Junior B.
907a39aaba
- gpu/modal_app.py: add the `pose` local entrypoint used for the HDAC2 pose-RMSD validation (run: `modal run gpu/modal_app.py::pose`). - pyproject [structure] extra: add the deps we actually use locally (gemmi, spyrmsd, meeko, modal) for reproducibility; document the non-pip tools (Vina binary, open-babel) and that Boltz/cuequivariance are Modal-image-only. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
59 lines
2.0 KiB
TOML
59 lines
2.0 KiB
TOML
[build-system]
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requires = ["setuptools>=68", "wheel"]
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build-backend = "setuptools.build_meta"
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[project]
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name = "reverso-mvp"
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version = "0.1.0"
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description = "Sickle cell drug repurposing MVP — disease signature + drug profile matching via CMap-style connectivity scoring"
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readme = "README.md"
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requires-python = ">=3.11,<3.14"
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license = { text = "Proprietary" }
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authors = [{ name = "Reverso" }]
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dependencies = [
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"pandas>=2.0",
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"numpy>=1.24",
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"scipy>=1.11",
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"requests>=2.31",
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"chembl_webresource_client>=0.10", # ChEMBL API client
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"GEOparse>=2.0", # GEO dataset access
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"pydeseq2>=0.4", # Differential expression in Python
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"cmapPy>=4.0", # Reference CMap connectivity implementation
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"pyarrow>=14.0", # Parquet I/O
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"jupyter>=1.0",
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"matplotlib>=3.7", # Sanity-check plots
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"seaborn>=0.13",
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"pydantic>=2.0", # Schema validation for signatures/profiles
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"mygene>=3.2", # Gene symbol -> Entrez/Ensembl mapping
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]
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[project.optional-dependencies]
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dev = [
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"pytest>=8.0",
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"ruff>=0.5",
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]
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# Structure-based binding track (PLAN §12); see docs/structure_binding_notes.md.
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# Non-pip tools (install separately): AutoDock Vina binary (tools/vina, from the AutoDock-Vina
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# GitHub release) and open-babel (brew). Boltz-2 + cuequivariance run only in the Modal GPU image
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# (gpu/modal_app.py), not locally.
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structure = [
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"rdkit>=2024.3", # ligand prep, fingerprints
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"requests>=2.31", # PubChem / RCSB fetch
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"gemmi>=0.6", # structure parsing + superposition
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"spyrmsd>=0.9", # symmetry-corrected pose RMSD
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"meeko>=0.7", # production docking ligand prep
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"modal>=1.5", # ephemeral GPU orchestration
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]
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[tool.setuptools.packages.find]
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where = ["."]
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include = ["src*"]
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[tool.ruff]
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line-length = 100
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target-version = "py311"
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[tool.pytest.ini_options]
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testpaths = ["tests"]
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