dev-python/pynwb: reinstating package

This reverts commit 252693b1a06c119a2efe40661b957fb6d10c0ed5.

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

8 files changed, 229 insertions, 0 deletions

diff --git a/dev-python/pynwb/Manifest b/dev-python/pynwb/Manifest
new file mode 100644
index 000000000..3a1d1f7a9
--- /dev/null
+++ b/dev-python/pynwb/Manifest
@@ -0,0 +1,3 @@
+DIST pynwb-2.0.1.tar.gz 452718 BLAKE2B d29347d748bd37bdf9326e0f9cc88b84742714ba78e6b0c56a923a4dd723c94e69ab3f325b5a5c66aef3ef819228abd64704268240fbdd369dac41b25e226b43 SHA512 897fa3bce93e733222a94bf9f043ed39c606c29f392f932a21c1004eebc1866d4caf50905a8e59baca87744af04d93e9957a7efb7e775422af5022787c4d086e
+DIST pynwb-2.1.0.tar.gz 459375 BLAKE2B 3645c4cac9a9c8e8726d6a6bf38d1fa8946237c7496fde76162ee5dec66de4d0c86241a7f076d44ce857c8b411a33e9e52af47c1c5e74cf4eb84da484950c61c SHA512 11d5b23809de1e5b13baf4d02420200baf215aa99237b8e747a9d401830bef5356306eb7f9a464be36e88e64e8c50018606102b126daa450a7ee624c5babb025
+DIST pynwb-2.2.0.tar.gz 582890 BLAKE2B 7bc5774ddeb2144266af5457640d8721c9976d17dbfa9ce2b1027fdc736ca185935eb0f908aa7f4ad6c42df0c1e64f18221db6203f194f65493e9c61694a6ee0 SHA512 49e50be6be1856330abc87cc6621f94f7bddfd742bc024cddf31f4d693d8bce68e23839ae9a0dd76602a70b44b9e46019e05840c7840c4fccf5c9ffb6b4bfd57
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/files/pynwb-2.1.0-versions.patch b/dev-python/pynwb/files/pynwb-2.1.0-versions.patch
new file mode 100644
index 000000000..8c816d226
--- /dev/null
+++ b/dev-python/pynwb/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/pynwb/files/pynwb-2.2.0-versions.patch b/dev-python/pynwb/files/pynwb-2.2.0-versions.patch
new file mode 100644
index 000000000..6141f629a
--- /dev/null
+++ b/dev-python/pynwb/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/pynwb/metadata.xml b/dev-python/pynwb/metadata.xml
new file mode 100644
index 000000000..1e30097b2
--- /dev/null
+++ b/dev-python/pynwb/metadata.xml
@@ -0,0 +1,24 @@
+<?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>
+	<upstream>
+		<remote-id type="pypi">pynwb</remote-id>
+		<remote-id type="github">NeurodataWithoutBorders/pynwb</remote-id>
+	</upstream>
+</pkgmetadata>
diff --git a/dev-python/pynwb/pynwb-2.0.1.ebuild b/dev-python/pynwb/pynwb-2.0.1.ebuild
new file mode 100644
index 000000000..3fe21370f
--- /dev/null
+++ b/dev-python/pynwb/pynwb-2.0.1.ebuild
@@ -0,0 +1,39 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DISTUTILS_USE_PEP517=setuptools
+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="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
+
+SLOT="0"
+LICENSE="BSD"
+KEYWORDS="~amd64 ~x86"
+
+RDEPEND="
+	sci-libs/hdf5[ros3(-)]
+	<dev-python/hdmf-3.3.2[${PYTHON_USEDEP}]
+	dev-python/h5py[${PYTHON_USEDEP}]
+	dev-python/numpy[${PYTHON_USEDEP}]
+	dev-python/pandas[${PYTHON_USEDEP}]
+	dev-python/python-dateutil[${PYTHON_USEDEP}]
+	"
+BDEPEND=""
+
+EPYTEST_DESELECT=(
+	# Reported upsream:
+	# https://github.com/NeurodataWithoutBorders/pynwb/issues/1425
+	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
diff --git a/dev-python/pynwb/pynwb-2.1.0-r1.ebuild b/dev-python/pynwb/pynwb-2.1.0-r1.ebuild
new file mode 100644
index 000000000..c24dae23a
--- /dev/null
+++ b/dev-python/pynwb/pynwb-2.1.0-r1.ebuild
@@ -0,0 +1,43 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DISTUTILS_USE_PEP517=setuptools
+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="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
+
+SLOT="0"
+LICENSE="BSD"
+KEYWORDS="~amd64 ~x86"
+
+RDEPEND="
+	sci-libs/hdf5[ros3(-)]
+	>=dev-python/hdmf-3.3.2[${PYTHON_USEDEP}]
+	dev-python/h5py[${PYTHON_USEDEP}]
+	dev-python/numpy[${PYTHON_USEDEP}]
+	dev-python/pandas[${PYTHON_USEDEP}]
+	dev-python/python-dateutil[${PYTHON_USEDEP}]
+	"
+BDEPEND=""
+
+PATCHES=(
+	"${FILESDIR}/${P}-versions.patch"
+	)
+
+EPYTEST_DESELECT=(
+	# Reported upsream:
+	# https://github.com/NeurodataWithoutBorders/pynwb/issues/1425
+	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
diff --git a/dev-python/pynwb/pynwb-2.2.0.ebuild b/dev-python/pynwb/pynwb-2.2.0.ebuild
new file mode 100644
index 000000000..6ea595a8f
--- /dev/null
+++ b/dev-python/pynwb/pynwb-2.2.0.ebuild
@@ -0,0 +1,57 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DISTUTILS_USE_PEP517=setuptools
+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="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
+
+SLOT="0"
+LICENSE="BSD"
+KEYWORDS="~amd64 ~x86"
+
+RDEPEND="
+	sci-libs/hdf5[ros3(-)]
+	>=dev-python/hdmf-3.3.2[${PYTHON_USEDEP}]
+	dev-python/h5py[${PYTHON_USEDEP}]
+	dev-python/numpy[${PYTHON_USEDEP}]
+	dev-python/pandas[${PYTHON_USEDEP}]
+	dev-python/python-dateutil[${PYTHON_USEDEP}]
+	"
+BDEPEND=""
+
+PATCHES=(
+	"${FILESDIR}/${P}-versions.patch"
+	)
+
+EPYTEST_DESELECT=(
+	# Reported upsream:
+	# https://github.com/NeurodataWithoutBorders/pynwb/issues/1580
+	tests/back_compat/test_read.py::TestReadOldVersions::test_read
+	tests/back_compat/test_read.py::TestReadOldVersions::test_read_imageseries_non_external_format
+	tests/back_compat/test_read.py::TestReadOldVersions::test_read_imageseries_nonmatch_starting_frame
+	tests/unit/test_image.py::ImageSeriesConstructor::test_external_file_with_data
+	tests/unit/test_image.py::ImageSeriesConstructor::test_external_file_with_data_construct_mode
+	tests/unit/test_image.py::ImageSeriesConstructor::test_external_file_with_incorrect_format
+	tests/unit/test_image.py::ImageSeriesConstructor::test_external_file_with_incorrect_format_construct_mode
+	tests/unit/test_image.py::ImageSeriesConstructor::test_external_file_with_incorrect_starting_frame
+	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