From nobody Thu Oct 20 20:31:41 2022 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 4MtfQQ12B1z4gVx6; Thu, 20 Oct 2022 20:31:42 +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 "R3" (verified OK)) by mx1.freebsd.org (Postfix) with ESMTPS id 4MtfQQ0NNQz3Ncw; Thu, 20 Oct 2022 20:31:42 +0000 (UTC) (envelope-from git@FreeBSD.org) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1666297902; 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=/Nz8TqmGbjuwK3HVglusgCHWEYOvHhyvRE/QuSCMyEI=; b=brVo2waiakS7VQtQup5hvhYL84YM0D70Eq5IenprdZmMmiV5FsoYdGEqtA5rJPup1qC0/M cecMASBYV4C7sZMlpAiKb2j99BD/JArWj9rSj521ZnrNwFepLF0y5+gd6cWC8KfLgcdzob TcjZnUkteF4YwJMyw1kCmf2k+Y7hJCxFyoVrL/QNj9MLL1S2IG8VWFSR3hB3Dlhfeb2ECt Z/Xu02TablWMo8evdq/Ol/iyoIiL7AFa3PXMr4W2zAxIpmwXK2r7MRwCIbhlR1msFa1UL4 +7ojE1OHwMdS9md+IcMXFL8yUHcKlVFs0YbT9vDo6WK5om5eY9tAEYiqs/ilIg== 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 4MtfQP6Z5Jz10Bd; Thu, 20 Oct 2022 20:31:41 +0000 (UTC) (envelope-from git@FreeBSD.org) Received: from gitrepo.freebsd.org ([127.0.1.44]) by gitrepo.freebsd.org (8.16.1/8.16.1) with ESMTP id 29KKVf17000832; Thu, 20 Oct 2022 20:31:41 GMT (envelope-from git@gitrepo.freebsd.org) Received: (from git@localhost) by gitrepo.freebsd.org (8.16.1/8.16.1/Submit) id 29KKVf3A000831; Thu, 20 Oct 2022 20:31:41 GMT (envelope-from git) Date: Thu, 20 Oct 2022 20:31:41 GMT Message-Id: <202210202031.29KKVf3A000831@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: 2e0d3b8d4533 - main - science/smoldyn: Update 2.68 -> 2.69; Fix tests 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: Sender: owner-dev-commits-ports-main@freebsd.org X-BeenThere: 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: 2e0d3b8d4533f5472ade919e5c3e71aaefad9da4 Auto-Submitted: auto-generated ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1666297902; 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=/Nz8TqmGbjuwK3HVglusgCHWEYOvHhyvRE/QuSCMyEI=; b=WkVJQ8gB3yqw3P7TALl8S8phvfET6RCdrcyZyLjVl5dut8XvDFKUtx5ZAMPsTiDSqbqdyW jve31il0va1Iw4ZMn2sx5LDBjTZdJVgUqfC5NppMiyCWwfsdjBZK62M0xTJNJNTqcEhogC OTEZvehvXdRPN+zJI0x9UegXuO3CJnPfiD8PkMF6kQbJV4tUutAEBCBdyC81HRgBDMTquA BfCMO1hZRo4Zr2A9zfND1IE5tQILSeufczu5ruPcEOvVT3wXTeK5tqMoE48qAiHmV0LzNg 05Coc1m36f8L7fKeEuAEVeRFZOJRA9oDvoYX8o324zUIyG/0fo0SPY8ki61vpQ== ARC-Seal: i=1; s=dkim; d=freebsd.org; t=1666297902; a=rsa-sha256; cv=none; b=hOHvF1O+lJzOU8IpJornJCQ61aKrUfoyKLjogTbABLEf3LWGf3TLlB75/S3OmJSF4UQMIj RXGNe90vJyd1WqM23DSj8x7qvoMvMOHbBYbc7q9qyzcNpyDYStlUVvKHoFUKfr6hI3josY INrEydE07FNXpasKYAvadz2jV3XuimrEczA2mkL/i/NBwplcB2QIoZMSRDYhjviwBVXylp HemtLX04iMdBNf2Bm6IIxSBwDzgnTELfcMZZdqUvK1uE7EjAYbSCpBM8wmPakcxX6rcfDB