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872b054d5c
* 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.
56 lines
1.3 KiB
C++
56 lines
1.3 KiB
C++
//
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// Copyright (C) 2003-2019 Greg Landrum and Rational Discovery LLC
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//
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// @@ All Rights Reserved @@
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// This file is part of the RDKit.
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// The contents are covered by the terms of the BSD license
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// which is included in the file license.txt, found at the root
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// of the RDKit source tree.
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//
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#include "rdmolops.h"
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#include <RDBoost/python.h>
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#include <RDGeneral/types.h>
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#include <RDBoost/Wrap.h>
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#include <RDBoost/import_array.h>
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#include <RDGeneral/Exceptions.h>
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#include <GraphMol/SanitException.h>
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#ifdef RDK_BUILD_THREADSAFE_SSS
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#include <mutex>
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#endif
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namespace python = boost::python;
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using namespace RDKit;
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#ifdef RDK_BUILD_THREADSAFE_SSS
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static std::once_flag s_rdmolops_numpy_init_flag;
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#endif
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void rdkit_rdmolops_ensure_numpy() {
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#ifdef RDK_BUILD_THREADSAFE_SSS
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std::call_once(s_rdmolops_numpy_init_flag, rdkit_import_array);
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#else
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static bool initialized = false;
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if (!initialized) {
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initialized = true;
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rdkit_import_array();
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}
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#endif
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}
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void wrap_molops();
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void wrap_chiralityops();
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BOOST_PYTHON_MODULE(rdmolops) {
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python::scope().attr("__doc__") =
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"Module containing RDKit functionality for manipulating molecules.";
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// ******************************
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// Functions from MolOps
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//****************************
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wrap_molops();
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wrap_chiralityops();
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}
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