Release 3.1.1
This commit is contained in:
Antonio Trande
parent
8bdf4b9ebb
commit
032161a547
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@ -8,3 +8,4 @@ openbabel-2.0.2.tar.gz
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/openbabel-3a63a9849f8d9719c5989c43875d51be50c53019.tar.gz
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/openbabel-2-4-0.tar.gz
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/openbabel-2-4-1.tar.gz
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/openbabel-openbabel-3-1-1.tar.gz
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@ -0,0 +1,44 @@
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From 4ba2fec17b786afebadfae800a015704ad533843 Mon Sep 17 00:00:00 2001
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From: dkoes <dkoes@pitt.edu>
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Date: Mon, 7 Jun 2021 11:04:25 -0400
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Subject: [PATCH] Resolve ImportError with make test
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This change will build _openbabel.so in scripts/python/openbabel instead
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of the default build/lib. This is necessary because openbabel.py tries
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to import _openbabel like this:
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if __package__ or "." in __name__:
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from . import _openbabel
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else:
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import _openbabel
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This results in a circular import error when running make test (the
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first branch of the if is triggered). This code appears to be generated by
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SWIG with no obvious way to change it to catch the ImportError and call
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import _openbabel instead. Note the PYTHONPATH is set to include
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build/lib, but it doesn't matter because SWIG is forcing the import to
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happen in scripts/python/openbabel.
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I'm not sure why this hasn't been a problem in the past, perhaps there's
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been a change in SWIG. This is with SWIG 4.0.1 and cmake 3.18.6.
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I think the best solution is to move all the files that are being built
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in /scripts to the build directory rather than polluting the src tree
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with them, but this would require changing all the bindings and I'm not
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up for building and testing every binding.
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---
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scripts/CMakeLists.txt | 1 +
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1 file changed, 1 insertion(+)
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diff --git a/scripts/CMakeLists.txt b/scripts/CMakeLists.txt
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index b715a546dd..56821641fe 100644
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--- a/scripts/CMakeLists.txt
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+++ b/scripts/CMakeLists.txt
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@@ -106,6 +106,7 @@ if (DO_PYTHON_BINDINGS)
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set_target_properties(bindings_python PROPERTIES
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OUTPUT_NAME _openbabel
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PREFIX ""
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+ LIBRARY_OUTPUT_DIRECTORY "${openbabel_SOURCE_DIR}/scripts/python/openbabel/"
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SUFFIX .so )
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execute_process(
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COMMAND
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@ -0,0 +1,39 @@
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From 7de27f309db5f7ec026ef5c5235e5b33bf7d1a85 Mon Sep 17 00:00:00 2001
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From: John Bollinger <John.Bollinger@StJude.org>
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Date: Thu, 14 May 2020 08:46:40 -0500
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Subject: [PATCH] Fix test failure with Python 3
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When run with Python 3.6, test/testdistgeom.py fails with a SyntaxError
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about a malformed character escape. This arises from a failure to escape
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literal backslash characters in single-quoted SMILES strings (several
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occurrences). Python 2 accepts this and does the right things with it,
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but Python 3 rejects it.
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Fixes #2217
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---
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test/testdistgeom.py | 10 +++++-----
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1 file changed, 5 insertions(+), 5 deletions(-)
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diff --git a/test/testdistgeom.py b/test/testdistgeom.py
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index 0fa5adb576..fc3a7515b9 100644
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--- a/test/testdistgeom.py
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+++ b/test/testdistgeom.py
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@@ -42,13 +42,13 @@ def testSMItoSMI(self):
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'C1CC[C@H]2[C@@H](C1)CCCC2', # cis-decalin
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'C1CC[C@@H]2[C@@H](C1)CCCC2', # trans-decalin
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'[C@H]1(NC[C@H]2[C@H]1N2)OC',
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- 'Clc1cccc(Cl)c1\C=N\NC(=O)c1cccs1',
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- 'O=C1NC(=S)S\C1=C/c1ccco1',
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+ 'Clc1cccc(Cl)c1\\C=N\\NC(=O)c1cccs1',
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+ 'O=C1NC(=S)S\\C1=C/c1ccco1',
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'S=C1NC(=O)/C(=C/c2ccco2)/S1',
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- 'O=C1NC(=S)N\C1=C\c1ccncc1',
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+ 'O=C1NC(=S)N\\C1=C\\c1ccncc1',
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'S=C1NC(=O)C(=C)N1',
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- 'CC(=O)N\N=C\c1ccncc1',
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- 'N/N=c/1\sc2c(n1C)cccc2',
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+ 'CC(=O)N\\N=C\\c1ccncc1',
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+ 'N/N=c/1\\sc2c(n1C)cccc2',
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'OCCN/C=C\\1/C(=NN(C1=O)c1ccccc1)C',
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'Cc1ccc(o1)/C=C/C=O',
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# disabled to make test run faster:
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@ -0,0 +1,34 @@
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From b75c392b75b3494d9dae15176f38facf7e61db17 Mon Sep 17 00:00:00 2001
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From: John Bollinger <John.Bollinger@StJude.org>
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Date: Fri, 15 May 2020 11:30:27 -0500
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Subject: [PATCH] Fix UB in UFF parameter parsing
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When evaluating atom coordination number, method
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OBForceFieldUFF::ParseParamFile() assumed that it may access a third character
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of the atom type string, but in fact that produces undefined behavior if the
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string is only one character long. A one-character atom type occurs in
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practice with the default parameter file (for deuterium).
