Periodic dependency maintainance #78
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## main #78 +/- ##
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Coverage 89.22% 89.22%
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This commit tries to fix some flakiness of the test execution over MacOS-based instances over GitHub Actions. It appears to be an issue of the `tables` dependency. From the logs of the CI: (https://github.com/bancaditalia/black-it/actions/runs/7121188681/job/19389914846?pr=78#step:5:62) ``` Fatal Python error: Illegal instruction Current thread 0x000000011783c600 (most recent call first): File "/Users/runner/work/black-it/black-it/.tox/py310/lib/python3.10/site-packages/tables/node.py", line 246 in __init__ File "/Users/runner/work/black-it/black-it/.tox/py310/lib/python3.10/site-packages/tables/leaf.py", line 264 in __init__ File "/Users/runner/work/black-it/black-it/.tox/py310/lib/python3.10/site-packages/tables/carray.py", line 200 in __init__ File "/Users/runner/work/black-it/black-it/.tox/py310/lib/python3.10/site-packages/tables/earray.py", line 143 in __init__ File "/Users/runner/work/black-it/black-it/.tox/py310/lib/python3.10/site-packages/tables/file.py", line 1345 in create_earray File "/Users/runner/work/black-it/black-it/black_it/utils/json_pandas_checkpointing.py", line 211 in save_calibrator_state File "/Users/runner/work/black-it/black-it/tests/test_utils/test_pandas_json_checkpointing.py", line 58 in test_save_and_load_calibrator_state File "/Users/runner/work/black-it/black-it/.tox/py310/lib/python3.10/site-packages/_pytest/python.py", line 194 in pytest_pyfunc_call File "/Users/runner/work/black-it/black-it/.tox/py310/lib/python3.10/site-packages/pluggy/_callers.py", line 77 in _multicall File "/Users/runner/work/black-it/black-it/.tox/py310/lib/python3.10/site-packages/pluggy/_manager.py", line 115 in _hookexec File "/Users/runner/work/black-it/black-it/.tox/py310/lib/python3.10/site-packages/pluggy/_hooks.py", line 493 in __call__ File "/Users/runner/work/black-it/black-it/.tox/py310/lib/python3.10/site-packages/_pytest/python.py", line 1792 in runtest File "/Users/runner/work/black-it/black-it/.tox/py310/lib/python3.10/site-packages/_pytest/runner.py", line 169 in pytest_runtest_call File "/Users/runner/work/black-it/black-it/.tox/py310/lib/python3.10/site-packages/pluggy/_callers.py", line 77 in _multicall File "/Users/runner/work/black-it/black-it/.tox/py310/lib/python3.10/site-packages/pluggy/_manager.py", line 115 in _hookexec File "/Users/runner/work/black-it/black-it/.tox/py310/lib/python3.10/site-packages/pluggy/_hooks.py", line 493 in __call__ File "/Users/runner/work/black-it/black-it/.tox/py310/lib/python3.10/site-packages/_pytest/runner.py", line 262 in <lambda> File "/Users/runner/work/black-it/black-it/.tox/py310/lib/python3.10/site-packages/_pytest/runner.py", line 341 in from_call File "/Users/runner/work/black-it/black-it/.tox/py310/lib/python3.10/site-packages/_pytest/runner.py", line 261 in call_runtest_hook File "/Users/runner/work/black-it/black-it/.tox/py310/lib/python3.10/site-packages/_pytest/runner.py", line 222 in call_and_report File "/Users/runner/work/black-it/black-it/.tox/py310/lib/python3.10/site-packages/_pytest/runner.py", line 133 in runtestprotocol File "/Users/runner/work/black-it/black-it/.tox/py310/lib/python3.10/site-packages/_pytest/runner.py", line 114 in pytest_runtest_protocol File "/Users/runner/work/black-it/black-it/.tox/py310/lib/python3.10/site-packages/pluggy/_callers.py", line 77 in _multicall File "/Users/runner/work/black-it/black-it/.tox/py310/lib/python3.10/site-packages/pluggy/_manager.py", line 115 in _hookexec File "/Users/runner/work/black-it/black-it/.tox/py310/lib/python3.10/site-packages/pluggy/_hooks.py", line 