9 Commits

Author SHA1 Message Date
Yakov Pechersky
872b054d5c Defer numpy initialization to first use (#9127)
* Defer numpy initialization to first use in rdchem, rdmolops, cDataStructs

`from rdkit import Chem` unconditionally bootstrapped numpy (~120ms) via
import_array()/boost::python::numpy::initialize() in module init functions,
even when no numpy-dependent APIs were called. This is costly in cold-start
environments like AWS Lambda.

Move numpy initialization behind lazy guards (static bool + first-call init)
in rdchem.so, rdmolops.so, and cDataStructs.so. Numpy now loads only when
an API that actually needs it is invoked (GetDistanceMatrix, GetPositions,
SetPositions, GetAdjacencyMatrix, ConvertToNumpyArray, etc.).

Also change Conformer::SetPos to accept python::object instead of
np::ndarray to prevent Boost.Python from requiring numpy type conversion
before the lazy guard runs.

Adds test_lazy_numpy.py with subprocess-based tests verifying:
- `from rdkit import Chem` does not load numpy
- SmilesToMol/MolToSmiles work without numpy
- numpy loads on demand when array APIs are called

* skip inchi tests if not available

* switch to threadsafe once_flag, like elsewhere

* finish ifdef style

* switch to magic static style

* Revert "switch to magic static style"

This reverts commit 7300188db7.
2026-02-23 18:42:42 +01:00
Greg Landrum
da6cd73168 Run clang-format across everything (#7849)
* run clang-format-18 across Code/*.cpp and Code/*.h

* run clang-format-18 across External
2024-09-26 13:39:02 +02:00
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
Jan Domański
56234066b8 Conformer GetPos returns a numpy array rather than a tuple of tuples (#1087)
* Conformer GetPos returns a numpy array rather than a tuple of tuples

* Add missing method binding to GetPositions for a conformer

* Minor fixes
- avoid copying the coordinates,
- add a test
2016-10-14 05:02:59 +02:00
Greg Landrum
e08e0d16d8 first pass, using google style 2015-11-14 14:58:11 +01:00
Greg Landrum
f3fbef45c5 update copyright statements 2010-09-26 17:04:37 +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
Greg Landrum
75a79b6327 initial import 2006-05-06 22:20:08 +00:00