.. DO NOT EDIT. .. THIS FILE WAS AUTOMATICALLY GENERATED BY SPHINX-GALLERY. .. TO MAKE CHANGES, EDIT THE SOURCE PYTHON FILE: .. "emd_tutorials/04_utilities/emd_tutorial_04_utils_01_support.py" .. LINE NUMBERS ARE GIVEN BELOW. .. only:: html .. note:: :class: sphx-glr-download-link-note :ref:`Go to the end ` to download the full example code .. rst-class:: sphx-glr-example-title .. _sphx_glr_emd_tutorials_04_utilities_emd_tutorial_04_utils_01_support.py: Check install and run tests =========================== The ``emd.support`` submodule contains a few functions relating to the installation and testing of EMD on your system. Most users will not need to use these functions most of the time but they can be helpful for checking that EMD is properly installed. .. GENERATED FROM PYTHON SOURCE LINES 12-14 Firstly, we can use ``emd.support.get_installed_version`` to confirm which version of EMD we have installed. .. GENERATED FROM PYTHON SOURCE LINES 14-21 .. code-block:: Python # sphinx_gallery_thumbnail_path = '_static/emd_pytest_thumb.png' import emd print(emd.support.get_installed_version()) .. rst-class:: sphx-glr-script-out .. code-block:: none 0.6.2 .. GENERATED FROM PYTHON SOURCE LINES 22-25 Secondly, we can identify where the EMD files are installed on the computer by calling ``emd.support.get_install_dir``. This can be useful if you have a couple of EMD versions and want to be sure which is currently in use. .. GENERATED FROM PYTHON SOURCE LINES 25-28 .. code-block:: Python print(emd.support.get_install_dir()) .. rst-class:: sphx-glr-script-out .. code-block:: none /home/docs/checkouts/readthedocs.org/user_builds/emd/checkouts/stable/emd .. GENERATED FROM PYTHON SOURCE LINES 29-32 Finally, if you have installed EMD from source (rather than via conda or pypi) you can run the test suit directly from the support module. (Note that this will not create any output on the website.) .. GENERATED FROM PYTHON SOURCE LINES 32-34 .. code-block:: Python print(emd.support.run_tests()) .. rst-class:: sphx-glr-script-out .. code-block:: none ============================= test session starts ============================== platform linux -- Python 3.11.6, pytest-8.1.1, pluggy-1.4.0 rootdir: /home/docs/checkouts/readthedocs.org/user_builds/emd/checkouts/stable configfile: setup.cfg plugins: cov-4.1.0 collected 49 items ../../../../emd/tests/test_cycles.py ......... [ 18%] ../../../../emd/tests/test_imftools.py . [ 20%] ../../../../emd/tests/test_logger.py .... [ 28%] ../../../../emd/tests/test_sift.py ......................... [ 79%] ../../../../emd/tests/test_spectra.py ........ [ 95%] ../../../../emd/tests/test_utils.py .. [100%]/home/docs/checkouts/readthedocs.org/user_builds/emd/envs/stable/lib/python3.11/site-packages/coverage/inorout.py:519: CoverageWarning: Module emd was previously imported, but not measured (module-not-measured) self.warn(msg, slug="module-not-measured") =============================== warnings summary =============================== emd/tests/test_cycles.py::TestCyclesObject::test_cycle_object_iteration /home/docs/checkouts/readthedocs.org/user_builds/emd/checkouts/stable/emd/cycles.py:530: DeprecationWarning: `alltrue` is deprecated as of NumPy 1.25.0, and will be removed in NumPy 2.0. Please use `all` instead. ensure_equal_dims((ip, x), ('ip', 'x'), 'phase_align') emd/tests/test_cycles.py::TestCyclesObject::test_cycle_object_iteration /home/docs/checkouts/readthedocs.org/user_builds/emd/envs/stable/lib/python3.11/site-packages/scipy/interpolate/_interpolate.py:710: RuntimeWarning: divide by zero encountered in divide slope = (y_hi - y_lo) / (x_hi - x_lo)[:, None] emd/tests/test_imftools.py::TestAssessHarmonicCriteria::test_input_length emd/tests/test_imftools.py::TestAssessHarmonicCriteria::test_input_length /home/docs/checkouts/readthedocs.org/user_builds/emd/checkouts/stable/emd/imftools.py:407: DeprecationWarning: `alltrue` is deprecated as of NumPy 1.25.0, and will be removed in NumPy 2.0. Please use `all` instead. ensure_equal_dims((IP, IF, IA), ('IP', 'IF', 'IA'), 'assess_harmonic_criteria') emd/tests/test_imftools.py::TestAssessHarmonicCriteria::test_input_length emd/tests/test_imftools.py::TestAssessHarmonicCriteria::test_input_length emd/tests/test_imftools.py::TestAssessHarmonicCriteria::test_input_length emd/tests/test_imftools.py::TestAssessHarmonicCriteria::test_input_length /home/docs/checkouts/readthedocs.org/user_builds/emd/envs/stable/lib/python3.11/site-packages/dcor/_hypothesis.py:34: DeprecationWarning: HypothesisTest will cease to be iterable. warnings.warn( emd/tests/test_sift.py::TestSiftDefaults::test_ensemble_sift_default emd/tests/test_sift.py::TestSiftDefaults::test_ensemble_sift_default emd/tests/test_sift.py::TestSiftDefaults::test_ensemble_sift_default emd/tests/test_sift.py::TestSiftDefaults::test_ensemble_sift_default emd/tests/test_sift.py::TestSiftDefaults::test_ensemble_sift_default emd/tests/test_sift.py::TestSiftDefaults::test_ensemble_sift_default emd/tests/test_sift.py::TestSiftDefaults::test_ensemble_sift_default emd/tests/test_sift.py::TestSiftDefaults::test_ensemble_sift_default /home/docs/checkouts/readthedocs.org/user_builds/emd/checkouts/stable/emd/sift.py:671: DeprecationWarning: `alltrue` is deprecated as of NumPy 1.25.0, and will be removed in NumPy 2.0. Please use `all` instead. ensure_equal_dims([X, noise], ['X', 'noise'], '_sift_with_noise', dim=0) emd/tests/test_sift.py::TestIsIMF::test_is_imf_on_abreu emd/tests/test_sift.py::TestIsIMF::test_is_imf_on_abreu /home/docs/checkouts/readthedocs.org/user_builds/emd/checkouts/stable/emd/tests/test_sift.py:430: DeprecationWarning: `alltrue` is deprecated as of NumPy 1.25.0, and will be removed in NumPy 2.0. Please use `all` instead. out = is_imf(imf) emd/tests/test_sift.py::TestIsIMF::test_is_imf_on_sinusoid /home/docs/checkouts/readthedocs.org/user_builds/emd/checkouts/stable/emd/tests/test_sift.py:422: DeprecationWarning: `alltrue` is deprecated as of NumPy 1.25.0, and will be removed in NumPy 2.0. Please use `all` instead. out = is_imf(self.y) emd/tests/test_spectra.py::TestSpectra::test_hilberthuang emd/tests/test_spectra.py::TestSpectra::test_hilberthunang_1d emd/tests/test_spectra.py::TestSpectra::test_hilberthunang_1d emd/tests/test_spectra.py::TestSpectra::test_hilberthunang_1d /home/docs/checkouts/readthedocs.org/user_builds/emd/checkouts/stable/emd/spectra.py:596: DeprecationWarning: `alltrue` is deprecated as of NumPy 1.25.0, and will be removed in NumPy 2.0. Please use `all` instead. ensure_equal_dims((IF, IA), ('IF', 'IA'), 'hilberthuang') emd/tests/test_spectra.py::TestHolospectrum::test_holo /home/docs/checkouts/readthedocs.org/user_builds/emd/checkouts/stable/emd/spectra.py:747: DeprecationWarning: `alltrue` is deprecated as of NumPy 1.25.0, and will be removed in NumPy 2.0. Please use `all` instead. ensure_equal_dims((IF, IF2, IA2), ('IF', 'IF2', 'IA2'), 'holospectrum', dim=0) emd/tests/test_spectra.py::TestHolospectrum::test_holo /home/docs/checkouts/readthedocs.org/user_builds/emd/checkouts/stable/emd/spectra.py:748: DeprecationWarning: `alltrue` is deprecated as of NumPy 1.25.0, and will be removed in NumPy 2.0. Please use `all` instead. ensure_equal_dims((IF, IF2, IA2), ('IF', 'IF2', 'IA2'), 'holospectrum', dim=1) -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html ---------- coverage: platform linux, python 3.11.6-final-0 ----------- Name Stmts Miss Cover Missing -------------------------------------------------------------------------------------------------------------------------------- /home/docs/checkouts/readthedocs.org/user_builds/emd/checkouts/stable/emd/__init__.py 13 13 0% 7-39 /home/docs/checkouts/readthedocs.org/user_builds/emd/checkouts/stable/emd/_cycles_support.py 149 83 44% 5-57, 70-75, 85, 93, 96-100, 105, 