[gentoo-commits] proj/sci:master commit in: sci-biology/neuroconv/
commit: 73916dd3680ffd92e5bd3d32b262e5d78c86a448 Author: Horea Christian chymera eu> AuthorDate: Tue Apr 2 23:56:26 2024 + Commit: Horea Christian gmail com> CommitDate: Wed Apr 3 00:00:03 2024 + URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=73916dd3 sci-biology/neuroconv: dependency revbump Signed-off-by: Horea Christian chymera.eu> .../neuroconv/{neuroconv-0.4.8.ebuild => neuroconv-0.4.8-r1.ebuild} | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/sci-biology/neuroconv/neuroconv-0.4.8.ebuild b/sci-biology/neuroconv/neuroconv-0.4.8-r1.ebuild similarity index 97% rename from sci-biology/neuroconv/neuroconv-0.4.8.ebuild rename to sci-biology/neuroconv/neuroconv-0.4.8-r1.ebuild index a3012611f..b21c2fd8e 100644 --- a/sci-biology/neuroconv/neuroconv-0.4.8.ebuild +++ b/sci-biology/neuroconv/neuroconv-0.4.8-r1.ebuild @@ -17,20 +17,21 @@ KEYWORDS="~amd64" IUSE="+ecephys +icephys +ophys" RDEPEND=" + dev-python/docstring-parser[${PYTHON_USEDEP}] dev-python/h5py[${PYTHON_USEDEP}] - dev-python/hdmf[${PYTHON_USEDEP}] dev-python/hdmf-zarr[${PYTHON_USEDEP}] + dev-python/hdmf[${PYTHON_USEDEP}] dev-python/jsonschema[${PYTHON_USEDEP}] dev-python/numpy[${PYTHON_USEDEP}] dev-python/nwbinspector[${PYTHON_USEDEP}] dev-python/pandas[${PYTHON_USEDEP}] dev-python/parse[${PYTHON_USEDEP}] dev-python/psutil[${PYTHON_USEDEP}] + dev-python/pydantic[${PYTHON_USEDEP}] dev-python/pynwb[${PYTHON_USEDEP}] dev-python/pyyaml[${PYTHON_USEDEP}] dev-python/scipy[${PYTHON_USEDEP}] dev-python/tqdm[${PYTHON_USEDEP}] - dev-python/pydantic[${PYTHON_USEDEP}] ecephys? ( dev-python/spikeinterface[${PYTHON_USEDEP}] )
[gentoo-commits] proj/sci:master commit in: sci-biology/neuroconv/
commit: 597997e35db5451deb6079df099686bc085b732a Author: Horea Christian chymera eu> AuthorDate: Thu Mar 21 22:10:03 2024 + Commit: Horea Christian gmail com> CommitDate: Thu Mar 21 22:15:29 2024 + URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=597997e3 sci-biology/neuroconv: version bump, treeclean Signed-off-by: Horea Christian chymera.eu> sci-biology/neuroconv/neuroconv-0.2.4.ebuild | 56 -- ...conv-0.4.6-r1.ebuild => neuroconv-0.4.8.ebuild} | 6 +++ 2 files changed, 6 insertions(+), 56 deletions(-) diff --git a/sci-biology/neuroconv/neuroconv-0.2.4.ebuild b/sci-biology/neuroconv/neuroconv-0.2.4.ebuild deleted file mode 100644 index c554ce791..0 --- a/sci-biology/neuroconv/neuroconv-0.2.4.ebuild +++ /dev/null @@ -1,56 +0,0 @@ -# Copyright 2021-2023 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=8 - -PYTHON_COMPAT=( python3_{10..11} ) -DISTUTILS_USE_PEP517=setuptools -inherit distutils-r1 - -DESCRIPTION="Create NWB files from proprietary formats." -HOMEPAGE="https://github.com/catalystneuro/neuroconv"; -SRC_URI="https://github.com/catalystneuro/neuroconv/archive/refs/tags/v${PV}.tar.gz -> ${P}.gh.tar.gz" - -LICENSE="BSD" -SLOT="0" -KEYWORDS="~amd64" -IUSE="+ecephys +icephys +ophys" - -RDEPEND=" - dev-python/h5py[${PYTHON_USEDEP}] - dev-python/hdmf[${PYTHON_USEDEP}] - dev-python/jsonschema[${PYTHON_USEDEP}] - dev-python/numpy[${PYTHON_USEDEP}] - dev-python/pandas[${PYTHON_USEDEP}] - dev-python/psutil[${PYTHON_USEDEP}] - dev-python/pynwb[${PYTHON_USEDEP}] - dev-python/pyyaml[${PYTHON_USEDEP}] - dev-python/scipy[${PYTHON_USEDEP}] - dev-python/tqdm[${PYTHON_USEDEP}] - dev-vcs/dandi-cli[${PYTHON_USEDEP}] - ecephys? ( - dev-python/spikeinterface[${PYTHON_USEDEP}] - ) - icephys? ( - dev-python/neo[${PYTHON_USEDEP}] - ) - ophys? ( - sci-biology/roiextractors[${PYTHON_USEDEP}] - ) -" -BDEPEND=" - test? ( - dev-python/parameterized[${PYTHON_USEDEP}] - ) -" - -distutils_enable_tests pytest - -python_test() { - # Additional tests require complex data getting infrastructure, ophys tests still have issues: - # https://github.com/catalystneuro/neuroconv/issues/305 - local my_tests=( "tests/test_minimal" ) - use ecephys && my_tests+=( "tests/test_ecephys" ) - #use ophys && my_tests+=( "tests/test_ophys" ) - epytest ${my_tests[*]// /|} -} diff --git a/sci-biology/neuroconv/neuroconv-0.4.6-r1.ebuild b/sci-biology/neuroconv/neuroconv-0.4.8.ebuild similarity index 88% rename from sci-biology/neuroconv/neuroconv-0.4.6-r1.ebuild rename to sci-biology/neuroconv/neuroconv-0.4.8.ebuild index 1676aa6b7..a3012611f 100644 --- a/sci-biology/neuroconv/neuroconv-0.4.6-r1.ebuild +++ b/sci-biology/neuroconv/neuroconv-0.4.8.ebuild @@ -49,6 +49,12 @@ BDEPEND=" distutils_enable_tests pytest +# Reported upstream: +# https://github.com/catalystneuro/neuroconv/issues/785 +EPYTEST_DESELECT=( + tests/test_ecephys/test_mock_recording_interface.py::TestMockRecordingInterface::test_conversion_as_lone_interface +) + python_test() { # Additional tests require complex data getting infrastructure, ophys tests still have issues: # https://github.com/catalystneuro/neuroconv/issues/305
[gentoo-commits] proj/sci:master commit in: sci-biology/neuroconv/
commit: f9f093aa8035bb4656c98d054e00b5159e059153 Author: Horea Christian chymera eu> AuthorDate: Thu Jan 25 12:20:31 2024 + Commit: Horea Christian gmail com> CommitDate: Thu Jan 25 12:20:31 2024 + URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=f9f093aa sci-biology/neuroconv: updated dependency Signed-off-by: Horea Christian chymera.eu> .../neuroconv/{neuroconv-0.4.6.ebuild => neuroconv-0.4.6-r1.ebuild} | 1 + 1 file changed, 1 insertion(+) diff --git a/sci-biology/neuroconv/neuroconv-0.4.6.ebuild b/sci-biology/neuroconv/neuroconv-0.4.6-r1.ebuild similarity index 97% rename from sci-biology/neuroconv/neuroconv-0.4.6.ebuild rename to sci-biology/neuroconv/neuroconv-0.4.6-r1.ebuild index ac28a2da6..1676aa6b7 100644 --- a/sci-biology/neuroconv/neuroconv-0.4.6.ebuild +++ b/sci-biology/neuroconv/neuroconv-0.4.6-r1.ebuild @@ -19,6 +19,7 @@ IUSE="+ecephys +icephys +ophys" RDEPEND=" dev-python/h5py[${PYTHON_USEDEP}] dev-python/hdmf[${PYTHON_USEDEP}] + dev-python/hdmf-zarr[${PYTHON_USEDEP}] dev-python/jsonschema[${PYTHON_USEDEP}] dev-python/numpy[${PYTHON_USEDEP}] dev-python/nwbinspector[${PYTHON_USEDEP}]
