[juliendrapeau]

Summary

• Consolidate data/, results/, and sweeps/ under experiments/<stage>/<exp>/ to keep all per-experiment artifacts co-located.
• Reorganize hpc/ config files into hpc/config/; replace hardcoded CLUSTER_ROOTS dict with a clusters.yaml file that users copy from a template.
• Add workflow/plots/ matplotlib style infrastructure (common utilities + 4 mplstyles: default, one-column, two-column, presentation).
• Add use_hash option and duplicate-path detection to ConfigSet.slugify_all.

Changes

experiments/ directory structure

data/, results/, and sweeps/ are replaced by a unified experiments/ tree:

experiments/<stage>/<exp>/
  sweeps/          ← sweep scripts and summary.csv (tracked example)
  data/            ← per-job outputs (gitignored)
  results/         ← aggregated CSVs (gitignored)

Updated Snakefile, rules, workflow_example.yaml, docs, and all template snippets. The old data/ and results/ root directories remain gitignored for backward compat.

hpc/config/ reorganization

hpc/config_example.yaml and hpc/submit_example.yaml move to hpc/config/. A new hpc/config/clusters_example.yaml replaces the hardcoded CLUSTER_ROOTS dict in lifecycle.py: users copy it to hpc/config/clusters.yaml (gitignored) and fill in their SSH host aliases and scratch paths. The --profile hpc flag in run_snakemake.sh is updated to --profile hpc/config.

workflow/plots/ matplotlib style infrastructure

New workflow/plots/ package with common.py (use_style, read_results_csv, style constants) and four mplstyles: default, one_column, two_column, and presentation.

ConfigSet.slugify_all improvements

• use_hash=True uses each config's content hash as the directory name instead of a human-readable slug — guarantees uniqueness when slugs would collide.
• After assigning paths, duplicate detection raises ValueError listing all collisions.
• Both options are threaded through generate_and_save.

Version

Bumped to 0.5.0.

[github-actions]

☂️ Python Coverage

current status: ✅

Overall Coverage

Lines	Covered	Coverage	Threshold	Status
59	55	93%	90%	🟢

New Files

No new covered files...

Modified Files

No covered modified files...

updated for commit: 2cc818f by action🐍