From nobody Fri Nov 15 09:20:32 2024 X-Original-To: dev-commits-ports-main@mlmmj.nyi.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2610:1c1:1:606c::19:1]) by mlmmj.nyi.freebsd.org (Postfix) with ESMTP id 4XqWhd1RFqz5ctDk; Fri, 15 Nov 2024 09:20:33 +0000 (UTC) (envelope-from git@FreeBSD.org) Received: from mxrelay.nyi.freebsd.org (mxrelay.nyi.freebsd.org [IPv6:2610:1c1:1:606c::19:3]) (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 client-signature RSA-PSS (4096 bits) client-digest SHA256) (Client CN "mxrelay.nyi.freebsd.org", Issuer "R10" (verified OK)) by mx1.freebsd.org (Postfix) with ESMTPS id 4XqWhd0zmlz4H90; Fri, 15 Nov 2024 09:20:33 +0000 (UTC) (envelope-from git@FreeBSD.org) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1731662433; h=from:from:reply-to:subject:subject:date:date:message-id:message-id: to:to:cc:mime-version:mime-version:content-type:content-type: content-transfer-encoding:content-transfer-encoding; bh=bCykkP01L+r63R6FQN0j8UGr9QLfmFuRyQau+LokeJY=; b=WP24v2HIcUTWQPvmnPNS9DTQGVdkZtHfKx5QkM9TbooNUuNftcnzLzu9gjJUZpT7cfryjD m2E2LeKVSab87HkL8r3tgeXb0piVHTi1e+nI10V6QrNuZa/jhjU2F699T8XDbxi4wUeuLV G0Jo8kEE6h8B57VocgEXHxnGBrZ1DcKi/uqhz3ZCnR1f+G+SiJQY19YFMCoof2uvpszX0h 0QZ3/MulJwEIwNK2pVpwJ3BjIloS9BxwUFEHA8bLz0tTeCz+OBtMZquIEtrLgXCOxu12QW ZaNHVJ8LIdCjjaXGD8Wbk7VEOmSKT133hzF8qrHq9cagQuNfLLl/jH0DASQotA== ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1731662433; h=from:from:reply-to:subject:subject:date:date:message-id:message-id: to:to:cc:mime-version:mime-version:content-type:content-type: content-transfer-encoding:content-transfer-encoding; bh=bCykkP01L+r63R6FQN0j8UGr9QLfmFuRyQau+LokeJY=; b=ZzUMqtfOghtIALyFNyK2Dg3H8wqIsojb1LiVTlgt9+spl+hvtKGoq46W0q+zArJw8fhJNy 43tJh2IEXVTlJ/H2y9dwd3TEFYF7Bi4ypoV7OnX9YUbvJgB+SsX/XMK7SonJ+s9SjKofS8 w7Xjb9HHdRkKhWaAy2SG4owTZUR0YYh9RrGfbVDFjgetTpu788jhwD447v/eHdE3/FGjUn d43KgxQwina6bs6e+imzdxRX0UKH5pGK9StmmGDexf5rwxS3PlVaW5azELVRUaWYfF0iZ9 FX9fvnikXV1H1b5QHvv8IGm17vSTfKYy8VunSdQoC8WwYkK9OyzON9BIkjIsPQ== ARC-Authentication-Results: i=1; mx1.freebsd.org; none ARC-Seal: i=1; s=dkim; d=freebsd.org; t=1731662433; a=rsa-sha256; cv=none; b=jR+fvOU0P4wq/GWdZgnd/re61sNXzcpFm3tmSVqYYgyxeAwXNO0vfoPehwS7uq8cEtePFt T3tkUdC9YAhSTl6wW9zlmHTiwlQB0Jsvy4dmqVhdYgmWfyVPnsitjo270naTw/LauyYnRu 0IE7LfvRHd4oPzmipQNGLev4koHLk+EG3M6TNkTPGqRMjjiYaUPdSZ94KJyq2JNrmp3OT7 xXe+u1kLittVczNFSPK8IsKQpNS9iZR79CIkinZmkierBhNg7L3R+mrMkEJZoBMK78wtHM s2MldCH/5SuX7WB6GAJp5fCz+iW2rgdvG8HsbOl6rnLgMxZzw1HyMV1aFxwSKg== Received: from gitrepo.freebsd.org (gitrepo.freebsd.org [IPv6:2610:1c1:1:6068::e6a:5]) (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) (Client did not present a certificate) by mxrelay.nyi.freebsd.org (Postfix) with ESMTPS id 4XqWhd0bhJzHTh; Fri, 15 Nov 2024 09:20:33 +0000 (UTC) (envelope-from git@FreeBSD.org) Received: from gitrepo.freebsd.org ([127.0.1.44]) by gitrepo.freebsd.org (8.18.1/8.18.1) with ESMTP id 4AF9KWsc056319; Fri, 15 Nov 2024 09:20:32 GMT (envelope-from git@gitrepo.freebsd.org) Received: (from git@localhost) by gitrepo.freebsd.org (8.18.1/8.18.1/Submit) id 4AF9KWZo056316; Fri, 15 Nov 2024 09:20:32 GMT (envelope-from git) Date: Fri, 15 Nov 2024 09:20:32 GMT Message-Id: <202411150920.4AF9KWZo056316@gitrepo.freebsd.org> To: ports-committers@FreeBSD.org, dev-commits-ports-all@FreeBSD.org, dev-commits-ports-main@FreeBSD.org From: Yuri Victorovich Subject: git: 8a8942be51f0 - main - science/py-pymatgen: update 2022.7.19 =?utf-8?Q?=E2=86=92?