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Pixi / myloasm / quickbinner / etc#296

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wwood wants to merge 189 commits intorhysnewell:devfrom
wwood:myloasm
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Pixi / myloasm / quickbinner / etc#296
wwood wants to merge 189 commits intorhysnewell:devfrom
wwood:myloasm

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@wwood wwood commented Feb 20, 2026

Some huge number of commits here. Some headline changes, beyond those mentioned in #275

  • Before gtdbtk, singlem, eggnog bins are filtered according to 50/5 and bins put in data/filtered_bins (bin_info still has all bins tho)
  • added the quickbin binner. It is so fast that it should probably be a standard binner, not an extra one, actually
  • singlem is not run on reads or appraise by default. Issue is that there's a performance regression in singlem - will need to fix that upstream
  • help messages are now via bird_tool_utils so the example style for -h, and --full-help drops to man
  • snakemake v9
  • aviary complete worked on hybrid input all the way to the end of annotation (admittedly there was some bugfixes along the way which hopefully didn't break anything)

wwood and others added 30 commits April 20, 2025 21:04
@wwood
pixi: First steps.
612d657
@wwood
pixi: First workflow w/o conda.
b3e8705
@wwood
admin: Towards pixi.
2631207
@wwood
test: Use pytest and adjust actions.
5aab998
@wwood
pixi: Further steps.
e9517dd
@wwood
pixi: First version with test_integration passing except batch.
a065812
@wwood
batch: Remove it.
3b021da 
Batch had at least 2 problems:
1. The test in test_integration was failing (need to add --cluster?)
2. There was a hard-coded ~/git/aviary path in the code.
@wwood
Merge remote-tracking branch 'origin/dev' into pixi
b049c28
@wwood
taxvamb: Update to v5.
9846488
@wwood
pixi: Run frozen and with a defined manifest.
06bbedf
@AroneyS
test pixi files within aviary package dir
7d0785b
@AroneyS
fix manifest path
127266b
@AroneyS
move pixi properly into aviary package dir
c107856 
use `pixi install -a --manifest-path aviary/pixi.toml` to install to aviary/.pixi/envs
@AroneyS
add manifest path arg to tests
a227450
@AroneyS
fix coassembly bug
e4b68b9
@AroneyS
remove references to CONDA_ENV_PATH env variable
3fc97fc
@AroneyS
convert --build arg to pixi install
0a6ba77
@AroneyS
add build subcommand
7cbed8a
@AroneyS
remove more conda-prefix references
3f1a880
@AroneyS
remove more references to conda
0ec71d1
@AroneyS
fix test
afc89e0
@AroneyS
mark build tests as expensive
d74eb77
@AroneyS
ignore "None" tmp_dir arg
8707b4a
@AroneyS
move resources before --configfile to prevent target_rule being consi…
59aa46e 
…dered under resources

fixes error `not enough values to unpack (expected 2, got 1)`
@AroneyS
create done file when skipping refinery
8e5c807
@AroneyS
add metabuli db path arg to all commands
c9662f5
@AroneyS
move package installation to task to prevent dependency lockup
eb1681f 
updating requirements.txt depends on the installed pixi env which depends on requirements.txt to install the local package...
pixi.toml pypi dependencies do not currently support `--no-deps`
@AroneyS
fix binner gpu environments
75a1b36 
ensure that they are actually using the gpu
installed on machine with H100s and worked on machine with A100s
@AroneyS
download all if none specified
09a0294
@AroneyS
fix default download arg
cb26b09
wwood and others added 25 commits January 16, 2026 09:53
@wwood
Merge remote-tracking branch 'wwood/quickbin' into myloasm
54ac686
@wwood
test_recover: Fix quickbin test.
112283e
@wwood
finalise_stats: Fix it.
e77270e
@wwood
qc_short_reads: Workaround hpc-related temp() snakemake bug.
cdb2d63
@wwood
actions: Attempt fix.
89391aa
@wwood
actions: Attempt fix 2.
3d50dd3
@wwood
actions and README: Workaround dead .pixi link issue.
b772890
@wwood
actions: Attempt fix 4.
75a4b45
@wwood
postinstall: Create symlinks.
21e6a54
@wwood
actions: Attempt fix 5.
3485164
@wwood
actions: Attempt fix 6.
f7e1160
@wwood
pixi.toml: Clean up.
31e956a
@AroneyS @wwood
fix pandas dtypes
9b69b57
@AroneyS @wwood
fix mispelling in disable-adapter-trimming arg
b22c5b1
@wwood
Refine singlem bin filtering workflow and tests
31436cd
@wwood
appraise: Further steps towards.
e576dc1
@wwood
appraise: No assign taxonomy.
c37d919
@wwood
Rename quality filter rule and make contamination threshold inclusive
50dc397
@wwood
singlem_appraise: Do not run by default.
e4c0c37 
It is computationally prohibitive at the moment, and not strictly necessary.
@wwood
Merge remote-tracking branch 'wwood/codex/create-unified-filter-rule-…
ff0e12b 
…for-bins' into myloasm
@wwood
Adjust singlem_pipe_reads expectations in workflow tests
5d1ec15
@wwood
Set singlem_appraise expectations to default-disabled
78c8951
@wwood
Clear existing GTDB-Tk output before classify_wf
99ff0ae
@wwood
Align max contamination CLI help wording
7d0767a
@wwood
Add QuickBin and myloasm citations
b369996
@wwood wwood mentioned this pull request Feb 20, 2026
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@AroneyS AroneyS self-requested a review February 20, 2026 04:49
AroneyS
AroneyS approved these changes Feb 20, 2026
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I assume run-tests-at-cmr succeeds?

@wwood wwood closed this Mar 31, 2026
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