fix(workflows): parse and use manifest isotopes list #207
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Add support for explicit isotopes list in manifest to control which isotopes are analyzed. Previously, the isotopes field in manifest YAML was completely ignored, causing all natural isotopes to be included. Changes: - Add isotopes field to ManifestData with format validation - Parse isotopes from YAML frontmatter in extract_manifest - Use manifest isotopes as priority 2 in _get_isotope_composition: 1. User-specified isotopes (highest) 2. Manifest isotopes list (new) 3. Enrichment dict 4. Natural abundance (fallback) 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude Opus 4.5 <[email protected]>
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Pull request overview
This PR successfully fixes issue #206 by implementing support for parsing and using a manifest isotopes list in resonance analysis workflows. The implementation adds a new priority level for isotope composition determination, allowing users to specify an explicit list of isotopes in the manifest that takes precedence over enrichment values but can still be overridden by user-specified isotopes.
Key changes:
- Added
isotopes: list[str] | Nonefield toManifestDatawith comprehensive validation for isotope format (Element-MassNumber) - Integrated isotopes list into priority hierarchy as level 2 (between user-specified and enrichment)
- Comprehensive test coverage with 15 new unit tests covering all edge cases and priority interactions
Reviewed changes
Copilot reviewed 3 out of 3 changed files in this pull request and generated no comments.
| File | Description |
|---|---|
src/pleiades/workflows/models.py |
Added isotopes field to ManifestData with @field_validator that validates isotope format using regex pattern ^[A-Z][a-z]?-\d+$ |
src/pleiades/workflows/resonance.py |
Updated extract_manifest() to parse isotopes from YAML frontmatter and modified _get_isotope_composition() to use manifest isotopes as priority level 2 with equal weights |
tests/unit/pleiades/workflows/test_resonance.py |
Added 15 comprehensive unit tests covering ManifestData validation, extract_manifest parsing, and _get_isotope_composition priority order with various edge cases |
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Summary
Fixes #206 - Manifest isotopes list is ignored during resonance analysis.
isotopes: list[str] | Nonefield toManifestDatawith format validationisotopesfrom YAML frontmatter inextract_manifest()_get_isotope_composition():Test plan
🤖 Generated with Claude Code