`get_python_source` gets called on shared object file and causes SyntaxError #1160

P403n1x87 · 2021-05-06T15:05:49Z

Describe the bug

While testing with pytest-cov we started noticing some failures due to an "internal" error. Digging deeper, it looks like somehow a shared object (.so) file has made its way to get_python_source, which then fails with

INTERNALERROR> SyntaxError: invalid or missing encoding declaration

with the actual issue being

INTERNALERROR> Traceback (most recent call last):
INTERNALERROR>   File "/Users/gabriele.tornetta/.pyenv/versions/3.5.10/lib/python3.5/tokenize.py", line 392, in find_cookie
INTERNALERROR>     line_string = line.decode('utf-8')
INTERNALERROR> UnicodeDecodeError: 'utf-8' codec can't decode byte 0xcf in position 0: invalid continuation byte

Whilst it's maybe the case that the issue is more upstream (maybe .so files should not make it this far?), perhaps get_python_source should be enhanced to catch these potential cases. For instance, the extension check at

coveragepy/coverage/python.py

Lines 42 to 45 in c776c90

 if ext == ".py" and env.WINDOWS: 

 exts = [".py", ".pyw"] 

 else: 

 exts = [ext]

could be enhanced?

To Reproduce

Unfortunately, it's not clear to me how to reproduce this problem, as it has appeared all of a sudden, and I don't see any changes in the dependency versions that are currently being pulled in the CI jobs. The project that is being tested contains some Cythonized code, and this is where the shared object is coming from.

What version of Python are you using? 3.5, 3.6, 3.8
What version of coverage.py are you using? The output of coverage debug sys is helpful. 5.5
What versions of what packages do you have installed? The output of pip freeze is helpful.
What code are you running? Give us a specific commit of a specific repo that we can check out.
What commands did you run?

Expected behavior

No internal errors 🙂

The text was updated successfully, but these errors were encountered:

nedbat · 2021-05-09T14:46:43Z

Can you try a few things?

coverage debug data what does this show?
Can you try running your test suite under coverage without the pytest-cov plugin? Instead of "pytest blah blah" use "coverage run -m pytest blah blah", and then "coverage html". Does the same thing happen?
It could also be useful to run your test suite as you do now, but with these environment variables: "COVERAGE_DEBUG=trace COVERAGE_DEBUG_FILE=/tmp/debug.out"

P403n1x87 · 2021-05-10T11:44:48Z

coverage debug data

-- data ------------------------------------------------------
path: .coverage
has_arcs: False

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As described in nedbat#1160, occasionally some shared object paths make their way into the coverage report. When they get to `get_python_source` the call to `source_encoding` fails because the content of these files is binary. The change allows `get_python_source` to handle these cases gracefully while still reporting the issue. Fixes nedbat#1160.

nedbat · 2021-10-17T17:56:16Z

Is this still happening for you? The debug output seems mysterious until I realized the empty strings were because of HTML-tag-like things that Markdown is hiding.

bdice · 2021-10-17T20:23:11Z

@nedbat I just saw this error message with coverage==5.5 and pytest-cov==2.12.1, and also with coverage==6.0.2 and pytest-cov==3.0.0 on Python 3.9. This is a new failure for our package, which also uses compiled Cython modules. I added some new doctests in this PR and this error started appearing.

CI logs for coverage==5.5 and pytest-cov==2.12.1: https://app.circleci.com/pipelines/github/glotzerlab/freud/3247/workflows/dbe8c8c9-ff33-408f-8d23-f90091dfda31/jobs/12802

CI logs for coverage==6.0.2 and pytest-cov==3.0.0: https://app.circleci.com/pipelines/github/glotzerlab/freud/3248/workflows/13ccdc97-a04e-4c31-b765-db37561b7c01/jobs/12808

These commands all cause the failure:

coverage -m pytest
python -m pytest --cov
python -m pytest --cov --cov-config=setup.cfg --cov-report=xml tests/ -v

Calling pytest via python -m pytest without coverage succeeds.

I have attached the debug information requested above:

$ coverage debug data

-- data ------------------------------------------------------ path: /root/ci/freud/.coverage has_arcs: True 22 files: /root/ci/freud/freud/__init__.py: 8 lines /root/ci/freud/freud/box.cpython-39-x86_64-linux-gnu.so: 1 lines /root/ci/freud/freud/box.pyx: 208 lines [Cython.Coverage.Plugin] /root/ci/freud/freud/cluster.cpython-39-x86_64-linux-gnu.so: 1 lines /root/ci/freud/freud/cluster.pyx: 38 lines [Cython.Coverage.Plugin] /root/ci/freud/freud/data.py: 87 lines /root/ci/freud/freud/density.cpython-39-x86_64-linux-gnu.so: 1 lines /root/ci/freud/freud/density.pyx: 103 lines [Cython.Coverage.Plugin] /root/ci/freud/freud/diffraction.cpython-39-x86_64-linux-gnu.so: 4 lines /root/ci/freud/freud/diffraction.pyx: 125 lines [Cython.Coverage.Plugin] /root/ci/freud/freud/environment.cpython-39-x86_64-linux-gnu.so: 6 lines /root/ci/freud/freud/environment.pyx: 177 lines [Cython.Coverage.Plugin] /root/ci/freud/freud/errors.py: 5 lines /root/ci/freud/freud/interface.pyx: 9 lines [Cython.Coverage.Plugin] /root/ci/freud/freud/locality.pyx: 147 lines [Cython.Coverage.Plugin] /root/ci/freud/freud/msd.pyx: 47 lines [Cython.Coverage.Plugin] /root/ci/freud/freud/order.cpython-39-x86_64-linux-gnu.so: 2 lines /root/ci/freud/freud/order.pyx: 132 lines [Cython.Coverage.Plugin] /root/ci/freud/freud/parallel.pyx: 10 lines [Cython.Coverage.Plugin] /root/ci/freud/freud/plot.py: 237 lines /root/ci/freud/freud/pmft.pyx: 91 lines [Cython.Coverage.Plugin] /root/ci/freud/freud/util.pyx: 35 lines [Cython.Coverage.Plugin]

debug.out

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'' Tracing '' Tracing '' Tracing '' Tracing '/root/ci/freud/freud/environment.pyx': will be traced by Tracing '' Tracing '' Tracing '' Tracing '' Tracing '' Tracing '' Tracing '' Tracing '' Tracing '' Tracing '' Tracing '' Tracing '' Tracing '' Tracing '' Tracing '' Tracing '' Tracing '' Tracing '' Tracing '' Tracing '' Tracing '' Tracing '' Tracing '' Tracing '' Tracing '' Tracing '' Tracing '/root/ci/freud/freud/interface.pyx': will be traced by Tracing '/root/ci/freud/freud/msd.pyx': will be traced by Tracing '/root/ci/freud/freud/pmft.pyx': will be traced by Not tracing '/usr/lib/python3.9/urllib/parse.py': falls outside the --source spec Not tracing '/root/ci/freud/venv/lib/python3.9/site-packages/pytest_cov/compat.py': falls outside the --source spec Not tracing '/root/ci/freud/venv/lib/python3.9/site-packages/coverage/control.py': falls outside the --source spec Not tracing '/root/ci/freud/venv/lib/python3.9/site-packages/coverage/collector.py': falls outside the --source spec

P403n1x87 · 2021-10-17T20:37:24Z

Is this still happening for you? The debug output seems mysterious until I realized the empty strings were because of HTML-tag-like things that Markdown is hiding.

It was still happening until a few weeks ago. I should have said that we have some Cythonised code, and that's where the .so files are coming from. The issue arises only for those tests that exercise mostly Cython call paths.

nedbat · 2021-10-17T22:11:40Z

@bdice Can you give me reproduction instructions? The circleci links want me to log in. What repo should I clone, what commit should I check out, and what dependencies should I install, and what commands should I run?

nedbat · 2021-10-17T22:54:33Z

@P403n1x87 "It was still happening until a few weeks ago" Do you know what changed a few weeks ago? If it's still happening somehow, can you give me reproduction steps?

bdice · 2021-10-17T23:06:02Z

@nedbat I tried to create a reproduction locally, but I'm having some difficulty getting it to trigger locally with dependencies installed from conda. It occurred on CircleCI. I have included the tracebacks from CircleCI here. I'll try to see if I can reproduce the error in a local copy of the Docker container that our CI server uses.

CI logs for coverage==5.5 and pytest-cov==2.12.1: https://app.circleci.com/pipelines/github/glotzerlab/freud/3247/workflows/dbe8c8c9-ff33-408f-8d23-f90091dfda31/jobs/12802

============================= test session starts ==============================
platform linux -- Python 3.9.0, pytest-6.2.5, py-1.10.0, pluggy-1.0.0 -- /root/ci/freud/venv/bin/python3.9
cachedir: .pytest_cache
rootdir: /root/ci/freud, configfile: setup.cfg
plugins: cov-2.12.1
collecting ... 
collecting 48 items                                                            
collecting 55 items                                                            
collecting 184 items                                                           
collecting 305 items                                                           
collected 403 items                                                            

