[gentoo-commits] proj/sci:master commit in: dev-python/heudiconv/files/, dev-python/heudiconv/

[Horea Christian]

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>gentoo@×××××××.eu</email>
+		<name>Horea Christian</name>
+	</maintainer>
+	<maintainer type="project">
+		<email>sci@g.o</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>