[WIP] a demonstration of/documentation for some Storage functionality
#1758
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commit 3268907 Author: C. Titus Brown <titus@idyll.org> Date: Fri Jul 2 05:38:56 2021 -0700 remove leftover merge code commit 3b53de9 Merge: 0f7dc81 21f5e63 Author: C. Titus Brown <titus@idyll.org> Date: Fri Jul 2 05:35:54 2021 -0700 Merge branch 'latest' of https://github.com/sourmash-bio/sourmash into add/zipfile_use_storage commit 0f7dc81 Author: C. Titus Brown <titus@idyll.org> Date: Fri Jun 25 10:45:34 2021 -0700 fix error message commit fc0c6fe Merge: 65646fb a5a52b1 Author: C. Titus Brown <titus@idyll.org> Date: Fri Jun 25 10:17:33 2021 -0700 Merge branch 'latest' of https://github.com/sourmash-bio/sourmash into add/zipfile_use_storage commit 65646fb Author: C. Titus Brown <titus@idyll.org> Date: Thu Jun 24 11:35:55 2021 -0700 fix merge commit dec537a Merge: c039fd6 9dbd8b5 Author: C. Titus Brown <titus@idyll.org> Date: Thu Jun 24 11:31:47 2021 -0700 Merge branch 'latest' of https://github.com/sourmash-bio/sourmash into add/zipfile_use_storage commit c039fd6 Merge: 89fad20 8cc96cd Author: C. Titus Brown <titus@idyll.org> Date: Wed Jun 23 17:48:50 2021 -0700 Merge branch 'add/picklist_zf_manifests' into add/zipfile_use_storage commit 8cc96cd Author: C. Titus Brown <titus@idyll.org> Date: Wed Jun 23 15:43:19 2021 -0700 fix tests for a CLEAN test-data/prot/ directory commit 5e49336 Author: C. Titus Brown <titus@idyll.org> Date: Wed Jun 23 10:32:49 2021 -0700 update docstring commit 2438d90 Merge: 873592d 0ff54e7 Author: C. Titus Brown <titus@idyll.org> Date: Wed Jun 23 10:34:23 2021 -0700 Merge branch 'latest' of https://github.com/sourmash-bio/sourmash into add/picklist_zf_manifests commit 89fad20 Merge: c6a8ad7 0ff54e7 Author: C. Titus Brown <titus@idyll.org> Date: Wed Jun 23 10:33:13 2021 -0700 Merge branch 'latest' of https://github.com/sourmash-bio/sourmash into add/zipfile_use_storage commit c6a8ad7 Author: C. Titus Brown <titus@idyll.org> Date: Wed Jun 23 10:32:49 2021 -0700 update docstring commit bd753d2 Author: C. Titus Brown <titus@idyll.org> Date: Wed Jun 23 09:04:56 2021 -0700 fix a few more things commit 86ac7ad Merge: 41438a6 873592d Author: C. Titus Brown <titus@idyll.org> Date: Wed Jun 23 09:03:35 2021 -0700 Merge branch 'add/picklist_zf_manifests' into add/zipfile_use_storage commit 873592d Merge: b6d5547 1992de9 Author: C. Titus Brown <titus@idyll.org> Date: Wed Jun 23 08:48:31 2021 -0700 Merge branch 'latest' of https://github.com/sourmash-bio/sourmash into add/picklist_zf_manifests commit b6d5547 Author: C. Titus Brown <titus@idyll.org> Date: Wed Jun 23 08:47:02 2021 -0700 add test for multiple selects commit 8ebac0d Author: C. Titus Brown <titus@idyll.org> Date: Wed Jun 23 08:37:25 2021 -0700 remove print statements commit 701878b Author: C. Titus Brown <titus@idyll.org> Date: Wed Jun 23 08:36:45 2021 -0700 update test files to have manifest, update tests commit faad6ee Author: C. Titus Brown <titus@idyll.org> Date: Wed Jun 23 08:17:40 2021 -0700 don't test manifest content commit 44aba07 Author: C. Titus Brown <titus@idyll.org> Date: Wed Jun 23 08:08:58 2021 -0700 more refactor zipfile select commit 61ce0f2 Author: C. Titus Brown <titus@idyll.org> Date: Wed Jun 23 07:37:53 2021 -0700 refactor zipfile select commit 5879ff2 Author: C. Titus Brown <titus@idyll.org> Date: Wed Jun 23 07:37:28 2021 -0700 check compatibility in MinHash.intersection_and_union commit e1c44a6 Merge: 6c1f9da d473199 Author: C. Titus Brown <titus@idyll.org> Date: Wed Jun 23 07:14:38 2021 -0700 Merge branch 'latest' of http://github.com/sourmash-bio/sourmash into add/picklist_zf_manifests commit 6c1f9da Author: C. Titus Brown <titus@idyll.org> Date: Wed Jun 23 07:12:58 2021 -0700 more manifest testing for zipfiles commit 1b2cf73 Author: C. Titus Brown <titus@idyll.org> Date: Wed Jun 23 07:04:47 2021 -0700 add use_manifest fixture, refactor manifest loading commit 38ec792 Author: C. Titus Brown <titus@idyll.org> Date: Wed Jun 23 06:50:13 2021 -0700 add sig manifest tests for other file types commit 6905d40 Author: C. Titus Brown <titus@idyll.org> Date: Wed Jun 23 06:42:51 2021 -0700 update sig manifest to error when manifests cannot be generated commit fa47667 Author: C. Titus Brown <titus@idyll.org> Date: Wed Jun 23 06:19:51 2021 -0700 rename signatures_with_internal to _signatures_with_internal commit 096b141 Author: C. Titus Brown <titus@idyll.org> Date: Wed Jun 23 05:46:32 2021 -0700 add manifests to default zip collection output commit 99199ee Author: C. Titus Brown <titus@idyll.org> Date: Wed Jun 23 05:32:52 2021 -0700 move manifest stuff to manifest.py commit 0adee52 Author: C. Titus Brown <titus@idyll.org> Date: Wed Jun 23 05:28:54 2021 -0700 remove print commit 83e387e Merge: fe83b68 9bb6a9b Author: C. Titus Brown <titus@idyll.org> Date: Tue Jun 22 18:15:48 2021 -0700 Merge branch 'add/picklist_manifests_sbt' into add/picklist_zf_manifests commit fe83b68 Author: C. Titus Brown <titus@idyll.org> Date: Tue Jun 22 18:07:23 2021 -0700 revert collection to multiindex commit 60a6eec Author: C. Titus Brown <titus@idyll.org> Date: Tue Jun 22 14:08:34 2021 -0700 change LoadedCollection back over to MultiIndex; remove LazyMultiIndex commit 9bb6a9b Author: C. Titus Brown <titus@idyll.org> Date: Tue Jun 22 12:53:40 2021 -0700 fix header writing commit 7486871 Merge: 4221fc9 c3f1a3d Author: C. Titus Brown <titus@idyll.org> Date: Tue Jun 22 12:53:03 2021 -0700 Merge branch 'add/picklist_zf_manifests' into add/picklist_manifests_sbt commit 41438a6 Author: C. Titus Brown <titus@idyll.org> Date: Tue Jun 22 12:52:32 2021 -0700 fix header writing commit 4026855 Merge: 6b18439 c3f1a3d Author: C. Titus Brown <titus@idyll.org> Date: Tue Jun 22 12:48:33 2021 -0700 Merge branch 'add/picklist_zf_manifests' into add/zipfile_use_storage commit c3f1a3d Author: C. Titus Brown <titus@idyll.org> Date: Tue Jun 22 12:42:38 2021 -0700 reverse order of adding to seen set commit 71b81ed