[MRG] Remove deprecated minhash functions #1149
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* move sourmash._minhash to sourmash.minhash * deprecate max_hash throughout * change MinHash.add(...) to MinHash.add_kmer(...) * remove update and is_molecule_type from MinHash * remove subtract_mins * rename downsample_n to downsample_num * switch to hashes property instead of using get_mins() * replace get_mins(...) with hashes thruout * change deprecated 'compare' usage to 'similarity' in test_jaccard * elminate most of the deprecation warnings in test__minhash by switching compare to similarity * fix remaining tests in test__minhash * fix compat message * restore removed functions, sigh :) * minor upd * add deprecations * use a wrapper object for .hashes and make it read-only * refactor to use downsample(num/scaled= * refactor to use downsample(scaled=...) * return two deleted tests * fixed test that was masked by another test * add explicit check for length of kmer in add_kmer * fix ordering in hash retrieval * fix more tests for py2 <khaaaaaaaaaan> * add 'flatten' method to MinHash * add test for MinHash.flatten * add tests for add and add_kmer * remove nonsense test * test the (now deprecated) get_mins function * test (deprecated) get_hashes * add tests for downsample and is_molecule_type * test moltype properties more explicitly * fix py27 * move translate_codon to module level * put a stub in place of _minhash with a FutureWarning * adjust import req * remove __future__ imports * remove sys.version checks for py 2 * remove requirement for enum34 * remove __reduce__ from MinHash class (#1144) * avoid the DeprecationWarning * update docs: only python 3.7 and 3.8 * remove 2.7 from travis * remove _compat from signature.py * remove _compat from exceptions.py * remove _compat from index and sbt_storage * remove _compat from nodegraph * remove _compat completely * make signature -> sig in CLI using py3 'aliases' * put back assert that didn't work in py2 * Update sourmash/minhash.py Co-authored-by: Luiz Irber <luizirber@users.noreply.github.com> Co-authored-by: Luiz Irber <luizirber@users.noreply.github.com>
Codecov Report
@@ Coverage Diff @@
## latest #1149 +/- ##
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Coverage ? 92.62%
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Files ? 71
Lines ? 5698
Branches ? 0
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Hits ? 5278
Misses ? 420
Partials ? 0 Continue to review full report at Codecov.
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luizirber
approved these changes
Aug 6, 2020
This was referenced Aug 9, 2020
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Per #1128 remove all of the MinHash functions deprecated in 3.5 / to be removed in 4.0.
Fixes #1148.
make testDid it pass the tests?make coverageIs the new code covered?without a major version increment. Changing file formats also requires a
major version number increment.
changes were made?