Date: Sat, 14 Sep 2024 13:23:34 GMT From: "Jason W. Bacon" <jwb@FreeBSD.org> To: ports-committers@FreeBSD.org, dev-commits-ports-all@FreeBSD.org, dev-commits-ports-main@FreeBSD.org Subject: git: fbb86e94a87c - main - biology/py-macs3: Update to 3.0.2 Message-ID: <202409141323.48EDNYgR025996@gitrepo.freebsd.org>
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The branch main has been updated by jwb: URL: https://cgit.FreeBSD.org/ports/commit/?id=fbb86e94a87c238d1214b49f06b0f955e0f517a0 commit fbb86e94a87c238d1214b49f06b0f955e0f517a0 Author: Jason W. Bacon <jwb@FreeBSD.org> AuthorDate: 2024-09-14 13:22:03 +0000 Commit: Jason W. Bacon <jwb@FreeBSD.org> CommitDate: 2024-09-14 13:23:32 +0000 biology/py-macs3: Update to 3.0.2 Some minor enhancements and improved docs Changes: https://github.com/macs3-project/MACS/releases Reported by: portscout --- biology/py-macs3/Makefile | 9 ++++----- biology/py-macs3/distinfo | 6 +++--- biology/py-macs3/files/patch-pyproject.toml | 6 +++--- biology/py-macs3/files/patch-requirements.txt | 19 +++++++++++-------- biology/py-macs3/files/patch-setup.py | 11 ----------- 5 files changed, 21 insertions(+), 30 deletions(-) diff --git a/biology/py-macs3/Makefile b/biology/py-macs3/Makefile index 56f6bdc9c904..2ca2822457a4 100644 --- a/biology/py-macs3/Makefile +++ b/biology/py-macs3/Makefile @@ -1,6 +1,6 @@ PORTNAME= MACS3 DISTVERSIONPREFIX= v -DISTVERSION= 3.0.1 +DISTVERSION= 3.0.2 CATEGORIES= biology python PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} @@ -14,15 +14,14 @@ LICENSE_FILE= ${WRKSRC}/LICENSE NOT_FOR_ARCHS= i386 NOT_FOR_ARCHS_REASON_i386=Requires _Float16 -BUILD_DEPENDS= ${PY_SETUPTOOLS} \ - ${PYTHON_PKGNAMEPREFIX}wheel>0:devel/py-wheel@${PY_FLAVOR} \ +BUILD_DEPENDS= ${PYTHON_PKGNAMEPREFIX}wheel>0:devel/py-wheel@${PY_FLAVOR} \ ${PYNUMPY} \ simde>0:devel/simde \ ${PYTHON_PKGNAMEPREFIX}cykhash>0:devel/py-cykhash@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}hmmlearn>0:math/py-hmmlearn@${PY_FLAVOR} + ${PYTHON_PKGNAMEPREFIX}hmmlearn>=0.3.2:math/py-hmmlearn@${PY_FLAVOR} RUN_DEPENDS= ${PYNUMPY} \ ${PYTHON_PKGNAMEPREFIX}cykhash>0:devel/py-cykhash@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}hmmlearn>0:math/py-hmmlearn@${PY_FLAVOR} + ${PYTHON_PKGNAMEPREFIX}hmmlearn>=0.3.2:math/py-hmmlearn@${PY_FLAVOR} TEST_DEPENDS= ${PYTHON_PKGNAMEPREFIX}pytest>0:devel/py-pytest@${PY_FLAVOR} \ bash:shells/bash diff --git a/biology/py-macs3/distinfo b/biology/py-macs3/distinfo index b742493c53a1..bacae8bd911a 100644 --- a/biology/py-macs3/distinfo +++ b/biology/py-macs3/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1713397031 -SHA256 (macs3-project-MACS-v3.0.1_GH0.tar.gz) = 