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This change addresses the issue by verifying that the second character of
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each atom type string is not a C string terminator as a precondition for
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accessing the third. If the second is a string terminator then the same
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default behavior is provided as if the type were two characters long.
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Fixes #2223
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---
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src/forcefields/forcefielduff.cpp | 2 +-
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1 file changed, 1 insertion(+), 1 deletion(-)
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diff --git a/src/forcefields/forcefielduff.cpp b/src/forcefields/forcefielduff.cpp
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index 9bff879c9c..2e98e0e804 100644
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--- a/src/forcefields/forcefielduff.cpp
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+++ b/src/forcefields/forcefielduff.cpp
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@@ -1647,7 +1647,7 @@ namespace OpenBabel {
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parameter.b = 0; // used for tracking number of angles in 5-coordinate
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parameter.c = 0;
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- char coord = vs[1][2]; // 3rd character of atom type
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+ char coord = vs[1][1] ? vs[1][2] : '\0'; // 3rd character of atom type, if any
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switch (coord) {
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case '1': // linear
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parameter._ipar.push_back(1);
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@ -1,21 +1,21 @@
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diff -up openbabel-openbabel-2-4-1/test/CMakeLists.txt.s390x openbabel-openbabel-2-4-1/test/CMakeLists.txt
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--- openbabel-openbabel-2-4-1/test/CMakeLists.txt.s390x 2016-10-10 17:56:17.000000000 +0200
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+++ openbabel-openbabel-2-4-1/test/CMakeLists.txt 2019-01-27 19:32:21.568052461 +0100
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@@ -62,7 +62,7 @@ set(origtests
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diff -up a/test/CMakeLists.txt.s390x b/test/CMakeLists.txt
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--- a/test/CMakeLists.txt.s390x 2016-10-10 17:56:17.000000000 +0200
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+++ b/test/CMakeLists.txt 2019-01-27 19:32:21.568052461 +0100
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@@ -74,7 +74,7 @@
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)
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set (atom_parts 1 2 3 4)
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set (ffmmff94_parts 1 2)
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set (ffmmff94_parts 1 2 3 4 5 6)
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-set (math_parts 1 2 3 4)
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+set (math_parts 1 2 3)
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set (pdbreadfile_parts 1 2 3 4)
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if(BUILD_SHARED)
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if(LIBXML2_FOUND)
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@@ -238,7 +238,7 @@ endif(NOT MINGW AND NOT CYGWIN)
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if (PYTHON_BINDINGS)
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@@ -250,8 +250,6 @@
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include(UsePythonTest)
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set(pybindtests
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- bindings _pybel example)
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+ bindings example)
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foreach(pybindtest ${pybindtests})
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SET_SOURCE_FILES_PROPERTIES(test${pybindtest}.py PROPERTIES
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PYTHONPATH "${CMAKE_SOURCE_DIR}/scripts/python:${CMAKE_BINARY_DIR}/lib${LIB_SUFFIX}"
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bindings
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- _pybel
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- example
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obconv_writers
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cdjsonformat
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pcjsonformat
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@ -1,16 +1,16 @@
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diff -up openbabel-openbabel-2-4-0/test/CMakeLists.txt.tests openbabel-openbabel-2-4-0/test/CMakeLists.txt
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--- openbabel-openbabel-2-4-0/test/CMakeLists.txt.tests 2016-09-21 21:55:37.000000000 +0200
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+++ openbabel-openbabel-2-4-0/test/CMakeLists.txt 2016-10-10 13:48:52.726803964 +0200
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@@ -34,7 +34,7 @@ set (implicitH_parts 1)
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set (lssr_parts 1 2 3 4 5)
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set (isomorphism_parts 1 2 3 4 5 6 7 8)
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diff -up a/test/CMakeLists.txt.tests b/test/CMakeLists.txt