mHhvNiAUKZ9udfWRt7I50R6KB5hQ86lK5Whvr3MYCucPKbuh4hQ5shTkjebklA== ARC-Authentication-Results: i=1; mx1.freebsd.org; none X-ThisMailContainsUnwantedMimeParts: N The branch main has been updated by yuri: URL: https://cgit.FreeBSD.org/ports/commit/?id=2e0d3b8d4533f5472ade919e5c3e71aaefad9da4 commit 2e0d3b8d4533f5472ade919e5c3e71aaefad9da4 Author: Yuri Victorovich AuthorDate: 2022-10-20 14:51:06 +0000 Commit: Yuri Victorovich CommitDate: 2022-10-20 20:31:39 +0000 science/smoldyn: Update 2.68 -> 2.69; Fix tests PYTHON options was added but it is disabled because one dependency is missing. Tests, however, pass with PYTHON=ON (and only with PYTHON=ON). --- science/smoldyn/Makefile | 31 ++++++++++++++++++++++--------- science/smoldyn/distinfo | 6 +++--- science/smoldyn/pkg-plist | 28 ++++++++++++++++++++++++++++ 3 files changed, 53 insertions(+), 12 deletions(-) diff --git a/science/smoldyn/Makefile b/science/smoldyn/Makefile index a58d63dfaa30..631cc762f026 100644 --- a/science/smoldyn/Makefile +++ b/science/smoldyn/Makefile @@ -1,5 +1,5 @@ PORTNAME= smoldyn -DISTVERSION= 2.68 +DISTVERSION= 2.69 CATEGORIES= science MASTER_SITES= https://www.smoldyn.org/ @@ -11,22 +11,35 @@ LICENSE= LGPL3 LICENSE_FILE= ${WRKSRC}/License.txt LIB_DEPENDS= libtiff.so:graphics/tiff +TEST_DEPENDS= ${PYTHON_PKGNAMEPREFIX}flaky>0:devel/py-flaky@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}matplotlib>0:math/py-matplotlib@${PY_FLAVOR} \ + ${PYNUMPY} -USES= cmake:testing compiler:c++11-lang gl localbase:ldflags tar:tgz python:test shebangfix xorg +USES= cmake:testing compiler:c++11-lang gl localbase:ldflags python:test tar:tgz shebangfix xorg USE_GL= gl glu glut USE_XORG= xi xmu USE_LDCONFIG= yes SHEBANG_GLOB= *.py.in -CMAKE_OFF= OPTION_PYTHON CMAKE_TESTING_ON= OPTION_EXAMPLES # all tests fail to run, see https://github.com/ssandrews/Smoldyn/issues/127 -PLIST_FILES= bin/${PORTNAME} \ - include/libsmoldyn.h \ - include/smoldyn.h \ - include/smoldynconfigure.h \ - lib/libsmoldyn_shared.so \ - lib/libsmoldyn_static.a +OPTIONS_DEFINE= PYTHON +OPTIONS_DEFAULT= # PYTHON Tests ONLY pass when PYTHON=ON despite biology/py-biosimulators-utils being missing +OPTIONS_SUB= yes + +PYTHON_CMAKE_BOOL= OPTION_PYTHON +PYTHON_USES= python +PYTHON_CMAKE_ON= -DPython3_EXECUTABLE=${PYTHON_CMD} +PYTHON_BUILD_DEPENDS= ${PYTHON_PKGNAMEPREFIX}setuptools>0:devel/py-setuptools@${PY_FLAVOR} +PYTHON_RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}biosimulators-utils>0:biology/py-biosimulators-utils@${PY_FLAVOR} +PYTHON_BROKEN= pending biology/py-biosimulators-utils completion + +post-extract: # see https://github.com/ssandrews/Smoldyn/issues/127 + @${CHMOD} +x ${WRKSRC}/scripts/run_pyscript.py.in + +do-install-PYTHON-on: # workaround for https://github.com/ssandrews/Smoldyn/issues/129 + @cd ${BUILD_WRKSRC}/py && ${COPYTREE_SHARE} ${PORTNAME} ${STAGEDIR}${PYTHON_SITELIBDIR} + @${RM} ${STAGEDIR}${PYTHON_SITELIBDIR}/${PORTNAME}/.DS_Store .include diff --git a/science/smoldyn/distinfo b/science/smoldyn/distinfo index eaef8f3533d5..dab6130f445b 100644 --- a/science/smoldyn/distinfo +++ b/science/smoldyn/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1659253902 -SHA256 (smoldyn-2.68.tgz) = f84f8bc214110453039ef76b61fd9b8c37bc6a8b584c8bae85171c7e7543df7f -SIZE (smoldyn-2.68.tgz) = 32722229 +TIMESTAMP = 1666163797 +SHA256 (smoldyn-2.69.tgz) = ad0b76cea376419202cd064bad04c2fb47e624ea74db0b96512c54494b44e6ad +SIZE (smoldyn-2.69.tgz) = 32837854 diff --git a/science/smoldyn/pkg-plist b/science/smoldyn/pkg-plist new file mode 100644 index 000000000000..f664bfef6faa --- /dev/null +++ b/science/smoldyn/pkg-plist @@ -0,0 +1,28 @@ +bin/smoldyn +include/libsmoldyn.h +include/smoldyn.h +include/smoldynconfigure.h +lib/libsmoldyn_shared.so +lib/libsmoldyn_static.a +%%PYTHON%%%%PYTHON_SITELIBDIR%%/smoldyn/__init__.py +%%PYTHON%%%%PYTHON_SITELIBDIR%%/smoldyn/__main__.py +%%PYTHON%%%%PYTHON_SITELIBDIR%%/smoldyn/__pycache__/__init__%%PYTHON_EXT_SUFFIX%%.pyc +%%PYTHON%%%%PYTHON_SITELIBDIR%%/smoldyn/__pycache__/smoldyn%%PYTHON_EXT_SUFFIX%%.pyc +%%PYTHON%%%%PYTHON_SITELIBDIR%%/smoldyn/__pycache__/types%%PYTHON_EXT_SUFFIX%%.pyc +%%PYTHON%%%%PYTHON_SITELIBDIR%%/smoldyn/__pycache__/utils%%PYTHON_EXT_SUFFIX%%.pyc +%%PYTHON%%%%PYTHON_SITELIBDIR%%/smoldyn/_smoldyn.cpython-310-darwin.so +%%PYTHON%%%%PYTHON_SITELIBDIR%%/smoldyn/_smoldyn%%PYTHON_EXT_SUFFIX%%-darwin.so +%%PYTHON%%%%PYTHON_SITELIBDIR%%/smoldyn/_smoldyn%%PYTHON_EXT_SUFFIX%%.so +%%PYTHON%%%%PYTHON_SITELIBDIR%%/smoldyn/biosimulators/__init__.py +%%PYTHON%%%%PYTHON_SITELIBDIR%%/smoldyn/biosimulators/__main__.py +%%PYTHON%%%%PYTHON_SITELIBDIR%%/smoldyn/biosimulators/__pycache__/__init__%%PYTHON_EXT_SUFFIX%%.pyc +%%PYTHON%%%%PYTHON_SITELIBDIR%%/smoldyn/biosimulators/__pycache__/_version%%PYTHON_EXT_SUFFIX%%.pyc +%%PYTHON%%%%PYTHON_SITELIBDIR%%/smoldyn/biosimulators/__pycache__/combine%%PYTHON_EXT_SUFFIX%%.pyc +%%PYTHON%%%%PYTHON_SITELIBDIR%%/smoldyn/biosimulators/__pycache__/data_model%%PYTHON_EXT_SUFFIX%%.pyc +%%PYTHON%%%%PYTHON_SITELIBDIR%%/smoldyn/biosimulators/_version.py +%%PYTHON%%%%PYTHON_SITELIBDIR%%/smoldyn/biosimulators/combine.py +%%PYTHON%%%%PYTHON_SITELIBDIR%%/smoldyn/biosimulators/data_model.py +%%PYTHON%%%%PYTHON_SITELIBDIR%%/smoldyn/biosimulators/utils.py +%%PYTHON%%%%PYTHON_SITELIBDIR%%/smoldyn/smoldyn.py +%%PYTHON%%%%PYTHON_SITELIBDIR%%/smoldyn/types.py +%%PYTHON%%%%PYTHON_SITELIBDIR%%/smoldyn/utils.py