Add tests for pyopia.cli generate-config and modify-config - #394
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First pass at #142. Confirms typer's CliRunner works cleanly under pytest in this environment, and that the TensorFlow/pytest incompatibility noted in the issue (filed 2023) no longer applies with current TF/Keras versions. Scoped to the simple, side-effect-light commands for now (generate-config for each instrument, modify-config). Heavier commands (process, init-project, process-realtime) that exercise full pipeline runs and downloads are left for a follow-up, following the example-data patterns already used in test_pipeline.py.
Adds coverage for docs, --version, init-project, process, process-realtime, merge-mfdata, convert-raw-images, make-montage, and export-to-ecotaxa, alongside the existing generate-config/modify-config tests. Commands that need real particle stats/ROI images to exercise (process, merge-mfdata, convert-raw-images, make-montage, export-to-ecotaxa) share a single real end-to-end pipeline run against the downloaded SilCam example image via session-scoped fixtures in conftest.py, consistent with the real-download/real-processing approach already used in test_pipeline.py and test_classify.py. The --version test targets the --version option added in PR #386, which has not yet merged into main; it will start passing once that PR lands and this branch is rebased. Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
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Now updated with a full set of tests for all CLI options. |
emlynjdavies
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Jul 30, 2026
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this test works for me locally! I was not aware of this way of defining pytest fixtures. could this be a way of helping to simplify the code in the test_* files (perhaps as a future housework issue)?
need to update version number when ready
# Conflicts: # pyopia/__init__.py
This was referenced Jul 30, 2026
emlynjdavies
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Aug 5, 2026
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Summary
First pass at #142. The issue noted TensorFlow had problems running in a pytest environment back in 2023 — that no longer reproduces with current TF/Keras versions (confirmed
pyopia.classifyimports and runs fine under pytest in this environment), andtyper.testing.CliRunnerworks cleanly againstpyopia.cli.app.Scoped to the simple, side-effect-light commands for this first PR:
generate-configfor each instrument (silcam, holo, uvp)modify-configLeft for a follow-up: heavier commands (
process,init-project,process-realtime) that exercise full pipeline runs and downloads — these would follow the same example-data patterns already used intest_pipeline.py. Also skippeddocs(callstyper.launch()to open a browser — not suitable for CI).Test plan
pytest pyopia/tests/test_cli.pypasses (4 passed)flake8 pyopia/tests/test_cli.pyclean