Migration#2

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pmayd wants to merge 141 commits intodevfrom

Commits on Nov 28, 2025

Commits on Dec 9, 2025

ruff check
pmayd
committed

Commits on Dec 27, 2025

fix header merge forward-fill for group headers like observations_category

Michael Aydinbas
and
claude
committed
use Excel merge metadata for header forward-fill instead of heuristics

Michael Aydinbas
and
claude
committed
fix openpyxl warning filter to match submodules

Michael Aydinbas
and
claude
committed
perf: replace Excel merge metadata with synonym validation (6.6x faster)

Michael Aydinbas
and
claude
committed
fix: convert height from cm to m before BMI calculation

Michael Aydinbas
and
claude
committed

Commits on Dec 28, 2025

fix: date parsing truncated dd-Mon-yyyy format (11 chars) to 10

Michael Aydinbas
and
claude
committed
test: add R extraction error exceptions for Mandalay trackers

Michael Aydinbas
and
claude
committed
test: add R extraction error exception for NPH tracker

Michael Aydinbas
and
claude
committed
fix: calculate age/t1d_diagnosis_age from DOB, handle Excel errors

Michael Aydinbas
and
claude
committed

Commits on Feb 20, 2026

Commits on Feb 25, 2026

Commits on Feb 26, 2026

format code
Michael Aydinbas
committed
Add clean output, CLI step output, and setup guide
Michael Aydinbas
committed
rename just commands, fix error in tests, fix max_workers not working for run-local
Michael Aydinbas
committed

Commits on Feb 27, 2026

Improve CLI UX, GCS performance, and GCP setup
Michael Aydinbas
committed

Commits on Feb 28, 2026

Add backup-bq and fix logs-job in justfile
Michael Aydinbas
committed

Commits on Mar 1, 2026

Audit and update docs: remove obsolete files, update to reflect current state
Michael Aydinbas
committed
Move all GCP resources to asia-southeast2 (Jakarta) for data residency
Michael Aydinbas
committed
Fix uv not found in Docker and update justfile region to Jakarta
Michael Aydinbas
committed
Fix Docker build: add UV_PYTHON_DOWNLOADS and copy README.md
Michael Aydinbas
committed
Fix Docker build: split uv sync to avoid editable install before src/ exists
Michael Aydinbas
committed
Add gcloud command to list images in Artifact Registry after docker-push
Michael Aydinbas
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Add local Docker test instructions and docker-smoke just command
Michael Aydinbas
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Add --provenance=false to docker-build to suppress attestation manifests
Michael Aydinbas
committed
Add git-SHA tagging strategy and rollback command to justfile
Michael Aydinbas
committed
Add docker-list command to justfile
Michael Aydinbas
committed
Reorder and group justfile into logical sections
Michael Aydinbas
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Fix E402: move warnings.filterwarnings after imports in cli.py
Michael Aydinbas
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Fix ty type errors: PolarsDataType annotation and tqdm isinstance check
Michael Aydinbas
committed
Update Cloud Run Job spec: bump to 8 vCPU / 8 GiB, add jobs list command
Michael Aydinbas
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Code cleanup: remove unused imports, fix forward reference, reformat
Michael Aydinbas
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Add --platform=linux/amd64 to docker-build for Cloud Run compatibility
Michael Aydinbas
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Fix CI test failures by excluding slow and integration tests
Michael Aydinbas
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Fix reference_data path resolution in Docker/Cloud Run
Michael Aydinbas
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Switch parallel processing from ProcessPoolExecutor to ThreadPoolExecutor
Michael Aydinbas
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Update SETUP.md: fix BigQuery IAM grant command
Michael Aydinbas
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Restore clean console output for parallel pipeline runs
Michael Aydinbas
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Revert to ProcessPoolExecutor; add docker-clean command
Michael Aydinbas
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Fix GCS upload: timestamped prefix, upload only tables and logs
Michael Aydinbas
committed
Fix BigQuery loading: delete-before-recreate and update logs clustering
Michael Aydinbas
committed
Add clinic_data_static table creation
Michael Aydinbas
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Add error_code classification to pipeline logs
Michael Aydinbas
committed
Fix CLI test runner for CI environment
Michael Aydinbas
committed