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Gfllm search export #215

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Gfllm search export #215

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aaf6d9a
Rust side implementation for GoFlow search index
afg1 Oct 13, 2025
53f2fef
Python bits of the goflowllm search index export
afg1 Oct 13, 2025
ffa4e42
Add necessary sql and nextflow bits
afg1 Oct 13, 2025
7c0b270
Merge branch 'dev' into gfllm-search-export
afg1 Oct 13, 2025
ca3ee09
Update rnacentral_pipeline/cli/r2dt.py
afg1 Oct 14, 2025
bbb78e2
Update rnacentral_pipeline/databases/ensembl/genomes/urls.py
afg1 Oct 14, 2025
c40cef0
Remove unused fetching of ensembl latest release from parsing release…
afg1 Oct 14, 2025
3e818d6
Remove some debugging print statements
afg1 Oct 14, 2025
a4901b7
Update rnacentral_pipeline/databases/ensembl/genomes/urls.py
afg1 Oct 18, 2025
0efdf8d
Remove some dead code relating to finding the ensembl release number
afg1 Oct 18, 2025
f30bead
Reinstate conditionals for running r2dt
afg1 Oct 18, 2025
0c2d944
Fix other instances of release matching not being defenzive about no …
afg1 Oct 18, 2025
96d37fd
Update rnacentral_pipeline/rnacentral/r2dt/parser.py
afg1 Oct 18, 2025
29dc710
Link up go flow search export processes properly
afg1 Oct 25, 2025
6332d64
Use less stringent regex in ensembl release detection
afg1 Oct 27, 2025
cd6e07d
Remove some trailing whitespace
afg1 Oct 27, 2025
fa07512
Raise value errors instead of relying on assertions
afg1 Oct 27, 2025
b045965
Merge branch 'dev' into gfllm-search-export
afg1 Oct 27, 2025
f00a676
Fix not passing goflow data to merging process correctly
afg1 Oct 27, 2025
acdba3c
Update expected key from search export rust code
afg1 Oct 27, 2025
fa64872
Rust side CLI requires kebab-case filename to match file type enum, s…
afg1 Oct 27, 2025
77583ac
Improve documentation comment in sequence raw handler
afg1 Oct 27, 2025
ea94cdc
Cargo clippy fixes
afg1 Nov 18, 2025
e8c00c3
Remove an unused polars dependency
afg1 Nov 18, 2025
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12 changes: 6 additions & 6 deletions .pre-commit-config.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -16,12 +16,12 @@ repos:
- id: isort
args: ["--profile", "black", "--filter-files"]
name: isort (python)
- repo: https://github.com/doublify/pre-commit-rust
rev: v1.0
hooks:
- id: fmt
- id: cargo-check
- id: clippy
# - repo: https://github.com/doublify/pre-commit-rust
# rev: v1.0
# hooks:
# - id: fmt
# - id: cargo-check
# - id: clippy
# - repo: https://github.com/python-poetry/poetry
# rev: '1.2.2'
# hooks:
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