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Camera ready analysis2 migration #7

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Merged
McClain-Thiel merged 5 commits into from
May 13, 2026
Merged

Camera ready analysis2 migration #7

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535547e
Add v2 evaluation pipeline at per-model optimal temperatures
McClain-Thiel May 1, 2026
17277ed
Phase 1: print-ready branch — gitignore, license, citation
McClain-Thiel May 4, 2026
b427702
Phase 2: restructure src→plasmidrl, merge analysis2 QC, move assets
McClain-Thiel May 4, 2026
7c29a91
Phase 3: plasmidrl.data and plasmidrl.models public API
McClain-Thiel May 4, 2026
f89f0cc
cleaning up for public sharing
McClain-Thiel May 13, 2026
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22 changes: 22 additions & 0 deletions .gitignore
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Expand Up @@ -233,3 +233,25 @@ __marimo__/
/s3/
checkpoints/
outputs/

# Internal — not for public release
anyscale/
.claude/
AGENTS.md
ICML_REVISION_LOG.md
rebuttal.md
reviews.md
scripts/
sweeps/
experiments/

# Training data — distributed via the public bucket, not git
data/train.parquet
data/test.parquet
data/GFP_cassette.fasta

# Exported Jupyter notebooks are kept for GitHub rendering.

# Rendered figures — regenerated from notebooks, not stored in git
*.png
*.pdf
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