[gentoo-commits] proj/sci:master commit in: dev-python/pynwb/
commit: 7f1649f287ef810d3ad4745e0736501d329ff744
Author: Horea Christian chymera eu>
AuthorDate: Thu Mar 21 16:55:56 2024 +
Commit: Horea Christian gmail com>
CommitDate: Thu Mar 21 22:15:29 2024 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=7f1649f2
dev-python/pynwb: add 2.6.0, drop 2.3.2
Signed-off-by: Horea Christian chymera.eu>
dev-python/pynwb/{pynwb-2.3.2.ebuild => pynwb-2.6.0.ebuild} | 11 +--
1 file changed, 9 insertions(+), 2 deletions(-)
diff --git a/dev-python/pynwb/pynwb-2.3.2.ebuild
b/dev-python/pynwb/pynwb-2.6.0.ebuild
similarity index 81%
rename from dev-python/pynwb/pynwb-2.3.2.ebuild
rename to dev-python/pynwb/pynwb-2.6.0.ebuild
index 6599fbf8f..2f403981c 100644
--- a/dev-python/pynwb/pynwb-2.3.2.ebuild
+++ b/dev-python/pynwb/pynwb-2.6.0.ebuild
@@ -15,14 +15,14 @@ LICENSE="BSD"
KEYWORDS="~amd64 ~x86"
RDEPEND="
- >=sci-libs/hdf5-1.12.2
>=dev-python/hdmf-3.3.2[${PYTHON_USEDEP}]
+ >=sci-libs/hdf5-1.12.2
dev-python/h5py[${PYTHON_USEDEP}]
dev-python/numpy[${PYTHON_USEDEP}]
dev-python/pandas[${PYTHON_USEDEP}]
dev-python/python-dateutil[${PYTHON_USEDEP}]
+ dev-python/requests[${PYTHON_USEDEP}]
"
-BDEPEND=""
EPYTEST_DESELECT=(
# Reported upsream:
@@ -39,6 +39,13 @@ EPYTEST_DESELECT=(
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
+ # Reported upstream:
+ # https://github.com/NeurodataWithoutBorders/pynwb/issues/1800
+ tests/unit/test_file.py::TestNoCacheSpec::test_simple
+ # Not sandboxed, reported upstream:
+ # https://github.com/NeurodataWithoutBorders/pynwb/issues/1800
+
tests/read_dandi/test_read_dandi.py::TestReadNWBDandisets::test_read_first_nwb_asset
+ tests/unit/test_base.py::TestTimeSeries::test_repr_html
)
distutils_enable_tests pytest
[gentoo-commits] proj/sci:master commit in: dev-python/pynwb/files/
commit: 0816f5a2b5a64c71ed56bed9f9bfbb29b5d5dd12
Author: Michael Mair-Keimberger levelnine at>
AuthorDate: Sat Dec 30 17:50:14 2023 +
Commit: Andrew Ammerlaan gentoo org>
CommitDate: Sun Dec 31 08:50:15 2023 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=0816f5a2
dev-python/pynwb: remove unused patch(es)
Signed-off-by: Michael Mair-Keimberger levelnine.at>
Signed-off-by: Andrew Ammerlaan 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 -
.../pynwb/files/pynwb-2.3.1-pkg_resources.patch| 54 --
dev-python/pynwb/files/pynwb-2.3.1-typing.patch| 13 --
5 files changed, 130 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..0
--- 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..0
--- 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..0
--- 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/files/pynwb-2.3.1-pkg_resources.patch
b/dev-python/pynwb/files/pynwb-2.3.1-pkg_resources.patch
deleted file mode 100644
index bf496b900..0
--- a/dev-python/pynwb/files/pynwb-2.3.1-pkg_resources.patch
+++ /dev/null
@@ -1,54 +0,0 @@
-From df0f7ed71defb8d12a7ff72746b93211304c4d4b Mon Sep 17 00:00:00 2001
-From: rly
-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",
-
[gentoo-commits] proj/sci:master commit in: dev-python/pynwb/
commit: 975e4101b9bcdf67bcfce0c05db3fa1d5ffa3bca
Author: Horea Christian chymera eu>
AuthorDate: Tue Dec 12 04:31:23 2023 +
Commit: Horea Christian gmail com>
CommitDate: Tue Dec 12 04:31:23 2023 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=975e4101
dev-python/pynwb: add 2.5.0
Signed-off-by: Horea Christian chymera.eu>
dev-python/pynwb/pynwb-2.5.0.ebuild | 50 +
1 file changed, 50 insertions(+)
diff --git a/dev-python/pynwb/pynwb-2.5.0.ebuild
b/dev-python/pynwb/pynwb-2.5.0.ebuild
new file mode 100644
index 0..ca11c3dbe
--- /dev/null
+++ b/dev-python/pynwb/pynwb-2.5.0.ebuild
@@ -0,0 +1,50 @@
+# 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;
+
+SLOT="0"
+LICENSE="BSD"
+KEYWORDS="~amd64 ~x86"
+
+RDEPEND="
+ >=dev-python/hdmf-3.3.2[${PYTHON_USEDEP}]
+ >=sci-libs/hdf5-1.12.2
+ dev-python/h5py[${PYTHON_USEDEP}]
+ dev-python/numpy[${PYTHON_USEDEP}]
+ dev-python/pandas[${PYTHON_USEDEP}]
