git: a9aeb9e24985 - main - science/py-dipy: update 1.7.0 → 1.8.0

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From: Yuri Victorovich <yuri_at_FreeBSD.org>
Date: Sun, 17 Dec 2023 19:01:52 UTC
The branch main has been updated by yuri:

URL: https://cgit.FreeBSD.org/ports/commit/?id=a9aeb9e2498534106633e6510e029bd86be77928

commit a9aeb9e2498534106633e6510e029bd86be77928
Author:     Yuri Victorovich <yuri@FreeBSD.org>
AuthorDate: 2023-12-17 19:01:28 +0000
Commit:     Yuri Victorovich <yuri@FreeBSD.org>
CommitDate: 2023-12-17 19:01:49 +0000

    science/py-dipy: update 1.7.0 → 1.8.0
    
    Reported by:    portscout
---
 science/py-dipy/Makefile                   |   18 +-
 science/py-dipy/distinfo                   |    6 +-
 science/py-dipy/files/patch-pyproject.toml |   24 +
 science/py-dipy/pkg-plist                  | 1118 +++++++++++++++++++++++++++-
 4 files changed, 1153 insertions(+), 13 deletions(-)

diff --git a/science/py-dipy/Makefile b/science/py-dipy/Makefile
index 77cf214c7636..5df423531231 100644
--- a/science/py-dipy/Makefile
+++ b/science/py-dipy/Makefile
@@ -1,5 +1,5 @@
 PORTNAME=	dipy
-DISTVERSION=	1.7.0
+DISTVERSION=	1.8.0
 CATEGORIES=	science python
 MASTER_SITES=	PYPI
 PKGNAMEPREFIX=	${PYTHON_PKGNAMEPREFIX}
@@ -15,8 +15,11 @@ PY_DEPENDS=	${PYTHON_PKGNAMEPREFIX}h5py>0:science/py-h5py@${PY_FLAVOR} \
 		${PYTHON_PKGNAMEPREFIX}nibabel>0:science/py-nibabel@${PY_FLAVOR} \
 		${PYNUMPY} \
 		${PYTHON_PKGNAMEPREFIX}scipy>0:science/py-scipy@${PY_FLAVOR} \
-		${PYTHON_PKGNAMEPREFIX}tqdm>0:misc/py-tqdm@${PY_FLAVOR}
-BUILD_DEPENDS=	${PY_DEPENDS}
+		${PYTHON_PKGNAMEPREFIX}tqdm>0:misc/py-tqdm@${PY_FLAVOR} \
+		${PYTHON_PKGNAMEPREFIX}trx-python>0:science/py-trx-python@${PY_FLAVOR}
+BUILD_DEPENDS=	${PY_DEPENDS} \
+		${PYTHON_PKGNAMEPREFIX}meson-python>0:devel/meson-python@${PY_FLAVOR} \
+		${PYTHON_PKGNAMEPREFIX}wheel>0:devel/py-wheel@${PY_FLAVOR}
 RUN_DEPENDS=	${PY_DEPENDS}
 TEST_DEPENDS=	${PYTHON_PKGNAMEPREFIX}pandas>0:math/py-pandas@${PY_FLAVOR} \
 		${PYTHON_PKGNAMEPREFIX}scikit-learn>0:science/py-scikit-learn@${PY_FLAVOR} \
@@ -27,14 +30,17 @@ TEST_DEPENDS+=	${PYTHON_PKGNAMEPREFIX}fury>0:graphics/py-fury@${PY_FLAVOR} \
 TEST_DEPENDS+=	${PYTHON_PKGNAMEPREFIX}cvxpy>0:math/py-cvxpy@${PY_FLAVOR} # "doc" extra dependencies, see dipy/info.py
 
 USES=		python shebangfix
-USE_PYTHON=	distutils cython concurrent autoplist pytest # pkg-plist also exists and contains files missing from the python-generated plist
+USE_PYTHON=	pep517 concurrent cython pytest # autoplist is broken: it produces incorrect entries and unnecessary files are also placed under doc/
 
