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91 Commits

Author SHA1 Message Date
Greg Landrum
7e6600f3be Fixes #2516 (#2519) 
* RDStreams now installed properly

* skip Wrap directories if RDK_BUILD_PYTHON_WRAPPERS is not set

Fixes #2516
 2019-06-28 09:57:00 -04:00
Greg Landrum
ec31bea97b clang-tidy-7 pass (#2408) 2019-04-16 12:05:47 -04:00
Greg Landrum
b337415094 Fix github #2311 (#2394) 
* Fixes #2311
at least I hope it does

* Stop using deprecated boost functionality

* allow the Murtagh module to import even if the code isn't built
update the associated tests

* update release notes

* typo

* fix integer division
 2019-04-04 10:20:56 +02:00
greg landrum
92ca0da5f9 Merge branch 'doc-update' of https://github.com/greglandrum/rdkit into greglandrum-doc-update 2019-03-07 21:15:00 +01:00
Greg Landrum
24f1737839 Remove a bunch of Python2-related warts (#2315) 
* remove all of the "from __future__" imports

* remove the first batch of rdkit.six imports/uses

* next step of rdkit.six removal

* removing xrange, range, and some maps

* next round of removals

* next round of cleanups

* fix inchi test

* last bits of "from rdkit.six" are gone

* and the last of the six stuff is gone

* strange importlib problem
 2019-03-06 20:43:49 -05:00
Greg Landrum
fb5e325705 update docstrings in the wrappers too 2019-03-05 11:40:28 +01:00
Brian Kelley
373a89021e Change boost int types to std types (#2233) 2019-01-22 17:45:03 +01:00
Greg Landrum
2738c35178 Fixes #1903 (#1971) 
* Fixes #1903

* update SWIG bindings too
 2018-07-25 09:14:17 +02:00
Paolo Tosco
c08ea49bda - enable building DLLs on Windows (#1861) 
* - enable building DLLs on Windows

* - export.h and test.h are now auto-generated by CMake
 2018-05-16 08:42:41 +02:00
Greg Landrum
87786c08b5 Merge branch 'master' into modern_cxx 
# Conflicts:
#	.travis.yml
#	Code/GraphMol/FileParsers/MolFileParser.cpp
#	Code/GraphMol/FileParsers/MolFileStereochem.cpp
#	Code/GraphMol/ForceFieldHelpers/UFF/testUFFHelpers.cpp
#	Code/GraphMol/MolAlign/testMolAlign.cpp
#	Code/GraphMol/MolDraw2D/MolDraw2D.cpp
#	Code/GraphMol/MolDraw2D/Wrap/rdMolDraw2D.cpp
#	Code/GraphMol/QueryOps.cpp
#	Code/GraphMol/ROMol.cpp
#	Code/GraphMol/SmilesParse/test.cpp
#	Code/GraphMol/Trajectory/Trajectory.cpp
#	Code/GraphMol/Wrap/Atom.cpp
#	Code/GraphMol/Wrap/Bond.cpp
#	Code/GraphMol/new_canon.cpp
#	Code/RDGeneral/testDict.cpp
#	Code/SimDivPickers/Wrap/MaxMinPicker.cpp
 2017-10-05 05:58:38 +02:00
Brian Kelley
7488840ac4 Fix/urange check (#1506) 
* Fixes atom documentation

* Fixes #1461

This is a complicated one.  Basically URANGE_CHECK when
used on unsigned integers has a problem when the size of
the range it’s checking is 0.  The standard operations is
to check

URANGE(num, size-1)

Which (for unsigned integers) obviously rolls over.

This fixes all usage cases to be

URANGE(num+1, size)

And fixes the bugs found.  (addBond and the mmff tests)

* Fixes #1461 - Updates URANGE_CHECK to be 0<=x<hi
 2017-09-11 21:17:33 +02:00
Greg Landrum
7c0bb0b743 clang-tidy output 2017-04-22 17:09:24 +02:00
gedeck
e9af48ffd7 Issue1071/yapf (#1078) 
* Issue #1071: add yapf configuration file

