mirror of
https://github.com/rdkit/rdkit.git
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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.
140 lines
4.5 KiB
C++
140 lines
4.5 KiB
C++
// $Id$
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//
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// Copyright (c) 2001-2006 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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#define PY_ARRAY_UNIQUE_SYMBOL rddatastructs_array_API
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#ifdef RDK_BUILD_THREADSAFE_SSS
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#include <mutex>
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#endif
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#include <RDBoost/python.h>
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#include <RDBoost/Wrap.h>
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#include <DataStructs/BitVects.h>
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#include <DataStructs/DiscreteValueVect.h>
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#include <DataStructs/SparseIntVect.h>
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#include <DataStructs/RealValueVect.h>
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#include <RDBoost/boost_numpy.h>
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#include <numpy/npy_common.h>
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#include <RDBoost/import_array.h>
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#include <RDBoost/pyint_api.h>
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namespace python = boost::python;
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void wrap_SBV();
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void wrap_EBV();
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void wrap_BitOps();
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void wrap_Utils();
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void wrap_discreteValVect();
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void wrap_realValVect();
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void wrap_sparseIntVect();
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void wrap_FPB();
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#ifdef RDK_BUILD_THREADSAFE_SSS
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static std::once_flag s_ds_numpy_init_flag;
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#endif
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static void ds_ensure_numpy() {
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#ifdef RDK_BUILD_THREADSAFE_SSS
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std::call_once(s_ds_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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namespace {
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template <typename T, typename U>
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void converter(const T &v, python::object destArray, U func) {
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ds_ensure_numpy();
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if (!PyArray_Check(destArray.ptr())) {
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throw_value_error("Expecting a Numeric array object");
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}
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auto *destP = (PyArrayObject *)destArray.ptr();
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npy_intp ndims[1];
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ndims[0] = v.size();
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PyArray_Dims dims;
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dims.ptr = ndims;
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dims.len = 1;
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PyArray_Resize(destP, &dims, 0, NPY_ANYORDER);
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for (unsigned int i = 0; i < v.size(); ++i) {
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PyObject *iItem = func(v[i]);
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PyArray_SETITEM(destP, static_cast<char *>(PyArray_GETPTR1(destP, i)),
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iItem);
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Py_DECREF(iItem);
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}
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}
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} // namespace
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template <typename T>
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void convertToIntNumpyArray(const T &v, python::object destArray) {
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converter(v, destArray, PyLong_FromLong);
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}
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template <typename T>
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void convertToDoubleNumpyArray(const T &v, python::object destArray) {
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converter(v, destArray, PyFloat_FromDouble);
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}
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BOOST_PYTHON_MODULE(cDataStructs) {
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python::scope().attr("__doc__") =
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"Module containing an assortment of functionality for basic data "
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"structures.\n"
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"\n"
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"At the moment the data structures defined are:\n"
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" Bit Vector classes (for storing signatures, fingerprints and the "
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"like:\n"
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" - ExplicitBitVect: class for relatively small (10s of thousands of "
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"bits) or\n"
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" dense bit vectors.\n"
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" - SparseBitVect: class for large, sparse bit vectors\n"
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" DiscreteValueVect: class for storing vectors of integers\n"
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" SparseIntVect: class for storing sparse vectors of integers\n";
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wrap_Utils();
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wrap_SBV();
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wrap_EBV();
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wrap_BitOps();
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wrap_discreteValVect();
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wrap_realValVect();
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wrap_sparseIntVect();
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wrap_FPB();
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python::def(
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"ConvertToNumpyArray",
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(void (*)(const ExplicitBitVect &, python::object))convertToIntNumpyArray,
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(python::arg("bv"), python::arg("destArray")));
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python::def("ConvertToNumpyArray",
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(void (*)(const RDKit::DiscreteValueVect &,
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python::object))convertToIntNumpyArray,
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(python::arg("bv"), python::arg("destArray")));
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python::def("ConvertToNumpyArray",
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(void (*)(const RDKit::SparseIntVect<std::int32_t> &,
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python::object))convertToIntNumpyArray,
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(python::arg("bv"), python::arg("destArray")));
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python::def("ConvertToNumpyArray",
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(void (*)(const RDKit::SparseIntVect<boost::int64_t> &,
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python::object))convertToIntNumpyArray,
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(python::arg("bv"), python::arg("destArray")));
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python::def("ConvertToNumpyArray",
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(void (*)(const RDKit::SparseIntVect<std::uint32_t> &,
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python::object))convertToIntNumpyArray,
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(python::arg("bv"), python::arg("destArray")));
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python::def("ConvertToNumpyArray",
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(void (*)(const RDKit::SparseIntVect<boost::uint64_t> &,
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python::object))convertToIntNumpyArray,
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(python::arg("bv"), python::arg("destArray")));
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python::def("ConvertToNumpyArray",
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(void (*)(const RDKit::RealValueVect &,
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python::object))convertToDoubleNumpyArray,
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(python::arg("rvv"), python::arg("destArray")));
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}
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