Chore/release v2.0.6

[aslgraefe]

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[Copilot]

Pull request overview

Release v2.0.6 updates RareLink to RD-CDM v2.0.3, refreshes CDM field identifiers (Sex at Birth → LOINC 76689-9), and improves the Phenopacket export pipeline with routing + validation.

Changes:

• Replace the Personal Information “Sex at birth” field identifier from snomedct_281053000 to loinc_76689_9 across schemas, mappings, fixtures, and tests.
• Enhance Phenopacket export: camelCase JSON output, structured pipeline result reporting, write-time validation, and new ontology routing adapter with tests.
• Restructure packaging/dependencies for extras and remove unused RD-CDM codegen/sync modules and related tests.

Reviewed changes

Copilot reviewed 85 out of 95 changed files in this pull request and generated 2 comments.

Show a summary per file

File	Description
tests/utils/test_processor.py	Updates test mapping/config keys for Sex at birth to LOINC field id.
tests/rd_cdm/test_scaffold_and_force.py	Removes RD-CDM scaffold/force tests along with removed generator code.
tests/rd_cdm/test_normalize_and_build_schema.py	Removes CSV version rewrite tests (code removed).
tests/rd_cdm/test_ensure_types_and_codegen.py	Removes LinkML codegen test (code removed).
tests/rd_cdm/test_csv_update.py	Removes duplicate CSV update tests (code removed).
tests/phenopackets/test_pipeline.py	Updates tests to new PipelineResult and correct patch paths.
tests/phenopackets/test_data/sample_records_rarelink_cdm_1.json	Updates sample record Sex at birth key to loinc_76689_9.
tests/phenopackets/test_data/sample_records_rarelink_cdm.json	Updates sample record Sex at birth key to loinc_76689_9.
tests/phenopackets/adapter/test_ontology_routing_adapter.py	Adds tests for new ontology routing adapter behavior.
submodules/tofhir	Removes tofhir git submodule pointer.
src/rarelink/utils/label_fetching.py	Adds caching for BioPortal label lookup.
src/rarelink/tofhir/schemas/Rarelink_2_personal_information.json	Updates Sex at birth element id/path to LOINC field id.
src/rarelink/tofhir/mappings/ips.patient.json	Updates toFHIR mapping references to LOINC field id.
src/rarelink/tofhir/docker-compose.yml	Pins Kafka to bitnamilegacy/kafka:3.7.0.
src/rarelink/rd_cdm/sync.py	Removes unused RD-CDM sync + generation script.
src/rarelink/rd_cdm/schema_template.py	Removes unused LinkML schema template helper.
src/rarelink/rd_cdm/codegen_cli.py	Removes unused codegen CLI entrypoint.
src/rarelink/rd_cdm/codegen.py	Removes unused RD-CDM codegen logic.
src/rarelink/rd_cdm/cli.py	Removes unused RD-CDM CLI wrapper.
src/rarelink/rd_cdm/init.py	Removes empty __all__.
src/rarelink/rarelink_cdm/schema_definitions/rarelink_code_systems.yaml	Updates code system versions for the release.
src/rarelink/rarelink_cdm/schema_definitions/rarelink_6_4_family_history.yaml	Adjusts Sex at birth meaning metadata (now LOINC-coded in diff).
src/rarelink/rarelink_cdm/schema_definitions/rarelink_2_personal_information.yaml	Renames Sex at birth slot to loinc_76689_9 and updates enum meaning metadata.
src/rarelink/rarelink_cdm/rarelink_cdm_datadictionary - v2_0_5.csv	Updates REDCap data dictionary variable name/id for Sex at birth.
src/rarelink/rarelink_cdm/python_datamodel/rarelink_code_systems.py	Regenerates code systems datamodel with updated versions/imports.
src/rarelink/rarelink_cdm/python_datamodel/rarelink_cdm.py	Updates datamodel attribute/slot name for Sex at birth to loinc_76689_9.
src/rarelink/rarelink_cdm/python_datamodel/rarelink_2_personal_information.py	Updates module datamodel attribute/slot name for Sex at birth to loinc_76689_9.
src/rarelink/rarelink_cdm/mappings/redcap/template.json	Updates REDCap mapping template key to loinc_76689_9.
src/rarelink/rarelink_cdm/mappings/redcap/map_2_personal_information.py	Updates field mappings to loinc_76689_9.
src/rarelink/rarelink_cdm/mappings/phenopackets/resources.py	Updates code system version constants used in phenopacket metadata/resources.
src/rarelink/rarelink_cdm/mappings/phenopackets/individual.py	Updates phenopacket “sex_field” mapping to LOINC field id.
src/rarelink/phenopackets/write.py	Switches JSON serialization to camelCase and adds optional validation callbacks.
src/rarelink/phenopackets/validate.py	Adds Python-native validation + prefix-placement warnings + optional CLI stage.
src/rarelink/phenopackets/pipeline.py	Introduces PipelineResult, adds callbacks, captures warnings, writes failure/warning reports.
src/rarelink/phenopackets/mappings/variation_descriptor_mapper.py	Emits mapper issues via warnings.warn() for pipeline capture.
