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- Add kompot smooth section with usage, options, and examples - Add smooth to overview, quick start workflow, config templates, help - Fix all \\ to single \ in code-block directives (RST renders literally)
The per-command basic examples repeated the same info as the workflow block above and the detailed command sections below.
…abels - Exclude compute_differential_abundance/expression from automodule - Add smooth_expression automodule (exclude deprecated compute_smoothed_expression) - Add RunInfo.to_settings() and call_args() to documented members - Rename "Gene Expression Imputation" to "Smoothing" in toctree
- Add --dry-run flag to kompot de: estimates resource requirements without running the analysis - JSON output to stdout (or -o file), human-readable report to stderr - Exit code 0 if feasible, 1 if not - Add ResourcePlan.to_dict() for machine-parseable serialization - Add configure_logging() to redirect kompot logger stream - CLI now logs to stderr by default (keeps stdout clean for machine-parseable output like --dry-run and --table-output) - Document --dry-run in CLI docs with pipeline examples
Users would likely reuse the same args as the real run, which would overwrite their h5ad output with a JSON file. Stdout-only is safer.
- Add dry_run=False to all 8 DE test Namespace objects (run_de now accesses args.dry_run from the --dry-run flag added in this PR) - Update actions/checkout v4→v6 and actions/setup-python v5→v6 to resolve Node.js 20 deprecation warnings
- Add TestCLIDryRun: covers --dry-run JSON output, infeasible exit code 1, and output validation skip when dry_run=True - Add TestConfigureLogging: covers stream redirection and default - Fix codecov action: file→files (v5 API change) - Add --cov-report=term-missing to pytest so coverage stats appear in CI logs
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Summary
--dry-runflag tokompot deCLI: outputs JSON resource plan to stdout, human report to stderrkompot.configure_logging(stream)so CLI logs to stderr by defaultkompot smoothto CLI docs with full command reference[Unreleased]changelog sectionTest plan
kompot de --dry-runoutputs valid JSON to stdout