-}
diff --git a/sci-mathematics/acl2/acl2-8.4.ebuild b/sci-mathematics/acl2/acl2-8.4.ebuild
new file mode 100644
index 000000000..dfc3967ed
--- /dev/null
+++ b/sci-mathematics/acl2/acl2-8.4.ebuild
@@ -0,0 +1,86 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+inherit elisp-common
+
+DESCRIPTION="Industrial strength theorem prover"
+HOMEPAGE="https://www.cs.utexas.edu/users/moore/acl2/"
+SRC_URI="https://github.com/acl2/acl2/archive/${PV}/${P}.tar.gz"
+
+SLOT="0"
+LICENSE="BSD"
+KEYWORDS="~amd64 ~x86"
+IUSE="books doc emacs"
+
+BDEPEND="
+ >=dev-lisp/sbcl-1.5.2
+ emacs? ( >=app-editors/emacs-23.1:* )
+"
+DEPEND="
+ dev-lisp/sbcl:=
+ books? ( dev-lang/perl )
+ doc? ( dev-lang/perl )
+"
+RDEPEND="${DEPEND}"
+
+PATCHES=( "${FILESDIR}"/${PN}-use_make_variable.patch )
+
+src_prepare() {
+ find . -type f -name "*.bak" -delete
+ find . -type f -name "*.orig" -delete
+ # Remove sparc binary inadvertently included in upstream
+ rm books/workshops/2003/schmaltz-al-sammane-et-al/support/acl2link || die
+ default
+}
+
+src_compile() {
+ emake LISP="sbcl --noinform --noprint \
+ --no-sysinit --no-userinit --disable-debugger"
+
+ if use books; then
+ emake "ACL2=${S}/saved_acl2" basic
+ fi
+
+ if use doc; then
+ emake "ACL2=${S}/saved_acl2" DOC
+ fi
+
+ if use emacs; then
+ elisp-compile emacs/*.el
+ fi
+}
+
+src_install() {
+ local SAVED_NAME=saved_acl2
+ sed -e "s:${S}:/usr/share/acl2:g" -i ${SAVED_NAME} || die
+ dobin ${SAVED_NAME}
+
+ insinto /usr/share/acl2
+ doins ${SAVED_NAME}.core
+ if use books; then
+ sed -e "/5/a export ACL2_SYSTEM_BOOKS=/usr/share/acl2/books/" \
+ -i ${SAVED_NAME} || die
+ doins -r books
+ fi
+
+ DOCS=( books/README.md )
+ if use doc; then
+ HTML_DOCS=( doc/HTML/. )
+ fi
+ einstalldocs
+
+ if use emacs; then
+ elisp-install ${PN} emacs/*{.el,elc}
+ doins TAGS
+ fi
+}
+
+pkg_postinst() {
+ use emacs && elisp-site-regen
+}
+
+pkg_postrm() {
+ use emacs && elisp-site-regen
+}
diff --git a/sci-mathematics/acl2/files/acl2-use_make_variable.patch b/sci-mathematics/acl2/files/acl2-use_make_variable.patch
new file mode 100644
index 000000000..32e0f05da
--- /dev/null
+++ b/sci-mathematics/acl2/files/acl2-use_make_variable.patch
@@ -0,0 +1,13 @@
+use make variable to avoid QA issue: "make[1]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule"
+
+--- a/GNUmakefile
++++ b/GNUmakefile
+@@ -576,7 +576,7 @@ doc/home-page.html: doc/home-page.lisp
+ # xdoc::save that populates doc/manual/ (not under books/).