src/rarelink/phenopackets/mappings/phenotypic_feature_mapper.py	Emits mapper issues via warnings.warn().
src/rarelink/phenopackets/mappings/metadata_mapper.py	Emits CodeSystemsContainer autoload failures via warnings.warn().
src/rarelink/phenopackets/mappings/medical_action_mapper.py	Emits mapper issues via warnings.warn().
src/rarelink/phenopackets/mappings/measurement_mapper.py	Emits parsing issues via warnings.warn().
src/rarelink/phenopackets/mappings/interpretation_mapper.py	Emits mapper issues via warnings.warn().
src/rarelink/phenopackets/mappings/base_mapper.py	Cleans up comments and keeps mapping behavior stable.
src/rarelink/phenopackets/adapter/ontology_routing_adapter.py	Adds ontology routing adapter + prefix placement checker.
src/rarelink/phenopackets/adapter/multi_onset.py	Minor comment cleanup in existing adapter.
src/rarelink/phenopackets/adapter/init.py	Exposes new routing adapter APIs.
src/rarelink/cli/redcap/upload_records.py	Imports validate_linkml_data directly (removes lazy wrapper).
src/rarelink/cli/redcap/download_records.py	Imports validate_linkml_data directly (removes lazy wrapper).
res/evaluation_cohort/redcap/evaluation_cohort_rarelink-cdm-linkml.json	Updates cohort fixture Sex at birth keys to loinc_76689_9.
res/evaluation_cohort/phenopackets/failures.json	Removes obsolete failures report fixture.
res/evaluation_cohort/phenopackets/1.json	Updates example phenopacket JSON to camelCase output and new content.
res/evaluation_cohort/phenopackets/2.json	Updates example phenopacket JSON to camelCase output and version resources.
res/evaluation_cohort/phenopackets/3.json	Updates example phenopacket JSON to camelCase output.
res/evaluation_cohort/phenopackets/4.json	Updates example phenopacket JSON to camelCase output.
res/evaluation_cohort/phenopackets/5.json	Updates example phenopacket JSON to camelCase output.
res/evaluation_cohort/phenopackets/6.json	Updates example phenopacket JSON to camelCase output.
res/evaluation_cohort/phenopackets/7.json	Updates example phenopacket JSON to camelCase output.
res/evaluation_cohort/phenopackets/8.json	Updates example phenopacket JSON to camelCase output.
res/evaluation_cohort/phenopackets/9.json	Updates example phenopacket JSON to camelCase output.
res/evaluation_cohort/phenopackets/10.json	Updates example phenopacket JSON to camelCase output.
pytest.ini	Ignores UserWarning from phenopacket mappers in test output.
pyproject.toml	Bumps project version, trims core deps, adds extras, updates package data inclusion.
docs/index.rst	Updates overview text and section links.
docs/conf.py	Removes numpy/pandas intersphinx/doctest setup and simplifies mapping.
docs/_static/res/import_mapper_tsvs/rarelink_cdm_sssom_template.tsv	Updates Sex at birth predicate to loinc_76689_9.
docs/_static/res/import_mapper_tsvs/example_1_sssom.tsv	Updates Sex at birth predicate/object examples.
docs/_static/rarelink_cdm_datadictionary - v2_0_5.csv	Updates embedded data dictionary Sex at birth variable text/id.
docs/_build/html/_static/res/import_mapper_tsvs/rarelink_cdm_sssom_template.tsv	Updates built-doc artifact template TSV.
docs/_build/html/_static/res/import_mapper_tsvs/example_1_sssom.tsv	Updates built-doc artifact example TSV.
docs/_build/html/_static/rarelink_cdm_datadictionary - v2_0_5.csv	Updates built-doc artifact data dictionary CSV.
docs/_build/html/_sources/4_user_guide/4_2_import_mapper.rst.txt	Updates built-doc artifact import mapper text.
docs/_build/html/_sources/2_rarelink_framework/2_2_rarelink_cdm.rst.txt	Updates built-doc artifact CDM text.
docs/_build/html/_downloads/951a4999946d3dff534dce54032556ef/rarelink_cdm_datadictionary - v2_0_5.csv	Updates built-doc artifact downloadable CSV.
docs/_build/html/4_user_guide/4_2_import_mapper.html	Updates built-doc artifact import mapper HTML.
docs/_build/html/2_rarelink_framework/2_2_rarelink_cdm.html	Updates built-doc artifact CDM HTML link/field references.
docs/6_changelog.rst	Adds v2.0.6 changelog entry and release notes.
docs/4_user_guide/4_3_phenopackets.rst	Adds adapter documentation and updates TOC structure.
docs/4_user_guide/4_2_import_mapper.rst	Updates Sex at birth predicate/object examples.
docs/4_user_guide/4_1_manual_data_capture.rst	Updates mutation validation guidance links.
docs/3_installation/3_1_setup_rarelink_framework.rst	Updates install instructions for extras/dev workflow.
docs/2_rarelink_framework/2_2_rarelink_cdm.rst	Updates Sex at birth field reference to loinc_76689_9.
docs/2_rarelink_framework/2_1_rarelink_overview.rst	Switches overview figure to PNG and updates descriptive text.
README.md	Updates installation instructions and marks RD-CDM version badge to 2.0.3.
.gitignore	Adds .DS_Store patterns and ignores dev/.

