Add test suite, CI/codecov, and packaging docs; fix two latent bugs#4
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Tests: expand from 52 to 154 passing tests across the package (network, pathway analysis, workflows, repair, prior reconciliation, simulation, and comparison modules). Fixes: - network.py: add missing `verbose` param to extract_indra_prior (referenced an undefined name -> NameError on every call) - models.py: correct `node_name not in "Output"` substring checks to `"Output" not in node_name`, matching the read-site predicates Chore: add CI workflow (lint + pytest + Codecov upload), coverage badge, LICENSE/CONTRIBUTING/CHANGELOG, and point all repo URLs at Vitek-Lab/Causomic. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
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📝 WalkthroughWalkthroughThis PR adds CI/packaging infrastructure and project docs, introduces a new pathway over-representation/diversity-selection/Cytoscape-export module, fixes an output-node gating bug in causal models, threads a ChangesProject Infrastructure and Packaging
Library Verbose Flags, Pathway Analysis, and Cleanup
Estimated code review effort: 4 (Complex) | ~75 minutes Sequence Diagram(s)sequenceDiagram
participant User
participant workflows as run_toxicity_detection_workflow
participant graph_construction as query_forward_paths
participant network as estimate_posterior_dag
participant repair as repair_confounding
User->>workflows: call with input_data, verbose
workflows->>graph_construction: build INDRA prior
graph_construction-->>workflows: prior graph
workflows->>network: estimate_posterior_dag(verbose=verbose)
network-->>workflows: posterior_network
workflows->>repair: repair_confounding(verbose=verbose)
repair-->>workflows: repaired_network
workflows-->>User: (indra_prior, posterior_network, repaired_network)
Poem
✨ Finishing Touches📝 Generate docstrings
🧪 Generate unit tests (beta)
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Tests: expand from 52 to 154 passing tests across the package (network, pathway analysis, workflows, repair, prior reconciliation, simulation, and comparison modules).
Fixes:
verboseparam to extract_indra_prior (referenced an undefined name -> NameError on every call)node_name not in "Output"substring checks to"Output" not in node_name, matching the read-site predicatesChore: add CI workflow (lint + pytest + Codecov upload), coverage badge, LICENSE/CONTRIBUTING/CHANGELOG, and point all repo URLs at Vitek-Lab/Causomic.
Motivation and context
This change expands the package with broader analysis, simulation, validation, and workflow support while adding substantial test coverage. It also fixes two latent bugs: an undefined
verbosereference inextract_indra_prior, and incorrect"Output"substring checks in the causal model code. In parallel, the repository is made more production-ready with CI, packaging, documentation, and branding updates.Changes
Vitek-Lab/Causomic.LICENSECONTRIBUTING.mdCHANGELOG.mdcausal_modeldata_analysisgraph_constructionsimulationvalidationextract_indra_priorby adding the missingverboseparameter."Output"node detection logic inmodels.py.main()demo entry points..gitignorefor local dev artifacts.Tests
Added or expanded coverage for:
Coding guidelines violated
None identified.