+ acl2-manual: check-books
+ rm -rf doc/manual books/system/doc/acl2-manual.cert
+- cd books ; make USE_QUICKLISP=1 system/doc/acl2-manual.cert
++ cd books ; $(MAKE) USE_QUICKLISP=1 system/doc/acl2-manual.cert
+ rm -rf doc/manual/download/*
+
+ # WARNING: The dependency list just below isn't complete, since it
diff --git a/sci-mathematics/acl2/metadata.xml b/sci-mathematics/acl2/metadata.xml
index 6035ff684..b3d826757 100644
--- a/sci-mathematics/acl2/metadata.xml
+++ b/sci-mathematics/acl2/metadata.xml
@@ -20,6 +20,6 @@
<flag name="books">build community books, the canonical collection of open-source libraries</flag>
</use>
<upstream>
- <remote-id type="github">acl2-devel/acl2-devel</remote-id>
+ <remote-id type="github">acl2/acl2</remote-id>
</upstream>
</pkgmetadata>
diff --git a/sci-mathematics/flocq/flocq-3.4.0.ebuild b/sci-mathematics/flocq/flocq-3.4.0-r1.ebuild
index e629d5628..f0e6c73a8 100644
--- a/sci-mathematics/flocq/flocq-3.4.0.ebuild
+++ b/sci-mathematics/flocq/flocq-3.4.0-r1.ebuild
@@ -1,7 +1,9 @@
# Copyright 1999-2021 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=7
+EAPI=8
+
+inherit multiprocessing
DESCRIPTION="A floating-point formalization for the Coq system"
HOMEPAGE="http://flocq.gforge.inria.fr/"
@@ -26,7 +28,7 @@ src_configure() {
}
src_compile() {
- ./remake || die "emake failed"
+ ./remake --jobs=$(makeopts_jobs) || die "emake failed"
}
src_install() {
diff --git a/sci-misc/europa-bin/Manifest b/sci-misc/europa-bin/Manifest
new file mode 100644
index 000000000..24c662f60
--- /dev/null
+++ b/sci-misc/europa-bin/Manifest
@@ -0,0 +1 @@
+DIST europa-bin-1.0.0.tar.xz 47742444 BLAKE2B 6729c49f48d399fa4b80661c1efada0b6268ccf83eb548e73af708e375d3377e847d3fa52219007ee0aec0ce16bd0df839ea88c09cb2cfe7bad1979d24611f68 SHA512 f0c37d162246eddc7c2c19878aae0128afdae82b2ac2584a4a441fb12ef19429387ea62230fc50928d10b89add747b1c8b42637eaf63d58fa3c43a20ad02e7c7
diff --git a/sci-misc/europa-bin/europa-bin-1.0.0.ebuild b/sci-misc/europa-bin/europa-bin-1.0.0.ebuild
new file mode 100644
index 000000000..ad502cfac
--- /dev/null
+++ b/sci-misc/europa-bin/europa-bin-1.0.0.ebuild
@@ -0,0 +1,57 @@
+# Copyright 2019-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+inherit xdg
+
+DESCRIPTION="JupyterLab's Desktop client in electron"
+HOMEPAGE="https://github.com/suyashmahar/europa"
+SRC_URI="https://drive.google.com/uc?export=download&id=1c6NYXJgioU4_2v-CQ6oxtb1jzMMhDeMo -> ${P}.tar.xz"
+
+KEYWORDS="-* ~amd64"
+LICENSE="GPL-3"
+SLOT="0"
+
+RDEPEND="
+ app-accessibility/at-spi2-atk:2
+ dev-libs/atk
+ dev-libs/expat
+ dev-libs/libappindicator
+ dev-libs/nspr
+ dev-libs/nss
+ dev-python/jupyterlab
+ media-libs/alsa-lib
+ net-print/cups
+ x11-libs/cairo
+ x11-libs/gdk-pixbuf:2
+ x11-libs/gtk+:3
+ x11-libs/libnotify
+ x11-libs/libxcb
+ x11-libs/libX11
+ x11-libs/libXcomposite
+ x11-libs/libXcursor
+ x11-libs/libXdamage
+ x11-libs/libXext
+ x11-libs/libXfixes
+ x11-libs/libXi
+ x11-libs/libxkbcommon
+ x11-libs/libXrandr
+ x11-libs/libXrender
+ x11-libs/libXtst
+ x11-libs/libXScrnSaver
+ x11-libs/pango
+"
+
+QA_PREBUILT="/opt/${PN//-bin}*"
+
+S="${WORKDIR}"
+
+src_install() {
+ # Move icon to correct dir
+ mv usr/share/icons/hicolor/0x0 usr/share/icons/hicolor/256x256 || die
+ # Write name in desktop file with capital letter
+ sed -i -e 's/Name=europa/Name=Europa/g' usr/share/applications/europa.desktop || die