tests/test_box_Box.py::TestBox::test_construct PASSED                    [  0%]
tests/test_box_Box.py::TestBox::test_get_length PASSED                   [  0%]
tests/test_box_Box.py::TestBox::test_set_length PASSED                   [  0%]
tests/test_box_Box.py::TestBox::test_get_tilt_factor PASSED              [  0%]
tests/test_box_Box.py::TestBox::test_set_tilt_factor PASSED              [  1%]
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tests/test_locality_NeighborQuery.py::TestNeighborQueryLinkCell::test_query_to_nlist PASSED [ 61%]
tests/test_locality_NeighborQuery.py::TestNeighborQueryLinkCell::test_reciprocal PASSED [ 61%]
tests/test_locality_NeighborQuery.py::TestNeighborQueryLinkCell::test_reciprocal_twoset PASSED [ 62%]
tests/test_locality_NeighborQuery.py::TestNeighborQueryLinkCell::test_exclude_ii PASSED [ 62%]
tests/test_locality_NeighborQuery.py::TestNeighborQueryLinkCell::test_exhaustive_search PASSED [ 62%]
tests/test_locality_NeighborQuery.py::TestNeighborQueryLinkCell::test_exhaustive_search_asymmetric PASSED [ 62%]
tests/test_locality_NeighborQuery.py::TestNeighborQueryLinkCell::test_attributes PASSED [ 63%]
tests/test_locality_NeighborQuery.py::TestNeighborQueryLinkCell::test_no_bonds PASSED [ 63%]
tests/test_locality_NeighborQuery.py::TestNeighborQueryLinkCell::test_corner_2d PASSED [ 63%]
tests/test_locality_NeighborQuery.py::TestNeighborQueryLinkCell::test_random_system_query PASSED [ 63%]
tests/test_locality_NeighborQuery.py::TestNeighborQueryLinkCell::test_duplicate_cell_shells PASSED [ 64%]
tests/test_locality_NeighborQuery.py::TestNeighborQueryLinkCell::test_duplicate_cell_shells2 PASSED [ 64%]
tests/test_locality_NeighborQuery.py::TestNeighborQueryLinkCell::test_2d_box_3d_points PASSED [ 64%]
tests/test_locality_NeighborQuery.py::TestNeighborQueryLinkCell::test_plot_3d PASSED [ 64%]
tests/test_locality_NeighborQuery.py::TestNeighborQueryLinkCell::test_plot_2d PASSED [ 65%]
tests/test_locality_NeighborQuery.py::TestNeighborQueryLinkCell::test_chaining PASSED [ 65%]
tests/test_locality_NeighborQuery.py::TestNeighborQueryLinkCell::test_default_cell_width PASSED [ 65%]
tests/test_locality_NeighborQuery.py::TestMultipleMethods::test_alternating_points PASSED [ 65%]
tests/test_locality_PeriodicBuffer.py::TestPeriodicBuffer::test_square PASSED [ 66%]
tests/test_locality_PeriodicBuffer.py::TestPeriodicBuffer::test_cube PASSED [ 66%]
tests/test_locality_PeriodicBuffer.py::TestPeriodicBuffer::test_fcc_unit_cell PASSED [ 66%]
tests/test_locality_PeriodicBuffer.py::TestPeriodicBuffer::test_triclinic PASSED [ 66%]
tests/test_locality_PeriodicBuffer.py::TestPeriodicBuffer::test_repr PASSED [ 66%]
tests/test_locality_Voronoi.py::TestVoronoi::test_random_2d PASSED       [ 67%]
tests/test_locality_Voronoi.py::TestVoronoi::test_random_3d PASSED       [ 67%]
tests/test_locality_Voronoi.py::TestVoronoi::test_voronoi_tess_2d PASSED [ 67%]
tests/test_locality_Voronoi.py::TestVoronoi::test_voronoi_tess_3d PASSED [ 67%]
tests/test_locality_Voronoi.py::TestVoronoi::test_voronoi_neighbors_wrapped PASSED [ 68%]
tests/test_locality_Voronoi.py::TestVoronoi::test_voronoi_weights_fcc PASSED [ 68%]
tests/test_locality_Voronoi.py::TestVoronoi::test_repr PASSED            [ 68%]
tests/test_locality_Voronoi.py::TestVoronoi::test_attributes PASSED      [ 68%]
tests/test_locality_Voronoi.py::TestVoronoi::test_repr_png PASSED        [ 69%]
tests/test_msd_MSD.py::TestMSD::test_attribute_access PASSED             [ 69%]
tests/test_msd_MSD.py::TestMSD::test_MSD PASSED                          [ 69%]
tests/test_msd_MSD.py::TestMSD::test_repr PASSED                         [ 69%]
tests/test_order_Cubatic.py::TestCubatic::test_ordered PASSED            [ 70%]
tests/test_order_Cubatic.py::TestCubatic::test_disordered PASSED         [ 70%]
tests/test_order_Cubatic.py::TestCubatic::test_valid_inputs PASSED       [ 70%]
tests/test_order_Cubatic.py::TestCubatic::test_repr PASSED               [ 70%]
tests/test_order_Hexatic.py::TestHexatic::test_getK PASSED               [ 71%]
tests/test_order_Hexatic.py::TestHexatic::test_getK_pass PASSED          [ 71%]
tests/test_order_Hexatic.py::TestHexatic::test_order_size PASSED         [ 71%]
tests/test_order_Hexatic.py::TestHexatic::test_compute_random PASSED     [ 71%]
tests/test_order_Hexatic.py::TestHexatic::test_compute PASSED            [ 72%]
tests/test_order_Hexatic.py::TestHexatic::test_weighted_random PASSED    [ 72%]
tests/test_order_Hexatic.py::TestHexatic::test_weighted_square PASSED    [ 72%]
tests/test_order_Hexatic.py::TestHexatic::test_weighted_hex PASSED       [ 72%]
tests/test_order_Hexatic.py::TestHexatic::test_normalization PASSED      [ 73%]
tests/test_order_Hexatic.py::TestHexatic::test_3d_box PASSED             [ 73%]
tests/test_order_Hexatic.py::TestHexatic::test_repr PASSED               [ 73%]
tests/test_order_Hexatic.py::TestHexatic::test_repr_png PASSED           [ 73%]
tests/test_order_Nematic.py::TestNematicOrder::test_perfect PASSED       [ 74%]
tests/test_order_Nematic.py::TestNematicOrder::test_imperfect PASSED     [ 74%]
tests/test_order_Nematic.py::TestNematicOrder::test_repr PASSED          [ 74%]
tests/test_order_RotationalAutocorrelation.py::TestRotationalAutocorrelation::test_equality PASSED [ 74%]
tests/test_order_RotationalAutocorrelation.py::TestRotationalAutocorrelation::test_attributes PASSED [ 75%]
tests/test_order_RotationalAutocorrelation.py::TestRotationalAutocorrelation::test_data PASSED [ 75%]
tests/test_order_RotationalAutocorrelation.py::TestRotationalAutocorrelation::test_repr PASSED [ 75%]
tests/test_order_SolidLiquid.py::TestSolidLiquid::test_shape PASSED      [ 75%]
tests/test_order_SolidLiquid.py::TestSolidLiquid::test_nlist PASSED      [ 76%]
tests/test_order_SolidLiquid.py::TestSolidLiquid::test_identical_environments PASSED [ 76%]
tests/test_order_SolidLiquid.py::TestSolidLiquid::test_attribute_access PASSED [ 76%]
tests/test_order_SolidLiquid.py::TestSolidLiquid::test_repr PASSED       [ 76%]
tests/test_order_Steinhardt.py::TestSteinhardt::test_shape PASSED        [ 77%]
tests/test_order_Steinhardt.py::TestSteinhardt::test_qlmi[3] PASSED      [ 77%]
tests/test_order_Steinhardt.py::TestSteinhardt::test_qlmi[4] PASSED      [ 77%]
tests/test_order_Steinhardt.py::TestSteinhardt::test_qlmi[5] PASSED      [ 77%]
tests/test_order_Steinhardt.py::TestSteinhardt::test_qlmi[6] PASSED      [ 78%]
tests/test_order_Steinhardt.py::TestSteinhardt::test_qlmi[7] PASSED      [ 78%]
tests/test_order_Steinhardt.py::TestSteinhardt::test_l_axis_aligned PASSED [ 78%]
tests/test_order_Steinhardt.py::TestSteinhardt::test_identical_environments_ql PASSED [ 78%]
tests/test_order_Steinhardt.py::TestSteinhardt::test_identical_environments_ql_near PASSED [ 79%]
tests/test_order_Steinhardt.py::TestSteinhardt::test_identical_environments_wl PASSED [ 79%]
tests/test_order_Steinhardt.py::TestSteinhardt::test_identical_environments_wl_near PASSED [ 79%]
tests/test_order_Steinhardt.py::TestSteinhardt::test_weighted PASSED     [ 79%]
tests/test_order_Steinhardt.py::TestSteinhardt::test_attribute_access PASSED [ 80%]
tests/test_order_Steinhardt.py::TestSteinhardt::test_compute_twice_norm PASSED [ 80%]
tests/test_order_Steinhardt.py::TestSteinhardt::test_rotational_invariance PASSED [ 80%]
tests/test_order_Steinhardt.py::TestSteinhardt::test_repr PASSED         [ 80%]
tests/test_order_Steinhardt.py::TestSteinhardt::test_repr_png PASSED     [ 81%]
tests/test_order_Steinhardt.py::TestSteinhardt::test_no_neighbors PASSED [ 81%]
tests/test_order_Steinhardt.py::TestSteinhardt::test_multiple_l PASSED   [ 81%]
tests/test_order_Translational.py::TestTranslational::test_simple PASSED [ 81%]
tests/test_order_Translational.py::TestTranslational::test_repr PASSED   [ 82%]
tests/test_parallel.py::TestParallel::test_set PASSED                    [ 82%]
tests/test_parallel.py::TestParallel::test_NumThreads PASSED             [ 82%]
tests/test_pmft.py::TestPMFTR12::test_box PASSED                         [ 82%]
tests/test_pmft.py::TestPMFTR12::test_bins PASSED                        [ 83%]
tests/test_pmft.py::TestPMFTR12::test_attribute_access PASSED            [ 83%]
tests/test_pmft.py::TestPMFTR12::test_two_particles PASSED               [ 83%]
tests/test_pmft.py::TestPMFTR12::test_repr PASSED                        [ 83%]
tests/test_pmft.py::TestPMFTR12::test_pcf PASSED                         [ 84%]
tests/test_pmft.py::TestPMFTR12::test_2d_box_3d_points PASSED            [ 84%]
tests/test_pmft.py::TestPMFTR12::test_points_ne_query_points PASSED      [ 84%]
tests/test_pmft.py::TestPMFTXYT::test_box PASSED                         [ 84%]
tests/test_pmft.py::TestPMFTXYT::test_bins PASSED                        [ 85%]
tests/test_pmft.py::TestPMFTXYT::test_attribute_access PASSED            [ 85%]
tests/test_pmft.py::TestPMFTXYT::test_two_particles PASSED               [ 85%]
tests/test_pmft.py::TestPMFTXYT::test_repr PASSED                        [ 85%]
tests/test_pmft.py::TestPMFTXYT::test_pcf PASSED                         [ 86%]
tests/test_pmft.py::TestPMFTXYT::test_2d_box_3d_points PASSED            [ 86%]
tests/test_pmft.py::TestPMFTXYT::test_points_ne_query_points PASSED      [ 86%]
