diff --git a/.gitignore b/.gitignore index 33b4b49..67ed05c 100644 --- a/.gitignore +++ b/.gitignore @@ -18,3 +18,4 @@ pymol-1.4-20110402svn3938.tar.gz /pymol-open-source-2.3.0.tar.gz /pymol.png /pymol-open-source-2.4.0.tar.gz +/pymol-open-source-2.5.0.tar.gz diff --git a/pymol-2.4.0-fix_bug119.patch b/pymol-2.4.0-fix_bug119.patch deleted file mode 100644 index 6251205..0000000 --- a/pymol-2.4.0-fix_bug119.patch +++ /dev/null @@ -1,34 +0,0 @@ -From 885891cf60371674406cdff16b395e25cc13d8ae Mon Sep 17 00:00:00 2001 -From: Sebastian Keller -Date: Tue, 28 Jul 2020 22:50:53 +0200 -Subject: [PATCH] Don't drop the last model when updating the selector table - -The last assigned model in the Obj vector was at position modelCnt. -Resizing the vector to modelCnt removes the last model, which later -results in a crash when trying to access it. - -See https://github.com/schrodinger/pymol-open-source/issues/119 ---- - layer3/Selector.cpp | 2 +- - 1 file changed, 1 insertion(+), 1 deletion(-) - -diff --git a/layer3/Selector.cpp b/layer3/Selector.cpp -index 546725b..637cd60 100644 ---- a/layer3/Selector.cpp -+++ b/layer3/Selector.cpp -@@ -7284,11 +7284,11 @@ static sele_array_t SelectorUpdateTableSingleObject(PyMOLGlobals * G, ObjectMole - result[obj->SeleBase + at] = tag; - } - } - } - } -- I->Obj.resize(modelCnt); -+ I->Obj.resize(modelCnt + 1); - I->Table.resize(c); - - PRINTFD(G, FB_Selector) - "SelectorUpdateTableSingleObject-Debug: leaving...\n" ENDFD; - --- -libgit2 1.0.1 - diff --git a/pymol-2.5.0-bug186.patch b/pymol-2.5.0-bug186.patch new file mode 100644 index 0000000..343a6d4 --- /dev/null +++ b/pymol-2.5.0-bug186.patch @@ -0,0 +1,13 @@ +--- a/layer1/Basis.orig.h 2021-05-10 20:38:37.000000000 +0200 ++++ b/layer1/Basis.h 2021-10-05 20:07:14.567410004 +0200 +@@ -38,6 +38,10 @@ + + */ + ++#ifdef None ++#undef None ++#endif ++ + enum class cCylCap { + None = 0, + Flat = 1, diff --git a/pymol-python3.patch b/pymol-python3.patch deleted file mode 100644 index 4fd3053..0000000 --- a/pymol-python3.patch +++ /dev/null @@ -1,374 +0,0 @@ -diff -rup pymol-open-source-2.3.0.orig/test/headerTest.py pymol-open-source-2.3.0/test/headerTest.py ---- pymol-open-source-2.3.0.orig/test/headerTest.py 2019-02-11 14:08:10.000000000 +0000 -+++ pymol-open-source-2.3.0/test/headerTest.py 2019-12-31 00:58:56.747925023 +0000 -@@ -7,28 +7,28 @@ import os - if len(sys.argv)>1: - p = sys.argv[1:] - else: -- print "Usage: pymol -cq ./headerTest.py -- MTZTestDirectory" -+ print("Usage: pymol -cq ./headerTest.py -- MTZTestDirectory") - sys.exit(1) - - - for curPath in p: -- print "Processing MTZ files in path: '%s'" % curPath -+ print("Processing MTZ files in path: '%s'" % curPath) - - l = glob.glob(curPath + os.sep + "*.mtz") - - d = {} - - for mtzFile in l: -- print "Processing %s." % mtzFile -+ print("Processing %s." % mtzFile) - d[mtzFile] = headering.MTZHeader(mtzFile) - - for f in d: -- print "Columns for file '%s':" % f -+ print("Columns for file '%s':" % f) - pprint.pprint(d[f].getColumns()) -- print "" -+ print("") - - for f in d: -- print "Columns of type W ofr file '%s':" % f -+ print("Columns of type W ofr file '%s':" % f) - pprint.pprint(d[f].getColumnsOfType("W")) -- print "" -+ print("") - -diff -rup pymol-open-source-2.3.0.orig/test/inp/B01.py pymol-open-source-2.3.0/test/inp/B01.py ---- pymol-open-source-2.3.0.orig/test/inp/B01.py 2019-02-11 14:08:10.000000000 +0000 -+++ pymol-open-source-2.3.0/test/inp/B01.py 2019-12-31 01:05:14.326755274 +0000 -@@ -50,7 +50,7 @@ def load(): - try: - cmd.set("suspend_updates","1") - cmd.delete('pdb') -- print file,last1,last2,c,"of",l -+ print(file,last1,last2,c,"of",l) - last2 = last1 - last1 = file - cmd.load(file,'pdb') -diff -rup pymol-open-source-2.3.0.orig/test/inp/B02.py pymol-open-source-2.3.0/test/inp/B02.py ---- pymol-open-source-2.3.0.orig/test/inp/B02.py 2019-02-11 14:08:10.000000000 +0000 -+++ pymol-open-source-2.3.0/test/inp/B02.py 2019-12-31 01:06:50.254201459 +0000 -@@ -26,7 +26,7 @@ def load(): - # list.pop(0) - for file in list: - try: -- print file -+ print(file) - cmd.delete('pdb') - cmd.load(file,'pdb') - cmd.orient('pdb') -diff -rup pymol-open-source-2.3.0.orig/test/inp/B04.py pymol-open-source-2.3.0/test/inp/B04.py ---- pymol-open-source-2.3.0.orig/test/inp/B04.py 2019-02-11 14:08:10.000000000 +0000 -+++ pymol-open-source-2.3.0/test/inp/B04.py 2019-12-31 01:07:35.787938573 +0000 -@@ -42,15 +42,15 @@ def load(): - l=f.readlines() - f.close() - if len(l): -- print -+ print() - for a in l: -- print a, -+ print(a,) - # save it so we have something to look at... - os.system("/bin/cp -f %s %s_s"%(cmp_file,cmp_file)) - os.system("/bin/cp -f %s %s_s"%(ref_file,ref_file)) - os.system("/bin/cp -f %s %s_src"%(out_file,cmp_file)) - os.system("/bin/cp -f %s %s_src"%(file,ref_file)) -- print file -+ print(file) - else: - sys.__stdout__.write(".") - sys.__stdout__.flush() -diff -rup pymol-open-source-2.3.0.orig/test/inp/B06.py pymol-open-source-2.3.0/test/inp/B06.py ---- pymol-open-source-2.3.0.orig/test/inp/B06.py 2019-02-11 14:08:10.000000000 +0000 -+++ pymol-open-source-2.3.0/test/inp/B06.py 2019-12-31 01:00:00.870564958 +0000 -@@ -26,7 +26,7 @@ def load(): - # while list[0]!="pdb/f8/pdb1f8u": - # list.pop(0) - for file in list: -- print file -+ print(file) - cmd.delete('pdb') - cmd.load(file,'pdb') - cmd.orient('pdb') -diff -rup pymol-open-source-2.3.0.orig/test/inp/B07.py pymol-open-source-2.3.0/test/inp/B07.py ---- pymol-open-source-2.3.0.orig/test/inp/B07.py 2019-02-11 14:08:10.000000000 +0000 -+++ pymol-open-source-2.3.0/test/inp/B07.py 2019-12-31 01:08:26.179647638 +0000 -@@ -33,10 +33,10 @@ def load(): - idx = ch.insert_model(model) - - ch.pattern_orient_bonds(idx) -- print " %5d"%cmd.count_atoms(),"%5d"%len(ch.pattern_get_string(idx)), -+ print(" %5d"%cmd.count_atoms(),"%5d"%len(ch.pattern_get_string(idx)),) - ch.pattern_detect_chirality(idx) - pat = ch.pattern_get_string(idx) -- print "%5d"%len(pat),pat[0:22]+"..."