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CI tests fails due to pytest-cov requiring toml instead of tomli #1392

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weiji14 opened this issue Jul 21, 2021 · 1 comment · Fixed by #1401 or #1564
Closed

CI tests fails due to pytest-cov requiring toml instead of tomli #1392

weiji14 opened this issue Jul 21, 2021 · 1 comment · Fixed by #1401 or #1564
Labels
maintenance Boring but important stuff for the core devs
Milestone
0.4.1

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@weiji14
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weiji14 commented Jul 21, 2021

Description of the problem

A large chunk of the Python ecosystem is switching from toml to tomli, and this has been causing some breakages lately (mostly temporary as people deal with dependency hell). See nedbat/coveragepy#1180 for a comprehensive list.

Anyways, the GMT Dev Test started failing on 19 Jul 2021 (https://github.com/GenericMappingTools/pygmt/runs/3099541749?check_suite_focus=true#step:15:95), and I've tracked it down to be due to coverage releasing v6.0b1 on the same day (https://pypi.org/project/coverage/6.0b1/). coverage switched to using tomli in nedbat/coveragepy#1186, but pytest-cov 2.12.1 (released 2 Jun 2021) still seems to use toml, hence the breakage (I think).

Error message

Traceback (most recent call last):
  File "/usr/share/miniconda3/envs/pygmt/bin/pytest", line 8, in <module>
    sys.exit(console_main())
  File "/usr/share/miniconda3/envs/pygmt/lib/python3.9/site-packages/_pytest/config/__init__.py", line 185, in console_main
    code = main()
  File "/usr/share/miniconda3/envs/pygmt/lib/python3.9/site-packages/_pytest/config/__init__.py", line 143, in main
    config = _prepareconfig(args, plugins)
  File "/usr/share/miniconda3/envs/pygmt/lib/python3.9/site-packages/_pytest/config/__init__.py", line 318, in _prepareconfig
    config = pluginmanager.hook.pytest_cmdline_parse(
  File "/usr/share/miniconda3/envs/pygmt/lib/python3.9/site-packages/pluggy/hooks.py", line 281, in __call__
    return self._hookexec(self, self.get_hookimpls(), kwargs)
  File "/usr/share/miniconda3/envs/pygmt/lib/python3.9/site-packages/pluggy/manager.py", line 93, in _hookexec
    return self._inner_hookexec(hook, methods, kwargs)
  File "/usr/share/miniconda3/envs/pygmt/lib/python3.9/site-packages/pluggy/manager.py", line 84, in <lambda>
    self._inner_hookexec = lambda hook, methods, kwargs: _multicall(
  File "/usr/share/miniconda3/envs/pygmt/lib/python3.9/site-packages/pluggy/callers.py", line 130, in _multicall
    gen.send(outcome)
  File "/usr/share/miniconda3/envs/pygmt/lib/python3.9/site-packages/_pytest/helpconfig.py", line 100, in pytest_cmdline_parse
    config: Config = outcome.get_result()
  File "/usr/share/miniconda3/envs/pygmt/lib/python3.9/site-packages/pluggy/callers.py", line 80, in get_result
    raise ex[1].with_traceback(ex[2])
  File "/usr/share/miniconda3/envs/pygmt/lib/python3.9/site-packages/pluggy/callers.py", line 114, in _multicall
    res = hook_impl.function(*args)
  File "/usr/share/miniconda3/envs/pygmt/lib/python3.9/site-packages/_pytest/config/__init__.py", line 1003, in pytest_cmdline_parse
    self.parse(args)
  File "/usr/share/miniconda3/envs/pygmt/lib/python3.9/site-packages/_pytest/config/__init__.py", line 1283, in parse
    self._preparse(args, addopts=addopts)
  File "/usr/share/miniconda3/envs/pygmt/lib/python3.9/site-packages/_pytest/config/__init__.py", line 1191, in _preparse
    self.hook.pytest_load_initial_conftests(
  File "/usr/share/miniconda3/envs/pygmt/lib/python3.9/site-packages/pluggy/hooks.py", line 281, in __call__
    return self._hookexec(self, self.get_hookimpls(), kwargs)
  File "/usr/share/miniconda3/envs/pygmt/lib/python3.9/site-packages/pluggy/manager.py", line 93, in _hookexec
    return self._inner_hookexec(hook, methods, kwargs)
  File "/usr/share/miniconda3/envs/pygmt/lib/python3.9/site-packages/pluggy/manager.py", line 84, in <lambda>
    self._inner_hookexec = lambda hook, methods, kwargs: _multicall(
  File "/usr/share/miniconda3/envs/pygmt/lib/python3.9/site-packages/pluggy/callers.py", line 135, in _multicall
    return outcome.get_result()
  File "/usr/share/miniconda3/envs/pygmt/lib/python3.9/site-packages/pluggy/callers.py", line 80, in get_result
    raise ex[1].with_traceback(ex[2])
  File "/usr/share/miniconda3/envs/pygmt/lib/python3.9/site-packages/pluggy/callers.py", line 114, in _multicall
    res = hook_impl.function(*args)
  File "/usr/share/miniconda3/envs/pygmt/lib/python3.9/site-packages/pytest_cov/plugin.py", line 126, in pytest_load_initial_conftests
    plugin = CovPlugin(options, early_config.pluginmanager)
  File "/usr/share/miniconda3/envs/pygmt/lib/python3.9/site-packages/pytest_cov/plugin.py", line 177, in __init__
    self.start(engine.Central)
  File "/usr/share/miniconda3/envs/pygmt/lib/python3.9/site-packages/pytest_cov/plugin.py", line 199, in start
    self.cov_controller.start()
  File "/usr/share/miniconda3/envs/pygmt/lib/python3.9/site-packages/pytest_cov/engine.py", line 44, in ensure_topdir_wrapper
    return meth(self, *args, **kwargs)
  File "/usr/share/miniconda3/envs/pygmt/lib/python3.9/site-packages/pytest_cov/engine.py", line 209, in start
    self.cov = coverage.Coverage(source=self.cov_source,
  File "/usr/share/miniconda3/envs/pygmt/lib/python3.9/site-packages/coverage/control.py", line 196, in __init__
    self.config = read_coverage_config(
  File "/usr/share/miniconda3/envs/pygmt/lib/python3.9/site-packages/coverage/config.py", line 544, in read_coverage_config
    config_read = config.from_file(fname, our_file=our_file)
  File "/usr/share/miniconda3/envs/pygmt/lib/python3.9/site-packages/coverage/config.py", line 273, in from_file
    files_read = cp.read(filename)
  File "/usr/share/miniconda3/envs/pygmt/lib/python3.9/site-packages/coverage/tomlconfig.py", line 59, in read
    raise CoverageException(msg.format(filename))
coverage.exceptions.CoverageException: Can't read '../pyproject.toml' without TOML support. Install with [toml] extra
make: *** [Makefile:39: test] Error 1