[gentoo-commits] proj/sci:master commit in: sci-biology/neuroconv/
commit: a3e64508c08297dfc5951fd5d7d6d92961fe45ad Author: Horea Christian chymera eu> AuthorDate: Thu Jan 25 11:46:22 2024 + Commit: Horea Christian gmail com> CommitDate: Thu Jan 25 11:46:22 2024 + URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=a3e64508 sci-biology/neuroconv: add 0.4.6 Signed-off-by: Horea Christian chymera.eu> sci-biology/neuroconv/neuroconv-0.4.6.ebuild | 58 1 file changed, 58 insertions(+) diff --git a/sci-biology/neuroconv/neuroconv-0.4.6.ebuild b/sci-biology/neuroconv/neuroconv-0.4.6.ebuild new file mode 100644 index 0..ac28a2da6 --- /dev/null +++ b/sci-biology/neuroconv/neuroconv-0.4.6.ebuild @@ -0,0 +1,58 @@ +# Copyright 2021-2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{10..11} ) +DISTUTILS_USE_PEP517=setuptools +inherit distutils-r1 + +DESCRIPTION="Create NWB files from proprietary formats." +HOMEPAGE="https://github.com/catalystneuro/neuroconv"; +SRC_URI="https://github.com/catalystneuro/neuroconv/archive/refs/tags/v${PV}.tar.gz -> ${P}.gh.tar.gz" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64" +IUSE="+ecephys +icephys +ophys" + +RDEPEND=" + dev-python/h5py[${PYTHON_USEDEP}] + dev-python/hdmf[${PYTHON_USEDEP}] + dev-python/jsonschema[${PYTHON_USEDEP}] + dev-python/numpy[${PYTHON_USEDEP}] + dev-python/nwbinspector[${PYTHON_USEDEP}] + dev-python/pandas[${PYTHON_USEDEP}] + dev-python/parse[${PYTHON_USEDEP}] + dev-python/psutil[${PYTHON_USEDEP}] + dev-python/pynwb[${PYTHON_USEDEP}] + dev-python/pyyaml[${PYTHON_USEDEP}] + dev-python/scipy[${PYTHON_USEDEP}] + dev-python/tqdm[${PYTHON_USEDEP}] + dev-python/pydantic[${PYTHON_USEDEP}] + ecephys? ( + dev-python/spikeinterface[${PYTHON_USEDEP}] + ) + icephys? ( + dev-python/neo[${PYTHON_USEDEP}] + ) + ophys? ( + sci-biology/roiextractors[${PYTHON_USEDEP}] + ) +" +BDEPEND=" + test? ( + dev-python/parameterized[${PYTHON_USEDEP}] + ) +" + +distutils_enable_tests pytest + +python_test() { + # Additional tests require complex data getting infrastructure, ophys tests still have issues: + # https://github.com/catalystneuro/neuroconv/issues/305 + local my_tests=( "tests/test_minimal" ) + use ecephys && my_tests+=( "tests/test_ecephys" ) + #use ophys && my_tests+=( "tests/test_ophys" ) + epytest ${my_tests[*]// /|} +}
[gentoo-commits] proj/sci:master commit in: sci-biology/neuroconv/
commit: 116d00a2964bcf136fd7e093bd8ad415a670 Author: Horea Christian chymera eu> AuthorDate: Tue May 2 23:41:13 2023 + Commit: Horea Christian gmail com> CommitDate: Tue May 2 23:41:13 2023 + URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=116d00a2 sci-biology/neuroconv: enable py3.11 Signed-off-by: Horea Christian chymera.eu> sci-biology/neuroconv/neuroconv-0.2.4.ebuild | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/sci-biology/neuroconv/neuroconv-0.2.4.ebuild b/sci-biology/neuroconv/neuroconv-0.2.4.ebuild index 39046a1a5..c554ce791 100644 --- a/sci-biology/neuroconv/neuroconv-0.2.4.ebuild +++ b/sci-biology/neuroconv/neuroconv-0.2.4.ebuild @@ -3,7 +3,7 @@ EAPI=8 -PYTHON_COMPAT=( python3_{10..10} ) +PYTHON_COMPAT=( python3_{10..11} ) DISTUTILS_USE_PEP517=setuptools inherit distutils-r1
