CI tests fails due to pytest-cov requiring toml instead of tomli #1392
Description
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 1Easiest solution would be to add the toml package to this line:
pygmt/.github/workflows/ci_tests_dev.yaml
Lines 88 to 89 in c341628
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 🙂