+ dev-python/python-dateutil[${PYTHON_USEDEP}]
+ dev-python/requests[${PYTHON_USEDEP}]
+ "
+
+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
+ # Reported upstream:
+ # https://github.com/NeurodataWithoutBorders/pynwb/issues/1800
+ tests/unit/test_file.py::TestNoCacheSpec::test_simple
+ # Not sandboxed, reported upstream:
+ # https://github.com/NeurodataWithoutBorders/pynwb/issues/1800
+
tests/read_dandi/test_read_dandi.py::TestReadNWBDandisets::test_read_first_nwb_asset
+)
+
+distutils_enable_tests pytest
[gentoo-commits] proj/sci:master commit in: dev-python/pynwb/
commit: ca5f9e39188f379372ca5a8f5dc29c1146d8cf59
Author: Horea Christian chymera eu>
AuthorDate: Tue Dec 12 04:31:41 2023 +
Commit: Horea Christian gmail com>
CommitDate: Tue Dec 12 04:31:41 2023 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=ca5f9e39
dev-python/pynwb: drop 2.2.0-r1, 2.3.1-r1
Signed-off-by: Horea Christian chymera.eu>
dev-python/pynwb/pynwb-2.2.0-r1.ebuild | 56 --
dev-python/pynwb/pynwb-2.3.1-r1.ebuild | 50 --
2 files changed, 106 deletions(-)
diff --git a/dev-python/pynwb/pynwb-2.2.0-r1.ebuild
b/dev-python/pynwb/pynwb-2.2.0-r1.ebuild
deleted file mode 100644
index 5a286c3b6..0
--- a/dev-python/pynwb/pynwb-2.2.0-r1.ebuild
+++ /dev/null
@@ -1,56 +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="A Python API for working with Neurodata stored in the NWB Format "
-HOMEPAGE="https://github.com/NeurodataWithoutBorders/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[${PYTHON_USEDEP}]
- "
-BDEPEND=""
-
-PATCHES=(
- "${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
diff --git a/dev-python/pynwb/pynwb-2.3.1-r1.ebuild
b/dev-python/pynwb/pynwb-2.3.1-r1.ebuild
deleted file mode 100644
index 382bfdb60..0
--- a/dev-python/pynwb/pynwb-2.3.1-r1.ebuild
+++ /dev/null
@@ -1,50 +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="A Python API for working with Neurodata stored in the NWB Format "
-HOMEPAGE="https://github.com/NeurodataWithoutBorders/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 both 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
-
[gentoo-commits] proj/sci:master commit in: dev-python/pynwb/, dev-python/pynwb/files/
commit: ee5933c91a1a18023763a6dc2f25e1c9199a4360
Author: Horea Christian chymera eu>
AuthorDate: Mon May 22 11:06:04 2023 +
Commit: Horea Christian gmail com>
CommitDate: Mon May 22 11:06:04 2023 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=ee5933c9
dev-python/pynwb: update SRC_URI
Signed-off-by: Horea Christian chymera.eu>
.../df0f7ed71defb8d12a7ff72746b93211304c4d4b.patch | 54 --
dev-python/pynwb/pynwb-2.2.0-r1.ebuild | 3 +-
dev-python/pynwb/pynwb-2.3.1-r1.ebuild | 1 -
dev-python/pynwb/pynwb-2.3.1.ebuild| 1 -
4 files changed, 1 insertion(+), 58 deletions(-)
diff --git
a/dev-python/pynwb/files/df0f7ed71defb8d12a7ff72746b93211304c4d4b.patch
b/dev-python/pynwb/files/df0f7ed71defb8d12a7ff72746b93211304c4d4b.patch
deleted file mode 100644
index bf496b900..0
--- a/dev-python/pynwb/files/df0f7ed71defb8d12a7ff72746b93211304c4d4b.patch
+++ /dev/null
@@ -1,54 +0,0 @@
-From df0f7ed71defb8d12a7ff72746b93211304c4d4b Mon Sep 17 00:00:00 2001
-From: rly
-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-2.2.0-r1.ebuild
b/dev-python/pynwb/pynwb-2.2.0-r1.ebuild
index 52fab7a63..5a286c3b6 100644
--- a/dev-python/pynwb/pynwb-2.2.0-r1.ebuild
+++ b/dev-python/pynwb/pynwb-2.2.0-r1.ebuild
@@ -5,11 +5,10 @@ EAPI=8
DISTUTILS_USE_PEP517=setuptools
PYTHON_COMPAT=( python3_{10..11} )
-inherit distutils-r1
+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="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
SLOT="0"
LICENSE="BSD"
diff --git a/dev-python/pynwb/pynwb-2.3.1-r1.ebuild
b/dev-python/pynwb/pynwb-2.3.1-r1.ebuild
index 585dcc37d..382bfdb60 100644
--- a/dev-python/pynwb/pynwb-2.3.1-r1.ebuild
+++ b/dev-python/pynwb/pynwb-2.3.1-r1.ebuild
@@ -9,7 +9,6 @@ inherit distutils-r1 pypi
DESCRIPTION="A Python API for working with Neurodata stored in the NWB Format "
