mirror of https://github.com/TREX-CoE/trexio.git
Merge pull request #126 from TREX-CoE/text-fallback-python
Text fallback when building python API
This commit is contained in:
GitHub
commit
81818a40ab
25
Makefile.am
25
Makefile.am
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@ -37,7 +37,7 @@ CLEANFILES = trexio.mod
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if HAVE_FORTRAN
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BUILT_SOURCES = trexio.mod
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else
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BUILT_SOURCES =
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BUILT_SOURCES =
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endif
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EXTRA_DIST = .git_hash
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@ -261,10 +261,18 @@ pytrexio_i = $(srcdir)/src/pytrexio.i
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numpy_i = $(srcdir)/src/numpy.i
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if HAVE_HDF5
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python-test: $(TEST_PY)
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python3 -m pytest -v --all $(TEST_PY)
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$(RM) -r -- __pycache__
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$(RM) -f -- test_file_py.h5 unsafe_test_file_py.h5
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$(RM) -rf -- test_file_py.dir unsafe_test_file_py.dir
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else
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python-test: $(TEST_PY)
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python3 -m pytest -v $(TEST_PY)
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$(RM) -r -- __pycache__
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$(RM) -f -- test_file_py.h5 unsafe_test_file_py.h5
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$(RM) -r -- __pycache__
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$(RM) -rf -- test_file_py.dir unsafe_test_file_py.dir
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endif
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python-install: $(pytrexio_py) $(setup_py) $(setup_cfg)
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cd python && \
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@ -274,11 +282,15 @@ python-sdist: $(pytrexio_py) $(setup_py) $(setup_cfg)
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cd python && \
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python3 -m build --sdist
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if HAVE_HDF5
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$(pytrexio_py): $(pytrexio_c)
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cd tools && ./prepare_python.sh
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else
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$(pytrexio_py): $(pytrexio_c)
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cd tools && ./prepare_python.sh --without-hdf5
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endif
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# Build Python module and C wrapper code for TREXIO using SWIG
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# [?] swig -python -threads pytrexio.i ----> Add thread support for all the interface
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$(pytrexio_c): $(ORG_FILES) $(GENERATOR_FILES) $(trexio_h) $(pytrexio_i) $(numpy_i)
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@if [[ $(SWIG).x != ".x" ]] ; then \
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cp $(trexio_h) src/ ; \
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@ -307,7 +319,7 @@ DEB_FILES = \
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helpers-debian/libtrexio0.install \
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helpers-debian/libtrexio-dev.install \
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helpers-debian/source \
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helpers-debian/README.source
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helpers-debian/README.source
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debian_from_dist: $(DEB_FILES) $(SOURCES) $(trexio_h)
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cp ../trexio-$(PACKAGE_VERSION).tar.gz ../libtrexio_$(PACKAGE_VERSION).orig.tar.gz
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@ -317,6 +329,9 @@ debian_from_dist: $(DEB_FILES) $(SOURCES) $(trexio_h)
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CLEANFILES += $(pytrexio_c) \
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$(pytrexio_py) \
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$(trexio_py) \
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$(srcdir)/src/trexio.py \
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$(srcdir)/src/pytrexio.py \
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$(srcdir)/src/trexio.h \
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python/src/*.c \
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python/src/*.h
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@ -4,6 +4,7 @@ include examples/notebooks/*
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include examples/README.md
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include requirements.txt tools/set_NUMPY_INCLUDEDIR.sh
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include test/benzene_data.py
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include test/conftest.py
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exclude examples/LICENSE
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exclude examples/requirements.txt
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@ -40,7 +40,7 @@ if numpy_isUndefined and not do_sdist:
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rootpath = os.path.dirname(os.path.abspath(__file__))
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srcpath = os.path.join(rootpath, 'src')
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c_files = ['trexio.c', 'trexio_hdf5.c', 'trexio_text.c', 'pytrexio_wrap.c']
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c_files = ['trexio.c', 'trexio_text.c']
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with open("README.md", "r") as fh:
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@ -61,12 +61,15 @@ if not version_r:
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# The block below is needed to derive additional flags related to the HDF5 library,
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# which is required to build pytrexio extension module during the setup.py execution
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h5_present = False
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h5_ldflags_withl = os.environ.get("H5_LDFLAGS", None)
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h5_cflags_withI = os.environ.get("H5_CFLAGS", None)
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h5_ldflags_isUndefined = h5_ldflags_withl is None or h5_ldflags_withl==""
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h5_cflags_isUndefined = h5_cflags_withI is None or h5_cflags_withI==""
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h5_present = (not h5_ldflags_isUndefined) & (not h5_cflags_isUndefined)
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if (h5_ldflags_isUndefined or h5_cflags_isUndefined) and not do_sdist:
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try:
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@ -76,31 +79,51 @@ if (h5_ldflags_isUndefined or h5_cflags_isUndefined) and not do_sdist:
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try:
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assert pk.exists('hdf5')
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h5_present = True
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except AssertionError:
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raise Exception("pkg-config could not locate HDF5")
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print("pkg-config could not locate HDF5; installing TREXIO with TEXT back-end only!")