tests/test_pmft.py::TestPMFTXYT::test_nontrivial_orientations PASSED     [ 86%]
tests/test_pmft.py::TestPMFTXY::test_box PASSED                          [ 87%]
tests/test_pmft.py::TestPMFTXY::test_bins PASSED                         [ 87%]
tests/test_pmft.py::TestPMFTXY::test_attribute_access PASSED             [ 87%]
tests/test_pmft.py::TestPMFTXY::test_two_particles PASSED                [ 87%]
tests/test_pmft.py::TestPMFTXY::test_repr PASSED                         [ 88%]
tests/test_pmft.py::TestPMFTXY::test_pcf PASSED                          [ 88%]
tests/test_pmft.py::TestPMFTXY::test_2d_box_3d_points PASSED             [ 88%]
tests/test_pmft.py::TestPMFTXY::test_repr_png PASSED                     [ 88%]
tests/test_pmft.py::TestPMFTXY::test_points_ne_query_points PASSED       [ 89%]
tests/test_pmft.py::TestPMFTXY::test_query_args_nn PASSED                [ 89%]
tests/test_pmft.py::TestPMFTXY::test_orientation_with_query_points PASSED [ 89%]
tests/test_pmft.py::TestPMFTXY::test_orientation_with_fewer_query_points PASSED [ 89%]
tests/test_pmft.py::TestPMFTXYZ::test_box PASSED                         [ 90%]
tests/test_pmft.py::TestPMFTXYZ::test_bins PASSED                        [ 90%]
tests/test_pmft.py::TestPMFTXYZ::test_attribute_access PASSED            [ 90%]
tests/test_pmft.py::TestPMFTXYZ::test_repr PASSED                        [ 90%]
tests/test_pmft.py::TestPMFTXYZ::test_pcf PASSED                         [ 91%]
tests/test_pmft.py::TestPMFTXYZ::test_two_particles PASSED               [ 91%]
tests/test_pmft.py::TestPMFTXYZ::test_shift_two_particles_dead_pixel PASSED [ 91%]
tests/test_pmft.py::TestPMFTXYZ::test_query_args_nn PASSED               [ 91%]
tests/test_pmft.py::TestPMFTXYZ::test_orientation_with_query_points PASSED [ 92%]
tests/test_pmft.py::TestPMFTXYZ::test_orientation_with_fewer_query_points PASSED [ 92%]
tests/test_pmft.py::TestPMFTR12ManagedArray::test_saved_values PASSED    [ 92%]
tests/test_pmft.py::TestPMFTXYTManagedArray::test_saved_values PASSED    [ 92%]
tests/test_pmft.py::TestPMFTXYManagedArray::test_saved_values PASSED     [ 93%]
tests/test_pmft.py::TestPMFTXYZManagedArray::test_saved_values PASSED    [ 93%]
tests/test_pmft.py::TestCompare::test_XY_XYZ PASSED                      [ 93%]
tests/test_pmft.py::TestCompare::test_XY_XYT PASSED                      [ 93%]
tests/test_util.py::TestCommon::test_convert_array PASSED                [ 94%]
tests/test_util.py::TestCommon::test_convert_matrix_box PASSED           [ 94%]
tests/test_util.py::TestCommon::test_convert_tuple_box PASSED            [ 94%]
tests/test_util.py::TestCommon::test_convert_dict_box PASSED             [ 94%]
tests/test_util.py::TestCommon::test_convert_array_len_2_box PASSED      [ 95%]
tests/test_util.py::TestCommon::test_convert_array_len_3_box PASSED      [ 95%]
tests/test_util.py::TestCommon::test_convert_array_len_6_box PASSED      [ 95%]
tests/integration/test_reader_integrations.py::TestReaderIntegrations::test_mdanalysis_gsd SKIPPED [ 95%]
tests/integration/test_reader_integrations.py::TestReaderIntegrations::test_mdanalysis_dcd SKIPPED [ 96%]
tests/integration/test_reader_integrations.py::TestReaderIntegrations::test_gsd_gsd PASSED [ 96%]
tests/integration/test_reader_integrations.py::TestReaderIntegrations::test_garnett_gsd PASSED [ 96%]
tests/integration/test_reader_integrations.py::TestReaderIntegrations::test_garnett_dcd PASSED [ 96%]
tests/integration/test_reader_integrations.py::TestReaderIntegrations::test_ovito_gsd SKIPPED [ 97%]
tests/validation/test_Minkowski_Structure_Metrics.py::TestMinkowski::test_minkowski_structure_metrics[fcc] PASSED [ 97%]
tests/validation/test_Minkowski_Structure_Metrics.py::TestMinkowski::test_minkowski_structure_metrics[bcc] PASSED [ 97%]
tests/validation/test_Minkowski_Structure_Metrics.py::TestMinkowski::test_minkowski_structure_metrics[hcp] PASSED [ 97%]
tests/validation/test_Minkowski_Structure_Metrics.py::TestMinkowski::test_minkowski_structure_metrics[sc] PASSED [ 98%]
tests/validation/test_Steinhardt_Average.py::TestSteinhardtReferenceValues::test_gc_radius PASSED [ 98%]
tests/validation/test_Steinhardt_Average.py::TestSteinhardtReferenceValues::test_gc_radius_ave PASSED [ 98%]
tests/validation/test_Steinhardt_Average.py::TestSteinhardtReferenceValues::test_rvd_msm PASSED [ 98%]
tests/validation/test_Steinhardt_Average.py::TestSteinhardtReferenceValues::test_rvd_msm_ave PASSED [ 99%]
tests/validation/test_Steinhardt_Average.py::TestSteinhardtReferenceValues::test_msm_calc[q-False-False] PASSED [ 99%]
tests/validation/test_Steinhardt_Average.py::TestSteinhardtReferenceValues::test_msm_calc[w-False-True] PASSED [ 99%]
tests/validation/test_Steinhardt_Average.py::TestSteinhardtReferenceValues::test_msm_calc[avq-True-False] PASSED [ 99%]
tests/validation/test_Steinhardt_Average.py::TestSteinhardtReferenceValues::test_msm_calc[avw-True-True] PASSED [100%]
INTERNALERROR> Traceback (most recent call last):
INTERNALERROR>   File "/usr/lib/python3.9/tokenize.py", line 330, in find_cookie
INTERNALERROR>     line_string = line.decode('utf-8')
INTERNALERROR> UnicodeDecodeError: 'utf-8' codec can't decode byte 0xc5 in position 25: invalid continuation byte
INTERNALERROR> 
INTERNALERROR> During handling of the above exception, another exception occurred:
INTERNALERROR> 
INTERNALERROR> Traceback (most recent call last):
INTERNALERROR>   File "/root/ci/freud/venv/lib/python3.9/site-packages/_pytest/main.py", line 269, in wrap_session
INTERNALERROR>     session.exitstatus = doit(config, session) or 0
INTERNALERROR>   File "/root/ci/freud/venv/lib/python3.9/site-packages/_pytest/main.py", line 323, in _main
INTERNALERROR>     config.hook.pytest_runtestloop(session=session)
INTERNALERROR>   File "/root/ci/freud/venv/lib/python3.9/site-packages/pluggy/_hooks.py", line 265, in __call__
INTERNALERROR>     return self._hookexec(self.name, self.get_hookimpls(), kwargs, firstresult)
INTERNALERROR>   File "/root/ci/freud/venv/lib/python3.9/site-packages/pluggy/_manager.py", line 80, in _hookexec
INTERNALERROR>     return self._inner_hookexec(hook_name, methods, kwargs, firstresult)
INTERNALERROR>   File "/root/ci/freud/venv/lib/python3.9/site-packages/pluggy/_callers.py", line 55, in _multicall
INTERNALERROR>     gen.send(outcome)
INTERNALERROR>   File "/root/ci/freud/venv/lib/python3.9/site-packages/pytest_cov/plugin.py", line 271, in pytest_runtestloop
INTERNALERROR>     self.cov_controller.finish()
INTERNALERROR>   File "/root/ci/freud/venv/lib/python3.9/site-packages/pytest_cov/engine.py", line 44, in ensure_topdir_wrapper
INTERNALERROR>     return meth(self, *args, **kwargs)
INTERNALERROR>   File "/root/ci/freud/venv/lib/python3.9/site-packages/pytest_cov/engine.py", line 196, in summary
INTERNALERROR>     total = self.cov.xml_report(ignore_errors=True, outfile=output)
INTERNALERROR>   File "/root/ci/freud/venv/lib/python3.9/site-packages/coverage/control.py", line 994, in xml_report
INTERNALERROR>     return render_report(self.config.xml_output, XmlReporter(self), morfs)
INTERNALERROR>   File "/root/ci/freud/venv/lib/python3.9/site-packages/coverage/report.py", line 35, in render_report
INTERNALERROR>     return reporter.report(morfs, outfile=outfile)
INTERNALERROR>   File "/root/ci/freud/venv/lib/python3.9/site-packages/coverage/xmlreport.py", line 76, in report
INTERNALERROR>     for fr, analysis in get_analysis_to_report(self.coverage, morfs):
INTERNALERROR>   File "/root/ci/freud/venv/lib/python3.9/site-packages/coverage/report.py", line 70, in get_analysis_to_report
INTERNALERROR>     analysis = coverage._analyze(fr)
INTERNALERROR>   File "/root/ci/freud/venv/lib/python3.9/site-packages/coverage/control.py", line 808, in _analyze
INTERNALERROR>     return Analysis(data, it, self._file_mapper)
INTERNALERROR>   File "/root/ci/freud/venv/lib/python3.9/site-packages/coverage/results.py", line 20, in __init__
INTERNALERROR>     self.statements = self.file_reporter.lines()
INTERNALERROR>   File "/root/ci/freud/venv/lib/python3.9/site-packages/coverage/python.py", line 191, in lines
INTERNALERROR>     return self.parser.statements
INTERNALERROR>   File "/root/ci/freud/venv/lib/python3.9/site-packages/coverage/python.py", line 182, in parser
INTERNALERROR>     self._parser = PythonParser(
INTERNALERROR>   File "/root/ci/freud/venv/lib/python3.9/site-packages/coverage/parser.py", line 44, in __init__
INTERNALERROR>     self.text = get_python_source(self.filename)
INTERNALERROR>   File "/root/ci/freud/venv/lib/python3.9/site-packages/coverage/python.py", line 65, in get_python_source
INTERNALERROR>     source = source.decode(source_encoding(source), "replace")
INTERNALERROR>   File "/root/ci/freud/venv/lib/python3.9/site-packages/coverage/phystokens.py", line 261, in _source_encoding_py3
INTERNALERROR>     return tokenize.detect_encoding(readline)[0]
INTERNALERROR>   File "/usr/lib/python3.9/tokenize.py", line 371, in detect_encoding
INTERNALERROR>     encoding = find_cookie(first)
INTERNALERROR>   File "/usr/lib/python3.9/tokenize.py", line 335, in find_cookie
INTERNALERROR>     raise SyntaxError(msg)
INTERNALERROR>   File "<string>", line None
INTERNALERROR> SyntaxError: invalid or missing encoding declaration

