fix consolidate training run outputs into a single runs/ directory

[sudhansu-24]

Describe your changes

Training and evaluation artifacts are written under a single directory runs/<run-name>/: ModelCheckpoint uses runs/<run-name>/checkpoints/, Trainer(default_root_dir=...) keeps Lightning CSV logs under that run instead of a top-level lightning_logs/, and WandbLogger / CustomMLFlowLogger use save_dir=run_dir so internal logger paths and code using self.logger.save_dir (e.g. plots) stay under the run root. Checkpoints remain outside W&B’s wandb/ subtree so large files are not synced by default.

Motivation: Issue #293 and maintainer feedback (W&B selective sync, common run root, MLflow temp images not in CWD).
Dependencies: None

Issue Link

closes #293

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• 🐛 Bug fix (non-breaking change that fixes an issue)
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[joeloskarsson]

@sadamov assigning you here to decide later if this should be closed in favor of #297 or what is the best path forward with this.

[sudhansu-24]

thanks @sadamov for clarifying.

I’ll continue implementation/revisions on #580 and coordinate here.
@Shyam-Sunder-saini @techaadii, if you have any pending changes or preferences from your earlier work that should be included please share them and i will incorporate them into this pr so we can converge quickly

[Shyam-Sunder-saini]

Thanks @sudhansu-24 for taking this forward!

From my side, I’ve aligned all training artifacts so they are now scoped under runs/<run-name>/, including checkpoints, Lightning logs, W&B, and MLflow outputs.

I also updated the logger setup so that both WandbLogger and CustomMLFlowLogger use the same save_dir (run directory). Additionally, MLflow now falls back to the run directory if MLFLOW_TRACKING_URI is not set.

Currently, only one logger is active at a time (default is W&B), and MLflow artifacts are generated when explicitly running with --logger mlflow.

If there are any preferences around structure or logging behavior from earlier work, I’m happy to incorporate them.

Let me know if you’d like me to push any additional changes to the PR.

[sudhansu-24]

Thanks @Shyam-Sunder-saini

could you share the exact changes you want added beyond the current #580 state (especially around the MLFLOW_TRACKING_URI fallback) either as:

a short checklist by file, or a commit/PR branch we can cherry-pick from?

if you post that i will incorporate it quickly so we can finalize review.