fix(tracking)!: switch mlflow from deprecated mlruns to sqllite db by pizzajojo · Pull Request #122 · CAIIVS/raitap

pizzajojo · 2026-05-08T15:32:57Z

Summary

- Migrate the default local MLflow tracking backend from deprecated filesystem storage to SQLite.

- Add persistent MLflow UI behavior so `tracking.open_when_done=true` leaves the local UI/server available after a run.

- Remove the stale `mlflow_server.yaml` preset from the old standalone launcher path.

- Update MLflow tracking docs and tests for the new SQLite-backed default.

Key Changes

- Default backend store URI is now `sqlite:///mlflow/mlflow.db`.

- Default artifact root is now `./mlflow/artifacts`.

- Local MLflow server startup now passes `--backend-store-uri` and `--default-artifact-root`.

- Direct SQLite UI startup uses `mlflow ui --backend-store-uri ...`.

- When reusing an already-open direct SQLite UI port, RAITAP now logs a warning that the existing UI may point to a different backend.

- Added constants for the default MLflow UI host/port instead of hardcoded literals.

- `tracking.output_forwarding_url` remains the supported way to connect to an existing/company MLflow server.

Checklist

CI — Required checks are green
Breaking changes — If this PR breaks compatibility (API, configs, file formats, etc.), the title uses ! after the type or scope (e.g. feat!: or feat(transparency)!:). I understand that this change will have a direct, disruptive impact on package users. I ensured that this change is absolutely necessary and cannot be delayed.
Contributor guide — I’ve read Pull requests and commit messages before requesting review.

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Issue — A GitHub issues is linked to this PR ("Development" section in the right sidebar).
Docs — User or contributor docs updated where needed.
Tests — New or updated tests cover the change.

Copilot

Pull request overview

Warning

The PR contains breaking changes, but the tiles does not contain "!". Please mark it as breaking by adding "!" after the type or scope (e.g. feat!: or feat(api)!:).

This PR migrates RAITAP’s default local MLflow tracking storage from the deprecated file-store layout (./mlruns) to a SQLite-backed store, and updates the MLflow launcher behavior so tracking.open_when_done=true keeps the local UI/server available after a run.

Changes:

Default local MLflow backend store switched to sqlite:///mlflow/mlflow.db with artifact root ./mlflow/artifacts, and local server/UI startup now passes these explicitly.
MLFlowTracker now ensures local paths exist, ensures direct-store experiments exist (with an explicit artifact location), and preserves spawned UI/server processes when open_when_done=true.
Tests and documentation updated for the SQLite-backed default; legacy mlflow_server.yaml removed.

Reviewed changes

Copilot reviewed 8 out of 8 changed files in this pull request and generated 5 comments.

Show a summary per file

File	Description
src/raitap/tracking/mlflow_tracker.py	Implements SQLite default backend/artifact roots, server/UI CLI args, local path preparation, and new UI persistence behavior.
src/raitap/configs/tracking/mlflow.yaml	Adds default `backend_store_uri` and `default_artifact_root` to the MLflow tracking preset.
src/raitap/configs/tracking/mlflow_server.yaml	Removes obsolete standalone launcher preset.
src/raitap/configs/schema.py	Extends `TrackingConfig` with `backend_store_uri` and `default_artifact_root`.
src/raitap/tracking/tests/test_mlflow_tracker.py	Adds/updates mock-driven tests covering SQLite defaults, server/UI invocation, and terminate behavior.
src/raitap/tracking/README.md	Updates tracking smoke-test docs and adds migration guidance for existing `mlruns` histories.
docs/modules/tracking/frameworks-and-libraries.md	Documents the new SQLite default and migration command.
docs/modules/tracking/configuration.md	Updates `output_forwarding_url` default behavior text and CLI example for enabling tracking.

stanlrt · 2026-05-08T20:12:31Z

  log_model: true

-:cli: tracking=mlflow tracking.log_model=true
+:cli: +tracking=mlflow tracking.log_model=true


because tracking is not in our default config.yaml. + is used in mflow to add a property/config without it you overwrite existing config/properties. see below:\

❯ uv run raitap tracking=mlflow Built raitap @ file:///Users/jonasvonderhagen/raitap Uninstalled 1 package in 7ms Installed 1 package in 2ms Could not override 'tracking'. No match in the defaults list. To append to your default list use +tracking=mlflow

we can also add tracking=null to config.yaml

stanlrt · 2026-05-08T20:13:01Z

 _target_: MLFlowTracker
-output_forwarding_url: http://127.0.0.1:5000
+output_forwarding_url: http://127.0.0.1:5001
+backend_store_uri: sqlite:///mlflow/mlflow.db


why are we setting the default values?

