[gentoo-commits] proj/sci:master commit in: dev-python/hdmf/
commit: 660cac741c12de9ea6e4b98195b2be6a07821f0e
Author: Horea Christian chymera eu>
AuthorDate: Thu Mar 21 21:34:50 2024 +
Commit: Horea Christian gmail com>
CommitDate: Thu Mar 21 22:15:29 2024 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=660cac74
dev-python/hdmf: version and PYTHON_COMPAT bump, treeclean
Signed-off-by: Horea Christian chymera.eu>
.../{hdmf-3.11.0.ebuild => hdmf-3.13.0.ebuild} | 4 +--
dev-python/hdmf/hdmf-3.5.1.ebuild | 28 -
dev-python/hdmf/hdmf-3.5.2.ebuild | 29 --
3 files changed, 2 insertions(+), 59 deletions(-)
diff --git a/dev-python/hdmf/hdmf-3.11.0.ebuild
b/dev-python/hdmf/hdmf-3.13.0.ebuild
similarity index 88%
rename from dev-python/hdmf/hdmf-3.11.0.ebuild
rename to dev-python/hdmf/hdmf-3.13.0.ebuild
index 2463ccc1a..7068afb01 100644
--- a/dev-python/hdmf/hdmf-3.11.0.ebuild
+++ b/dev-python/hdmf/hdmf-3.13.0.ebuild
@@ -4,7 +4,7 @@
EAPI=8
DISTUTILS_USE_PEP517=hatchling
-PYTHON_COMPAT=( python3_{10..11} )
+PYTHON_COMPAT=( python3_{10..12} )
inherit distutils-r1 pypi
DESCRIPTION="The Hierarchical Data Modeling Framework"
@@ -25,7 +25,7 @@ RDEPEND="
"
PATCHES=(
- "${FILESDIR}/${P}-no_test_coverage.patch"
+ "${FILESDIR}/${PN}-3.11.0-no_test_coverage.patch"
)
distutils_enable_tests pytest
diff --git a/dev-python/hdmf/hdmf-3.5.1.ebuild
b/dev-python/hdmf/hdmf-3.5.1.ebuild
deleted file mode 100644
index 883b5b95b..0
--- a/dev-python/hdmf/hdmf-3.5.1.ebuild
+++ /dev/null
@@ -1,28 +0,0 @@
-# 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
-
-DESCRIPTION="The Hierarchical Data Modeling Framework"
-HOMEPAGE="https://github.com/hdmf-dev/hdmf;
-SRC_URI="https://github.com/hdmf-dev/hdmf/releases/download/${PV}/${P}.tar.gz;
-
-SLOT="0"
-LICENSE="BSD"
-KEYWORDS="~amd64 ~x86"
-
-RDEPEND="
- dev-python/h5py[${PYTHON_USEDEP}]
- dev-python/jsonschema[${PYTHON_USEDEP}]
- dev-python/numpy[${PYTHON_USEDEP}]
- dev-python/pandas[${PYTHON_USEDEP}]
- dev-python/ruamel-yaml[${PYTHON_USEDEP}]
- dev-python/scipy[${PYTHON_USEDEP}]
- "
-BDEPEND=""
-
-distutils_enable_tests pytest
diff --git a/dev-python/hdmf/hdmf-3.5.2.ebuild
b/dev-python/hdmf/hdmf-3.5.2.ebuild
deleted file mode 100644
index ee978516e..0
--- a/dev-python/hdmf/hdmf-3.5.2.ebuild
+++ /dev/null
@@ -1,29 +0,0 @@
-# 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="The Hierarchical Data Modeling Framework"
-HOMEPAGE="https://github.com/hdmf-dev/hdmf;
-SRC_URI="$(pypi_sdist_url hdmf)"
-#SRC_URI="https://github.com/hdmf-dev/hdmf/releases/download/${PV}/${P}.tar.gz;
-
-SLOT="0"
-LICENSE="BSD"
-KEYWORDS="~amd64 ~x86"
-
-RDEPEND="
- dev-python/h5py[${PYTHON_USEDEP}]
- dev-python/jsonschema[${PYTHON_USEDEP}]
- dev-python/numpy[${PYTHON_USEDEP}]
- dev-python/pandas[${PYTHON_USEDEP}]
- dev-python/ruamel-yaml[${PYTHON_USEDEP}]
- dev-python/scipy[${PYTHON_USEDEP}]
- "
-BDEPEND=""
-
-distutils_enable_tests pytest
[gentoo-commits] proj/sci:master commit in: dev-python/hdmf-zarr/, dev-python/hdmf-zarr/files/
commit: 5f89fde86285ba2b98d3b026165554b4c0d5d9f2
Author: Horea Christian chymera eu>
AuthorDate: Thu Jan 25 11:28:46 2024 +
Commit: Horea Christian gmail com>
CommitDate: Thu Jan 25 11:28:46 2024 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=5f89fde8
dev-python/hdmf-zarr: new package, add 0.5.0
Signed-off-by: Horea Christian chymera.eu>
.../hdmf-zarr/files/hdmf-zarr-0.5.0-coverage.patch | 28 +++
dev-python/hdmf-zarr/hdmf-zarr-0.5.0.ebuild| 32 ++
dev-python/hdmf-zarr/metadata.xml | 16 +++
3 files changed, 76 insertions(+)
diff --git a/dev-python/hdmf-zarr/files/hdmf-zarr-0.5.0-coverage.patch
b/dev-python/hdmf-zarr/files/hdmf-zarr-0.5.0-coverage.patch
new file mode 100644
index 0..d82c30960
--- /dev/null
+++ b/dev-python/hdmf-zarr/files/hdmf-zarr-0.5.0-coverage.patch
@@ -0,0 +1,28 @@
+diff --git a/pyproject.toml b/pyproject.toml
+index 4008b3b..40e281a 100644
+--- a/pyproject.toml
b/pyproject.toml
+@@ -62,9 +62,6 @@ exclude = [".git_archival.txt"]
+ [tool.hatch.build.targets.wheel]
+ packages = ["src/hdmf_zarr"]
+
+-[tool.pytest.ini_options]
+-addopts = "--cov --cov-report html"
+-
+ [tool.codespell]
+ skip =
"htmlcov,.git,.mypy_cache,.pytest_cache,.coverage,*.pdf,*.svg,venvs,.tox,./docs/_build/*,*.ipynb"
+ ignore-words-list = "datas"
+diff --git a/tox.ini b/tox.ini
+index 720a97f..66d0df3 100644
+--- a/tox.ini
b/tox.ini
+@@ -28,8 +28,7 @@ commands =
+ [testenv:localcoverage]
+ basepython = python3.11
+ commands =
+-pytest --cov=hdmf_zarr
+-coverage html -d tests/coverage/htmlcov
++pytest
+
+ # Test with python 3.11; pinned dev and optional reqs
+ [testenv:py311-optional]
diff --git a/dev-python/hdmf-zarr/hdmf-zarr-0.5.0.ebuild
b/dev-python/hdmf-zarr/hdmf-zarr-0.5.0.ebuild
new file mode 100644
index 0..692197867
--- /dev/null
+++ b/dev-python/hdmf-zarr/hdmf-zarr-0.5.0.ebuild