HOMEPAGE="https://github.com/NeurodataWithoutBorders/pynwb;
-SRC_URI="$(pypi_sdist_url pynwb)"
SLOT="0"
LICENSE="BSD"
diff --git a/dev-python/pynwb/pynwb-2.3.1.ebuild
b/dev-python/pynwb/pynwb-2.3.1.ebuild
index cce90c5d1..e36e65dbe 100644
--- a/dev-python/pynwb/pynwb-2.3.1.ebuild
+++ b/dev-python/pynwb/pynwb-2.3.1.ebuild
@@ -9,7 +9,6 @@ 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="$(pypi_sdist_url pynwb)"
SLOT="0"
LICENSE="BSD"
[gentoo-commits] proj/sci:master commit in: dev-python/pynwb/
commit: aceee28fad7e9f381ac376e195df19877bb21bbc
Author: Horea Christian chymera eu>
AuthorDate: Mon May 22 11:12:08 2023 +
Commit: Horea Christian gmail com>
CommitDate: Mon May 22 11:12:08 2023 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=aceee28f
dev-python/pynwb: drop 2.3.1
Signed-off-by: Horea Christian chymera.eu>
dev-python/pynwb/pynwb-2.3.1.ebuild | 49 -
1 file changed, 49 deletions(-)
diff --git a/dev-python/pynwb/pynwb-2.3.1.ebuild
b/dev-python/pynwb/pynwb-2.3.1.ebuild
deleted file mode 100644
index e36e65dbe..0
--- a/dev-python/pynwb/pynwb-2.3.1.ebuild
+++ /dev/null
@@ -1,49 +0,0 @@
-# Copyright 1999-2023 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-DISTUTILS_USE_PEP517=setuptools
-PYTHON_COMPAT=( python3_{10..11} )
-inherit distutils-r1 pypi
-
-DESCRIPTION="A Python API for working with Neurodata stored in the NWB Format "
-HOMEPAGE="https://github.com/NeurodataWithoutBorders/pynwb;
-
-SLOT="0"
-LICENSE="BSD"
-KEYWORDS="~amd64 ~x86"
-
-RDEPEND="
- >=sci-libs/hdf5-1.12.2
- >=dev-python/hdmf-3.3.2[${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"
- )
-
-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
[gentoo-commits] proj/sci:master commit in: dev-python/pynwb/
commit: 69e782ccfd16db0a1efb0d494de1c052a3ae4335
Author: Horea Christian chymera eu>
AuthorDate: Mon May 22 11:11:42 2023 +
Commit: Horea Christian gmail com>
CommitDate: Mon May 22 11:11:42 2023 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=69e782cc
dev-python/pynwb: add 2.3.2
Signed-off-by: Horea Christian chymera.eu>
dev-python/pynwb/pynwb-2.3.2.ebuild | 44 +
1 file changed, 44 insertions(+)
diff --git a/dev-python/pynwb/pynwb-2.3.2.ebuild
b/dev-python/pynwb/pynwb-2.3.2.ebuild
new file mode 100644
index 0..6599fbf8f
--- /dev/null
+++ b/dev-python/pynwb/pynwb-2.3.2.ebuild
@@ -0,0 +1,44 @@
+# 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;
+
+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=""
+
+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
[gentoo-commits] proj/sci:master commit in: dev-python/pynwb/
commit: d33365ba84ea3e62c9c90c2dc17fe4c2030ddc62
Author: Horea Christian chymera eu>
AuthorDate: Mon May 22 11:04:47 2023 +
Commit: Horea Christian gmail com>
CommitDate: Mon May 22 11:04:47 2023 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=d33365ba
dev-python/pynwb: drop 2.1.0-r2
Signed-off-by: Horea Christian chymera.eu>
dev-python/pynwb/pynwb-2.1.0-r2.ebuild | 43 --
1 file changed, 43 deletions(-)
diff --git a/dev-python/pynwb/pynwb-2.1.0-r2.ebuild
b/dev-python/pynwb/pynwb-2.1.0-r2.ebuild
deleted file mode 100644
index e95649217..0
--- a/dev-python/pynwb/pynwb-2.1.0-r2.ebuild
+++ /dev/null
@@ -1,43 +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="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/hdf5-1.12.2
- >=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[${PYTHON_USEDEP}]
- "
-BDEPEND=""
-
-PATCHES=(
- "${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
[gentoo-commits] proj/sci:master commit in: dev-python/pynwb/files/, dev-python/pynwb/
commit: 5017407dd9e589abb913af53da82de7e487e6114 Author: Horea Christian chymera eu> AuthorDate: Sat Mar 25 03:07:12 2023 + Commit: Horea Christian gmail com> CommitDate: Sat Mar 25 03:07:12 2023 + URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=5017407d dev-python/pynwb: revbump for deprecated pkg_resources Signed-off-by: Horea Christian 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 0..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 +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 0..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 +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__", +