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h5_cflags_withI = pk.cflags('hdf5')
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h5_ldflags_withl = pk.libs('hdf5')
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if h5_present:
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h5_cflags_withI = pk.cflags('hdf5')
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h5_ldflags_withl = pk.libs('hdf5')
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h5_cflags = h5_cflags_withI.replace("-I","").split(" ")[0] if not do_sdist else ""
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h5_ldflags = h5_ldflags_withl.split(" ")[0] if not do_sdist else ""
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if h5_present:
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h5_cflags = h5_cflags_withI.replace("-I","").split(" ")[0] if not do_sdist else ""
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h5_ldflags = h5_ldflags_withl.split(" ")[0] if not do_sdist else ""
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c_files.append('trexio_hdf5.c')
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# ============================ End of the HDF5 block ============================ #
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# Define pytrexio extension module based on TREXIO source codes + SWIG-generated wrapper
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pytrexio_module = Extension('pytrexio._pytrexio',
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c_files.append('pytrexio_wrap.c')
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compile_args = [
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'-std=c99',
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'-Wno-discarded-qualifiers',
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'-Wno-unused-variable',
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'-Wno-unused-but-set-variable'
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]
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# if config.h is present then we are building via Autotools
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if os.path.isfile(os.path.join(srcpath, "config.h")):
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compile_args.append('-DHAVE_CONFIG_H')
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# explicit hack needed when building from sdist tarball
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if h5_present:
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compile_args.append('-DHAVE_HDF5')
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# define C extension module
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if h5_present:
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pytrexio_module = Extension('pytrexio._pytrexio',
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sources = [os.path.join(srcpath, code) for code in c_files],
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include_dirs = [h5_cflags, srcpath, numpy_includedir],
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libraries = ['hdf5' ],
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extra_compile_args = [
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'-std=c99',
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'-Wno-discarded-qualifiers',
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'-Wno-unused-variable',
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'-Wno-unused-but-set-variable'
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],
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extra_compile_args = compile_args,
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extra_link_args = [h5_ldflags]
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)
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else:
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pytrexio_module = Extension('pytrexio._pytrexio',
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sources = [os.path.join(srcpath, code) for code in c_files],
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include_dirs = [srcpath, numpy_includedir],
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extra_compile_args = compile_args
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)
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setup(name = 'trexio',
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@ -0,0 +1,17 @@
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# content of conftest.py
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import pytest
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def pytest_addoption(parser):
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parser.addoption(
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"--all", action="store_true", help="Run all back-ends"
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)
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def pytest_generate_tests(metafunc):
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if "backend" in metafunc.fixturenames:
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if metafunc.config.getoption("all"):
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backends = ['hdf5', 'text']
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else:
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backends = ['text']
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metafunc.parametrize("backend", backends)
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@ -6,19 +6,22 @@ import trexio
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from benzene_data import *
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FILENAME = 'test_file_py.h5'
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BACK_END = trexio.TREXIO_HDF5
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def clean():
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def clean(back_end, filename):
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"""Remove test files."""
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import os
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try:
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os.remove(FILENAME)
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os.remove('unsafe_' + FILENAME)
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except FileNotFoundError:
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pass
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if back_end == trexio.TREXIO_HDF5:
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import os
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try:
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os.remove(filename)
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os.remove('unsafe_' + filename)
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except FileNotFoundError:
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pass
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else:
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import shutil
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try:
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shutil.rmtree(filename)
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shutil.rmtree('unsafe_' + filename)
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except FileNotFoundError:
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pass
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def test_info():
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@ -29,7 +32,7 @@ def test_info():
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def test_void():
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"""Check raise of an error upon I/O on non-existing file."""