+
+ mv "${S}"/* "${ED}" || die
+}
diff --git a/sci-misc/europa-bin/metadata.xml b/sci-misc/europa-bin/metadata.xml
new file mode 100644
index 000000000..0c2747670
--- /dev/null
+++ b/sci-misc/europa-bin/metadata.xml
@@ -0,0 +1,12 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <upstream>
+ <remote-id type="github">suyashmahar/europa</remote-id>
+ <bugs-to>https://github.com/suyashmahar/europa/issues</bugs-to>
+ </upstream>
+ <maintainer type="project">
+ <email>sci@gentoo.org</email>
+ <name>Gentoo Science Project</name>
+ </maintainer>
+</pkgmetadata>
diff --git a/sci-misc/irstlm/files/irstlm-6.00.05-doc-obey-docdir.patch b/sci-misc/irstlm/files/irstlm-6.00.05-doc-obey-docdir.patch
new file mode 100644
index 000000000..0b25ead22
--- /dev/null
+++ b/sci-misc/irstlm/files/irstlm-6.00.05-doc-obey-docdir.patch
@@ -0,0 +1,22 @@
+Remove doc/irstlm-manual.pdf from install in --prefix to instead obey --docdir
+
+--- a/doc/Makefile.am
++++ b/doc/Makefile.am
+@@ -1,5 +1,3 @@
+-documentationdir = @prefix@/doc
+-
+ if DOC_COMPILATION
+
+ irstlm-manual.pdf: irstlm-manual.tex
+@@ -14,10 +12,6 @@ clean-local:
+
+ all: irstlm-manual.pdf
+
+-dist_documentation_SCRIPTS = irstlm-manual.pdf
++dist_doc_DATA = irstlm-manual.pdf
+
+ endif
+-
+-EXTRA_DIST = irstlm-manual.tex
+-
+-
diff --git a/sci-misc/irstlm/files/irstlm-6.00.05-remove-lib-linking.patch b/sci-misc/irstlm/files/irstlm-6.00.05-remove-lib-linking.patch
new file mode 100644
index 000000000..c0cfcfe32
--- /dev/null
+++ b/sci-misc/irstlm/files/irstlm-6.00.05-remove-lib-linking.patch
@@ -0,0 +1,18 @@
+Remove Makefile.am lib linking operation
+Taken from upstream PR: https://github.com/irstlm-team/irstlm/pull/12
+
+--- a/Makefile.am
++++ b/Makefile.am
+@@ -7,12 +7,3 @@ SUBDIRS = src scripts doc
+ EXTRA_DIST = README RELEASE Copyright
+
+ ACLOCAL_AMFLAGS = -I m4
+-
+-LN_S=@LN_S@
+-
+-install-exec-hook:
+- cd ${exec_prefix}/ && \
+- ${LN_S} -n -f lib lib64
+-
+-dist-hook:
+- rm -rf `find $(distdir)/doc -type d -name .svn`
diff --git a/sci-misc/irstlm/irstlm-6.00.05-r1.ebuild b/sci-misc/irstlm/irstlm-6.00.05-r1.ebuild
new file mode 100644
index 000000000..73786fd4a
--- /dev/null
+++ b/sci-misc/irstlm/irstlm-6.00.05-r1.ebuild
@@ -0,0 +1,38 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+inherit autotools
+
+DESCRIPTION="A tool to estimate, store, and access very large n-gram language models"
+HOMEPAGE="https://hlt-mt.fbk.eu/technologies/irstlm"
+SRC_URI="https://github.com/irstlm-team/${PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="LGPL-3"
+SLOT="0"
+KEYWORDS="~amd64"
+IUSE="doc static-libs"
+
+BDEPEND="doc? ( app-text/texlive[extra] )"
+
+PATCHES=(
+ "${FILESDIR}"/${P}-remove-lib-linking.patch
+ "${FILESDIR}"/${P}-doc-obey-docdir.patch
+)
+
+src_prepare() {
+ default
+ # Remove AM_CXXFLAGS that are breaking the package or should not be there
+ # Bug: https://bugs.gentoo.org/755473
+ sed -e 's/-static -isystem\/usr\/include -W //' -i src/Makefile.am || die
+ # Needed for doc
+ cp "${S}/doc/RELEASE" "${S}/RELEASE.tex" || die
+ eautoreconf
+}
+
+src_configure() {
+ econf \
+ $(use_enable static-libs static) \
+ $(use_enable doc)
+}
diff --git a/scripts/setup-and-run-repoman.sh b/scripts/setup-and-run-repoman.sh
index f9e45a9cf..e2e10c78e 100755
--- a/scripts/setup-and-run-repoman.sh