[gentoo-commits] proj/sci:master commit in: dev-python/pynwb/
commit: fb68d10fc0b5f4b96772f83365eace1be3a4b8f4
Author: Horea Christian chymera eu>
AuthorDate: Sat Mar 25 03:07:52 2023 +
Commit: Horea Christian gmail com>
CommitDate: Sat Mar 25 03:07:52 2023 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=fb68d10f
dev-python/pynwb: comment clarification
Signed-off-by: Horea Christian chymera.eu>
dev-python/pynwb/pynwb-2.3.1-r1.ebuild | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/dev-python/pynwb/pynwb-2.3.1-r1.ebuild
b/dev-python/pynwb/pynwb-2.3.1-r1.ebuild
index 9f5f42370..585dcc37d 100644
--- a/dev-python/pynwb/pynwb-2.3.1-r1.ebuild
+++ b/dev-python/pynwb/pynwb-2.3.1-r1.ebuild
@@ -25,7 +25,7 @@ RDEPEND="
"
BDEPEND=""
-# Remove in next release
+# Remove both in next release
PATCHES=(
"${FILESDIR}/${P}-typing.patch"
"${FILESDIR}/${P}-pkg_resources.patch"
[gentoo-commits] proj/sci:master commit in: dev-python/pynwb/
commit: 18fa2218a3c92cf5650c1a65ed0ef12eae76c127
Author: Horea Christian chymera eu>
AuthorDate: Wed Mar 22 19:43:52 2023 +
Commit: Horea Christian gmail com>
CommitDate: Wed Mar 22 19:43:52 2023 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=18fa2218
dev-python/pynwb: enable py3.11
Signed-off-by: Horea Christian chymera.eu>
dev-python/pynwb/pynwb-2.1.0-r2.ebuild | 2 +-
dev-python/pynwb/pynwb-2.2.0-r1.ebuild | 2 +-
2 files changed, 2 insertions(+), 2 deletions(-)
diff --git a/dev-python/pynwb/pynwb-2.1.0-r2.ebuild
b/dev-python/pynwb/pynwb-2.1.0-r2.ebuild
index 14eed0e2f..e95649217 100644
--- a/dev-python/pynwb/pynwb-2.1.0-r2.ebuild
+++ b/dev-python/pynwb/pynwb-2.1.0-r2.ebuild
@@ -4,7 +4,7 @@
EAPI=8
DISTUTILS_USE_PEP517=setuptools
-PYTHON_COMPAT=( python3_10 )
+PYTHON_COMPAT=( python3_{10..11} )
inherit distutils-r1
DESCRIPTION="A Python API for working with Neurodata stored in the NWB Format "
diff --git a/dev-python/pynwb/pynwb-2.2.0-r1.ebuild
b/dev-python/pynwb/pynwb-2.2.0-r1.ebuild
index 041418fbb..52fab7a63 100644
--- a/dev-python/pynwb/pynwb-2.2.0-r1.ebuild
+++ b/dev-python/pynwb/pynwb-2.2.0-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="A Python API for working with Neurodata stored in the NWB Format "
[gentoo-commits] proj/sci:master commit in: dev-python/pynwb/, dev-python/pynwb/files/
commit: 16797f5b3289b8970625b8c03645e9a6a5fcaa04
Author: Horea Christian chymera eu>
AuthorDate: Wed Mar 22 19:39:12 2023 +
Commit: Horea Christian gmail com>
CommitDate: Wed Mar 22 19:39:12 2023 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=16797f5b
dev-python/pynwb: add 2.3.1
Signed-off-by: Horea Christian chymera.eu>
dev-python/pynwb/files/pynwb-2.3.1-typing.patch | 13 +++
dev-python/pynwb/pynwb-2.3.1.ebuild | 50 +
2 files changed, 63 insertions(+)
diff --git a/dev-python/pynwb/files/pynwb-2.3.1-typing.patch
b/dev-python/pynwb/files/pynwb-2.3.1-typing.patch
new file mode 100644
index 0..e672f243b
--- /dev/null
+++ b/dev-python/pynwb/files/pynwb-2.3.1-typing.patch
@@ -0,0 +1,13 @@
+diff --git a/src/pynwb/ophys.py b/src/pynwb/ophys.py
+index b09267ff6..e3d9f8f6d 100644
+--- a/src/pynwb/ophys.py
b/src/pynwb/ophys.py
+@@ -192,7 +192,7 @@ def __init__(self, **kwargs):
+ args_to_set = popargs_to_dict(keys_to_set, kwargs)
+ super().__init__(**kwargs)
+
+-if args_to_set["binning"] < 0:
++if args_to_set["binning"] is not None and args_to_set["binning"] < 0:
+ raise ValueError(f"Binning value must be >= 0:
{args_to_set['binning']}")
+ if isinstance(args_to_set["binning"], int):
+ args_to_set["binning"] = np.uint(args_to_set["binning"])
diff --git a/dev-python/pynwb/pynwb-2.3.1.ebuild
b/dev-python/pynwb/pynwb-2.3.1.ebuild
new file mode 100644
index 0..cce90c5d1
--- /dev/null
+++ b/dev-python/pynwb/pynwb-2.3.1.ebuild
@@ -0,0 +1,50 @@
+# 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"