113-114, 120-144, 155, 164, 173-183, 192, 198-206, 211, 215-227, 232, 237, 244, 250-256, 260, 264, 269, 273, 278, 283-296, 303-308 /home/docs/checkouts/readthedocs.org/user_builds/emd/checkouts/stable/emd/_sift_core.py 230 63 73% 5-23, 68-69, 95, 110, 134, 170, 176, 181, 185, 196-200, 207, 324, 332, 334, 337-350, 361-362, 364-365, 370, 404-406, 409-411, 416-458, 487, 498, 518, 523, 532-533, 544-545, 550 /home/docs/checkouts/readthedocs.org/user_builds/emd/checkouts/stable/emd/_version.py 1 1 0% 4 /home/docs/checkouts/readthedocs.org/user_builds/emd/checkouts/stable/emd/cycles.py 609 297 51% 5-72, 133-134, 141, 146-147, 157, 174-175, 197, 223, 252-299, 349-350, 368-378, 396, 431, 437-440, 448-483, 533, 539, 545-546, 554, 558, 573-754, 773, 779, 782, 791, 799, 812-813, 818, 823-855, 953, 976, 981, 986, 990, 995-1004, 1009, 1014-1025, 1029, 1033-1034, 1038, 1042, 1055, 1063-1072, 1085, 1091, 1093-1096, 1100-1107, 1111-1120, 1126-1181, 1201-1202, 1212-1234, 1237, 1248-1266, 1272, 1283, 1286, 1294, 1298, 1301-1302, 1311, 1313, 1318, 1322, 1333, 1342, 1347, 1352, 1358, 1361, 1374, 1389, 1400, 1414, 1420, 1422, 1424, 1426, 1428, 1432 /home/docs/checkouts/readthedocs.org/user_builds/emd/checkouts/stable/emd/imftools.py 199 82 59% 5-25, 63, 98, 112-114, 123, 147, 150, 158-159, 167, 247-351, 417, 490-550, 572, 577-579, 597-668 /home/docs/checkouts/readthedocs.org/user_builds/emd/checkouts/stable/emd/logger.py 123 69 44% 5-89, 93-140, 157, 171, 175, 177, 189, 199, 207, 213-215, 223-237, 243, 252-260, 265-269, 289-298, 301-303, 306, 308, 314, 317 /home/docs/checkouts/readthedocs.org/user_builds/emd/checkouts/stable/emd/plotting.py 221 221 0% 5-540 /home/docs/checkouts/readthedocs.org/user_builds/emd/checkouts/stable/emd/sift.py 579 201 65% 5-58, 126, 128-129, 157-172, 181, 186, 215-256, 292-374, 378-383, 390-392, 523, 582-583, 598-605, 611-619, 691-693, 758, 769, 801-803, 879, 935, 979, 1061, 1110-1112, 1240-1241, 1257, 1280, 1290-1292, 1420-1424, 1426-1427, 1433-1439, 1472-1474, 1481, 1485-1492, 1509, 1512-1514, 1522-1524, 1540, 1549-1598, 1633, 1635, 1653-1656, 1662, 1673, 1679-1680, 1684-1699, 1713-1735, 1742, 1746, 1752-1756, 1762-1763, 1769-1770, 1778-1792, 1866-1873, 1887, 1906, 1915, 1919 /home/docs/checkouts/readthedocs.org/user_builds/emd/checkouts/stable/emd/simulate.py 50 44 12% 5-96, 159-209 /home/docs/checkouts/readthedocs.org/user_builds/emd/checkouts/stable/emd/spectra.py 304 155 49% 5-44, 120-179, 200-284, 328-333, 336, 341, 373, 398-484, 620, 776-889, 939-940, 942-943, 947-948, 959-964, 969-970, 975, 1037, 1113, 1147, 1181-1183, 1187, 1195, 1226, 1234, 1257, 1260, 1266, 1271, 1274, 1278-1279 /home/docs/checkouts/readthedocs.org/user_builds/emd/checkouts/stable/emd/support.py 97 49 49% 5-34, 40-78, 83-84, 94, 125-134, 169-172, 174-177, 185, 233-236, 272-285 /home/docs/checkouts/readthedocs.org/user_builds/emd/checkouts/stable/emd/tests/__init__.py 0 0 100% /home/docs/checkouts/readthedocs.org/user_builds/emd/checkouts/stable/emd/tests/test_cycles.py 131 0 100% /home/docs/checkouts/readthedocs.org/user_builds/emd/checkouts/stable/emd/tests/test_imftools.py 21 0 100% /home/docs/checkouts/readthedocs.org/user_builds/emd/checkouts/stable/emd/tests/test_logger.py 31 2 94% 52-53 /home/docs/checkouts/readthedocs.org/user_builds/emd/checkouts/stable/emd/tests/test_sift.py 300 5 98% 134, 217-219, 223 /home/docs/checkouts/readthedocs.org/user_builds/emd/checkouts/stable/emd/tests/test_spectra.py 86 0 100% /home/docs/checkouts/readthedocs.org/user_builds/emd/checkouts/stable/emd/tests/test_utils.py 30 0 100% -------------------------------------------------------------------------------------------------------------------------------- TOTAL 3174 1285 60% ======================= 49 passed, 25 warnings in 2.23s ======================== --- Logging error --- Traceback (most recent call last): File "/home/docs/.asdf/installs/python/3.11.6/lib/python3.11/logging/__init__.py", line 