Author: C. Titus Brown <titus@idyll.org> Date: Tue Jun 22 12:41:33 2021 -0700 add docstring commit ed5fb7a Author: C. Titus Brown <titus@idyll.org> Date: Tue Jun 22 12:40:43 2021 -0700 rename matches_siginfo to matches_manifest_row commit 2756e7d Author: C. Titus Brown <titus@idyll.org> Date: Tue Jun 22 12:28:37 2021 -0700 add save/load test commit ba2e53c Merge: c243b0e c04f137 Author: C. Titus Brown <titus@idyll.org> Date: Tue Jun 22 11:12:07 2021 -0700 Merge branch 'latest' of github.com:dib-lab/sourmash into add/picklist_zf_manifests commit c243b0e Author: C. Titus Brown <titus@idyll.org> Date: Tue Jun 22 11:10:20 2021 -0700 add manifest tests commit e301645 Author: C. Titus Brown <titus@idyll.org> Date: Tue Jun 22 10:07:35 2021 -0700 add a test for sig manifest commit e315c90 Merge: d95813e 0814bcc Author: C. Titus Brown <titus@idyll.org> Date: Tue Jun 22 09:58:29 2021 -0700 Merge branch 'latest' of github.com:dib-lab/sourmash into add/picklist_zf_manifests commit d95813e Author: C. Titus Brown <titus@idyll.org> Date: Sat Jun 19 13:52:50 2021 -0700 add manifest versions commit 4221fc9 Merge: d4a9a2e 31018df Author: C. Titus Brown <titus@idyll.org> Date: Fri Jun 18 05:47:28 2021 -0700 Merge branch 'add/picklist_zf_manifests' into add/picklist_manifests_sbt commit 6b18439 Merge: 9ff0eab 31018df Author: C. Titus Brown <titus@idyll.org> Date: Fri Jun 18 05:46:39 2021 -0700 Merge branch 'add/picklist_zf_manifests' into add/zipfile_use_storage commit 31018df Merge: 9e46ff8 74de59a Author: C. Titus Brown <titus@idyll.org> Date: Fri Jun 18 05:44:38 2021 -0700 Merge branch 'latest' of github.com:dib-lab/sourmash into add/picklist_zf_manifests commit 9ff0eab Merge: 9c530a5 9e46ff8 Author: C. Titus Brown <titus@idyll.org> Date: Thu Jun 17 14:02:08 2021 -0700 Merge branch 'add/picklist_zf_manifests' into add/zipfile_use_storage commit d4a9a2e Author: C. Titus Brown <titus@idyll.org> Date: Thu Jun 17 14:01:48 2021 -0700 fix test for manifests commit 2da0085 Merge: a7e153a 9e46ff8 Author: C. Titus Brown <titus@idyll.org> Date: Thu Jun 17 14:01:27 2021 -0700 Merge branch 'add/picklist_zf_manifests' into add/picklist_manifests_sbt commit 9e46ff8 Author: C. Titus Brown <titus@idyll.org> Date: Thu Jun 17 13:55:21 2021 -0700 cleanup of comments etc. commit e1e367a Author: C. Titus Brown <titus@idyll.org> Date: Thu Jun 17 13:49:21 2021 -0700 remove @ctb comments commit 5cad5ff Merge: 54ea3f9 8812142 Author: C. Titus Brown <titus@idyll.org> Date: Thu Jun 17 12:22:46 2021 -0700 Merge branch 'add/picklist_selectors' into add/picklist_zf_manifests commit 8812142 Author: C. Titus Brown <titus@idyll.org> Date: Thu Jun 17 12:20:45 2021 -0700 further attempt to fix test commit 54ea3f9 Author: C. Titus Brown <titus@idyll.org> Date: Thu Jun 17 12:17:27 2021 -0700 only match picklist at end of 'select' commit 122d043 Merge: f697ec4 de6f3c4 Author: C. Titus Brown <titus@idyll.org> Date: Thu Jun 17 11:40:39 2021 -0700 Merge branch 'add/picklist_selectors' into