Easiest solution would be to add the toml package to this line:

pygmt/.github/workflows/ci_tests_dev.yaml

Lines 88 to 89 in c341628

pip install --pre numpy pandas xarray netCDF4 packaging \
ipython pytest-cov pytest-mpl pytest>=6.0 sphinx-gallery

However, this could also just resolve itself in the next few days, depending on when pytest-cov creates a tagged release. So we could just wait and see if things get fixed automatically 🙂
@weiji14 weiji14 added the maintenance Boring but important stuff for the core devs label Jul 21, 2021
@weiji14 weiji14 mentioned this issue Jul 31, 2021
Merged
5 tasks
@seisman seisman added this to the 0.4.1 milestone Aug 5, 2021
weiji14 added a commit that referenced this issue Aug 5, 2021
@weiji14
Add tomli as a dependency in GMT Dev Tests (#1401)
1f9ab43 
Adding tomli to fix the GMT Dev Tests breakages reported
in #1392. This is a temporary measure until `pytest-cov`
releases a new version > 2.12.1.
@weiji14
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weiji14 commented Oct 3, 2021

Reopening because coverage=6.0 was just released on PyPI (https://pypi.org/project/coverage/6.0/) and conda-forge (https://anaconda.org/conda-forge/coverage/files?version=6.0) and breaking the tests again... See https://github.com/GenericMappingTools/pygmt/runs/3781356743?check_suite_focus=true#step:11:93

coverage.exceptions.CoverageException: Can't read '../pyproject.toml' without TOML support. Install with [toml] extra

@weiji14 weiji14 reopened this Oct 3, 2021
weiji14 added a commit that referenced this issue Oct 3, 2021
@weiji14
Add tomli as a dependency in GitHub Actions CI
543be1e 
Adding tomli to fix the GitHub Actions CI test
breakages reported in #1392. This is a temporary
measure until `pytest-cov>2.12.1` is released.
@weiji14 weiji14 mentioned this issue Oct 3, 2021
Merged
5 tasks
@weiji14 weiji14 changed the title GMT dev test fails due to pytest-cov requiring toml instead of tomli CI tests fails due to pytest-cov requiring toml instead of tomli Oct 3, 2021
weiji14 added a commit that referenced this issue Oct 3, 2021
@weiji14
Add tomli as a dependency in GitHub Actions CI (#1564)
b0335cd 
Adding tomli to fix the GitHub Actions CI test
breakages reported in #1392. This is a temporary
measure until `pytest-cov>2.12.1` is released.

* Remove coverage dependency since it is required by pytest-cov already
@seisman seisman mentioned this issue Aug 23, 2022
Merged
6 tasks
sixy6e pushed a commit to sixy6e/pygmt that referenced this issue Dec 21, 2022
@weiji14
Add tomli as a dependency in GMT Dev Tests (GenericMappingTools#1401)
25490a0 
Adding tomli to fix the GMT Dev Tests breakages reported
in GenericMappingTools#1392. This is a temporary measure until `pytest-cov`
releases a new version > 2.12.1.
sixy6e pushed a commit to sixy6e/pygmt that referenced this issue Dec 21, 2022
@weiji14
Add tomli as a dependency in GitHub Actions CI (GenericMappingTools#1564
ddc8115 
)

Adding tomli to fix the GitHub Actions CI test
breakages reported in GenericMappingTools#1392. This is a temporary
measure until `pytest-cov>2.12.1` is released.

* Remove coverage dependency since it is required by pytest-cov already
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@seisman @weiji14