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openforcefield / openff-toolkit

The Open Forcefield Toolkit provides implementations of the SMIRNOFF format, parameterization engine, and other tools. Documentation available at http://open-forcefield-toolkit.readthedocs.io
http://openforcefield.org
MIT License
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Re-run cookbooks #1819

Closed mattwthompson closed 5 months ago

mattwthompson commented 5 months ago

The cookbooks are consistently failing in CI and I'm not sure why ... I re-ran them locally with nbconvert and also captured an expected error as text to avoid returning an exit code.

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codecov[bot] commented 5 months ago

Codecov Report

Merging #1819 (c0f4535) into main (d0e63b9) will not change coverage. The diff coverage is n/a.

Additional details and impacted files
mattwthompson commented 5 months ago

This will take more digging (or somebody who is more familiar with this particular location)


Run pytest -v --no-cov --durations=5 --nbval --ignore docs/_build/ docs/
  pytest -v --no-cov --durations=5 --nbval --ignore docs/_build/ docs/
  shell: /usr/bin/bash -l {0}
  env:
    OE_LICENSE: /home/runner/work/openff-toolkit/openff-toolkit/oe_license.txt
    PACKAGE: openff
    PYTEST_ARGS: -r fE --tb=short -nauto
    COV: --cov=openff/toolkit --cov-config=setup.cfg --cov-append --cov-report=xml
    ENVFILE: test_env
    JOBNAME: RDKit and OpenEye
    TOOLKIT_CHECKS: RDKIT OPENEYE
    PACKAGES_TO_REMOVE: 
    MAMBA_ROOT_PREFIX: /home/runner/micromamba
    MAMBA_EXE: /home/runner/micromamba-bin/micromamba
    CONDARC: /home/runner/work/_temp/setup-micromamba/.condarc
============================= test session starts ==============================
platform linux -- Python 3.9.18, pytest-8.0.0, pluggy-1.4.0 -- /home/runner/micromamba/envs/openff-toolkit-test/bin/python3.9
cachedir: .pytest_cache
rootdir: /home/runner/work/openff-toolkit/openff-toolkit
configfile: setup.cfg
plugins: xdist-3.5.0, cov-4.1.0, rerunfailures-13.0, nbval-0.10.0
collecting ... collected 31 items

docs/users/molecule_cookbook::ipynb::Cell 0 FAILED                       [  3%]
docs/users/molecule_cookbook::ipynb::Cell 1 PASSED                       [  6%]
docs/users/molecule_cookbook::ipynb::Cell [2](https://github.com/openforcefield/openff-toolkit/actions/runs/7748589247/job/21131478456#step:18:2) PASSED                       [  9%]
docs/users/molecule_cookbook::ipynb::Cell [3](https://github.com/openforcefield/openff-toolkit/actions/runs/7748589247/job/21131478456#step:18:3) PASSED                       [ 12%]
docs/users/molecule_cookbook::ipynb::Cell [4](https://github.com/openforcefield/openff-toolkit/actions/runs/7748589247/job/21131478456#step:18:4) PASSED                       [ 16%]
docs/users/molecule_cookbook::ipynb::Cell [5](https://github.com/openforcefield/openff-toolkit/actions/runs/7748589247/job/21131478456#step:18:5) PASSED                       [ 19%]
docs/users/molecule_cookbook::ipynb::Cell [6](https://github.com/openforcefield/openff-toolkit/actions/runs/7748589247/job/21131478456#step:18:6) PASSED                       [ 22%]
docs/users/molecule_cookbook::ipynb::Cell [7](https://github.com/openforcefield/openff-toolkit/actions/runs/7748589247/job/21131478456#step:18:7) PASSED                       [ 25%]
docs/users/molecule_cookbook::ipynb::Cell [8](https://github.com/openforcefield/openff-toolkit/actions/runs/7748589247/job/21131478456#step:18:8) PASSED                       [ 2[9](https://github.com/openforcefield/openff-toolkit/actions/runs/7748589247/job/21131478456#step:18:9)%]
docs/users/molecule_cookbook::ipynb::Cell 9 PASSED                       [ 32%]
docs/users/molecule_cookbook::ipynb::Cell [10](https://github.com/openforcefield/openff-toolkit/actions/runs/7748589247/job/21131478456#step:18:10) PASSED                      [ 35%]
docs/users/molecule_cookbook::ipynb::Cell [11](https://github.com/openforcefield/openff-toolkit/actions/runs/7748589247/job/21131478456#step:18:11) PASSED                      [ 38%]
docs/users/molecule_cookbook::ipynb::Cell [12](https://github.com/openforcefield/openff-toolkit/actions/runs/7748589247/job/21131478456#step:18:12) PASSED                      [ 41%]
docs/users/molecule_cookbook::ipynb::Cell [13](https://github.com/openforcefield/openff-toolkit/actions/runs/7748589247/job/21131478456#step:18:13) PASSED                      [ 45%]
docs/users/molecule_cookbook::ipynb::Cell [14](https://github.com/openforcefield/openff-toolkit/actions/runs/7748589247/job/21131478456#step:18:14) PASSED                      [ 48%]
docs/users/molecule_cookbook::ipynb::Cell [15](https://github.com/openforcefield/openff-toolkit/actions/runs/7748589247/job/21131478456#step:18:15) PASSED                      [ 51%]
docs/users/molecule_cookbook::ipynb::Cell [16](https://github.com/openforcefield/openff-toolkit/actions/runs/7748589247/job/21131478456#step:18:17) PASSED                      [ 54%]
docs/users/molecule_cookbook::ipynb::Cell [17](https://github.com/openforcefield/openff-toolkit/actions/runs/7748589247/job/21131478456#step:18:18) PASSED                      [ 58%]
docs/users/molecule_cookbook::ipynb::Cell [18](https://github.com/openforcefield/openff-toolkit/actions/runs/7748589247/job/21131478456#step:18:19) PASSED                      [ 61%]
docs/users/molecule_cookbook::ipynb::Cell [19](https://github.com/openforcefield/openff-toolkit/actions/runs/7748589247/job/21131478456#step:18:20) PASSED                      [ 64%]
docs/users/molecule_cookbook::ipynb::Cell [20](https://github.com/openforcefield/openff-toolkit/actions/runs/7748589247/job/21131478456#step:18:21) PASSED                      [ 67%]
docs/users/molecule_cookbook::ipynb::Cell [21](https://github.com/openforcefield/openff-toolkit/actions/runs/7748589247/job/21131478456#step:18:22) PASSED                      [ 70%]
docs/users/molecule_cookbook::ipynb::Cell [22](https://github.com/openforcefield/openff-toolkit/actions/runs/7748589247/job/21131478456#step:18:23) PASSED                      [ 74%]
docs/users/molecule_cookbook::ipynb::Cell [23](https://github.com/openforcefield/openff-toolkit/actions/runs/7748589247/job/21131478456#step:18:24) PASSED                      [ 77%]
docs/users/molecule_cookbook::ipynb::Cell [24](https://github.com/openforcefield/openff-toolkit/actions/runs/7748589247/job/21131478456#step:18:25) PASSED                      [ 80%]
docs/users/pdb_cookbook/index::ipynb::Cell 0 PASSED                      [ 83%]
docs/users/pdb_cookbook/index::ipynb::Cell 1 PASSED                      [ 87%]
docs/users/pdb_cookbook/index::ipynb::Cell 2 PASSED                      [ 90%]
docs/users/pdb_cookbook/index::ipynb::Cell 3 PASSED                      [ 93%]
docs/users/pdb_cookbook/index::ipynb::Cell 4 PASSED                      [ 96%]
docs/users/pdb_cookbook/index::ipynb::Cell 5 PASSED                      [100%]