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with pytest.raises(trexio.Error):
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_ = trexio.File('void.file', 'r', BACK_END)
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_ = trexio.File('void.file', 'r', trexio.TREXIO_TEXT)
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def test_orbital_list():
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@ -53,20 +56,30 @@ def test_bitfield_list():
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class TestIO:
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"""Unit tests for writing/reading different blocks of the TREXIO file."""
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filename = FILENAME
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back_end = BACK_END
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mode = 'w'
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test_file = None
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clean()
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@pytest.fixture(autouse=True)
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def setup(self, backend):
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self.mode = 'w'
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self.test_file = None
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if backend == 'hdf5':
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self.back_end = trexio.TREXIO_HDF5
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self.filename = 'test_file_py.h5'
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elif backend == 'text':
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self.back_end = trexio.TREXIO_TEXT
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self.filename = 'test_file_py.dir'
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else:
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raise ValueError("Wrong TREXIO back-end supplied to pytest.")
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def __del__(self):
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if self.test_file:
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if self.test_file.isOpen:
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self.test_file.close()
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def test_clean(self):
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"""Clean existing files."""
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clean(self.back_end, self.filename)
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#def __del__(self):
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# """Class destructor."""
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# if self.test_file:
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# if self.test_file.isOpen:
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# self.test_file.close()
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def open(self, filename=None, mode=None, back_end=None):
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"""Create a TREXIO file and open it for writing."""
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if not filename:
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@ -107,12 +120,17 @@ class TestIO:
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with pytest.raises(trexio.Error):
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trexio.write_nucleus_num(self.test_file, nucleus_num * 2)
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if self.test_file.isOpen:
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self.test_file.close()
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def test_num(self):
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"""Write a number."""
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self.open()
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trexio.write_nucleus_num(self.test_file, nucleus_num)
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assert trexio.has_nucleus_num(self.test_file)
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if self.test_file.isOpen:
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self.test_file.close()
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def test_str(self):
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@ -120,6 +138,8 @@ class TestIO:
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self.open()
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trexio.write_nucleus_point_group(self.test_file, point_group)
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assert trexio.has_nucleus_point_group(self.test_file)
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if self.test_file.isOpen:
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self.test_file.close()
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def test_array_str(self):
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@ -129,6 +149,8 @@ class TestIO:
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self.test_num()
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trexio.write_nucleus_label(self.test_file, nucleus_label)
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assert trexio.has_nucleus_label(self.test_file)
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if self.test_file.isOpen:
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self.test_file.close()
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def test_array_1D(self):
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@ -138,6 +160,8 @@ class TestIO:
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self.test_num()
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trexio.write_nucleus_charge(self.test_file, nucleus_charge)
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assert trexio.has_nucleus_charge(self.test_file)
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if self.test_file.isOpen:
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self.test_file.close()
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def test_array_2D(self):
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@ -147,6 +171,8 @@ class TestIO:
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self.test_num()
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trexio.write_nucleus_coord(self.test_file, nucleus_coord)
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assert trexio.has_nucleus_coord(self.test_file)
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if self.test_file.isOpen:
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self.test_file.close()
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def test_indices(self):
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@ -159,6 +185,8 @@ class TestIO:
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# now write the indices
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trexio.write_basis_nucleus_index(self.test_file, indices_np)
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assert trexio.has_basis_nucleus_index(self.test_file)
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if self.test_file.isOpen:
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self.test_file.close()
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def test_sparse(self):
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@ -170,6 +198,8 @@ class TestIO:
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offset = 0
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trexio.write_ao_2e_int_eri(self.test_file, offset, num_integrals, indices, values)
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assert trexio.has_ao_2e_int_eri(self.test_file)
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if self.test_file.isOpen:
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self.test_file.close()
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def test_determinant(self):
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@ -189,31 +219,39 @@ class TestIO:
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assert trexio.has_determinant_coefficient(self.test_file)
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# manually check the consistency between coefficient_size and number of determinants
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assert trexio.read_determinant_coefficient_size(self.test_file) == trexio.read_determinant_num(self.test_file)
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if self.test_file.isOpen:
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self.test_file.close()
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def test_delete_group(self):
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"""Delete a group."""