-SHEBANG_GLOB=	*.sh
+SHEBANG_GLOB=	*.sh *.py
 
 TEST_ENV=	${MAKE_ENV} PYTHONPATH=${STAGEDIR}${PYTHONPREFIX_SITELIBDIR}
 
 post-install:
-	${STRIP_CMD} ${STAGEDIR}${PYTHONPREFIX_SITELIBDIR}/${PORTNAME}/*/*.so
+	# strip binaries
+	@${STRIP_CMD} ${STAGEDIR}${PYTHONPREFIX_SITELIBDIR}/${PORTNAME}/*/*.so
+	# remove doc files
+	@${RM} -rf ${STAGEDIR}${PREFIX}/doc
 
 do-test:
 	cd ${WRKSRC} && ${SETENV} ${TEST_ENV} tools/ci/run_tests.sh
diff --git a/science/py-dipy/distinfo b/science/py-dipy/distinfo
index d31d0a143861..2abe0c2f1a9e 100644
--- a/science/py-dipy/distinfo
+++ b/science/py-dipy/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1686151055
-SHA256 (dipy-1.7.0.tar.gz) = 59bb647128aae7793215c813bb8ea35dae260ac9f0d938c724064f0af5a05cc3
-SIZE (dipy-1.7.0.tar.gz) = 12389209
+TIMESTAMP = 1702799716
+SHA256 (dipy-1.8.0.tar.gz) = cc3845585b6ccd5d7bf43094d52a00eb73111072eee36c2149fabdb1b071f008
+SIZE (dipy-1.8.0.tar.gz) = 6494141
diff --git a/science/py-dipy/files/patch-pyproject.toml b/science/py-dipy/files/patch-pyproject.toml
new file mode 100644
index 000000000000..d37ccaa7aeb2
--- /dev/null
+++ b/science/py-dipy/files/patch-pyproject.toml
@@ -0,0 +1,24 @@
+--- pyproject.toml.orig	2023-12-17 07:57:19 UTC
++++ pyproject.toml
+@@ -137,10 +137,10 @@ requires = [
+     "packaging>21.0",
+     "wheel",
+     "numpy==1.19.5; python_version=='3.8' and platform_python_implementation != 'PyPy'",
+-    "numpy==1.22.4; python_version=='3.9' and platform_python_implementation != 'PyPy'",
+-    "numpy==1.22.4; python_version=='3.10' and platform_system=='Windows' and platform_python_implementation != 'PyPy'",
+-    "numpy==1.22.4; python_version=='3.10' and platform_system != 'Windows' and platform_python_implementation != 'PyPy'",
+-    "numpy==1.23.3; python_version=='3.11' and platform_python_implementation != 'PyPy'",
++    "numpy>=1.22.4; python_version=='3.9' and platform_python_implementation != 'PyPy'",
++    "numpy>=1.22.4; python_version=='3.10' and platform_system=='Windows' and platform_python_implementation != 'PyPy'",
++    "numpy>=1.22.4; python_version=='3.10' and platform_system != 'Windows' and platform_python_implementation != 'PyPy'",
++    "numpy>=1.23.3; python_version=='3.11' and platform_python_implementation != 'PyPy'",
+     "numpy>=1.26.0b1; python_version>='3.12'",
