From nobody Sun Nov 17 18:10:47 2024 X-Original-To: dev-commits-ports-all@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 4XrzMX3Kvmz5dDGC; Sun, 17 Nov 2024 18:10:48 +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 4XrzMW5RN7z4lqJ; Sun, 17 Nov 2024 18:10:47 +0000 (UTC) (envelope-from git@FreeBSD.org) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1731867047; 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=P816EajR6HyXBEY8p92eBBJS8YQAGweQbsHa2W3qpKA=; b=e8z/xvv42z1lGdfJAUw3eoiHE34b1HPTJ9YgNbgaJe8JVnh4Kb3T5GE5wkypAg2NNuQ8vP O93KEx53L+uws9EOUyVmrSJo+51x2UetxXxAj6/iLUed1olR3JHz+RkmztGF6keOGFyNfG t8joeX3Aw2TN/LGYxofav8x6iDvpSgYP0o77jojDbTl80EfbqL69Kfj1qVqLjtS2Mc11XC H3qW8BH88kW55/y1dCLAGgUJJxd2R4+sGD/CLwEHOiJDJJ6Inwo8uR5j9wWH000YQ1QYf3 VXTKKIBndOghrWQGelrMT6K3U3U5THimD/ZJBqjLnpi71iNziIJ4m1JsyF9tgg== ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1731867047; 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=P816EajR6HyXBEY8p92eBBJS8YQAGweQbsHa2W3qpKA=; b=igPVVeoopz9kSG49Q8aZm9UtOlYhzYwTDEk5WCINSIL/jVnGADZbRY4Xnn1zIkwY/5m5GB ZOPcHRIar83/UEwdvnvHJxd1jEh+42VEdKjIj41qdulH3uoO1cY6eTqEz6B9zi4TmUpuhJ 90PJzgEYsh1o2RwDru3h0vmjJan9SpuHnB6ouTn1buNd0T/kdnRThSXNwH1HYxgmPwCjgM oN6Kvh6n/FjnDan4D1yBZNL0uroH+emaVnMJ+e/lD8dXApDuRTuOQOTMJUQuQUKSKmli5m 75+ITuEeal45GOQe1CWOLbR1il4njPlJaQvODK9/HWTUluEULeuQr0A1klWibg== ARC-Authentication-Results: i=1; mx1.freebsd.org; none ARC-Seal: i=1; s=dkim; d=freebsd.org; t=1731867047; a=rsa-sha256; cv=none; b=jI1/Z3IWM/bl/nAMejPpqEuWApXCmH5VLGz8dCRCbuQtvjg+Wb6crffQLAubzxpYmqjemm KDkCwqrSYVgjlPAdKQ8Vd2SqVPjjkM/o4EoM/qd/NyLpWlNz8meESY/olpMKdsyfA11SNW nYgK1MDwnF8mMJ2unJE99EOXbaxX9eZj/tv/2+iseSCx3Bq+yoJJIeUCD6MqF8r5vhfuv6 OPwervFy/xSwcC6dCgv95HnUdgMxbkgQzqUcZD3y/dEGonDNDWWCqIn6i0Rxdtt/623XB0 J9ZgHem0/sojVPQBjgivt0s5EAobKdYi5GAVoCRAPAd9bo19vUqtRVDCaMOWhA== 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 4XrzMW44R2z12Pv; Sun, 17 Nov 2024 18:10:47 +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 4AHIAleR089663; Sun, 17 Nov 2024 18:10:47 GMT (envelope-from git@gitrepo.freebsd.org) Received: (from git@localhost) by gitrepo.freebsd.org (8.18.1/8.18.1/Submit) id 4AHIAlNW089660; Sun, 17 Nov 2024 18:10:47 GMT (envelope-from git) Date: Sun, 17 Nov 2024 18:10:47 GMT Message-Id: <202411171810.4AHIAlNW089660@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: 01e2cd169e9d - main - science/py-pymol: update 2.5.0-97 =?utf-8?Q?=E2=86=92?= 3.0.0 List-Id: Commit messages for all branches of the ports repository List-Archive: https://lists.freebsd.org/archives/dev-commits-ports-all List-Help: List-Post: List-Subscribe: List-Unsubscribe: X-BeenThere: dev-commits-ports-all@freebsd.org Sender: owner-dev-commits-ports-all@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: 01e2cd169e9dd073cdd84302dbeba9fe158a50ec Auto-Submitted: auto-generated The branch main has been updated by yuri: URL: https://cgit.FreeBSD.org/ports/commit/?id=01e2cd169e9dd073cdd84302dbeba9fe158a50ec commit 01e2cd169e9dd073cdd84302dbeba9fe158a50ec Author: Yuri Victorovich AuthorDate: 2024-11-17 17:31:31 +0000 Commit: Yuri Victorovich CommitDate: 2024-11-17 18:10:32 +0000 science/py-pymol: update 2.5.0-97 → 3.0.0 --- science/py-pymol/Makefile | 11 ++++------- science/py-pymol/distinfo | 6 +++--- science/py-pymol/files/patch-setup.py | 22 +++++++++++----------- science/py-pymol/pkg-plist | 31 +++++++++++++++++++++++++++---- 4 files changed, 45 insertions(+), 25 deletions(-) diff --git a/science/py-pymol/Makefile b/science/py-pymol/Makefile index b31b04de6cb9..de37dcd75e05 100644 --- a/science/py-pymol/Makefile +++ b/science/py-pymol/Makefile @@ -1,8 +1,6 @@ PORTNAME= pymol DISTVERSIONPREFIX= v -DISTVERSION= 2.5.0-97 -PORTREVISION= 2 -DISTVERSIONSUFFIX= -gd24468af +DISTVERSION= 3.0.0 CATEGORIES= science biology python PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} @@ -19,15 +17,14 @@ BUILD_DEPENDS= ${PYNUMPY} \ ${LOCALBASE}/include/glm/glm.hpp:math/glm \ ${LOCALBASE}/include/mmtf.hpp:science/mmtf-cpp LIB_DEPENDS= libfreetype.so:print/freetype2 \ - libpng.so:graphics/png \ - libmsgpackc.so:devel/msgpack-c \ - libnetcdf.so:science/netcdf + libnetcdf.so:science/netcdf \ + libpng16.so:graphics/png RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}msgpack>0:devel/py-msgpack@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}Pmw>0:x11-toolkits/py-Pmw@${PY_FLAVOR} \ ${PYNUMPY} USES= compiler:c++11-lang gl gnome python tar:bz2 -USE_GL= gl glew glu glut +USE_GL= gl glew glu USE_GNOME= libxml2 USE_PYTHON= distutils concurrent # autoplist is broken: https://github.com/schrodinger/pymol-open-source/issues/99 diff --git a/science/py-pymol/distinfo b/science/py-pymol/distinfo index bb74283b993b..b47da168396a 100644 --- a/science/py-pymol/distinfo +++ b/science/py-pymol/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1669581024 -SHA256 (schrodinger-pymol-open-source-v2.5.0-97-gd24468af_GH0.tar.gz) = 801e8e71a02c56c07aacd241044e397586a435a4435b74845d779d9846c994af -SIZE (schrodinger-pymol-open-source-v2.5.0-97-gd24468af_GH0.tar.gz) = 10495556 +TIMESTAMP = 1731825743 +SHA256 (schrodinger-pymol-open-source-v3.0.0_GH0.tar.gz) = 45e800a02680cec62dff7a0f92283f4be7978c13a02934a43ac6bb01f67622cf +SIZE (schrodinger-pymol-open-source-v3.0.0_GH0.tar.gz) = 29510174 diff --git a/science/py-pymol/files/patch-setup.py b/science/py-pymol/files/patch-setup.py index fe1059c10949..6378d80ded89 100644 --- a/science/py-pymol/files/patch-setup.py +++ b/science/py-pymol/files/patch-setup.py @@ -1,15 +1,15 @@ ---- setup.py.orig 2021-05-10 18:38:37 UTC +--- setup.py.orig 2024-04-09 16:59:46 UTC +++ setup.py -@@ -53,6 +53,8 @@ try: - "shared library; no: disable fast MMTF load support") - parser.add_argument('--help-distutils', action="store_true", - help="show help for distutils options and exit") -+ parser.add_argument('--single-version-externally-managed', action="store_true", -+ help="single-version-externally-managed") - parser.add_argument('--testing', action="store_true", - help="Build C-level tests") - parser.add_argument('--openvr', dest='openvr', action='store_true') -@@ -282,7 +284,7 @@ if DEBUG and not WIN: +@@ -60,6 +60,8 @@ parser.add_argument('--help-distutils', action="store_ + "shared library; no: disable fast MMTF load support") + parser.add_argument('--help-distutils', action="store_true", + help="show help for distutils options and exit") ++parser.add_argument('--single-version-externally-managed', action="store_true", ++ help="single-version-externally-managed") + parser.add_argument('--testing', action="store_true", + help="Build C-level tests") + parser.add_argument('--openvr', dest='openvr', action='store_true') +@@ -295,7 +297,7 @@ ext_comp_args = [ libs = ["png", "freetype"] lib_dirs = [] ext_comp_args = [ diff --git a/science/py-pymol/pkg-plist b/science/py-pymol/pkg-plist index cac539fae865..3363a43e5cb1 100644 --- a/science/py-pymol/pkg-plist +++ b/science/py-pymol/pkg-plist @@ -287,10 +287,6 @@ bin/pymol %%PYTHON_SITELIBDIR%%/pmg_tk/startup/__pycache__/__init__%%PYTHON_EXT_SUFFIX%%.opt-1.pyc %%PYTHON_SITELIBDIR%%/pmg_tk/startup/__pycache__/__init__%%PYTHON_EXT_SUFFIX%%.pyc %%PYTHON_SITELIBDIR%%/pmg_tk/volume.py -%%PYTHON_SITELIBDIR%%/pymol-2.6.0a0-py%%PYTHON_VER%%.egg-info/PKG-INFO -%%PYTHON_SITELIBDIR%%/pymol-2.6.0a0-py%%PYTHON_VER%%.egg-info/SOURCES.txt -%%PYTHON_SITELIBDIR%%/pymol-2.6.0a0-py%%PYTHON_VER%%.egg-info/dependency_links.txt -%%PYTHON_SITELIBDIR%%/pymol-2.6.0a0-py%%PYTHON_VER%%.egg-info/top_level.txt %%PYTHON_SITELIBDIR%%/pymol/Qt/__init__.py %%PYTHON_SITELIBDIR%%/pymol/Qt/__pycache__/__init__%%PYTHON_EXT_SUFFIX%%.opt-1.pyc %%PYTHON_SITELIBDIR%%/pymol/Qt/__pycache__/__init__%%PYTHON_EXT_SUFFIX%%.pyc @@ -499,6 +495,10 @@ bin/pymol %%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/chempy/fragments/asp.pkl %%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/chempy/fragments/asph.pkl %%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/chempy/fragments/atp.pkl +%%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/chempy/fragments/atpA.pkl +%%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/chempy/fragments/atpB.pkl +%%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/chempy/fragments/atp_ttpA.pkl +%%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/chempy/fragments/atp_ttpB.pkl %%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/chempy/fragments/benzene.pkl %%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/chempy/fragments/benzocycloheptane.pkl %%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/chempy/fragments/butane.pkl @@ -530,6 +530,10 @@ bin/pymol %%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/chempy/fragments/ct_tyr.pkl %%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/chempy/fragments/ct_val.pkl %%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/chempy/fragments/ctp.pkl +%%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/chempy/fragments/ctpA.pkl +%%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/chempy/fragments/ctpB.pkl +%%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/chempy/fragments/ctp_gtpA.pkl +%%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/chempy/fragments/ctp_gtpB.pkl %%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/chempy/fragments/cyanide.pkl %%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/chempy/fragments/cyclobutane.pkl %%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/chempy/fragments/cycloheptane.pkl @@ -547,6 +551,10 @@ bin/pymol %%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/chempy/fragments/gluh.pkl %%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/chempy/fragments/gly.pkl %%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/chempy/fragments/gtp.pkl +%%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/chempy/fragments/gtpA.pkl +%%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/chempy/fragments/gtpB.pkl +%%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/chempy/fragments/gtp_ctpA.pkl +%%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/chempy/fragments/gtp_ctpB.pkl %%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/chempy/fragments/hid.pkl %%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/chempy/fragments/hie.pkl %%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/chempy/fragments/hip.pkl @@ -601,8 +609,13 @@ bin/pymol %%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/chempy/fragments/trifluoromethane.pkl %%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/chempy/fragments/trp.pkl %%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/chempy/fragments/ttp.pkl +%%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/chempy/fragments/ttpA.pkl +%%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/chempy/fragments/ttpB.pkl +%%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/chempy/fragments/ttp_atpA.pkl +%%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/chempy/fragments/ttp_atpB.pkl %%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/chempy/fragments/tyr.pkl %%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/chempy/fragments/utp.pkl +%%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/chempy/fragments/utpA.pkl %%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/chempy/fragments/val.pkl %%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/chempy/sidechains/generate1.py %%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/chempy/sidechains/generate2.py @@ -664,7 +677,12 @@ bin/pymol %%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/pymol/icons/icon2.svg %%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/pymol/matrices/BLOSUM62 %%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/pymol/splash.png +%%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/setting_help.csv %%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/shaders/anaglyph_header.fs +%%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/shaders/bezier.fs +%%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/shaders/bezier.tsc +%%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/shaders/bezier.tse +%%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/shaders/bezier.vs %%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/shaders/bg.fs %%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/shaders/bg.vs %%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/shaders/call_compute_color_for_light.fs @@ -705,6 +723,11 @@ bin/pymol %%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/shaders/webgl_header.fs %%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/shaders/webgl_header.vs %%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/startup/README.txt +%%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/startup/apbs_gui/__init__.py +%%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/startup/apbs_gui/apbs.ui +%%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/startup/apbs_gui/creating.py +%%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/startup/apbs_gui/electrostatics.py +%%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/startup/apbs_gui/qtwidgets.py %%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/startup/lightingsettings_gui/__init__.py %%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/startup/lightingsettings_gui/main.py %%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/test/double.png