================== 399 passed, 4 skipped in 64.15s (0:01:04) ===================

Exited with code exit status 3

CI logs for coverage==6.0.2 and pytest-cov==3.0.0: https://app.circleci.com/pipelines/github/glotzerlab/freud/3248/workflows/13ccdc97-a04e-4c31-b765-db37561b7c01/jobs/12808

============================= test session starts ==============================
platform linux -- Python 3.9.0, pytest-6.2.5, py-1.10.0, pluggy-1.0.0 -- /root/ci/freud/venv/bin/python3.9
cachedir: .pytest_cache
rootdir: /root/ci/freud, configfile: setup.cfg
plugins: cov-3.0.0
collecting ... 
collecting 48 items                                                            
collecting 81 items                                                            
collecting 184 items                                                           
collecting 305 items                                                           
collected 403 items                                                            

tests/test_box_Box.py::TestBox::test_construct PASSED                    [  0%]
tests/test_box_Box.py::TestBox::test_get_length PASSED                   [  0%]
tests/test_box_Box.py::TestBox::test_set_length PASSED                   [  0%]
tests/test_box_Box.py::TestBox::test_get_tilt_factor PASSED              [  0%]
tests/test_box_Box.py::TestBox::test_set_tilt_factor PASSED              [  1%]
tests/test_box_Box.py::TestBox::test_box_volume PASSED                   [  1%]
tests/test_box_Box.py::TestBox::test_wrap_single_particle PASSED         [  1%]
tests/test_box_Box.py::TestBox::test_wrap_multiple_particles PASSED      [  1%]
tests/test_box_Box.py::TestBox::test_wrap_multiple_images PASSED         [  2%]
tests/test_box_Box.py::TestBox::test_wrap PASSED                         [  2%]
tests/test_box_Box.py::TestBox::test_wrap_out_provided_with_input_array PASSED [  2%]
tests/test_box_Box.py::TestBox::test_wrap_out_provided_with_new_array PASSED [  2%]
tests/test_box_Box.py::TestBox::test_wrap_out_provided_with_array_with_wrong_shape PASSED [  3%]
tests/test_box_Box.py::TestBox::test_wrap_out_provided_with_array_with_wrong_dtype PASSED [  3%]
tests/test_box_Box.py::TestBox::test_wrap_out_provided_with_array_with_wrong_order PASSED [  3%]
tests/test_box_Box.py::TestBox::test_unwrap PASSED                       [  3%]
tests/test_box_Box.py::TestBox::test_unwrap_with_out PASSED              [  4%]
tests/test_box_Box.py::TestBox::test_images_3d PASSED                    [  4%]
tests/test_box_Box.py::TestBox::test_images_2d PASSED                    [  4%]
tests/test_box_Box.py::TestBox::test_center_of_mass PASSED               [  4%]
tests/test_box_Box.py::TestBox::test_center_of_mass_weighted PASSED      [  5%]
tests/test_box_Box.py::TestBox::test_center PASSED                       [  5%]
tests/test_box_Box.py::TestBox::test_center_weighted PASSED              [  5%]
tests/test_box_Box.py::TestBox::test_absolute_coordinates PASSED         [  5%]
tests/test_box_Box.py::TestBox::test_absolute_coordinates_out PASSED     [  6%]
tests/test_box_Box.py::TestBox::test_fractional_coordinates PASSED       [  6%]
tests/test_box_Box.py::TestBox::test_fractional_coordinates_out PASSED   [  6%]
tests/test_box_Box.py::TestBox::test_vectors PASSED                      [  6%]
tests/test_box_Box.py::TestBox::test_periodic PASSED                     [  7%]
tests/test_box_Box.py::TestBox::test_equal PASSED                        [  7%]
tests/test_box_Box.py::TestBox::test_repr PASSED                         [  7%]
tests/test_box_Box.py::TestBox::test_str PASSED                          [  7%]
tests/test_box_Box.py::TestBox::test_to_dict PASSED                      [  8%]
tests/test_box_Box.py::TestBox::test_from_box PASSED                     [  8%]
tests/test_box_Box.py::TestBox::test_matrix PASSED                       [  8%]
tests/test_box_Box.py::TestBox::test_set_dimensions PASSED               [  8%]
tests/test_box_Box.py::TestBox::test_2_dimensional PASSED                [  9%]
tests/test_box_Box.py::TestBox::test_cube PASSED                         [  9%]
tests/test_box_Box.py::TestBox::test_square PASSED                       [  9%]
tests/test_box_Box.py::TestBox::test_multiply PASSED                     [  9%]
tests/test_box_Box.py::TestBox::test_plot_3d PASSED                      [ 10%]
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tests/test_locality_Voronoi.py::TestVoronoi::test_attributes PASSED      [ 68%]
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tests/test_msd_MSD.py::TestMSD::test_attribute_access PASSED             [ 69%]
tests/test_msd_MSD.py::TestMSD::test_MSD PASSED                          [ 69%]
tests/test_msd_MSD.py::TestMSD::test_repr PASSED                         [ 69%]
tests/test_order_Cubatic.py::TestCubatic::test_ordered PASSED            [ 70%]
tests/test_order_Cubatic.py::TestCubatic::test_disordered PASSED         [ 70%]
tests/test_order_Cubatic.py::TestCubatic::test_valid_inputs PASSED       [ 70%]
tests/test_order_Cubatic.py::TestCubatic::test_repr PASSED               [ 70%]
tests/test_order_Hexatic.py::TestHexatic::test_getK PASSED               [ 71%]
tests/test_order_Hexatic.py::TestHexatic::test_getK_pass PASSED          [ 71%]
tests/test_order_Hexatic.py::TestHexatic::test_order_size PASSED         [ 71%]
tests/test_order_Hexatic.py::TestHexatic::test_compute_random PASSED     [ 71%]
tests/test_order_Hexatic.py::TestHexatic::test_compute PASSED            [ 72%]
tests/test_order_Hexatic.py::TestHexatic::test_weighted_random PASSED    [ 72%]
tests/test_order_Hexatic.py::TestHexatic::test_weighted_square PASSED    [ 72%]
tests/test_order_Hexatic.py::TestHexatic::test_weighted_hex PASSED       [ 72%]
tests/test_order_Hexatic.py::TestHexatic::test_normalization PASSED      [ 73%]
tests/test_order_Hexatic.py::TestHexatic::test_3d_box PASSED             [ 73%]
tests/test_order_Hexatic.py::TestHexatic::test_repr PASSED               [ 73%]
tests/test_order_Hexatic.py::TestHexatic::test_repr_png PASSED           [ 73%]
tests/test_order_Nematic.py::TestNematicOrder::test_perfect PASSED       [ 74%]
tests/test_order_Nematic.py::TestNematicOrder::test_imperfect PASSED     [ 74%]
tests/test_order_Nematic.py::TestNematicOrder::test_repr PASSED          [ 74%]
tests/test_order_RotationalAutocorrelation.py::TestRotationalAutocorrelation::test_equality PASSED [ 74%]
tests/test_order_RotationalAutocorrelation.py::TestRotationalAutocorrelation::test_attributes PASSED [ 75%]
tests/test_order_RotationalAutocorrelation.py::TestRotationalAutocorrelation::test_data PASSED [ 75%]
tests/test_order_RotationalAutocorrelation.py::TestRotationalAutocorrelation::test_repr PASSED [ 75%]
tests/test_order_SolidLiquid.py::TestSolidLiquid::test_shape PASSED      [ 75%]
tests/test_order_SolidLiquid.py::TestSolidLiquid::test_nlist PASSED      [ 76%]
tests/test_order_SolidLiquid.py::TestSolidLiquid::test_identical_environments PASSED [ 76%]
tests/test_order_SolidLiquid.py::TestSolidLiquid::test_attribute_access PASSED [ 76%]
tests/test_order_SolidLiquid.py::TestSolidLiquid::test_repr PASSED       [ 76%]
tests/test_order_Steinhardt.py::TestSteinhardt::test_shape PASSED        [ 77%]
tests/test_order_Steinhardt.py::TestSteinhardt::test_qlmi[3] PASSED      [ 77%]
tests/test_order_Steinhardt.py::TestSteinhardt::test_qlmi[4] PASSED      [ 77%]
tests/test_order_Steinhardt.py::TestSteinhardt::test_qlmi[5] PASSED      [ 77%]
tests/test_order_Steinhardt.py::TestSteinhardt::test_qlmi[6] PASSED      [ 78%]
tests/test_order_Steinhardt.py::TestSteinhardt::test_qlmi[7] PASSED      [ 78%]
tests/test_order_Steinhardt.py::TestSteinhardt::test_l_axis_aligned PASSED [ 78%]
tests/test_order_Steinhardt.py::TestSteinhardt::test_identical_environments_ql PASSED [ 78%]
tests/test_order_Steinhardt.py::TestSteinhardt::test_identical_environments_ql_near PASSED [ 79%]
tests/test_order_Steinhardt.py::TestSteinhardt::test_identical_environments_wl PASSED [ 79%]
tests/test_order_Steinhardt.py::TestSteinhardt::test_identical_environments_wl_near PASSED [ 79%]
tests/test_order_Steinhardt.py::TestSteinhardt::test_weighted PASSED     [ 79%]
tests/test_order_Steinhardt.py::TestSteinhardt::test_attribute_access PASSED [ 80%]
tests/test_order_Steinhardt.py::TestSteinhardt::test_compute_twice_norm PASSED [ 80%]
tests/test_order_Steinhardt.py::TestSteinhardt::test_rotational_invariance PASSED [ 80%]
tests/test_order_Steinhardt.py::TestSteinhardt::test_repr PASSED         [ 80%]
tests/test_order_Steinhardt.py::TestSteinhardt::test_repr_png PASSED     [ 81%]
tests/test_order_Steinhardt.py::TestSteinhardt::test_no_neighbors PASSED [ 81%]
tests/test_order_Steinhardt.py::TestSteinhardt::test_multiple_l PASSED   [ 81%]
tests/test_order_Translational.py::TestTranslational::test_simple PASSED [ 81%]
tests/test_order_Translational.py::TestTranslational::test_repr PASSED   [ 82%]
tests/test_parallel.py::TestParallel::test_set PASSED                    [ 82%]
tests/test_parallel.py::TestParallel::test_NumThreads PASSED             [ 82%]
tests/test_pmft.py::TestPMFTR12::test_box PASSED                         [ 82%]
tests/test_pmft.py::TestPMFTR12::test_bins PASSED                        [ 83%]
tests/test_pmft.py::TestPMFTR12::test_attribute_access PASSED            [ 83%]
tests/test_pmft.py::TestPMFTR12::test_two_particles PASSED               [ 83%]
tests/test_pmft.py::TestPMFTR12::test_repr PASSED                        [ 83%]
tests/test_pmft.py::TestPMFTR12::test_pcf PASSED                         [ 84%]
tests/test_pmft.py::TestPMFTR12::test_2d_box_3d_points PASSED            [ 84%]
tests/test_pmft.py::TestPMFTR12::test_points_ne_query_points PASSED      [ 84%]
tests/test_pmft.py::TestPMFTXYT::test_box PASSED                         [ 84%]
