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Probe-Particle / ppafm

Classical force field model for simulating atomic force microscopy images.
MIT License
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Automatic tests failed: #295

Closed ondrejkrejci closed 3 weeks ago

ondrejkrejci commented 1 month ago

It looks to me, like a bug in GitHub or lowering down the policy, since all tests have died at 4 minutes marks. I did not changed any part of the "active code", only README and a commented part. Anyway the test stopped with the following error for python3.7:

Run PPAFM_RECOMPILE=1 pytest tests examples/PTCDA_Hartree_dz2 -v --cov --cov-report json
============================= test session starts ==============================
platform linux -- Python 3.7.17, pytest-7.4.4, pluggy-1.2.0 -- /opt/hostedtoolcache/Python/3.7.17/x64/bin/python
cachedir: .pytest_cache
rootdir: /home/runner/work/ppafm/ppafm
configfile: pyproject.toml
plugins: cov-4.1.0
collecting ... collected 12 items

tests/test_afmulator.py::test_afmulator_save_load PASSED                 [  8%]
tests/test_atomicUtils.py::test_ZsToElems PASSED                         [ 16%]
tests/test_common.py::test_get_df_weight PASSED                          [ 25%]
tests/test_common.py::test_get_simple_df_weight PASSED                   [ 33%]
tests/test_common.py::test_sphere_tangent_space PASSED                   [ 41%]
tests/test_datagrid.py::test_power PASSED                                [ 50%]
tests/test_datagrid.py::test_tip_interp PASSED                           [ 58%]
tests/test_generator.py::test_GeneratorAFMtrainer PASSED                 [ 66%]
tests/test_io.py::test_xyz PASSED                                        [ 75%]
tests/test_io.py::test_parse_comment_ase PASSED                          [ 83%]
tests/test_io.py::test_load_aims PASSED                                  [ 91%]
Error: The operation was canceled.

The python 3.11 seems an interesting one:

Run PPAFM_RECOMPILE=1 pytest tests examples/PTCDA_Hartree_dz2 -v --cov --cov-report json
============================= test session starts ==============================
platform linux -- Python 3.11.9, pytest-8.3.2, pluggy-1.5.0 -- /opt/hostedtoolcache/Python/3.11.9/x64/bin/python
cachedir: .pytest_cache
rootdir: /home/runner/work/ppafm/ppafm
configfile: pyproject.toml
plugins: cov-5.0.0
collecting ... collected 12 items

tests/test_afmulator.py::test_afmulator_save_load PASSED                 [  8%]
tests/test_atomicUtils.py::test_ZsToElems PASSED                         [ 16%]
tests/test_common.py::test_get_df_weight PASSED                          [ 25%]
tests/test_common.py::test_get_simple_df_weight PASSED                   [ 33%]
tests/test_common.py::test_sphere_tangent_space PASSED                   [ 41%]
tests/test_datagrid.py::test_power PASSED                                [ 50%]
tests/test_datagrid.py::test_tip_interp PASSED                           [ 58%]
tests/test_generator.py::test_GeneratorAFMtrainer PASSED                 [ 66%]
tests/test_io.py::test_xyz PASSED                                        [ 75%]
tests/test_io.py::test_parse_comment_ase PASSED                          [ 83%]
tests/test_io.py::test_load_aims PASSED                                  [ 91%]
/home/runner/work/_temp/a2a60b1b-2468-44ab-93c7-89e20eb061a1.sh: line 1:  1839 Segmentation fault      (core dumped) PPAFM_RECOMPILE=1 pytest tests examples/PTCDA_Hartree_dz2 -v --cov --cov-report json
examples/PTCDA_Hartree_dz2/example_ptcda_hartree.py::example_ptcda_hartree 
Error: Process completed with exit code 139.

Similarly 3.12 is having problems with the PTCDA_Hartree_dz2 example:

Run PPAFM_RECOMPILE=1 pytest tests examples/PTCDA_Hartree_dz2 -v --cov --cov-report json
============================= test session starts ==============================
platform linux -- Python 3.12.4, pytest-8.3.2, pluggy-1.5.0 -- /opt/hostedtoolcache/Python/3.12.4/x64/bin/python
cachedir: .pytest_cache
rootdir: /home/runner/work/ppafm/ppafm
configfile: pyproject.toml
plugins: cov-5.0.0
collecting ... collected 12 items

