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[ypriverol]

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ℹ️ Review info

⚙️ Run configuration

Configuration used: defaults

Review profile: CHILL

Plan: Pro

Run ID: c5cb2133-2bec-4a9d-8eb5-4dc7377011b2

📥 Commits

Reviewing files that changed from the base of the PR and between c3bec9b and 5c5cbd7.

⛔ Files ignored due to path filters (4)

• docs/images/favicon.svg is excluded by !**/*.svg
• docs/logo/mokume_logo.svg is excluded by !**/*.svg
• docs/logo/mokume_logo_darkbg.svg is excluded by !**/*.svg
• docs/logo/mokume_mark.svg is excluded by !**/*.svg

📒 Files selected for processing (32)

• .github/workflows/deploy-docs.yml
• .gitignore
• docs/overrides/main.html
• mkdocs.yml
• mokume/core/dataset.py
• mokume/core/duckdb_backend.py
• mokume/core/registry.py
• mokume/core/schema.py
• mokume/export/__init__.py
• mokume/export/anndata.py
• mokume/export/csv.py
• mokume/harmonization/__init__.py
• mokume/harmonization/base.py
• mokume/harmonization/combat.py
• mokume/harmonization/correction.py
• mokume/harmonization/models.py
• mokume/imputation/base.py
• mokume/imputation/knn.py
• mokume/imputation/simple.py
• mokume/io/qpx_adapter.py
• mokume/normalization/base.py
• mokume/normalization/feature_normalizers.py
• mokume/normalization/sample_normalizers.py
• mokume/pipeline/flows/__init__.py
• mokume/pipeline/flows/directlfq.py
• mokume/pipeline/flows/ratio.py
• mokume/pipeline/flows/standard.py
• mokume/pipeline/runner.py
• mokume/quantification/median.py
• tests/test_cecilia_integration.py
• tests/test_dataset.py
• tests/test_registry.py

✨ Finishing Touches

🧪 Generate unit tests (beta)

• Create PR with unit tests
• Commit unit tests in branch docs/quantms-theme-update

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[codacy-production]

Not up to standards ⛔

🔴 Issues 71 high · 12 medium · 17 minor

Alerts:
⚠ 100 issues (≤ 0 issues of at least minor severity)

Results:
100 new issues

Category	Results
UnusedCode	10 medium 2 minor
Documentation	14 minor
ErrorProne	7 high
Security	2 medium 64 high
CodeStyle	1 minor

View in Codacy

🟢 Metrics 577 complexity · 5 duplication

Metric	Results
Complexity	577
Duplication	5

View in Codacy

_{TIP This summary will be updated as you push new changes. Give us feedback}

[ypriverol]

Replaced by clean PR with only deployment workflow changes