tests/test_pmft.py::TestPMFTXYT::test_bins PASSED                        [ 85%]
tests/test_pmft.py::TestPMFTXYT::test_attribute_access PASSED            [ 85%]
tests/test_pmft.py::TestPMFTXYT::test_two_particles PASSED               [ 85%]
tests/test_pmft.py::TestPMFTXYT::test_repr PASSED                        [ 85%]
tests/test_pmft.py::TestPMFTXYT::test_pcf PASSED                         [ 86%]
tests/test_pmft.py::TestPMFTXYT::test_2d_box_3d_points PASSED            [ 86%]
tests/test_pmft.py::TestPMFTXYT::test_points_ne_query_points PASSED      [ 86%]
tests/test_pmft.py::TestPMFTXYT::test_nontrivial_orientations PASSED     [ 86%]
tests/test_pmft.py::TestPMFTXY::test_box PASSED                          [ 87%]
tests/test_pmft.py::TestPMFTXY::test_bins PASSED                         [ 87%]
tests/test_pmft.py::TestPMFTXY::test_attribute_access PASSED             [ 87%]
tests/test_pmft.py::TestPMFTXY::test_two_particles PASSED                [ 87%]
tests/test_pmft.py::TestPMFTXY::test_repr PASSED                         [ 88%]
tests/test_pmft.py::TestPMFTXY::test_pcf PASSED                          [ 88%]
tests/test_pmft.py::TestPMFTXY::test_2d_box_3d_points PASSED             [ 88%]
tests/test_pmft.py::TestPMFTXY::test_repr_png PASSED                     [ 88%]
tests/test_pmft.py::TestPMFTXY::test_points_ne_query_points PASSED       [ 89%]
tests/test_pmft.py::TestPMFTXY::test_query_args_nn PASSED                [ 89%]
tests/test_pmft.py::TestPMFTXY::test_orientation_with_query_points PASSED [ 89%]
tests/test_pmft.py::TestPMFTXY::test_orientation_with_fewer_query_points PASSED [ 89%]
tests/test_pmft.py::TestPMFTXYZ::test_box PASSED                         [ 90%]
tests/test_pmft.py::TestPMFTXYZ::test_bins PASSED                        [ 90%]
tests/test_pmft.py::TestPMFTXYZ::test_attribute_access PASSED            [ 90%]
tests/test_pmft.py::TestPMFTXYZ::test_repr PASSED                        [ 90%]
tests/test_pmft.py::TestPMFTXYZ::test_pcf PASSED                         [ 91%]
tests/test_pmft.py::TestPMFTXYZ::test_two_particles PASSED               [ 91%]
tests/test_pmft.py::TestPMFTXYZ::test_shift_two_particles_dead_pixel PASSED [ 91%]
tests/test_pmft.py::TestPMFTXYZ::test_query_args_nn PASSED               [ 91%]
tests/test_pmft.py::TestPMFTXYZ::test_orientation_with_query_points PASSED [ 92%]
tests/test_pmft.py::TestPMFTXYZ::test_orientation_with_fewer_query_points PASSED [ 92%]
tests/test_pmft.py::TestPMFTR12ManagedArray::test_saved_values PASSED    [ 92%]
tests/test_pmft.py::TestPMFTXYTManagedArray::test_saved_values PASSED    [ 92%]
tests/test_pmft.py::TestPMFTXYManagedArray::test_saved_values PASSED     [ 93%]
tests/test_pmft.py::TestPMFTXYZManagedArray::test_saved_values PASSED    [ 93%]
tests/test_pmft.py::TestCompare::test_XY_XYZ PASSED                      [ 93%]
tests/test_pmft.py::TestCompare::test_XY_XYT PASSED                      [ 93%]
tests/test_util.py::TestCommon::test_convert_array PASSED                [ 94%]
tests/test_util.py::TestCommon::test_convert_matrix_box PASSED           [ 94%]
tests/test_util.py::TestCommon::test_convert_tuple_box PASSED            [ 94%]
tests/test_util.py::TestCommon::test_convert_dict_box PASSED             [ 94%]
tests/test_util.py::TestCommon::test_convert_array_len_2_box PASSED      [ 95%]
tests/test_util.py::TestCommon::test_convert_array_len_3_box PASSED      [ 95%]
tests/test_util.py::TestCommon::test_convert_array_len_6_box PASSED      [ 95%]
tests/integration/test_reader_integrations.py::TestReaderIntegrations::test_mdanalysis_gsd SKIPPED [ 95%]
tests/integration/test_reader_integrations.py::TestReaderIntegrations::test_mdanalysis_dcd SKIPPED [ 96%]
tests/integration/test_reader_integrations.py::TestReaderIntegrations::test_gsd_gsd PASSED [ 96%]
tests/integration/test_reader_integrations.py::TestReaderIntegrations::test_garnett_gsd PASSED [ 96%]
tests/integration/test_reader_integrations.py::TestReaderIntegrations::test_garnett_dcd PASSED [ 96%]
tests/integration/test_reader_integrations.py::TestReaderIntegrations::test_ovito_gsd SKIPPED [ 97%]
tests/validation/test_Minkowski_Structure_Metrics.py::TestMinkowski::test_minkowski_structure_metrics[fcc] PASSED [ 97%]
tests/validation/test_Minkowski_Structure_Metrics.py::TestMinkowski::test_minkowski_structure_metrics[bcc] PASSED [ 97%]
tests/validation/test_Minkowski_Structure_Metrics.py::TestMinkowski::test_minkowski_structure_metrics[hcp] PASSED [ 97%]
tests/validation/test_Minkowski_Structure_Metrics.py::TestMinkowski::test_minkowski_structure_metrics[sc] PASSED [ 98%]
tests/validation/test_Steinhardt_Average.py::TestSteinhardtReferenceValues::test_gc_radius PASSED [ 98%]
tests/validation/test_Steinhardt_Average.py::TestSteinhardtReferenceValues::test_gc_radius_ave PASSED [ 98%]
tests/validation/test_Steinhardt_Average.py::TestSteinhardtReferenceValues::test_rvd_msm PASSED [ 98%]
tests/validation/test_Steinhardt_Average.py::TestSteinhardtReferenceValues::test_rvd_msm_ave PASSED [ 99%]
tests/validation/test_Steinhardt_Average.py::TestSteinhardtReferenceValues::test_msm_calc[q-False-False] PASSED [ 99%]
tests/validation/test_Steinhardt_Average.py::TestSteinhardtReferenceValues::test_msm_calc[w-False-True] PASSED [ 99%]
tests/validation/test_Steinhardt_Average.py::TestSteinhardtReferenceValues::test_msm_calc[avq-True-False] PASSED [ 99%]
tests/validation/test_Steinhardt_Average.py::TestSteinhardtReferenceValues::test_msm_calc[avw-True-True] PASSED [100%]
INTERNALERROR> Traceback (most recent call last):
INTERNALERROR>   File "/usr/lib/python3.9/tokenize.py", line 330, in find_cookie
INTERNALERROR>     line_string = line.decode('utf-8')
INTERNALERROR> UnicodeDecodeError: 'utf-8' codec can't decode byte 0xc5 in position 25: invalid continuation byte
INTERNALERROR> 
INTERNALERROR> During handling of the above exception, another exception occurred:
INTERNALERROR> 
INTERNALERROR> Traceback (most recent call last):
INTERNALERROR>   File "/root/ci/freud/venv/lib/python3.9/site-packages/_pytest/main.py", line 269, in wrap_session
INTERNALERROR>     session.exitstatus = doit(config, session) or 0
INTERNALERROR>   File "/root/ci/freud/venv/lib/python3.9/site-packages/_pytest/main.py", line 323, in _main
INTERNALERROR>     config.hook.pytest_runtestloop(session=session)
INTERNALERROR>   File "/root/ci/freud/venv/lib/python3.9/site-packages/pluggy/_hooks.py", line 265, in __call__
INTERNALERROR>     return self._hookexec(self.name, self.get_hookimpls(), kwargs, firstresult)
INTERNALERROR>   File "/root/ci/freud/venv/lib/python3.9/site-packages/pluggy/_manager.py", line 80, in _hookexec
INTERNALERROR>     return self._inner_hookexec(hook_name, methods, kwargs, firstresult)
INTERNALERROR>   File "/root/ci/freud/venv/lib/python3.9/site-packages/pluggy/_callers.py", line 55, in _multicall
INTERNALERROR>     gen.send(outcome)
INTERNALERROR>   File "/root/ci/freud/venv/lib/python3.9/site-packages/pytest_cov/plugin.py", line 294, in pytest_runtestloop
INTERNALERROR>     self.cov_controller.finish()
INTERNALERROR>   File "/root/ci/freud/venv/lib/python3.9/site-packages/pytest_cov/engine.py", line 44, in ensure_topdir_wrapper
INTERNALERROR>     return meth(self, *args, **kwargs)
INTERNALERROR>   File "/root/ci/freud/venv/lib/python3.9/site-packages/pytest_cov/engine.py", line 196, in summary
INTERNALERROR>     total = self.cov.xml_report(ignore_errors=True, outfile=output)
INTERNALERROR>   File "/root/ci/freud/venv/lib/python3.9/site-packages/coverage/control.py", line 1009, in xml_report
INTERNALERROR>     return render_report(self.config.xml_output, XmlReporter(self), morfs)
INTERNALERROR>   File "/root/ci/freud/venv/lib/python3.9/site-packages/coverage/report.py", line 34, in render_report
INTERNALERROR>     return reporter.report(morfs, outfile=outfile)
INTERNALERROR>   File "/root/ci/freud/venv/lib/python3.9/site-packages/coverage/xmlreport.py", line 73, in report
INTERNALERROR>     for fr, analysis in get_analysis_to_report(self.coverage, morfs):
INTERNALERROR>   File "/root/ci/freud/venv/lib/python3.9/site-packages/coverage/report.py", line 69, in get_analysis_to_report
INTERNALERROR>     analysis = coverage._analyze(fr)
INTERNALERROR>   File "/root/ci/freud/venv/lib/python3.9/site-packages/coverage/control.py", line 822, in _analyze
INTERNALERROR>     return Analysis(data, self.config.precision, it, self._file_mapper)
INTERNALERROR>   File "/root/ci/freud/venv/lib/python3.9/site-packages/coverage/results.py", line 20, in __init__
INTERNALERROR>     self.statements = self.file_reporter.lines()
INTERNALERROR>   File "/root/ci/freud/venv/lib/python3.9/site-packages/coverage/python.py", line 191, in lines
INTERNALERROR>     return self.parser.statements
INTERNALERROR>   File "/root/ci/freud/venv/lib/python3.9/site-packages/coverage/python.py", line 182, in parser
INTERNALERROR>     self._parser = PythonParser(
INTERNALERROR>   File "/root/ci/freud/venv/lib/python3.9/site-packages/coverage/parser.py", line 42, in __init__
INTERNALERROR>     self.text = get_python_source(self.filename)
INTERNALERROR>   File "/root/ci/freud/venv/lib/python3.9/site-packages/coverage/python.py", line 66, in get_python_source
INTERNALERROR>     source = source.decode(source_encoding(source), "replace")
INTERNALERROR>   File "/root/ci/freud/venv/lib/python3.9/site-packages/coverage/phystokens.py", line 195, in source_encoding
INTERNALERROR>     return tokenize.detect_encoding(readline)[0]
INTERNALERROR>   File "/usr/lib/python3.9/tokenize.py", line 371, in detect_encoding
INTERNALERROR>     encoding = find_cookie(first)
INTERNALERROR>   File "/usr/lib/python3.9/tokenize.py", line 335, in find_cookie
INTERNALERROR>     raise SyntaxError(msg)
INTERNALERROR>   File "<string>", line None
INTERNALERROR> SyntaxError: invalid or missing encoding declaration

