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) server-digest SHA256) (No client certificate requested) by finch.gentoo.org (Postfix) with ESMTPS id 95669158010 for ; Tue, 31 Jan 2023 21:27:31 +0000 (UTC) Received: from pigeon.gentoo.org (localhost [127.0.0.1]) by pigeon.gentoo.org (Postfix) with SMTP id 599C1E0AB6; Tue, 31 Jan 2023 21:27:30 +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 391DCE0AAE for ; Tue, 31 Jan 2023 21:27:30 +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 E15EE340CD9 for ; Tue, 31 Jan 2023 21:27:28 +0000 (UTC) Received: from localhost.localdomain (localhost [IPv6:::1]) by oystercatcher.gentoo.org (Postfix) with ESMTP id 63E8962F for ; Tue, 31 Jan 2023 21:27:26 +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: <1675200284.70e2057641f5a42ec3eb46de196fea112a6955d0.chymera@gentoo> Subject: [gentoo-commits] proj/sci:master commit in: dev-python/heudiconv/files/, dev-python/heudiconv/ X-VCS-Repository: proj/sci X-VCS-Files: dev-python/heudiconv/files/pynwb-2.0.0-versions.patch dev-python/heudiconv/files/pynwb-2.1.0-versions.patch dev-python/heudiconv/files/pynwb-2.2.0-versions.patch dev-python/heudiconv/heudiconv-0.11.6.ebuild dev-python/heudiconv/metadata.xml X-VCS-Directories: dev-python/heudiconv/files/ dev-python/heudiconv/ X-VCS-Committer: chymera X-VCS-Committer-Name: Horea Christian X-VCS-Revision: 70e2057641f5a42ec3eb46de196fea112a6955d0 X-VCS-Branch: master Date: Tue, 31 Jan 2023 21:27:26 +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: 7c48e5f9-f9bd-4767-b468-1bced7c7c016 X-Archives-Hash: 9d020ca2899b753c7ff167483498e592 commit: 70e2057641f5a42ec3eb46de196fea112a6955d0 Author: Horea Christian chymera eu> AuthorDate: Tue Jan 31 21:24:44 2023 +0000 Commit: Horea Christian gmail com> CommitDate: Tue Jan 31 21:24:44 2023 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=70e20576 dev-python/heudiconv: new package, add 0.11.6 Signed-off-by: Horea Christian chymera.eu> .../heudiconv/files/pynwb-2.0.0-versions.patch | 21 +++++++++ .../heudiconv/files/pynwb-2.1.0-versions.patch | 21 +++++++++ .../heudiconv/files/pynwb-2.2.0-versions.patch | 21 +++++++++ dev-python/heudiconv/heudiconv-0.11.6.ebuild | 51 ++++++++++++++++++++++ dev-python/heudiconv/metadata.xml | 16 +++++++ 5 files changed, 130 insertions(+) diff --git a/dev-python/heudiconv/files/pynwb-2.0.0-versions.patch b/dev-python/heudiconv/files/pynwb-2.0.0-versions.patch new file mode 100644 index 000000000..d09c50594 --- /dev/null +++ b/dev-python/heudiconv/files/pynwb-2.0.0-versions.patch @@ -0,0 +1,21 @@ +diff --git a/setup.py b/tmp/setup.py +index 39e75824..f7948f64 100755 +--- a/setup.py ++++ b/setup.py +@@ -19,11 +19,11 @@ print('found these packages:', pkgs) + schema_dir = 'nwb-schema/core' + + reqs = [ +- 'h5py>=2.9,<4', +- 'hdmf>=3.1.1,<4', +- 'numpy>=1.16,<1.22', +- 'pandas>=1.0.5,<2', +- 'python-dateutil>=2.7,<3', ++ 'h5py', ++ 'hdmf', ++ 'numpy', ++ 'pandas', ++ 'python-dateutil', + 'setuptools' + ] + diff --git a/dev-python/heudiconv/files/pynwb-2.1.0-versions.patch b/dev-python/heudiconv/files/pynwb-2.1.0-versions.patch new file mode 100644 index 000000000..8c816d226 --- /dev/null +++ b/dev-python/heudiconv/files/pynwb-2.1.0-versions.patch @@ -0,0 +1,21 @@ +diff --git a/setup.py b/tmp/setup.py +index 39e75824..f7948f64 100755 +--- a/setup.py ++++ b/setup.py +@@ -19,11 +19,11 @@ print('found these packages:', pkgs) + schema_dir = 'nwb-schema/core' + + reqs = [ +- 'h5py>=2.10,<4', +- 'hdmf>=3.3.2,<4', +- 'numpy>=1.16,<1.23', +- 'pandas>=1.0.5,<2', +- 'python-dateutil>=2.7,<3', ++ 'h5py', ++ 'hdmf', ++ 'numpy', ++ 'pandas', ++ 'python-dateutil', + 'setuptools' + ] + diff --git a/dev-python/heudiconv/files/pynwb-2.2.0-versions.patch b/dev-python/heudiconv/files/pynwb-2.2.0-versions.patch new file mode 100644 index 000000000..6141f629a --- /dev/null +++ b/dev-python/heudiconv/files/pynwb-2.2.0-versions.patch @@ -0,0 +1,21 @@ +diff --git a/setup.py b/tmp/setup.py +index 39e75824..f7948f64 100755 +--- a/setup.py ++++ b/setup.py +@@ -19,11 +19,11 @@ print('found these packages:', pkgs) + schema_dir = 'nwb-schema/core' + + reqs = [ +- 'h5py>=2.10,<4', +- 'hdmf>=3.4.2,<4', +- 'numpy>=1.16,<1.24', +- 'pandas>=1.1.5,<2', +- 'python-dateutil>=2.7.3,<3', ++ 'h5py', ++ 'hdmf', ++ 'numpy', ++ 'pandas', ++ 'python-dateutil', + 'setuptools' + ] + diff --git a/dev-python/heudiconv/heudiconv-0.11.6.ebuild b/dev-python/heudiconv/heudiconv-0.11.6.ebuild new file mode 100644 index 000000000..6c3c6b59d --- /dev/null +++ b/dev-python/heudiconv/heudiconv-0.11.6.ebuild @@ -0,0 +1,51 @@ +# 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 ) +inherit distutils-r1 + +DESCRIPTION="Flexible DICOM conversion to structured directory layouts" +HOMEPAGE=" + https://github.com/nipy/heudiconv + https://heudiconv.readthedocs.io/en/latest/ +" +SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz" + +SLOT="0" +LICENSE="Apache-2.0" +KEYWORDS="~amd64 ~x86" + +RDEPEND=" + sci-libs/nibabel[${PYTHON_USEDEP}] + sci-libs/pydicom[${PYTHON_USEDEP}] + sci-libs/nipype[${PYTHON_USEDEP}] + sci-biology/dcmstack[${PYTHON_USEDEP}] + dev-python/filelock[${PYTHON_USEDEP}] + dev-python/versioningit[${PYTHON_USEDEP}] + " +BDEPEND=" + test? ( + dev-python/six[${PYTHON_USEDEP}] + ) +" + +# Reported upstream: +# https://github.com/nipy/heudiconv/issues/627 +EPYTEST_DESELECT=( + "heudiconv/tests/test_convert.py::test_b0dwi_for_fmap" + "heudiconv/tests/test_dicoms.py::test_embed_dicom_and_nifti_metadata" + "heudiconv/tests/test_heuristics.py::test_reproin_largely_smoke" + "heudiconv/tests/test_heuristics.py::test_scans_keys_reproin" + "heudiconv/tests/test_heuristics.py::test_scout_conversion" + "heudiconv/tests/test_heuristics.py::test_notop[bidsoptions0]" + "heudiconv/tests/test_heuristics.py::test_notop[bidsoptions1]" + "heudiconv/tests/test_heuristics.py::test_phoenix_doc_conversion" + "heudiconv/tests/test_main.py::test_prepare_for_datalad" + "heudiconv/tests/test_main.py::test_cache" + "heudiconv/tests/test_regression.py::test_grouping[merged]" +) + +distutils_enable_tests pytest diff --git a/dev-python/heudiconv/metadata.xml b/dev-python/heudiconv/metadata.xml new file mode 100644 index 000000000..a98cbf459 --- /dev/null +++ b/dev-python/heudiconv/metadata.xml @@ -0,0 +1,16 @@ + + + + + gentoo@chymera.eu + Horea Christian + + + sci@gentoo.org + Gentoo Science Project + + + heudiconv + nipy/heudiconv + +