=================================== FAILURES ===================================
__________________ docs/users/molecule_cookbook.ipynb::Cell 0 __________________
Notebook cell execution failed
Cell 0: Cell outputs differ

Input:
# Workaround for https://github.com/conda-forge/qcfractal-feedstock/issues/43
try:
    import qcportal  # noqa
except ImportError:
    pass

import sys

ipython = get_ipython()  # noqa

def hide_traceback(
    exc_tuple=None,
    filename=None,
    tb_offset=None,
    exception_only=False,
    running_compiled_code=False,
):
    """Hide tracebacks for simpler errors."""
    etype, value, _ = sys.exc_info()
    value.__cause__ = None  # suppress chained exceptions
    return ipython._showtraceback(
        etype,
        value,
        ipython.InteractiveTB.get_exception_only(etype, value),
    )

ipython.showtraceback = hide_traceback

# Hide NumPy warnings
import warnings

warnings.filterwarnings(
    "ignore",
    r"The value of the smallest subnormal for ",
)

Traceback:
Unexpected output fields from running code: {'stderr'}

============================= slowest 5 durations ==============================
45.12s call     docs/users/pdb_cookbook/index.ipynb::Cell 4
15.78s call     docs/users/pdb_cookbook/index.ipynb::Cell 2
11.82s call     docs/users/pdb_cookbook/index.ipynb::Cell 3
7.61s call     docs/users/pdb_cookbook/index.ipynb::Cell 1
6.81s call     docs/users/molecule_cookbook.ipynb::Cell 14
=========================== short test summary info ============================
FAILED docs/users/molecule_cookbook.ipynb::Cell 0
=================== 1 failed, [30](https://github.com/openforcefield/openff-toolkit/actions/runs/7748589247/job/21131478456#step:18:31) passed in 95.97s (0:01:[35](https://github.com/openforcefield/openff-toolkit/actions/runs/7748589247/job/21131478456#step:18:36)) ====================
j-wags commented 5 months ago

Huh, thanks for taking a look at this. It pains me to say it, but since this is cosmetic I'd be in favor of going ahead with the release today and then I'll dig into this afterwards.

j-wags commented 5 months ago

Oh rats. I was thinking that this was just a problem in the testing framework, but now that I look at the rendered docs preview I see that the molecule cookbook outputs are broken.

Weird, I can run manually just fine. I'll dig into this.

mattwthompson commented 5 months ago

For posterity the ❌ results from a bug in which OEChem thought a license expiring in April 2024 actually expires on January 30, 2024. It'd still be nice to re-run these notebooks once in a while, but that's a separate thread from what got me started here.