= 2024.11.13 List-Id: Commits to the main branch of the FreeBSD ports repository List-Archive: https://lists.freebsd.org/archives/dev-commits-ports-main List-Help: List-Post: List-Subscribe: List-Unsubscribe: X-BeenThere: dev-commits-ports-main@freebsd.org Sender: owner-dev-commits-ports-main@FreeBSD.org MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: 8bit X-Git-Committer: yuri X-Git-Repository: ports X-Git-Refname: refs/heads/main X-Git-Reftype: branch X-Git-Commit: 8a8942be51f0bae0f8923377b06da9cfc9dc9860 Auto-Submitted: auto-generated The branch main has been updated by yuri: URL: https://cgit.FreeBSD.org/ports/commit/?id=8a8942be51f0bae0f8923377b06da9cfc9dc9860 commit 8a8942be51f0bae0f8923377b06da9cfc9dc9860 Author: Yuri Victorovich AuthorDate: 2024-11-14 14:58:13 +0000 Commit: Yuri Victorovich CommitDate: 2024-11-15 09:20:24 +0000 science/py-pymatgen: update 2022.7.19 → 2024.11.13 --- science/py-pymatgen/Makefile | 69 +++++++++++++++----------- science/py-pymatgen/distinfo | 6 +-- science/py-pymatgen/files/patch-pyproject.toml | 13 +++++ 3 files changed, 55 insertions(+), 33 deletions(-) diff --git a/science/py-pymatgen/Makefile b/science/py-pymatgen/Makefile index cd4f348020dc..6060a6f4b40d 100644 --- a/science/py-pymatgen/Makefile +++ b/science/py-pymatgen/Makefile @@ -1,49 +1,58 @@ PORTNAME= pymatgen -DISTVERSION= 2022.7.19 -PORTREVISION= 1 +DISTVERSIONPREFIX= v +DISTVERSION= 2024.11.13 CATEGORIES= science python -MASTER_SITES= PYPI +#MASTER_SITES= PYPI # no tests PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} MAINTAINER= yuri@FreeBSD.org COMMENT= Python Materials Genomics is a robust materials analysis code -WWW= https://pymatgen.org/ +WWW= https://pymatgen.org/ \ + https://github.com/materialsproject/pymatgen LICENSE= MIT -LICENSE_FILE= ${WRKSRC}/LICENSE.rst - -BUILD_DEPENDS= ${PYNUMPY} -RUN_DEPENDS= ${PYNUMPY} \ - ${PYTHON_PKGNAMEPREFIX}beautifulsoup>0:www/py-beautifulsoup@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}matplotlib>0:math/py-matplotlib@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}monty>0:devel/py-monty@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}networkx>0:math/py-networkx@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}palettable>=3.3.0:misc/py-palettable@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}pandas>0:math/py-pandas@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}plotly>0:graphics/py-plotly@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}requests>0:www/py-requests@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}ruamel.yaml>0:devel/py-ruamel.yaml@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}scipy>=1.7.3:science/py-scipy@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}six>0:devel/py-six@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}spglib>0:science/py-spglib@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}sympy>0:math/py-sympy@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}tabulate>0:devel/py-tabulate@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}tqdm>0:misc/py-tqdm@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}typing-extensions>0:devel/py-typing-extensions@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}uncertainties>=3.1.6:math/py-uncertainties@${PY_FLAVOR} +LICENSE_FILE= ${WRKSRC}/LICENSE + +BUILD_DEPENDS= ${PYNUMPY} \ + ${PYTHON_PKGNAMEPREFIX}wheel>0:devel/py-wheel@${PY_FLAVOR} +RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}beautifulsoup>0:www/py-beautifulsoup@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}joblib>=1:devel/py-joblib@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}matplotlib>=3.8:math/py-matplotlib@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}monty>=2024.10.21:devel/py-monty@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}networkx>=2.7:math/py-networkx@${PY_FLAVOR} \ + ${PYNUMPY} \ + ${PYTHON_PKGNAMEPREFIX}palettable>=3.3.3:misc/py-palettable@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}pandas>=2:math/py-pandas@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}plotly>=4.5.0:graphics/py-plotly@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}pybtex>=0.24.0:textproc/py-pybtex@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}requests>=2.32:www/py-requests@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}ruamel.yaml>=0.17.0:devel/py-ruamel.yaml@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}scipy>=1.13.0:science/py-scipy@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}scipy>=1.14.1:science/py-scipy@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}spglib>=2.5.0:science/py-spglib@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}sympy>=1.3:math/py-sympy@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}tabulate>=0.9:devel/py-tabulate@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}tqdm>=4.60:misc/py-tqdm@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}uncertainties>=3.1.4:math/py-uncertainties@${PY_FLAVOR} TEST_DEPENDS= ${PYTHON_PKGNAMEPREFIX}pybtex>0:textproc/py-pybtex@${PY_FLAVOR} USES= compiler:c++11-lang python -USE_PYTHON= distutils cython concurrent autoplist pytest +USE_PYTHON= pep517 cython concurrent autoplist pytest + +USE_GITHUB= yes +GH_ACCOUNT= materialsproject + +TEST_ENV= ${MAKE_ENV} PYTHONPATH=${STAGEDIR}${PYTHONPREFIX_SITELIBDIR} +TEST_WRKSRC= ${WRKSRC}/tests -post-install: +post-install: # strip binaries @cd ${STAGEDIR}${PYTHONPREFIX_SITELIBDIR}/${PORTNAME} && ${STRIP_CMD} \ optimization/linear_assignment*.so \ optimization/neighbors*.so \ util/coord_cython*.so -# tests fail: https://github.com/materialsproject/pymatgen/issues/2275, https://github.com/materialsproject/pymatgen/issues/2592 -pre-test: - @cd ${WRKSRC} && ${PYTHON_CMD} ${PYSETUP} build_ext --inplace +# tests fail to find some files: https://github.com/materialsproject/pymatgen/issues/4172 +xpre-test: + @cd ${TEST_WRKSRC} && ${PYTHON_CMD} ${PYSETUP} build_ext --inplace .include diff --git a/science/py-pymatgen/distinfo b/science/py-pymatgen/distinfo index 36bf2e7b4e7e..ae9b145d0114 100644 --- a/science/py-pymatgen/distinfo +++ b/science/py-pymatgen/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1659081267 -SHA256 (pymatgen-2022.7.19.tar.gz) = 4557fb7ee0f25753d97fa0cd8bcfb9d36ea7d422ee12b416cae05c7fb50531d7 -SIZE (pymatgen-2022.7.19.tar.gz) = 2610811 +TIMESTAMP = 1731622067 +SHA256 (materialsproject-pymatgen-v2024.11.13_GH0.tar.gz) = b780cc395007f5793d1823d4b0b83ed99cfec10d4834bb8e640e92c65627dbe5 +SIZE (materialsproject-pymatgen-v2024.11.13_GH0.tar.gz) = 262224927 diff --git a/science/py-pymatgen/files/patch-pyproject.toml b/science/py-pymatgen/files/patch-pyproject.toml new file mode 100644 index 000000000000..dc9a546031bc --- /dev/null +++ b/science/py-pymatgen/files/patch-pyproject.toml @@ -0,0 +1,13 @@ +--- pyproject.toml.orig 2024-11-14 18:47:14 UTC ++++ pyproject.toml +@@ -3,8 +3,8 @@ requires = [ + "Cython>=0.29.23", + # Building against NPY2 will support both NPY1 and NPY2 + # https://numpy.org/devdocs/dev/depending_on_numpy.html#build-time-dependency +- "numpy>=2.1.0", +- "setuptools>=65.0.0", ++ "numpy", ++ "setuptools", + ] + build-backend = "setuptools.build_meta" +