================== 399 passed, 4 skipped in 62.00s (0:01:01) ===================

Exited with code exit status 3

bdice · 2021-10-17T23:40:56Z

@nedbat I recreated the exact same environment in a local Docker container, to the best of my ability, but everything appears to work as desired. However, I was able to SSH into the CircleCI server and reproduce the error repeatedly. Is there a particular test you'd suggest for me to try on the CI server to attempt to further triage or resolve this issue? In the meantime I'll look into the source of coverage and PR #1164 to see if I can learn more.

nedbat · 2021-10-18T01:44:22Z

@bdice: two things to try: first, can you reproduce the problem without pytest-cov? coverage run and coverage xml are the two commands you'd need to use. Second, can you set COVERAGE_DEBUG=trace in the environment? That will produce some more diagnostic output. Is it possible to get the .coverage data from from the test run? Thanks!

nedbat · 2021-10-18T01:47:00Z

It does seem like Cython is involved in this problem. @P403n1x87 Do you use the Cython.Coverage coverage.py plugin?

bdice · 2021-10-18T02:52:56Z

coverage run -m pytest does not show an error. python -m pytest --cov does show an error. However, I reported above that the coverage run -m pytest command did generate an error, so I'm unsure if I misread the output last time or if the error has gone away as mysteriously as it began. edit: I can generate the error with or without pytest-cov. I was incorrectly calling coverage run before and not passing in the setup.cfg configuration.

I have examined the traceback a little more. Let me break down the last few pieces:

INTERNALERROR>   File "/root/ci/freud/venv/lib/python3.9/site-packages/coverage/python.py", line 182, in parser
INTERNALERROR>     self._parser = PythonParser(
INTERNALERROR>   File "/root/ci/freud/venv/lib/python3.9/site-packages/coverage/parser.py", line 42, in __init__
INTERNALERROR>     self.text = get_python_source(self.filename)
INTERNALERROR>   File "/root/ci/freud/venv/lib/python3.9/site-packages/coverage/python.py", line 66, in get_python_source
INTERNALERROR>     source = source.decode(source_encoding(source), "replace")
INTERNALERROR>   File "/root/ci/freud/venv/lib/python3.9/site-packages/coverage/phystokens.py", line 195, in source_encoding
INTERNALERROR>     return tokenize.detect_encoding(readline)[0]
INTERNALERROR>   File "/usr/lib/python3.9/tokenize.py", line 371, in detect_encoding
INTERNALERROR>     encoding = find_cookie(first)
INTERNALERROR>   File "/usr/lib/python3.9/tokenize.py", line 335, in find_cookie
INTERNALERROR>     raise SyntaxError(msg)
INTERNALERROR>   File "<string>", line None
INTERNALERROR> SyntaxError: invalid or missing encoding declaration

On coverage/parser.py", line 42, in __init__: self.text = get_python_source(self.filename), I see that self.filename is pointing to a Cython library, /root/ci/freud/freud/box.cpython-39-x86_64-linux-gnu.so.

I see it's passing the first "line" of this library file here: coverage/phystokens.py", line 195, in source_encoding: return tokenize.detect_encoding(readline)[0]. The tokenize library is then trying and failing to determine the encoding of the first "line" of the shared library (embedded below). This string has some bytes that aren't valid UTF-8, causing the failure.

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I went up a few frames in the backtrace and found the list of file_reporters in report.py contained my .so file:

[<CythonModuleReporter filename='/root/ci/freud/freud/density.pyx'>, <CythonModuleReporter filename='/root/ci/freud/freud/pmft.pyx'>, <CythonModuleReporter filename='/root/ci/freud/freud/parallel.pyx'>, <CythonModuleReporter filename='/root/ci/freud/freud/box.pyx'>, <PythonFileReporter '/root/ci/freud/freud/data.py'>, <CythonModuleReporter filename='/root/ci/freud/freud/locality.pyx'>, <PythonFileReporter '/root/ci/freud/freud/__init__.py'>, <PythonFileReporter '/root/ci/freud/freud/box.cpython-39-x86_64-linux-gnu.so'>, <CythonModuleReporter filename='/root/ci/freud/freud/order.pyx'>, <PythonFileReporter '/root/ci/freud/freud/plot.py'>, <PythonFileReporter '/root/ci/freud/freud/errors.py'>, <CythonModuleReporter filename='/root/ci/freud/freud/util.pyx'>]

I also see that coverage.config.plugins is set to ['Cython.Coverage'].

It seems that the solution to this might be to ensure that *.so and other binary files are not parsed for source coverage? At this point I'm still unsure if it's coverage or pytest-cov or the Cython plugin that need to be changed.

It's possible that this issue arises ONLY when the first "line" of the built *.so library contains an invalid byte for UTF-8... that could be why it's so hard to reproduce.

bdice · 2021-10-18T03:10:00Z

this issue arises ONLY when the first "line" of the built *.so library contains an invalid byte for UTF-8... that could be why it's so hard to reproduce.

I did some more investigation and I'm almost certain this is why reproducing the issue is very difficult. It's dependent on so many factors that affect compilation and whether an invalid UTF-8 byte occurs before the first character interpreted as a line break.

bdice · 2021-10-18T04:00:27Z

coverage.zip
Attached is the .coverage SQLite database showing this error. It embeds coverage information for the .so file. That file shows two matching records in the arc table, from line -1 to line 1 and from line 1 to line -1.

Also, I was able to make it fail with only coverage run -m pytest -k box and coverage xml. My previous issue with replicating the error was because I didn't correctly pass my setup.cfg file to coverage. I don't think this issue is caused by pytest-cov.

P403n1x87 · 2021-10-18T09:33:41Z

@nedbat these steps should do

git clone --depth=1 https://github.com/datadog/dd-trace-py
cd dd-trace-py
# Linux
sed -i "s/profiling.run pytest --no-cov/profiling.run pytest/g" tox.ini
# OSX
# sed -i "" "s/profiling.run pytest --no-cov/profiling.run pytest/g" tox.ini
pip install tox
tox -e py37-profile-minreqs-gevent

You can change py37 with any other Python version that is supported (3.5-3.10) if needed

nedbat · 2021-10-18T11:34:57Z

@P403n1x87 Thanks, this reproduces it. I'll see what I can figure out (I'm a Cython newb!)

nedbat · 2021-10-18T11:37:26Z

BTW, this is a faster command to reproduce it, since we don't need all of the tests in your impressively extensive test suite:

.tox/py37-profile-minreqs-gevent/bin/python -m tests.profiling.run pytest --capture=no --verbose --benchmark-disable -k q tests/profiling

P403n1x87 · 2021-10-18T12:00:25Z

Ah, sorry for that. I haven't tried with a small subset of the tests as we normally see the results from the CI report.

nedbat · 2021-10-19T02:03:50Z

I have a fix for this in commit afe6cf3.

The problem happened with Cython files containing other generated code (@P403n1x87 had attrs, @bdice had doctests).

Thanks for the bug! :)

bdice · 2021-10-19T02:06:43Z

@nedbat Amazing! I really appreciate your insight and support on this, I wouldn’t have thought of that root cause. 😊

nedbat · 2021-10-30T11:47:26Z

This is now released as part of coverage 6.1.