8a2f5b2dccfc255ea2fd5e54e0d6aa9c12f5ce83762b17b779ce2546ade860ce -SIZE (macs3-project-MACS-v3.0.1_GH0.tar.gz) = 197400439 +TIMESTAMP = 1725973815 +SHA256 (macs3-project-MACS-v3.0.2_GH0.tar.gz) = 33e877460f1b621ee85c78221b52d1e067b8f5aacdaf4d16bd887485bf636e08 +SIZE (macs3-project-MACS-v3.0.2_GH0.tar.gz) = 197484503 diff --git a/biology/py-macs3/files/patch-pyproject.toml b/biology/py-macs3/files/patch-pyproject.toml index 15f55a86a701..94a5699aa764 100644 --- a/biology/py-macs3/files/patch-pyproject.toml +++ b/biology/py-macs3/files/patch-pyproject.toml @@ -1,7 +1,7 @@ ---- pyproject.toml.orig 2024-02-23 05:43:44 UTC +--- pyproject.toml.orig 2024-09-07 16:11:35 UTC +++ pyproject.toml @@ -1,3 +1,3 @@ [build-system] --requires=['setuptools>=60.0', 'numpy>=1.24.2', 'scipy>=1.11.4', 'cykhash>=2.0,<3.0', 'Cython~=3.0', 'scikit-learn>=1.2.1', 'hmmlearn>=0.3'] -+requires=['setuptools>=60.0', 'numpy>=1.24.2', 'scipy>=1.11.1', 'cykhash>=2.0,<3.0', 'Cython>=0', 'scikit-learn>=1.2.1', 'hmmlearn>=0.3'] +-requires=['setuptools>=68.0', 'numpy>=1.25,<2.0.0', 'scipy>=1.12', 'cykhash>=2.0,<3.0', 'Cython>=3.0,<3.1', 'scikit-learn>=1.3', 'hmmlearn>=0.3.2'] ++requires=['setuptools>=63.0', 'numpy>=1.25,<2.0.0', 'scipy>=1.11.1', 'cykhash>=2.0,<3.0', 'Cython>=0.29.37', 'scikit-learn>=1.3', 'hmmlearn>=0.3.2'] diff --git a/biology/py-macs3/files/patch-requirements.txt b/biology/py-macs3/files/patch-requirements.txt index 81c9a1f75f88..ceac91b3141e 100644 --- a/biology/py-macs3/files/patch-requirements.txt +++ b/biology/py-macs3/files/patch-requirements.txt @@ -1,11 +1,14 @@ ---- requirements.txt.orig 2024-02-23 05:43:44 UTC +--- requirements.txt.orig 2024-09-07 16:11:35 UTC +++ requirements.txt -@@ -1,6 +1,6 @@ --Cython~=3.0 -+Cython>=0 - numpy>=1.24.2 --scipy>=1.11.4 +@@ -1,8 +1,8 @@ +-Cython>=3.0,<3.1 ++Cython>=0.29.37 + numpy>=1.25,<2.0.0 +-scipy>=1.12 +scipy>=1.11.1 - scikit-learn>=1.2.1 - hmmlearn>=0.3 + scikit-learn>=1.3 + hmmlearn>=0.3.2 cykhash>=2.0,<3.0 + pytest>=7.0 +-setuptools>=68.0 ++setuptools>=63.0 diff --git a/biology/py-macs3/files/patch-setup.py b/biology/py-macs3/files/patch-setup.py deleted file mode 100644 index f309f3139736..000000000000 --- a/biology/py-macs3/files/patch-setup.py +++ /dev/null @@ -1,11 +0,0 @@ ---- setup.py.orig 2024-02-24 14:39:02 UTC -+++ setup.py -@@ -70,7 +70,7 @@ def main(): - - if not clang: - try: -- gcc_version_check = subprocess.check_output( ["gcc", "--version"], universal_newlines=True) -+ gcc_version_check = subprocess.check_output( ["cc", "--version"], universal_newlines=True) - if gcc_version_check.find("clang") != -1: - clang = True - else:
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