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self.open(filename='unsafe_' + self.filename, mode='u', back_end=self.back_end)
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self.test_num()
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self.test_array_1D()
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self.test_array_2D()
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trexio.write_nucleus_num(self.test_file, nucleus_num)
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trexio.write_nucleus_charge(self.test_file, nucleus_charge)
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trexio.flush(self.test_file)
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assert trexio.has_nucleus_num(self.test_file)
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assert trexio.has_nucleus_charge(self.test_file)
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assert trexio.has_nucleus(self.test_file)
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trexio.delete_nucleus(self.test_file)
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assert not trexio.has_nucleus_num(self.test_file)
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assert not trexio.has_nucleus_charge(self.test_file)
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assert not trexio.has_nucleus_coord(self.test_file)
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assert not trexio.has_nucleus(self.test_file)
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if self.test_file.isOpen:
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self.test_file.close()
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||||
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||||
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def test_has_group(self):
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"""Check existense of a group."""
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self.open()
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assert trexio.has_nucleus(self.test_file)
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assert not trexio.has_rdm(self.test_file)
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if self.test_file.isOpen:
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self.test_file.close()
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def test_context_manager(self):
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@ -231,6 +269,8 @@ class TestIO:
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self.open(mode='r')
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num_r = trexio.read_nucleus_num(self.test_file)
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assert num_r == nucleus_num
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if self.test_file.isOpen:
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self.test_file.close()
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||||
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def test_read_array_1D(self):
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|
@ -240,6 +280,8 @@ class TestIO:
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assert charges_np_r.dtype is np.dtype(np.float64)
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assert charges_np_r.size == nucleus_num
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np.testing.assert_array_almost_equal(charges_np_r, np.array(nucleus_charge), decimal=8)
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||||
if self.test_file.isOpen:
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self.test_file.close()
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||||
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def test_read_array_2D(self):
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|
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@ -250,6 +292,8 @@ class TestIO:
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assert coords_np.dtype is np.dtype(np.float64)
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assert coords_np.size == nucleus_num * 3
|
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np.testing.assert_array_almost_equal(coords_np, np.array(nucleus_coord).reshape(nucleus_num,3), decimal=8)
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if self.test_file.isOpen:
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self.test_file.close()
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||||
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||||
def test_read_errors(self):
|
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|
|
@ -258,6 +302,8 @@ class TestIO:
|
|||
# unsafe call to read_safe should fail with error message corresponding to TREXIO_UNSAFE_ARRAY_DIM
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||||
with pytest.raises(trexio.Error):
|
||||
_ = trexio.read_nucleus_charge(self.test_file, dim=nucleus_num/2)
|
||||
if self.test_file.isOpen:
|
||||
self.test_file.close()
|
||||
|
||||
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def test_read_integers(self):
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|
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@ -276,7 +322,8 @@ class TestIO:
|
|||
assert indices_np_64.dtype is np.dtype(np.int64)
|
||||
assert indices_np_64.size == basis_shell_num
|
||||
assert (indices_np_64 == np.array(nucleus_index)).all()
|
||||
|
||||
if self.test_file.isOpen:
|
||||
self.test_file.close()
|
||||
|
||||
def test_sparse_read(self):
|
||||
"""Read a sparse array."""
|
||||
|
|
@ -300,7 +347,8 @@ class TestIO:
|
|||
assert read_buf_size == (num_integrals - buf_size)
|
||||
assert indices_sparse_np[0][0] == offset_file * 4
|
||||
assert indices_sparse_np[read_buf_size-1][3] == (offset_file + read_buf_size) * 4 - 1
|
||||
|
||||
if self.test_file.isOpen:
|
||||
self.test_file.close()
|
||||
|
||||
def test_determinant_read(self):
|
||||
"""Read the CI determinants."""
|
||||
|
|
@ -320,7 +368,8 @@ class TestIO:
|
|||
#print(f'First complete read of determinant coefficients: {read_buf_size}')
|
||||
assert not eof
|
||||
assert read_buf_size == buf_size
|
||||
|
||||
if self.test_file.isOpen:
|
||||
self.test_file.close()
|
||||
|
||||
def test_array_str_read(self):
|
||||
"""Read an array of strings."""