+     "numpy; python_version>='3.8' and platform_python_implementation=='PyPy'",
+ ]
+@@ -177,4 +177,4 @@ Metrics = [
+ addopts = "--ignore=dipy/testing/decorators.py --ignore-glob='bench*.py' --ignore-glob=**/benchmarks/*"
+ filterwarnings = [
+     'ignore:.*You do not have FURY installed.*:UserWarning',
+-]
+\ No newline at end of file
++]
diff --git a/science/py-dipy/pkg-plist b/science/py-dipy/pkg-plist
index a0aa59d2df04..7c8789a9ee0c 100644
--- a/science/py-dipy/pkg-plist
+++ b/science/py-dipy/pkg-plist
@@ -1,4 +1,1114 @@
-%%PYTHON_SITELIBDIR%%/dipy/COMMIT_INFO.txt
-%%PYTHON_SITELIBDIR%%/dipy/__config__.py
-%%PYTHON_SITELIBDIR%%/dipy/__pycache__/__config__.cpython-%%PYTHON_SUFFIX%%.opt-1.pyc
-%%PYTHON_SITELIBDIR%%/dipy/__pycache__/__config__.cpython-%%PYTHON_SUFFIX%%.pyc
+bin/dipy_align_affine
+bin/dipy_align_syn
+bin/dipy_apply_transform
+bin/dipy_buan_lmm
+bin/dipy_buan_profiles
+bin/dipy_buan_shapes
+bin/dipy_bundlewarp
+bin/dipy_correct_motion
+bin/dipy_denoise_lpca
+bin/dipy_denoise_mppca
+bin/dipy_denoise_nlmeans
+bin/dipy_denoise_patch2self
+bin/dipy_evac_plus
+bin/dipy_fetch
+bin/dipy_fit_csa
+bin/dipy_fit_csd
+bin/dipy_fit_dki
+bin/dipy_fit_dti
+bin/dipy_fit_ivim
+bin/dipy_fit_mapmri
+bin/dipy_gibbs_ringing
+bin/dipy_horizon
+bin/dipy_info
+bin/dipy_labelsbundles
+bin/dipy_mask
+bin/dipy_median_otsu
+bin/dipy_recobundles
+bin/dipy_reslice
+bin/dipy_slr
+bin/dipy_snr_in_cc
+bin/dipy_split
+bin/dipy_track
+bin/dipy_track_pft
+%%PYTHON_SITELIBDIR%%/dipy-1.8.0.dist-info/LICENSE
+%%PYTHON_SITELIBDIR%%/dipy-1.8.0.dist-info/METADATA
+%%PYTHON_SITELIBDIR%%/dipy-1.8.0.dist-info/RECORD
+%%PYTHON_SITELIBDIR%%/dipy-1.8.0.dist-info/WHEEL
+%%PYTHON_SITELIBDIR%%/dipy-1.8.0.dist-info/entry_points.txt
+%%PYTHON_SITELIBDIR%%/dipy/__init__.py
+%%PYTHON_SITELIBDIR%%/dipy/__pycache__/__init__%%PYTHON_EXT_SUFFIX%%.opt-1.pyc
+%%PYTHON_SITELIBDIR%%/dipy/__pycache__/__init__%%PYTHON_EXT_SUFFIX%%.pyc
+%%PYTHON_SITELIBDIR%%/dipy/__pycache__/conftest%%PYTHON_EXT_SUFFIX%%.opt-1.pyc
+%%PYTHON_SITELIBDIR%%/dipy/__pycache__/conftest%%PYTHON_EXT_SUFFIX%%.pyc
+%%PYTHON_SITELIBDIR%%/dipy/__pycache__/pkg_info%%PYTHON_EXT_SUFFIX%%.opt-1.pyc
+%%PYTHON_SITELIBDIR%%/dipy/__pycache__/pkg_info%%PYTHON_EXT_SUFFIX%%.pyc
+%%PYTHON_SITELIBDIR%%/dipy/__pycache__/version%%PYTHON_EXT_SUFFIX%%.opt-1.pyc
+%%PYTHON_SITELIBDIR%%/dipy/__pycache__/version%%PYTHON_EXT_SUFFIX%%.pyc
