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BlueBrain / BluePyMM

Blue Brain Python Cell Model Management
https://bluepymm.readthedocs.io/en/latest/
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py38 functional tests run forever #236

Open anilbey opened 2 years ago

anilbey commented 2 years ago

The run step freezes after bluepymm.select_combos: test select_combos based on example simple1 test is executed.

Here is the last log produced, nothing else gets written after this log. 

   bluepymm.select_combos: test select_combos based on example simple1 ... /home/runner/work/BluePyMM/BluePyMM/bluepymm/select_combos/reporting.py:379: FutureWarning: The frame.append method is deprecated and will be removed from pandas in a future version. Use pandas.concat instead.
    ext_neurondb = ext_neurondb.append(emodel_ext_neurondb_rows)
  /home/runner/work/BluePyMM/BluePyMM/bluepymm/select_combos/reporting.py:381: FutureWarning: The frame.append method is deprecated and will be removed from pandas in a future version. Use pandas.concat instead.
    megate_passed_all = megate_passed_all.append(
  /home/runner/work/BluePyMM/BluePyMM/bluepymm/select_combos/reporting.py:383: FutureWarning: The frame.append method is deprecated and will be removed from pandas in a future version. Use pandas.concat instead.
    median_scores = median_scores.append(emodel_median_scores)
  /home/runner/work/BluePyMM/BluePyMM/bluepymm/select_combos/reporting.py:384: FutureWarning: The frame.append method is deprecated and will be removed from pandas in a future version. Use pandas.concat instead.
    passed_combos = passed_combos.append(emodel_passed_combos)
  /home/runner/work/BluePyMM/BluePyMM/bluepymm/select_combos/reporting.py:379: FutureWarning: The frame.append method is deprecated and will be removed from pandas in a future version. Use pandas.concat instead.
    ext_neurondb = ext_neurondb.append(emodel_ext_neurondb_rows)
  /home/runner/work/BluePyMM/BluePyMM/bluepymm/select_combos/reporting.py:381: FutureWarning: The frame.append method is deprecated and will be removed from pandas in a future version. Use pandas.concat instead.
    megate_passed_all = megate_passed_all.append(
  /home/runner/work/BluePyMM/BluePyMM/bluepymm/select_combos/reporting.py:383: FutureWarning: The frame.append method is deprecated and will be removed from pandas in a future version. Use pandas.concat instead.
    median_scores = median_scores.append(emodel_median_scores)
  /home/runner/work/BluePyMM/BluePyMM/bluepymm/select_combos/reporting.py:384: FutureWarning: The frame.append method is deprecated and will be removed from pandas in a future version. Use pandas.concat instead.
    passed_combos = passed_combos.append(emodel_passed_combos)
  /home/runner/work/BluePyMM/BluePyMM/bluepymm/select_combos/reporting.py:313: UserWarning: Tight layout not applied. The bottom and top margins cannot be made large enough to accommodate all axes decorations.
    plt.tight_layout()
  ok
wvangeit commented 2 years ago

yeah, can we login on these github actions nodes?

anilbey commented 2 years ago

It is possible it seems. I haven't tried that before. I am busy with other tasks at the moment. I can look at it the next week. https://github.com/marketplace/actions/debugging-with-ssh

wvangeit commented 2 years ago

Sure, no hurry

anilbey commented 2 years ago

237 fixes this

anilbey commented 2 years ago

Update: #237 does not fix this. Github CI sometimes get stuck. It sometimes works when I manually restart it. In 237 py3.9 was getting stuck. It worked after I restarted but are we to restart the jobs from time to time?

Is this problem bluepymm specific or does it happen in the other repos as well? @AurelienJaquier

If it's happening only in BluePyMM, ipyparallel engines might be the cause.

AurelienJaquier commented 2 years ago

I haven't seen this in other repos.