* [gentoo-commits] proj/sci:master commit in: sci-biology/neuroconv/
@ 2024-01-25 11:46 Horea Christian
0 siblings, 0 replies; 8+ messages in thread
From: Horea Christian @ 2024-01-25 11:46 UTC (permalink / raw
To: gentoo-commits
commit: a3e64508c08297dfc5951fd5d7d6d92961fe45ad
Author: Horea Christian <chr <AT> chymera <DOT> eu>
AuthorDate: Thu Jan 25 11:46:22 2024 +0000
Commit: Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Thu Jan 25 11:46:22 2024 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=a3e64508
sci-biology/neuroconv: add 0.4.6
Signed-off-by: Horea Christian <chr <AT> 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 000000000..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 ${my_tests[*]// /|}
+}
^ permalink raw reply related [flat|nested] 8+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/neuroconv/
@ 2024-04-03 0:00 Horea Christian
0 siblings, 0 replies; 8+ messages in thread
From: Horea Christian @ 2024-04-03 0:00 UTC (permalink / raw
To: gentoo-commits
commit: 73916dd3680ffd92e5bd3d32b262e5d78c86a448
Author: Horea Christian <chr <AT> chymera <DOT> eu>
AuthorDate: Tue Apr 2 23:56:26 2024 +0000
Commit: Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Wed Apr 3 00:00:03 2024 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=73916dd3
sci-biology/neuroconv: dependency revbump
Signed-off-by: Horea Christian <chr <AT> chymera.eu>
.../neuroconv/{neuroconv-0.4.8.ebuild => neuroconv-0.4.8-r1.ebuild} | 5 +++--
1 file changed, 3 insertions(+), 2 deletions(-)
diff --git a/sci-biology/neuroconv/neuroconv-0.4.8.ebuild b/sci-biology/neuroconv/neuroconv-0.4.8-r1.ebuild
similarity index 97%
rename from sci-biology/neuroconv/neuroconv-0.4.8.ebuild
rename to sci-biology/neuroconv/neuroconv-0.4.8-r1.ebuild
index a3012611f..b21c2fd8e 100644
--- a/sci-biology/neuroconv/neuroconv-0.4.8.ebuild
+++ b/sci-biology/neuroconv/neuroconv-0.4.8-r1.ebuild
@@ -17,20 +17,21 @@ KEYWORDS="~amd64"
IUSE="+ecephys +icephys +ophys"
RDEPEND="
+ dev-python/docstring-parser[${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[${PYTHON_USEDEP}]
)
^ permalink raw reply related [flat|nested] 8+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/neuroconv/
@ 2024-03-21 22:15 Horea Christian
0 siblings, 0 replies; 8+ messages in thread
From: Horea Christian @ 2024-03-21 22:15 UTC (permalink / raw
To: gentoo-commits
commit: 597997e35db5451deb6079df099686bc085b732a
Author: Horea Christian <chr <AT> chymera <DOT> eu>
AuthorDate: Thu Mar 21 22:10:03 2024 +0000
Commit: Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Thu Mar 21 22:15:29 2024 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=597997e3
sci-biology/neuroconv: version bump, treeclean
Signed-off-by: Horea Christian <chr <AT> chymera.eu>
sci-biology/neuroconv/neuroconv-0.2.4.ebuild | 56 ----------------------
...conv-0.4.6-r1.ebuild => neuroconv-0.4.8.ebuild} | 6 +++
2 files changed, 6 insertions(+), 56 deletions(-)
diff --git a/sci-biology/neuroconv/neuroconv-0.2.4.ebuild b/sci-biology/neuroconv/neuroconv-0.2.4.ebuild
deleted file mode 100644
index c554ce791..000000000
--- a/sci-biology/neuroconv/neuroconv-0.2.4.ebuild
+++ /dev/null
@@ -1,56 +0,0 @@
-# Copyright 2021-2023 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-PYTHON_COMPAT=( python3_{10..11} )
-DISTUTILS_USE_PEP517=setuptools
-inherit distutils-r1
-
-DESCRIPTION="Create NWB files from proprietary formats."