@@ -0,0 +1,32 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+PYTHON_COMPAT=( python3_{10..11} )
+DISTUTILS_USE_PEP517=hatchling
+
+inherit distutils-r1 pypi
+
+DESCRIPTION="Zarr I/O backend for HDMF"
+HOMEPAGE="https://github.com/hdmf-dev/hdmf-zarr;
+#SRC_URI="https://github.com/hdmf-dev/hdmf-zarr/archive/refs/tags/${PV}.tar.gz
-> ${P}.tar.gz"
+KEYWORDS="~amd64 ~x86"
+
+LICENSE="BSD"
+SLOT="0"
+
+RDEPEND="
+ dev-python/hdmf[${PYTHON_USEDEP}]
+ dev-python/numcodecs[${PYTHON_USEDEP}]
+ dev-python/numpy[${PYTHON_USEDEP}]
+ dev-python/pynwb[${PYTHON_USEDEP}]
+ dev-python/threadpoolctl[${PYTHON_USEDEP}]
+ dev-python/zarr[${PYTHON_USEDEP}]
+"
+DEPEND="${RDEPEND}"
+
+PATCHES=(
+ "${FILESDIR}/${P}-coverage.patch"
+)
+
+distutils_enable_tests pytest
diff --git a/dev-python/hdmf-zarr/metadata.xml
b/dev-python/hdmf-zarr/metadata.xml
new file mode 100644
index 0..1ced471a1
--- /dev/null
+++ b/dev-python/hdmf-zarr/metadata.xml
@@ -0,0 +1,16 @@
+
+http://www.gentoo.org/dtd/metadata.dtd;>
+
+
+ gen...@chymera.eu
+ Horea Christian
+
+
+ s...@gentoo.org
+ Gentoo Science Project
+
+
+ hdmf-dev/hdmf-zarr
+ hdmf-zarr
+
+
[gentoo-commits] proj/sci:master commit in: dev-python/hdmf/files/
commit: 4da1b60b772c1c2a8ede9d728bb8564e3b8352cc
Author: Michael Mair-Keimberger levelnine at>
AuthorDate: Sat Dec 30 17:49:41 2023 +
Commit: Andrew Ammerlaan gentoo org>
CommitDate: Sun Dec 31 08:50:13 2023 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=4da1b60b
dev-python/hdmf: remove unused patches
Signed-off-by: Michael Mair-Keimberger levelnine.at>
Signed-off-by: Andrew Ammerlaan gentoo.org>
dev-python/hdmf/files/hdmf-3.3.2-versions.patch | 20 ---
dev-python/hdmf/files/hdmf-3.5.0-open_links.patch | 170 --
2 files changed, 190 deletions(-)
diff --git a/dev-python/hdmf/files/hdmf-3.3.2-versions.patch
b/dev-python/hdmf/files/hdmf-3.3.2-versions.patch
deleted file mode 100644
index aaf62e115..0
--- a/dev-python/hdmf/files/hdmf-3.3.2-versions.patch
+++ /dev/null
@@ -1,20 +0,0 @@
a/setup.py 2022-01-31 02:48:24.645837186 -0500
-+++ b/setup.py 2022-01-31 02:49:55.066949247 -0500
-@@ -18,12 +18,12 @@
- schema_dir = 'common/hdmf-common-schema/common'
-
- reqs = [
--'h5py>=2.10,<4',
--'jsonschema>=2.6.0,<5',
--'numpy>=1.16,<1.23',
--'pandas>=1.0.5,<2',
--'ruamel.yaml>=0.16,<1',
--'scipy>=1.1,<2',
-+'h5py',
-+'jsonschema',
-+'numpy',
-+'pandas',
-+'ruamel.yaml',
-+'scipy',
- 'setuptools',
- ]
diff --git a/dev-python/hdmf/files/hdmf-3.5.0-open_links.patch
b/dev-python/hdmf/files/hdmf-3.5.0-open_links.patch
deleted file mode 100644
index 544bf8f4b..0
--- a/dev-python/hdmf/files/hdmf-3.5.0-open_links.patch
+++ /dev/null
@@ -1,170 +0,0 @@
-From 184b4a6711c60d90e073828ddcd3a6d328ee6a5e Mon Sep 17 00:00:00 2001
-From: Oliver Ruebel
-Date: Wed, 18 Jan 2023 16:05:57 -0800
-Subject: [PATCH 1/5] Fix #817 Check that __open_links exists before trying to
- clsoe links
-
- src/hdmf/backends/hdf5/h5tools.py | 13 +
- 1 file changed, 9 insertions(+), 4 deletions(-)
-
-diff --git a/src/hdmf/backends/hdf5/h5tools.py
b/src/hdmf/backends/hdf5/h5tools.py
-index ba8946c60..acf2061ad 100644
a/src/hdmf/backends/hdf5/h5tools.py
-+++ b/src/hdmf/backends/hdf5/h5tools.py
-@@ -746,10 +746,15 @@ def close_linked_files(self):
- not, which prevents the linked-to file from being deleted or
truncated. Use this method to close all opened,
- linked-to files.
- """
--for obj in self.__open_links:
--if obj:
--obj.file.close()
--self.__open_links = []
-+# Make sure
-+try:
-+for obj in self.__open_links:
-+if obj:
-+obj.file.close()
-+except AttributeError: # In case that self.__open_links does not
exist on delete
-+pass
-+finally:
-+self.__open_links = []
-
- @docval({'name': 'builder', 'type': GroupBuilder, 'doc': 'the
GroupBuilder object representing the HDF5 file'},
- {'name': 'link_data', 'type': bool,
-
-From c12ea0851f4632c59ecdd626556bee6ddc22b632 Mon Sep 17 00:00:00 2001
-From: Oliver Ruebel
-Date: Wed, 18 Jan 2023 17:32:20 -0800
-Subject: [PATCH 2/5] Catch possible missing HDF5IO.__file error
-
- src/hdmf/backends/hdf5/h5tools.py | 19 +++
- 1 file changed, 15 insertions(+), 4 deletions(-)
-
-diff --git a/src/hdmf/backends/hdf5/h5tools.py
b/src/hdmf/backends/hdf5/h5tools.py
-index acf2061ad..75044a64a 100644
a/src/hdmf/backends/hdf5/h5tools.py
-+++ b/src/hdmf/backends/hdf5/h5tools.py
-@@ -736,8 +736,15 @@ def close(self, close_links=True):
- """
- if close_links:
- self.close_linked_files()
--if self.__file is not None:
--self.__file.close()
-+try:
-+if self.__file is not None:
-+self.__file.close()
-+except AttributeError:
-+# Do not do anything in case that self._file does not exist. This
-+# may happen in case that an error occurs before HDF5IO has been
fully
-+# setup in __init__, e.g,. if a child class such as NWBHDF5IO
raises
-+# and error before self.__file has been created
-+warnings.warn("HDF5IO was not fully initialized before close.
