Round rank output, modernise the docs, add diagrams - #121
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The numeric columns were written at full float precision, so a mutability of 8.09229314668869e-08 claimed a precision that a binomial test on single-digit counts does not have, and made the table hard to read. Four significant figures. read_protein_mutations_MAF also aborted the whole file on one row with the wrong number of fields, so rank failed on real TCGA files that motif and profile read without complaint; the other readers learned to skip such rows in 1.1.0. And a ranking that produced no rows wrote an empty file in silence rather than saying the input needs protein annotations. The examples in rank_doc showed the old precision, so they now show the real output.
Switches to Furo and adds mermaid diagrams where prose was doing badly: how the subcommands chain together, the FILTER decision, the precedence of the overlapping cohort arguments, and the re-run swap. The rank examples showed fifteen-digit numbers the command no longer prints, so they now show its actual output, and the tables they sit in are rebuilt to match.
The check grepped for 'MutaGene X.Y.Z documentation', which is alabaster's title. Furo uses html_title, so changing the theme read as a version mismatch. It matches the version alone now.
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rankprinted8.09229314668869e-08— fifteen significant figures for an estimate from a binomial test on single-digit counts. Now four:Two bugs found while checking that:
read_protein_mutations_MAFaborted the whole file on one row with the wrong field count, sorankdied ontests/motifs/data/tcga_A3JM-01.maf— a filemotifandprofileread fine. The other readers learned to skip such rows in 1.1.0; this one hadn't. With it fixed, that fixture ranks CTNNB1 S37C and TP53 R248P.Docs: Furo theme, and mermaid diagrams where prose was doing badly — how the subcommands chain, the FILTER decision, the cohort argument precedence, and the re-run swap. The rank examples showed the old precision, so they now show real output.
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minor: the rank output format changes.