+%%PYTHON_SITELIBDIR%%/dipy/align/__init__.py
+%%PYTHON_SITELIBDIR%%/dipy/align/__pycache__/__init__%%PYTHON_EXT_SUFFIX%%.opt-1.pyc
+%%PYTHON_SITELIBDIR%%/dipy/align/__pycache__/__init__%%PYTHON_EXT_SUFFIX%%.pyc
+%%PYTHON_SITELIBDIR%%/dipy/align/__pycache__/_public%%PYTHON_EXT_SUFFIX%%.opt-1.pyc
+%%PYTHON_SITELIBDIR%%/dipy/align/__pycache__/_public%%PYTHON_EXT_SUFFIX%%.pyc
+%%PYTHON_SITELIBDIR%%/dipy/align/__pycache__/cpd%%PYTHON_EXT_SUFFIX%%.opt-1.pyc
+%%PYTHON_SITELIBDIR%%/dipy/align/__pycache__/cpd%%PYTHON_EXT_SUFFIX%%.pyc
+%%PYTHON_SITELIBDIR%%/dipy/align/__pycache__/imaffine%%PYTHON_EXT_SUFFIX%%.opt-1.pyc
+%%PYTHON_SITELIBDIR%%/dipy/align/__pycache__/imaffine%%PYTHON_EXT_SUFFIX%%.pyc
+%%PYTHON_SITELIBDIR%%/dipy/align/__pycache__/imwarp%%PYTHON_EXT_SUFFIX%%.opt-1.pyc
+%%PYTHON_SITELIBDIR%%/dipy/align/__pycache__/imwarp%%PYTHON_EXT_SUFFIX%%.pyc
+%%PYTHON_SITELIBDIR%%/dipy/align/__pycache__/metrics%%PYTHON_EXT_SUFFIX%%.opt-1.pyc
+%%PYTHON_SITELIBDIR%%/dipy/align/__pycache__/metrics%%PYTHON_EXT_SUFFIX%%.pyc
+%%PYTHON_SITELIBDIR%%/dipy/align/__pycache__/reslice%%PYTHON_EXT_SUFFIX%%.opt-1.pyc
+%%PYTHON_SITELIBDIR%%/dipy/align/__pycache__/reslice%%PYTHON_EXT_SUFFIX%%.pyc
+%%PYTHON_SITELIBDIR%%/dipy/align/__pycache__/scalespace%%PYTHON_EXT_SUFFIX%%.opt-1.pyc
+%%PYTHON_SITELIBDIR%%/dipy/align/__pycache__/scalespace%%PYTHON_EXT_SUFFIX%%.pyc
+%%PYTHON_SITELIBDIR%%/dipy/align/__pycache__/streamlinear%%PYTHON_EXT_SUFFIX%%.opt-1.pyc
+%%PYTHON_SITELIBDIR%%/dipy/align/__pycache__/streamlinear%%PYTHON_EXT_SUFFIX%%.pyc
+%%PYTHON_SITELIBDIR%%/dipy/align/__pycache__/streamwarp%%PYTHON_EXT_SUFFIX%%.opt-1.pyc
+%%PYTHON_SITELIBDIR%%/dipy/align/__pycache__/streamwarp%%PYTHON_EXT_SUFFIX%%.pyc
+%%PYTHON_SITELIBDIR%%/dipy/align/_public.py
+%%PYTHON_SITELIBDIR%%/dipy/align/bundlemin%%PYTHON_EXT_SUFFIX%%.so
+%%PYTHON_SITELIBDIR%%/dipy/align/cpd.py
+%%PYTHON_SITELIBDIR%%/dipy/align/crosscorr%%PYTHON_EXT_SUFFIX%%.so
+%%PYTHON_SITELIBDIR%%/dipy/align/expectmax%%PYTHON_EXT_SUFFIX%%.so
+%%PYTHON_SITELIBDIR%%/dipy/align/fused_types.pxd
+%%PYTHON_SITELIBDIR%%/dipy/align/imaffine.py
+%%PYTHON_SITELIBDIR%%/dipy/align/imwarp.py
+%%PYTHON_SITELIBDIR%%/dipy/align/metrics.py
+%%PYTHON_SITELIBDIR%%/dipy/align/parzenhist%%PYTHON_EXT_SUFFIX%%.so
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