|
||||
|
|
@ -328,6 +377,8 @@ class TestIO:
|
|||
labels_r = trexio.read_nucleus_label(self.test_file)
|
||||
assert len(labels_r) == nucleus_num
|
||||
assert labels_r == nucleus_label
|
||||
if self.test_file.isOpen:
|
||||
self.test_file.close()
|
||||
|
||||
|
||||
def test_str_read(self):
|
||||
|
|
@ -335,3 +386,5 @@ class TestIO:
|
|||
self.open(mode='r')
|
||||
point_group_r = trexio.read_nucleus_point_group(self.test_file)
|
||||
assert point_group_r == point_group
|
||||
if self.test_file.isOpen:
|
||||
self.test_file.close()
|
||||
|
|
|
|||
|
|
@ -853,6 +853,14 @@ class File:
|
|||
|
||||
return self.state
|
||||
|
||||
|
||||
def flush(self):
|
||||
"""Flush the data on disk."""
|
||||
rc = pytr.trexio_flush(self.pytrexio_s)
|
||||
if rc != TREXIO_SUCCESS:
|
||||
raise Error(rc)
|
||||
|
||||
|
||||
def inquire(self):
|
||||
"""Inquire whether a TREXIO file exists."""
|
||||
self.exists = _inquire(self.filename)
|
||||
|
|
@ -1506,7 +1514,7 @@ def flush(trexio_file):
|
|||
Parameter is a ~trexio_file~ object that has been created by a call to ~open~ function.
|
||||
"""
|
||||
|
||||
rc = pytr.trexio_flush(trexio_file)
|
||||
rc = pytr.trexio_flush(trexio_file.pytrexio_s)
|
||||
if rc != TREXIO_SUCCESS:
|
||||
raise Error(rc)
|
||||
#+end_src
|
||||
|
|
@ -2139,7 +2147,7 @@ trexio_read_$group_num$_64 (trexio_t* const file, $group_num_dtype_double$* cons
|
|||
if (trexio_has_$group_num$(file) != TREXIO_SUCCESS) return TREXIO_ATTR_MISSING;
|
||||
|
||||
trexio_exit_code rc = TREXIO_GROUP_READ_ERROR;
|
||||
|
||||
|
||||
switch (file->back_end) {
|
||||
|
||||
case TREXIO_TEXT:
|
||||
|
|
@ -3370,7 +3378,7 @@ trexio_read_$group_dset$(trexio_t* const file,
|
|||
|
||||
/* Find the maximal value along all dimensions to define the compression technique in the back end */
|
||||
int64_t max_dim = unique_dims[0];
|
||||
#if (unique_rank != 1)
|
||||
#if (unique_rank != 1)
|
||||
for (uint32_t i = 1; i < unique_rank; i++) {
|
||||
if (unique_dims[i] > max_dim) max_dim = unique_dims[i];
|
||||
}
|
||||
|
|
@ -3503,7 +3511,7 @@ trexio_write_$group_dset$(trexio_t* const file,
|
|||
|
||||
/* Find the maximal value along all dimensions to define the compression technique in the back end */
|
||||
int64_t max_dim = unique_dims[0];
|
||||
#if (unique_rank != 1)
|
||||
#if (unique_rank != 1)
|
||||
for (uint32_t i = 1; i < unique_rank; i++) {
|
||||
if (unique_dims[i] > max_dim) max_dim = unique_dims[i];
|
||||
}
|
||||
|
|
|
|||
|
|
@ -1,5 +1,4 @@
|
|||
#define TEST_BACKEND_TEXT
|
||||
#define TEST_BACKEND_HDF5
|
||||
#define TREXIO_FILE_PREFIX "io_dset_float"
|
||||
#include "test_macros.h"
|
||||
#include "io_dset_float.c"
|
||||
|
||||
|
|
|
|||
|
|
@ -2,4 +2,3 @@
|
|||
#define TREXIO_FILE_PREFIX "io_dset_float"
|
||||
#include "test_macros.h"
|
||||
#include "io_dset_float.c"
|
||||
|
||||
|
|
|
|||
|
|
@ -1,4 +1,4 @@
|
|||
#define TEST_BACKEND_TEXT
|
||||
#define TEST_BACKEND_HDF5
|
||||
#define TREXIO_FILE_PREFIX "io_dset_int"
|
||||
#include "test_macros.h"
|
||||
#include "io_dset_int.c"
|
||||
|
|
|
|||
|
|
@ -2,4 +2,3 @@
|
|||
#define TREXIO_FILE_PREFIX "io_dset_int"
|
||||
#include "test_macros.h"
|
||||
#include "io_dset_int.c"
|
||||
|
||||
|
|
|
|||
|
|
@ -1,11 +1,22 @@
|
|||
#!/bin/bash
|
||||
|
||||
# We want the script to crash on the 1st error:
|
||||
set -e
|
||||
|
||||
# Check that script is executed from tools directory
|
||||
if [[ $(basename $PWD) != "tools" ]] ; then
|
||||
echo "This script should run in the tools directory"
|
||||
exit -1
|
||||
fi
|
||||
|
||||
DO_HDF5=0
|
||||
if [[ -z ${1} ]] && [[ "${1}" == "--without-hdf5" ]] ; then
|
||||
echo "Compiling Python API without the HDF5 back end."