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--- a/test/CMakeLists.txt.tests 2016-09-21 21:55:37.000000000 +0200
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+++ b/test/CMakeLists.txt 2016-10-10 13:48:52.726803964 +0200
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@@ -39,7 +39,7 @@
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set (isomorphism_parts 1 2 3 4 5 6 7 8 9)
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set (multicml_parts 1)
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-set (regressions_parts 1 221 222 223 224)
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set (periodic_parts 1 2 3 4)
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-set (regressions_parts 1 221 222 223 224 225 226 227 228 240 241 242 1794 2111)
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+set (regressions_parts 222 223 224)
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set (rotor_parts 1 2 3 4)
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set (shuffle_parts 1 2 3 4 5)
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set (smiles_parts 1 2 3)
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@@ -177,7 +177,7 @@ if(WITH_INCHI)
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@@ -188,7 +188,7 @@
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set_target_properties(test_inchiwrite PROPERTIES LINK_SEARCH_END_STATIC TRUE)
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endif()
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# files in test/inchi -- both .sdf and .txt
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@ -19,11 +19,11 @@ diff -up openbabel-openbabel-2-4-0/test/CMakeLists.txt.tests openbabel-openbabel
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set(inchidata ${CMAKE_SOURCE_DIR}/test/inchi)
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foreach(test ${inchitests})
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add_test(inchi${test}_Test
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@@ -215,7 +215,7 @@ if(NOT MINGW AND NOT CYGWIN)
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@@ -226,7 +226,7 @@
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include(UsePythonTest)
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if(PYTHON_EXECUTABLE)
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set(pytests
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- babel sym smartssym fastsearch unique kekule pdbformat)
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- babel sym smartssym fastsearch distgeom unique kekule pdbformat RInChI)
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+ babel smartssym fastsearch unique kekule pdbformat)
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foreach(pytest ${pytests})
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SET_SOURCE_FILES_PROPERTIES(test${pytest}.py PROPERTIES
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@ -1,11 +1,12 @@
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diff -up openbabel-openbabel-2-4-1/openbabel-2.0.pc.cmake.p openbabel-openbabel-2-4-1/openbabel-2.0.pc.cmake
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--- openbabel-openbabel-2-4-1/openbabel-2.0.pc.cmake.p 2016-10-10 17:56:17.000000000 +0200
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+++ openbabel-openbabel-2-4-1/openbabel-2.0.pc.cmake 2019-01-27 10:47:00.905546971 +0100
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diff -up a/openbabel-3.pc.cmake.p b/openbabel-3.pc.cmake
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--- a/openbabel-3.pc.cmake.p
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+++ b/openbabel-3.pc.cmake
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@@ -1,6 +1,6 @@
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prefix=@CMAKE_INSTALL_PREFIX@
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exec_prefix=${prefix}
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-libdir=${exec_prefix}/@LIB_INSTALL_DIR@
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+libdir=${exec_prefix}/lib@LIB_SUFFIX@
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includedir=${prefix}/include
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pkgincludedir=${includedir}/openbabel-2.0
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pkgincludedir=${includedir}/openbabel@BABEL_MAJ_VER@
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@ -1,33 +0,0 @@
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diff -up openbabel-3a63a9849f8d9719c5989c43875d51be50c53019/src/formats/pngformat.cpp.nc openbabel-3a63a9849f8d9719c5989c43875d51be50c53019/src/formats/pngformat.cpp
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--- openbabel-3a63a9849f8d9719c5989c43875d51be50c53019/src/formats/pngformat.cpp.nc 2016-02-16 23:47:25.000000000 +0100
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+++ openbabel-3a63a9849f8d9719c5989c43875d51be50c53019/src/formats/pngformat.cpp 2016-02-18 19:01:40.509752461 +0100
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@@ -218,7 +218,7 @@ bool PNGFormat::ReadMolecule(OBBase* pOb
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_count=0;
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_hasInputPngFile=true;
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}
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- const char pngheader[] = {-119,80,78,71,13,10,26,10,0};
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+ const signed char pngheader[] = {-119,80,78,71,13,10,26,10,0};
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char readbytes[9];
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ifs.read(readbytes, 8);
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diff -up openbabel-3a63a9849f8d9719c5989c43875d51be50c53019/src/formats/yasaraformat.cpp.nc openbabel-3a63a9849f8d9719c5989c43875d51be50c53019/src/formats/yasaraformat.cpp
