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commit: 67e6080551c80d384ee79713470e20396317a8f1 |
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Author: Horea Christian <chr <AT> chymera <DOT> eu> |
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AuthorDate: Mon Jan 31 08:15:27 2022 +0000 |
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Commit: Horea Christian <horea.christ <AT> gmail <DOT> com> |
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CommitDate: Mon Jan 31 08:15:27 2022 +0000 |
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URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=67e60805 |
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|
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dev-python/pynwb: new package (DANDI stack) |
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|
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Package-Manager: Portage-3.0.30, Repoman-3.0.3 |
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Signed-off-by: Horea Christian <chr <AT> chymera.eu> |
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|
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dev-python/pynwb/ChangeLog | 6 +++ |
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dev-python/pynwb/files/pynwb-2.0.0-versions.patch | 21 ++++++++++ |
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dev-python/pynwb/metadata.xml | 20 ++++++++++ |
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dev-python/pynwb/pynwb-2.0.0.ebuild | 46 ++++++++++++++++++++++ |
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dev-python/pynwb/pynwb-2.0.0_p0.ebuild | 47 +++++++++++++++++++++++ |
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5 files changed, 140 insertions(+) |
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|
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diff --git a/dev-python/pynwb/ChangeLog b/dev-python/pynwb/ChangeLog |
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new file mode 100644 |
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index 000000000..1eee46e49 |
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--- /dev/null |
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+++ b/dev-python/pynwb/ChangeLog |
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@@ -0,0 +1,6 @@ |
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+*pynwb-2.0.0_p0 (31 Jan 2022) |
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+ |
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+ 31 Jan 2022; <chymera@g.o> +files/pynwb-2.0.0-versions.patch, |
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+ +pynwb-2.0.0_p0.ebuild, pynwb-2.0.0.ebuild: |
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+ dev-python/pynwb: version bump and test skip linking skipped test reports on |
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+ upstream issue treacker |
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|
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diff --git a/dev-python/pynwb/files/pynwb-2.0.0-versions.patch b/dev-python/pynwb/files/pynwb-2.0.0-versions.patch |
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new file mode 100644 |
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index 000000000..d09c50594 |
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--- /dev/null |
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+++ b/dev-python/pynwb/files/pynwb-2.0.0-versions.patch |
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@@ -0,0 +1,21 @@ |
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+diff --git a/setup.py b/tmp/setup.py |
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+index 39e75824..f7948f64 100755 |
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+--- a/setup.py |
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++++ b/setup.py |
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+@@ -19,11 +19,11 @@ print('found these packages:', pkgs) |
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+ schema_dir = 'nwb-schema/core' |
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+ |
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+ reqs = [ |
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+- 'h5py>=2.9,<4', |
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+- 'hdmf>=3.1.1,<4', |
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+- 'numpy>=1.16,<1.22', |
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+- 'pandas>=1.0.5,<2', |
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+- 'python-dateutil>=2.7,<3', |
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++ 'h5py', |
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++ 'hdmf', |
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++ 'numpy', |
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++ 'pandas', |
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++ 'python-dateutil', |
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+ 'setuptools' |
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+ ] |
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+ |
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|
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diff --git a/dev-python/pynwb/metadata.xml b/dev-python/pynwb/metadata.xml |
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new file mode 100644 |
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index 000000000..99512b574 |
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--- /dev/null |
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+++ b/dev-python/pynwb/metadata.xml |
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@@ -0,0 +1,20 @@ |
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+<?xml version='1.0' encoding='UTF-8'?> |
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+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> |
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+<pkgmetadata> |
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+ <maintainer type="person"> |
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+ <email>gentoo@×××××××.eu</email> |
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+ <name>Horea Christian</name> |
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+ </maintainer> |
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+ <maintainer type="project"> |
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+ <email>sci@g.o</email> |
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+ <name>Gentoo Science Project</name> |
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+ </maintainer> |
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+ <longdescription lang="en"> |
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+ PyNWB is a Python package for working with NWB files. It provides a |
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+ high-level API for efficiently working with Neurodata stored in the NWB |
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+ format. Neurodata Without Borders: Neurophysiology (NWB:N) is a project |
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+ to develop a unified data format for cellular-based neurophysiology |
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+ data, focused on the dynamics of groups of neurons measured under a |
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+ large range of experimental conditions. |
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+ </longdescription> |
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+</pkgmetadata> |
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|
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diff --git a/dev-python/pynwb/pynwb-2.0.0.ebuild b/dev-python/pynwb/pynwb-2.0.0.ebuild |
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new file mode 100644 |
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index 000000000..b0294a4e0 |
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--- /dev/null |
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+++ b/dev-python/pynwb/pynwb-2.0.0.ebuild |
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@@ -0,0 +1,46 @@ |
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+# Copyright 1999-2022 Gentoo Authors |
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+# Distributed under the terms of the GNU General Public License v2 |
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+ |
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+EAPI=8 |
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+ |