|
||||
DO_HDF5=1
|
||||
else
|
||||
echo "Compiling Python API with the HDF5 back end."
|
||||
fi
|
||||
|
||||
TREXIO_ROOT=$(dirname "${PWD}../")
|
||||
|
||||
# First define readonly global variables.
|
||||
|
|
@ -14,9 +25,7 @@ readonly INCLUDIR=${TREXIO_ROOT}/include
|
|||
readonly TOOLS=${TREXIO_ROOT}/tools
|
||||
readonly PYDIR=${TREXIO_ROOT}/python
|
||||
readonly PYTREXIODIR=${PYDIR}/pytrexio
|
||||
|
||||
# We want the script to crash on the 1st error:
|
||||
set -e
|
||||
readonly PYDIR_TREXIO_H=${PYDIR}/src/trexio.h
|
||||
|
||||
# Create src and trexio directories in the python folder if not yet done
|
||||
mkdir -p ${PYDIR}/src
|
||||
|
|
@ -25,22 +34,16 @@ mkdir -p ${PYTREXIODIR}
|
|||
# Copy all the source code and header files in the corresponding python directory
|
||||
cp ${SRC}/pytrexio.py ${PYTREXIODIR}/pytrexio.py
|
||||
cp ${SRC}/trexio.py ${PYDIR}/trexio.py
|
||||
cp ${SRC}/*.c ${PYDIR}/src
|
||||
cp ${SRC}/*.h ${PYDIR}/src
|
||||
cp ${INCLUDIR}/trexio.h ${PYDIR}/src
|
||||
cp ${SRC}/trexio.c ${SRC}/trexio_s.h ${SRC}/trexio_private.h ${PYDIR}/src
|
||||
cp ${SRC}/trexio_text.{c,h} ${PYDIR}/src
|
||||
cp ${SRC}/pytrexio_wrap.c ${PYDIR}/src/pytrexio_wrap.c
|
||||
cp ${INCLUDIR}/trexio.h ${PYDIR}/src
|
||||
cp ${INCLUDIR}/config.h ${PYDIR}/src
|
||||
|
||||
# fix needed to define HAVE_HDF5 symbol so that Python extension is always compiled with HDF5 (without including config.h)
|
||||
# add "#define HAVE_HDF5 1" line after "#include stdint.h" using awk and sed
|
||||
export LINE_NO=$(($(awk '/stdint.h/{print NR}' ${PYDIR}/src/trexio.h) + 1))
|
||||
# sed on MacOS is different from GNU sed on Linux and requires special treatment
|
||||
if [[ "$OSTYPE" == "darwin"* ]]; then
|
||||
sed -i '' -e "$LINE_NO"'i \
|
||||
#define HAVE_HDF5 1' "${PYDIR}/src/trexio.h"
|
||||
else
|
||||
sed -i -e "$LINE_NO"'i \
|
||||
#define HAVE_HDF5 1' "${PYDIR}/src/trexio.h"
|
||||
|
||||
if [[ ${DO_HDF5} == 0 ]] ; then
|
||||
cp ${SRC}/trexio_hdf5.{c,h} ${PYDIR}/src
|
||||
fi
|
||||
|
||||
# Copy additional info
|
||||
cp ${TREXIO_ROOT}/AUTHORS ${TREXIO_ROOT}/LICENSE ${PYDIR}
|
||||
|
||||
|
|
|
|||
Loading…
Reference in New Issue