diff options
| -rw-r--r-- | sci-biology/bx-python/Manifest | 3 | ||||
| -rw-r--r-- | sci-biology/bx-python/bx-python-0.12.0.ebuild | 41 | ||||
| -rw-r--r-- | sci-biology/bx-python/bx-python-0.8.9.ebuild | 35 | ||||
| -rw-r--r-- | sci-biology/bx-python/bx-python-0.9.0.ebuild | 35 | ||||
| -rw-r--r-- | sci-biology/bx-python/bx-python-9999.ebuild | 35 | ||||
| -rw-r--r-- | sci-biology/bx-python/files/no-doctest.patch | 9 | ||||
| -rw-r--r-- | sci-biology/bx-python/metadata.xml | 4 |
7 files changed, 51 insertions, 111 deletions
diff --git a/sci-biology/bx-python/Manifest b/sci-biology/bx-python/Manifest index 90147dff7..69572ef1e 100644 --- a/sci-biology/bx-python/Manifest +++ b/sci-biology/bx-python/Manifest @@ -1,2 +1 @@ -DIST bx-python-0.8.9.gh.tar.gz 1651514 BLAKE2B ee75d08aaae8102c2af5be0175c75200382e157abc0c0c723a67b55d5542ab2d4b6ccd4e256975b0a2d00b39b2249d73df0c6f4324b3a74757c3e18e2aeb6c1a SHA512 37863c92258dc06a12b566b02697502f68bbf7e4d9decd8fc63af10ee58b614dd0e7cff35e9977ba1ddf913f176c49e7969728d8e64a9f78ac7100da4a3d70ea -DIST bx-python-0.9.0.gh.tar.gz 1667445 BLAKE2B 0814792a2af8bfb7af5ef5fe1ddc184ed14a68df060a8286f4eba334388497363dc002f6c0de72836b5654452fe28f4cef67cd31b765a4a121c84f3af0634ea0 SHA512 955f396614d8e6d19a74e94a6612f7752a45f752a4a59c95853474dd363ed1960d20a340f17eb1815fda3aaf26d907dc30d37aa8c23608d718742b68864ca1bc +DIST bx-python-0.12.0.gh.tar.gz 1660806 BLAKE2B 0eddb9b9a93520319d275001067a3518015483605cf4d096729ec92e14c0eb35f2ceb34db964216dd3c6687351a7415c46061960b1f66a7564c90efeba3a587b SHA512 821b33841dd2935485669f6c112277d404475b1cd778deb3eaa1194f3b21594335a219d9345e279e7afc3adb1e347e71e60f0029712fc58e95d1e70f9e8fbb55 diff --git a/sci-biology/bx-python/bx-python-0.12.0.ebuild b/sci-biology/bx-python/bx-python-0.12.0.ebuild new file mode 100644 index 000000000..1a00b0395 --- /dev/null +++ b/sci-biology/bx-python/bx-python-0.12.0.ebuild @@ -0,0 +1,41 @@ +# Copyright 1999-2024 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +DISTUTILS_USE_PEP517=setuptools +DISTUTILS_EXT=1 +PYTHON_COMPAT=( python3_{10..12} ) + +inherit distutils-r1 + +DESCRIPTION="Library for rapid implementation of genome scale analyses" +HOMEPAGE="https://github.com/bxlab/bx-python" +SRC_URI="https://github.com/bxlab/bx-python/archive/v${PV}.tar.gz -> ${P}.gh.tar.gz" + +LICENSE="MIT" +SLOT="0" +KEYWORDS="~amd64 ~x86" + +RDEPEND="dev-python/numpy[${PYTHON_USEDEP}]" +DEPEND="dev-python/cython[${PYTHON_USEDEP}]" + +# doctests have external deps +PATCHES=( + "${FILESDIR}/no-doctest.patch" +) + +distutils_enable_tests pytest + +# https://github.com/bxlab/bx-python/issues/101 +EPYTEST_DESELECT=( + lib.linux-x86_64-cpython-312/bx/binned_array_tests.py::test_file_lzo + lib.linux-x86_64-cpython-312/bx/binned_array_tests.py::test_binned_array_writer +) + +python_test() { + cd "${BUILD_DIR}/build" || die + ln -s "${S}/pytest.ini" . || die + ln -s "${S}/test_data" . || die + epytest +} diff --git a/sci-biology/bx-python/bx-python-0.8.9.ebuild b/sci-biology/bx-python/bx-python-0.8.9.ebuild deleted file mode 100644 index 6cffba1be..000000000 --- a/sci-biology/bx-python/bx-python-0.8.9.ebuild +++ /dev/null @@ -1,35 +0,0 @@ -# Copyright 1999-2023 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=8 - -PYTHON_COMPAT=( python3_{10..10} ) - -inherit distutils-r1 - -DESCRIPTION="Library for rapid implementation of genome scale analyses" -HOMEPAGE="https://github.com/bxlab/bx-python" -SRC_URI="https://github.com/bxlab/bx-python/archive/v${PV}.tar.gz -> ${P}.gh.tar.gz" - -LICENSE="MIT" -SLOT="0" -KEYWORDS="~amd64 ~x86" -# Tests