Version 6.4.4 — 2022-08-16 -------------------------- - Wheels are now provided for Python 3.11. .. _changes_6-4-3: Version 6.4.3 — 2022-08-06 -------------------------- - Fix a failure when combining data files if the file names contained glob-like patterns (`pull 1405`_). Thanks, Michael Krebs and Benjamin Schubert. - Fix a messaging failure when combining Windows data files on a different drive than the current directory. (`pull 1430`_, fixing `issue 1428`_). Thanks, Lorenzo Micò. - Fix path calculations when running in the root directory, as you might do in a Docker container: `pull 1403`_, thanks Arthur Rio. - Filtering in the HTML report wouldn't work when reloading the index page. This is now fixed (`pull 1413`_). Thanks, Marc Legendre. - Fix a problem with Cython code measurement (`pull 1347`_, fixing `issue 972`_). Thanks, Matus Valo. .. _issue 972: nedbat/coveragepy#972 .. _pull 1347: nedbat/coveragepy#1347 .. _pull 1403: nedbat/coveragepy#1403 .. _pull 1405: nedbat/coveragepy#1405 .. _pull 1413: nedbat/coveragepy#1413 .. _issue 1428: nedbat/coveragepy#1428 .. _pull 1430: nedbat/coveragepy#1430 .. _changes_6-4-2: Version 6.4.2 — 2022-07-12 -------------------------- - Updated for a small change in Python 3.11.0 beta 4: modules now start with a line with line number 0, which is ignored. This line cannnot be executed, so coverage totals were thrown off. This line is now ignored by coverage.py, but this also means that truly empty modules (like ``__init__.py``) have no lines in them, rather than one phantom line. Fixes `issue 1419`_. - Internal debugging data added to sys.modules is now an actual module, to avoid confusing code that examines everything in sys.modules. Thanks, Yilei Yang (`pull 1399`_). .. _pull 1399: nedbat/coveragepy#1399 .. _issue 1419: nedbat/coveragepy#1419 .. _changes_6-4-1: Version 6.4.1 — 2022-06-02 -------------------------- - Greatly improved performance on PyPy, and other environments that need the pure Python trace function. Thanks, Carl Friedrich Bolz-Tereick (`pull 1381`_ and `pull 1388`_). Slightly improved performance when using the C trace function, as most environments do. Closes `issue 1339`_. - The conditions for using tomllib from the standard library have been made more precise, so that 3.11 alphas will continue to work. Closes `issue 1390`_. .. _issue 1339: nedbat/coveragepy#1339 .. _pull 1381: nedbat/coveragepy#1381 .. _pull 1388: nedbat/coveragepy#1388 .. _issue 1390: nedbat/coveragepy#1390 .. _changes_64: Version 6.4 — 2022-05-22 ------------------------ - A new setting, :ref:`config_run_sigterm`, controls whether a SIGTERM signal handler is used. In 6.3, the signal handler was always installed, to capture data at unusual process ends. Unfortunately, this introduced other problems (see `issue 1310`_). Now the signal handler is only used if you opt-in by setting ``[run] sigterm = true``. - Small changes to the HTML report: - Added links to next and previous file, and more keyboard shortcuts: ``[`` and ``]`` for next file and previous file; ``u`` for up to the index; and ``?`` to open/close the help panel. Thanks, `J. M. F. Tsang <pull 1364_>`_. - The timestamp and version are displayed at the top of the report. Thanks, `Ammar Askar <pull 1354_>`_. Closes `issue 1351`_. - A new debug option ``debug=sqldata`` adds more detail to ``debug=sql``, logging all the data being written to the database. - Previously, running ``coverage report`` (or any of the reporting commands) in an empty directory would create a .coverage data file. Now they do not, fixing `issue 1328`_. - On Python 3.11, the ``[toml]`` extra no longer installs tomli, instead using tomllib from the standard library. Thanks `Shantanu <pull 1359_>`_. - In-memory CoverageData objects now properly update(), closing `issue 1323`_. .. _issue 1310: nedbat/coveragepy#1310 .. _issue 1323: nedbat/coveragepy#1323 .. _issue 1328: nedbat/coveragepy#1328 .. _issue 1351: nedbat/coveragepy#1351 .. _pull 1354: nedbat/coveragepy#1354 .. _pull 1359: nedbat/coveragepy#1359 .. _pull 1364: nedbat/coveragepy#1364 .. _changes_633: Version 6.3.3 — 2022-05-12 -------------------------- - Fix: Coverage.py now builds successfully on CPython 3.11 (3.11.0b1) again. Closes `issue 1367`_. Some results for generators may have changed. .. _issue 1367: nedbat/coveragepy#1367 .. _changes_632: Version 6.3.2 — 2022-02-20 -------------------------- - Fix: adapt to pypy3.9's decorator tracing behavior. It now traces function decorators like CPython 3.8: both the @-line and the def-line are traced. Fixes `issue 1326`_. - Debug: added ``pybehave`` to the list of :ref:`coverage debug <cmd_debug>` and :ref:`cmd_run_debug` options. - Fix: show an intelligible error message if ``--concurrency=multiprocessing`` is used without a configuration file. Closes `issue 1320`_. .. _issue 1320: nedbat/coveragepy#1320 .. _issue 1326: nedbat/coveragepy#1326 .. _changes_631: Version 6.3.1 — 2022-02-01 -------------------------- - Fix: deadlocks could occur when terminating processes. Some of these deadlocks (described in `issue 1310`_) are now fixed. - Fix: a signal handler was being set from multiple threads, causing an error: "ValueError: signal only works in main thread". This is now fixed, closing `issue 1312`_. - Fix: ``--precision`` on the command-line was being ignored while considering ``--fail-under``. This is now fixed, thanks to `Marcelo Trylesinski <pull 1317_>`_. - Fix: releases no longer provide 3.11.0-alpha wheels. Coverage.py uses CPython internal fields which are moving during the alpha phase. Fixes `issue 1316`_. .. _issue 1310: nedbat/coveragepy#1310 .. _issue 1312: nedbat/coveragepy#1312 .. _issue 1316: nedbat/coveragepy#1316 .. _pull 1317: nedbat/coveragepy#1317 .. _changes_63: Version 6.3 — 2022-01-25 ------------------------ - Feature: Added the ``lcov`` command to generate reports in LCOV format. Thanks, `Bradley Burns <pull 1289_>`_. Closes issues `587 <issue 587_>`_ and `626 <issue 626_>`_. - Feature: the coverage data file can now be specified on the command line with the ``--data-file`` option in any command that reads or writes data. This is in addition to the existing ``COVERAGE_FILE`` environment variable. Closes `issue 624`_. Thanks, `Nikita Bloshchanevich <pull 1304_>`_. - Feature: coverage measurement data will now be written when a SIGTERM signal is received by the process. This includes :meth:`Process.terminate <python:multiprocessing.Process.terminate>`, and other ways to terminate a process. Currently this is only on Linux and Mac; Windows is not supported. Fixes `issue 1307`_. - Dropped support for Python 3.6, which reached end-of-life on 2021-12-23. - Updated Python 3.11 support to 3.11.0a4, fixing `issue 1294`_. - Fix: the coverage data file is now created in a more robust way, to avoid problems when multiple processes are trying to write data at once. Fixes issues `1303 <issue 1303_>`_ and `883 <issue 883_>`_. - Fix: a .gitignore file will only be written into the HTML report output directory if the directory is empty. This should prevent certain unfortunate accidents of writing the file where it is not wanted. - Releases now have MacOS arm64 wheels for Apple Silicon, fixing `issue 1288`_. .. _issue 587: nedbat/coveragepy#587 .. _issue 624: nedbat/coveragepy#624 .. _issue 626: nedbat/coveragepy#626 .. _issue 883: nedbat/coveragepy#883 .. _issue 1288: nedbat/coveragepy#1288 .. _issue 1294: nedbat/coveragepy#1294 .. _issue 1303: nedbat/coveragepy#1303 .. _issue 1307: nedbat/coveragepy#1307 .. _pull 1289: nedbat/coveragepy#1289 .. _pull 1304: nedbat/coveragepy#1304 .. _changes_62: Version 6.2 — 2021-11-26 ------------------------ - Feature: Now the ``--concurrency`` setting can now have a list of values, so that threads and another lightweight threading package can be measured together, such as ``--concurrency=gevent,thread``. Closes `issue 1012`_ and `issue 1082`_. - Fix: A module specified as the ``source`` setting is imported during startup, before the user program imports it. This could cause problems if the rest of the program isn't ready yet. For example, `issue 1203`_ describes a Django setting that is accessed before settings have been configured. Now the early import is wrapped in a try/except so errors then don't stop execution. - Fix: A colon in a decorator expression would cause an exclusion to end too early, preventing the exclusion of the decorated function. This is now fixed. - Fix: The HTML report now will not overwrite a .gitignore file that already exists in the HTML output directory (follow-on for `issue 1244`_). - API: The exceptions raised by Coverage.py have been specialized, to provide finer-grained catching of exceptions by third-party code. - API: Using ``suffix=False`` when constructing a Coverage object with multiprocessing wouldn't suppress the data file suffix (`issue 989`_). This is now fixed. - Debug: The ``coverage debug data`` command will now sniff out combinable data files, and report on all of them. - Debug: The ``coverage debug`` command used to accept a number of topics at a time, and show all of them, though this was never documented. This no longer works, to allow for command-line options in the future. .. _issue 989: nedbat/coveragepy#989 .. _issue 1012: nedbat/coveragepy#1012 .. _issue 1082: nedbat/coveragepy#1082 .. _issue 1203: nedbat/coveragepy#1203 .. _changes_612: Version 6.1.2 — 2021-11-10 -------------------------- - Python 3.11 is supported (tested with 3.11.0a2). One still-open issue has to do with `exits through with-statements <issue 1270_>`_. - Fix: When remapping file paths through the ``[paths]`` setting while combining, the ``[run] relative_files`` setting was ignored, resulting in absolute paths for remapped file names (`issue 1147`_). This is now fixed. - Fix: Complex conditionals over excluded lines could have incorrectly reported a missing branch (`issue 1271`_). This is now fixed. - Fix: More exceptions are now handled when trying to parse source files for reporting. Problems that used to terminate coverage.py can now be handled with ``[report] ignore_errors``. This helps with plugins failing to read files (`django_coverage_plugin issue 78`_). - Fix: Removed another vestige of jQuery from the source tarball (`issue 840`_). - Fix: Added a default value for a new-to-6.x argument of an internal class. This unsupported class is being used by coveralls (`issue 1273`_). Although I'd rather not "fix" unsupported interfaces, it's actually nicer with a default value. .. _django_coverage_plugin issue 78: nedbat/django_coverage_plugin#78 .. _issue 1147: nedbat/coveragepy#1147 .. _issue 1270: nedbat/coveragepy#1270 .. _issue 1271: nedbat/coveragepy#1271 .. _issue 1273: nedbat/coveragepy#1273 .. _changes_611: