Get notebooks building again #27

Yoshanuikabundi · 2023-12-18T10:35:18Z

For some reason I though GitHub would tell me when all the actions on this repo were failing.

TODOS:

Get things working by explicitly skipping some notebooks
Automatically skip notebooks that can't execute
Notify package owners when their notebook isn't on the examples page

github-actions · 2023-12-18T10:35:34Z

This repository caches data generated from notebooks stored in other repositories in the _cookbook_data_* branches. Regenerating this cache takes about half an hour, so it is not done automatically in PRs. The current value of the cache from the main branch has been copied over to this PR's cache.

To regenerate the cache for this PR, create a comment on this PR consisting only of the string:

/regenerate-cache

Yoshanuikabundi · 2023-12-18T10:52:08Z

/regenerate-cache

github-actions · 2023-12-18T10:52:33Z

A workflow has been dispatched to regenerate the cookbook cache for this PR.

Run ID: 7247042253
Triggering actor: github-actions[bot]
Target branch: fix-actions
Deployment branch: _cookbook_data_PR27

github-actions · 2023-12-18T10:58:38Z

A workflow dispatched to regenerate the cookbook cache for this PR has just finished.

Run ID: 7247042253
Triggering actor: github-actions[bot]
Target branch: fix-actions
Deployment branch: _cookbook_data_PR27
Status: failure

If the workflow was successful, changes will only be visible in the ReadTheDocs preview after it has been rebuilt.

Yoshanuikabundi · 2023-12-18T11:35:35Z

---------------------------------------------------------------------------
AssertionError                            Traceback (most recent call last)
Cell In[16], line 30
     23 energy_difference = abs(off_ene - omm_ene)
     26 # For some reason, there is a slight coordinate/energy difference between the OpenFF
     27 # TIP5P virtual sites and the OpenMM TIP5P virtual sites. The energy difference appears
     28 # to be entirely due to slightly different geometry.
     29 assert (
---> 30     coordinate_difference < 0.04
     31 ), f"Coordinates differ by a norm of {coordinate_difference}"
     32 assert (
     33     energy_difference < 1.0 * openmm.unit.kilojoule_per_mole
     34 ), f"Energies differ by {energy_difference}"

AssertionError: Coordinates differ by a norm of 3.0895671596164282


During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/runner/micromamba/envs/openff-docs-examples/lib/python3.10/multiprocessing/pool.py", line 125, in worker
    result = (True, func(*args, **kwds))
  File "/home/runner/work/openff-docs/openff-docs/source/_ext/proc_examples.py", line 202, in execute_notebook
    raise ValueError(f"Exception encountered while executing {src_rel}")
ValueError: Exception encountered while executing openforcefield/openff-toolkit/virtual_sites/vsite_showcase.ipynb
"""

I can reproduce locally. Will pin a version of the toolkit that doesn't have this error.

Yoshanuikabundi · 2023-12-18T11:37:22Z

/regenerate-cache

github-actions · 2023-12-18T11:37:43Z

A workflow has been dispatched to regenerate the cookbook cache for this PR.

Run ID: 7247520513
Triggering actor: github-actions[bot]
Target branch: fix-actions
Deployment branch: _cookbook_data_PR27

github-actions · 2023-12-18T11:38:12Z

A workflow dispatched to regenerate the cookbook cache for this PR has just finished.

Run ID: 7247520513
Triggering actor: github-actions[bot]
Target branch: fix-actions
Deployment branch: _cookbook_data_PR27
Status: failure

If the workflow was successful, changes will only be visible in the ReadTheDocs preview after it has been rebuilt.

Yoshanuikabundi · 2023-12-18T11:40:47Z

/regenerate-cache

github-actions · 2023-12-18T11:41:10Z

A workflow has been dispatched to regenerate the cookbook cache for this PR.

Run ID: 7247550785
Triggering actor: github-actions[bot]
Target branch: fix-actions
Deployment branch: _cookbook_data_PR27

github-actions · 2023-12-18T11:58:58Z

A workflow dispatched to regenerate the cookbook cache for this PR has just finished.

