From mboxrd@z Thu Jan 1 00:00:00 1970 Return-Path: Received: from lists.gentoo.org (pigeon.gentoo.org [208.92.234.80]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) key-exchange X25519 server-signature RSA-PSS (2048 bits)) (No client certificate requested) by finch.gentoo.org (Postfix) with ESMTPS id 2910415A7D9 for ; Wed, 22 Mar 2023 19:39:28 +0000 (UTC) Received: from pigeon.gentoo.org (localhost [127.0.0.1]) by pigeon.gentoo.org (Postfix) with SMTP id 08E5EE07E1; Wed, 22 Mar 2023 19:39:27 +0000 (UTC) Received: from smtp.gentoo.org (woodpecker.gentoo.org [140.211.166.183]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) key-exchange X25519 server-signature RSA-PSS (4096 bits) server-digest SHA256) (No client certificate requested) by pigeon.gentoo.org (Postfix) with ESMTPS id DF7E7E07E1 for ; Wed, 22 Mar 2023 19:39:26 +0000 (UTC) Received: from oystercatcher.gentoo.org (oystercatcher.gentoo.org [148.251.78.52]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) key-exchange X25519 server-signature RSA-PSS (4096 bits) server-digest SHA256) (No client certificate requested) by smtp.gentoo.org (Postfix) with ESMTPS id 63E46340B1C for ; Wed, 22 Mar 2023 19:39:25 +0000 (UTC) Received: from localhost.localdomain (localhost [IPv6:::1]) by oystercatcher.gentoo.org (Postfix) with ESMTP id 91EE97F5 for ; Wed, 22 Mar 2023 19:39:23 +0000 (UTC) From: "Horea Christian" To: gentoo-commits@lists.gentoo.org Content-Transfer-Encoding: 8bit Content-type: text/plain; charset=UTF-8 Reply-To: gentoo-dev@lists.gentoo.org, "Horea Christian" Message-ID: <1679513952.16797f5b3289b8970625b8c03645e9a6a5fcaa04.chymera@gentoo> Subject: [gentoo-commits] proj/sci:master commit in: dev-python/pynwb/, dev-python/pynwb/files/ X-VCS-Repository: proj/sci X-VCS-Files: dev-python/pynwb/files/pynwb-2.3.1-typing.patch dev-python/pynwb/pynwb-2.3.1.ebuild X-VCS-Directories: dev-python/pynwb/ dev-python/pynwb/files/ X-VCS-Committer: chymera X-VCS-Committer-Name: Horea Christian X-VCS-Revision: 16797f5b3289b8970625b8c03645e9a6a5fcaa04 X-VCS-Branch: master Date: Wed, 22 Mar 2023 19:39:23 +0000 (UTC) Precedence: bulk List-Post: List-Help: List-Unsubscribe: List-Subscribe: List-Id: Gentoo Linux mail X-BeenThere: gentoo-commits@lists.gentoo.org X-Auto-Response-Suppress: DR, RN, NRN, OOF, AutoReply X-Archives-Salt: fda2c0fb-631b-48a6-bb4f-b6772de01835 X-Archives-Hash: d018976c198f9a65b68c4c2681b348a4 commit: 16797f5b3289b8970625b8c03645e9a6a5fcaa04 Author: Horea Christian chymera eu> AuthorDate: Wed Mar 22 19:39:12 2023 +0000 Commit: Horea Christian gmail com> CommitDate: Wed Mar 22 19:39:12 2023 +0000 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 000000000..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 000000000..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