Missing self.__file")
-
- def close_linked_files(self):
- """Close all opened, linked-to files.
-@@ -751,8 +758,12 @@ def close_linked_files(self):
- for obj in self.__open_links:
- if obj:
- obj.file.close()
--except AttributeError: # In case that self.__open_links does not
exist on delete
--pass
-+except AttributeError:
-+# Do not do anything in case that self.__open_links does not
exist. This
-+# may happen in case that an error occurs before HDF5IO has been
fully
-+# setup in __init__, e.g,. if a child class such as NWBHDF5IO
raises
-+# and error before self.__open_links has been created.
-+
[gentoo-commits] proj/sci:master commit in: dev-python/hdmf/, dev-python/hdmf/files/
commit: e574813b07a27fb7240d5d4636a5909bb0a17fc4
Author: Horea Christian chymera eu>
AuthorDate: Mon Dec 11 17:19:09 2023 +
Commit: Horea Christian gmail com>
CommitDate: Mon Dec 11 17:19:09 2023 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=e574813b
dev-python/hdmf: add 3.11.0
Signed-off-by: Horea Christian chymera.eu>
.../hdmf/files/hdmf-3.11.0-no_test_coverage.patch | 10 +++
dev-python/hdmf/hdmf-3.11.0.ebuild | 31 ++
2 files changed, 41 insertions(+)
diff --git a/dev-python/hdmf/files/hdmf-3.11.0-no_test_coverage.patch
b/dev-python/hdmf/files/hdmf-3.11.0-no_test_coverage.patch
new file mode 100644
index 0..e44a68902
--- /dev/null
+++ b/dev-python/hdmf/files/hdmf-3.11.0-no_test_coverage.patch
@@ -0,0 +1,10 @@
+--- a/pyproject.toml 2020-02-01 19:00:00.0 -0500
b/pyproject.toml 2023-12-11 12:00:19.368474488 -0500
+@@ -76,7 +76,6 @@
+ # verbose = 1
+
+ [tool.pytest.ini_options]
+-addopts = "--cov --cov-report html"
+ norecursedirs = "tests/unit/helpers"
+
+ [tool.codespell]
diff --git a/dev-python/hdmf/hdmf-3.11.0.ebuild
b/dev-python/hdmf/hdmf-3.11.0.ebuild
new file mode 100644
index 0..2463ccc1a
--- /dev/null
+++ b/dev-python/hdmf/hdmf-3.11.0.ebuild
@@ -0,0 +1,31 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DISTUTILS_USE_PEP517=hatchling
+PYTHON_COMPAT=( python3_{10..11} )
+inherit distutils-r1 pypi
+
+DESCRIPTION="The Hierarchical Data Modeling Framework"
+HOMEPAGE="https://github.com/hdmf-dev/hdmf;
+SRC_URI="$(pypi_sdist_url hdmf)"
+
+SLOT="0"
+LICENSE="BSD"
+KEYWORDS="~amd64 ~x86"
+
+RDEPEND="
+ dev-python/h5py[${PYTHON_USEDEP}]
+ dev-python/jsonschema[${PYTHON_USEDEP}]
+ dev-python/numpy[${PYTHON_USEDEP}]
+ dev-python/pandas[${PYTHON_USEDEP}]
+ dev-python/ruamel-yaml[${PYTHON_USEDEP}]
+ dev-python/scipy[${PYTHON_USEDEP}]
+ "
+
+PATCHES=(
+ "${FILESDIR}/${P}-no_test_coverage.patch"
+ )
+
+distutils_enable_tests pytest
[gentoo-commits] proj/sci:master commit in: dev-python/hdmf/
commit: 536677a07349f8be4a549ea7ac9aff2ed579d2c8
Author: Horea Christian chymera eu>
AuthorDate: Mon Dec 11 17:19:56 2023 +
Commit: Horea Christian gmail com>
CommitDate: Mon Dec 11 17:19:56 2023 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=536677a0
dev-python/hdmf: drop 3.4.7, 3.5.0_p1
Signed-off-by: Horea Christian chymera.eu>
dev-python/hdmf/hdmf-3.4.7.ebuild| 28 ---
dev-python/hdmf/hdmf-3.5.0_p1.ebuild | 37
2 files changed, 65 deletions(-)
diff --git a/dev-python/hdmf/hdmf-3.4.7.ebuild
b/dev-python/hdmf/hdmf-3.4.7.ebuild
deleted file mode 100644
index 883b5b95b..0
--- a/dev-python/hdmf/hdmf-3.4.7.ebuild
+++ /dev/null
@@ -1,28 +0,0 @@
-# Copyright 1999-2023 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-DISTUTILS_USE_PEP517=setuptools
-PYTHON_COMPAT=( python3_{10..11} )
-inherit distutils-r1
-
-DESCRIPTION="The Hierarchical Data Modeling Framework"
-HOMEPAGE="https://github.com/hdmf-dev/hdmf;
-SRC_URI="https://github.com/hdmf-dev/hdmf/releases/download/${PV}/${P}.tar.gz;
-
-SLOT="0"
-LICENSE="BSD"
-KEYWORDS="~amd64 ~x86"
-
-RDEPEND="
- dev-python/h5py[${PYTHON_USEDEP}]
- dev-python/jsonschema[${PYTHON_USEDEP}]
- dev-python/numpy[${PYTHON_USEDEP}]
- dev-python/pandas[${PYTHON_USEDEP}]
- dev-python/ruamel-yaml[${PYTHON_USEDEP}]
- dev-python/scipy[${PYTHON_USEDEP}]
- "
-BDEPEND=""
-
-distutils_enable_tests pytest
diff --git a/dev-python/hdmf/hdmf-3.5.0_p1.ebuild
b/dev-python/hdmf/hdmf-3.5.0_p1.ebuild
deleted file mode 100644
index 053831f8d..0
--- a/dev-python/hdmf/hdmf-3.5.0_p1.ebuild
+++ /dev/null
@@ -1,37 +0,0 @@
