Allow range- or scalar-defined, index-based filtering of samples #367
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…ound even if set_desired_range is invoked.
…ed limit, skip, and converting range to bounds as new functions within utils.py.
* update description and remove shorter option name to keep one-character norm * refactor and use the range determination utilities; #324 * avoid extending namedtuple * remove commented-out code * condense implementation by sharing common pattern * Correcting logic for skip range and setting default lower bound to '1' instead of '0'. #324 * If upper range is greater than total sample number, default to sample number as upper range instead of crashing. #324 * simplify conditional and avoid second cast * improve interval type name and implementation; union intervals rather than set diff; generalize typing annotations * avoid full list construction * fix type name * add hypothesis to test requirements * add docs * ignore hypothesis output * better error subtyping to narrow catch clauses * start and stub tests for natural range; apply formatter * handle null as argument to upper bound for range parser * make upper bound required when parsing range from string * fix error message, implement basic data type methods * remove unused namedtuple type; add type annotations * remove handling of null for upper bound on string parse of range * prohibit bogus input as just delimiter to parse * Replaced SAMPLE_NAME_ATTR with sample_table_index where seen. Closes #338 * fix error message * finish tests for natural range type * narrow error type; protect against flipped bounds * fix off-by-one in single-value skipping case * test the sample indexing helpers for ranges * remove unused test generator * use the parser validation * fix parser validation * add tests for parser validation * ignore tempfile left sometimes during testing; #364 * better test naming, import sorting * acct for default=None making unspecified opts be present in namespace * fix attr/opt checking * better test helpers naming and handling of standard streams * apply formatter * try looper dotfile as fixture for cleanup in teardown; #364 * do type conversions to allow string membership tests * helper for sample indexing from --skip and --limit --------- Co-authored-by: Donald C <125581724+donaldcampbelljr@users.noreply.github.com> Co-authored-by: Aaron O'Brien <obrien.aaron.g@gmail.com> Co-authored-by: ayobi <knq8ng@virginia.edu>
vreuter
requested review from
nsheff,
ayobi,
khoroshevskyi and
donaldcampbelljr
donaldcampbelljr
approved these changes
Apr 20, 2023
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Close #324
Close #320