Matt Swain
e57b7a9bc8
Use numpy not numeric for boost 1.65+ - fixes #1581 ( #1664 )
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boost python numeric no longer exists in boost 1.65, so check boost version and conditionally use boost python numpy.
2017-11-20 05:44:19 +01:00
Greg Landrum
f94e277856
another pass of clang modernize
2017-10-12 06:35:51 +02:00
Greg Landrum
87786c08b5
Merge branch 'master' into modern_cxx
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# 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
Greg Landrum
96b092177e
[WIP] add threshold argument to maxmin picker ( #1587 )
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* add threshold argument
* expose the new options to python
not yet tested, but it at least compiles
* support threshold on the python side;
fix a bug with the way the threshold is returned
2017-09-26 12:49:33 -04:00
Greg Landrum
fd3524f77c
Optimization of the MaxMin diversity picker ( #1574 )
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* initial submission; needs review
* minor
* line endings
* remove cache functionality since it's now redundant
* add test data
* add a test
* changes from review
2017-09-17 09:13:14 -04:00
Greg Landrum
85488fb3ae
fixes #1421 ( #1422 )
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* fixes #1421
* change suggested in review
2017-07-02 10:24:26 +02:00
Greg Landrum
a19d6fec0b
fixes #1421 ( #1422 )
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* fixes #1421
* change suggested in review
2017-05-22 17:29:00 -04:00
Greg Landrum
7c0bb0b743
clang-tidy output
2017-04-22 17:09:24 +02:00
gedeck
e9af48ffd7
Issue1071/yapf ( #1078 )
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* 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
Brian Kelley
5d3a2a7262
Merge pull request #797 from greglandrum/fix/cleanup_register_execption
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Remove extra calls to python::register_exception_translator
2016-03-12 08:03:45 -05:00
Greg Landrum
b9ba12f8f9
Remove extra calls to python::register_exception_translator
2016-03-01 06:36:54 +01:00
Greg Landrum
a2f2c9805f
add a basic test of specific results for the lazy picker
2016-02-25 16:25:10 +01:00
Greg Landrum
ed62f46a4d
require numpy 1.7, not 1.8
2015-12-01 04:39:28 +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
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
237861136b
Fixes more Boost warning suppression
2015-10-18 16:08:11 -04:00
Brian Kelley
daa7e62258
Fixes signed conversion issues (use rdcast)
2015-10-18 15:16:38 -04:00
Brian Kelley
403a3d6b7c
Suppresses Boost warnings
2015-10-18 13:41:03 -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
e6a1327822
Code/RDBoost/Exceptions.h moved to Code/RDGeneral
2015-03-16 21:40:40 +01:00
Riccardo Vianello
95f60d21bc
python3 portability fixes for pandas and the ipython notebook
2014-09-11 23:49:45 +02:00
Greg Landrum
7946261aae
Fixes #294
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also adds direct diversity picking using fingerprints from python (efficiency win)
2014-08-07 09:22:11 +02:00
Greg Landrum
fac600885b
fix the simdivfilters problem with python3. This has now been tested on py3 and should, hopefully, not cause the travis build to fail
2014-08-05 05:26:25 +02:00
Greg Landrum
d2fdb3d075
Fixes #294
2014-08-03 12:03:35 +02:00
Riccardo Vianello
3358ec5925
initial set of changes introducing python3 support
2014-06-17 18:26:41 +02:00
Greg Landrum
bf2416032e
docstring cleanup
2012-01-07 15:10:42 +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
052ec66542
cleanups:
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remove x bit from headers and sources;
remove a couple empty files from Code/GraphMol
2010-09-08 04:25:57 +00:00
Greg Landrum
cb6cdb99b3
merge in a set of changes from Riccardo V. to install .h files as well;
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this needs more testing.
2010-09-04 14:07:22 +00:00
Greg Landrum
b3f6b9376c
add seed options for MaxMinPicker
2010-04-07 19:29:23 +00:00
Greg Landrum
53485592ca
builds on windows with visual studio; need to pass back to linux now
2009-10-01 13:35:48 +00:00
Greg Landrum
76297b0fff
builds and passes tests on linux
2009-09-28 11:02:18 +00:00
Greg Landrum
f0b288cfed
big changes again (repeat the 979, 980 disaster on the correct branch)
2009-02-04 20:13:44 +00:00
Greg Landrum
8bf7a4c187
now all tests pass here as well
2009-02-03 05:26:10 +00:00
Greg Landrum
2580fbaaa2
this is probably a ways from done, but now at least we can run bjam under mingw without it immediately erroring out
2008-11-15 17:14:13 +00:00
Greg Landrum
89a34d1a39
get this building on Darwin; NOTE: this may not work on win or linux yet
2008-09-03 19:24:35 +00:00
Greg Landrum
a3e6cb057e
this is a mass of cleanup stuff; mostly line endings
2008-07-07 13:21:24 +00:00
Greg Landrum
ac5a7d72c7
these are no longer needed
2008-07-07 06:36:34 +00:00
Greg Landrum
c9eb4e91e1
merge revs 736:741 from branch http://rdkit.svn.sourceforge.net/svnroot/rdkit/branches/NumPyPort_27June2008
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This removes the numeric python dependency and switches to relying on numpy.
current status of tests from branch: pass on lin32 and 64 and win32.
2008-07-05 07:42:38 +00:00
Greg Landrum
e8f3536845
remove a bunch of compiler warnings
2008-05-26 20:05:57 +00:00
Greg Landrum
8424d36830
get things building on windows.
2008-04-08 18:24:56 +00:00
Greg Landrum
d3aea154ef
switch everything over to dynamic linking in order to try and solve
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the horrible cross-library exception handling mess on linux. This may well break things on windows, which
might want these things static. Regardless, even as it is, this should be considered experimental
2008-04-08 10:24:57 +00:00
Greg Landrum
26a4124ad9
remove files for old build system
2008-02-20 17:06:59 +00:00
Greg Landrum
1e772eb335
merge in functionality for lazy picking (don't need to do the whole
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distance matrix in advance) + initial picks (pick a set that's
diverse w.r.t. the ones passed in);
Throw ValueErrorExceptions instead of invariants on bad input.
2007-11-24 06:26:46 +00:00
Greg Landrum
430a83bd96
merge in the jamfiles from the bjam branch;
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various and sundry minor code cleanups;
this probably does not yet build on windows... that is next
2007-11-23 15:55:30 +00:00