-# Copyright 1999-2023 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-DISTUTILS_USE_PEP517=setuptools
-PYTHON_COMPAT=( python3_{10..11} )
-inherit distutils-r1
-
-MY_PV="${PV//_p*/}"
-MY_P="${PN}-${MY_PV}"
-
-DESCRIPTION="The Hierarchical Data Modeling Framework"
-HOMEPAGE="https://github.com/hdmf-dev/hdmf;
-SRC_URI="https://github.com/hdmf-dev/hdmf/releases/download/${MY_PV}/${MY_P}.tar.gz;
-
-SLOT="0"
-LICENSE="BSD"
-KEYWORDS="~amd64 ~x86"
-
-RDEPEND="
- dev-python/h5py[${PYTHON_USEDEP}]
- dev-python/jsonschema[${PYTHON_USEDEP}]
- dev-python/numpy[${PYTHON_USEDEP}]
- dev-python/pandas[${PYTHON_USEDEP}]
- dev-python/ruamel-yaml[${PYTHON_USEDEP}]
- dev-python/scipy[${PYTHON_USEDEP}]
- "
-BDEPEND=""
-
-PATCHES=(
- "${FILESDIR}/${MY_P}-open_links.patch"
-)
-
-distutils_enable_tests pytest
-
-S="${WORKDIR}/${MY_P}"
[gentoo-commits] proj/sci:master commit in: dev-python/hdmf/
commit: 55fa52c89e98d6ca75d514c60877bc806cc0f8f1
Author: Horea Christian chymera eu>
AuthorDate: Wed Mar 22 15:08:20 2023 +
Commit: Horea Christian gmail com>
CommitDate: Wed Mar 22 15:08:20 2023 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=55fa52c8
dev-python/hdmf: add 3.5.2
Signed-off-by: Horea Christian chymera.eu>
dev-python/hdmf/hdmf-3.5.2.ebuild | 29 +
1 file changed, 29 insertions(+)
diff --git a/dev-python/hdmf/hdmf-3.5.2.ebuild
b/dev-python/hdmf/hdmf-3.5.2.ebuild
new file mode 100644
index 0..ee978516e
--- /dev/null
+++ b/dev-python/hdmf/hdmf-3.5.2.ebuild
@@ -0,0 +1,29 @@
+# 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="The Hierarchical Data Modeling Framework"
+HOMEPAGE="https://github.com/hdmf-dev/hdmf;
+SRC_URI="$(pypi_sdist_url hdmf)"
+#SRC_URI="https://github.com/hdmf-dev/hdmf/releases/download/${PV}/${P}.tar.gz;
+
+SLOT="0"
+LICENSE="BSD"
+KEYWORDS="~amd64 ~x86"
+
+RDEPEND="
+ dev-python/h5py[${PYTHON_USEDEP}]
+ dev-python/jsonschema[${PYTHON_USEDEP}]
+ dev-python/numpy[${PYTHON_USEDEP}]
+ dev-python/pandas[${PYTHON_USEDEP}]
+ dev-python/ruamel-yaml[${PYTHON_USEDEP}]
+ dev-python/scipy[${PYTHON_USEDEP}]
+ "
+BDEPEND=""
+
+distutils_enable_tests pytest
[gentoo-commits] proj/sci:master commit in: dev-python/hdmf/files/, dev-python/hdmf/
commit: 8b5ce5c1066e797f6cbf5abb21bd1dfe41d897eb
Author: Horea Christian chymera eu>
AuthorDate: Wed Mar 22 14:56:19 2023 +
Commit: Horea Christian gmail com>
CommitDate: Wed Mar 22 14:56:19 2023 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=8b5ce5c1
dev-python/hdmf: treeclean and rm deprecated commented lines
Signed-off-by: Horea Christian chymera.eu>
dev-python/hdmf/files/hdmf-3.1.1-versions.patch | 21
dev-python/hdmf/hdmf-3.3.2-r1.ebuild| 32 -
dev-python/hdmf/hdmf-3.4.7.ebuild | 4
dev-python/hdmf/hdmf-3.5.1.ebuild | 4
4 files changed, 61 deletions(-)
diff --git a/dev-python/hdmf/files/hdmf-3.1.1-versions.patch
b/dev-python/hdmf/files/hdmf-3.1.1-versions.patch
deleted file mode 100644
index 58822989d..0
--- a/dev-python/hdmf/files/hdmf-3.1.1-versions.patch
+++ /dev/null
@@ -1,21 +0,0 @@
a/setup.py 2022-01-31 02:48:24.645837186 -0500
-+++ b/setup.py 2022-01-31 02:49:55.066949247 -0500
-@@ -12,12 +12,12 @@
- schema_dir = 'common/hdmf-common-schema/common'
-
- reqs = [
--'h5py>=2.10,<4',
--'numpy>=1.16,<1.22',
--'scipy>=1.1,<2',
--'pandas>=1.0.5,<2',
--'ruamel.yaml>=0.16,<1',
--'jsonschema>=2.6.0,<4',
-+'h5py',
-+'numpy',
-+'scipy',
-+'pandas',
-+'ruamel.yaml',
-+'jsonschema',
- 'setuptools',
- ]
-
diff --git a/dev-python/hdmf/hdmf-3.3.2-r1.ebuild
b/dev-python/hdmf/hdmf-3.3.2-r1.ebuild
deleted file mode 100644
index 0efdd8f92..0
--- a/dev-python/hdmf/hdmf-3.3.2-r1.ebuild
+++ /dev/null
@@ -1,32 +0,0 @@
-# Copyright 1999-2022 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-DISTUTILS_USE_PEP517=setuptools
-PYTHON_COMPAT=( python3_{10..11} )
-inherit distutils-r1
-
-DESCRIPTION="The Hierarchical Data Modeling Framework"
-HOMEPAGE="https://github.com/hdmf-dev/hdmf;
-SRC_URI="https://github.com/hdmf-dev/hdmf/releases/download/${PV}/${P}.tar.gz;
-
-SLOT="0"
-LICENSE="BSD"
-KEYWORDS="~amd64 ~x86"
-
-RDEPEND="
- dev-python/h5py[${PYTHON_USEDEP}]
- dev-python/jsonschema[${PYTHON_USEDEP}]
- dev-python/numpy[${PYTHON_USEDEP}]
- dev-python/pandas[${PYTHON_USEDEP}]
- dev-python/ruamel-yaml[${PYTHON_USEDEP}]