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--- openbabel-3a63a9849f8d9719c5989c43875d51be50c53019/src/formats/yasaraformat.cpp.nc 2016-02-16 23:47:25.000000000 +0100
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+++ openbabel-3a63a9849f8d9719c5989c43875d51be50c53019/src/formats/yasaraformat.cpp 2016-02-18 23:22:23.786793588 +0100
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@@ -472,7 +472,7 @@ bool YOBFormat::WriteMolecule(OBBase* pO
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// bool hetatom;
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char buffer[32],/*resname[4],*/atomname[5];
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- char double1[8]={0,0,0,0,0,0,-16,0x3f};
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+ const signed char double1[8]={0,0,0,0,0,0,-16,0x3f};
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// char *str;
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int i,j,/*m,q,*/pos;
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int /*resno,chainNum,link,linktype,*/atoms,element,links/*,chain*/;
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@@ -500,7 +500,7 @@ bool YOBFormat::WriteMolecule(OBBase* pO
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mem_set(buffer,0,8);
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for (i=0;i<4;i++)
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{ for (j=0;j<4;j++)
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- { if (i==j) ofs.write(double1,8);
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+ { if (i==j) ofs.write(reinterpret_cast<const char*>(double1),8);
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else ofs.write(buffer,8); } }
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storeint32le(buffer,MOB_INFOEND);
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storeint32le(&buffer[4],MOB_INFOENDSIZE);
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@ -1,12 +1,35 @@
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diff -up openbabel-75414ad4e043f16ba72ae51c7ca60f448576688d/CMakeLists.txt.plugindir openbabel-75414ad4e043f16ba72ae51c7ca60f448576688d/CMakeLists.txt
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--- openbabel-75414ad4e043f16ba72ae51c7ca60f448576688d/CMakeLists.txt.plugindir 2015-02-07 21:42:44.431479900 +0100
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+++ openbabel-75414ad4e043f16ba72ae51c7ca60f448576688d/CMakeLists.txt 2015-02-07 21:43:29.000429326 +0100
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@@ -266,7 +266,7 @@ if(NOT MSVC)
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diff -up a/CMakeLists.txt.plugindir b/CMakeLists.txt
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--- a/CMakeLists.txt.plugindir 2015-02-07 21:42:44.431479900 +0100
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+++ b/CMakeLists.txt 2015-02-07 21:43:29.000429326 +0100
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@@ -24,7 +24,7 @@
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# had too many 1.100.1 releases. :-)
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set(BABEL_MAJ_VER 3)
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set(BABEL_MIN_VER 1)
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-set(BABEL_PATCH_VER 0)
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+set(BABEL_PATCH_VER 1)
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# This should be phased out in preference for just using the target name
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set(BABEL_LIBRARY openbabel)
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@@ -276,7 +276,7 @@
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}
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" SCANDIR_NEEDS_CONST)
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- set(OB_MODULE_PATH "${CMAKE_INSTALL_PREFIX}/${OB_PLUGIN_INSTALL_DIR}"
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+ set(OB_MODULE_PATH "${OB_PLUGIN_INSTALL_DIR}"
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CACHE PATH "Set to system install for bindings only build")
|
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add_definitions(-DOB_MODULE_PATH="\\"${OB_MODULE_PATH}\\"")
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- set(OB_MODULE_PATH "${CMAKE_INSTALL_PREFIX}/${OB_PLUGIN_INSTALL_DIR}")
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+ set(OB_MODULE_PATH "${LIB_INSTALL_DIR}/openbabel3")
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# Add some visibility support when using GCC
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# note: Altough MinGW g++ 4.4 passes this test, visibility can't be used
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@@ -751,11 +751,11 @@
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# Now to configure the installed config file.
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set(OB_CONFIG_DIR "${LIB_INSTALL_DIR}/cmake/openbabel3")
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-set(OpenBabel3_INCLUDE_DIRS "\${OpenBabel3_INSTALL_PREFIX}/${OB_INCLUDE_DIRS}")
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+set(OpenBabel3_INCLUDE_DIRS "\${INCLUDE_INSTALL_DIR}/openbabel3")
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set(OpenBabel3_LIBRARIES "$<TARGET_FILE:openbabel>")
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||||
|
||||
set(OB_EXPORTS_FILE
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- "\${OpenBabel3_INSTALL_PREFIX}/${OB_CONFIG_DIR}/OpenBabel3_EXPORTS.cmake")
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+ "\${LIB_INSTALL_DIR}/cmake/openbabel3/OpenBabel3_EXPORTS.cmake")
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set(REL_REF)
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if(NOT WIN32)
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set(REL_REF "/../../..")