add/picklist_zf_manifests commit de6f3c4 Author: C. Titus Brown <titus@idyll.org> Date: Thu Jun 17 11:38:35 2021 -0700 remove order dependence from test commit f697ec4 Author: C. Titus Brown <titus@idyll.org> Date: Thu Jun 17 09:31:18 2021 -0700 fix coltypes commit 7937292 Merge: bba101c 4d156e9 Author: C. Titus Brown <titus@idyll.org> Date: Thu Jun 17 09:24:38 2021 -0700 Merge branch 'add/picklist_selectors' into add/picklist_zf_manifests commit 4d156e9 Author: C. Titus Brown <titus@idyll.org> Date: Thu Jun 17 09:13:52 2021 -0700 add docs commit ab286cf Author: C. Titus Brown <titus@idyll.org> Date: Thu Jun 17 08:50:57 2021 -0700 remove debugging print commit c965648 Author: C. Titus Brown <titus@idyll.org> Date: Thu Jun 17 08:44:32 2021 -0700 add a test for using prefetch CSV as picklist commit ca6ea4f Author: C. Titus Brown <titus@idyll.org> Date: Thu Jun 17 08:34:08 2021 -0700 add picklist test that checks indexing-and-then-search == index commit bba101c Merge: 39abe57 ba5c8bc Author: C. Titus Brown <titus@idyll.org> Date: Thu Jun 17 08:13:05 2021 -0700 Merge branch 'add/picklist_selectors' into add/picklist_zf_manifests commit ba5c8bc Author: C. Titus Brown <titus@idyll.org> Date: Thu Jun 17 07:47:13 2021 -0700 block multiple picklists on SBTs and LCAs, for now commit a074127 Author: C. Titus Brown <titus@idyll.org> Date: Thu Jun 17 07:38:45 2021 -0700 add picklists to lca index commit a0335a3 Author: C. Titus Brown <titus@idyll.org> Date: Thu Jun 17 07:32:10 2021 -0700 add picklists to sourmash compare commit c0e5781 Author: C. Titus Brown <titus@idyll.org> Date: Thu Jun 17 07:25:59 2021 -0700 add picklists to prefetch commit 7a30b20 Author: C. Titus Brown <titus@idyll.org> Date: Thu Jun 17 07:12:17 2021 -0700 add picklists and tests for search, gather, index commit ced72d2 Author: C. Titus Brown <titus@idyll.org> Date: Thu Jun 17 06:25:01 2021 -0700 add picklist args throughout, eek. commit 984a557 Author: C. Titus Brown <titus@idyll.org> Date: Thu Jun 17 06:14:23 2021 -0700 fix space commit fddf141 Author: C. Titus Brown <titus@idyll.org> Date: Thu Jun 17 06:14:09 2021 -0700 move picklist reporting into sourmash_args commit b3c6bb9 Author: C. Titus Brown <titus@idyll.org> Date: Thu Jun 17 06:09:40 2021 -0700 move picklist.py from sourmash.sig into sourmash commit 21ce4b7 Author: C. Titus Brown <titus@idyll.org> Date: Wed Jun 16 15:41:51 2021 -0700 fix tests for new SignaturePicklist commit b8f4bb8 Merge: 8e5fb8d b787b75 Author: C. Titus Brown <titus@idyll.org> Date: Wed Jun 16 15:40:10 2021 -0700 Merge branch 'latest' of github.com:dib-lab/sourmash into add/picklist_selectors commit 8e5fb8d Merge: 5ac4671 04c209c Author: C. Titus Brown <titus@idyll.org> Date: Wed Jun 16 12:05:31 2021 -0700 Merge branch 'add/picklist' into add/picklist_selectors commit 04c209c Author: C. Titus Brown <titus@idyll.org> Date: Wed Jun 16 11:27:21 2021 -0700 remove comment commit 14b87d4 Author: C. Titus Brown <titus@idyll.org> Date: Wed Jun 16 11:18:32 2021 -0700 