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[EXP] a simple JSON RPC client for sourmash search #1644

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[EXP] a simple JSON RPC client for sourmash search #1644

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@ctb ctb commented Jun 27, 2021 •
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Note: PR into #1619

See #1484 and https://github.com/ctb/2021-sourmash-jsonrpc for more information.

ctb added 30 commits June 12, 2021 07:17
@ctb
various cleanups of sourmash_args
0997834
@ctb
cleanup flakes errors
66b0599
@ctb
clean up sourmash.sig submodule
3a583a9
@ctb
initial picklist implementation
bb794ec
@ctb
integrate picklists into sourmash sig extract
3ecfb48
@ctb
basic tests for picklist functionality
505b04f
@ctb
track found etc
74f31f5
@ctb
add picklists to selectors
b1fc982
@ctb
split pickfile out a little bit
a817843
@ctb
split column_type out of SignaturePicklist a bit
def1933
@ctb
picklist tests for .signatures() methods on Index classes
de6fc06
@ctb
split pickfile out a little bit
1bdf88e
@ctb
split column_type out of SignaturePicklist a bit
3c05f95
@ctb
Merge branch 'add/picklist' into add/picklist_selectors
03cc61b
@ctb
test 'Index.find' on picklists for SBTs and LCAs
54407a3
@ctb
factor out picklist checks to 'passes_all_picklists' fn
a88b66d
@ctb
support special picklist interactions with zipfile collections
b57b2b3
@ctb
special case md5 prefixes, for prefetch
e205e64
@ctb
try out manifests
6593a42
@ctb
hacky but functional manifest support
14a5ee1
@ctb
add missing manifest CLI file
b2547f3
@ctb
build out a manifest class a bit
17b9576
@ctb
provide 'select' more generically on manifests
01d33fc
@ctb
get started adding manifests to MultiIndex
cb8e28d
@ctb
work through manifests for MultiIndex
2f2269b
@ctb
update comment about picklist.found
1d7e0cf
@ctb
more comment
67a9be1
@ctb
Merge branch 'latest' of github.com:dib-lab/sourmash into add/picklist
031522c
@ctb
Merge branch 'add/picklist' into add/picklist_selectors
5ac4671
@ctb
Merge branch 'add/picklist_selectors' into add/picklist_zf_manifests
23c1531
ctb added 25 commits June 22, 2021 12:28
@ctb
add save/load test
2756e7d
@ctb
rename matches_siginfo to matches_manifest_row
ed5fb7a
@ctb
add docstring
71b81ed
@ctb
reverse order of adding to seen set
c3f1a3d
@ctb
Merge branch 'add/picklist_zf_manifests' into add/picklist_manifests_sbt
7486871
@ctb
fix header writing
9bb6a9b
@ctb
Merge branch 'add/picklist_zf_manifests' into add/manifest_lazy_sigfile
6ebec9c
@ctb
change LoadedCollection back over to MultiIndex; remove LazyMultiIndex
60a6eec
@ctb
revert collection to multiindex
fe83b68
@ctb
Merge branch 'add/picklist_manifests_sbt' into add/picklist_zf_manifests
83e387e
@ctb
remove print
0adee52
@ctb
move manifest stuff to manifest.py
99199ee
@ctb
Merge branch 'add/picklist_manifests_sbt' into add/manifest_lazy_sigfile
0a982cb
@ctb
Merge branch 'add/picklist_zf_manifests' into add/manifest_lazy_sigfile
da381a1
@ctb
re-add LazyMultiIndex here
6e17c1a
@ctb
Merge branch 'latest' of https://github.com/sourmash-bio/sourmash int…
b633db1 
…o add/manifest_lazy_sigfile
@ctb
fix manifest code
a60438e
@ctb
Merge branch 'latest' of https://github.com/sourmash-bio/sourmash int…
cc44288 
…o add/manifest_lazy_sigfile
@ctb
upgrade debugging output on _load_database
75ba72b
@ctb
restore LazyLoadedSigfile, add comments/docstrings
02c485d
@ctb
doc strings, comments, etc
61c1b24
@ctb
some basic tests of the lazy loading indices
cc3b643
@ctb
change from sigfile to lca file for no manifests :)
3a25095
@ctb
add manifest_of_manifests
cb1594f
@ctb
support a simple JSON RPC mechanism for databases
7718240
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codecov bot commented Jun 27, 2021 •
edited
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Codecov Report

Merging #1644 (7718240) into add/manifest_lazy_sigfile (cb1594f) will decrease coverage by 19.05%.
The diff coverage is 35.29%.

Impacted file tree graph

@@                      Coverage Diff                       @@
##           add/manifest_lazy_sigfile    #1644       +/-   ##
==============================================================
- Coverage                      88.86%   69.81%   -19.06%     
==============================================================
  Files                             85       85               
  Lines                           7860     7875       +15     
  Branches                        1451     1452        +1     
==============================================================
- Hits                            6985     5498     -1487     
- Misses                           619     2122     +1503     
+ Partials                         256      255        -1
Flag Coverage Δ
python 69.81% <35.29%> (-19.06%) ⬇️

Flags with carried forward coverage won't be shown. Click here to find out more.

Impacted Files Coverage Δ
src/sourmash/sourmash_args.py 57.86% <21.42%> (-36.31%) ⬇️
src/sourmash/search.py 36.53% <100.00%> (-60.38%) ⬇️
src/sourmash/compare.py 17.56% <0.00%> (-82.44%) ⬇️
src/sourmash/commands.py 18.70% <0.00%> (-67.69%) ⬇️
src/sourmash/sig/__main__.py 42.65% <0.00%> (-48.25%) ⬇️
src/sourmash/lca/command_index.py 47.00% <0.00%> (-42.50%) ⬇️
src/sourmash/lca/command_classify.py 38.46% <0.00%> (-42.31%) ⬇️
src/sourmash/sbt_storage.py 70.18% <0.00%> (-20.19%) ⬇️
... and 14 more

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@ctb ctb mentioned this pull request Jun 27, 2021
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@ctb ctb force-pushed the add/manifest_lazy_sigfile branch from 0f03178 to 79c0b86 Compare July 5, 2021 13:21
@ctb ctb mentioned this pull request Aug 21, 2022
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@ctb ctb mentioned this pull request Sep 3, 2022
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