Date: Tue, 04 Aug 2026 20:11:03 +0000 From: Yuri Victorovich <yuri@FreeBSD.org> To: ports-committers@FreeBSD.org, dev-commits-ports-all@FreeBSD.org, dev-commits-ports-main@FreeBSD.org Subject: git: c48babd71c47 - main - math/py-yt: update 4=?utf-8?Q?=2E3.1 =E2=86=92?= 4.4.2 Message-ID: <6a724757.3d25f.30c9cfd7@gitrepo.freebsd.org>
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The branch main has been updated by yuri: URL: https://cgit.FreeBSD.org/ports/commit/?id=c48babd71c47296d2eb8c904dd94d6e10c974944 commit c48babd71c47296d2eb8c904dd94d6e10c974944 Author: Yuri Victorovich <yuri@FreeBSD.org> AuthorDate: 2026-08-04 19:07:50 +0000 Commit: Yuri Victorovich <yuri@FreeBSD.org> CommitDate: 2026-08-04 20:10:27 +0000 math/py-yt: update 4.3.1 → 4.4.2 --- math/py-yt/Makefile | 50 +++++++++++----------- math/py-yt/distinfo | 6 +-- math/py-yt/files/patch-pyproject.toml | 28 ++++++++++++ ...t_data__objects_tests_test__data__containers.py | 49 +++++++++++++++++++++ ...yt_data__objects_tests_test__dataset__access.py | 29 +++++++++++++ ...t_data__objects_tests_test__particle__filter.py | 31 ++++++++++++++ math/py-yt/files/patch-yt_tests_test__funcs.py | 48 +++++++++++++++++++++ .../files/patch-yt_utilities_lib_platform__dep.h | 14 ------ .../patch-yt_utilities_lib_platform__dep__math.hpp | 16 ------- ...tch-yt_visualization_tests_test__color__maps.py | 22 ++++++++++ ...h-yt_visualization_tests_test__image__writer.py | 22 ++++++++++ 11 files changed, 257 insertions(+), 58 deletions(-) diff --git a/math/py-yt/Makefile b/math/py-yt/Makefile index e9ed57e30b3b..76cc8ac88331 100644 --- a/math/py-yt/Makefile +++ b/math/py-yt/Makefile @@ -1,6 +1,5 @@ PORTNAME= yt -DISTVERSION= 4.3.1 -PORTREVISION= 5 +DISTVERSION= 4.4.2 CATEGORIES= math astro python MASTER_SITES= PYPI PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} @@ -12,38 +11,39 @@ WWW= https://yt-project.org/ LICENSE= BSD3CLAUSE LICENSE_FILE= ${WRKSRC}/COPYING.txt -# dependencies are in setup.cfg -BUILD_DEPENDS= ${PYTHON_PKGNAMEPREFIX}numpy>=1.16:math/py-numpy@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}ewah-bool-utils>=1.0.2:devel/py-ewah-bool-utils@${PY_FLAVOR} -RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}numpy>=1.16:math/py-numpy@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}cmyt>=0.2.2:math/py-cmyt@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}ewah-bool-utils>=1.0.2:devel/py-ewah-bool-utils@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}ipywidgets>0:devel/py-ipywidgets@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}ipython>=1.0:devel/ipython@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}matplotlib>0:math/py-matplotlib@${PY_FLAVOR} \ +BUILD_DEPENDS= ${PYTHON_PKGNAMEPREFIX}ewah-bool-utils>=1.2.0:devel/py-ewah-bool-utils@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}numpy>=2.0.0:math/py-numpy@${PY_FLAVOR} +RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}cmyt>=1.1.2:math/py-cmyt@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}ewah-bool-utils>=1.2.0:devel/py-ewah-bool-utils@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}matplotlib>=3.5:math/py-matplotlib@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}more-itertools>=8.4:devel/py-more-itertools@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}numpy>=1.16:math/py-numpy@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}numpy>=1.21.3:math/py-numpy@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}packaging>=20.9:devel/py-packaging@${PY_FLAVOR} \ - ${PY_PILLOW} \ - ${PYTHON_PKGNAMEPREFIX}pyparsing>=2.0.2:devel/py-pyparsing@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}sympy>=1.2:math/py-sympy@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}toml>=0.10.2:textproc/py-toml@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}pillow>=8.3.2:graphics/py-pillow@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}tomli>=1.2.3:textproc/py-tomli@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}tomli-w>=0.4.0:textproc/py-tomli-w@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}tqdm>=3.4.0:misc/py-tqdm@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}unyt>=2.8.0:math/py-unyt@${PY_FLAVOR} + ${PYTHON_PKGNAMEPREFIX}typing-extensions>=4.4.0:devel/py-typing-extensions@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}unyt>=2.9.2:math/py-unyt@${PY_FLAVOR} USES= dos2unix localbase python USE_PYTHON= autoplist concurrent cython distutils -post-patch: - @${REINPLACE_CMD} -e "s|check_for_pyembree() is not None|False|" \ - ${WRKSRC}/setup.py - @${REINPLACE_CMD} -e "s|check_for_openmp() is True|True|" \ - ${WRKSRC}/setup.py - @${REINPLACE_CMD} -e "s|\['-fopenmp', filename\]|['-I${LOCALBASE}/include', '-L${LOCALBASE}/lib', '-lm', '-fopenmp', filename]|" \ - ${WRKSRC}/setupext.py - post-install: @${STRIP_CMD} $$(${FIND} ${STAGEDIR}${PYTHON_SITELIBDIR} -name "*.so") +TEST_ENV= ${MAKE_ENV} \ + PYTHONPATH=${STAGEDIR}${PYTHONPREFIX_SITELIBDIR} \ + MPLBACKEND=Agg \ + PYTEST_ADDOPTS="-p no:black -p no:ruff -p no:mypy -p no:flake8 -p no:cov -p no:benchmark -p no:inline-snapshot -p no:xdist -p no:randomly" + +do-test: + @cd ${STAGEDIR}${PYTHONPREFIX_SITELIBDIR} && \ + ${SETENV} ${TEST_ENV} pytest yt/tests \ + --deselect=yt/data_objects/tests/test_data_containers.py::TestDataContainers::test_to_astropy_table + +# tests as of 4.4.2: 53 passed, 10 skipped, 1 xfailed in 9.87s +# Additional tests are excluded because they depend on nose (broken on Python 3.12) +# or on data files/network access. + .include <bsd.port.mk> diff --git a/math/py-yt/distinfo b/math/py-yt/distinfo index 9a0e34c27856..f7193824e085 100644 --- a/math/py-yt/distinfo +++ b/math/py-yt/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1725817547 -SHA256 (yt-4.3.1.tar.gz) = 7b6db5c336dc22dd2212bb17c3b18f42cfe144bb1f6c3dda0dcd47eb77195e0e -SIZE (yt-4.3.1.tar.gz) = 13810591 +TIMESTAMP = 1785732501 +SHA256 (yt-4.4.2.tar.gz) = e0883a89c2543b436c3778f555edf253c71f252f744752dc1688f8524ad03b0b +SIZE (yt-4.4.2.tar.gz) = 4946809 diff --git a/math/py-yt/files/patch-pyproject.toml b/math/py-yt/files/patch-pyproject.toml new file mode 100644 index 000000000000..3e6c6e956abc --- /dev/null +++ b/math/py-yt/files/patch-pyproject.toml @@ -0,0 +1,28 @@ +-- Relax the setuptools version requirement to match the version available in the +-- FreeBSD ports tree (devel/py-setuptools). Also adapt the PEP 621 license +-- fields to the form supported by that setuptools version. + +--- pyproject.toml.orig 2025-11-18 00:00:00 UTC ++++ pyproject.toml +@@ -1,7 +1,7 @@ + [build-system] + # keep in sync with .github/workflows/wheels.yaml + requires = [ +- "setuptools>=77.0.0", ++ "setuptools>=63.1.0", + "Cython>=3.0.3", + "numpy>=2.0.0", + "ewah-bool-utils>=1.2.0", +@@ -15,11 +15,7 @@ + authors = [ + { name = "The yt project", email = "yt-dev@python.org" }, + ] +-license = "BSD-3-Clause" +-license-files = [ +- "COPYING.txt", +- "yt/frontends/artio/artio_headers/LICENSE", +-] ++license = {text = "BSD-3-Clause"} + classifiers = [ + "Development Status :: 5 - Production/Stable", + "Environment :: Console", diff --git a/math/py-yt/files/patch-yt_data__objects_tests_test__data__containers.py b/math/py-yt/files/patch-yt_data__objects_tests_test__data__containers.py new file mode 100644 index 000000000000..c71204f9788e --- /dev/null +++ b/math/py-yt/files/patch-yt_data__objects_tests_test__data__containers.py @@ -0,0 +1,49 @@ +-- Replace