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* Add discovery of Python packages (#151) * Fix Docker entrypoint * Attempt to fix Circle CI pip install * Run each CRISPResso command in the conda environment * Update `--base_editor_output` parameter name for Circle CI * Update tests Makefile and batch expected output * Fix QWC inference across amplicons (#137) * Mckay/be plot improvements (#136) * trying to get the figure to fit nicely, increased element size to 100 * custom figsize to display without cutting off increased figsize in report template * Allow messages to be served in CLI reports (#134) (pinellolab#583) * Fix deletion at second position (#131) * Fix bug when there is a deletion starting at the second position This bug only happens when a deletion starts are the second position, before the fix, it would report that the deletion started at the first position. It is fixed now, so deletions at the second position are reported correctly. * Update CRISPRessoCOREResources.c due to change in .pyx * Add tests for find_indels_substitutions for deletions at the end * Fix 1bp deletions at the end, and off by one error This ensures that when a deletion occurs at the end of a read, the entire deletion is accounted for. * Update CRISPRessoCOREResources.c to reflect fixes for deletions at the end of alignments * Add extra asserts to deletion checks * Point to new test branch * Reafctor deletion_coordinates to go past the end of the string for deletions at the end of the sequence * Point tests to master * Allow messages to be served in CLI reports * Point to cole/messages test branch * Point tests back to master * point to tests branch * typo * testing github actions * remove test * point tests to master --------- Co-authored-by: Cole Lyman <[email protected]> * Update inferred QWC tests to reflect correct intended behavior * Fix inferring QWC to match intended behavior * Add more test cases and fix bug discovered in single bp QWC * Add even more test cases testing indels outside the QWC * Point tests to cole/fix-qwc-deletion * update plotly.js (#138) * Change order of amplicon inference alignment so that 1st amplicon is the reference This makes a difference because it changes the values of `s1inds`, and therefore the value of the inferred quantification window coordinates. * Point integration tests back to master * Update CHANGELOG.md --------- Co-authored-by: mbowcut2 <[email protected]> * Update setup.py and pyproject.toml to find all modules and packages * Convert pyproject.toml to Unix file endings --------- Co-authored-by: mbowcut2 <[email protected]> * Guardrail dropdowns * Revert changes to .c files * Closed guardrail warning by default * .c fix * Revert .c files to match master Co-Authored-By: Claude Opus 4.6 <[email protected]> * Revert .c files back to master * Update CHANGELOG.md * Update CHANGELOG.md --------- Co-authored-by: Cole Lyman <[email protected]> Co-authored-by: mbowcut2 <[email protected]> Co-authored-by: Claude Opus 4.6 <[email protected]>
Colelyman
reviewed
Feb 20, 2026
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Use pixi to run integration tests, pin versions, import pro.