Fix CI - #58
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## Description Release PR merging `dev` into `main`, bringing `main` from `1.0.0` up to `1.0.4`. This covers several bug fixes (annotation timing, path resolution, CLI argument names), a dependency floor bump for `pyhmmer` (0.12.0, required for compatibility with its `bytes`→`str` API change), removal of unsupported/dead CLI options, a large documentation overhaul (developer guide, API reference, citation guide, quick-start), and CI workflow cleanup. ## What changed - **Fixes:** - Fixed annotation monitoring accumulating elapsed time across pangenomes instead of per-pangenome (#48). - Fixed relative path resolution so `pangenome.h5` is found correctly regardless of where the pangenome TSV/CLI is invoked from (#54). - Fixed wrong argument names in the `compare_spots`/`compare_systems` commands. - Fixed a CI failure (#49). - **Dependencies:** - Pinned `pyhmmer>=0.12.0` in `pyproject.toml` and `panorama.yml`; updated `genInput.py`, `macsymodel_translator.py`, and `hmm_search.py` to use plain `str` access on HMM/Hit/Sequence/Alignment attributes now that pyhmmer 0.12+ returns `str` instead of `bytes` (#58). - **Removed:** - Removed unsupported `--conserved_spots` option from `write_flat.py` (#56). - Removed the automatic version-bump GitHub Actions workflow (#52). - **Utilities:** - Added a `resolve_path` utility, integrated into `check_tsv_sanity` for robust pangenome path resolution. - **CI:** - Scoped the Ruff format/lint workflow to `panorama`/`tests` only (`src` input), so it no longer lints unrelated paths like `.github/scripts/`. - Skipped test/Ruff workflow runs on `doc/*` branches and fixed duplicate doc-check workflow runs. - **Documentation:** - Added a "How to cite" guide and citation `.bib` files (#55). - Added a pull request template for contributions (#51). - Large developer-guide and API-documentation restructuring: new I/O layer and detection-workflow pages, cleaned-up autosummary/API structure, removed several outdated developer docs. - Numerous formatting/typo/link fixes across user and modeler documentation; added PANORAMA logo and citation/paper badges to the README. ## Testing **Test environment:** - Dataset used: no external `PANORAMA_test` dataset run as part of this release PR itself — each underlying change was tested/verified individually in its own PR (see #48, #49, #51, #52, #54, #55, #56, #57, #58). - Key parameters: N/A (aggregation PR). **Results:** - All constituent PRs passed CI (Ruff + pytest, Ubuntu/macOS, Python 3.12) individually before merging into `dev`. - Recommend a final CI run on this PR against `main` before merging. ## Documentation - [x] Added/updated code comments - [x] Added/updated docstring - [x] Updated README or docs if needed - [ ] Added example usage (if relevant) ## Checklist - [x] My code follows the project guidelines - [x] Complex logic is commented - [x] No unnecessary files or debug code included - [ ] My PR is targeting the `dev` branch (this PR targets `main`, as a release merge) ## Additional notes `VERSION` is already at `1.0.4` on `dev` (bumped incrementally across the merged PRs); no further manual bump should be needed for this release. Anyone with an existing `panorama` conda env built before `pyhmmer>=0.12.0` was pinned should recreate/update it to match the new floor.
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Description
pyhmmer0.12.0 changedHMM.name/.accession/.description(and the matchingHit/Sequence/Alignmentattributes) frombytestostr. Since the dependency was unpinned (>=0.11.1), CI picked up 0.12.x and every.decode("UTF-8")call on these attributes started raisingAttributeError: 'str' object has no attribute 'decode'. This brokepanorama utils --hmm, which cascaded into failures fortest_write_systems,test_pansystems_command,test_compare_spots_command, andtest_compare_systems_commandsince none of the shared test pangenomes ever got systems detected.Separately, the Ruff CI workflow was linting the entire repo instead of just
panorama//tests/, failing on an unrelated formatting issue in.github/scripts/.What changed
pyhmmer>=0.12.0inpyproject.tomlandpanorama.yml, and updatedpanorama/utility/genInput.py,panorama/utility/translate/macsymodel_translator.py, andpanorama/annotate/hmm_search.pyto use plainstraccess on HMM/Hit/Sequence/Alignment attributes (dropped all.decode("UTF-8")/.encode("UTF-8")calls).assign_hit()andannot_with_hmmscan()'s debug callback inhmm_search.py, which had the same latent bug on thehmmscanfallback path (not exercised by CI's small test dataset, but would break on real large-data runs)..github/workflows/ruff.ymltosrc: "panorama tests"so it only lints the paths it's supposed to, instead of the whole repo.Testing
Test environment:
PANORAMA_test); verified manually against the realpyhmmer0.12.1 install in the project'spanoramaconda env.HMM/TextSequenceobjects viapyhmmer.plan7.HMM.sample/pyhmmer.easel.TextSequence.Results:
parse_hmm_info,write_hmm,process_hmm_name,process_hmm_accessionall run correctly end-to-end against pyhmmer 0.12.1 (previously raisedAttributeError).TextSequence/MSA name-and-accession assignment/digitization confirmed working with plainstr.ruff format --checkandruff checkpass cleanly when scoped topanorama tests(verified locally with ruff 0.15.22, matching CI).pytest/ruffnot installed in thepanoramaconda env) — recommend CI confirms the previously-failing tests now pass.Documentation
Checklist
devbranchAdditional notes
Anyone with an existing
panoramaconda env built before this change should recreate/update it (pyhmmer>=0.12.0) to match the new floor.