trap errors and be nice to users commit 4f8e20c Author: C. Titus Brown <titus@idyll.org> Date: Wed Jun 16 11:16:49 2021 -0700 cover untested code with tests commit 8f65f22 Author: C. Titus Brown <titus@idyll.org> Date: Wed Jun 16 10:17:50 2021 -0700 test with --md5 selector commit 9d60e32 Author: C. Titus Brown <titus@idyll.org> Date: Wed Jun 16 10:15:06 2021 -0700 documentation commit 3d23d87 Author: C. Titus Brown <titus@idyll.org> Date: Wed Jun 16 09:39:59 2021 -0700 add --picklist-require-all &c commit 14a88a7 Author: C. Titus Brown <titus@idyll.org> Date: Wed Jun 16 09:34:43 2021 -0700 verify output commit 207a813 Author: C. Titus Brown <titus@idyll.org> Date: Wed Jun 16 09:31:22 2021 -0700 more picklist tests commit 9b50748 Author: C. Titus Brown <titus@idyll.org> Date: Wed Jun 16 09:19:40 2021 -0700 fix tests :) commit aaa4548 Author: C. Titus Brown <titus@idyll.org> Date: Wed Jun 16 09:18:08 2021 -0700 update comments, constructor, etc. commit a7e153a Author: C. Titus Brown <titus@idyll.org> Date: Wed Jun 16 07:22:39 2021 -0700 fix tests commit 9c530a5 Author: C. Titus Brown <titus@idyll.org> Date: Wed Jun 16 07:12:46 2021 -0700 add comment about Storage encapsulation commit 48fd900 Author: C. Titus Brown <titus@idyll.org> Date: Wed Jun 16 07:07:17 2021 -0700 all tests pass, w00t commit d6a48c1 Author: C. Titus Brown <titus@idyll.org> Date: Wed Jun 16 07:01:34 2021 -0700 refactor ZipFileLinearIndex to use ZipStorage underneath commit 5a185bb Author: C. Titus Brown <titus@idyll.org> Date: Wed Jun 16 06:45:42 2021 -0700 change internal zipfile writing to use ZipStorage commit c356842 Author: C. Titus Brown <titus@idyll.org> Date: Wed Jun 16 06:12:24 2021 -0700 done, I think? commit 75dc079 Merge: 1dd8170 39abe57 Author: C. Titus Brown <titus@idyll.org> Date: Wed Jun 16 05:25:38 2021 -0700 Merge branch 'add/picklist_zf_manifests' into add/picklist_manifests_sbt commit 39abe57 Author: C. Titus Brown <titus@idyll.org> Date: Wed Jun 16 05:23:42 2021 -0700 CSV output function commit 1dd8170 Author: C. Titus Brown <titus@idyll.org> Date: Wed Jun 16 05:20:35 2021 -0700 add manifests to SBTs commit 72d8497 Author: C. Titus Brown <titus@idyll.org> Date: Wed Jun 16 04:23:48 2021 -0700 move manifest stuff into manifest class commit a4057e6 Author: C. Titus Brown <titus@idyll.org> Date: Tue Jun 15 10:33:09 2021 -0700 create LazyMultiIndex commit 730a717 Author: C. Titus Brown <titus@idyll.org> Date: Tue Jun 15 09:40:45 2021 -0700 more cleanup and docs commit 230c793 Author: C. Titus Brown <titus@idyll.org> Date: Tue Jun 15 09:28:09 2021 -0700 cleanup and simplification of ZipFile stuff commit 8a8c3b2 Author: C. Titus Brown <titus@idyll.org> Date: Tue Jun 15 08:54:23 2021 -0700 shift signature metadata matching from manifests over to picklist commit ab0fc0e Author: C. Titus Brown <titus@idyll.org> Date: Tue Jun 15 08:45:06 2021 -0700 misc cleanup commit c3b6fc0 Author: C. Titus Brown <titus@idyll.org> Date: Tue Jun 15 08:36:08 2021 -0700 more cleanup