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-rw-r--r--sci-biology/afni/afni-24.0.04-r1.ebuild (renamed from sci-biology/afni/afni-24.0.04.ebuild)1
-rw-r--r--sci-biology/afni/afni-24.0.08-r1.ebuild (renamed from sci-biology/afni/afni-24.0.08.ebuild)1
-rw-r--r--sci-biology/fsl/fsl-6.0.4.ebuild4
-rw-r--r--sci-biology/neuroconv/Manifest3
-rw-r--r--sci-biology/neuroconv/neuroconv-0.2.4.ebuild56
-rw-r--r--sci-biology/neuroconv/neuroconv-0.4.8-r1.ebuild (renamed from sci-biology/neuroconv/neuroconv-0.4.6-r1.ebuild)11
6 files changed, 12 insertions, 64 deletions
diff --git a/sci-biology/afni/afni-24.0.04.ebuild b/sci-biology/afni/afni-24.0.04-r1.ebuild
index c00ef846f..557fbd579 100644
--- a/sci-biology/afni/afni-24.0.04.ebuild
+++ b/sci-biology/afni/afni-24.0.04-r1.ebuild
@@ -40,7 +40,6 @@ RDEPEND="
sci-libs/gts
sys-devel/llvm:*
sys-libs/libomp
- dev-libs/libpthread-stubs
virtual/jpeg-compat:62
x11-libs/libGLw
x11-libs/libXft
diff --git a/sci-biology/afni/afni-24.0.08.ebuild b/sci-biology/afni/afni-24.0.08-r1.ebuild
index 75ff5b6b6..20293877f 100644
--- a/sci-biology/afni/afni-24.0.08.ebuild
+++ b/sci-biology/afni/afni-24.0.08-r1.ebuild
@@ -40,7 +40,6 @@ RDEPEND="
sci-libs/gts
sys-devel/llvm:*
sys-libs/libomp
- dev-libs/libpthread-stubs
virtual/jpeg-compat:62
x11-libs/libGLw
x11-libs/libXft
diff --git a/sci-biology/fsl/fsl-6.0.4.ebuild b/sci-biology/fsl/fsl-6.0.4.ebuild
index cd91cf192..6e5d6e779 100644
--- a/sci-biology/fsl/fsl-6.0.4.ebuild
+++ b/sci-biology/fsl/fsl-6.0.4.ebuild
@@ -151,8 +151,8 @@ src_compile() {
# define the default build system to match upstream official standard
# -> individual projects may overwrite the '-std=' flag
- export ANSI_CFLAGS="-std=c99"
- export ANSI_CXXFLAGS="-std=c++98"
+ export ANSI_CFLAGS="-std=c11"
+ export ANSI_CXXFLAGS="-std=c++11"
export USERLDFLAGS="${LDFLAGS}"
export USERCFLAGS="${CFLAGS}"
diff --git a/sci-biology/neuroconv/Manifest b/sci-biology/neuroconv/Manifest
index 1963b7225..35c461b92 100644
--- a/sci-biology/neuroconv/Manifest
+++ b/sci-biology/neuroconv/Manifest
@@ -1,2 +1 @@
-DIST neuroconv-0.2.4.gh.tar.gz 757136 BLAKE2B a3a21b3a00667bde4461d91ade514891c8710f309413b100e1cccfd2684dfcbf9b21feaf4f58b3c5ff845aa08e69bf47467b411926eeb7d3b2862753302b1d9b SHA512 293038feae2704442b81ba0f012d775ba96d7bdffb6aaacaaebd09ca2f8b39e91ef4ea69c972abf060f0f9ab8cb76fedb77dda67455fa992edd52f0e6e504b0d
-DIST neuroconv-0.4.6.gh.tar.gz 1000357 BLAKE2B 24fc43a4c7c1cb588b5af49c1da2348f775506efd0c36b838b7882cf4a03520dac6e0fe6fd17310c17ae84371d3eeb8e3aec4b16fc3b07c10bec2e3c46e51dff SHA512 eeccc6900b6ae9f053f67503a93c4040033afc8b056b8869ad562f7cd2dd802cce2b7a467b5ccaa20fe84a188697821c328043b6177302d1913a30a5a789ae15
+DIST neuroconv-0.4.8.gh.tar.gz 1020546 BLAKE2B 880d7c4bdce3faf3bc969c9a0fd4206e1fd9d57254e40aa1181cf2d8f48abd72491b8b66d8ccc1988a623f8b2a8be160f2575f59ea69080a8bb6ed501c389881 SHA512 d06a625823a71f21a5eac957e452ab80b6fb847fc5f8c8e68fb6c46360402c4bc338f7fc611537272e72c0b72555a2951c346d38aa89c8ac8b209921ea7af72d
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 ${my_tests[*]// /|}
-}
diff --git a/sci-biology/neuroconv/neuroconv-0.4.6-r1.ebuild b/sci-biology/neuroconv/neuroconv-0.4.8-r1.ebuild
index 1676aa6b7..b21c2fd8e 100644
--- a/sci-biology/neuroconv/neuroconv-0.4.6-r1.ebuild
+++ b/sci-biology/neuroconv/neuroconv-0.4.8-r1.ebuild
@@ -17,20 +17,21 @@ KEYWORDS="~amd64"
IUSE="+ecephys +icephys +ophys"
RDEPEND="
+ dev-python/docstring-parser[${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}]
)
@@ -49,6 +50,12 @@ 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