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+PYTHON_COMPAT=( python3_{8..10} ) |
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+inherit distutils-r1 |
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+ |
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+DESCRIPTION="A Python API for working with Neurodata stored in the NWB Format " |
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+HOMEPAGE="https://github.com/NeurodataWithoutBorders/pynwb" |
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+SRC_URI="https://github.com/NeurodataWithoutBorders/pynwb/releases/download/${PV}/${P}.tar.gz" |
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+ |
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+SLOT="0" |
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+LICENSE="BSD" |
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+KEYWORDS="~amd64 ~x86" |
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+ |
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+RDEPEND=" |
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+ sci-libs/hdf5[ros3] |
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+ dev-python/hdmf[${PYTHON_USEDEP}] |
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+ dev-python/h5py[${PYTHON_USEDEP}] |
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+ dev-python/numpy[${PYTHON_USEDEP}] |
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+ dev-python/pandas[${PYTHON_USEDEP}] |
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+ dev-python/python-dateutil[${PYTHON_USEDEP}] |
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+ " |
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+BDEPEND="" |
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+ |
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+PATCHES=( |
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+ "${FILESDIR}/${P}-versions.patch" |
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+ ) |
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+ |
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+EPYTEST_DESELECT=( |
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+ # Reported upsream: |
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+ # https://github.com/dandi/dandischema/issues/87 |
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+ tests/validation/test_validate.py::TestValidateScript::test_validate_file_cached |
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+ tests/validation/test_validate.py::TestValidateScript::test_validate_file_cached_bad_ns |
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+ tests/validation/test_validate.py::TestValidateScript::test_validate_file_cached_hdmf_common |
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+ tests/validation/test_validate.py::TestValidateScript::test_validate_file_cached_ignore |
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+ tests/validation/test_validate.py::TestValidateScript::test_validate_file_no_cache |
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+ tests/validation/test_validate.py::TestValidateScript::test_validate_file_no_cache_bad_ns |
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+ # Reported upstream and fixed in newer version: |
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+ # https://github.com/NeurodataWithoutBorders/pynwb/issues/1412#issuecomment-934153799 |
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+ tests/integration/ros3/test_ros3.py::TestRos3Streaming::test_dandi_read |
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+ tests/integration/ros3/test_ros3.py::TestRos3Streaming::test_read |
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+) |
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+ |
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+distutils_enable_tests pytest |
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|
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diff --git a/dev-python/pynwb/pynwb-2.0.0_p0.ebuild b/dev-python/pynwb/pynwb-2.0.0_p0.ebuild |
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new file mode 100644 |
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index 000000000..fba3e6319 |
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--- /dev/null |
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+++ b/dev-python/pynwb/pynwb-2.0.0_p0.ebuild |
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@@ -0,0 +1,47 @@ |
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+# Copyright 1999-2022 Gentoo Authors |
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+# Distributed under the terms of the GNU General Public License v2 |
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+ |
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+EAPI=8 |
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+ |
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+PYTHON_COMPAT=( python3_{8..10} ) |
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+inherit distutils-r1 |
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+ |
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+MY_PV="${PV/_p/.post}.dev5" |
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+MY_P="${PN}-${MY_PV}" |
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+ |
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+DESCRIPTION="A Python API for working with Neurodata stored in the NWB Format " |
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+HOMEPAGE="https://github.com/NeurodataWithoutBorders/pynwb" |
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+SRC_URI="https://github.com/NeurodataWithoutBorders/pynwb/releases/download/latest/${MY_P}.tar.gz" |
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+ |
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+SLOT="0" |
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+LICENSE="BSD" |
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+KEYWORDS="~amd64 ~x86" |
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+ |
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+RDEPEND=" |
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+ sci-libs/hdf5[ros3] |
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+ dev-python/hdmf[${PYTHON_USEDEP}] |
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+ dev-python/h5py[${PYTHON_USEDEP}] |
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+ dev-python/numpy[${PYTHON_USEDEP}] |
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+ dev-python/pandas[${PYTHON_USEDEP}] |
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+ dev-python/python-dateutil[${PYTHON_USEDEP}] |
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+ " |
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+BDEPEND="" |
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+ |
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+PATCHES=( |
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+ "${FILESDIR}/${PN}-2.0.0-versions.patch" |
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+ ) |
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+ |
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+S="${WORKDIR}/${MY_P}" |
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+ |
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+EPYTEST_DESELECT=( |
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+ # Reported upsream |
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+ # https://github.com/dandi/dandischema/issues/87 |
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+ tests/validation/test_validate.py::TestValidateScript::test_validate_file_cached |
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+ tests/validation/test_validate.py::TestValidateScript::test_validate_file_cached_bad_ns |
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+ tests/validation/test_validate.py::TestValidateScript::test_validate_file_cached_hdmf_common |
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+ tests/validation/test_validate.py::TestValidateScript::test_validate_file_cached_ignore |
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+ tests/validation/test_validate.py::TestValidateScript::test_validate_file_no_cache |
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+ tests/validation/test_validate.py::TestValidateScript::test_validate_file_no_cache_bad_ns |
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+) |
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+ |
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+distutils_enable_tests pytest |