Run ID: 7247550785
Triggering actor: github-actions[bot]
Target branch: fix-actions
Deployment branch: _cookbook_data_PR27
Status: failure

If the workflow was successful, changes will only be visible in the ReadTheDocs preview after it has been rebuilt.

mattwthompson · 2023-12-18T12:58:40Z

I though GitHub would tell me when all the actions on this repo were failing.

I've been getting emails since ~Friday. I previously thought the most recent committer to the default branch got these, now I guess not

Yoshanuikabundi · 2023-12-18T13:41:45Z

/regenerate-cache

github-actions · 2023-12-18T13:42:23Z

A workflow has been dispatched to regenerate the cookbook cache for this PR.

Run ID: 7248916071
Triggering actor: github-actions[bot]
Target branch: fix-actions
Deployment branch: _cookbook_data_PR27

Yoshanuikabundi · 2023-12-18T13:42:50Z

I found an option in my account settings to be notified about failing GitHub actions and I'm getting them now :)

github-actions · 2023-12-18T13:43:53Z

A workflow dispatched to regenerate the cookbook cache for this PR has just finished.

Run ID: 7248916071
Triggering actor: github-actions[bot]
Target branch: fix-actions
Deployment branch: _cookbook_data_PR27
Status: failure

If the workflow was successful, changes will only be visible in the ReadTheDocs preview after it has been rebuilt.

Yoshanuikabundi · 2023-12-18T13:54:56Z

/regenerate-cache

github-actions · 2023-12-18T13:55:18Z

A workflow has been dispatched to regenerate the cookbook cache for this PR.

Run ID: 7249054053
Triggering actor: github-actions[bot]
Target branch: fix-actions
Deployment branch: _cookbook_data_PR27

github-actions · 2023-12-18T14:07:51Z

A workflow dispatched to regenerate the cookbook cache for this PR has just finished.

Run ID: 7249054053
Triggering actor: github-actions[bot]
Target branch: fix-actions
Deployment branch: _cookbook_data_PR27
Status: failure

If the workflow was successful, changes will only be visible in the ReadTheDocs preview after it has been rebuilt.

Yoshanuikabundi · 2023-12-18T14:11:26Z

/regenerate-cache

github-actions · 2023-12-18T14:11:51Z

A workflow has been dispatched to regenerate the cookbook cache for this PR.

Run ID: 7249260096
Triggering actor: github-actions[bot]
Target branch: fix-actions
Deployment branch: _cookbook_data_PR27

github-actions · 2023-12-18T14:35:29Z

A workflow dispatched to regenerate the cookbook cache for this PR has just finished.

Run ID: 7249260096
Triggering actor: github-actions[bot]
Target branch: fix-actions
Deployment branch: _cookbook_data_PR27
Status: failure

If the workflow was successful, changes will only be visible in the ReadTheDocs preview after it has been rebuilt.

github-actions · 2023-12-19T05:32:14Z

A workflow has been dispatched to regenerate the cookbook cache for this PR.

Run ID: 7257811427
Triggering actor: github-actions[bot]
Target branch: fix-actions
Deployment branch: _cookbook_data_PR27

github-actions · 2023-12-19T05:57:24Z

A workflow dispatched to regenerate the cookbook cache for this PR has just finished.

Run ID: 7257811427
Triggering actor: github-actions[bot]
Target branch: fix-actions
Deployment branch: _cookbook_data_PR27
Status: failure

If the workflow was successful, changes will only be visible in the ReadTheDocs preview after it has been rebuilt.

Yoshanuikabundi · 2024-03-19T01:30:04Z

/regenerate-cache

github-actions · 2024-03-19T01:30:25Z

A workflow has been dispatched to regenerate the cookbook cache for this PR.

Run ID: 8336134619
Triggering actor: github-actions[bot]
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github-actions · 2024-03-19T01:30:54Z

A workflow dispatched to regenerate the cookbook cache for this PR has just finished.

Run ID: 8336134619
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Deployment branch: _cookbook_data_PR27
Status: failure

If the workflow was successful, changes will only be visible in the ReadTheDocs preview after it has been rebuilt.