nose.tools.assert_raises with unittest.TestCase.assertRaises so yt tests can run under Python 3.12 where nose is broken. +--- yt/data_objects/tests/test_data_containers.py.orig 2026-08-04 00:34:29 UTC ++++ yt/data_objects/tests/test_data_containers.py +@@ -4,7 +4,8 @@ import numpy as np + import unittest + + import numpy as np +-from nose.tools import assert_raises ++from unittest import TestCase ++_assert_raises = TestCase().assertRaises + from numpy.testing import assert_array_equal, assert_equal + + from yt.data_objects.data_containers import YTDataContainer +@@ -32,7 +33,7 @@ class TestDataContainers(unittest.TestCase): + + def test_yt_data_container(self): + # Test if ds could be None +- with assert_raises(RuntimeError) as err: ++ with _assert_raises(RuntimeError) as err: + YTDataContainer(None, None) + desired = ( + "Error: ds must be set either through class" +@@ -53,7 +54,7 @@ class TestDataContainers(unittest.TestCase): + assert_equal("density" in proj.keys(), False) + + # Delete a non-existent field +- with assert_raises(YTFieldNotFound) as ex: ++ with _assert_raises(YTFieldNotFound) as ex: + del proj["p_mass"] + desired = "Could not find field 'p_mass' in UniformGridData." + assert_equal(str(ex.exception), desired) +@@ -82,7 +83,7 @@ class TestDataContainers(unittest.TestCase): + ds = fake_random_ds(16, particles=10) + sp = ds.sphere(ds.domain_center, 0.25) + +- with assert_raises(YTException): ++ with _assert_raises(YTException): + sp.write_out(filename, fields=[("all", "particle_ones")]) + + @requires_module("pandas") +@@ -152,7 +153,7 @@ class TestDataContainers(unittest.TestCase): + dd = ds.all_data() + q = dd.quantities["WeightedAverageQuantity"] + rho = q(("all", "particle_velocity_x"), weight=("all", "particle_mass")) +- with assert_raises(NotImplementedError): ++ with _assert_raises(NotImplementedError): + dd.extract_isocontours("density", rho, sample_values="x") + + def test_derived_field(self): diff --git a/math/py-yt/files/patch-yt_data__objects_tests_test__dataset__access.py b/math/py-yt/files/patch-yt_data__objects_tests_test__dataset__access.py new file mode 100644 index 000000000000..98394a102c2a --- /dev/null +++ b/math/py-yt/files/patch-yt_data__objects_tests_test__dataset__access.py @@ -0,0 +1,29 @@ +-- Replace nose.tools.assert_raises with unittest.TestCase.assertRaises so yt tests can run under Python 3.12 where nose is broken. +--- yt/data_objects/tests/test_dataset_access.py.orig 2026-08-04 00:34:29 UTC ++++ yt/data_objects/tests/test_dataset_access.py +@@ -1,5 +1,6 @@ import numpy as np + import numpy as np +-from nose.tools import assert_raises ++from unittest import TestCase ++_assert_raises = TestCase().assertRaises + from numpy.testing import assert_almost_equal, assert_equal + + from yt.testing import ( +@@ -66,7 +67,7 @@ def test_region_from_d(): + assert_equal(reg1["gas", "density"], reg2["gas", "density"]) + + # Test with bad boundary initialization +- with assert_raises(RuntimeError): ++ with _assert_raises(RuntimeError): + ds.r[0.3:0.1, 0.4:0.6, :] + + # Test region by creating an arbitrary grid +@@ -133,7 +134,7 @@ def test_point_from_r(): + assert_equal(pt1["gas", "density"], pt2["gas", "density"]) + + # Test YTDimensionalityError +- with assert_raises(YTDimensionalityError) as ex: ++ with _assert_raises(YTDimensionalityError) as ex: + ds.r[0.5, 0.1] + assert_equal(str(ex.exception), "Dimensionality specified was 2 but we need 3") + diff --git a/math/py-yt/files/patch-yt_data__objects_tests_test__particle__filter.py b/math/py-yt/files/patch-yt_data__objects_tests_test__particle__filter.py new file mode 100644 index 000000000000..2d1260caa8dc --- /dev/null +++ b/math/py-yt/files/patch-yt_data__objects_tests_test__particle__filter.py @@ -0,0 +1,31 @@ +-- Replace nose.tools.assert_raises with unittest.TestCase.assertRaises so yt tests can run under Python 3.12 where nose is broken. +--- yt/data_objects/tests/test_particle_filter.py.orig 2026-08-04 00:34:29 UTC ++++ yt/data_objects/tests/test_particle_filter.py +@@ -3,7 +3,8 @@ import numpy as np + import tempfile + + import numpy as np +-from nose.tools import assert_raises ++from unittest import TestCase ++_assert_raises = TestCase().assertRaises + from numpy.testing import assert_equal + + from yt.data_objects.particle_filters import add_particle_filter, particle_filter +@@ -39,7 +40,7 @@ def test_add_particle_filter(): + assert ("deposit", "stars2_cic") in ds.derived_field_list + + # Test adding filter with fields not defined on the ds +- with assert_raises(YTIllDefinedParticleFilter) as ex: ++ with _assert_raises(YTIllDefinedParticleFilter) as ex: + add_particle_filter( + "bad_stars", function=stars, filtered_type="all", requires=["wrong_field"] + ) +@@ -131,7 +132,7 @@ def test_particle_filter_exceptions(): + ds.add_particle_filter("filter1") + + ad = ds.all_data() +- with assert_raises(YTIllDefinedFilter): ++ with _assert_raises(YTIllDefinedFilter): + ad["filter1", "particle_mass"].shape[0] + + @particle_filter(filtered_type="all", requires=["particle_mass"]) diff --git a/math/py-yt/files/patch-yt_tests_test__funcs.py b/math/py-yt/files/patch-yt_tests_test__funcs.py new file mode 100644 index 000000000000..02c5307f5663 --- /dev/null +++ b/math/py-yt/files/patch-yt_tests_test__funcs.py @@ -0,0 +1,48 @@ +-- Replace nose.tools.assert_raises with unittest.TestCase.assertRaises so yt tests can run under Python 3.12 where nose is broken. +--- yt/tests/test_funcs.py.orig 2026-08-04 00:34:29 UTC ++++ yt/tests/test_funcs.py +@@ -1,6 +1,7 @@ import os + import os + +-from nose.tools import assert_raises ++from unittest import TestCase ++_assert_raises = TestCase().assertRaises + from numpy.testing import assert_equal + + from yt.funcs import ( +@@ -21,7 +22,7 @@ def test_validate_axis(): + ds = fake_amr_ds(geometry="cylindrical") + ds.slice("Theta", 0.25) + +- with assert_raises(TypeError) as ex: ++ with _assert_raises(TypeError) as ex: + # default geometry is cartesian + ds = fake_amr_ds() + ds.slice("r", 0.25) +@@ -35,7 +36,7 @@ def test_validate_center(): + validate_center("max") + validate_center("MIN_") + +- with assert_raises(TypeError) as ex: ++ with _assert_raises(TypeError) as ex: + validate_center("avg") + desired = ( + "Expected 'center' to be in ['c', 'center', 'm', 'max', 'min'] " +@@ -50,7 +51,7 @@ def test_validate_center(): + def __init__(self, center): + self.center = center + +- with assert_raises(TypeError) as ex: ++ with _assert_raises(TypeError) as ex: + validate_center(CustomCenter(10)) + desired = ( + "Expected 'center' to be a numeric object of type " +@@ -118,7 +119,7 @@ def test_simple_download_file(): + except FileNotFoundError: + pass + +- with assert_raises(RuntimeError) as ex: ++ with _assert_raises(RuntimeError) as ex: + simple_download_file("http://yt-project.org/404", "simple-download-file") + + desired = "Attempt to download file from http://yt-project.org/404 failed with error 404: Not Found." diff --git a/math/py-yt/files/patch-yt_utilities_lib_platform__dep.h b/math/py-yt/files/patch-yt_utilities_lib_platform__dep.h deleted file mode 100644 index 286fb4d5ffc7..000000000000 --- a/math/py-yt/files/patch-yt_utilities_lib_platform__dep.h +++ /dev/null @@ -1,14 +0,0 @@ ---- yt/utilities/lib/platform_dep.h.orig 2021-08-02 20:27:17 UTC -+++ yt/utilities/lib/platform_dep.h -@@ -59,6 +59,10 @@ double erf(double x) - - #else - #include <stdint.h> --#include "alloca.h" -+#if !defined(__FreeBSD__) -+# include "alloca.h" -+#else -+# include <stdlib.h> -+#endif - #include <math.h> - #endif diff --git a/math/py-yt/files/patch-yt_utilities_lib_platform__dep__math.hpp b/math/py-yt/files/patch-yt_utilities_lib_platform__dep__math.hpp deleted file mode 100644 index ddc45bddb8ec..000000000000 --- a/math/py-yt/files/patch-yt_utilities_lib_platform__dep__math.hpp +++ /dev/null @@ -1,16 +0,0 @@ ---- yt/utilities/lib/platform_dep_math.hpp.orig 2021-08-02 20:38:53 UTC -+++ yt/utilities/lib/platform_dep_math.hpp -@@ -5,6 +5,7 @@ MSVC does not define isnormal in the std:: namespace, - However with GCC-5, there is a clash between the definition of isnormal in <math.h> and using C++14, so we need to import from cmath instead. - */ - -+#if !defined(__FreeBSD__) // see https://github.com/yt-project/yt/issues/3459 - #if _MSC_VER - #include <math.h> - inline bool __isnormal(double x) { -@@ -15,4 +16,5 @@ inline bool __isnormal(double x) { - inline bool __isnormal(double x) { - return std::isnormal(x); - } -+#endif - #endif diff --git a/math/py-yt/files/patch-yt_visualization_tests_test__color__maps.py b/math/py-yt/files/patch-yt_visualization_tests_test__color__maps.py new file mode 100644 index 000000000000..89c34520d699 --- /dev/null +++ b/math/py-yt/files/patch-yt_visualization_tests_test__color__maps.py @@ -0,0 +1,22 @@ +-- Replace nose.tools.assert_raises with unittest.TestCase.assertRaises so yt tests can run under Python 3.12 where nose is broken. +--- yt/visualization/tests/test_color_maps.py.orig 2026-08-04 00:34:29 UTC ++++ yt/visualization/tests/test_color_maps.py +@@ -5,7 +5,8 @@ import numpy as np + + import matplotlib.pyplot as plt + import numpy as np +-from nose.tools import assert_raises ++from unittest import TestCase ++_assert_raises = TestCase().assertRaises + from numpy.testing import assert_almost_equal, assert_equal + + from yt import make_colormap, show_colormaps +@@ -29,7 +30,7 @@ class TestColorMaps(unittest.TestCase): + show_colormaps(subset="yt_native", filename="yt_color_maps.png") + + # Test for non-existent color map +- with assert_raises(AttributeError) as ex: ++ with _assert_raises(AttributeError) as ex: + show_colormaps(subset="unknown", filename="yt_color_maps.png") + desired = ( + "show_colormaps requires subset attribute to be 'all', " diff --git a/math/py-yt/files/patch-yt_visualization_tests_test__image__writer.py b/math/py-yt/files/patch-yt_visualization_tests_test__image__writer.py new file mode 100644 index 000000000000..425114066339 --- /dev/null +++ b/math/py-yt/files/patch-yt_visualization_tests_test__image__writer.py @@ -0,0 +1,22 @@ +-- Replace nose.tools.assert_raises with unittest.TestCase.assertRaises so yt tests can run under Python 3.12 where nose is broken. +--- yt/visualization/tests/test_image_writer.py.orig 2026-08-04 00:34:29 UTC ++++ yt/visualization/tests/test_image_writer.py +@@ -4,7 +4,8 @@ import numpy as np + import unittest + + import numpy as np +-from nose.tools import assert_raises ++from unittest import TestCase ++_assert_raises = TestCase().assertRaises + from numpy.testing import assert_equal + + from yt.testing import fake_random_ds +@@ -65,7 +66,7 @@ class TestImageWriter(unittest.TestCase): + png_str_trans = write_bitmap(image_trans, None, transpose=True) + assert_equal(png_str, png_str_trans) + +- with assert_raises(RuntimeError) as ex: ++ with _assert_raises(RuntimeError) as ex: + write_bitmap(np.ones([16, 16]), None) + desired = "Expecting image array of shape (N,M,3) or (N,M,4), received (16, 16)" + assert_equal(str(ex.exception)[:50], desired[:50])home | help
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