Issue with PyTables on the GitHub Actions runner for MacOS 12.7.1

[marcofavoritobi]

This issue describes a problem when running tests over MacOS 12.7.1.

The following text is taken by a commit from #77, 2489f3f:

This change was needed because of a nondeterminism in how the macos-12 (=macos-latest at the time of writing) runner image was instantiated by GitHub Actions.
In particular, for runner version 2.311.0, the operating system was nondeterministically chosen between 12.6.9 and 12.7.1, as it can be seen in these two GH runs:

• https://github.com/bancaditalia/black-it/actions/runs/7128997647/job/19412070642
• https://github.com/bancaditalia/black-it/actions/runs/7128997647/job/19412070868

This is a known issue in the community: see actions/runner-images#8642

Furthermore, at the time of writing, it is suspected that Python code that uses pytables is not stable over macos at version 12.7.1 (but this problem does not occur on v12.6.9!), as witnessed by this issue: PyTables/PyTables#1093

What happened in our CI workflow is that tests resulted in a flaky outcome, but not because of our tests, but due to the nondeterminism in how the macos runner was instantiated by GitHub Actions.

This was not our unique attempt. In fact, we first tried to improve the preliminary configuration steps for the testing environment, as follows:

• if: matrix.os == 'macos-latest'
  name: Install dependencies (macos-latest)
  run: |
  # for some reason this seems to be a necessary step for MacOS images, but not for Ubuntu and Windows
  brew install hdf5
  brew install c-blosc
  # https://stackoverflow.com/questions/73029883/could-not-find-hdf5-installation-for-pytables-on-m1-mac
  echo "HDF5_DIR=/usr/local/" >> $GITHUB_ENV
  echo "BLOSC_DIR=/usr/local/" >> $GITHUB_ENV

This attempt consisted in installing HDF5 and C-blosc explicitly in the preliminary steps on CI for MacOS images. By the way, 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 , although it seems this step is not actually needed.
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.

However, despite our efforts in this direction, the issue with pytables persisted. 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>

The purpose of this GH issue is to keep track of the workaround, and try to solve it as soon as the problem is solved by GH Actions or PyTables.