Run built-in app tests#

Goal#

Execute the integration tests that ship inside each PlayMolecule app, to confirm the app and its environment are working before you build real jobs around it.

Minimal example#

from playmolecule.apps import proteinprepare

print(proteinprepare.tests)               # list available tests
proteinprepare.tests.simple.run()         # run one

Each named test runs the app end-to-end in a temporary directory, waits for completion, and asserts that the manifest’s expected_outputs files appear.

Discover tests#

print(proteinprepare.tests)

Each entry has a description, arguments, and an expected_outputs list:

[simple] 'Prepare 3PTB structure from RCSB'
- Arguments:
  pdbid = 3ptb
- Expected outputs:
  output.pdb
  pka_plot.png
  details.csv

[reprotonation] 'Prepare 3PTB but reprotonate specific residues'
...

Tests come from the app manifest’s tests block.

Run locally#

proteinprepare.tests.simple.run()

The test runs in a tempfile.TemporaryDirectory and prints a 🎉 Test '<name>' succeeded in N seconds! 🎉 line on success. Any missing expected output raises RuntimeError.

Run on SLURM#

proteinprepare.tests.simple.run(
    queue="slurm",
    dir="/shared/scratch/tests/",
    partition="normalCPU",
    ncpu=1,
    ngpu=0,
)

When queue="slurm", you must pass dir= pointing to a path visible from the worker nodes — the default temp directory under /tmp/ won’t be there.

All extra kwargs are forwarded to run(), which forwards SLURM-specific ones to the queue.

Pin a test to a specific version#

To detect manifest drift across upgrades, call the test on a pinned version:

proteinprepare.v1.proteinprepare.tests.simple.run()

Gotchas#

Tests don’t return anything — they raise on failure. Wrap in try/except if you’re driving them from a larger script.
Test names that don’t start with a letter, or contain characters other than [A-Za-z0-9_], are renamed at load time (- becomes _, leading digit becomes test_<n>). Use dir(app.tests) to see the actual attribute names.
Test failures will leave the temp directory deleted (it’s a context manager). If you need to debug, pass dir="./debug-runs/" and inspect the leftover contents — but note that for queue=None (local) the cleanup still runs.