Paper2Agent_decoupleRpy

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Paper2Agent_decoupleRpy

3.23 MB

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5 contributors

History: 336 commits

Annie Voigt

chore: keep agent working notes local; gitleaks allowlist no longer needs the scrubbed key value

dd4c2cb unverified 7 days ago

.github
chore(dependabot): ignore major/minor python base-image bumps about 2 months ago
deploy
fix(uploads): make the deployed malware-scan posture explicit and honest 26 days ago
docker
feat(exec): sandboxed per-session exec-kernel executor (ADR-0007 Phase 1) about 2 months ago
docs
docs: Loveless prod e2e verified (both sc UMAPs) + Werba pseudobulk→DESeq2 clean; ADR-0006 items 7/8 closed 12 days ago
resources
feat(mouse): thin mouse-intake path — staging script, ENSMUSG→MGI map, nested-batch guard 16 days ago
scripts
fix(hooks): chain git-lfs pre-push after the ADR-0014 security scan 13 days ago
security
feat(upload): assemble raw counts/TPM/metadata into an h5ad inside the gate 14 days ago
src
fix: dataset_load Path P now returns the h5ad; re-pin biodata-registry 0.1.16 12 days ago
tests
feat(ui): collapsed 'what happened' provenance panel after every run 13 days ago
.dockerignore
856 Bytes
feat(exec): real MCP handshake + container-launch fixes (ADR-0007 Phase 1 validation) about 2 months ago
.gitattributes
2.01 kB
chore(git): union-merge the append-style bookkeeping files 19 days ago
.gitignore
515 Bytes
chore: keep agent working notes local; gitleaks allowlist no longer needs the scrubbed key value 7 days ago
.gitleaks.toml
2.15 kB
chore: keep agent working notes local; gitleaks allowlist no longer needs the scrubbed key value 7 days ago
.pre-commit-config.yaml
971 Bytes
chore(security): add ruff+pre-commit baseline, record clean 2026-07-06 scan about 2 months ago
Makefile
1.49 kB
feat(security): ADR-0014 CI security scanning + shared scan definition about 2 months ago
README.md
2.46 kB
merge: security-review-prep (README orientation + _resolve_env_vars docstring) 23 days ago
TCGA_PAAD_scope.md
15.4 kB
Add TCGA-PAAD scoping doc, dataset assembly scripts, ignore .claude/ 3 months ago
app.py
1.99 kB
style: apply ruff lint --fix + ruff format across the tree about 2 months ago
bandit.yaml
885 Bytes
feat(security): ADR-0014 CI security scanning + shared scan definition about 2 months ago
fastmcp.json
193 Bytes
Flatten mcp/ folder and move mcp_server/ into src/ 4 months ago
gradio_ui.py
90.6 kB
feat(ui): collapsed 'what happened' provenance panel after every run 13 days ago
images.png
2.19 kB
Initial commit: DecoupleRpy agent 4 months ago
mcp_config.yaml
2.38 kB
Use python3 instead of bare python for decoupleRpy MCP server command 2 months ago
packages.txt
127 Bytes
Unpin lib*-dev in packages.txt to avoid build breaks on Debian security updates 2 months ago
prompts.yaml
50.1 kB
feat(de): surface the results-CSV schema; prompt bans schema-sniff re-reads 13 days ago
pytest.ini
637 Bytes
chore(scripts): rename the limma probe so pytest stops collecting it 19 days ago
requirements.in
6.1 kB
fix: dataset_load Path P now returns the h5ad; re-pin biodata-registry 0.1.16 12 days ago
requirements.txt
12.7 kB
fix: dataset_load Path P now returns the h5ad; re-pin biodata-registry 0.1.16 12 days ago
ruff.toml
1.17 kB
chore(security): add ruff+pre-commit baseline, record clean 2026-07-06 scan about 2 months ago
server.py
8.91 kB
style: apply ruff lint --fix + ruff format across the tree about 2 months ago
ui_formatting.py
29.9 kB
feat(ui): collapsed 'what happened' provenance panel after every run 13 days ago