tests/test_afmulator.py::test_afmulator_save_load PASSED                 [  8%]
tests/test_atomicUtils.py::test_ZsToElems PASSED                         [ 16%]
tests/test_common.py::test_get_df_weight PASSED                          [ 25%]
tests/test_common.py::test_get_simple_df_weight PASSED                   [ 33%]
tests/test_common.py::test_sphere_tangent_space PASSED                   [ 41%]
tests/test_datagrid.py::test_power PASSED                                [ 50%]
tests/test_datagrid.py::test_tip_interp PASSED                           [ 58%]
tests/test_generator.py::test_GeneratorAFMtrainer PASSED                 [ 66%]
tests/test_io.py::test_xyz PASSED                                        [ 75%]
tests/test_io.py::test_parse_comment_ase PASSED                          [ 83%]
tests/test_io.py::test_load_aims PASSED                                  [ 91%]
/opt/hostedtoolcache/Python/3.12.4/x64/lib/python3.12/site-packages/coverage/report_core.py:115: CoverageWarning: Couldn't parse '/home/runner/work/ppafm/ppafm/_opt_hostedtoolcache_Python_3_12_4_x64_lib_python3_12_site_packages_reikna_algorithms_reduce_mako': No source for code: '/home/runner/work/ppafm/ppafm/_opt_hostedtoolcache_Python_3_12_4_x64_lib_python3_12_site_packages_reikna_algorithms_reduce_mako'. (couldnt-parse)
  coverage._warn(msg, slug="couldnt-parse")
/opt/hostedtoolcache/Python/3.12.4/x64/lib/python3.12/site-packages/coverage/report_core.py:115: CoverageWarning: Couldn't parse '/home/runner/work/ppafm/ppafm/_opt_hostedtoolcache_Python_3_12_4_x64_lib_python3_12_site_packages_reikna_algorithms_scan_mako': No source for code: '/home/runner/work/ppafm/ppafm/_opt_hostedtoolcache_Python_3_12_4_x64_lib_python3_12_site_packages_reikna_algorithms_scan_mako'. (couldnt-parse)
  coverage._warn(msg, slug="couldnt-parse")
/opt/hostedtoolcache/Python/3.12.4/x64/lib/python3.12/site-packages/coverage/report_core.py:115: CoverageWarning: Couldn't parse '/home/runner/work/ppafm/ppafm/_opt_hostedtoolcache_Python_3_12_4_x64_lib_python3_12_site_packages_reikna_algorithms_transpose_mako': No source for code: '/home/runner/work/ppafm/ppafm/_opt_hostedtoolcache_Python_3_12_4_x64_lib_python3_12_site_packages_reikna_algorithms_transpose_mako'. (couldnt-parse)
  coverage._warn(msg, slug="couldnt-parse")
/opt/hostedtoolcache/Python/3.12.4/x64/lib/python3.12/site-packages/coverage/report_core.py:115: CoverageWarning: Couldn't parse '/home/runner/work/ppafm/ppafm/_opt_hostedtoolcache_Python_3_12_4_x64_lib_python3_12_site_packages_reikna_cluda_functions_mako': No source for code: '/home/runner/work/ppafm/ppafm/_opt_hostedtoolcache_Python_3_12_4_x64_lib_python3_12_site_packages_reikna_cluda_functions_mako'. (couldnt-parse)
  coverage._warn(msg, slug="couldnt-parse")
/opt/hostedtoolcache/Python/3.12.4/x64/lib/python3.12/site-packages/coverage/report_core.py:115: CoverageWarning: Couldn't parse '/home/runner/work/ppafm/ppafm/_opt_hostedtoolcache_Python_3_12_4_x64_lib_python3_12_site_packages_reikna_cluda_kernel_mako': No source for code: '/home/runner/work/ppafm/ppafm/_opt_hostedtoolcache_Python_3_12_4_x64_lib_python3_12_site_packages_reikna_cluda_kernel_mako'. (couldnt-parse)
  coverage._warn(msg, slug="couldnt-parse")
/opt/hostedtoolcache/Python/3.12.4/x64/lib/python3.12/site-packages/coverage/report_core.py:115: CoverageWarning: Couldn't parse '/home/runner/work/ppafm/ppafm/_opt_hostedtoolcache_Python_3_12_4_x64_lib_python3_12_site_packages_reikna_cluda_vsize_mako': No source for code: '/home/runner/work/ppafm/ppafm/_opt_hostedtoolcache_Python_3_12_4_x64_lib_python3_12_site_packages_reikna_cluda_vsize_mako'. (couldnt-parse)
  coverage._warn(msg, slug="couldnt-parse")
/opt/hostedtoolcache/Python/3.12.4/x64/lib/python3.12/site-packages/coverage/report_core.py:115: CoverageWarning: Couldn't parse '/home/runner/work/ppafm/ppafm/_opt_hostedtoolcache_Python_3_12_4_x64_lib_python3_12_site_packages_reikna_fft_fft_mako': No source for code: '/home/runner/work/ppafm/ppafm/_opt_hostedtoolcache_Python_3_12_4_x64_lib_python3_12_site_packages_reikna_fft_fft_mako'. (couldnt-parse)
  coverage._warn(msg, slug="couldnt-parse")
/opt/hostedtoolcache/Python/3.12.4/x64/lib/python3.12/site-packages/coverage/report_core.py:115: CoverageWarning: Couldn't parse '/home/runner/work/ppafm/ppafm/_opt_hostedtoolcache_Python_3_12_4_x64_lib_python3_12_site_packages_reikna_fft_fftshift_mako': No source for code: '/home/runner/work/ppafm/ppafm/_opt_hostedtoolcache_Python_3_12_4_x64_lib_python3_12_site_packages_reikna_fft_fftshift_mako'. (couldnt-parse)
  coverage._warn(msg, slug="couldnt-parse")
examples/PTCDA_Hartree_dz2/example_ptcda_hartree.py::example_ptcda_hartree PASSED [100%]