+ )
+
+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
[gentoo-commits] proj/sci:master commit in: dev-python/pynwb/
commit: 1c183aee3e1acb043ebcee0de027835d9dbe40a5
Author: Horea Christian chymera eu>
AuthorDate: Mon Jan 30 11:53:59 2023 +
Commit: Horea Christian gmail com>
CommitDate: Mon Jan 30 11:53:59 2023 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=1c183aee
dev-python/pynwb: drop 2.0.1-r1
Signed-off-by: Horea Christian chymera.eu>
dev-python/pynwb/pynwb-2.0.1-r1.ebuild | 39 --
1 file changed, 39 deletions(-)
diff --git a/dev-python/pynwb/pynwb-2.0.1-r1.ebuild
b/dev-python/pynwb/pynwb-2.0.1-r1.ebuild
deleted file mode 100644
index 3d3e0cbb9..0
--- a/dev-python/pynwb/pynwb-2.0.1-r1.ebuild
+++ /dev/null
@@ -1,39 +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 )
-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/hdf5-1.12.2
- 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
[gentoo-commits] proj/sci:master commit in: dev-python/pynwb/
commit: 8489010298163161a2b45a13c70016fb9e926b48
Author: Horea Christian chymera eu>
AuthorDate: Thu Jan 12 10:12:59 2023 +
Commit: Horea Christian gmail com>
CommitDate: Thu Jan 12 10:12:59 2023 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=84890102
dev-python/pynwb: fully deprecated ros3 flag of hdf5 dep
Signed-off-by: Horea Christian chymera.eu>
dev-python/pynwb/{pynwb-2.0.1.ebuild => pynwb-2.0.1-r1.ebuild}| 2 +-
dev-python/pynwb/{pynwb-2.1.0-r1.ebuild => pynwb-2.1.0-r2.ebuild} | 2 +-
dev-python/pynwb/{pynwb-2.2.0.ebuild => pynwb-2.2.0-r1.ebuild}| 2 +-
3 files changed, 3 insertions(+), 3 deletions(-)
diff --git a/dev-python/pynwb/pynwb-2.0.1.ebuild
b/dev-python/pynwb/pynwb-2.0.1-r1.ebuild
similarity index 97%
rename from dev-python/pynwb/pynwb-2.0.1.ebuild
rename to dev-python/pynwb/pynwb-2.0.1-r1.ebuild
index d713c6bcb..719e308b3 100644
--- a/dev-python/pynwb/pynwb-2.0.1.ebuild
+++ b/dev-python/pynwb/pynwb-2.0.1-r1.ebuild
@@ -16,7 +16,7 @@ LICENSE="BSD"
KEYWORDS="~amd64 ~x86"
RDEPEND="
- >=sci-libs/hdf5-1.12.2[ros3(+)]
+ >=sci-libs/hdf5-1.12.2
[gentoo-commits] proj/sci:master commit in: dev-python/pynwb/
commit: 763713a088a11b16c7f00b2f391f4cdaafbf7504 Author: Horea Christian chymera eu> AuthorDate: Thu Jan 12 09:41:55 2023 + Commit: Horea Christian gmail com> CommitDate: Thu Jan 12 09:48:37 2023 + URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=763713a0 dev-python/pynwb: fixing hd5 dependency ros3 USE flag requirement Signed-off-by: Horea Christian chymera.eu> dev-python/pynwb/pynwb-2.0.1.ebuild| 4 ++-- dev-python/pynwb/pynwb-2.1.0-r1.ebuild | 4 ++-- dev-python/pynwb/pynwb-2.2.0.ebuild| 4 ++-- 3 files changed, 6 insertions(+), 6 deletions(-) diff --git a/dev-python/pynwb/pynwb-2.0.1.ebuild b/dev-python/pynwb/pynwb-2.0.1.ebuild index 3fe21370f..d713c6bcb 100644 --- a/dev-python/pynwb/pynwb-2.0.1.ebuild +++ b/dev-python/pynwb/pynwb-2.0.1.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2022 Gentoo Authors +# Copyright 1999-2023 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=8 @@ -16,7 +16,7 @@ LICENSE="BSD" KEYWORDS="~amd64 ~x86" RDEPEND=" - sci-libs/hdf5[ros3(-)] + >=sci-libs/hdf5-1.12.2[ros3(+)]
[gentoo-commits] proj/sci:master commit in: dev-python/pynwb/, dev-python/pynwb/files/
commit: 56843b9298ba13771fd05ed1b4a55e13aa81
Author: Horea Christian chymera eu>
AuthorDate: Thu Jan 12 09:35:54 2023 +
Commit: Horea Christian gmail com>
CommitDate: Thu Jan 12 09:48:19 2023 +
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 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 0..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 0..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 0..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 0..1e30097b2
--- /dev/null
+++ b/dev-python/pynwb/metadata.xml
@@ -0,0 +1,24 @@
+
+http://www.gentoo.org/dtd/metadata.dtd;>
+
+
+ gen...@chymera.eu
+ Horea Christian
+
+
+ s...@gentoo.org
+ Gentoo Science Project
+
+
+ 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.
