* [gentoo-commits] proj/sci:master commit in: dev-python/pynwb/files/, dev-python/pynwb/
@ 2022-01-31 8:15 Horea Christian
0 siblings, 0 replies; 5+ messages in thread
From: Horea Christian @ 2022-01-31 8:15 UTC (permalink / raw
To: gentoo-commits
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; <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/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
^ permalink raw reply related [flat|nested] 5+ messages in thread
* [gentoo-commits] proj/sci:master commit in: dev-python/pynwb/files/, dev-python/pynwb/
@ 2022-07-19 4:58 Horea Christian
0 siblings, 0 replies; 5+ messages in thread
From: Horea Christian @ 2022-07-19 4:58 UTC (permalink / raw
To: gentoo-commits
commit: 5ec641ea8274723cbc1b13a0144201b3a6de2623
Author: Horea Christian <chr <AT> chymera <DOT> eu>
AuthorDate: Tue Jul 19 04:57:49 2022 +0000
Commit: Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Tue Jul 19 04:57:49 2022 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=5ec641ea
dev-python/pynwb: patched upstream versioncheck
Package-Manager: Portage-3.0.30, Repoman-3.0.3
Signed-off-by: Horea Christian <chr <AT> chymera.eu>
dev-python/pynwb/files/pynwb-2.1.0-versions.patch | 21 +++++++++++++++++++++
.../{pynwb-2.1.0.ebuild => pynwb-2.1.0-r1.ebuild} | 4 ++++
2 files changed, 25 insertions(+)
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/pynwb-2.1.0.ebuild b/dev-python/pynwb/pynwb-2.1.0-r1.ebuild
similarity index 96%
rename from dev-python/pynwb/pynwb-2.1.0.ebuild
rename to dev-python/pynwb/pynwb-2.1.0-r1.ebuild
index a53c4bbb0..c24dae23a 100644
--- a/dev-python/pynwb/pynwb-2.1.0.ebuild
+++ b/dev-python/pynwb/pynwb-2.1.0-r1.ebuild
@@ -25,6 +25,10 @@ RDEPEND="
"
BDEPEND=""
+PATCHES=(
+ "${FILESDIR}/${P}-versions.patch"
+ )
+
EPYTEST_DESELECT=(
# Reported upsream:
# https://github.com/NeurodataWithoutBorders/pynwb/issues/1425
^ permalink raw reply related [flat|nested] 5+ messages in thread
* [gentoo-commits] proj/sci:master commit in: dev-python/pynwb/files/, dev-python/pynwb/
@ 2022-11-02 21:10 Horea Christian
0 siblings, 0 replies; 5+ messages in thread
From: Horea Christian @ 2022-11-02 21:10 UTC (permalink / raw
To: gentoo-commits
commit: 299f323d9a54d449992ea9156fc0004d15cf934b
Author: Horea Christian <chr <AT> chymera <DOT> eu>
AuthorDate: Wed Nov 2 21:09:45 2022 +0000
Commit: Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Wed Nov 2 21:09:45 2022 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=299f323d
dev-python/pynwb: add 2.2.0
Signed-off-by: Horea Christian <chr <AT> chymera.eu>
dev-python/pynwb/files/pynwb-2.2.0-versions.patch | 21 +++++++++
dev-python/pynwb/pynwb-2.2.0.ebuild | 57 +++++++++++++++++++++++
2 files changed, 78 insertions(+)
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/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
^ permalink raw reply related [flat|nested] 5+ messages in thread
* [gentoo-commits] proj/sci:master commit in: dev-python/pynwb/files/, dev-python/pynwb/
@ 2023-01-03 18:16 Andrew Ammerlaan
0 siblings, 0 replies; 5+ messages in thread
From: Andrew Ammerlaan @ 2023-01-03 18:16 UTC (permalink / raw
To: gentoo-commits
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@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