require dev-python/pytest-cython (currently not in ::gentoo or ::science) -# (and might need some more work beyond that) -RESTRICT=test - -RDEPEND=" - dev-python/numpy[${PYTHON_USEDEP}] - dev-python/six[${PYTHON_USEDEP}] -" -BDEPEND=" - dev-python/cython[${PYTHON_USEDEP}] -" - -# has file collision with sci-biology/RSeQC - -# ToDo: fix doc building: -# Reason: TemplateNotFound('i') -#distutils_enable_sphinx doc/source - -distutils_enable_tests pytest diff --git a/sci-biology/bx-python/bx-python-0.9.0.ebuild b/sci-biology/bx-python/bx-python-0.9.0.ebuild deleted file mode 100644 index 6cffba1be..000000000 --- a/sci-biology/bx-python/bx-python-0.9.0.ebuild +++ /dev/null @@ -1,35 +0,0 @@ -# Copyright 1999-2023 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=8 - -PYTHON_COMPAT=( python3_{10..10} ) - -inherit distutils-r1 - -DESCRIPTION="Library for rapid implementation of genome scale analyses" -HOMEPAGE="https://github.com/bxlab/bx-python" -SRC_URI="https://github.com/bxlab/bx-python/archive/v${PV}.tar.gz -> ${P}.gh.tar.gz" - -LICENSE="MIT" -SLOT="0" -KEYWORDS="~amd64 ~x86" -# Tests require dev-python/pytest-cython (currently not in ::gentoo or ::science) -# (and might need some more work beyond that) -RESTRICT=test - -RDEPEND=" - dev-python/numpy[${PYTHON_USEDEP}] - dev-python/six[${PYTHON_USEDEP}] -" -BDEPEND=" - dev-python/cython[${PYTHON_USEDEP}] -" - -# has file collision with sci-biology/RSeQC - -# ToDo: fix doc building: -# Reason: TemplateNotFound('i') -#distutils_enable_sphinx doc/source - -distutils_enable_tests pytest diff --git a/sci-biology/bx-python/bx-python-9999.ebuild b/sci-biology/bx-python/bx-python-9999.ebuild deleted file mode 100644 index b29975b58..000000000 --- a/sci-biology/bx-python/bx-python-9999.ebuild +++ /dev/null @@ -1,35 +0,0 @@ -# Copyright 1999-2023 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=8 - -PYTHON_COMPAT=( python3_{10..10} ) - -inherit distutils-r1 git-r3 - -DESCRIPTION="Library for rapid implementation of genome scale analyses" -HOMEPAGE="https://github.com/bxlab/bx-python" -EGIT_REPO_URI="https://github.com/bxlab/bx-python" - -LICENSE="MIT" -SLOT="0" -KEYWORDS="" -# Tests require dev-python/pytest-cython (currently not in ::gentoo or ::science) -# (and might need some more work beyond that) -RESTRICT=test - -RDEPEND=" - dev-python/numpy[${PYTHON_USEDEP}] - dev-python/six[${PYTHON_USEDEP}] -" -BDEPEND=" - dev-python/cython[${PYTHON_USEDEP}] -" - -# has file collision with sci-biology/RSeQC - -# ToDo: fix doc building: -# Reason: TemplateNotFound('i') -#distutils_enable_sphinx doc/source - -distutils_enable_tests pytest diff --git a/sci-biology/bx-python/files/no-doctest.patch b/sci-biology/bx-python/files/no-doctest.patch new file mode 100644 index 000000000..d0c2b2e62 --- /dev/null +++ b/sci-biology/bx-python/files/no-doctest.patch @@ -0,0 +1,9 @@ +diff --git a/pytest.ini b/pytest.ini +index e77e08f..4184247 100644 +--- a/pytest.ini ++++ b/pytest.ini +@@ -1,4 +1,3 @@ + [pytest] +-addopts = --doctest-cython --doctest-modules + python_files = *_tests.py + testpaths = lib script_tests/ diff --git a/sci-biology/bx-python/metadata.xml b/sci-biology/bx-python/metadata.xml index f1fc4360e..2ead27d78 100644 --- a/sci-biology/bx-python/metadata.xml +++ b/sci-biology/bx-python/metadata.xml @@ -5,10 +5,6 @@ <email>mschu.dev@gmail.com</email> <name>Michael Schubert</name> </maintainer> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> <upstream> <remote-id type="github">bxlab/bx-python</remote-id> <remote-id type="pypi">bx-python</remote-id> |