Remove support for --conserved_spots in write_flat.py - #56
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Jul 23, 2026
## 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restructuring: new I/O layer and detection-workflow pages, cleaned-up autosummary/API structure, removed several outdated developer docs.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
Write_flat does not support to write conserved_spot anymore. This has been moved directly to the compare_spot command. This PR remove the argument from the command.
What changed
conserved_spotargument is not checked anymoreDocumentation
Checklist
devbranch