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|
|
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|
@ -1,15 +0,0 @@
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diff -up openbabel-openbabel-2-4-1/scripts/CMakeLists.txt.py3 openbabel-openbabel-2-4-1/scripts/CMakeLists.txt
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--- openbabel-openbabel-2-4-1/scripts/CMakeLists.txt.py3 2019-03-04 11:12:54.369464503 +0100
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+++ openbabel-openbabel-2-4-1/scripts/CMakeLists.txt 2019-03-04 11:59:39.323264995 +0100
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@@ -84,7 +84,10 @@ if (DO_PYTHON_BINDINGS)
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COMMAND ${CMAKE_COMMAND} -E echo " try:" >> ob.py
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COMMAND ${CMAKE_COMMAND} -E echo " import dl" >> ob.py
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COMMAND ${CMAKE_COMMAND} -E echo " except ImportError:" >> ob.py
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- COMMAND ${CMAKE_COMMAND} -E echo " import DLFCN as dl" >> ob.py
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+ COMMAND ${CMAKE_COMMAND} -E echo " try:" >> ob.py
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+ COMMAND ${CMAKE_COMMAND} -E echo " import DLFCN as dl" >> ob.py
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||||
+ COMMAND ${CMAKE_COMMAND} -E echo " except ImportError:" >> ob.py
|
||||
+ COMMAND ${CMAKE_COMMAND} -E echo " import ctypes as dl" >> ob.py
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||||
COMMAND ${CMAKE_COMMAND} -E echo " sys.setdlopenflags(sys.getdlopenflags() | dl.RTLD_GLOBAL)" >> ob.py
|
||||
COMMAND cat ${openbabel_SOURCE_DIR}/scripts/python/openbabel.py >> ob.py
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||||
COMMAND ${CMAKE_COMMAND} -E copy ob.py ${openbabel_SOURCE_DIR}/scripts/python/openbabel.py
|
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|
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@ -1,32 +0,0 @@
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diff -up openbabel-openbabel-2-4-1/test/testpdbformat.py.taberror openbabel-openbabel-2-4-1/test/testpdbformat.py
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--- openbabel-openbabel-2-4-1/test/testpdbformat.py.taberror 2016-10-10 17:56:17.000000000 +0200
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+++ openbabel-openbabel-2-4-1/test/testpdbformat.py 2019-03-04 11:09:24.786801658 +0100
|
||||
@@ -24,12 +24,12 @@ class TestPDBFormat(BaseTest):
|
||||
|
||||
def testInsertionCodes(self):
|
||||
"""
|
||||
- Testing a PDB entry with insertion codes to distinguish residues
|
||||
- upon conversion to FASTA.
|
||||
+ Testing a PDB entry with insertion codes to distinguish residues
|
||||
+ upon conversion to FASTA.
|
||||
"""
|
||||
self.canFindExecutable("babel")
|
||||
|
||||
- self.entryPDBwithInsertioncodes="""ATOM 406 N VAL L 29 58.041 17.797 48.254 1.00 0.00 N
|
||||
+ self.entryPDBwithInsertioncodes="""ATOM 406 N VAL L 29 58.041 17.797 48.254 1.00 0.00 N
|
||||
ATOM 407 CA VAL L 29 57.124 18.088 47.170 1.00 0.00 C
|
||||
ATOM 408 C VAL L 29 55.739 17.571 47.538 1.00 0.00 C
|
||||
ATOM 409 O VAL L 29 55.535 16.362 47.550 1.00 0.00 O
|
||||
@@ -100,9 +100,9 @@ ATOM 473 HE1 TYR L 32 48.512
|
||||
ATOM 474 HE2 TYR L 32 48.145 19.172 44.648 1.00 0.00 H
|
||||
ATOM 475 HH TYR L 32 46.462 17.658 44.280 1.00 0.00 H
|
||||
"""
|
||||
- output, error = run_exec(self.entryPDBwithInsertioncodes,
|
||||
- "babel -ipdb -ofasta")
|
||||
- self.assertEqual(output.rstrip().rsplit("\n",1)[1], "VSSSY")
|
||||
+ output, error = run_exec(self.entryPDBwithInsertioncodes,
|
||||
+ "babel -ipdb -ofasta")
|
||||
+ self.assertEqual(output.rstrip().rsplit("\n",1)[1], "VSSSY")
|
||||
|
||||
if __name__ == "__main__":
|
||||
testsuite = []
|
||||
115
openbabel.spec
115
openbabel.spec
|
|
@ -1,55 +1,54 @@
|