1113, in emit stream.write(msg + self.terminator) ValueError: I/O operation on closed file. Call stack: File "", line 198, in _run_module_as_main File "", line 88, in _run_code File "/home/docs/checkouts/readthedocs.org/user_builds/emd/envs/stable/lib/python3.11/site-packages/sphinx/__main__.py", line 7, in raise SystemExit(main(sys.argv[1:])) File "/home/docs/checkouts/readthedocs.org/user_builds/emd/envs/stable/lib/python3.11/site-packages/sphinx/cmd/build.py", line 341, in main return build_main(argv) File "/home/docs/checkouts/readthedocs.org/user_builds/emd/envs/stable/lib/python3.11/site-packages/sphinx/cmd/build.py", line 293, in build_main app = Sphinx(args.sourcedir, args.confdir, args.outputdir, File "/home/docs/checkouts/readthedocs.org/user_builds/emd/envs/stable/lib/python3.11/site-packages/sphinx/application.py", line 272, in __init__ self._init_builder() File "/home/docs/checkouts/readthedocs.org/user_builds/emd/envs/stable/lib/python3.11/site-packages/sphinx/application.py", line 343, in _init_builder self.events.emit('builder-inited') File "/home/docs/checkouts/readthedocs.org/user_builds/emd/envs/stable/lib/python3.11/site-packages/sphinx/events.py", line 97, in emit results.append(listener.handler(self.app, *args)) File "/home/docs/checkouts/readthedocs.org/user_builds/emd/envs/stable/lib/python3.11/site-packages/sphinx_gallery/gen_gallery.py", line 632, in generate_gallery_rst ) = generate_dir_rst(src_dir, target_dir, gallery_conf, seen_backrefs) File "/home/docs/checkouts/readthedocs.org/user_builds/emd/envs/stable/lib/python3.11/site-packages/sphinx_gallery/gen_rst.py", line 531, in generate_dir_rst intro, title, (t, mem) = generate_file_rst( File "/home/docs/checkouts/readthedocs.org/user_builds/emd/envs/stable/lib/python3.11/site-packages/sphinx_gallery/gen_rst.py", line 1203, in generate_file_rst output_blocks, time_elapsed = execute_script( File "/home/docs/checkouts/readthedocs.org/user_builds/emd/envs/stable/lib/python3.11/site-packages/sphinx_gallery/gen_rst.py", line 1108, in execute_script execute_code_block( File "/home/docs/checkouts/readthedocs.org/user_builds/emd/envs/stable/lib/python3.11/site-packages/sphinx_gallery/gen_rst.py", line 970, in execute_code_block is_last_expr, mem_max = _exec_and_get_memory( File "/home/docs/checkouts/readthedocs.org/user_builds/emd/envs/stable/lib/python3.11/site-packages/sphinx_gallery/gen_rst.py", line 811, in _exec_and_get_memory mem_last, _ = gallery_conf["call_memory"]( File "/home/docs/checkouts/readthedocs.org/user_builds/emd/envs/stable/lib/python3.11/site-packages/sphinx_gallery/gen_gallery.py", line 244, in call_memory return 0.0, func() File "/home/docs/checkouts/readthedocs.org/user_builds/emd/envs/stable/lib/python3.11/site-packages/sphinx_gallery/gen_rst.py", line 722, in __call__ exec(self.code, self.fake_main.__dict__) File "/home/docs/checkouts/readthedocs.org/user_builds/emd/checkouts/stable/doc/source/tutorials/04_utilities/emd_tutorial_04_utils_01_support.py", line 33, in print(emd.support.run_tests()) File "/home/docs/checkouts/readthedocs.org/user_builds/emd/checkouts/stable/emd/support.py", line 73, in run_tests logger.info('EMD package tests passed') Message: 'EMD package tests passed' Arguments: () None .. rst-class:: sphx-glr-timing **Total running time of the script:** (0 minutes 2.659 seconds) .. _sphx_glr_download_emd_tutorials_04_utilities_emd_tutorial_04_utils_01_support.py: .. only:: html .. container:: sphx-glr-footer sphx-glr-footer-example .. container:: sphx-glr-download sphx-glr-download-jupyter :download:`Download Jupyter notebook: emd_tutorial_04_utils_01_support.ipynb ` .. container:: sphx-glr-download sphx-glr-download-python :download:`Download Python source code: emd_tutorial_04_utils_01_support.py ` .. only:: html .. rst-class:: sphx-glr-signature `Gallery generated by Sphinx-Gallery `_