git: 01e2cd169e9d - main - science/py-pymol: update 2.5.0-97 → 3.0.0

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From: Yuri Victorovich <yuri_at_FreeBSD.org>
Date: Sun, 17 Nov 2024 18:10:47 UTC
The branch main has been updated by yuri:

URL: https://cgit.FreeBSD.org/ports/commit/?id=01e2cd169e9dd073cdd84302dbeba9fe158a50ec

commit 01e2cd169e9dd073cdd84302dbeba9fe158a50ec
Author:     Yuri Victorovich <yuri@FreeBSD.org>
AuthorDate: 2024-11-17 17:31:31 +0000
Commit:     Yuri Victorovich <yuri@FreeBSD.org>
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