+
+
+ pynwb
+ NeurodataWithoutBorders/pynwb
+
+
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 0..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(-)]
+ https://github.com/NeurodataWithoutBorders/pynwb/issues/1425
+
tests/validation/test_validate.py::TestValidateScript::test_validate_file_cached
+
[gentoo-commits] proj/sci:master commit in: dev-python/pynwb/files/, dev-python/pynwb/
commit: 252693b1a06c119a2efe40661b957fb6d10c0ed5
Author: Andrew Ammerlaan gentoo org>
AuthorDate: Tue Jan 3 18:15:06 2023 +
Commit: Andrew Ammerlaan gentoo org>
CommitDate: Tue Jan 3 18:15:12 2023 +
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 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..0
--- 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..0
--- 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..0
--- 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..0
--- a/dev-python/pynwb/metadata.xml
+++ /dev/null
@@ -1,24 +0,0 @@
-
-http://www.gentoo.org/dtd/metadata.dtd;>
-
-
- gen...@chymera.eu
- Horea Christian
-
-
- s...@gentoo.org
- Gentoo Science Project
-
-
- 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.
-
-
- pynwb
- NeurodataWithoutBorders/pynwb
-
-
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..0
--- 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(-)]
- https://github.com/NeurodataWithoutBorders/pynwb/issues/1425
-
tests/validation/test_validate.py::TestValidateScript::test_validate_file_cached
-
[gentoo-commits] proj/sci:master commit in: dev-python/pynwb/
commit: 9ab6b069325b69e6833bdb7c517ae5acf3124e38
Author: Horea Christian chymera eu>
AuthorDate: Wed Nov 2 21:10:04 2022 +
Commit: Horea Christian gmail com>
CommitDate: Wed Nov 2 21:10:04 2022 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=9ab6b069
dev-python/pynwb: drop 2.0.0
Signed-off-by: Horea Christian chymera.eu>
dev-python/pynwb/pynwb-2.0.0.ebuild | 46 -
1 file changed, 46 deletions(-)
diff --git a/dev-python/pynwb/pynwb-2.0.0.ebuild
b/dev-python/pynwb/pynwb-2.0.0.ebuild
deleted file mode 100644
index e133d027b..0
--- a/dev-python/pynwb/pynwb-2.0.0.ebuild
+++ /dev/null
@@ -1,46 +0,0 @@
-# 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(-)]
- 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
- # 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
[gentoo-commits] proj/sci:master commit in: dev-python/pynwb/files/, dev-python/pynwb/
commit: 299f323d9a54d449992ea9156fc0004d15cf934b
Author: Horea Christian chymera eu>
AuthorDate: Wed Nov 2 21:09:45 2022 +
Commit: Horea Christian gmail com>
CommitDate: Wed Nov 2 21:09:45 2022 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=299f323d
dev-python/pynwb: add 2.2.0
Signed-off-by: Horea Christian 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 0..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 0..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
[gentoo-commits] proj/sci:master commit in: dev-python/pynwb/files/, dev-python/pynwb/
commit: 5ec641ea8274723cbc1b13a0144201b3a6de2623
Author: Horea Christian chymera eu>
AuthorDate: Tue Jul 19 04:57:49 2022 +
Commit: Horea Christian gmail com>
CommitDate: Tue Jul 19 04:57:49 2022 +
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 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 0..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
[gentoo-commits] proj/sci:master commit in: dev-python/pynwb/
commit: 75cb88a8a0d3dbc52dee2df510b2a84236dcafee
Author: Horea Christian chymera eu>
AuthorDate: Tue Jul 12 15:29:11 2022 +
Commit: Horea Christian gmail com>
CommitDate: Tue Jul 12 15:29:11 2022 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=75cb88a8
dev-python/pynwb: version bump, fixed dependency versions
Package-Manager: Portage-3.0.30, Repoman-3.0.3
Signed-off-by: Horea Christian chymera.eu>
dev-python/pynwb/pynwb-2.0.0.ebuild | 4 ++--
dev-python/pynwb/pynwb-2.0.1.ebuild | 6 +++---
dev-python/pynwb/{pynwb-2.0.1.ebuild => pynwb-2.1.0.ebuild} | 6 +++---
3 files changed, 8 insertions(+), 8 deletions(-)
diff --git a/dev-python/pynwb/pynwb-2.0.0.ebuild
b/dev-python/pynwb/pynwb-2.0.0.ebuild
index d9afd62e7..e133d027b 100644
--- a/dev-python/pynwb/pynwb-2.0.0.ebuild
+++ b/dev-python/pynwb/pynwb-2.0.0.ebuild
@@ -16,7 +16,7 @@ KEYWORDS="~amd64 ~x86"
RDEPEND="
sci-libs/hdf5[ros3(-)]
- dev-python/hdmf[${PYTHON_USEDEP}]
+ https://github.com/dandi/dandischema/issues/87
+ # https://github.com/NeurodataWithoutBorders/pynwb/issues/1425