493 in __call__ File "/Users/runner/work/black-it/black-it/.tox/py310/lib/python3.10/site-packages/_pytest/main.py", line 350 in pytest_runtestloop File "/Users/runner/work/black-it/black-it/.tox/py310/lib/python3.10/site-packages/pluggy/_callers.py", line 77 in _multicall File "/Users/runner/work/black-it/black-it/.tox/py310/lib/python3.10/site-packages/pluggy/_manager.py", line 115 in _hookexec File "/Users/runner/work/black-it/black-it/.tox/py310/lib/python3.10/site-packages/pluggy/_hooks.py", line 493 in __call__ File "/Users/runner/work/black-it/black-it/.tox/py310/lib/python3.10/site-packages/_pytest/main.py", line 325 in _main File "/Users/runner/work/black-it/black-it/.tox/py310/lib/python3.10/site-packages/_pytest/main.py", line 271 in wrap_session File "/Users/runner/work/black-it/black-it/.tox/py310/lib/python3.10/site-packages/_pytest/main.py", line 318 in pytest_cmdline_main File "/Users/runner/work/black-it/black-it/.tox/py310/lib/python3.10/site-packages/pluggy/_callers.py", line 77 in _multicall File "/Users/runner/work/black-it/black-it/.tox/py310/lib/python3.10/site-packages/pluggy/_manager.py", line 115 in _hookexec File "/Users/runner/work/black-it/black-it/.tox/py310/lib/python3.10/site-packages/pluggy/_hooks.py", line 493 in __call__ File "/Users/runner/work/black-it/black-it/.tox/py310/lib/python3.10/site-packages/_pytest/config/__init__.py", line 169 in main File "/Users/runner/work/black-it/black-it/.tox/py310/lib/python3.10/site-packages/_pytest/config/__init__.py", line 192 in console_main File "/Users/runner/work/black-it/black-it/.tox/py310/bin/pytest", line 8 in <module> ``` A successful workaround seems to install HDF5 and C-blosc explicitly in the preliminary steps on CI for MacOS images. This step was part of the installation instructions of PyTables v3.9.2: https://github.com/PyTables/PyTables/blob/v3.9.2/README.rst#installation Moreover, as explained here: https://stackoverflow.com/questions/73029883/could-not-find-hdf5-installation-for-pytables-on-m1-mac, sometimes must be explicitly set the environment path variables where HDF5 ahd C-blosc are installed. For some reason this is not needed on Ubuntu and Windows runners.
marcofavoritobi
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Just run `poetry lock --no-update` with poetry at version 1.7.1.
Note by muxator: executing this command on 2024-02-23 printed the following
warning with no information about which package is originating it:
Warning: The locked version 2.0.0 for executing is a yanked version. Reason
for being yanked: Released 2.0.1 which is equivalent but added
'python_requires = >=3.5' so that pip install with Python 2 uses the
previous version 1.2.0.
Without the --no-update flag, the command will update the versions of the dependencies to the latest possible.
The dependency 'ipykernel' is not a direct dependency of the package.
This can be verified by grepping import statements involving ipykernel package:
$ grep -r "import ipykernel"
$ grep -r "from ipykernel import"
Both commands do not return any result.
Note: this is not a complete approach to detect direct uses of a package, but it
is a *reasonably* complete approach.
This commit removes the line for ipykernel in pyproject.toml. Then, it runs
`poetry lock`. Note that no dependency has changed in poetry.lock, meaning that
ipykernel is a subdependency of another direct dependency (e.g. see ipywidgets
dependencies).
muxator
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|
v2: Since this sort of PRs is time-dependent, I've rewritten it applying the exact same steps from @marcofavoritobi. |
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Proposed changes
poetry lock --no-updatewith poetry at version 1.7.1