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Merged
VEK239 merged 5 commits into from
Oct 4, 2026
Merged

Package RTP-CODEC and organize manuscript code and documentation #8

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1eaa530
Package RTP-CODEC and organize manuscript workflows
VEK239 Oct 4, 2026
51684ab
Track source subpackages and declare plotting dependencies
VEK239 Oct 4, 2026
37ffe78
Include relocated data examples and preparation launchers
VEK239 Oct 4, 2026
eb0cfb6
Keep large historical AIRR data outside the source distribution
VEK239 Oct 4, 2026
1b2e1cb
Include grouped reporting launchers in the source tree
VEK239 Oct 4, 2026
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4 changes: 4 additions & 0 deletions .gitattributes
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Expand Up @@ -8,3 +8,7 @@
*.tsv text eol=lf whitespace=-blank-at-eol
*.csv text eol=lf
*.json text eol=lf
*.toml text eol=lf
*.cff text eol=lf
*.ipynb text eol=lf
*.txt text eol=lf
7 changes: 4 additions & 3 deletions .github/workflows/tests.yml
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Expand Up @@ -12,7 +12,8 @@ jobs:
python-version: '3.11'
cache: pip
- run: python -m pip install torch==2.4.1 --index-url https://download.pytorch.org/whl/cpu
- run: python -m pip install -r requirements-dev.txt
- run: python -m compileall -q irrm_codec benchmark scripts tests
- run: python -m pip install -e ".[dev]"
- run: python -m compileall -q src tests
- run: python -m pytest -q
- run: find scripts slurm benchmark/slurm -type f \( -name '*.sh' -o -name '*.sbatch' \) -print0 | xargs -0 -n1 bash -n
- run: rtp-codec --help && rtp-codec train --help && rtp-codec encode --help
- run: find scripts -type f \( -name '*.sh' -o -name '*.sbatch' \) -print0 | xargs -0 -n1 bash -n
15 changes: 9 additions & 6 deletions .gitignore
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Expand Up @@ -40,23 +40,26 @@ Thumbs.db
*.log

# Project artifacts
artifacts/
/artifacts/

# Local data
data/
/data/

# Reports
reports/
/reports/

# Generated experiments and local publication scratch
.publish-*/
.tmp*/
tmp/
output/
manuscript/
/tmp/
/output/
/manuscript/
*.pt
*.pth
*.npy
*.npz
experiments/**/wandb/
experiments/**/predictions/

# Generated training runs (versioned presets live in configs/)
/experiments/
19 changes: 19 additions & 0 deletions CITATION.cff
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@@ -0,0 +1,19 @@
cff-version: 1.2.0
message: "Please cite the RTP-CODEC manuscript and this repository when using the code."
title: "RTP-CODEC: Learning Compact TCR Representations from Multiple Biological Objectives"
type: software
version: 0.1.0
url: "https://github.com/VEK239/rtp-codec"
repository-code: "https://github.com/VEK239/rtp-codec"
license: GPL-3.0-only
authors:
- family-names: Vlasova
given-names: Elizaveta
- family-names: Grigorev
given-names: Petr
- family-names: Demidova
given-names: Mariia
- family-names: Muravyov
given-names: Sergey
- family-names: Shugay
given-names: Mikhail
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