WIP: Add bcrlarch to cf-paired-loci phylo benchmarking framework#336
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davidrich27 wants to merge 5 commits intopsathyrella:mainfrom
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WIP: Add bcrlarch to cf-paired-loci phylo benchmarking framework#336davidrich27 wants to merge 5 commits intopsathyrella:mainfrom
davidrich27 wants to merge 5 commits intopsathyrella:mainfrom
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add_to_scan_cmd crashed with TypeError when vstr was Python None (rather than string 'None'), which occurs when all scan variables have single values. Also add bcrl_methods to the padded_seq_info_list initialization so bcrlarch-pars gets proper ambiguous base handling. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Add --smoke-test flag that runs the full bcrlarch-pars pipeline with minimal settings (1 event, 1 time point, 1 replicate, no parallelism) for end-to-end validation. Also update default output path to _benchmark_output/ and add _temp/ and _benchmark_output/ to .gitignore. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
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Summary
bcrlarchas a phylogenetic inference method in partis so it can be benchmarked alongside iqtree, raxml, gctree, gctree-mut-mult, igphyml via thecf-paired-loci.pyvalidation pipelinerun-validation.shwrapper script for running the pipeline with standard parametersChanges
partis/treeutils.py— register bcrlarch in the phylo inference machinery:inf_anc_methodsandall_phylo_methodsmethod listsgetcmd(): generate arun.shthat activates thebcr-larch-experimentspixi environment and runsbcrlarch-run.py(same pattern as raxml's shell wrapper)ofn(): outputtree.nwk/inferred-seqs.fa(same as gctree/igphyml)read_inf_seqs(): read inferred ancestors frominferred-seqs.fa(same pattern as gctree)test/cf-paired-loci.py— add'bcrlarch'tophylo_actions, which auto-generatesbcrlarch-tree-perfand wires it into--actions bcrlarchand--actions tree-perfrun-validation.sh(new) — wrapper script for the validation pipeline with standard parameters (obs-times, sim-events, carry-cap, etc.) and a--tree-perf-basicshortcut that includes bcrlarchNotes
bcr-larch-experiments/is a sibling directory topartis/, resolved viaos.path.dirname(utils.get_partis_dir())pixi shell-hookfor environment activation (unlike gctree/igphyml which use mamba)bcrlarch-run.pyrunner script follows the same interface as gctree/igphyml:--infname,--outdir,--root-label; outputstree.nwkandinferred-seqs.faTest plan
./run-validation.sh --actions bcrlarch --dry-runtree.nwkandinferred-seqs.faoutput./run-validation.sh --actions bcrlarch-tree-perf