+pat[-10:] -+ print("%5d"%len(pat),pat[0:22]+"..."+pat[-10:]) - - cmd.feedback('disable','symmetry objectmolecule executive','everything') - load() -diff -rup pymol-open-source-2.3.0.orig/test/inp/C1050fitting.py pymol-open-source-2.3.0/test/inp/C1050fitting.py ---- pymol-open-source-2.3.0.orig/test/inp/C1050fitting.py 2019-02-11 14:08:10.000000000 +0000 -+++ pymol-open-source-2.3.0/test/inp/C1050fitting.py 2019-12-31 01:09:57.017123219 +0000 -@@ -5,11 +5,11 @@ from pymol import cmd - - from random import random,seed - --print "BEGIN-LOG" -+print("BEGIN-LOG") - - seed(123) - --print "the 1st random number should be %8.3f\notherwise the rest of the test is meaningless...\n"%pymol.random() -+print("the 1st random number should be %8.3f\notherwise the rest of the test is meaningless...\n"%pymol.random()) - - pymol.random = random - -@@ -23,29 +23,29 @@ for a in xrange(1,11): - - - cmd.frame(1) --print "%8.3f"%cmd.fit("ref","trg") -+print("%8.3f"%cmd.fit("ref","trg")) - - # asdf - - - for a in xrange(1,14): -- print a, -- print "%8.3f"%cmd.fit("ref and resi %d"%a,"trg"), -- print "%8.3f"%cmd.rms("ref","trg"), -- print "%8.3f"%cmd.rms_cur("ref","trg") -+ print(a,) -+ print("%8.3f"%cmd.fit("ref and resi %d"%a,"trg"),) -+ print("%8.3f"%cmd.rms("ref","trg"),) -+ print("%8.3f"%cmd.rms_cur("ref","trg")) - - cmd.frame(10) - --print "%8.3f"%cmd.fit("ref","trg") -+print("%8.3f"%cmd.fit("ref","trg")) - for a in xrange(1,14): -- print a, -- print "%8.3f"%cmd.fit("ref and resi %d"%a,"trg"), -- print "%8.3f"%cmd.rms("ref","trg"), -- print "%8.3f"%cmd.rms_cur("ref","trg") -+ print(a,) -+ print("%8.3f"%cmd.fit("ref and resi %d"%a,"trg"),) -+ print("%8.3f"%cmd.rms("ref","trg"),) -+ print("%8.3f"%cmd.rms_cur("ref","trg")) - - - a = 1 --print "%8.3f"%cmd.fit("ref","trg") -+print("%8.3f"%cmd.fit("ref","trg")) - for b in xrange(1,11): - cmd._dump_floats(cmd.intra_fit("trg and resi %d"%a,b)) - cmd._dump_floats(cmd.intra_rms("trg",b)) -@@ -56,7 +56,7 @@ cmd.do("intra_fit (trg and resi 1),10") - cmd.do("intra_rms (trg),10") - cmd.do("intra_rms_cur (trg),10") - --print "END-LOG" -+print("END-LOG") - - - -diff -rup pymol-open-source-2.3.0.orig/test/inp/C1060controlling.py pymol-open-source-2.3.0/test/inp/C1060controlling.py ---- pymol-open-source-2.3.0.orig/test/inp/C1060controlling.py 2019-02-11 14:08:10.000000000 +0000 -+++ pymol-open-source-2.3.0/test/inp/C1060controlling.py 2019-12-31 01:12:25.376266687 +0000 -@@ -2,30 +2,30 @@ - - from pymol import cmd - --print "BEGIN-LOG" -+print("BEGIN-LOG") - --print cmd.set_key('F1',lambda :cmd.turn('x',10)) --print cmd.set_key('F12',lambda :cmd.turn('x',10)) -+print(cmd.set_key('F1',lambda :cmd.turn('x',10))) -+print(cmd.set_key('F12',lambda :cmd.turn('x',10))) - --print cmd.set_key('left',lambda :cmd.turn('x',10)) --print cmd.set_key('right',lambda :cmd.turn('x',10)) --print cmd.set_key('pgup',lambda :cmd.turn('x',10)) --print cmd.set_key('pgdn',lambda :cmd.turn('x',10)) --print cmd.set_key('home',lambda :cmd.turn('x',10)) --print cmd.set_key('insert',lambda :cmd.turn('x',10)) -+print(cmd.set_key('left',lambda :cmd.turn('x',10))) -+print(cmd.set_key('right',lambda :cmd.turn('x',10))) -+print(cmd.set_key('pgup',lambda :cmd.turn('x',10))) -+print(cmd.set_key('pgdn',lambda :cmd.turn('x',10))) -+print(cmd.set_key('home',lambda :cmd.turn('x',10))) -+print(cmd.set_key('insert',lambda :cmd.turn('x',10))) - --print cmd.set_key('ALT-A',lambda :cmd.turn('y',10)) -+print(cmd.set_key('ALT-A',lambda :cmd.turn('y',10))) - --print cmd.set_key('CTRL-C',lambda :cmd.turn('z',10)) -+print(cmd.set_key('CTRL-C',lambda :cmd.turn('z',10))) - --print cmd.set_key('SHFT-F1', lambda :cmd.turn('z',10)) -+print(cmd.set_key('SHFT-F1', lambda :cmd.turn('z',10))) - --print cmd.set_key('ALT-F1', lambda :cmd.turn('y',10)) -+print(cmd.set_key('ALT-F1', lambda :cmd.turn('y',10))) - --print cmd.set_key('CTRL-F8', lambda :cmd.move('x',1)) -+print(cmd.set_key('CTRL-F8', lambda :cmd.move('x',1))) - - --print "END-LOG" -+print("END-LOG") - - - -diff -rup pymol-open-source-2.3.0.orig/test/inp/C1100do.py pymol-open-source-2.3.0/test/inp/C1100do.py ---- pymol-open-source-2.3.0.orig/test/inp/C1100do.py 2019-02-11 14:08:10.000000000 +0000 -+++ pymol-open-source-2.3.0/test/inp/C1100do.py 2019-12-31 01:12:44.051158878 +0000 -@@ -2,7 +2,7 @@ - - from pymol import cmd - --print "BEGIN-LOG" -+print("BEGIN-LOG") - - cmd.do(""" - load dat/pept.pdb -@@ -27,16 +27,16 @@ cmd.do('ray') - - # see if when can embed Python blocks inside of PyMOL inside of Python - --cmd.do('for a in range(1,10):\\\n print a\\\n print a+10') -+cmd.do('for a in range(1,10):\\\n print (a)\\\n print (a+10)') - - cmd.do(r""" - for a in range(11,21):\ -- print a\ -- print a+10 -+ print (a)\ -+ print (a+10) - """) - - --print "END-LOG" -+print("END-LOG") - - - -diff -rup pymol-open-source-2.3.0.orig/test/inp/C2000returns.py pymol-open-source-2.3.0/test/inp/C2000returns.py ---- pymol-open-source-2.3.0.orig/test/inp/C2000returns.py 2019-02-11 14:08:10.000000000 +0000 -+++ pymol-open-source-2.3.0/test/inp/C2000returns.py 2019-12-31 01:14:11.048656595 +0000 -@@ -1,6 +1,6 @@ - # -c - --print "BEGIN-LOG" -+print("BEGIN-LOG") - - import pymol - from pymol import cmd -@@ -8,18 +8,18 @@ from pymol import cmd - # need to do this for all supported file types because the load routines diverge... - - def x(st): -- print st -+ print(st) - cmd.set("raise_exceptions",0) - valu = eval(st) -- print valu -+ print(valu) - if cmd.is_error(valu): - cmd.set("raise_exceptions",1) - try: -- print eval(st) -+ print(eval(st)) - except pymol.CmdException: -- print "CmdException raised." -+ print("CmdException raised.") - except cmd.QuietException: -- print "QuietException raised." -+ print("QuietException raised.") - - map(x,[ - 'cmd.load("dat/pept.pdb")' , -@@ -55,12 +55,12 @@ map(x,[ - cmd.delete("all") - cmd.load("dat/pept.pdb") - mdl = cmd.get_model("pept") --print mdl.__class__ --print len(mdl.atom) -+print(mdl.__class__) -+print(len(mdl.atom)) - - mdl = cmd.get_model("none") --print mdl.__class__ --print len(mdl.atom) -+print(mdl.__class__) -+print(len(mdl.atom)) - - map( x, [ - 'cmd.get_model("nonexistent")', -@@ -119,7 +119,7 @@ map( x, [ - - - --print "END-LOG" -+print("END-LOG") - - TODO=""" - -diff -rup pymol-open-source-2.3.0.orig/test/inp/T04.py pymol-open-source-2.3.0/test/inp/T04.py ---- pymol-open-source-2.3.0.orig/test/inp/T04.py 2019-02-11 14:08:10.000000000 +0000 -+++ pymol-open-source-2.3.0/test/inp/T04.py 2019-12-31 01:00:30.116396114 +0000 -@@ -34,7 +34,7 @@ def centers(): - cmd.center("(resi %d)"%resi) - time.sleep(random.random()*0.30) - except: -- print "exception" -+ print("exception") - - t = threading.Thread(target=centers) - t.setDaemon(1) -@@ -146,7 +146,7 @@ def carts(): - time.sleep(random.random()*0.03) - - except: -- print "exception" -+ print("exception") - - t = threading.Thread(target=carts) - t.setDaemon(1) -diff -rup pymol-open-source-2.3.0.orig/test/win.py pymol-open-source-2.3.0/test/win.py ---- pymol-open-source-2.3.0.orig/test/win.py 2019-02-11 14:08:10.000000000 +0000 -+++ pymol-open-source-2.3.0/test/win.py 2019-12-31 01:15:21.879273187 +0000 -@@ -58,10 +58,10 @@ for test in tests: - tst = re.sub(r".*/|.*\\","",ifil) # get exact test name without suffix - tst = re.sub(r"\..*","",tst) - -- print " run_tests: "+tst+"..." -+ print(" run_tests: "+tst+"...") - - syscmd = cmmd+" -x -d pwd "+opt+" "+ifil+" > tmp.txt 2>&1" -- print syscmd -+ print(syscmd) - #os.system("c:\\pymolws\\pymol.exe") - os.system(syscmd) - # generate log file -@@ -94,10 +94,10 @@ for test in tests: - if (not lf) and not (lg): - break - if string.strip(lf)!=string.strip(lg): -- print "<",lf -- print ">",lg -+ print("<",lf) -+ print(">",lg) - --print "done" -+print("done") - time.sleep(360) - - # diff --git a/pymol-setup.py.patch b/pymol-setup.py.patch index 519e88d..894c8cb 100644 --- a/pymol-setup.py.patch +++ b/pymol-setup.py.patch @@ -1,11 +1,11 @@ --- pymol-open-source-2.3.0.orig/setup.py_orig 2016-10-07 10:52:09.874178679 -0400 +++ pymol-open-source-2.3.0/setup.py 2016-10-07 10:56:46.198125842 -0400 -@@ -273,7 +273,7 @@ +@@ -289,7 +289,7 @@ # legacy stuff '-Wno-char-subscripts', # optimizations - "-Og" if DEBUG else "-O3", + "-Og" if DEBUG else "-O2", - ] + ] if not WIN else [] ext_link_args = [] ext_objects = [] diff --git a/pymol.png b/pymol.png new file mode 100644 index 0000000..deda15d --- /dev/null +++ b/pymol.png @@ -0,0 +1,590 @@ + + + + + + Tree - rpms/pymol - src.fedoraproject.org + + + + + + + + + + + + + + + + + + +