+++ b/scripts/setup-and-run-repoman.sh
@@ -16,7 +16,7 @@ git clone https://github.com/gentoo/portage.git
cd portage
# Get all versions, and read into array
-mapfile -t RM_VERSIONS < <( git tag | grep repoman | sort -u )
+mapfile -t RM_VERSIONS < <( git tag | grep portage | sort -uV )
# Select latests version (last element in array)
RM_VERS="${RM_VERSIONS[-1]}"
diff --git a/sys-kernel/dkms/Manifest b/sys-kernel/dkms/Manifest
deleted file mode 100644
index c688e13d0..000000000
--- a/sys-kernel/dkms/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST dkms-2.8.4.tar.gz 104625 BLAKE2B 0bd9c47d2a4bf313426832ec88bbda9bd58a482c691de145ff87ce05d47d473132f2a300e8d0e6e0609b6dcdd47f8f9e521a104ae19cfa8b1ba453fc6de7a412 SHA512 1b8b987b239db8cf00f367ee4f5faf13dc41b450f09fb046dc719e51d6a762d6b700bf41156d8011c3ea7e139064119d6717b60c1bf7fa0a75ea1fc63887baa5
diff --git a/sys-kernel/dkms/dkms-2.8.4.ebuild b/sys-kernel/dkms/dkms-2.8.4.ebuild
deleted file mode 100644
index 895780135..000000000
--- a/sys-kernel/dkms/dkms-2.8.4.ebuild
+++ /dev/null
@@ -1,41 +0,0 @@
-# Copyright 1999-2020 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit linux-info
-
-DESCRIPTION="Dynamic Kernel Module Support"
-HOMEPAGE="https://github.com/dell/dkms"
-SRC_URI="https://github.com/dell/dkms/archive/v${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="GPL-2"
-KEYWORDS="~amd64 ~x86"
-SLOT="0"
-
-IUSE="doc"
-
-CONFIG_CHECK="~MODULES"
-
-RDEPEND="sys-apps/kmod"
-
-src_prepare() {
- # Install uncompressed version of man files
- sed -i \
- -e '\_gzip -c -9 dkms.8 > $(MAN)/dkms.8.gz_d' \
- -e '\_chmod 0644 $(MAN)/dkms.8.gz_d' \
- -e 's/dkms.8.gz/dkms.8/g' \
- Makefile || die
- default
-}
-
-src_compile() {
- # Nothing to do here
- return
-}
-
-src_install() {
- emake install DESTDIR="${D}" LIBDIR="${D}"/usr/$(get_libdir)/
- use doc && emake install-doc DOCDIR="${D}/usr/share/doc/${PF}"
- einstalldocs
-}
diff --git a/sys-kernel/dkms/metadata.xml b/sys-kernel/dkms/metadata.xml
deleted file mode 100644
index 71b8e5f86..000000000
--- a/sys-kernel/dkms/metadata.xml
+++ /dev/null
@@ -1,18 +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>
- <upstream>
- <remote-id type="github">dell/dkms</remote-id>
- </upstream>
- <longdescription lang="en">
- Dynamic Kernel Module Support (DKMS) is a program/framework that enables generating Linux kernel modules whose sources generally reside outside the kernel source tree. The concept is to have DKMS modules automatically rebuilt when a new kernel is installed.
- An essential feature of DKMS is that it automatically recompiles all DKMS modules if a new kernel version is installed. This allows drivers and devices outside of the mainline kernel to continue working after a Linux kernel upgrade.
- Another benefit of DKMS is that it allows the installation of a new driver on an existing system, running an arbitrary kernel version, without any need for manual compilation or precompiled packages provided by the vendor.
- DKMS was written by the Linux Engineering Team at Dell in 2003. It is included in many distributions, such as Ubuntu, Debian, Fedora, SUSE, and Arch. DKMS is free software released under the terms of the GNU General Public License (GPL) v2 or later.
- DKMS supports both the rpm and deb package formats out-of-the-box.
- </longdescription>
-</pkgmetadata>