[gentoo-commits] proj/sci:master commit in: sci-biology/neuroconv/
commit: 95e72af97822eef8d7f6273b1f2751b9f4fbb670 Author: Horea Christian chymera eu> AuthorDate: Tue May 2 22:46:33 2023 + Commit: Horea Christian gmail com> CommitDate: Tue May 2 22:47:38 2023 + URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=95e72af9 sci-biology/neuroconv: brought back This reverts commit 3f8ff1293b126e52932e381d68d6451f65f11229. Signed-off-by: Horea Christian chymera.eu> sci-biology/neuroconv/metadata.xml | 21 +++ sci-biology/neuroconv/neuroconv-0.2.4.ebuild | 56 2 files changed, 77 insertions(+) diff --git a/sci-biology/neuroconv/metadata.xml b/sci-biology/neuroconv/metadata.xml new file mode 100644 index 0..efd00647e --- /dev/null +++ b/sci-biology/neuroconv/metadata.xml @@ -0,0 +1,21 @@ + +http://www.gentoo.org/dtd/metadata.dtd";> + + + gen...@chymera.eu + Horea Christian + + + s...@gentoo.org + Gentoo Science Project + + + Extracellular electrophysiology interfaces + Intracellular electrophysiology interfaces + Optical physiology interfaces + + + catalystneuro/roiextractors + roiextractors + + diff --git a/sci-biology/neuroconv/neuroconv-0.2.4.ebuild b/sci-biology/neuroconv/neuroconv-0.2.4.ebuild new file mode 100644 index 0..39046a1a5 --- /dev/null +++ b/sci-biology/neuroconv/neuroconv-0.2.4.ebuild @@ -0,0 +1,56 @@ +# Copyright 2021-2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{10..10} ) +DISTUTILS_USE_PEP517=setuptools +inherit distutils-r1 + +DESCRIPTION="Create NWB files from proprietary formats." +HOMEPAGE="https://github.com/catalystneuro/neuroconv"; +SRC_URI="https://github.com/catalystneuro/neuroconv/archive/refs/tags/v${PV}.tar.gz -> ${P}.gh.tar.gz" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64" +IUSE="+ecephys +icephys +ophys" + +RDEPEND=" + dev-python/h5py[${PYTHON_USEDEP}] + dev-python/hdmf[${PYTHON_USEDEP}] + dev-python/jsonschema[${PYTHON_USEDEP}] + dev-python/numpy[${PYTHON_USEDEP}] + dev-python/pandas[${PYTHON_USEDEP}] + dev-python/psutil[${PYTHON_USEDEP}] + dev-python/pynwb[${PYTHON_USEDEP}] + dev-python/pyyaml[${PYTHON_USEDEP}] + dev-python/scipy[${PYTHON_USEDEP}] + dev-python/tqdm[${PYTHON_USEDEP}] + dev-vcs/dandi-cli[${PYTHON_USEDEP}] + ecephys? ( + dev-python/spikeinterface[${PYTHON_USEDEP}] + ) + icephys? ( + dev-python/neo[${PYTHON_USEDEP}] + ) + ophys? ( + sci-biology/roiextractors[${PYTHON_USEDEP}] + ) +" +BDEPEND=" + test? ( + dev-python/parameterized[${PYTHON_USEDEP}] + ) +" + +distutils_enable_tests pytest + +python_test() { + # Additional tests require complex data getting infrastructure, ophys tests still have issues: + # https://github.com/catalystneuro/neuroconv/issues/305 + local my_tests=( "tests/test_minimal" ) + use ecephys && my_tests+=( "tests/test_ecephys" ) + #use ophys && my_tests+=( "tests/test_ophys" ) + epytest ${my_tests[*]// /|} +}
