Plot fixes, filename centralization, and pre-release option lockout - #246
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RunpengLuo merged 4 commits intoJul 31, 2026
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…layout; prune dead config
Styling:
- Move all plot hyper-parameters into hatchet.yaml under plot_* keys, shared
across cluster-bins (plot-rdr-baf), plot-cn, and plot-panel via a single
get_plot_style(args); register them as hidden CLI flags
(add_arguments_plot_style).
cluster-bins plots:
- Split K plots into K{k}.pdf (1D/2D) + K{k}.diagnostic.pdf; only bulk.K{k}.pdf
copied to bbc/.
- Unify 1D onto the multi-sample layout matching plot-cn (all samples one page,
2 rows/sample); fix gray-axes box, drop "sample=" titles, snug legend, pad
mhBAF/RDR ranges.
plot-panel:
- Always show all clones; drop show_prop inlining and min_prop filtering, which
mishandled the multi-sample case (iloc[0]).
- Forward the resolved plot_* style to plot_1d2d sub-runs instead of dead
hardcoded constants.
compute-cn:
- Move run_plot_cn and plot_pareto_curve (was plot_pareto_pdf) into
plot_compute_cn.py; config-driven.
- Remove dead filtering() (superseded by cluster-bins filter_clusters);
reorder compute_cn_utils.py into labeled sections.
Cleanup:
- Remove dead show_prop config (hatchet.yaml + --show_prop flag).
- tests: fix snakemake config section names (underscore -> hyphen).
- gitignore: ignore .vscode/.
…labels - Add src/hatchet/filenames.py as the single source of truth for pipeline input/output/subdirectory names (constants + templated helpers). Wire cluster-bins, compute-cn, evaluate, plot, and utils through it so producer/consumer filename contracts (gammas, best.*.ucn, summary, results.*, objectives, sols/) cannot silently drift. Legacy evaluate_pool_solutions names (no current producer) are flagged, not faked. - plot_compute_cn: rename _format_pool_label -> _fmt_pool_label, add _fmt_prop, inline per-sample clone proportions in pool-panel y-labels.
- Drop the bin_dir U-initialization entirely: remove _random_tumor_matrix_bin_dir, its build_random_u branch, and the u_bin_p parameter from parser, yaml, compute_cn, and inference. - Hide cnt_cd from --mode choices and hide its companion args (--tree_file, --eps_fit) from --help. Both remain reachable internally and in tests; they are simply not user-selectable pre-release. - Sync docs (reference.md table, compute-cn.md --help usage).
Brand text only (package description, CI step name, docstrings, comments). Does not touch the lowercase env/bioconda identifier `hatchet3`.
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Groups four related changes on
feat/plot-fixes(squash-merges to one commit). Full test suite (63) passes; ruff check + format clean.Plot fixes
hatchet.yaml(plot_*keys, sharedget_plot_style); registered as hidden CLI flags.K{k}.pdf(1D/2D) +K{k}.diagnostic.pdf; 1D unified onto plot-cn's multi-sample layout; fix axes box, titles, legend, value ranges.show_prop/min_prop); forward resolved style toplot_1d2dsub-runs.Filename centralization
src/hatchet/filenames.py: single source of truth for all input/output/subdirectory names (constants + templated helpers). cluster-bins, compute-cn, evaluate, plot, and utils import from it so producer/consumer filename contracts cannot silently drift.Restrict pre-release solver options
bin_dirU-initialization entirely (parameter + code path).cnt_cdfrom--modeand its companion args (--tree_file,--eps_fit) from--help; still reachable internally and in tests, just not user-selectable pre-release.reference.md,compute-cn.md).Cleanup
run_plot_cn/plot_pareto_curveintoplot_compute_cn.py; remove deadfiltering(); reordercompute_cn_utils.pyinto sections.show_propconfig; fix snakemake test config section names (underscore -> hyphen); ignore.vscode/.HATCHet3->HATCHet(docs, metadata, test strings); the lowercasehatchet3env/bioconda identifier is intentionally unchanged.