Version 6.1.1 — 2021-10-31 -------------------------- - Fix: The sticky header on the HTML report didn't work unless you had branch coverage enabled. This is now fixed: the sticky header works for everyone. (Do people still use coverage without branch measurement!? j/k) - Fix: When using explicitly declared namespace packages, the "already imported a file that will be measured" warning would be issued (`issue 888`_). This is now fixed. .. _issue 888: nedbat/coveragepy#888 .. _changes_61: Version 6.1 — 2021-10-30 ------------------------ - Deprecated: The ``annotate`` command and the ``Coverage.annotate`` function will be removed in a future version, unless people let me know that they are using it. Instead, the ``html`` command gives better-looking (and more accurate) output, and the ``report -m`` command will tell you line numbers of missing lines. Please get in touch if you have a reason to use ``annotate`` over those better options: [email protected]. - Feature: Coverage now sets an environment variable, ``COVERAGE_RUN`` when running your code with the ``coverage run`` command. The value is not important, and may change in the future. Closes `issue 553`_. - Feature: The HTML report pages for Python source files now have a sticky header so the file name and controls are always visible. - Feature: The ``xml`` and ``json`` commands now describe what they wrote where. - Feature: The ``html``, ``combine``, ``xml``, and ``json`` commands all accept a ``-q/--quiet`` option to suppress the messages they write to stdout about what they are doing (`issue 1254`_). - Feature: The ``html`` command writes a ``.gitignore`` file into the HTML output directory, to prevent the report from being committed to git. If you want to commit it, you will need to delete that file. Closes `issue 1244`_. - Feature: Added support for PyPy 3.8. - Fix: More generated code is now excluded from measurement. Code such as `attrs`_ boilerplate, or doctest code, was being measured though the synthetic line numbers meant they were never reported. Once Cython was involved though, the generated .so files were parsed as Python, raising syntax errors, as reported in `issue 1160`_. This is now fixed. - Fix: When sorting human-readable names, numeric components are sorted correctly: file10.py will appear after file9.py. This applies to file names, module names, environment variables, and test contexts. - Performance: Branch coverage measurement is faster, though you might only notice on code that is executed many times, such as long-running loops. - Build: jQuery is no longer used or vendored (`issue 840`_ and `issue 1118`_). Huge thanks to Nils Kattenbeck (septatrix) for the conversion to vanilla JavaScript in `pull request 1248`_. .. _issue 553: nedbat/coveragepy#553 .. _issue 840: nedbat/coveragepy#840 .. _issue 1118: nedbat/coveragepy#1118 .. _issue 1160: nedbat/coveragepy#1160 .. _issue 1244: nedbat/coveragepy#1244 .. _pull request 1248: nedbat/coveragepy#1248 .. _issue 1254: nedbat/coveragepy#1254 .. _attrs: https://www.attrs.org/ .. _changes_602: Version 6.0.2 — 2021-10-11 -------------------------- - Namespace packages being measured weren't properly handled by the new code that ignores third-party packages. If the namespace package was installed, it was ignored as a third-party package. That problem (`issue 1231`_) is now fixed. - Packages named as "source packages" (with ``source``, or ``source_pkgs``, or pytest-cov's ``--cov``) might have been only partially measured. Their top-level statements could be marked as unexecuted, because they were imported by coverage.py before measurement began (`issue 1232`_). This is now fixed, but the package will be imported twice, once by coverage.py, then again by your test suite. This could cause problems if importing the package has side effects. - The :meth:`.CoverageData.contexts_by_lineno` method was documented to return a dict, but was returning a defaultdict. Now it returns a plain dict. It also no longer returns negative numbered keys. .. _issue 1231: nedbat/coveragepy#1231 .. _issue 1232: nedbat/coveragepy#1232 .. _changes_601: Version 6.0.1 — 2021-10-06 -------------------------- - In 6.0, the coverage.py exceptions moved from coverage.misc to coverage.exceptions. These exceptions are not part of the public supported API, CoverageException is. But a number of other third-party packages were importing the exceptions from coverage.misc, so they are now available from there again (`issue 1226`_). - Changed an internal detail of how tomli is imported, so that tomli can use coverage.py for their own test suite (`issue 1228`_). - Defend against an obscure possibility under code obfuscation, where a function can have an argument called "self", but no local named "self" (`pull request 1210`_). Thanks, Ben Carlsson. .. _pull request 1210: nedbat/coveragepy#1210 .. _issue 1226: nedbat/coveragepy#1226 .. _issue 1228: nedbat/coveragepy#1228 .. _changes_60: Version 6.0 — 2021-10-03 ------------------------ - The ``coverage html`` command now prints a message indicating where the HTML report was written. Fixes `issue 1195`_. - The ``coverage combine`` command now prints messages indicating each data file being combined. Fixes `issue 1105`_. - The HTML report now includes a sentence about skipped files due to ``skip_covered`` or ``skip_empty`` settings. Fixes `issue 1163`_. - Unrecognized options in the configuration file are no longer errors. They are now warnings, to ease the use of coverage across versions. Fixes `issue 1035`_. - Fix handling of exceptions through context managers in Python 3.10. A missing exception is no longer considered a missing branch from the with statement. Fixes `issue 1205`_. - Fix another rarer instance of "Error binding parameter 0 - probably unsupported type." (`issue 1010`_). - Creating a directory for the coverage data file now is safer against conflicts when two coverage runs happen simultaneously (`pull 1220`_). Thanks, Clément Pit-Claudel. .. _issue 1035: nedbat/coveragepy#1035 .. _issue 1105: nedbat/coveragepy#1105 .. _issue 1163: nedbat/coveragepy#1163 .. _issue 1195: nedbat/coveragepy#1195 .. _issue 1205: nedbat/coveragepy#1205 .. _pull 1220: nedbat/coveragepy#1220 .. _changes_60b1: Version 6.0b1 — 2021-07-18 -------------------------- - Dropped support for Python 2.7, PyPy 2, and Python 3.5. - Added support for the Python 3.10 ``match/case`` syntax. - Data collection is now thread-safe. There may have been rare instances of exceptions raised in multi-threaded programs. - Plugins (like the `Django coverage plugin`_) were generating "Already imported a file that will be measured" warnings about Django itself. These have been fixed, closing `issue 1150`_. - Warnings generated by coverage.py are now real Python warnings. - Using ``--fail-under=100`` with coverage near 100% could result in the self-contradictory message :code:`total of 100 is less than fail-under=100`. This bug (`issue 1168`_) is now fixed. - The ``COVERAGE_DEBUG_FILE`` environment variable now accepts ``stdout`` and ``stderr`` to write to those destinations. - TOML parsing now uses the `tomli`_ library. - Some minor changes to usually invisible details of the HTML report: - Use a modern hash algorithm when fingerprinting, for high-security environments (`issue 1189`_). When generating the HTML report, we save the hash of the data, to avoid regenerating an unchanged HTML page. We used to use MD5 to generate the hash, and now use SHA-3-256. This was never a security concern, but security scanners would notice the MD5 algorithm and raise a false alarm. - Change how report file names are generated, to avoid leading underscores (`issue 1167`_), to avoid rare file name collisions (`issue 584`_), and to avoid file names becoming too long (`issue 580`_). .. _Django coverage plugin: https://pypi.org/project/django-coverage-plugin/ .. _issue 580: nedbat/coveragepy#580 .. _issue 584: nedbat/coveragepy#584 .. _issue 1150: nedbat/coveragepy#1150 .. _issue 1167: nedbat/coveragepy#1167 .. _issue 1168: nedbat/coveragepy#1168 .. _issue 1189: nedbat/coveragepy#1189 .. _tomli: https://pypi.org/project/tomli/ .. _changes_56b1: Version 5.6b1 — 2021-04-13 -------------------------- Note: 5.6 final was never released. These changes are part of 6.0. - Third-party packages are now ignored in coverage reporting. This solves a few problems: - Coverage will no longer report about other people's code (`issue 876`_). This is true even when using ``--source=.`` with a venv in the current directory. - Coverage will no longer generate "Already imported a file that will be measured" warnings about coverage itself (`issue 905`_). - The HTML report uses j/k to move up and down among the highlighted chunks of code. They used to highlight the current chunk, but 5.0 broke that behavior. Now the highlighting is working again. - The JSON report now includes ``percent_covered_display``, a string with the total percentage, rounded to the same number of decimal places as the other reports' totals. .. _issue 876: nedbat/coveragepy#876 .. _issue 905: nedbat/coveragepy#905

P403n1x87 added the bug Something isn't working label May 6, 2021

P403n1x87 changed the title ~~Shared object file in get_python_source~~ get_python_source gets called on shared object file and causes SyntaxError May 6, 2021

brettlangdon mentioned this issue May 6, 2021

ci(coverage): disable coverage DataDog/dd-trace-py#2414

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P403n1x87 mentioned this issue May 24, 2021

fix(python): handle source decoding errors #1164

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bdice mentioned this issue Oct 17, 2021

Fix doctests to work with pytest. glotzerlab/freud#802

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nedbat added this to the Next milestone Oct 18, 2021

nedbat added a commit that referenced this issue Oct 19, 2021

fix: avoid measuring generated code. #1160

afe6cf3

nedbat added the fixed label Oct 19, 2021

nedbat closed this as completed Oct 19, 2021

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`get_python_source` gets called on shared object file and causes SyntaxError #1160

`get_python_source` gets called on shared object file and causes SyntaxError #1160

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get_python_source gets called on shared object file and causes SyntaxError #1160

get_python_source gets called on shared object file and causes SyntaxError #1160

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`get_python_source` gets called on shared object file and causes SyntaxError #1160

`get_python_source` gets called on shared object file and causes SyntaxError #1160

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