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

["Horea Christian" <horea.christ@gmail.com>]

commit:     16797f5b3289b8970625b8c03645e9a6a5fcaa04
Author:     Horea Christian <chr <AT> chymera <DOT> eu>
AuthorDate: Wed Mar 22 19:39:12 2023 +0000
Commit:     Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Wed Mar 22 19:39:12 2023 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=16797f5b

dev-python/pynwb: add 2.3.1

Signed-off-by: Horea Christian <chr <AT> chymera.eu>

 dev-python/pynwb/files/pynwb-2.3.1-typing.patch | 13 +++++++
 dev-python/pynwb/pynwb-2.3.1.ebuild             | 50 +++++++++++++++++++++++++
 2 files changed, 63 insertions(+)

diff --git a/dev-python/pynwb/files/pynwb-2.3.1-typing.patch b/dev-python/pynwb/files/pynwb-2.3.1-typing.patch
new file mode 100644
index 000000000..e672f243b
--- /dev/null
+++ b/dev-python/pynwb/files/pynwb-2.3.1-typing.patch
@@ -0,0 +1,13 @@
+diff --git a/src/pynwb/ophys.py b/src/pynwb/ophys.py
+index b09267ff6..e3d9f8f6d 100644
+--- a/src/pynwb/ophys.py
++++ b/src/pynwb/ophys.py
+@@ -192,7 +192,7 @@ def __init__(self, **kwargs):
+         args_to_set = popargs_to_dict(keys_to_set, kwargs)
+         super().__init__(**kwargs)
+ 
+-        if args_to_set["binning"] < 0:
++        if args_to_set["binning"] is not None and args_to_set["binning"] < 0:
+             raise ValueError(f"Binning value must be >= 0: {args_to_set['binning']}")
+         if isinstance(args_to_set["binning"], int):
+             args_to_set["binning"] = np.uint(args_to_set["binning"])

diff --git a/dev-python/pynwb/pynwb-2.3.1.ebuild b/dev-python/pynwb/pynwb-2.3.1.ebuild
new file mode 100644
index 000000000..cce90c5d1
--- /dev/null
+++ b/dev-python/pynwb/pynwb-2.3.1.ebuild
@@ -0,0 +1,50 @@
+# 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..11} )
+inherit distutils-r1 pypi
+
+DESCRIPTION="A Python API for working with Neurodata stored in the NWB Format "
+HOMEPAGE="https://github.com/NeurodataWithoutBorders/pynwb"
+SRC_URI="$(pypi_sdist_url pynwb)"
+
+SLOT="0"
+LICENSE="BSD"
+KEYWORDS="~amd64 ~x86"
+
+RDEPEND="
+	>=sci-libs/hdf5-1.12.2
+	>=dev-python/hdmf-3.3.2[${PYTHON_USEDEP}]
+	dev-python/h5py[${PYTHON_USEDEP}]
+	dev-python/numpy[${PYTHON_USEDEP}]
+	dev-python/pandas[${PYTHON_USEDEP}]
+	dev-python/python-dateutil[${PYTHON_USEDEP}]
+	"
+BDEPEND=""
+
+# Remove in next release
+PATCHES=(
+	"${FILESDIR}/${P}-typing.patch"
+	)
+
+EPYTEST_DESELECT=(
+	# Reported upsream:
+	# https://github.com/NeurodataWithoutBorders/pynwb/issues/1580
+	tests/validation/test_validate.py::TestValidateCLI::test_validate_file_cached
+	tests/validation/test_validate.py::TestValidateCLI::test_validate_file_cached_bad_ns
+	tests/validation/test_validate.py::TestValidateCLI::test_validate_file_cached_core
+	tests/validation/test_validate.py::TestValidateCLI::test_validate_file_cached_extension
+	tests/validation/test_validate.py::TestValidateCLI::test_validate_file_cached_extension_pass_ns
+	tests/validation/test_validate.py::TestValidateCLI::test_validate_file_cached_hdmf_common
+	tests/validation/test_validate.py::TestValidateCLI::test_validate_file_cached_ignore
+	tests/validation/test_validate.py::TestValidateCLI::test_validate_file_invalid
+	tests/validation/test_validate.py::TestValidateCLI::test_validate_file_list_namespaces_core
+	tests/validation/test_validate.py::TestValidateCLI::test_validate_file_list_namespaces_extension
+	tests/validation/test_validate.py::TestValidateCLI::test_validate_file_no_cache
+	tests/validation/test_validate.py::TestValidateCLI::test_validate_file_no_cache_bad_ns
+)
+
+distutils_enable_tests pytest