-HOMEPAGE="https://github.com/catalystneuro/neuroconv"
-SRC_URI="https://github.com/catalystneuro/neuroconv/archive/refs/tags/v${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
^ permalink raw reply related [flat|nested] 8+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/neuroconv/
@ 2024-01-25 12:25 Horea Christian
0 siblings, 0 replies; 8+ messages in thread
From: Horea Christian @ 2024-01-25 12:25 UTC (permalink / raw
To: gentoo-commits
commit: f9f093aa8035bb4656c98d054e00b5159e059153
Author: Horea Christian <chr <AT> chymera <DOT> eu>
AuthorDate: Thu Jan 25 12:20:31 2024 +0000
Commit: Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Thu Jan 25 12:20:31 2024 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=f9f093aa
sci-biology/neuroconv: updated dependency
Signed-off-by: Horea Christian <chr <AT> 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}]
^ permalink raw reply related [flat|nested] 8+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/neuroconv/
@ 2023-05-02 23:41 Horea Christian
0 siblings, 0 replies; 8+ messages in thread
From: Horea Christian @ 2023-05-02 23:41 UTC (permalink / raw
To: gentoo-commits
commit: 116d00a2964bcf136fd7e093bd99998ad415a670
Author: Horea Christian <chr <AT> chymera <DOT> eu>
AuthorDate: Tue May 2 23:41:13 2023 +0000
Commit: Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Tue May 2 23:41:13 2023 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=116d00a2
sci-biology/neuroconv: enable py3.11
Signed-off-by: Horea Christian <chr <AT> 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
^ permalink raw reply related [flat|nested] 8+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/neuroconv/
@ 2023-05-02 23:01 Horea Christian
0 siblings, 0 replies; 8+ messages in thread
From: Horea Christian @ 2023-05-02 23:01 UTC (permalink / raw
To: gentoo-commits
commit: 95e72af97822eef8d7f6273b1f2751b9f4fbb670
Author: Horea Christian <chr <AT> chymera <DOT> eu>
AuthorDate: Tue May 2 22:46:33 2023 +0000
Commit: Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Tue May 2 22:47:38 2023 +0000
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 <chr <AT> 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 000000000..efd00647e
--- /dev/null
+++ b/sci-biology/neuroconv/metadata.xml
@@ -0,0 +1,21 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <maintainer type="person">
+ <email>gentoo@chymera.eu</email>
+ <name>Horea Christian</name>
+ </maintainer>
+ <maintainer type="project">
+ <email>sci@gentoo.org</email>
+ <name>Gentoo Science Project</name>
+ </maintainer>
+ <use>
+ <flag name="ecephys">Extracellular electrophysiology interfaces</flag>
+ <flag name="icephys">Intracellular electrophysiology interfaces</flag>
+ <flag name="ophys">Optical physiology interfaces</flag>
+ </use>
+ <upstream>
+ <remote-id type="github">catalystneuro/roiextractors</remote-id>
+ <remote-id type="pypi">roiextractors</remote-id>
+ </upstream>
+</pkgmetadata>
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 000000000..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[*]// /|}
+}
^ permalink raw reply related [flat|nested] 8+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/neuroconv/
@ 2023-05-02 12:44 Andrew Ammerlaan
0 siblings, 0 replies; 8+ messages in thread
From: Andrew Ammerlaan @ 2023-05-02 12:44 UTC (permalink / raw
To: gentoo-commits
commit: 3f8ff1293b126e52932e381d68d6451f65f11229
Author: Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
AuthorDate: Tue May 2 12:44:23 2023 +0000
Commit: Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
CommitDate: Tue May 2 12:44:23 2023 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=3f8ff129
sci-biology/neuroconv: treeclean
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> 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..000000000
--- a/sci-biology/neuroconv/metadata.xml
+++ /dev/null
@@ -1,21 +0,0 @@
-<?xml version='1.0' encoding='UTF-8'?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <maintainer type="person">
- <email>gentoo@chymera.eu</email>
- <name>Horea Christian</name>
- </maintainer>
- <maintainer type="project">
- <email>sci@gentoo.org</email>
- <name>Gentoo Science Project</name>
- </maintainer>
- <use>
- <flag name="ecephys">Extracellular electrophysiology interfaces</flag>
- <flag name="icephys">Intracellular electrophysiology interfaces</flag>
- <flag name="ophys">Optical physiology interfaces</flag>
- </use>
- <upstream>
- <remote-id type="github">catalystneuro/roiextractors</remote-id>
- <remote-id type="pypi">roiextractors</remote-id>
- </upstream>
-</pkgmetadata>
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..000000000
--- 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[*]// /|}
-}
^ permalink raw reply related [flat|nested] 8+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/neuroconv/
@ 2023-02-20 18:45 Horea Christian
0 siblings, 0 replies; 8+ messages in thread
From: Horea Christian @ 2023-02-20 18:45 UTC (permalink / raw
To: gentoo-commits
commit: 6b9b4d6de57257950c5ed59ca8e484328c9ac2a9
Author: Horea Christian <chr <AT> chymera <DOT> eu>
AuthorDate: Mon Feb 20 18:45:34 2023 +0000
Commit: Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Mon Feb 20 18:45:34 2023 +0000
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 <chr <AT> 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 000000000..efd00647e
--- /dev/null
+++ b/sci-biology/neuroconv/metadata.xml
@@ -0,0 +1,21 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <maintainer type="person">
+ <email>gentoo@chymera.eu</email>
+ <name>Horea Christian</name>
+ </maintainer>
+ <maintainer type="project">
+ <email>sci@gentoo.org</email>
+ <name>Gentoo Science Project</name>
+ </maintainer>
+ <use>
+ <flag name="ecephys">Extracellular electrophysiology interfaces</flag>
+ <flag name="icephys">Intracellular electrophysiology interfaces</flag>
+ <flag name="ophys">Optical physiology interfaces</flag>
+ </use>
+ <upstream>
+ <remote-id type="github">catalystneuro/roiextractors</remote-id>
+ <remote-id type="pypi">roiextractors</remote-id>
+ </upstream>
+</pkgmetadata>
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 000000000..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[*]// /|}
+}
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