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© Red Hat, Inc. and others.
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+ + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/pymol.spec b/pymol.spec index a486d3b..9caafff 100644 --- a/pymol.spec +++ b/pymol.spec @@ -1,7 +1,7 @@ Name: pymol Summary: PyMOL Molecular Graphics System -Version: 2.4.0 -Release: 8%{?dist} +Version: 2.5.0 +Release: 1%{?dist} # Which files use following license: # BSD: main license of open source PyMOL and some plugins @@ -24,11 +24,8 @@ Patch2: %{name}-wmclass-pmgapp.patch Patch3: %{name}-mmtf.patch -# Fix brp-python-bytecompile script -Patch4: %{name}-python3.patch - -# Fix https://github.com/schrodinger/pymol-open-source/issues/119 -Patch5: %{name}-2.4.0-fix_bug119.patch +# https://github.com/schrodinger/pymol-open-source/issues/186 +Patch4: %{name}-2.5.0-bug186.patch BuildRequires: desktop-file-utils BuildRequires: libappstream-glib @@ -82,17 +79,13 @@ assist you in your research. %autosetup -n %{name}-open-source-%{version} -p1 ln -sr modules/web modules/pymol_web -sed -i 1d modules/pmg_tk/startup/apbs_tools.py - -# Fix shebang in individual files to ensure Python3 dependence -pathfix.py -pn -i "%{__python3}" test/cyg test/run test/show %build export CXXFLAGS="%{optflags}" -%py3_build -- --use-msgpackc=c++11 --glut +%py3_build -- --use-msgpackc=c++11 --use-openmp=yes --jobs `/usr/bin/getconf _NPROCESSORS_ONLN` %install -%py3_install -- --use-msgpackc=c++11 --glut --pymol-path=%{python3_sitearch}/%{name} +%py3_install -- --use-msgpackc=c++11 --use-openmp=yes --pymol-path=%{python3_sitearch}/%{name} # Create executable script for running PyMOL echo "#!/bin/sh" > pymol @@ -143,6 +136,9 @@ appstream-util validate-relax --nonet %{buildroot}/%{_metainfodir}/*.appdata.xml %{_datadir}/pixmaps/%{name}.png %changelog +* Tue Oct 05 2021 Antonio Trande 2.5.0-1 +- Release 2.5.0 + * Tue Aug 10 2021 Orion Poplawski - 2.4.0-8 - Rebuild for netcdf 4.8.0 diff --git a/sources b/sources index 7ed419d..fd5ad11 100644 --- a/sources +++ b/sources @@ -1,2 +1 @@ -SHA512 (pymol-open-source-2.4.0.tar.gz) = 2b19294197d58a808bf7bb7fa9f829c2ec582ba47a4380783a2b1eedda2ce4118cd398e01885db8c449e7fd5e4c08a1c40508e679ef42d8e183a6a52b031c02a -SHA512 (pymol.png) = 561f561905c1ef648b0c3b6779193dd056e676ccf0666f21affbf7eab32675e6e8eb91d3fff15e704e40806f5879ded001f1eb0c9251232c0e33235d70c2b6bc +SHA512 (pymol-open-source-2.5.0.tar.gz) = 19f21b8f735fda5314abf202d56f3c81c7251bf6ef0df73ccee534d9c08035f4ef6155ffb68e09d7717a0fb5ba7289bbfa440691bea4cec0de7199c9e858ea91