Develop branch merge into Main

[VarenyaJ]

Completed PRs/Issue

PR Title: PR #20 – Develop branch merge into Main (Branch: develop → main)
PR Type: Integration / Release
Status: Completed

Background

The develop branch had accumulated multiple major features, including expanded
Phenopacket support (genotypes, phenotypes, diseases, measurements, biosamples),
CLI commands (parse-excel, audit-excel, download), and refactored mapping
logic. This PR merged those updates into main to create the first feature-complete,
GA4GH-aligned release of the pipeline.

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Scope

Outline

Synchronize develop into main to release a working end-to-end pipeline for
Phenopacket generation from Excel workbooks.

Included/Required

• Merged feature branch feature/expand-phenopackets (Feature/expand phenopackets #19).
• Integrated VariationDescriptor support from exp/attempt_pyphetools (Draft Variant field for the Phenopacket #18).
• CLI commands:
  • p6 parse-excel: parse genotype/phenotype and emit JSON phenopackets.
  • p6 audit-excel: audit workbooks for headers, sheet classification, variant columns.
  • p6 download: fetch HPO JSON releases.
• Expanded data model:
  • DiseaseRecord, MeasurementRecord, BiosampleRecord.
• Refactored DefaultMapper into modular row-level helpers.
• Full unit and integration test suite.

Optional

• Graceful tolerance for chromosome inputs (chr16 vs 16).
• Strict vs non-strict HGVS consistency checks.
• Canonicalization of HGVS expressions.
• README expanded with new CLI references and examples.

Not included

• Full VariationDescriptor gene_context integration (still TODO).
• Visualization/dashboard layer.
• Privacy/PHI handling or linkage to genomic VCFs.

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Technical Plan / Implementation Details

• Integration of all work from PRs Draft Variant field for the Phenopacket #18 and Feature/expand phenopackets #19 into main.
• Refactored CLI (__main__.py) to support audit, parse, and download workflows.
• Mapper API stabilized: apply_mapping returns list[Phenopacket].
• Row-level parsing: genotype, phenotype, disease, measurement, biosample.
• Expanded loader (RENAME_MAP) with new standardized fields.
• Updated README with installation, CLI reference, and quickstart.
• Tests added:
  • tests/test_full_features.py
  • tests/test_cli_audit_excel.py
  • tests/test_download_mock.py
  • Unit tests for row-level mappers and HGVS consistency.

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Validation & Testing

• All tests passed in CI (unit + integration).
• test_full_features_parse_creates_all_blocks confirmed expanded JSON output.
• test_audit_excel_* validated CLI audit outputs (table + JSON).
• Mocked network calls for download ensured offline reproducibility.
• HGVS consistency checked in both strict and forgiving modes.

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Milestones

• Merge feature/expand-phenopackets (Feature/expand phenopackets #19).
• Merge VariationDescriptor draft (Draft Variant field for the Phenopacket #18).
• Stabilize CLI with parse-excel, audit-excel, download commands.
• Update README and developer docs.
• Confirm full CI test suite passing.

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Outcome

• main now contains a stable, feature-complete pipeline for generating
  GA4GH Phenopackets from Excel workbooks.
• CLI supports auditing, parsing, and ontology downloads.
• All five record types (genotypes, phenotypes, diseases, measurements, biosamples)
  are serialized into compliant JSON outputs.
• Project is ready for downstream adoption and further incremental releases.