|||
%global commit 3a63a9849f8d9719c5989c43875d51be50c53019
|
||||
%global shortcommit %(c=%{commit}; echo ${c:0:7})
|
||||
|
||||
%{!?perl_vendorarch:%global perl_vendorarch %(eval "`perl -V:installvendorarch`"; echo $installvendorarch)}
|
||||
|
||||
# we don't want to provide private Perl or Python extension libs
|
||||
%global __provides_exclude_from ^(%{perl_vendorarch}/auto|%{python3_sitearch})/.*\\.so$
|
||||
|
||||
Name: openbabel
|
||||
Version: 2.4.1
|
||||
Release: 39%{?dist}
|
||||
Version: 3.1.1
|
||||
Release: 3%{?dist}
|
||||
Summary: Chemistry software file format converter
|
||||
License: GPLv2
|
||||
URL: https://openbabel.org/
|
||||
Source0: https://github.com/openbabel/openbabel/archive/openbabel-%(echo %{version} | tr '.' '-').tar.gz
|
||||
Source0: https://github.com/openbabel/openbabel/archive/openbabel-openbabel-%(echo %{version} | tr '.' '-').tar.gz
|
||||
Source1: obgui.desktop
|
||||
|
||||
# fix perl modules install path
|
||||
Patch1: openbabel-perl.patch
|
||||
Patch0: %{name}-perl.patch
|
||||
|
||||
# fix plugin directory location (#680292, patch by lg)
|
||||
Patch4: openbabel-plugindir.patch
|
||||
Patch1: openbabel-plugindir.patch
|
||||
|
||||
# fix SWIG_init even when not using swig (#772149)
|
||||
Patch6: openbabel-noswig-rubymethod.patch
|
||||
Patch2: openbabel-noswig-rubymethod.patch
|
||||
|
||||
# On F-17, directory for C ruby files changed to use vendorarch directory
|
||||
Patch7: openbabel-ruby19-vendorarch.patch
|
||||
Patch3: openbabel-ruby19-vendorarch.patch
|
||||
|
||||
# temporarily disable some tests on:
|
||||
# - ppc64 and s390(x) to unblock other builds (#1108103)
|
||||
# - ARM (#1094491)
|
||||
# - aarch64 (#1094513)
|
||||
# Upstream bugs: https://sourceforge.net/p/openbabel/bugs/927/ https://sourceforge.net/p/openbabel/bugs/945/
|
||||
Patch8: openbabel-disable-tests.patch
|
||||
Patch9: openbabel-narrowing-conversion.patch
|
||||
Patch4: openbabel-disable-tests.patch
|
||||
|
||||
# Fix path to libdir in .pc file
|
||||
# https://bugzilla.redhat.com/show_bug.cgi?id=1669664
|
||||
Patch10: openbabel-fix-libdir-in-pkgconfig.patch
|
||||
Patch5: openbabel-fix-libdir-in-pkgconfig.patch
|
||||
|
||||
# Math 4 test is failing on s390x only
|
||||
Patch11: openbabel-disable-tests-s390x.patch
|
||||
Patch6: openbabel-disable-tests-s390x.patch
|
||||
|
||||
# Fix inconsistent whitespace
|
||||
Patch12: openbabel-taberror.patch
|
||||
|
||||
# Fix import of dl module in python3.7
|
||||
# https://github.com/openbabel/openbabel/pull/372
|
||||
Patch13: openbabel-python-dl.patch
|
||||
Patch7: openbabel-3.1.1-fix_bug2223.patch
|
||||
Patch8: openbabel-3.1.1-fix_bug2217.patch
|
||||
Patch9: openbabel-3.1.1-bug2378.patch
|
||||
|
||||
BuildRequires: make
|
||||
%if 0%{?el7}
|
||||
BuildRequires: boost169-devel
|
||||
%else
|
||||
BuildRequires: boost-devel
|
||||
%endif
|
||||
BuildRequires: swig
|
||||
BuildRequires: cmake3
|
||||
BuildRequires: dos2unix
|
||||
BuildRequires: desktop-file-utils
|
||||
|
|
@ -57,10 +56,10 @@ BuildRequires: eigen3-devel
|
|||
BuildRequires: gcc-c++
|
||||
BuildRequires: inchi-devel >= 1.0.3
|
||||
BuildRequires: libxml2-devel
|
||||
BuildRequires: swig
|
||||
BuildRequires: wxGTK3-devel
|
||||
BuildRequires: ImageMagick
|
||||
Requires: %{name}-libs%{?_isa} = %{version}-%{release}
|
||||
BuildRequires: rapidjson-devel
|
||||
Requires: %{name}-libs%{?_isa} = %{version}-%{release}
|
||||
|
||||
%description
|
||||
Open Babel is a free, open-source version of the Babel chemistry file
|
||||
|
|
@ -132,7 +131,7 @@ Requires: %{name}-libs%{?_isa} = %{version}-%{release}
|
|||
BuildRequires: python3-devel
|
||||
BuildRequires: python3-setuptools
|
||||
%{?python_provide:%python_provide python3-%{name}}
|
||||
Obsoletes: python2-%{name} < 2.4.1-21
|
||||
Obsoletes: python2-%{name} < 0:%{version}-%{release}
|
||||
|
||||
%description -n python3-%{name}
|
||||
Python3 wrapper for the Open Babel library.
