commit: 70e2057641f5a42ec3eb46de196fea112a6955d0 Author: Horea Christian <chr <AT> chymera <DOT> eu> AuthorDate: Tue Jan 31 21:24:44 2023 +0000 Commit: Horea Christian <horea.christ <AT> gmail <DOT> com> CommitDate: Tue Jan 31 21:24:44 2023 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=70e20576
dev-python/heudiconv: new package, add 0.11.6 Signed-off-by: Horea Christian <chr <AT> chymera.eu> .../heudiconv/files/pynwb-2.0.0-versions.patch | 21 +++++++++ .../heudiconv/files/pynwb-2.1.0-versions.patch | 21 +++++++++ .../heudiconv/files/pynwb-2.2.0-versions.patch | 21 +++++++++ dev-python/heudiconv/heudiconv-0.11.6.ebuild | 51 ++++++++++++++++++++++ dev-python/heudiconv/metadata.xml | 16 +++++++ 5 files changed, 130 insertions(+) diff --git a/dev-python/heudiconv/files/pynwb-2.0.0-versions.patch b/dev-python/heudiconv/files/pynwb-2.0.0-versions.patch new file mode 100644 index 000000000..d09c50594 --- /dev/null +++ b/dev-python/heudiconv/files/pynwb-2.0.0-versions.patch @@ -0,0 +1,21 @@ +diff --git a/setup.py b/tmp/setup.py +index 39e75824..f7948f64 100755 +--- a/setup.py ++++ b/setup.py +@@ -19,11 +19,11 @@ print('found these packages:', pkgs) + schema_dir = 'nwb-schema/core' + + reqs = [ +- 'h5py>=2.9,<4', +- 'hdmf>=3.1.1,<4', +- 'numpy>=1.16,<1.22', +- 'pandas>=1.0.5,<2', +- 'python-dateutil>=2.7,<3', ++ 'h5py', ++ 'hdmf', ++ 'numpy', ++ 'pandas', ++ 'python-dateutil', + 'setuptools' + ] + diff --git a/dev-python/heudiconv/files/pynwb-2.1.0-versions.patch b/dev-python/heudiconv/files/pynwb-2.1.0-versions.patch new file mode 100644 index 000000000..8c816d226 --- /dev/null +++ b/dev-python/heudiconv/files/pynwb-2.1.0-versions.patch @@ -0,0 +1,21 @@ +diff --git a/setup.py b/tmp/setup.py +index 39e75824..f7948f64 100755 +--- a/setup.py ++++ b/setup.py +@@ -19,11 +19,11 @@ print('found these packages:', pkgs) + schema_dir = 'nwb-schema/core' + + reqs = [ +- 'h5py>=2.10,<4', +- 'hdmf>=3.3.2,<4', +- 'numpy>=1.16,<1.23', +- 'pandas>=1.0.5,<2', +- 'python-dateutil>=2.7,<3', ++ 'h5py', ++ 'hdmf', ++ 'numpy', ++ 'pandas', ++ 'python-dateutil', + 'setuptools' + ] + diff --git a/dev-python/heudiconv/files/pynwb-2.2.0-versions.patch b/dev-python/heudiconv/files/pynwb-2.2.0-versions.patch new file mode 100644 index 000000000..6141f629a --- /dev/null +++ b/dev-python/heudiconv/files/pynwb-2.2.0-versions.patch @@ -0,0 +1,21 @@ +diff --git a/setup.py b/tmp/setup.py +index 39e75824..f7948f64 100755 +--- a/setup.py ++++ b/setup.py +@@ -19,11 +19,11 @@ print('found these packages:', pkgs) + schema_dir = 'nwb-schema/core' + + reqs = [ +- 'h5py>=2.10,<4', +- 'hdmf>=3.4.2,<4', +- 'numpy>=1.16,<1.24', +- 'pandas>=1.1.5,<2', +- 'python-dateutil>=2.7.3,<3', ++ 'h5py', ++ 'hdmf', ++ 'numpy', ++ 'pandas', ++ 'python-dateutil', + 'setuptools' + ] + diff --git a/dev-python/heudiconv/heudiconv-0.11.6.ebuild b/dev-python/heudiconv/heudiconv-0.11.6.ebuild new file mode 100644 index 000000000..6c3c6b59d --- /dev/null +++ b/dev-python/heudiconv/heudiconv-0.11.6.ebuild @@ -0,0 +1,51 @@ +# Copyright 1999-2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +DISTUTILS_USE_PEP517=setuptools +PYTHON_COMPAT=( python3_10 ) +inherit distutils-r1 + +DESCRIPTION="Flexible DICOM conversion to structured directory layouts" +HOMEPAGE=" + https://github.com/nipy/heudiconv + https://heudiconv.readthedocs.io/en/latest/ +" +SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz" + +SLOT="0" +LICENSE="Apache-2.0" +KEYWORDS="~amd64 ~x86" + +RDEPEND=" + sci-libs/nibabel[${PYTHON_USEDEP}] + sci-libs/pydicom[${PYTHON_USEDEP}] + sci-libs/nipype[${PYTHON_USEDEP}] + sci-biology/dcmstack[${PYTHON_USEDEP}] + dev-python/filelock[${PYTHON_USEDEP}] + dev-python/versioningit[${PYTHON_USEDEP}] + " +BDEPEND=" + test? ( + dev-python/six[${PYTHON_USEDEP}] + ) +" + +# Reported upstream: +# https://github.com/nipy/heudiconv/issues/627 +EPYTEST_DESELECT=( + "heudiconv/tests/test_convert.py::test_b0dwi_for_fmap" + "heudiconv/tests/test_dicoms.py::test_embed_dicom_and_nifti_metadata" + "heudiconv/tests/test_heuristics.py::test_reproin_largely_smoke" + "heudiconv/tests/test_heuristics.py::test_scans_keys_reproin" + "heudiconv/tests/test_heuristics.py::test_scout_conversion" + "heudiconv/tests/test_heuristics.py::test_notop[bidsoptions0]" + "heudiconv/tests/test_heuristics.py::test_notop[bidsoptions1]" + "heudiconv/tests/test_heuristics.py::test_phoenix_doc_conversion" + "heudiconv/tests/test_main.py::test_prepare_for_datalad" + "heudiconv/tests/test_main.py::test_cache" + "heudiconv/tests/test_regression.py::test_grouping[merged]" +) + +distutils_enable_tests pytest diff --git a/dev-python/heudiconv/metadata.xml b/dev-python/heudiconv/metadata.xml new file mode 100644 index 000000000..a98cbf459 --- /dev/null +++ b/dev-python/heudiconv/metadata.xml @@ -0,0 +1,16 @@ +<?xml version='1.0' encoding='UTF-8'?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="person"> + <email>gen...@chymera.eu</email> + <name>Horea Christian</name> + </maintainer> + <maintainer type="project"> + <email>s...@gentoo.org</email> + <name>Gentoo Science Project</name> + </maintainer> + <upstream> + <remote-id type="pypi">heudiconv</remote-id> + <remote-id type="github">nipy/heudiconv</remote-id> + </upstream> +</pkgmetadata>