…ow-ups Adds configurable length limits, a CI workflow, an end-to-end SLURM wiring test, and closes the remaining review follow-ups. Length filtering (issue #33 + requested total caps): - Skip folds before any job is created when they exceed a length limit, so an oversized complex never wastes a feature/GPU allocation that would only OOM. - max_total_length_alphafold2: 5000 / max_total_length_alphafold3: 7000 (selected by --fold_backend; optional single `max_total_length` override). - max_protein_length (0=off, issue #33): a protein over the limit drops every fold containing it, so it is never downloaded. - Lengths resolved at parse time: local FASTA -> data/<id>.fasta -> persistent cache <output_directory>/.sequence_lengths.tsv -> UniProt REST API (length_filter_fetch_uniprot, default true). Skipped folds + reasons go to <output_directory>/skipped_folds.tsv; unknown lengths fail open (kept). - Fixes copy-number parsing: AlphaPulldown spec is name:copies:region, so the copy count is the first ':' token after the name (A:2:1-100 = 2 copies), not the last. Review follow-ups: - #1: integration test feeds our computed mem_mb through the real SLURM plugin's get_submit_command and asserts it becomes `sbatch --mem <value>` (skips if the plugin is absent). - #2: GitHub Actions CI (.github/workflows/ci.yml) byte-compiles common.smk and runs the dependency-free unit suite on py3.10/3.12. - #5: AF2 precomputed-feature inference sizing now recovers length from the parse-time length cache (no FASTA / no AF3 JSON needed). - #6: AF3 ligand atoms are intentionally not counted (no sequence); documented, with a test asserting ligand entries contribute 0. The parse-time length cache is shared with memory sizing, so precomputed-feature runs get correct length-aware memory too. 18 unit tests pass; AF2/AF3/precomputed dry-runs build clean. Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>

Add instructions for snakemake setup in the documentation #5

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