Comments suppressed due to low confidence (10)

src/rarelink/phenopackets/validate.py:1

• sys.exit() is called but sys is not imported anywhere in this module, which will raise NameError when running python -m rarelink.phenopackets.validate ... or executing this file directly. Import sys at module level (near the other imports).
  src/rarelink/rarelink_cdm/schema_definitions/rarelink_2_personal_information.yaml:1
• The meaning for permissible value snomedct_248152002 (Female) has been changed to LOINC:76689-9, which is the Sex assigned at birth observation/field concept, not the code meaning “Female”. The permissible value meanings should remain the SNOMED CT concept identifiers (e.g., SNOMEDCT:248152002) while only the field/slot id changes to loinc_76689_9.
  src/rarelink/rarelink_cdm/schema_definitions/rarelink_6_4_family_history.yaml:1
• Same issue as in Personal Information: LOINC:76689-9 is not the meaning of “Female”. Keep permissible value meanings aligned to the actual value set codes (likely SNOMED CT), and only update the data element id / slot name to loinc_76689_9.
  src/rarelink/tofhir/mappings/ips.patient.json:1
• This mapping switches the source field to loinc_76689_9 but still hardcodes SNOMED CT system/version and SNOMED code 281053000 in the codeDefinition extension. If the data element is now defined by LOINC 76689-9, the codeDefinition (system/code/display) should be updated to LOINC (e.g., http://loinc.org + 76689-9) to avoid emitting inconsistent metadata.
  src/rarelink/tofhir/mappings/ips.patient.json:1
• This mapping switches the source field to loinc_76689_9 but still hardcodes SNOMED CT system/version and SNOMED code 281053000 in the codeDefinition extension. If the data element is now defined by LOINC 76689-9, the codeDefinition (system/code/display) should be updated to LOINC (e.g., http://loinc.org + 76689-9) to avoid emitting inconsistent metadata.
  src/rarelink/phenopackets/pipeline.py:1
• The docstring specifies progress_callback: callable(record_id, success, error), but the implementation calls it with keyword arguments (success=..., error=...). Callbacks implemented as simple positional-only callables (or lambda rid, ok, err: ...) may break if they don’t accept these keywords. Prefer calling with positional arguments (or update the documented callback contract/type hints to explicitly require these keyword names).
  src/rarelink/phenopackets/pipeline.py:1
• The docstring specifies progress_callback: callable(record_id, success, error), but the implementation calls it with keyword arguments (success=..., error=...). Callbacks implemented as simple positional-only callables (or lambda rid, ok, err: ...) may break if they don’t accept these keywords. Prefer calling with positional arguments (or update the documented callback contract/type hints to explicitly require these keyword names).
  src/rarelink/phenopackets/write.py:1
• File output should specify an explicit encoding (typically UTF-8) to avoid platform-dependent defaults and ensure consistent JSON output across environments. Open the file with encoding=\"utf-8\".
  src/rarelink/phenopackets/adapter/ontology_routing_adapter.py:1
• _PREFIX_RE is defined but not used anywhere in this module (prefix parsing is handled by process_code() and string splitting). Remove it to reduce dead code, or use it consistently in _get_prefix() if regex-based parsing is intended.
  src/rarelink/phenopackets/validate.py:1
• New validation behavior is introduced (structural checks, CURIE checks, optional CLI invocation). There’s existing phenopackets test coverage in tests/phenopackets/, but no tests are added here for validate_phenopackets()/_python_validate() outcomes (e.g., missing metaData keys, bad CURIE formats, and the branch where phenopacket-tools is not present). Add unit tests to lock down these rules and avoid regressions in what is considered a validation failure vs warning.

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