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[MRG] update to sourmash 4.1.0 #171

Merged
merged 35 commits into from
May 24, 2021
Merged

[MRG] update to sourmash 4.1.0 #171

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9a1054b
update to sourmash 4.1.0
taylorreiter May 18, 2021
f172ab2
Update env-sourmash.yml
taylorreiter May 18, 2021
7f409c0
Update env-reporting.yml
taylorreiter May 18, 2021
f4f7d84
start switch to 4.1. Prefect, zip of matches, load_file_as_signatures
taylorreiter May 19, 2021
be1704c
make gather stop when there aren't any more mh in the sig
taylorreiter May 19, 2021
fc634b6
rm div 0 in f_major calc, change match sig to zip, fix float point
taylorreiter May 19, 2021
39d2980
fix IndexError when empty sigs
taylorreiter May 19, 2021
18aa62c
change reporting env to >=4.1.0<5
taylorreiter May 19, 2021
304eda9
readd reporting file
taylorreiter May 19, 2021
cf8377b
switch test to load_file_as_signatures
taylorreiter May 19, 2021
38b2d8d
update snakemake test to matches.zip
taylorreiter May 19, 2021
475b4ce
add 2.fa to matches.zip with sourmash sig cat
taylorreiter May 19, 2021
41fd43d
tests/test_contigs_search.py
taylorreiter May 19, 2021
272e661
start switching to zip, still needs debug
taylorreiter May 19, 2021
4accd34
add test dataset
taylorreiter May 19, 2021
cc4144e
woops -- only break if len(mh) == 0
taylorreiter May 19, 2021
fc3d748
replace .get_mins() with .hashes
taylorreiter May 19, 2021
a0a322f
fix ValueError from threshold-bp
taylorreiter May 19, 2021
0e5bf65
woops rm thresholdbp print statement
taylorreiter May 19, 2021
2d01632
update to sourmash 1537 instead of 1537
taylorreiter May 20, 2021
8ca6da4
range for sourmash version
taylorreiter May 20, 2021
fe7997e
switch from gather to prefetch
taylorreiter May 20, 2021
3cbe754
add except for assertion error from sourmash assert db on empty sigs
taylorreiter May 20, 2021
ba291d9
refactor to not have pass block
taylorreiter May 20, 2021
bfc347a
refactor sum_ident
taylorreiter May 20, 2021
8d0b631
update threshold bp for prefetch to 3*scaled
taylorreiter May 20, 2021
21df7da
fix tests
ctb May 21, 2021
66f2a02
wups, remove test debugging
ctb May 21, 2021
c2086b5
remove sourmash 4.1.1 code
ctb May 21, 2021
9386006
remove --no-linear in prefetch bc its default
taylorreiter May 21, 2021
7a92847
fix load sig with file handle
taylorreiter May 21, 2021
716f02a
simplify while 1
taylorreiter May 21, 2021
9d1a895
Merge pull request #172 from dib-lab/update/tr_sourmash_by_ctb
taylorreiter May 21, 2021
cef2195
update to sourmash v4.1.1
ctb May 22, 2021
16bc5bc
Merge pull request #176 from dib-lab/ctb/update_sourmash_411
taylorreiter May 24, 2021
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2 changes: 1 addition & 1 deletion charcoal/conf/env-reporting.yml
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Expand Up @@ -12,5 +12,5 @@ dependencies:
- pip
- pip:
- git+https://github.com/dib-lab/charcoal.git
- sourmash==4.0.0a3
- sourmash==4.1.0
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- pyinterval
2 changes: 1 addition & 1 deletion charcoal/conf/env-sourmash.yml
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Expand Up @@ -11,5 +11,5 @@ dependencies:
- pip
- pip:
- git+https://github.com/dib-lab/charcoal.git
- sourmash==4.0.0a3
- sourmash==4.1.0
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- pyinterval
2 changes: 1 addition & 1 deletion environment.yml
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Expand Up @@ -10,4 +10,4 @@ dependencies:
- click
- pip
- pip:
- sourmash==4.0.0a3
- sourmash==4.1.0
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