[gentoo-commits] proj/sci:master commit in: sci-biology/neuroconv/
commit: 3f8ff1293b126e52932e381d68d6451f65f11229 Author: Andrew Ammerlaan gentoo org> AuthorDate: Tue May 2 12:44:23 2023 + Commit: Andrew Ammerlaan gentoo org> CommitDate: Tue May 2 12:44:23 2023 + URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=3f8ff129 sci-biology/neuroconv: treeclean Signed-off-by: Andrew Ammerlaan gentoo.org> sci-biology/neuroconv/metadata.xml | 21 --- sci-biology/neuroconv/neuroconv-0.2.4.ebuild | 56 2 files changed, 77 deletions(-) diff --git a/sci-biology/neuroconv/metadata.xml b/sci-biology/neuroconv/metadata.xml deleted file mode 100644 index efd00647e..0 --- a/sci-biology/neuroconv/metadata.xml +++ /dev/null @@ -1,21 +0,0 @@ - -http://www.gentoo.org/dtd/metadata.dtd";> - - - gen...@chymera.eu - Horea Christian - - - s...@gentoo.org - Gentoo Science Project - - - Extracellular electrophysiology interfaces - Intracellular electrophysiology interfaces - Optical physiology interfaces - - - catalystneuro/roiextractors - roiextractors - - diff --git a/sci-biology/neuroconv/neuroconv-0.2.4.ebuild b/sci-biology/neuroconv/neuroconv-0.2.4.ebuild deleted file mode 100644 index 39046a1a5..0 --- a/sci-biology/neuroconv/neuroconv-0.2.4.ebuild +++ /dev/null @@ -1,56 +0,0 @@ -# Copyright 2021-2023 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=8 - -PYTHON_COMPAT=( python3_{10..10} ) -DISTUTILS_USE_PEP517=setuptools -inherit distutils-r1 - -DESCRIPTION="Create NWB files from proprietary formats." -HOMEPAGE="https://github.com/catalystneuro/neuroconv"; -SRC_URI="https://github.com/catalystneuro/neuroconv/archive/refs/tags/v${PV}.tar.gz -> ${P}.gh.tar.gz" - -LICENSE="BSD" -SLOT="0" -KEYWORDS="~amd64" -IUSE="+ecephys +icephys +ophys" - -RDEPEND=" - dev-python/h5py[${PYTHON_USEDEP}] - dev-python/hdmf[${PYTHON_USEDEP}] - dev-python/jsonschema[${PYTHON_USEDEP}] - dev-python/numpy[${PYTHON_USEDEP}] - dev-python/pandas[${PYTHON_USEDEP}] - dev-python/psutil[${PYTHON_USEDEP}] - dev-python/pynwb[${PYTHON_USEDEP}] - dev-python/pyyaml[${PYTHON_USEDEP}] - dev-python/scipy[${PYTHON_USEDEP}] - dev-python/tqdm[${PYTHON_USEDEP}] - dev-vcs/dandi-cli[${PYTHON_USEDEP}] - ecephys? ( - dev-python/spikeinterface[${PYTHON_USEDEP}] - ) - icephys? ( - dev-python/neo[${PYTHON_USEDEP}] - ) - ophys? ( - sci-biology/roiextractors[${PYTHON_USEDEP}] - ) -" -BDEPEND=" - test? ( - dev-python/parameterized[${PYTHON_USEDEP}] - ) -" - -distutils_enable_tests pytest - -python_test() { - # Additional tests require complex data getting infrastructure, ophys tests still have issues: - # https://github.com/catalystneuro/neuroconv/issues/305 - local my_tests=( "tests/test_minimal" ) - use ecephys && my_tests+=( "tests/test_ecephys" ) - #use ophys && my_tests+=( "tests/test_ophys" ) - epytest ${my_tests[*]// /|} -}
