commit: 67e6080551c80d384ee79713470e20396317a8f1
Author: Horea Christian <chr <AT> chymera <DOT> eu>
AuthorDate: Mon Jan 31 08:15:27 2022 +0000
Commit: Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Mon Jan 31 08:15:27 2022 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=67e60805
dev-python/pynwb: new package (DANDI stack)
Package-Manager: Portage-3.0.30, Repoman-3.0.3
Signed-off-by: Horea Christian <chr <AT> chymera.eu>
dev-python/pynwb/ChangeLog | 6 +++
dev-python/pynwb/files/pynwb-2.0.0-versions.patch | 21 ++++++++++
dev-python/pynwb/metadata.xml | 20 ++++++++++
dev-python/pynwb/pynwb-2.0.0.ebuild | 46 ++++++++++++++++++++++
dev-python/pynwb/pynwb-2.0.0_p0.ebuild | 47 +++++++++++++++++++++++
5 files changed, 140 insertions(+)
diff --git a/dev-python/pynwb/ChangeLog b/dev-python/pynwb/ChangeLog
new file mode 100644
index 000000000..1eee46e49
--- /dev/null
+++ b/dev-python/pynwb/ChangeLog
@@ -0,0 +1,6 @@
+*pynwb-2.0.0_p0 (31 Jan 2022)
+
+ 31 Jan 2022; <chym...@gentoo.org> +files/pynwb-2.0.0-versions.patch,
+ +pynwb-2.0.0_p0.ebuild, pynwb-2.0.0.ebuild:
+ dev-python/pynwb: version bump and test skip linking skipped test reports on
+ upstream issue treacker
diff --git a/dev-python/pynwb/files/pynwb-2.0.0-versions.patch
b/dev-python/pynwb/files/pynwb-2.0.0-versions.patch
new file mode 100644
index 000000000..d09c50594
--- /dev/null
+++ b/dev-python/pynwb/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/pynwb/metadata.xml b/dev-python/pynwb/metadata.xml
new file mode 100644
index 000000000..99512b574
--- /dev/null
+++ b/dev-python/pynwb/metadata.xml
@@ -0,0 +1,20 @@
+<?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>
+ <longdescription lang="en">
+ PyNWB is a Python package for working with NWB files. It
provides a
+ high-level API for efficiently working with Neurodata stored in
the NWB
+ format. Neurodata Without Borders: Neurophysiology (NWB:N) is a
project
+ to develop a unified data format for cellular-based
neurophysiology
+ data, focused on the dynamics of groups of neurons measured
under a
+ large range of experimental conditions.
+ </longdescription>
+</pkgmetadata>
diff --git a/dev-python/pynwb/pynwb-2.0.0.ebuild
b/dev-python/pynwb/pynwb-2.0.0.ebuild
new file mode 100644
index 000000000..b0294a4e0
--- /dev/null
+++ b/dev-python/pynwb/pynwb-2.0.0.ebuild
@@ -0,0 +1,46 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{8..10} )
+inherit distutils-r1
+
+DESCRIPTION="A Python API for working with Neurodata stored in the NWB Format "
+HOMEPAGE="https://github.com/NeurodataWithoutBorders/pynwb";
+SRC_URI="https://github.com/NeurodataWithoutBorders/pynwb/releases/download/${PV}/${P}.tar.gz";
+
+SLOT="0"
+LICENSE="BSD"
+KEYWORDS="~amd64 ~x86"
+
+RDEPEND="
+ sci-libs/hdf5[ros3]
+ dev-python/hdmf[${PYTHON_USEDEP}]
+ dev-python/h5py[${PYTHON_USEDEP}]
+ dev-python/numpy[${PYTHON_USEDEP}]
+ dev-python/pandas[${PYTHON_USEDEP}]
+ dev-python/python-dateutil[${PYTHON_USEDEP}]
+ "
+BDEPEND=""
+
+PATCHES=(
+ "${FILESDIR}/${P}-versions.patch"
+ )
+
+EPYTEST_DESELECT=(
+ # Reported upsream:
+ # https://github.com/dandi/dandischema/issues/87
+
tests/validation/test_validate.py::TestValidateScript::test_validate_file_cached
+
tests/validation/test_validate.py::TestValidateScript::test_validate_file_cached_bad_ns
+
tests/validation/test_validate.py::TestValidateScript::test_validate_file_cached_hdmf_common
+
tests/validation/test_validate.py::TestValidateScript::test_validate_file_cached_ignore
+
tests/validation/test_validate.py::TestValidateScript::test_validate_file_no_cache
+
tests/validation/test_validate.py::TestValidateScript::test_validate_file_no_cache_bad_ns
+ # Reported upstream and fixed in newer version:
+ #
https://github.com/NeurodataWithoutBorders/pynwb/issues/1412#issuecomment-934153799
+ tests/integration/ros3/test_ros3.py::TestRos3Streaming::test_dandi_read
+ tests/integration/ros3/test_ros3.py::TestRos3Streaming::test_read
+)
+
+distutils_enable_tests pytest
diff --git a/dev-python/pynwb/pynwb-2.0.0_p0.ebuild
b/dev-python/pynwb/pynwb-2.0.0_p0.ebuild
new file mode 100644
index 000000000..fba3e6319
--- /dev/null
+++ b/dev-python/pynwb/pynwb-2.0.0_p0.ebuild
@@ -0,0 +1,47 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{8..10} )
+inherit distutils-r1
+
+MY_PV="${PV/_p/.post}.dev5"
+MY_P="${PN}-${MY_PV}"
+
+DESCRIPTION="A Python API for working with Neurodata stored in the NWB Format "
+HOMEPAGE="https://github.com/NeurodataWithoutBorders/pynwb";
+SRC_URI="https://github.com/NeurodataWithoutBorders/pynwb/releases/download/latest/${MY_P}.tar.gz";
+
+SLOT="0"
+LICENSE="BSD"
+KEYWORDS="~amd64 ~x86"
+
+RDEPEND="
+ sci-libs/hdf5[ros3]
+ dev-python/hdmf[${PYTHON_USEDEP}]
+ dev-python/h5py[${PYTHON_USEDEP}]
+ dev-python/numpy[${PYTHON_USEDEP}]
+ dev-python/pandas[${PYTHON_USEDEP}]
+ dev-python/python-dateutil[${PYTHON_USEDEP}]
+ "
+BDEPEND=""
+
+PATCHES=(
+ "${FILESDIR}/${PN}-2.0.0-versions.patch"
+ )
+
+S="${WORKDIR}/${MY_P}"
+
+EPYTEST_DESELECT=(
+ # Reported upsream
+ # https://github.com/dandi/dandischema/issues/87
+
tests/validation/test_validate.py::TestValidateScript::test_validate_file_cached
+
tests/validation/test_validate.py::TestValidateScript::test_validate_file_cached_bad_ns
+
tests/validation/test_validate.py::TestValidateScript::test_validate_file_cached_hdmf_common
+
tests/validation/test_validate.py::TestValidateScript::test_validate_file_cached_ignore
+
tests/validation/test_validate.py::TestValidateScript::test_validate_file_no_cache
+
tests/validation/test_validate.py::TestValidateScript::test_validate_file_no_cache_bad_ns
+)
+
+distutils_enable_tests pytest
