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[EXP] test-merge of new find code and prefetch #1465

Closed
wants to merge 166 commits into from
Closed

[EXP] test-merge of new find code and prefetch #1465

wants to merge 166 commits into from

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ctb
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@ctb ctb commented Apr 16, 2021 •
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Experimenting with how #1392 affects #1370 and #1371.

ctb added 30 commits March 6, 2021 07:54
@ctb
add an initial prefetch command
e6d4e1c
@ctb
minor cleanup
310708a
@ctb
extract prefetch code out to search.py
db887a3
@ctb
csv output
0157782
@ctb
refactor to provide 'prefetch' on Index
583f19e
@ctb
enable gather --prefetch because why not?
07fbfd9
@ctb
add test for explicit downsampling
650784f
@ctb
refactor return signature of load_dbs_and_sigs
c43c6e8
@ctb
more refactor - filename stuff
23eea6d
@ctb
add 'location' to SBT objects
d7e3064
@ctb
finish removing filename
e7a13a3
@ctb
Merge branch 'refactor/databases' into add/prefetch_index
69f019e
@ctb
fix prefetch after merging in #1373
11251ab
@ctb
implement a CounterGatherIndex
9bfa690
@ctb
remove sort
033a764
@ctb
update counter logic to remove proper intersection
ff78a1b
@ctb
Merge branch 'latest' of github.com:dib-lab/sourmash into add/prefetc…
6b4be47 
…h_index
@ctb
make 'find' a generator
70168f1
@ctb
Merge branch 'latest' of github.com:dib-lab/sourmash into add/prefetc…
fb8ae9c 
…h_cli
@ctb
Merge branch 'add/prefetch_cli' into add/prefetch_index
6e2b2cf
@ctb
remove comment
6f30528
@ctb
Merge branch 'latest' into add/prefetch_cli
90f769a
@ctb
Merge branch 'add/prefetch_cli' into add/prefetch_index
d00cb4c
@ctb
begin refactoring 'categorize'
4c09f5b
@ctb
have the 'find' function for SBTs return signatures
af6fd84
@ctb
fix majority of tests
8a92936
@ctb
Merge branch 'latest' of github.com:dib-lab/sourmash into add/prefetc…
5138e83 
…h_cli
@ctb
Merge branch 'add/prefetch_cli' into add/prefetch_index
f3ed42f
@ctb
Merge branch 'latest' of github.com:dib-lab/sourmash into fix/sbt_find
c4adabf
@ctb
comment & then fix test
cdb4159
@ctb ctb mentioned this pull request Apr 17, 2021
Closed
ctb added 18 commits April 18, 2021 06:40
@ctb
better tests for gather --save-unassigned
7759314
@ctb
Merge branch 'refactor/index_find' of github.com:dib-lab/sourmash int…
8376ce5 
…o refactor/index_find
@ctb
Merge branch 'refactor/index_find' into merge_find_and_prefetch
e877490
@ctb
remove unused print
423fff4
@ctb
remove unnecessary check-me comment
593a907
@ctb
clear out docstring
4132162
@ctb
SBT search doesn't work on v1 and v2 SBTs b/c no min_n_below
23166df
@ctb
Merge branch 'latest' of github.com:dib-lab/sourmash into add/prefetc…
c494032 
…h_cli
@ctb
start adding tests
3cf42f0
@ctb
Merge branch 'latest' of github.com:dib-lab/sourmash into refactor/in…
3a5901e 
…dex_find
@ctb
Merge branch 'latest' of github.com:dib-lab/sourmash into add/prefetc…
4c0362e 
…h_cli
@ctb
test some basic prefetch stuff
18219ae
@ctb
Merge branch 'add/prefetch_cli' into merge_find_and_prefetch
50a94d4
@ctb
update index for prefetch
3ed4af0
@ctb
add fairly thorough tests
ba8beb6
@ctb
Merge branch 'add/prefetch_cli' into merge_find_and_prefetch
79e0166
@ctb
fix my dumb mistake with gather
57467cd
@ctb
Merge branch 'refactor/index_find' into merge_find_and_prefetch
06f5d03
Base automatically changed from refactor/index_find to latest April 22, 2021 02:17
@ctb
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ctb commented Apr 22, 2021

closed in favor of #1370, now that #1392 is in.

@ctb ctb closed this Apr 22, 2021
@ctb ctb deleted the merge_find_and_prefetch branch August 20, 2022 14:58
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@ctb @luizirber