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28 Commits

Author SHA1 Message Date
Greg Landrum
79e8295586 Support Python 3.11 (#5994) 
* remove some more deprecated numpy stuff

* workaround for changes to random.shuffle in python 3.11

* fix pickling of rdkit mols in python 3.11

* add py311 build to CI

* update py311 CI

* remove qt for py311 for the moment

* only use the new code with pyversion >=3.11

* use the new logic for all pickle_suites

* need to work with older py too
 2023-01-24 18:16:26 +01:00
Eisuke Kawashima
11532089de Run clang-format against cpp (#4358) 2021-10-20 04:25:27 +02:00
Brian Kelley
549f318f29 Add ToList method to Sparse/ExplicitBitVector (#4467) 
* Add ToList method to Sparse/ExplicitBitVector

* Pushed a change to an older version of the file, reverting

* Fix function name

* Merge with the change that actually compiles

* Add SparseIntVect ToList, Update tests

* Fix test

* Update Code/DataStructs/Wrap/SparseIntVect.cpp

Co-authored-by: Greg Landrum <greg.landrum@gmail.com>

* Update Code/DataStructs/Wrap/wrap_SparseBV.cpp

Co-authored-by: Greg Landrum <greg.landrum@gmail.com>

Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
 2021-09-09 06:26:15 +02:00
Greg Landrum
edd922c99c Cleanup warnings from clang-10 (#3238) 
* stop returning local memory in exceptions

* remove a couple unnecessary copies in loops

* fix a bug in the way the default MMFF aromatic parameters are constructed

* remove a bunch of loop-variable warnings

* remove a bunch of clang warnings

* disable clang warnings in python wrappers

* remove some warnings when building the python wrappers
 2020-06-19 17:16:22 -04:00
Brian Kelley
373a89021e Change boost int types to std types (#2233) 2019-01-22 17:45:03 +01:00
Greg Landrum
915cf08faa run clang-format with c++-11 style over that 2017-04-22 17:19:10 +02:00
Greg Landrum
7c0bb0b743 clang-tidy output 2017-04-22 17:09:24 +02:00
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
Brian Kelley
403a3d6b7c Suppresses Boost warnings 2015-10-18 13:41:03 -04:00
Greg Landrum
47931754da fix DbCLI tests; includes fixing the pickling of SparseIntVects 2014-06-24 07:17:12 +02:00
Greg Landrum
50332b599e get some of the pickle problems resolved; this probably only works with python3 and is not yet 100% functional 2014-06-19 06:05:42 +02:00
Greg Landrum
879efa3be3 add support for integer arithmatic ops on SparseIntVects. operator+ et al. do not yet work from python 2013-08-26 06:51:13 +02:00
Greg Landrum
29312e73e1 minor updates 2012-01-03 07:50:53 +00:00
Greg Landrum
f3fbef45c5 update copyright statements 2010-09-26 17:04:37 +00:00
Greg Landrum
1480eccb87 expose tanimoto similarity on SparseIntVects 2009-06-19 04:19:45 +00:00
Greg Landrum
423433a3e4 support Tversky similarity for SparseIntVects 2009-06-18 14:37:03 +00:00
Greg Landrum
b50e69b171 bad argument removed 2009-01-05 05:02:21 +00:00
Greg Landrum
299689095a operator== and operator!= should be const; support unsigned SparseIntVects as well 2008-07-28 03:40:30 +00:00
Greg Landrum
029e08d6b4 merge in the changes from the 64 bit port branch r703:717 2008-06-11 05:01:17 +00:00
Greg Landrum
a6c1a64d1a remove some compiler warnings 
rearrange the argument ordering for the Dice similarity stuff so 
that it can be invoked the same as the other similarity metrics.
 2008-04-24 19:03:34 +00:00
Greg Landrum
213c2323bd add returnDistances support to the SparseIntVects too 2008-04-24 12:06:29 +00:00
Greg Landrum
9bb88cb2cf - speed up Dice similarity between SparseIntVects (a lot) 
- add bulk Dice similarity for SIVs to wrapper
- speed up bulk Dice similarity for bit vects
- test a bit more
 2008-04-15 05:18:52 +00:00
Greg Landrum
93834a90bd remove support for the useAbs function; 
add bounds support on the dice metric
 2007-10-05 15:35:11 +00:00
Greg Landrum
0ab0653c18 move DiceSimilarity code into c++ 2007-10-04 03:34:06 +00:00
Greg Landrum
67f7dab587 fix a problem with __len__ in python (can't do it if we return a Long); 
wrap GetLength() instead;
add getNonzeroElements()
 2007-09-28 03:45:03 +00:00
Greg Landrum
7726cb9d8a getting close to right here; still needs windows testing 2007-09-23 06:54:37 +00:00
Greg Landrum
1fa8cd321b add SparseIntVect in both c++ and Python 
This still needs windows testing.
 2007-09-22 18:49:37 +00:00