commit 509eb45 Author: C. Titus Brown <titus@idyll.org> Date: Tue Jun 15 08:23:41 2021 -0700 remove MultiIndex commit af5eb86 Author: C. Titus Brown <titus@idyll.org> Date: Tue Jun 15 08:09:53 2021 -0700 fix test names for new LoadedCollection commit c6cb1af Author: C. Titus Brown <titus@idyll.org> Date: Tue Jun 15 08:08:46 2021 -0700 fix all the tests commit 915f847 Author: C. Titus Brown <titus@idyll.org> Date: Tue Jun 15 07:48:35 2021 -0700 cleanup/simplification of LoadedCollection commit be9ef77 Author: C. Titus Brown <titus@idyll.org> Date: Tue Jun 15 07:41:48 2021 -0700 create LoadedCollection to replace MultiIndex non-lazy loading commit 3c0c9cf Author: C. Titus Brown <titus@idyll.org> Date: Tue Jun 15 07:17:08 2021 -0700 try making manifests obligatory for MultiIndex commit 23c1531 Merge: 67a9be1 5ac4671 Author: C. Titus Brown <titus@idyll.org> Date: Mon Jun 14 13:35:20 2021 -0700 Merge branch 'add/picklist_selectors' into add/picklist_zf_manifests commit 5ac4671 Merge: a88b66d 031522c Author: C. Titus Brown <titus@idyll.org> Date: Mon Jun 14 13:35:04 2021 -0700 Merge branch 'add/picklist' into add/picklist_selectors commit 031522c Merge: 3c05f95 ff75ec0 Author: C. Titus Brown <titus@idyll.org> Date: Mon Jun 14 13:34:37 2021 -0700 Merge branch 'latest' of github.com:dib-lab/sourmash into add/picklist commit 67a9be1 Author: C. Titus Brown <titus@idyll.org> Date: Mon Jun 14 11:46:07 2021 -0700 more comment commit 1d7e0cf Author: C. Titus Brown <titus@idyll.org> Date: Mon Jun 14 11:41:22 2021 -0700 update comment about picklist.found commit 2f2269b Author: C. Titus Brown <titus@idyll.org> Date: Mon Jun 14 11:33:56 2021 -0700 work through manifests for MultiIndex commit cb8e28d Author: C. Titus Brown <titus@idyll.org> Date: Mon Jun 14 06:34:34 2021 -0700 get started adding manifests to MultiIndex commit 01d33fc Author: C. Titus Brown <titus@idyll.org> Date: Mon Jun 14 06:21:05 2021 -0700 provide 'select' more generically on manifests commit 17b9576 Author: C. Titus Brown <titus@idyll.org> Date: Mon Jun 14 06:12:39 2021 -0700 build out a manifest class a bit commit b2547f3 Author: C. Titus Brown <titus@idyll.org> Date: Sun Jun 13 20:20:28 2021 -0700 add missing manifest CLI file commit 14a5ee1 Author: C. Titus Brown <titus@idyll.org> Date: Sun Jun 13 08:59:00 2021 -0700 hacky but functional manifest support commit 6593a42 Author: C. Titus Brown <titus@idyll.org> Date: Sun Jun 13 08:37:05 2021 -0700 try out manifests commit e205e64 Author: C. Titus Brown <titus@idyll.org> Date: Sun Jun 13 07:39:47 2021 -0700 special case md5 prefixes, for prefetch commit b57b2b3 Author: C. Titus Brown <titus@idyll.org> Date: Sun Jun 13 07:23:46 2021 -0700 support special picklist interactions with zipfile collections commit a88b66d Author: C. Titus Brown <titus@idyll.org> Date: Sun Jun 13 06:32:38 2021 -0700 factor out picklist checks to 'passes_all_picklists' fn commit 54407a3 Author: C. Titus Brown <titus@idyll.org> Date: Sat Jun 12 11:16:02 2021 -0700 