Yoshanuikabundi · 2024-03-19T01:38:55Z

/regenerate-cache

github-actions · 2024-03-19T01:39:14Z

A workflow has been dispatched to regenerate the cookbook cache for this PR.

Run ID: 8336211463
Triggering actor: github-actions[bot]
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Deployment branch: _cookbook_data_PR27

github-actions · 2024-03-19T02:02:21Z

A workflow dispatched to regenerate the cookbook cache for this PR has just finished.

Run ID: 8336211463
Triggering actor: github-actions[bot]
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Deployment branch: _cookbook_data_PR27
Status: failure

If the workflow was successful, changes will only be visible in the ReadTheDocs preview after it has been rebuilt.

Yoshanuikabundi · 2024-03-19T11:20:03Z

/regenerate-cache

github-actions · 2024-03-19T11:20:24Z

A workflow has been dispatched to regenerate the cookbook cache for this PR.

Run ID: 8342106212
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Deployment branch: _cookbook_data_PR27

github-actions · 2024-03-19T11:24:52Z

A workflow dispatched to regenerate the cookbook cache for this PR has just finished.

Run ID: 8342106212
Triggering actor: github-actions[bot]
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Deployment branch: _cookbook_data_PR27
Status: failure

If the workflow was successful, changes will only be visible in the ReadTheDocs preview after it has been rebuilt.

Yoshanuikabundi · 2024-03-20T09:06:49Z

/regenerate-cache

github-actions · 2024-03-20T09:07:11Z

A workflow has been dispatched to regenerate the cookbook cache for this PR.

Run ID: 8356303774
Triggering actor: github-actions[bot]
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Deployment branch: _cookbook_data_PR27

github-actions · 2024-03-20T09:10:45Z

A workflow dispatched to regenerate the cookbook cache for this PR has just finished.

Run ID: 8356303774
Triggering actor: github-actions[bot]
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Status: failure

If the workflow was successful, changes will only be visible in the ReadTheDocs preview after it has been rebuilt.

Yoshanuikabundi · 2024-03-20T10:10:21Z

/regenerate-cache

github-actions · 2024-03-20T10:10:42Z

A workflow has been dispatched to regenerate the cookbook cache for this PR.

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github-actions · 2024-03-20T10:28:09Z

A workflow dispatched to regenerate the cookbook cache for this PR has just finished.

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Support tags with/without leading v

7fad3d5

attempt to fix lint

26feeba

Insist on Toolkit 0.14.5

8204280

Try unpinning nagl

df5318c

Let cookbook choose nagl tag

d018bab

Support subdirectories with colab

500eb24

Extend notebook cell timeout from 600 -> 1200

7b0e823

Get NAGL examples from fixed commit in openforcefield/openff-nagl#73

b8ef691

Yoshanuikabundi mentioned this pull request Jan 10, 2024

fix issue #29 #30

Merged

Merge branch 'main' into fix-actions

29a69e6

Update nagl and dgl in examples env

638b2ed

Yoshanuikabundi added 4 commits March 19, 2024 13:30

Get examples from latest nagl

b27a8fb

Clean up tag collection

204168b

Skip some broken notebooks

35ce09d

Skip some broken notebooks

58c2b2d

OMP_NUM_THREADS=1 -> 2 to fix toolkit showcase

7cbb304

Yoshanuikabundi mentioned this pull request Mar 20, 2024

The toolkit showcase stochastically fails with OMP_NUM_THREADS=1 and AmberToolsToolkitWrapper openforcefield/openff-toolkit#1842

Closed

Remove OMP_NUM_THREADS env var from execute_notebooks

897cd92

Yoshanuikabundi changed the title ~~Fix broken actions~~ Get notebooks building again Mar 20, 2024

Yoshanuikabundi merged commit 383a326 into main Mar 20, 2024
3 of 4 checks passed

Yoshanuikabundi mentioned this pull request Apr 4, 2024

Use Conda Forge DGL in examples environment #25

Closed

Get notebooks building again #27

Get notebooks building again #27

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Yoshanuikabundi commented Dec 18, 2023 •

edited

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