Rename --p-filter-unobserved-features-from-phylogeny to something shorter #312
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fedarko
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Closes biocore#312. Old: --p-filter-unobserved-features-from-phylogeny (45 chars) New: --p-shear-to-table (18 chars)
fedarko
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ElDeveloper
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) * ENH: Initial stab at "just tree/fm" plots #175 -TODO polish interface more, hide more stuff (barplots / sm menu) -TODO clean up code -TODO test * ENH: improve UI hiding re: level of data passed * ENH/BUG: make just-fm tree plots work ok Still need to add tons of tests and iron out bugs but this should close #175 * STY: linty mclintface * DOC: add example usages to makefile todo should update readme * DOC: update readme re community plot stuff * DOC: reword s.m. desc in community-plot since "tip-level animations" not what i was going for * ENH: accept different featuretable types+upd8 docs * TST: unbreak core tests * TST: unbreak + add basic integration tests * DOC/TST: mention limitations of curr integ tests * TST: test that comm plot reqs both tbl and sm * MNT: update Makefile and Travis stuff * MNT: abstract reused code btwn comm & tree plot * MNT: rename newickpath -> newickfmt to be clearer * DOC: add note re: 2 fm matching funcs (pls don't make me combine them ._____________________________.) * MNT: remove redundant var in empress-template html * MNT: simplify small qzv names * ENH: fix flash of unstyled content pbm for #175 UI this was already annoying with the feature metadata controls; now it's nicer * DOC: document _plot() funcs * ENH: more sophisticated ctrl hiding/showing stuff ... based on how much data is available. Now, there are these easy-to-add "needs-community-data", "needs-feature-metadata", and "needs-metadata" classes that we can use to keep track of stuff. also now rather than hiding stuff by default then unhiding it we go with showing by default and then hiding; since we now delay showing the ctrl panel at all until after loading p much done, this is ok * DOC: lets you -> helps * TST: test that isCommunityPlot/fmCols set ok #175 * STY: put big url on own line * TST: add tbl/sm none-chking to core init&test #175 * TST: test tree-plot fm stuff in more detail * TST: check fm filtering for tree-plot * TST test to_dict for tree plot #175 * TST: expand to_dict tests for tree plot * DOC: add note to core init abt tree plot junk * TST/DOC: rm note about TODO which I todid * TST: test some barplot panel JS #175 stuff also refactored the legend clear method to use jquery bc why not * TST: test getSampleCategories() if not comm plot * DOC: clarify split commands in README also added some extra context to first paragraph * DOC: "feature and/or sample metadata"->"metadata" For #175 -- avoids confusion in just-sm / just-fm plots. We could also dynamically change this text based on how much data was passed to Empress but ... that's a lotta work for marginal benefit * BUG: Actually, don't accept FT[Composition] inputs Since we convert tables to presence/absence anyway, pseudocounts will explode that. * STY: rm now-unused import of Composition * DOC: Rename / polish docs for shearing option Closes #312. Old: --p-filter-unobserved-features-from-phylogeny (45 chars) New: --p-shear-to-table (18 chars) * TST: update make-dev-page re: new flag name #312 * STY: flake8 * TST: unbreak tests due to #312 change * DOC: update readme re new shearing param name also tidy up subset table section * DOC: clarify filtered tbl discussion more * ENH: Make legend export UI require metadata Addresses @ElDeveloper comment. * Update .travis.yml Co-authored-by: Yoshiki Vázquez Baeza <[email protected]> * Update empress/core.py Co-authored-by: Yoshiki Vázquez Baeza <[email protected]> * DOC: remove old HTML todo thanks @ElDeveloper for catching! * ENH: Rename --p-shear-to-table to --p-shear-tree Based on discussion with @ElDeveloper Co-authored-by: Yoshiki Vázquez Baeza <[email protected]>
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Came up in discussion with @ElDeveloper and @kwcantrell -- typing the full thing out is difficult. Maybe
--p-filter-unobserved-features? Or--p-filter-nontable-features? Something like that.The text was updated successfully, but these errors were encountered: