docs: pre-stable-release audit of doc/*.rst#1113
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…t behavior Pre-stable-release audit of doc/*.rst found documented commands and identifiers that no longer match the current CLI: - export theta: supply the reference via -r/--reference, not a second positional argument (importexport.rst, heterogeneity.rst). - guess_baits.py: the access BED is -a/--access; -g is --min-gap. - genemetrics columns: nbins -> probes, seg_weight/seg_probes -> segment_weight/segment_probes (reports.rst). - segmetrics stat flags: --median, --stdev, --sem (were -median, --std, -sem). - import-rna: document -f rsem for RSEM input (the default format is counts); fix -output -> --output (rna.rst). - target: the bin-size flag is --avg-size, not --average-size (pipeline.rst). - export nexus-basic: list the gene and probe columns it actually emits. - baf: segment also consumes VCF b-allele frequencies. - nonhybrid: WGS --annotate is recommended, not required; convert a stray Markdown link to reStructuredText. - tumor: batch does emit default-threshold integer calls (.call.cns); it simply cannot apply purity/ploidy corrections. - quickstart: fix a dropped word; name a pooled reference my_reference.cnn rather than my_flat_reference.cnn. - pipeline: clarify that the call threshold-table example uses tighter germline/diploid inner cutoffs, not the tumor-safe defaults. - heterogeneity: render .call.cns as an inline literal.
… release - Add autodoc stubs for cnvlib.bintest, cnvlib.purity, cnvlib.cluster, and skgenome.cut, which back current functionality but were missing from the API reference; fix a cluster.py module-docstring list that broke under autodoc. - Correct the CNVkit self-citation year (2016, not 2014) and restore "DNA" to the paper title in both index.rst and CITATION; add the missing field separator in the CITATION BibTeX entry. - whoelse.rst: split into Software and Studies sections; drop dead commercial links (DNAnexus, Bina RAVE, Diploid InHelix); add recent CNVkit-using work (Villani 2023, Joanito 2022, Marjanovic 2020) and the nf-core/sarek pipeline. - Modernize legacy external links (the matplotlib customizing guide and config filename, and the IGV homepage).
The metadata-action step enabled the `latest` tag on `is_default_branch`, so `latest` tracked master (identical to `devel`) and was never applied on a release-tag push, contradicting both its own comment and the documented "latest stable release" meaning. Key it on v*.*.* tag refs instead.
Codecov Report✅ All modified and coverable lines are covered by tests. Additional details and impacted files@@ Coverage Diff @@
## master #1113 +/- ##
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Coverage 71.31% 71.31%
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Branches 1429 1429
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Partials 444 444
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Audit of every
doc/*.rstpage against the current CLI and code ahead of the next stable release. The Sphinx build is clean (no warnings), all:ref:/:doc:/toctree cross-references resolve, and all subcommand names and flags in the docs were diffed againstcnvkit.py ... --help.CLI accuracy (commands/flags/columns that no longer matched)
export theta: reference is supplied via-r/--reference, not a second positional (importexport, heterogeneity).guess_baits.py: access BED is-a/--access(-gis--min-gap).genemetricsoutput columns:nbins->probes,seg_weight/seg_probes->segment_weight/segment_probes.segmetricsstat flags:--median,--stdev,--sem(were-median,--std,-sem).import-rna: document-f rsemfor RSEM input (default format iscounts);-output->--output.target: bin-size flag is--avg-size.export nexus-basic: list thegeneandprobecolumns it emits.baf:segmentalso consumes VCF b-allele frequencies.--annotateis recommended, not required; fix a Markdown link that should be reStructuredText.batchdoes emit default-threshold integer calls (.call.cns); it just cannot apply purity/ploidy.my_reference.cnn, notmy_flat_reference.cnn.callthreshold-table example uses tighter germline/diploid inner cutoffs, not the tumor-safe defaults.API reference, citations, and links
cnvlib.bintest,cnvlib.purity,cnvlib.cluster, andskgenome.cut(back current functionality, were undocumented); fix acluster.pydocstring that broke under autodoc.CI
ci(docker): thelatestimage tag was keyed onis_default_branch, so it tracked master (identical todevel) and was never applied on a release tag, contradicting both its own comment and the documented meaning. It now keys onv*.*.*tag refs.All new citations were verified against CrossRef and the articles themselves (DOIs, authors, volume/pages, and confirmed CNVkit usage). Reviewed via three focused passes (correctness, conventions, scope) before pushing.