test 'Index.find' on picklists for SBTs and LCAs commit 03cc61b Merge: de6fc06 3c05f95 Author: C. Titus Brown <titus@idyll.org> Date: Sat Jun 12 10:48:59 2021 -0700 Merge branch 'add/picklist' into add/picklist_selectors commit 3c05f95 Author: C. Titus Brown <titus@idyll.org> Date: Sat Jun 12 10:48:15 2021 -0700 split column_type out of SignaturePicklist a bit commit 1bdf88e Author: C. Titus Brown <titus@idyll.org> Date: Sat Jun 12 10:28:23 2021 -0700 split pickfile out a little bit commit de6fc06 Author: C. Titus Brown <titus@idyll.org> Date: Sat Jun 12 10:48:30 2021 -0700 picklist tests for .signatures() methods on Index classes commit def1933 Author: C. Titus Brown <titus@idyll.org> Date: Sat Jun 12 10:48:15 2021 -0700 split column_type out of SignaturePicklist a bit commit a817843 Author: C. Titus Brown <titus@idyll.org> Date: Sat Jun 12 10:28:23 2021 -0700 split pickfile out a little bit commit b1fc982 Author: C. Titus Brown <titus@idyll.org> Date: Sat Jun 12 10:01:56 2021 -0700 add picklists to selectors commit 74f31f5 Author: C. Titus Brown <titus@idyll.org> Date: Sat Jun 12 09:21:58 2021 -0700 track found etc commit 505b04f Author: C. Titus Brown <titus@idyll.org> Date: Sat Jun 12 09:11:24 2021 -0700 basic tests for picklist functionality commit 3ecfb48 Author: C. Titus Brown <titus@idyll.org> Date: Sat Jun 12 08:55:28 2021 -0700 integrate picklists into sourmash sig extract commit bb794ec Author: C. Titus Brown <titus@idyll.org> Date: Sat Jun 12 08:38:24 2021 -0700 initial picklist implementation commit 3a583a9 Author: C. Titus Brown <titus@idyll.org> Date: Sat Jun 12 07:36:48 2021 -0700 clean up sourmash.sig submodule commit 66b0599 Author: C. Titus Brown <titus@idyll.org> Date: Sat Jun 12 07:23:13 2021 -0700 cleanup flakes errors commit 0997834 Author: C. Titus Brown <titus@idyll.org> Date: Sat Jun 12 07:17:44 2021 -0700 various cleanups of sourmash_args
…o add/zipfile_use_storage
…o add/zipfile_use_storage
Codecov Report
@@ Coverage Diff @@
## latest #1758 +/- ##
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+ Coverage 83.43% 90.09% +6.66%
==========================================
Files 113 87 -26
Lines 12119 8413 -3706
Branches 1557 1557
==========================================
- Hits 10111 7580 -2531
+ Misses 1750 575 -1175
Partials 258 258
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This PR provides a demo notebook showing how to use storage classes and manifests together.
There's also a notebook showcasing some desired functionality in rust, c.f. #1752.
Brainstorming a bit about what's worth putting up for merge here -
demo-load-from-storage-and-search.ipynbnotebook is probably not useful now (or maybe even ever) for regular users or developers.demo-storage-and-manifests.ipynbnotebook might be useful to keep around, either as a notebook (as is) or as a doctest. Probably want to make sure it's run as part of tests, tho.src/sourmash/manifest.pyandsrc/sourmash/sbt_storage.pyare good, just need some tests and docs.