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MCP: pileup draws its figure without gtf or bam; modules never fits again through options; version 0.18.3 - #39
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…gain through options; version 0.18.3 - `pileup` with `figure` and neither `gtf` nor `bam` always failed: the command drew only on a figure flag, a GTF or BAMs, so it printed the ASCII pileup and wrote no SVG. It now gets `--svg`, which puts it in figure mode (the annotation recorded with the data draws the genes, if any). The figure no longer warns that `--svg` is ignored: it writes just that. - `modules` refused only some of the options that make it fit again, so `--membership-alpha`, `--community-gamma`, `--gene-alpha`, `--shift-sd` or `--cell-sd` in `options` could refit and write over the tables. The refused flags are now read off the command from the blockmodel options `modules` holds against the tables' record (`cluster::MODEL_OPTIONS`), with every alias, so none can be missed.
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Two bugs in the MCP server, found in an audit of faba's MCP coverage.
pileupwithfigureand neithergtfnorbamalways failedThe
pileuptool'sfigureflag only chose the SVG as the output. The command enters figure mode on a figure flag,--gtfor--bam, and a recorded GFF isn't consulted until after the mode is chosen. So the child printed the ASCII pileup, wrote no SVG, and the call failed with "finished without writing ….miami.svg".--svgis blocked inoptions, so an agent couldn't work around it.--svgwhenfigureis asked withoutgtforbam. The gene model comes from the annotation recorded with the data, if any.pileup_argv, which a new test checks:--svgalone, orgtf/baminstead of it.--svgis ignored, since an SVG is what it writes.--format,--pngand--no-pdfstill warn.figureneedsgtforbam.modulescould refit, and write over its tables, throughoptionsMODULES_TAKENwas a hand-written list that had drifted from the optionsmodulesholds against a run's record. It lacked--membership-alpha,--community-gamma,--gene-alpha,--shift-sdand--cell-sd. Passing any of them inoptionsat a value different from the record madeplan()fit again, intodataitself, throughrun_reading, so the step was never recorded.modulescommand fromcluster::MODEL_OPTIONS(nowpub(crate)), every long flag, alias and short included, plus the sampler's--chains,--sweepsand--burn-in. An option added toMODEL_OPTIONSis refused without another list to update.--communitiesand--prior-strengthaliases, are refused.Version
0.18.3.
Testing
cargo fmt --all --check,cargo clippy --all-targets -- -D warningsandcargo test(733 unit tests and the integration suites) pass. The--features hdf5build was not run here (no libhdf5).mcp::tests::modules_refuses_every_option_that_would_fit_againandmcp::tests::a_pileup_figure_asked_alone_is_drawn.pileupfigure run end to end through the MCP server; the test checks the command line it builds.