commit: 56843b9298ba13771fd05ed1b49999a55e13aa81
Author: Horea Christian <chr <AT> chymera <DOT> eu>
AuthorDate: Thu Jan 12 09:35:54 2023 +0000
Commit: Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Thu Jan 12 09:48:19 2023 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=56843b92
dev-python/pynwb: reinstating package
This reverts commit 252693b1a06c119a2efe40661b957fb6d10c0ed5.
Signed-off-by: Horea Christian <chr <AT> chymera.eu>
dev-python/pynwb/files/pynwb-2.0.0-versions.patch | 21 +++++++++
dev-python/pynwb/files/pynwb-2.1.0-versions.patch | 21 +++++++++
dev-python/pynwb/files/pynwb-2.2.0-versions.patch | 21 +++++++++
dev-python/pynwb/metadata.xml | 24 ++++++++++
dev-python/pynwb/pynwb-2.0.1.ebuild | 39 ++++++++++++++++
dev-python/pynwb/pynwb-2.1.0-r1.ebuild | 43 +++++++++++++++++
dev-python/pynwb/pynwb-2.2.0.ebuild | 57 +++++++++++++++++++++++
7 files changed, 226 insertions(+)
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>[email protected]</email>
+ <name>Horea Christian</name>
+ </maintainer>
+ <maintainer type="project">
+ <email>[email protected]</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