tests/validation/test_validate.py::TestValidateScript::test_validate_file_cached
tests/validation/test_validate.py::TestValidateScript::test_validate_file_cached_bad_ns
tests/validation/test_validate.py::TestValidateScript::test_validate_file_cached_hdmf_common
diff --git a/dev-python/pynwb/pynwb-2.0.1.ebuild
b/dev-python/pynwb/pynwb-2.0.1.ebuild
index 9f84bdb80..3fe21370f 100644
--- a/dev-python/pynwb/pynwb-2.0.1.ebuild
+++ b/dev-python/pynwb/pynwb-2.0.1.ebuild
@@ -9,7 +9,7 @@ inherit distutils-r1
DESCRIPTION="A Python API for working with Neurodata stored in the NWB Format "
HOMEPAGE="https://github.com/NeurodataWithoutBorders/pynwb;
-SRC_URI="https://github.com/NeurodataWithoutBorders/pynwb/releases/download/${PV}/${P}.tar.gz;
+SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
SLOT="0"
LICENSE="BSD"
@@ -17,7 +17,7 @@ KEYWORDS="~amd64 ~x86"
RDEPEND="
sci-libs/hdf5[ros3(-)]
- dev-python/hdmf[${PYTHON_USEDEP}]
+ https://github.com/dandi/dandischema/issues/87
+ # https://github.com/NeurodataWithoutBorders/pynwb/issues/1425
tests/validation/test_validate.py::TestValidateScript::test_validate_file_cached
tests/validation/test_validate.py::TestValidateScript::test_validate_file_cached_bad_ns
tests/validation/test_validate.py::TestValidateScript::test_validate_file_cached_hdmf_common
diff --git a/dev-python/pynwb/pynwb-2.0.1.ebuild
b/dev-python/pynwb/pynwb-2.1.0.ebuild
similarity index 86%
copy from dev-python/pynwb/pynwb-2.0.1.ebuild
copy to dev-python/pynwb/pynwb-2.1.0.ebuild
index 9f84bdb80..a53c4bbb0 100644
--- a/dev-python/pynwb/pynwb-2.0.1.ebuild
+++ b/dev-python/pynwb/pynwb-2.1.0.ebuild
@@ -9,7 +9,7 @@ inherit distutils-r1
DESCRIPTION="A Python API for working with Neurodata stored in the NWB Format "
HOMEPAGE="https://github.com/NeurodataWithoutBorders/pynwb;
-SRC_URI="https://github.com/NeurodataWithoutBorders/pynwb/releases/download/${PV}/${P}.tar.gz;
+SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
SLOT="0"
LICENSE="BSD"
@@ -17,7 +17,7 @@ KEYWORDS="~amd64 ~x86"
RDEPEND="
sci-libs/hdf5[ros3(-)]
- dev-python/hdmf[${PYTHON_USEDEP}]
+ >=dev-python/hdmf-3.3.2[${PYTHON_USEDEP}]
dev-python/h5py[${PYTHON_USEDEP}]
dev-python/numpy[${PYTHON_USEDEP}]
dev-python/pandas[${PYTHON_USEDEP}]
@@ -27,7 +27,7 @@ BDEPEND=""
EPYTEST_DESELECT=(
# Reported upsream:
- # https://github.com/dandi/dandischema/issues/87
+ # https://github.com/NeurodataWithoutBorders/pynwb/issues/1425
tests/validation/test_validate.py::TestValidateScript::test_validate_file_cached
tests/validation/test_validate.py::TestValidateScript::test_validate_file_cached_bad_ns
tests/validation/test_validate.py::TestValidateScript::test_validate_file_cached_hdmf_common
[gentoo-commits] proj/sci:master commit in: dev-python/pynwb/
commit: e77189d1019c38f6df1b25b2da53f7669c92d295
Author: Horea Christian chymera eu>
AuthorDate: Tue Jul 12 14:41:51 2022 +
Commit: Horea Christian gmail com>
CommitDate: Tue Jul 12 14:41:51 2022 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=e77189d1
dev-python/pynwb: dropped ebuild with missing source
Package-Manager: Portage-3.0.30, Repoman-3.0.3
Signed-off-by: Horea Christian chymera.eu>
dev-python/pynwb/pynwb-2.0.0_p0.ebuild | 47 --
1 file changed, 47 deletions(-)
diff --git a/dev-python/pynwb/pynwb-2.0.0_p0.ebuild
b/dev-python/pynwb/pynwb-2.0.0_p0.ebuild
deleted file mode 100644
index 25672015c..0
--- a/dev-python/pynwb/pynwb-2.0.0_p0.ebuild
+++ /dev/null
@@ -1,47 +0,0 @@
-# Copyright 1999-2022 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-PYTHON_COMPAT=( python3_{8..10} )
-inherit distutils-r1
-
-MY_PV="${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
[gentoo-commits] proj/sci:master commit in: dev-python/pynwb/
commit: 872c4f1ee5cfda29b12acc7ed09a923502d25484
Author: Horea Christian chymera eu>
AuthorDate: Tue Jul 12 14:40:13 2022 +
Commit: Horea Christian gmail com>
CommitDate: Tue Jul 12 14:40:13 2022 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=872c4f1e
dev-python/pynwb: version bump
Package-Manager: Portage-3.0.30, Repoman-3.0.3
Signed-off-by: Horea Christian chymera.eu>
dev-python/pynwb/metadata.xml | 4
dev-python/pynwb/pynwb-2.0.1.ebuild | 39 +
2 files changed, 43 insertions(+)
diff --git a/dev-python/pynwb/metadata.xml b/dev-python/pynwb/metadata.xml
index 99512b574..1e30097b2 100644
--- a/dev-python/pynwb/metadata.xml
+++ b/dev-python/pynwb/metadata.xml
@@ -17,4 +17,8 @@
data, focused on the dynamics of groups of neurons measured
under a
large range of experimental conditions.