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
^ permalink raw reply related [flat|nested] 5+ messages in thread
* [gentoo-commits] proj/sci:master commit in: dev-python/pynwb/files/, dev-python/pynwb/
@ 2023-03-25 3:08 Horea Christian
0 siblings, 0 replies; 5+ messages in thread
From: Horea Christian @ 2023-03-25 3:08 UTC (permalink / raw
To: gentoo-commits
commit: 5017407dd9e589abb913af53da82de7e487e6114
Author: Horea Christian <chr <AT> chymera <DOT> eu>
AuthorDate: Sat Mar 25 03:07:12 2023 +0000
Commit: Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Sat Mar 25 03:07:12 2023 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=5017407d
dev-python/pynwb: revbump for deprecated pkg_resources
Signed-off-by: Horea Christian <chr <AT> chymera.eu>
.../df0f7ed71defb8d12a7ff72746b93211304c4d4b.patch | 54 ++++++++++++++++++++++
.../pynwb/files/pynwb-2.3.1-pkg_resources.patch | 54 ++++++++++++++++++++++
dev-python/pynwb/pynwb-2.3.1-r1.ebuild | 51 ++++++++++++++++++++
3 files changed, 159 insertions(+)
diff --git a/dev-python/pynwb/files/df0f7ed71defb8d12a7ff72746b93211304c4d4b.patch b/dev-python/pynwb/files/df0f7ed71defb8d12a7ff72746b93211304c4d4b.patch
new file mode 100644
index 000000000..bf496b900
--- /dev/null
+++ b/dev-python/pynwb/files/df0f7ed71defb8d12a7ff72746b93211304c4d4b.patch
@@ -0,0 +1,54 @@
+From df0f7ed71defb8d12a7ff72746b93211304c4d4b Mon Sep 17 00:00:00 2001
+From: rly <rly@lbl.gov>
+Date: Fri, 24 Mar 2023 10:17:13 -0700
+Subject: [PATCH] Fix deprecation warning with pkg_resources
+
+---
+ src/pynwb/__init__.py | 14 +++++++++++---
+ tests/back_compat/test_import_structure.py | 1 -
+ 2 files changed, 11 insertions(+), 4 deletions(-)
+
+diff --git a/src/pynwb/__init__.py b/src/pynwb/__init__.py
+index 2df273d43..023cda237 100644
+--- a/src/pynwb/__init__.py
++++ b/src/pynwb/__init__.py
+@@ -15,16 +15,24 @@
+ import hdmf.common
+
+ CORE_NAMESPACE = 'core'
+-__core_ns_file_name = 'nwb.namespace.yaml'
+
+ from .spec import NWBDatasetSpec, NWBGroupSpec, NWBNamespace # noqa E402
+ from .validate import validate # noqa: F401, E402
+
+
+ def __get_resources():
+- from pkg_resources import resource_filename
++ try:
++ from importlib.resources import files
++ except ImportError:
++ # TODO: Remove when python 3.9 becomes the new minimum
++ from importlib_resources import files
++
++ __location_of_this_file = files(__name__)
++ __core_ns_file_name = 'nwb.namespace.yaml'
++ __schema_dir = 'nwb-schema/core'
++
+ ret = dict()
+- ret['namespace_path'] = os.path.join(resource_filename(__name__, 'nwb-schema/core'), __core_ns_file_name)
++ ret['namespace_path'] = str(__location_of_this_file / __schema_dir / __core_ns_file_name)
+ return ret
+
+
+diff --git a/tests/back_compat/test_import_structure.py b/tests/back_compat/test_import_structure.py
+index dba11a48a..e5f931f5d 100644
+--- a/tests/back_compat/test_import_structure.py
++++ b/tests/back_compat/test_import_structure.py
+@@ -34,7 +34,6 @@ def test_outer_import_structure(self):
+ "__TYPE_MAP",
+ "__builtins__",
+ "__cached__",
+- "__core_ns_file_name",
+ "__doc__",
+ "__file__",
+ "__get_resources",
diff --git a/dev-python/pynwb/files/pynwb-2.3.1-pkg_resources.patch b/dev-python/pynwb/files/pynwb-2.3.1-pkg_resources.patch