[gentoo-commits] proj/sci:master commit in: sci-biology/neuroconv/
commit: 6b9b4d6de57257950c5ed59ca8e484328c9ac2a9 Author: Horea Christian chymera eu> AuthorDate: Mon Feb 20 18:45:34 2023 + Commit: Horea Christian gmail com> CommitDate: Mon Feb 20 18:45:34 2023 + URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=6b9b4d6d sci-biology/neuroconv: new package, add 0.2.4 Signed-off-by: Horea Christian chymera.eu> sci-biology/neuroconv/metadata.xml | 21 +++ sci-biology/neuroconv/neuroconv-0.2.4.ebuild | 56 2 files changed, 77 insertions(+) diff --git a/sci-biology/neuroconv/metadata.xml b/sci-biology/neuroconv/metadata.xml new file mode 100644 index 0..efd00647e --- /dev/null +++ b/sci-biology/neuroconv/metadata.xml @@ -0,0 +1,21 @@ + +http://www.gentoo.org/dtd/metadata.dtd";> + + + gen...@chymera.eu + Horea Christian + + + s...@gentoo.org + Gentoo Science Project + + + Extracellular electrophysiology interfaces + Intracellular electrophysiology interfaces + Optical physiology interfaces + + + catalystneuro/roiextractors + roiextractors + + diff --git a/sci-biology/neuroconv/neuroconv-0.2.4.ebuild b/sci-biology/neuroconv/neuroconv-0.2.4.ebuild new file mode 100644 index 0..39046a1a5 --- /dev/null +++ b/sci-biology/neuroconv/neuroconv-0.2.4.ebuild @@ -0,0 +1,56 @@ +# Copyright 2021-2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{10..10} ) +DISTUTILS_USE_PEP517=setuptools +inherit distutils-r1 + +DESCRIPTION="Create NWB files from proprietary formats." +HOMEPAGE="https://github.com/catalystneuro/neuroconv"; +SRC_URI="https://github.com/catalystneuro/neuroconv/archive/refs/tags/v${PV}.tar.gz -> ${P}.gh.tar.gz" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64" +IUSE="+ecephys +icephys +ophys" + +RDEPEND=" + dev-python/h5py[${PYTHON_USEDEP}] + dev-python/hdmf[${PYTHON_USEDEP}] + dev-python/jsonschema[${PYTHON_USEDEP}] + dev-python/numpy[${PYTHON_USEDEP}] + dev-python/pandas[${PYTHON_USEDEP}] + dev-python/psutil[${PYTHON_USEDEP}] + dev-python/pynwb[${PYTHON_USEDEP}] + dev-python/pyyaml[${PYTHON_USEDEP}] + dev-python/scipy[${PYTHON_USEDEP}] + dev-python/tqdm[${PYTHON_USEDEP}] + dev-vcs/dandi-cli[${PYTHON_USEDEP}] + ecephys? ( + dev-python/spikeinterface[${PYTHON_USEDEP}] + ) + icephys? ( + dev-python/neo[${PYTHON_USEDEP}] + ) + ophys? ( + sci-biology/roiextractors[${PYTHON_USEDEP}] + ) +" +BDEPEND=" + test? ( + dev-python/parameterized[${PYTHON_USEDEP}] + ) +" + +distutils_enable_tests pytest + +python_test() { + # Additional tests require complex data getting infrastructure, ophys tests still have issues: + # https://github.com/catalystneuro/neuroconv/issues/305 + local my_tests=( "tests/test_minimal" ) + use ecephys && my_tests+=( "tests/test_ecephys" ) + #use ophys && my_tests+=( "tests/test_ophys" ) + epytest ${my_tests[*]// /|} +}