|
||||
|
|
@ -148,20 +147,21 @@ Ruby wrapper for the Open Babel library.
|
|||
|
||||
%prep
|
||||
%setup -q -n %{name}-%{name}-%(echo %{version} | tr '.' '-')
|
||||
%patch1 -p1 -b .perl_path
|
||||
%patch4 -p1 -b .plugindir
|
||||
%patch6 -p1 -b .noswig_ruby
|
||||
%patch7 -p1 -b .ruby_vendor
|
||||
%ifarch aarch64 %{arm} %{power64} s390 s390x
|
||||
%patch8 -p1 -b .tests
|
||||
%patch0 -p1 -b .perl_path
|
||||
%patch1 -p1 -b .plugindir
|
||||
%patch2 -p1 -b .noswig_ruby
|
||||
%patch3 -p1 -b .ruby_vendor
|
||||
%ifarch aarch64 %{arm} %{power64} s390x
|
||||
%patch4 -p1 -b .tests
|
||||
%endif
|
||||
%patch5 -p1 -b .s390x
|
||||
%ifarch s390x
|
||||
%patch11 -p1 -b .s390x
|
||||
%patch6 -p1 -b .backup
|
||||
%endif
|
||||
%patch9 -p1 -b .nc
|
||||
%patch10 -p1
|
||||
%patch12 -p1 -b .taberr
|
||||
%patch13 -p1 -b .py3dl
|
||||
%patch7 -p1 -b .backup
|
||||
%patch8 -p1 -b .backup
|
||||
%patch9 -p1 -b .backup
|
||||
|
||||
# convert to Unix line endings
|
||||
dos2unix -k \
|
||||
data/chemdrawcdx.h \
|
||||
|
|
@ -171,8 +171,6 @@ dos2unix -k \
|
|||
|
||||
convert src/GUI/babel.xpm -transparent white babel.png
|
||||
|
||||
cp -p %{SOURCE1} obgui.desktop
|
||||
|
||||
# Remove duplicate html files
|
||||
pushd doc
|
||||
for man in *.1; do
|
||||
|
|
@ -199,11 +197,22 @@ export CXXFLAGS="%{optflags} -DEIGEN_ALTIVEC_DISABLE_MMA"
|
|||
-DPYTHON_EXECUTABLE=%{__python3} \
|
||||
-DPERL_BINDINGS:BOOL=ON \
|
||||
-DRUBY_BINDINGS:BOOL=ON \
|
||||
-DWITH_MAEPARSER:BOOL=OFF \
|
||||
-DWITH_COORDGEN:BOOL=OFF \
|
||||
-DOPENBABEL_USE_SYSTEM_INCHI=true \
|
||||
-DENABLE_VERSIONED_FORMATS=false \
|
||||
-DRUN_SWIG=true \
|
||||
-DENABLE_TESTS:BOOL=ON \
|
||||
-DOPTIMIZE_NATIVE=OFF
|
||||
-DOPTIMIZE_NATIVE=OFF \
|
||||
-DGLIBC_24_COMPATIBLE:BOOL=OFF \
|
||||
%if 0%{?el7}
|
||||
-DBoost_FILESYSTEM_LIBRARY_RELEASE:FILEPATH=%{_libdir}/boost169/libboost_filesystem.so \
|
||||
-DBoost_SERIALIZATION_LIBRARY_RELEASE:FILEPATH=%{_libdir}/boost169/libboost_serialization.so \
|
||||
-DBoost_SYSTEM_LIBRARY_RELEASE:FILEPATH=%{_libdir}/boost169/libboost_system.so \
|
||||
-DBoost_INCLUDE_DIR:PATH=%{_includedir}/boost169 \
|
||||
-DBoost_LIBRARY_DIR_RELEASE:PATH=%{_libdir}/boost169
|
||||
%endif
|
||||
|
||||
%make_build -C %{_target_platform}
|
||||
|
||||
%install
|
||||
|
|
@ -211,7 +220,7 @@ export CXXFLAGS="%{optflags} -DEIGEN_ALTIVEC_DISABLE_MMA"
|
|||
|
||||
rm -f %{buildroot}%{_libdir}/cmake/openbabel2/*.cmake
|
||||
|
||||
desktop-file-install --dir=%{buildroot}%{_datadir}/applications obgui.desktop
|
||||
desktop-file-install --dir=%{buildroot}%{_datadir}/applications %{SOURCE1}
|
||||
install -Dpm644 babel.png %{buildroot}%{_datadir}/pixmaps/babel.png
|
||||
|
||||
%if 1
|
||||
|
|
@ -222,12 +231,8 @@ pushd %{_vpath_builddir}
|
|||
# rm the built ruby bindings for testsuite to succeed (Red Hat bugzilla ticket #1191173)
|
||||
rm -f %{_lib}/openbabel.so
|
||||
|
||||
# needed by openbabel python module
|