+
+ pynwb
+ NeurodataWithoutBorders/pynwb
+
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 0..9f84bdb80
--- /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="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[${PYTHON_USEDEP}]
+ "
+BDEPEND=""
+
+EPYTEST_DESELECT=(
+ # Reported upsream:
+ # https://github.com/dandi/dandischema/issues/87
+
tests/validation/test_validate.py::TestValidateScript::test_validate_file_cached
+
tests/validation/test_validate.py::TestValidateScript::test_validate_file_cached_bad_ns
+
tests/validation/test_validate.py::TestValidateScript::test_validate_file_cached_hdmf_common
+
tests/validation/test_validate.py::TestValidateScript::test_validate_file_cached_ignore
+
tests/validation/test_validate.py::TestValidateScript::test_validate_file_no_cache
+
tests/validation/test_validate.py::TestValidateScript::test_validate_file_no_cache_bad_ns
+)
+
+distutils_enable_tests pytest
[gentoo-commits] proj/sci:master commit in: dev-python/pynwb/
commit: 35bd9890236d3d3309e966f34048c4a0012d9b16
Author: Horea Christian chymera eu>
AuthorDate: Tue Feb 1 15:31:02 2022 +
Commit: Horea Christian gmail com>
CommitDate: Tue Feb 1 15:31:02 2022 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=35bd9890
dev-python/pynwb: flag assumed disabled if not present
Package-Manager: Portage-3.0.30, Repoman-3.0.3
Signed-off-by: Horea Christian chymera.eu>
dev-python/pynwb/pynwb-2.0.0.ebuild| 2 +-
dev-python/pynwb/pynwb-2.0.0_p0.ebuild | 2 +-
2 files changed, 2 insertions(+), 2 deletions(-)
diff --git a/dev-python/pynwb/pynwb-2.0.0.ebuild
b/dev-python/pynwb/pynwb-2.0.0.ebuild
index b0294a4e0..d9afd62e7 100644
--- a/dev-python/pynwb/pynwb-2.0.0.ebuild
+++ b/dev-python/pynwb/pynwb-2.0.0.ebuild
@@ -15,7 +15,7 @@ LICENSE="BSD"
KEYWORDS="~amd64 ~x86"
RDEPEND="
- sci-libs/hdf5[ros3]
+ sci-libs/hdf5[ros3(-)]
dev-python/hdmf[${PYTHON_USEDEP}]
dev-python/h5py[${PYTHON_USEDEP}]
dev-python/numpy[${PYTHON_USEDEP}]
diff --git a/dev-python/pynwb/pynwb-2.0.0_p0.ebuild
b/dev-python/pynwb/pynwb-2.0.0_p0.ebuild
index fba3e6319..25672015c 100644
--- a/dev-python/pynwb/pynwb-2.0.0_p0.ebuild
+++ b/dev-python/pynwb/pynwb-2.0.0_p0.ebuild
@@ -18,7 +18,7 @@ LICENSE="BSD"
KEYWORDS="~amd64 ~x86"
RDEPEND="
- sci-libs/hdf5[ros3]
+ sci-libs/hdf5[ros3(-)]
dev-python/hdmf[${PYTHON_USEDEP}]
dev-python/h5py[${PYTHON_USEDEP}]
dev-python/numpy[${PYTHON_USEDEP}]
[gentoo-commits] proj/sci:master commit in: dev-python/pynwb/
commit: e82aa77838def38e866bba6d9eaae5d60d4577c9 Author: Horea Christian chymera eu> AuthorDate: Mon Jan 31 08:19:05 2022 + Commit: Horea Christian gmail com> CommitDate: Mon Jan 31 08:19:05 2022 + URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=e82aa778 dev-python/pynwb: purged Changelog Package-Manager: Portage-3.0.30, Repoman-3.0.3 Signed-off-by: Horea Christian chymera.eu> dev-python/pynwb/ChangeLog | 6 -- 1 file changed, 6 deletions(-) diff --git a/dev-python/pynwb/ChangeLog b/dev-python/pynwb/ChangeLog deleted file mode 100644 index 1eee46e49..0 --- a/dev-python/pynwb/ChangeLog +++ /dev/null @@ -1,6 +0,0 @@ -*pynwb-2.0.0_p0 (31 Jan 2022) - - 31 Jan 2022; +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
[gentoo-commits] proj/sci:master commit in: dev-python/pynwb/files/, dev-python/pynwb/
commit: 67e6080551c80d384ee79713470e20396317a8f1
Author: Horea Christian chymera eu>
AuthorDate: Mon Jan 31 08:15:27 2022 +
Commit: Horea Christian gmail com>
CommitDate: Mon Jan 31 08:15:27 2022 +
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 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 0..1eee46e49
--- /dev/null
+++ b/dev-python/pynwb/ChangeLog
@@ -0,0 +1,6 @@
+*pynwb-2.0.0_p0 (31 Jan 2022)
+
+ 31 Jan 2022; +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 0..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 0..99512b574
--- /dev/null
+++ b/dev-python/pynwb/metadata.xml
@@ -0,0 +1,20 @@
+
+http://www.gentoo.org/dtd/metadata.dtd;>
+
+
+ gen...@chymera.eu
+ Horea Christian
+
+
+ s...@gentoo.org
+ Gentoo Science Project
+
+
+ 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.
+
+
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 0..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
