feat: support multiple DR parameter sets in a single prepare run#48
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Allow inline per-method parameter overrides in the -m flag using colon syntax with semicolon-separated params. This enables comparing the same DR method with different parameters in a single run without re-running the full pipeline. Example: -m "umap2:n_neighbors=15" -m "umap2:n_neighbors=50" -m pca2 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
Centralize the param-suffix rule used by ReductionPipeline._run_reductions into a single helper so cli/project.py can share it (follow-up commit). Includes a regression test for the mixed plain+override case (`-m umap2 -m umap2:n_neighbors=50`) which currently emits "ProtT5 — UMAP 2" and "ProtT5 — UMAP 2 (n=50)". Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
- Add _run_with_overridden_config(base, effective_params, method, dims, data) to pipeline.py to centralize the save/restore pattern for BaseProcessor.config. A leaked `precomputed` flag (or any temporary key) can no longer survive across reduction calls. - Update ReductionPipeline._run_reductions and cli/project.py to use both the new helper and disambiguation_suffix. cli/project.py previously set base.config without restoring it; this is now handled in one place. - Hoist the lazy in-test imports added in the previous commit to the top-level import block in tests/test_pipeline_utils.py. Addresses PR #48 review feedback. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
The precomputed-MDS branch in _run_reductions was the last call site still mutating self.base.config in place (set precomputed=True, then pop() after). Migrate it to _run_with_overridden_config so: - The save/restore pattern is consistent across all reduction call sites. - A precomputed flag can no longer survive in base.config if process_reduction raises mid-call. Regression tests cover both the happy path (flag is set during reduction, cleared after) and the exception path (flag is cleared even when reduction raises). Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
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- Add _run_with_overridden_config(base, effective_params, method, dims, data) to pipeline.py to centralize the save/restore pattern for BaseProcessor.config. A leaked `precomputed` flag (or any temporary key) can no longer survive across reduction calls. - Update ReductionPipeline._run_reductions and cli/project.py to use both the new helper and disambiguation_suffix. cli/project.py previously set base.config without restoring it; this is now handled in one place. - Hoist the lazy in-test imports added in the previous commit to the top-level import block in tests/test_pipeline_utils.py. Addresses PR tsenoner#48 review feedback. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
martinpycha
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May 20, 2026
feat: support multiple DR parameter sets in a single prepare run
martinpycha
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to d0rr4/PP1
that referenced
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May 20, 2026
Follow-up to PR tsenoner#48 review feedback. - docs/cli.md: rewrite -m flag description to spell out the comma-vs-semicolon rule explicitly, add an "Overridable parameters" subsection listing the 11 valid override keys with their abbreviations and types, and extend "Projection Naming" with an example of the parameter-suffix disambiguation behavior. - notebooks/ProtSpace_Preparation.ipynb: insert an informational markdown cell pointing power users at the CLI for parameter sweeps, since the toggle UI runs each method only once. No code or behavior changes; release-bot will not bump the version. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
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Summary
Closes #46.
-mflag:-m "umap2:n_neighbors=50;min_dist=0.1"-mis now repeatable:-m "umap2:n_neighbors=15" -m "umap2:n_neighbors=50" -m pca2ProtT5 — UMAP 2 (n=50))prepareandprojectcommands support the new syntaxNew types
MethodSpecfrozen dataclass:(method, dims, overrides)— replaces bare stringsparse_methods_arg(): parses repeatable-mwith comma+colon+semicolon syntaxFiles changed
pipeline.py—MethodSpec,parse_method_spec(),parse_methods_arg(),_run_reductions(), cache helpersembedding_set.py—format_param_suffix(), extendedformat_projection_name()common_options.py—Opt_Methodschanged fromstrtolist[str] | Noneprepare.py,project.py— wired up new parsingdocs/cli.md,CLAUDE.md, notebook — documentation updatedtest_pipeline_utils.py— 29 new tests (41 → 70)Test plan
uv run pytest tests/ -m "not slow")-m pca2,umap2works unchanged-m "umap2:n_neighbors=15" -m "umap2:n_neighbors=50" -m pca2produces 3 projections with correct namesProtT5 — UMAP 2 (n=15),ProtT5 — UMAP 2 (n=50),ProtT5 — PCA 2🤖 Generated with Claude Code