- dev-python/scipy[${PYTHON_USEDEP}]
- "
-BDEPEND=""
-
-PATCHES=(
- "${FILESDIR}/${P}-versions.patch"
-)
-
-distutils_enable_tests pytest
diff --git a/dev-python/hdmf/hdmf-3.4.7.ebuild
b/dev-python/hdmf/hdmf-3.4.7.ebuild
index 2d05ea71a..883b5b95b 100644
--- a/dev-python/hdmf/hdmf-3.4.7.ebuild
+++ b/dev-python/hdmf/hdmf-3.4.7.ebuild
@@ -25,8 +25,4 @@ RDEPEND="
"
BDEPEND=""
-#PATCHES=(
-# "${FILESDIR}/${P}-versions.patch"
-#)
-
distutils_enable_tests pytest
diff --git a/dev-python/hdmf/hdmf-3.5.1.ebuild
b/dev-python/hdmf/hdmf-3.5.1.ebuild
index 2d05ea71a..883b5b95b 100644
--- a/dev-python/hdmf/hdmf-3.5.1.ebuild
+++ b/dev-python/hdmf/hdmf-3.5.1.ebuild
@@ -25,8 +25,4 @@ RDEPEND="
"
BDEPEND=""
-#PATCHES=(
-# "${FILESDIR}/${P}-versions.patch"
-#)
-
distutils_enable_tests pytest
[gentoo-commits] proj/sci:master commit in: dev-python/hdmf/
commit: bfdbb5598e357f3123f1a1b7cea02b679797bdae
Author: Horea Christian chymera eu>
AuthorDate: Mon Jan 30 11:45:51 2023 +
Commit: Horea Christian gmail com>
CommitDate: Mon Jan 30 11:45:51 2023 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=bfdbb559
dev-python/hdmf: PYTHON_COMPAT bump 3.11
Signed-off-by: Horea Christian chymera.eu>
dev-python/hdmf/hdmf-3.3.2-r1.ebuild | 2 +-
dev-python/hdmf/hdmf-3.4.7.ebuild| 2 +-
dev-python/hdmf/hdmf-3.5.0_p1.ebuild | 2 +-
dev-python/hdmf/hdmf-3.5.1.ebuild| 2 +-
4 files changed, 4 insertions(+), 4 deletions(-)
diff --git a/dev-python/hdmf/hdmf-3.3.2-r1.ebuild
b/dev-python/hdmf/hdmf-3.3.2-r1.ebuild
index c63395b7d..0efdd8f92 100644
--- a/dev-python/hdmf/hdmf-3.3.2-r1.ebuild
+++ b/dev-python/hdmf/hdmf-3.3.2-r1.ebuild
@@ -4,7 +4,7 @@
EAPI=8
DISTUTILS_USE_PEP517=setuptools
-PYTHON_COMPAT=( python3_10 )
+PYTHON_COMPAT=( python3_{10..11} )
inherit distutils-r1
DESCRIPTION="The Hierarchical Data Modeling Framework"
diff --git a/dev-python/hdmf/hdmf-3.4.7.ebuild
b/dev-python/hdmf/hdmf-3.4.7.ebuild
index 4e9d47921..2d05ea71a 100644
--- a/dev-python/hdmf/hdmf-3.4.7.ebuild
+++ b/dev-python/hdmf/hdmf-3.4.7.ebuild
@@ -4,7 +4,7 @@
EAPI=8
DISTUTILS_USE_PEP517=setuptools
-PYTHON_COMPAT=( python3_10 )
+PYTHON_COMPAT=( python3_{10..11} )
inherit distutils-r1
DESCRIPTION="The Hierarchical Data Modeling Framework"
diff --git a/dev-python/hdmf/hdmf-3.5.0_p1.ebuild
b/dev-python/hdmf/hdmf-3.5.0_p1.ebuild
index 6e63271cd..053831f8d 100644
--- a/dev-python/hdmf/hdmf-3.5.0_p1.ebuild
+++ b/dev-python/hdmf/hdmf-3.5.0_p1.ebuild
@@ -4,7 +4,7 @@
EAPI=8
DISTUTILS_USE_PEP517=setuptools
-PYTHON_COMPAT=( python3_10 )
+PYTHON_COMPAT=( python3_{10..11} )
inherit distutils-r1
MY_PV="${PV//_p*/}"
diff --git a/dev-python/hdmf/hdmf-3.5.1.ebuild
b/dev-python/hdmf/hdmf-3.5.1.ebuild
index 4e9d47921..2d05ea71a 100644
--- a/dev-python/hdmf/hdmf-3.5.1.ebuild
+++ b/dev-python/hdmf/hdmf-3.5.1.ebuild
@@ -4,7 +4,7 @@
EAPI=8
DISTUTILS_USE_PEP517=setuptools
-PYTHON_COMPAT=( python3_10 )
+PYTHON_COMPAT=( python3_{10..11} )
inherit distutils-r1
DESCRIPTION="The Hierarchical Data Modeling Framework"
[gentoo-commits] proj/sci:master commit in: dev-python/hdmf/
commit: 9483693c1a9a9df2fd7aabfdfb86679a621fa0e0
Author: Horea Christian chymera eu>
AuthorDate: Mon Jan 30 11:43:42 2023 +
Commit: Horea Christian gmail com>
CommitDate: Mon Jan 30 11:43:42 2023 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=9483693c
dev-python/hdmf: drop 3.1.1-r1
Signed-off-by: Horea Christian chymera.eu>
dev-python/hdmf/hdmf-3.1.1-r1.ebuild | 38
1 file changed, 38 deletions(-)
diff --git a/dev-python/hdmf/hdmf-3.1.1-r1.ebuild
b/dev-python/hdmf/hdmf-3.1.1-r1.ebuild
deleted file mode 100644
index b3f479f18..0
--- a/dev-python/hdmf/hdmf-3.1.1-r1.ebuild
+++ /dev/null
@@ -1,38 +0,0 @@
-# Copyright 1999-2022 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-PYTHON_COMPAT=( python3_10 )
-DISTUTILS_USE_SETUPTOOLS=rdepend
-inherit distutils-r1
-
-DESCRIPTION="The Hierarchical Data Modeling Framework"
-HOMEPAGE="https://github.com/hdmf-dev/hdmf;
-SRC_URI="https://github.com/hdmf-dev/hdmf/releases/download/${PV}/${P}.tar.gz;
-
-SLOT="0"
-LICENSE="BSD"
-KEYWORDS="~amd64 ~x86"
-
-RDEPEND="
- dev-python/h5py[${PYTHON_USEDEP}]
- dev-python/jsonschema[${PYTHON_USEDEP}]
- dev-python/numpy[${PYTHON_USEDEP}]
- dev-python/pandas[${PYTHON_USEDEP}]
- dev-python/ruamel-yaml[${PYTHON_USEDEP}]
- dev-python/scipy[${PYTHON_USEDEP}]
- "
-BDEPEND=""
-
-distutils_enable_tests pytest
-
-# Known to upstream:
-# https://github.com/hdmf-dev/hdmf/issues/687
-EPYTEST_DESELECT=(
-
tests/unit/utils_test/test_labelleddict.py::TestLabelledDict::test_set_key_attr
-)
-
-PATCHES=(
- "${FILESDIR}/${P}-versions.patch"
-)
[gentoo-commits] proj/sci:master commit in: dev-python/hdmf/, dev-python/hdmf/files/
commit: e0e02abb64e2a95d94baff5bf8a3fac1f5878a95
Author: Horea Christian chymera eu>
AuthorDate: Mon Jan 30 11:42:48 2023 +
Commit: Horea Christian gmail com>
CommitDate: Mon Jan 30 11:42:48 2023 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=e0e02abb
dev-python/hdmf: add 3.4.7, 3.5.0_p1, 3.5.1
Signed-off-by: Horea Christian chymera.eu>
dev-python/hdmf/files/hdmf-3.5.0-open_links.patch | 170 ++
dev-python/hdmf/hdmf-3.4.7.ebuild | 32
dev-python/hdmf/hdmf-3.5.0_p1.ebuild | 37 +
dev-python/hdmf/hdmf-3.5.1.ebuild | 32
4 files changed, 271 insertions(+)
diff --git a/dev-python/hdmf/files/hdmf-3.5.0-open_links.patch
b/dev-python/hdmf/files/hdmf-3.5.0-open_links.patch
new file mode 100644
index 0..544bf8f4b
--- /dev/null
+++ b/dev-python/hdmf/files/hdmf-3.5.0-open_links.patch
@@ -0,0 +1,170 @@
+From 184b4a6711c60d90e073828ddcd3a6d328ee6a5e Mon Sep 17 00:00:00 2001
+From: Oliver Ruebel
+Date: Wed, 18 Jan 2023 16:05:57 -0800
+Subject: [PATCH 1/5] Fix #817 Check that __open_links exists before trying to
+ clsoe links
+
+---
+ src/hdmf/backends/hdf5/h5tools.py | 13 +
+ 1 file changed, 9 insertions(+), 4 deletions(-)
+
+diff --git a/src/hdmf/backends/hdf5/h5tools.py
b/src/hdmf/backends/hdf5/h5tools.py
+index ba8946c60..acf2061ad 100644
+--- a/src/hdmf/backends/hdf5/h5tools.py
b/src/hdmf/backends/hdf5/h5tools.py
+@@ -746,10 +746,15 @@ def close_linked_files(self):
+ not, which prevents the linked-to file from being deleted or
truncated. Use this method to close all opened,
+ linked-to files.
+ """
+-for obj in self.__open_links:
+-if obj:
+-obj.file.close()
+-self.__open_links = []
++# Make sure
++try:
++for obj in self.__open_links:
++if obj:
++obj.file.close()
++except AttributeError: # In case that self.__open_links does not
exist on delete
++pass
++finally:
++self.__open_links = []
+
+ @docval({'name': 'builder', 'type': GroupBuilder, 'doc': 'the
GroupBuilder object representing the HDF5 file'},
+ {'name': 'link_data', 'type': bool,
+
+From c12ea0851f4632c59ecdd626556bee6ddc22b632 Mon Sep 17 00:00:00 2001
+From: Oliver Ruebel
+Date: Wed, 18 Jan 2023 17:32:20 -0800
+Subject: [PATCH 2/5] Catch possible missing HDF5IO.__file error
+
+---
+ src/hdmf/backends/hdf5/h5tools.py | 19 +++
+ 1 file changed, 15 insertions(+), 4 deletions(-)
+
+diff --git a/src/hdmf/backends/hdf5/h5tools.py
b/src/hdmf/backends/hdf5/h5tools.py
+index acf2061ad..75044a64a 100644
+--- a/src/hdmf/backends/hdf5/h5tools.py
b/src/hdmf/backends/hdf5/h5tools.py
+@@ -736,8 +736,15 @@ def close(self, close_links=True):
+ """
+ if close_links:
+ self.close_linked_files()
+-if self.__file is not None:
+-self.__file.close()
++try:
++if self.__file is not None:
++self.__file.close()
++except AttributeError:
++# Do not do anything in case that self._file does not exist. This
++# may happen in case that an error occurs before HDF5IO has been
fully
++# setup in __init__, e.g,. if a child class such as NWBHDF5IO
raises
++# and error before self.__file has been created
++warnings.warn("HDF5IO was not fully initialized before close.
Missing self.__file")
+
+ def close_linked_files(self):
+ """Close all opened, linked-to files.
+@@ -751,8 +758,12 @@ def close_linked_files(self):
+ for obj in self.__open_links:
+ if obj:
+ obj.file.close()
+-except AttributeError: # In case that self.__open_links does not
exist on delete
+-pass
++except AttributeError:
++# Do not do anything in case that self.__open_links does not
exist. This
++# may happen in case that an error occurs before HDF5IO has been
fully
++# setup in __init__, e.g,. if a child class such as NWBHDF5IO
raises
++# and error before self.__open_links has been created.
++warnings.warn("HDF5IO was not fully initialized before close.
Missing self.__open_links.")
