[MRG] add test to confirm failure when summarizing on empty gather #1560
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Codecov Report
@@ Coverage Diff @@
## add-taxonomy #1560 +/- ##
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+ Coverage 81.34% 89.17% +7.83%
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Files 109 82 -27
Lines 10749 7041 -3708
Branches 1260 1260
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- Hits 8744 6279 -2465
+ Misses 1781 538 -1243
Partials 224 224
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14 tasks
hehouts
changed the title
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@bluegenes left a comment on the test im still working on |
…nto add-tax-tests
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@bluegenes I think this is ready to merge in now; the failed checks are in different tests |
bluegenes
reviewed
Jun 16, 2021
bluegenes
reviewed
Jun 16, 2021
bluegenes
reviewed
Jun 16, 2021
Codecov Report
@@ Coverage Diff @@
## add-taxonomy #1560 +/- ##
================================================
+ Coverage 81.37% 89.01% +7.63%
================================================
Files 110 83 -27
Lines 10944 7236 -3708
Branches 1315 1315
================================================
- Hits 8906 6441 -2465
+ Misses 1802 559 -1243
Partials 236 236
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Co-authored-by: Tessa Pierce Ward <[email protected]>
Co-authored-by: Tessa Pierce Ward <[email protected]>
…to add-tax-tests
hehouts
changed the title
bluegenes
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that referenced
this pull request
Jun 23, 2021
* provide a kind of ridiculous upgrade to lca index to better deal with identifiers/taxonomy * update load_taxonomy_assignments to be more flexible and pay attention to CLI * init structure for taxonomy subcommand * more init * syntax and add tax to init * init tax tests * working tax summarize command * fix main * init tests for new tax_utils * add ascending taxlist * init classify cmd * init tax cli testing * fix filename * change to function for classify threshold * add header * enable single gather result for summarize; mult for classify * add util script to take output of tax and format for krona viz (#1559) * get summarized working for summary and krona output * init test krona output * add write_summary function * get classify working again, both summary and krona output * test write_classification * init classify cli tests * init tests for load_taxonomy_assignments * enable force for getting past duplicated entries in taxonomy csv * handle and test missing taxonomy info * classify: handle, test empty gather results, gather results from csv * split identifiers by default * standardize spacing * comments * init add tax to docs * [MRG] add a function to take multiple sourmash tax summarize csvs and output a single "abundance" df (#1562) * add a function to take multiple sourmash tax summarize csvs and output a single 'abundance' df * add import dep. * rework format_tax_to_frac for easier testing and use; add tests * better name and docstring for agg_sumgather_csvs_by_lineage * init combine command * debugging code to help track down SBT duplicates/loss problem * fix, I think * remove unnecessary code * add test for duplicate signatures in SBT creation * see what happens when you run twice * add missing signatures, oops * initial refactoring that passes many tests * factor filename generation out of actual writing * refactor and cleanup * add more sigs to test, add note of concern L) * fix --append tests, too * refactor out save_exact in favor if save(..., overwrite=True) * fix some storage stuff in the tests * make test less confusing? * Update src/sourmash/sbt_storage.py Co-authored-by: Luiz Irber <[email protected]> * define list_sbts() on base Storage class * properly record duplicate signature names * move threshold arg parsing into cli/utils * init changes for multiquery input * use namedtuple for summarized gather results * init update for mult files * adjust for namedtuple output * mods for namedtuple * upd utils * add --from-file to summarize * working multifile summarize * --from-csv to --from-file * somewhat working classify again * updated classify * finish fixing combine test * make taxonomy_csv required * cleanup * more cleanup * use load_pathlist_from_file * test check_and_load_gather_csvs * properly restrict kwargs with * * allow lineage summary table output from summarize * require rank for krona, lineage summary output formats * add test for lineage summary output with format_lineage * add docstrings * punt cami to separate PR * raise ValueError on empty gather results * move notify * cleanup * remove tax combine; add tax label * verson of load_taxonomy that strictly uses headers * use new tax fn; enable mult taxonomy inputs * init tax docs * add classification status to classify output * add multi db gather test csv * fix typo * whoops, actually fix * handle accession in lineage csv header * fix line width * return available ranks from load_taxonomy_csv * [MRG] add test to confirm failure when summarizing on empty gather (#1560) * added summarize on empty gather.csv test * added empty taxonomy csv test * fix typo * Update test_tax.py * trouble shoot tests * troubleshooting empty gather test * fixed, maybe? (#1596) * trying to pull * cleaned up test_summarize_empty_gather_tax... * cleaned test_summarize_empty_gather * fixed test comments * removed comment * Update tests/test_tax.py Co-authored-by: Tessa Pierce Ward <[email protected]> * Update tests/test_tax.py Co-authored-by: Tessa Pierce Ward <[email protected]> * updated empty-gather test Co-authored-by: Tessa Pierce Ward <[email protected]> Co-authored-by: C. Titus Brown <[email protected]> * init standardize errs * add good valueerror for empty lineage csv file * better catch errs in __main__; test all cmds: empty gather, lineage files * check available ranks, bad gather headers, empty gather, etc * emit one (and only one) warning per 100% match * add all functions to __all__ ...is this desired? * change cli for better arg parsing; add examples to summarize docs * add mixed strain classify example and assoc data * doc formatting * more doc formatting * more tiny reformatting * Apply suggestions from code review Co-authored-by: C. Titus Brown <[email protected]> * add usage info for each subcommand; upd docs * minor cleanup and more informative warning * add checks for duplicated queries, better output for duplicated filenames; label --> annotate * better catch/print for valueerrors; pyflakes fixes * summary --> csv_summary * upd docs * two-sample lineage summary example * rename commands * upd function names too * minor doc upds * use f_unique_to_query * add output dir; add file output notifications * add cols to summary outputs; adjust accordingly * trigger GitHub actions Co-authored-by: C. Titus Brown <[email protected]> Co-authored-by: Taylor Reiter <[email protected]> Co-authored-by: Luiz Irber <[email protected]> Co-authored-by: Hannah Eve Houts <[email protected]>
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so far:
added "summarize on empty gather.csv" test
will add a few more tests
adds to PR Ref #1543