||||
cp -p %{_lib}/_openbabel.so ../scripts/python/
|
||||
|
||||
export CTEST_OUTPUT_ON_FAILURE=1
|
||||
export PYTHONPATH=%{buildroot}%{python3_sitearch}
|
||||
export LD_LIBRARY_PATH=%{buildroot}%{libdir}:%{buildroot}%{libdir}/openbabel:%{buildroot}%{perl_vendorarch}/*/Chemistry/OpenBabel:%{buildroot}%{ruby_vendorarchdir}
|
||||
%if 0%{?el7}
|
||||
ctest3 -j1 --force-new-ctest-process -E 'test_cifspacegroup_1|test_cifspacegroup_2'
|
||||
%else
|
||||
|
|
@ -245,7 +250,6 @@ ctest3 -j1 --force-new-ctest-process
|
|||
%endif
|
||||
|
||||
%files
|
||||
%{_bindir}/babel
|
||||
%{_bindir}/ob*
|
||||
%{_bindir}/roundtrip
|
||||
%{_mandir}/man1/*.1*
|
||||
|
|
@ -253,9 +257,11 @@ ctest3 -j1 --force-new-ctest-process
|
|||
%exclude %{_mandir}/man1/obgui.1*
|
||||
|
||||
%files devel
|
||||
%{_includedir}/%{name}-2.0
|
||||
%{_includedir}/%{name}3
|
||||
%{_libdir}/libopenbabel.so
|
||||
%{_libdir}/libopenbabel.so.7
|
||||
%{_libdir}/pkgconfig/*.pc
|
||||
%{_libdir}/cmake/openbabel3/
|
||||
|
||||
%files doc
|
||||
%doc doc/*.html doc/README* doc/dioxin.*
|
||||
|
|
@ -268,10 +274,10 @@ ctest3 -j1 --force-new-ctest-process
|
|||
|
||||
%files libs
|
||||
%license COPYING
|
||||
%doc NEWS.md THANKS AUTHORS authors.txt README.md
|
||||
%doc THANKS AUTHORS authors.txt README.md
|
||||
%{_datadir}/%{name}/
|
||||
%{_libdir}/%{name}/
|
||||
%{_libdir}/libopenbabel.so.*
|
||||
%{_libdir}/libopenbabel.so.7.0.0
|
||||
|
||||
%files -n perl-%{name}
|
||||
%{perl_vendorarch}/Chemistry/OpenBabel.pm
|
||||
|
|
@ -279,21 +285,26 @@ ctest3 -j1 --force-new-ctest-process
|
|||
%{perl_vendorarch}/*/Chemistry/OpenBabel/OpenBabel.so
|
||||
|
||||
%files -n python3-%{name}
|
||||
%{python3_sitearch}/_openbabel.so
|
||||
%{python3_sitearch}/openbabel.py
|
||||
%{python3_sitearch}/pybel.py
|
||||
%{python3_sitearch}/__pycache__/*
|
||||
%{python3_sitearch}/openbabel/
|
||||
|
||||
%files -n ruby-%{name}
|
||||
%{ruby_vendorarchdir}/openbabel.so
|
||||
|
||||
%changelog
|
||||
* Sat Nov 06 2021 Antonio Trande <sagitter@fedoraproject.org> - 3.1.1-3
|
||||
- Fix CMake config file
|
||||
|
||||
* Wed Sep 22 2021 Antonio Trande <sagitter@fedoraproject.org> - 3.1.1-2
|
||||
- Fix patches order
|
||||
|
||||
* Thu Sep 02 2021 Antonio Trande <sagitter@fedoraproject.org> - 3.1.1-1
|
||||
- Release 3.1.1
|
||||
|
||||
* Wed Sep 01 2021 Antonio Trande <sagitter@fedoraproject.org> - 2.4.1-39
|
||||
- Install license file and some release documentation
|
||||
|
||||
* Wed Sep 01 2021 Antonio Trande <sagitter@fedoraproject.org> - 2.4.1-38
|
||||
* Mon Aug 30 2021 Antonio Trande <sagitter@fedoraproject.org> - 2.4.1-38
|
||||
- Use CMake3 in EPEL7
|
||||
- Fix PPC64le builds (rhbz#1996330)
|
||||
|
||||
* Thu Jul 22 2021 Fedora Release Engineering <releng@fedoraproject.org> - 2.4.1-37
|
||||
- Rebuilt for https://fedoraproject.org/wiki/Fedora_35_Mass_Rebuild
|
||||
|
|
|
|||
Loading…
Reference in New Issue