new file mode 100644
index 000000000..bf496b900
--- /dev/null
+++ b/dev-python/pynwb/files/pynwb-2.3.1-pkg_resources.patch
@@ -0,0 +1,54 @@
+From df0f7ed71defb8d12a7ff72746b93211304c4d4b Mon Sep 17 00:00:00 2001
+From: rly <rly@lbl.gov>
+Date: Fri, 24 Mar 2023 10:17:13 -0700
+Subject: [PATCH] Fix deprecation warning with pkg_resources
+
+---
+ src/pynwb/__init__.py | 14 +++++++++++---
+ tests/back_compat/test_import_structure.py | 1 -
+ 2 files changed, 11 insertions(+), 4 deletions(-)
+
+diff --git a/src/pynwb/__init__.py b/src/pynwb/__init__.py
+index 2df273d43..023cda237 100644
+--- a/src/pynwb/__init__.py
++++ b/src/pynwb/__init__.py
+@@ -15,16 +15,24 @@
+ import hdmf.common
+
+ CORE_NAMESPACE = 'core'
+-__core_ns_file_name = 'nwb.namespace.yaml'
+
+ from .spec import NWBDatasetSpec, NWBGroupSpec, NWBNamespace # noqa E402
+ from .validate import validate # noqa: F401, E402
+
+
+ def __get_resources():
+- from pkg_resources import resource_filename
++ try:
++ from importlib.resources import files
++ except ImportError:
++ # TODO: Remove when python 3.9 becomes the new minimum
++ from importlib_resources import files
++
++ __location_of_this_file = files(__name__)
++ __core_ns_file_name = 'nwb.namespace.yaml'
++ __schema_dir = 'nwb-schema/core'
++
+ ret = dict()
+- ret['namespace_path'] = os.path.join(resource_filename(__name__, 'nwb-schema/core'), __core_ns_file_name)
++ ret['namespace_path'] = str(__location_of_this_file / __schema_dir / __core_ns_file_name)
+ return ret
+
+
+diff --git a/tests/back_compat/test_import_structure.py b/tests/back_compat/test_import_structure.py
+index dba11a48a..e5f931f5d 100644
+--- a/tests/back_compat/test_import_structure.py
++++ b/tests/back_compat/test_import_structure.py
+@@ -34,7 +34,6 @@ def test_outer_import_structure(self):
+ "__TYPE_MAP",
+ "__builtins__",
+ "__cached__",
+- "__core_ns_file_name",
+ "__doc__",
+ "__file__",
+ "__get_resources",
diff --git a/dev-python/pynwb/pynwb-2.3.1-r1.ebuild b/dev-python/pynwb/pynwb-2.3.1-r1.ebuild
new file mode 100644
index 000000000..9f5f42370
--- /dev/null
+++ b/dev-python/pynwb/pynwb-2.3.1-r1.ebuild
@@ -0,0 +1,51 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DISTUTILS_USE_PEP517=setuptools
+PYTHON_COMPAT=( python3_{10..11} )
+inherit distutils-r1 pypi
+
+DESCRIPTION="A Python API for working with Neurodata stored in the NWB Format "
+HOMEPAGE="https://github.com/NeurodataWithoutBorders/pynwb"
+SRC_URI="$(pypi_sdist_url pynwb)"
+
+SLOT="0"
+LICENSE="BSD"
+KEYWORDS="~amd64 ~x86"
+
+RDEPEND="
+ >=sci-libs/hdf5-1.12.2
+ >=dev-python/hdmf-3.3.2[${PYTHON_USEDEP}]
+ dev-python/h5py[${PYTHON_USEDEP}]
+ dev-python/numpy[${PYTHON_USEDEP}]
+ dev-python/pandas[${PYTHON_USEDEP}]
+ dev-python/python-dateutil[${PYTHON_USEDEP}]
+ "
+BDEPEND=""
+
+# Remove in next release
+PATCHES=(
+ "${FILESDIR}/${P}-typing.patch"
+ "${FILESDIR}/${P}-pkg_resources.patch"
+ )
+
+EPYTEST_DESELECT=(
+ # Reported upsream:
+ # https://github.com/NeurodataWithoutBorders/pynwb/issues/1580
+ 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
^ permalink raw reply related [flat|nested] 5+ messages in thread
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