=============================== warnings summary ===============================
../../../../../opt/hostedtoolcache/Python/3.12.4/x64/lib/python3.12/site-packages/pytools/persistent_dict.py:59
  /opt/hostedtoolcache/Python/3.12.4/x64/lib/python3.12/site-packages/pytools/persistent_dict.py:59: UserWarning: Unable to import recommended hash 'siphash24.siphash13', falling back to 'hashlib.sha256'. Run 'python3 -m pip install siphash24' to install the recommended hash.
    warn("Unable to import recommended hash 'siphash24.siphash13', "

ppafm/cli/plot_results.py:12
  /home/runner/work/ppafm/ppafm/ppafm/cli/plot_results.py:12: MatplotlibDeprecationWarning: Auto-close()ing of figures upon backend switching is deprecated since 3.8 and will be removed in 3.10.  To suppress this warning, explicitly call plt.close('all') first.
    mpl.use("Agg")

tests/test_afmulator.py::test_afmulator_save_load
tests/test_afmulator.py::test_afmulator_save_load
tests/test_afmulator.py::test_afmulator_save_load
examples/PTCDA_Hartree_dz2/example_ptcda_hartree.py::example_ptcda_hartree
examples/PTCDA_Hartree_dz2/example_ptcda_hartree.py::example_ptcda_hartree
  /home/runner/work/ppafm/ppafm/ppafm/fieldFFT.py:232: PendingDeprecationWarning: the matrix subclass is not the recommended way to represent matrices or deal with linear algebra (see https://docs.scipy.org/doc/numpy/user/numpy-for-matlab-users.html). Please adjust your code to use regular ndarray.
    return np.matrix(Lmat)

examples/PTCDA_Hartree_dz2/example_ptcda_hartree.py::example_ptcda_hartree
  /home/runner/work/ppafm/ppafm/ppafm/fieldFFT.py:18: PendingDeprecationWarning: the matrix subclass is not the recommended way to represent matrices or deal with linear algebra (see https://docs.scipy.org/doc/numpy/user/numpy-for-matlab-users.html). Please adjust your code to use regular ndarray.
    return np.matrix(lvec[1:])

examples/PTCDA_Hartree_dz2/example_ptcda_hartree.py::example_ptcda_hartree
  /opt/hostedtoolcache/Python/3.12.4/x64/lib/python3.12/site-packages/numpy/matrixlib/defmatrix.py:70: PendingDeprecationWarning: the matrix subclass is not the recommended way to represent matrices or deal with linear algebra (see https://docs.scipy.org/doc/numpy/user/numpy-for-matlab-users.html). Please adjust your code to use regular ndarray.
    return matrix(data, dtype=dtype, copy=False)

-- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html

---------- coverage: platform linux, python 3.12.4-final-0 -----------
Coverage JSON written to file coverage.json

================== 12 passed, 9 warnings in 203.48s (0:03:23) ==================
FileRead program: reading Q-0.10K0.50/OutFz.xsf file
XYZ dimensions are 62 202 202
Reading DONE
Error: The operation was canceled.
NikoOinonen commented 1 month ago

This seems to be the same issue as #279. We already disabled one of the tests, but it seems that the other one is failing randomly as well. I think the plan was to first resolve #232 since it might resolve this issue as well.

ondrejkrejci commented 3 weeks ago

Duplicate to #279