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| author |   Aisha Tammy <gentoo@aisha.cc> | 2021-05-21 02:01:45 +0000 |
|---|---|---|
| committer | Aisha Tammy <gentoo@aisha.cc> | 2021-05-21 02:02:03 +0000 |
| commit | baf55ad9bd948fa0762f6251d7388f3226c9920d (patch) | |
| tree | 7e2c6edc43897db019ad20c3ac5930c53417bf40 | |
| parent | media-libs/embree-bin: version bump to 3.13.0 (diff) | |
| download | sci-baf55ad9bd948fa0762f6251d7388f3226c9920d.tar.gz sci-baf55ad9bd948fa0762f6251d7388f3226c9920d.tar.bz2 sci-baf55ad9bd948fa0762f6251d7388f3226c9920d.zip | |
sci-biology/cutadapt: version bump to 3.3
Package-Manager: Portage-3.0.18, Repoman-3.0.3
Signed-off-by: Aisha Tammy <gentoo@aisha.cc>
| -rw-r--r-- | sci-biology/cutadapt/Manifest | 1 | ||||
| -rw-r--r-- | sci-biology/cutadapt/cutadapt-3.3.ebuild | 42 | ||||
| -rw-r--r-- | sci-biology/cutadapt/files/cutadapt-3.3-skiptest.patch | 13 |
3 files changed, 56 insertions, 0 deletions
diff --git a/sci-biology/cutadapt/Manifest b/sci-biology/cutadapt/Manifest index 2ae274012..30063661a 100644 --- a/sci-biology/cutadapt/Manifest +++ b/sci-biology/cutadapt/Manifest @@ -1 +1,2 @@ DIST cutadapt-2.10.tar.gz 282198 BLAKE2B 87784fd092d3417775f3a627d68bea1d3421f6392ae90f65e9b5f231f10a4da8cfacecc8c6fc3cd8420d0255ffc44ec72188bc901d1768f18f3b78077a165314 SHA512 afefb101a25daa071e5945e442de46cd594a6f4ba5915e9d11943280039223ff5d686b358de44f11b6367f203767d97b76fc529eae70b072139e55831189e594 +DIST cutadapt-3.3.tar.gz 294579 BLAKE2B 1cf833d65a9611e50d747b6ce544dbf639ccc8eab8c5e83425d47bfe5526a0a25faab10cec7b41fad5b012ccf0552948a778b81dac3d5768674326d210dd4540 SHA512 d8895453455aff31c613a4e031559c08646ce2bf072d85ed7b195e5863700a02a1ed44bfb409b63849aadf1db7cf40dea33d0ead4f056307365dc91aa6c93234 diff --git a/sci-biology/cutadapt/cutadapt-3.3.ebuild b/sci-biology/cutadapt/cutadapt-3.3.ebuild new file mode 100644 index 000000000..e1990f222 --- /dev/null +++ b/sci-biology/cutadapt/cutadapt-3.3.ebuild @@ -0,0 +1,42 @@ +# 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="Remove adapter sequences from high-throughput sequencing data" +HOMEPAGE="https://github.com/marcelm/cutadapt" +SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz" + +LICENSE="MIT" +SLOT="0" +KEYWORDS="~amd64 ~x86" + +DEPEND=" + dev-python/dnaio[${PYTHON_USEDEP}] + dev-python/xopen[${PYTHON_USEDEP}] +" +RDEPEND=" + ${PYTHON_DEPS} + ${DEPEND} +" +BDEPEND=" + test? ( + dev-python/cython + dev-python/pytest-mock + dev-python/pytest-timeout + ) +" + +PATCHES=( "${FILESDIR}"/${PN}-3.3-skiptest.patch ) + +distutils_enable_tests pytest + +# needs call to installed cutadapt executable +python_test() { + distutils_install_for_testing + pytest -vv || die "pytest failed with ${EPYTHON}" +} diff --git a/sci-biology/cutadapt/files/cutadapt-3.3-skiptest.patch b/sci-biology/cutadapt/files/cutadapt-3.3-skiptest.patch new file mode 100644 index 000000000..c2dc2a741 --- /dev/null +++ b/sci-biology/cutadapt/files/cutadapt-3.3-skiptest.patch @@ -0,0 +1,13 @@ +diff --git a/tests/test_command.py b/tests/test_command.py +index a81b04a..cf40233 100644 +--- a/tests/test_command.py ++++ b/tests/test_command.py +@@ -76,7 +76,7 @@ def test_force_fasta_output(tmpdir, cores): + assert_files_equal(cutpath("small.fasta"), out_path) + + +-@pytest.mark.skipif(sys.platform == "win32", reason="Maybe this can be made to work") ++@pytest.mark.skipif(reason="Maybe this can be made to work") + def test_non_utf8_locale(): + subprocess.check_call( + [sys.executable, "-m", "cutadapt", "-o", os.devnull, datapath("small.fastq")], |