+ finally:
+ self.__open_links = []
+
+
+From a43e65d13726936aa2ab49169e265a42c5a1be7f Mon Sep 17 00:00:00 2001
+From: Oliver Ruebel
+Date: Wed, 18 Jan 2023 17:32:55 -0800
+Subject: [PATCH 3/5] Add unit test for case where HDF5IO.close is called
+ before HDF5IO.__init__ is complete
+
+---
+ tests/unit/test_io_hdf5_h5tools.py | 34 ++
+ 1 file changed, 34 insertions(+)
+
+diff --git a/tests/unit/test_io_hdf5_h5tools.py
b/tests/unit/test_io_hdf5_h5tools.py
+index 8c03e72f8..0f2f81e31 100644
+--- a/tests/unit/test_io_hdf5_h5tools.py
[gentoo-commits] proj/sci:master commit in: dev-python/hdmf/
commit: 994ac92ee6990aeba470c2c6a166140be31efa9e
Author: Horea Christian chymera eu>
AuthorDate: Tue Jul 19 05:04:22 2022 +
Commit: Horea Christian gmail com>
CommitDate: Tue Jul 19 05:04:22 2022 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=994ac92e
dev-python/hdmf: removed explicit version listing in PATCHES
Package-Manager: Portage-3.0.30, Repoman-3.0.3
Signed-off-by: Horea Christian chymera.eu>
dev-python/hdmf/hdmf-3.1.1-r1.ebuild | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/dev-python/hdmf/hdmf-3.1.1-r1.ebuild
b/dev-python/hdmf/hdmf-3.1.1-r1.ebuild
index e9334b67a..866b5e553 100644
--- a/dev-python/hdmf/hdmf-3.1.1-r1.ebuild
+++ b/dev-python/hdmf/hdmf-3.1.1-r1.ebuild
@@ -34,5 +34,5 @@ EPYTEST_DESELECT=(
)
PATCHES=(
- "${FILESDIR}/${PN}-3.1.1-versions.patch"
+ "${FILESDIR}/${P}-versions.patch"
)
[gentoo-commits] proj/sci:master commit in: dev-python/hdmf/, dev-python/hdmf/files/
commit: cfe3213a1f7757442adb88a0aa8a84976c93ba0a
Author: Horea Christian chymera eu>
AuthorDate: Tue Jul 19 05:03:28 2022 +
Commit: Horea Christian gmail com>
CommitDate: Tue Jul 19 05:03:28 2022 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=cfe3213a
dev-python/hdmf: patched upstream versioncheck
Package-Manager: Portage-3.0.30, Repoman-3.0.3
Signed-off-by: Horea Christian chymera.eu>
dev-python/hdmf/files/hdmf-3.3.2-versions.patch | 20
.../hdmf/{hdmf-3.3.2.ebuild => hdmf-3.3.2-r1.ebuild} | 4
2 files changed, 24 insertions(+)
diff --git a/dev-python/hdmf/files/hdmf-3.3.2-versions.patch
b/dev-python/hdmf/files/hdmf-3.3.2-versions.patch
new file mode 100644
index 0..aaf62e115
--- /dev/null
+++ b/dev-python/hdmf/files/hdmf-3.3.2-versions.patch
@@ -0,0 +1,20 @@
+--- a/setup.py 2022-01-31 02:48:24.645837186 -0500
b/setup.py 2022-01-31 02:49:55.066949247 -0500
+@@ -18,12 +18,12 @@
+ schema_dir = 'common/hdmf-common-schema/common'
+
+ reqs = [
+-'h5py>=2.10,<4',
+-'jsonschema>=2.6.0,<5',
+-'numpy>=1.16,<1.23',
+-'pandas>=1.0.5,<2',
+-'ruamel.yaml>=0.16,<1',
+-'scipy>=1.1,<2',
++'h5py',
++'jsonschema',
++'numpy',
++'pandas',
++'ruamel.yaml',
++'scipy',
+ 'setuptools',
+ ]
diff --git a/dev-python/hdmf/hdmf-3.3.2.ebuild
b/dev-python/hdmf/hdmf-3.3.2-r1.ebuild
similarity index 93%
rename from dev-python/hdmf/hdmf-3.3.2.ebuild
rename to dev-python/hdmf/hdmf-3.3.2-r1.ebuild
index 071c5b9a0..1bec3913c 100644
--- a/dev-python/hdmf/hdmf-3.3.2.ebuild
+++ b/dev-python/hdmf/hdmf-3.3.2-r1.ebuild
@@ -25,4 +25,8 @@ RDEPEND="
"
BDEPEND=""
+PATCHES=(
+ "${FILESDIR}/${P}-versions.patch"
+)
+
distutils_enable_tests pytest
[gentoo-commits] proj/sci:master commit in: dev-python/hdmf/
commit: 39c10f0b4e0d0089476af6f612bdca51b8deb6a2
Author: Horea Christian chymera eu>
AuthorDate: Tue Jul 12 14:59:54 2022 +
Commit: Horea Christian gmail com>
CommitDate: Tue Jul 12 14:59:54 2022 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=39c10f0b
dev-python/hdmf: version bump, test and metadata update
Package-Manager: Portage-3.0.30, Repoman-3.0.3
Signed-off-by: Horea Christian chymera.eu>
dev-python/hdmf/hdmf-3.1.1-r1.ebuild| 6 ++
dev-python/hdmf/{hdmf-3.1.1-r1.ebuild => hdmf-3.3.2.ebuild} | 6 +-
dev-python/hdmf/metadata.xml| 4
3 files changed, 11 insertions(+), 5 deletions(-)
diff --git a/dev-python/hdmf/hdmf-3.1.1-r1.ebuild
b/dev-python/hdmf/hdmf-3.1.1-r1.ebuild
index 76d40c95f..e9334b67a 100644
--- a/dev-python/hdmf/hdmf-3.1.1-r1.ebuild
+++ b/dev-python/hdmf/hdmf-3.1.1-r1.ebuild
@@ -27,6 +27,12 @@ BDEPEND=""
distutils_enable_tests pytest
+# Known to upstream:
+# https://github.com/hdmf-dev/hdmf/issues/687
+EPYTEST_DESELECT=(
+
tests/unit/utils_test/test_labelleddict.py::TestLabelledDict::test_set_key_attr
+)
+
PATCHES=(
"${FILESDIR}/${PN}-3.1.1-versions.patch"
)
diff --git a/dev-python/hdmf/hdmf-3.1.1-r1.ebuild
b/dev-python/hdmf/hdmf-3.3.2.ebuild
similarity index 88%
copy from dev-python/hdmf/hdmf-3.1.1-r1.ebuild
copy to dev-python/hdmf/hdmf-3.3.2.ebuild
index 76d40c95f..071c5b9a0 100644
--- a/dev-python/hdmf/hdmf-3.1.1-r1.ebuild
+++ b/dev-python/hdmf/hdmf-3.3.2.ebuild
@@ -3,8 +3,8 @@
EAPI=8
+DISTUTILS_USE_PEP517=setuptools
PYTHON_COMPAT=( python3_{8..10} )
-DISTUTILS_USE_SETUPTOOLS=rdepend
inherit distutils-r1
DESCRIPTION="The Hierarchical Data Modeling Framework"
@@ -26,7 +26,3 @@ RDEPEND="
BDEPEND=""
distutils_enable_tests pytest
-
-PATCHES=(
- "${FILESDIR}/${PN}-3.1.1-versions.patch"
-)
diff --git a/dev-python/hdmf/metadata.xml b/dev-python/hdmf/metadata.xml
index 82da7c426..ac3f7a6cb 100644
--- a/dev-python/hdmf/metadata.xml
+++ b/dev-python/hdmf/metadata.xml
@@ -15,4 +15,8 @@
data models, reading and writing data to different storage
backends,
and representing data with Python object.
