Improve time and memory tracking for Babel runs

[gaurav]

Add benchmark: directives, localrules, and download resource limits

• Add benchmark: to every non-trivial rule across all 19 snakefiles, writing per-rule wall time / max_rss TSVs to babel_outputs/benchmarks/. Wildcard rules include the wildcard in the filename; loop-generated rules in reports.snakefile use an f-string path.
• Declare localrules for trivial done-marker rules (all, all_outputs, clean_compendia, clean_downloads, export_all_to_kgx, export_all_to_sapbert_training, export_all_{compendia,synonyms,}_to_duckdb, all_reports) so they run on the head node without a SLURM allocation.
• Add resources: mem="8G", cpus_per_task=1 to pure download rules in datacollect.snakefile and publications.snakefile; add runtime="6h" to large downloads (UniProtKB idmapping/trembl, UMLS).
• Add slurm/README.md documenting the profile, benchmark TSV fields, efficiency CSV, known resource hotspots, and future improvements.

[Copilot]

Pull request overview

Adds standardized benchmarking and SLURM-oriented execution tweaks across the Babel Snakemake workflow to improve per-rule time/memory tracking and reduce unnecessary cluster allocations.

Changes:

• Add benchmark: outputs for most non-trivial rules across the workflow, writing TSVs under babel_outputs/benchmarks/.
• Mark trivial aggregation/done-marker rules as localrules so they run on the head node (no SLURM allocation).
• Add explicit resources overrides for download-heavy rules and document the SLURM profile/benchmark outputs.

Reviewed changes

Copilot reviewed 22 out of 23 changed files in this pull request and generated 1 comment.

Show a summary per file

File	Description
uv.lock	Bumps rumdl lock entry to 0.1.26.
pyproject.toml	Updates dev dependency constraint to rumdl>=0.1.26.
Snakefile	Declares top-level localrules and adds benchmarking for uncompress_synonym_file.
src/snakefiles/anatomy.snakefile	Adds per-rule benchmark TSV outputs across anatomy rules.
src/snakefiles/cell_line.snakefile	Adds per-rule benchmark TSV outputs across cell line rules.
src/snakefiles/chemical.snakefile	Adds per-rule benchmark TSV outputs across chemical rules (incl. multi-step compendia).
src/snakefiles/datacollect.snakefile	Adds benchmark TSVs and sets resource overrides for download/I/O-heavy rules.
src/snakefiles/diseasephenotype.snakefile	Adds per-rule benchmark TSV outputs across disease/phenotype rules.
src/snakefiles/drugchemical.snakefile	Adds per-rule benchmark TSV outputs across drug/chemical conflation rules.
src/snakefiles/duckdb.snakefile	Marks aggregation exports as localrules; adds benchmarks for exports and DuckDB reports.
src/snakefiles/exports.snakefile	Marks export aggregators as localrules; adds benchmarks for per-file exports.
src/snakefiles/gene.snakefile	Adds per-rule benchmark TSV outputs across gene rules.
src/snakefiles/genefamily.snakefile	Adds per-rule benchmark TSV outputs across gene family rules.
src/snakefiles/geneprotein.snakefile	Adds per-rule benchmark TSV outputs across gene/protein conflation rules.
src/snakefiles/leftover_umls.snakefile	Adds benchmark TSV outputs for leftover UMLS and compression steps.
src/snakefiles/macromolecular_complex.snakefile	Adds per-rule benchmark TSV outputs across macromolecular complex rules.
src/snakefiles/process.snakefile	Adds per-rule benchmark TSV outputs across process/pathway rules.
src/snakefiles/protein.snakefile	Adds per-rule benchmark TSV outputs across protein rules.
src/snakefiles/publications.snakefile	Adds resource overrides for PubMed download and benchmarks across publication rules.
src/snakefiles/reports.snakefile	Marks all_reports as local; adds benchmarks including loop-generated per-compendium report rules.
src/snakefiles/taxon.snakefile	Adds per-rule benchmark TSV outputs across taxon rules.
slurm/README.md	Documents SLURM profile usage, benchmark TSV fields, and operational notes/hotspots.
docs/RunningBabel.md	Minor whitespace update at end of doc.

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[Copilot]

The README references run_babel_on_slurm.sh, but the repo script is named slurm/run-babel-on-slurm.sh (hyphens). Update the filename/path here so readers can find the script without guesswork.

Suggested change

	`run_babel_on_slurm.sh`) still reference the old conda environment and hardcoded paths.
	`slurm/run-babel-on-slurm.sh`) still reference the old conda environment and hardcoded paths.