* yapf formatting of Code directory

* yapf formatting of Contrib directory

* yapf formatting of Data directory

* yapf formatting of Docs directory

* yapf formatting of External directory

* yapf formatting of Projects directory

* yapf formatting of Regress directory

* yapf formatting of Scripts directory

* yapf formatting of Web directory

* yapf formatting of rdkit directory
 2016-09-23 04:58:46 +02:00
Greg Landrum
b9ba12f8f9 Remove extra calls to python::register_exception_translator 2016-03-01 06:36:54 +01:00
Greg Landrum
ed62f46a4d require numpy 1.7, not 1.8 2015-12-01 04:39:28 +01:00
Greg Landrum
f600b0310c Merge branch 'master' into fix/numpy-cleanup 2015-12-01 02:31:38 +01:00
Greg Landrum
4b15857baa Remove a few changes that caused windows builds to fail 2015-11-29 12:28:00 +01:00
Greg Landrum
79e1f8b1fa compiles without numpy warnings, all tests pass on ubuntu 15.04 with numpy 1.10 2015-11-28 06:49:34 +01:00
Greg Landrum
d07f2ccd05 replace oldnumeric imports 2015-11-28 02:38:58 +01:00
Greg Landrum
e08e0d16d8 first pass, using google style 2015-11-14 14:58:11 +01:00
Greg Landrum
e37296d7c7 post review 2015-11-14 08:08:14 +01:00
Greg Landrum
5618819c64 merge #641 2015-11-14 05:03:24 +01:00
Greg Landrum
1cde397acb merge commit 2015-10-30 02:58:46 +01:00
Brian Kelley
35e91e8b0e Silences unused variable 2015-10-18 21:17:55 -04:00
Brian Kelley
fb84c9f0b7 Switches to URANGE_CHECK when appropriate 2015-10-18 21:14:02 -04:00
Brian Kelley
4f48557d4e Silences unused parameters 2015-10-18 16:39:29 -04:00
Brian Kelley
5f59333a56 Silences unused parameters 2015-10-18 14:02:29 -04:00
Brian Kelley
403a3d6b7c Suppresses Boost warnings 2015-10-18 13:41:03 -04:00
Brian Kelley
a146c3826a Remove unused variables/functions and register keyword 2015-10-18 10:01:00 -04:00
Brian Kelley
12d562399a Merge branch 'master' into fix/const-string-ref 2015-10-13 07:08:00 -04:00
Brian Kelley
6ebbeb3bd3 Major conversion of std::string API to const std::string & 2015-09-25 15:15:59 -04:00
Greg Landrum
a743cff4d7 Fixes #573 2015-09-20 04:44:39 +02:00
Andrew Dalke
6d66534743 removed bare except statements 2015-09-07 13:27:14 +02:00
Riccardo Vianello
7c346d7c2e Code/RDBoost/Exceptions.h moved to Code/RDGeneral 2015-03-16 22:31:48 +01:00
Paolo Tosco
4f7482139f - fixed tests failing on Windows when retrieving sources through the 
Windows git client, which converts line terminators to CR+LF
- added a conditional compilation clause to Code/RDBoost/import_array.h
  to avoid a compilation error on Windows with Python3
 2015-02-22 21:49:40 +00:00
Greg Landrum
7a9cca2299 get this building on the mac 2014-09-18 08:08:08 +02:00
Greg Landrum
9012272794 Fixes #327 2014-09-16 05:55:43 +02:00
Riccardo Vianello
609009b1ec additional changes related to pickling. 
- fixed dependency from ordering of dict keys in a doctest
- replaced import of cPickle from the python2 lib w/ rdkit.six.moves.cPickle
- fixed a few more tests
- support pickle load/loads kw arguments with a portable interface
 2014-07-06 09:13:38 +02:00
Riccardo Vianello
3358ec5925 initial set of changes introducing python3 support 2014-06-17 18:26:41 +02:00
Greg Landrum
6bb981c4e2 Fixes #37 2014-05-01 07:16:03 +02:00
Greg Landrum
334aada835 merge 2014-03-28 04:56:21 -04:00
Greg Landrum
9f4471f872 more on #204 
A few other cleanups
 2014-02-06 06:43:28 +01:00
Greg Landrum
2114db0941 Fixes #204 
This covers at least the specific instances from the bug report.
Still need to figure out a general way to identify these automatically
to make sure all are fixed.
 2014-02-05 06:38:05 +01:00
Greg Landrum
800770a1df fix github issue 18 2013-04-16 11:22:03 +00:00
Greg Landrum
c6de27e945 this passes all tests on big-endian debian systems. 
note that in order to make it work, some lesser-used functionality (clustering and CMIM) had
to be disabled. This could be revisited in the future.
 2012-07-27 04:22:04 +00:00
Greg Landrum
e566afff2f merge in Riccardo Vianello's changes to make it easier to build c++ programs using the RDKit with cmake 2011-08-07 16:34:42 +00:00
Greg Landrum
b993f89afe remove the bjam-based build system 2010-09-27 03:54:07 +00:00
Greg Landrum
f3fbef45c5 update copyright statements 2010-09-26 17:04:37 +00:00
Greg Landrum
4db8233db6 sync with trunk 2010-09-10 05:12:41 +00:00
Greg Landrum
052ec66542 cleanups: 
remove x bit from headers and sources;
remove a couple empty files from Code/GraphMol
 2010-09-08 04:25:57 +00:00