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

[Andrew Ammerlaan]

commit:     252693b1a06c119a2efe40661b957fb6d10c0ed5
Author:     Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
AuthorDate: Tue Jan  3 18:15:06 2023 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
CommitDate: Tue Jan  3 18:15:12 2023 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=252693b1

dev-python/pynwb: treeclean

dep sci-libs/hdf5[ros3(-)] unavailable

Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> gentoo.org>

 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 deletions(-)

diff --git a/dev-python/pynwb/files/pynwb-2.0.0-versions.patch b/dev-python/pynwb/files/pynwb-2.0.0-versions.patch
deleted file mode 100644
index d09c50594..000000000
--- a/dev-python/pynwb/files/pynwb-2.0.0-versions.patch
+++ /dev/null
@@ -1,21 +0,0 @@
-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
deleted file mode 100644
index 8c816d226..000000000
--- a/dev-python/pynwb/files/pynwb-2.1.0-versions.patch
+++ /dev/null
@@ -1,21 +0,0 @@
-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
deleted file mode 100644
index 6141f629a..000000000
--- a/dev-python/pynwb/files/pynwb-2.2.0-versions.patch
+++ /dev/null
@@ -1,21 +0,0 @@
-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
deleted file mode 100644
index 1e30097b2..000000000
--- a/dev-python/pynwb/metadata.xml
+++ /dev/null
@@ -1,24 +0,0 @@
-<?xml version='1.0' encoding='UTF-8'?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>gentoo@×××××××.eu</email>
-		<name>Horea Christian</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci@g.o</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
deleted file mode 100644
index 3fe21370f..000000000
--- a/dev-python/pynwb/pynwb-2.0.1.ebuild
+++ /dev/null
@@ -1,39 +0,0 @@
-# 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
deleted file mode 100644
index c24dae23a..000000000
--- a/dev-python/pynwb/pynwb-2.1.0-r1.ebuild
+++ /dev/null
@@ -1,43 +0,0 @@
-# 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
deleted file mode 100644
index 6ea595a8f..000000000
--- a/dev-python/pynwb/pynwb-2.2.0.ebuild
+++ /dev/null
@@ -1,57 +0,0 @@
-# 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