+
+ hdmf-dev/hdmf
+ hdmf
+
[gentoo-commits] proj/sci:master commit in: dev-python/hdmf/files/, dev-python/hdmf/
commit: 53abb9d47d74a94be26890306eb605746e1f33ff
Author: Horea Christian chymera eu>
AuthorDate: Mon Jan 31 08:13:43 2022 +
Commit: Horea Christian gmail com>
CommitDate: Mon Jan 31 08:13:43 2022 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=53abb9d4
dev-python/hdmf: revbump for setup.py versions
Package-Manager: Portage-3.0.30, Repoman-3.0.3
Signed-off-by: Horea Christian chymera.eu>
.../hdmf/files/hdmf-3.1.1-new_jsonschema.patch | 10 --
dev-python/hdmf/files/hdmf-3.1.1-versions.patch | 21 +
.../{hdmf-3.1.1.ebuild => hdmf-3.1.1-r1.ebuild} | 4 ++--
3 files changed, 23 insertions(+), 12 deletions(-)
diff --git a/dev-python/hdmf/files/hdmf-3.1.1-new_jsonschema.patch
b/dev-python/hdmf/files/hdmf-3.1.1-new_jsonschema.patch
deleted file mode 100644
index 989332bb5..0
--- a/dev-python/hdmf/files/hdmf-3.1.1-new_jsonschema.patch
+++ /dev/null
@@ -1,10 +0,0 @@
a/setup.py 2021-09-24 00:51:55.892741725 -0400
-+++ b/setup.py 2021-10-27 14:33:20.733741241 -0400
-@@ -23,7 +23,7 @@
- 'scipy>=1.1,<2',
- 'pandas>=1.0.5,<2',
- 'ruamel.yaml>=0.16,<1',
--'jsonschema>=2.6.0,<4',
-+'jsonschema>=2.6.0',
- 'setuptools',
- ]
diff --git a/dev-python/hdmf/files/hdmf-3.1.1-versions.patch
b/dev-python/hdmf/files/hdmf-3.1.1-versions.patch
new file mode 100644
index 0..58822989d
--- /dev/null
+++ b/dev-python/hdmf/files/hdmf-3.1.1-versions.patch
@@ -0,0 +1,21 @@
+--- a/setup.py 2022-01-31 02:48:24.645837186 -0500
b/setup.py 2022-01-31 02:49:55.066949247 -0500
+@@ -12,12 +12,12 @@
+ schema_dir = 'common/hdmf-common-schema/common'
+
+ reqs = [
+-'h5py>=2.10,<4',
+-'numpy>=1.16,<1.22',
+-'scipy>=1.1,<2',
+-'pandas>=1.0.5,<2',
+-'ruamel.yaml>=0.16,<1',
+-'jsonschema>=2.6.0,<4',
++'h5py',
++'numpy',
++'scipy',
++'pandas',
++'ruamel.yaml',
++'jsonschema',
+ 'setuptools',
+ ]
+
diff --git a/dev-python/hdmf/hdmf-3.1.1.ebuild
b/dev-python/hdmf/hdmf-3.1.1-r1.ebuild
similarity index 88%
rename from dev-python/hdmf/hdmf-3.1.1.ebuild
rename to dev-python/hdmf/hdmf-3.1.1-r1.ebuild
index 1731b0d90..76d40c95f 100644
--- a/dev-python/hdmf/hdmf-3.1.1.ebuild
+++ b/dev-python/hdmf/hdmf-3.1.1-r1.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=8
@@ -28,5 +28,5 @@ BDEPEND=""
distutils_enable_tests pytest
PATCHES=(
- "${FILESDIR}/${PN}-3.1.1-new_jsonschema.patch"
+ "${FILESDIR}/${PN}-3.1.1-versions.patch"
)
[gentoo-commits] proj/sci:master commit in: dev-python/hdmf/files/, dev-python/hdmf/
commit: a67a1c84befd9b4a6653b197d1f5686e223b7cbb
Author: Horea Christian chymera eu>
AuthorDate: Fri Oct 29 11:58:58 2021 +
Commit: Horea Christian gmail com>
CommitDate: Fri Oct 29 11:58:58 2021 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=a67a1c84
dev-python/hdmf: new package (DANDI stack)
Package-Manager: Portage-3.0.28, Repoman-3.0.3
Signed-off-by: Horea Christian chymera.eu>
.../hdmf/files/hdmf-3.1.1-new_jsonschema.patch | 10 +++
dev-python/hdmf/hdmf-3.1.1.ebuild | 32 ++
dev-python/hdmf/metadata.xml | 18
3 files changed, 60 insertions(+)
diff --git a/dev-python/hdmf/files/hdmf-3.1.1-new_jsonschema.patch
b/dev-python/hdmf/files/hdmf-3.1.1-new_jsonschema.patch
new file mode 100644
index 0..989332bb5
--- /dev/null
+++ b/dev-python/hdmf/files/hdmf-3.1.1-new_jsonschema.patch
@@ -0,0 +1,10 @@
+--- a/setup.py 2021-09-24 00:51:55.892741725 -0400
b/setup.py 2021-10-27 14:33:20.733741241 -0400
+@@ -23,7 +23,7 @@
+ 'scipy>=1.1,<2',
+ 'pandas>=1.0.5,<2',
+ 'ruamel.yaml>=0.16,<1',
+-'jsonschema>=2.6.0,<4',
++'jsonschema>=2.6.0',
+ 'setuptools',
+ ]
diff --git a/dev-python/hdmf/hdmf-3.1.1.ebuild
b/dev-python/hdmf/hdmf-3.1.1.ebuild
new file mode 100644
index 0..1731b0d90
--- /dev/null
+++ b/dev-python/hdmf/hdmf-3.1.1.ebuild
@@ -0,0 +1,32 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{8..10} )
+DISTUTILS_USE_SETUPTOOLS=rdepend
+inherit distutils-r1
+
+DESCRIPTION="The Hierarchical Data Modeling Framework"
+HOMEPAGE="https://github.com/hdmf-dev/hdmf;
+SRC_URI="https://github.com/hdmf-dev/hdmf/releases/download/${PV}/${P}.tar.gz;
+
+SLOT="0"
+LICENSE="BSD"
+KEYWORDS="~amd64 ~x86"
+
+RDEPEND="
+ dev-python/h5py[${PYTHON_USEDEP}]
+ dev-python/jsonschema[${PYTHON_USEDEP}]
+ dev-python/numpy[${PYTHON_USEDEP}]
+ dev-python/pandas[${PYTHON_USEDEP}]
+ dev-python/ruamel-yaml[${PYTHON_USEDEP}]
+ dev-python/scipy[${PYTHON_USEDEP}]
+ "
+BDEPEND=""
+
+distutils_enable_tests pytest
+
+PATCHES=(
+ "${FILESDIR}/${PN}-3.1.1-new_jsonschema.patch"
+)
diff --git a/dev-python/hdmf/metadata.xml b/dev-python/hdmf/metadata.xml
new file mode 100644
index 0..82da7c426
--- /dev/null
+++ b/dev-python/hdmf/metadata.xml
@@ -0,0 +1,18 @@
+
+http://www.gentoo.org/dtd/metadata.dtd;>
+
+
+ gen...@chymera.eu
+ Horea Christian
+
+
+ s...@gentoo.org
+ Gentoo Science Project
+
+
+ The Hierarchical Data Modeling Framework, or HDMF, is a Python
package
+ for working with hierarchical data. It provides APIs for
specifying
+ data models, reading and writing data to different storage
backends,
+ and representing data with Python object.
+
+
