dev-python/pynwb: new package (DANDI stack)

Package-Manager: Portage-3.0.30, Repoman-3.0.3
Signed-off-by: Horea Christian <chr@chymera.eu>

6 files changed, 142 insertions, 0 deletions

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;  <chymera@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/Manifest b/dev-python/pynwb/Manifest
new file mode 100644
index 000000000..16b7c7287
--- /dev/null
+++ b/dev-python/pynwb/Manifest
@@ -0,0 +1,2 @@
+DIST pynwb-2.0.0.post0.dev5.tar.gz 450799 BLAKE2B 02aef74992dda44139e776eebf3d29924caa46bfc2a12da400ceaadff5856295b6205c6ad230483935e713eed9dd868b9109c2d51d7c69291dc93db806ef4761 SHA512 840a33cd0a2de5c491e785530e4dab589945015b9a60384ed127a27fbfe4c527b1b10d74a9ffe2a795a29c3bba65aafd007975973a2da68fca73bf71260b7b8b
+DIST pynwb-2.0.0.tar.gz 450082 BLAKE2B 3bfd17b8cbe5f12992630bc5a97144dbc7b3d583238e1fe0d59576029ae7a30acbd05b7af18ca89d6cba389df1bf543c97e75e83e04aeb4a4e44c4cd1a26be9d SHA512 4afc319fd9cce0c1e81589236237f9a28b69dd846d96849ae5cc554287a6dd124fd421f700736dbb714cfbe6f260e79f374d1dd63ee92c2776f5173654d61f9a
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>gentoo@chymera.eu</email>
+		<name>Horea Christian</name>
+	</maintainer>
+	<maintainer type="project">
+		<email>sci@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