I removed backend_store_uri, default_artifact_root, log_model, and open_when_done from the preset so it only defines the MLflow target and local server URL.

stanlrt · 2026-05-08T20:13:09Z

+default_artifact_root: ./mlflow/artifacts
 log_model: false
-open_when_done: true
+open_when_done: true


isnt this the default?

stanlrt · 2026-05-08T20:13:30Z

 class TrackingConfig:
    _target_: str = "MLFlowTracker"
    output_forwarding_url: str | None = None
+    backend_store_uri: str | None = None


that does not match the docs. if the defaults are MLFlow specific, it is correct to not set them here. but the docs should be updated (config and mlflow pages)

docs updated

stanlrt · 2026-05-08T20:15:38Z

                else:
                    logger.info("MLflow UI is ready at %s", url)
+            else:
+                logger.warning(


see #124 and

waiting for merge

rebased and addapted logging

Remove duplicated default values from the +tracking=mlflow preset and document MLFlowTracker-specific fallback behavior separately from generic TrackingConfig defaults. Align MLflow examples to the preset's 127.0.0.1:5001 server URL. Refs: - #122 (comment) - #122 (comment)

…eriment

…nishing run

…is taken on mac

Remove duplicated default values from the +tracking=mlflow preset and document MLFlowTracker-specific fallback behavior separately from generic TrackingConfig defaults. Align MLflow examples to the preset's 127.0.0.1:5001 server URL. Refs: - #122 (comment) - #122 (comment)

Copilot AI review requested due to automatic review settings May 8, 2026 15:32

pizzajojo linked an issue May 8, 2026 that may be closed by this pull request

Migrate MLFlow to the newer DB storage #109

Open

Copilot started reviewing on behalf of pizzajojo May 8, 2026 15:33 View session

Copilot AI reviewed May 8, 2026

View reviewed changes

Comment thread src/raitap/tracking/mlflow_tracker.py Outdated

Comment thread src/raitap/tracking/mlflow_tracker.py

Comment thread src/raitap/tracking/mlflow_tracker.py Outdated

Comment thread docs/modules/tracking/configuration.md

Comment thread src/raitap/tracking/tests/test_mlflow_tracker.py

pizzajojo requested a review from stanlrt May 8, 2026 16:59

pizzajojo self-assigned this May 8, 2026

pizzajojo changed the title ~~fix(tracking): switch mlflow from deprecated mlruns to sqllite db~~ fix(tracking)!: switch mlflow from deprecated mlruns to sqllite db May 8, 2026

stanlrt requested changes May 8, 2026

View reviewed changes

pizzajojo added 13 commits May 10, 2026 08:07

fix(tracking): switch from deprecated mlruns to sqllite db

fa8e609

refactor(tracking): remove unused MLflow server configuration

9a302a0

test(tracking): add test for reusing existing SQLite-based MLflow exp…

850ee79

…eriment

feat(tracking): open current experiment rather than main page upon fi…

99b643f

…nishing run

fix(tracking): update MLflow forwarding URL to use port 5001 as 5000 …

c22c10a

…is taken on mac

fix(tracking): normalize mlflow config fallbacks

07129c9

fix(tracking): avoid unused mlflow local storage setup

07abbdc

test(tracking): cover explicit sqlite mlflow path setup

ef62793

docs(tracking): document mlflow backend storage options

5998cd7

test(tracking): isolate mlflow tracker fixture storage

9ccce57

chore: fix ruff formatting

971b2b2

test(tracking): expect raitap_log warning for reused MLflow UI

38abd17

pizzajojo force-pushed the 109-migrate-mlflow-to-the-newer-db-storage branch from 1ffc521 to 38abd17 Compare May 10, 2026 06:18

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stanlrt May 8, 2026 • edited Loading Uh oh! There was an error while loading. Please reload this page.

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pizzajojo commented May 8, 2026 •

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stanlrt May 8, 2026 •

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