Scaffold Reverso MVP pipeline structure

Set up the project skeleton per PLAN.md §4:
- src/ package: identifiers, disease, drugs, scoring, provenance
  with pydantic schemas and confidence-tier logic (working);
  data-pull/compute functions stubbed per their build week
- 5 starter notebooks (01-05) with PLAN-referenced steps
- tests/test_scoring.py: tier-assignment tests pass; scoring
  reference test xfail until Week 3
- docs/: recovery_test_report, data_sources, known_limitations skeletons
- pyproject.toml (requires-python >=3.11,<3.14), .gitignore, README
- data/ tree preserved via .gitkeep; raw/processed/results gitignored

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

pyproject.toml

@@ -0,0 +1,46 @@
+[build-system]
+requires = ["setuptools>=68", "wheel"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "reverso-mvp"
+version = "0.1.0"
+description = "Sickle cell drug repurposing MVP — disease signature + drug profile matching via CMap-style connectivity scoring"
+readme = "README.md"
+requires-python = ">=3.11,<3.14"
+license = { text = "Proprietary" }
+authors = [{ name = "Reverso" }]
+
+dependencies = [
+    "pandas>=2.0",
+    "numpy>=1.24",
+    "scipy>=1.11",
+    "requests>=2.31",
+    "chembl_webresource_client>=0.10",   # ChEMBL API client
+    "GEOparse>=2.0",                      # GEO dataset access
+    "pydeseq2>=0.4",                      # Differential expression in Python
+    "cmapPy>=4.0",                        # Reference CMap connectivity implementation
+    "pyarrow>=14.0",                      # Parquet I/O
+    "jupyter>=1.0",
+    "matplotlib>=3.7",                    # Sanity-check plots
+    "seaborn>=0.13",
+    "pydantic>=2.0",                      # Schema validation for signatures/profiles
+    "mygene>=3.2",                        # Gene symbol -> Entrez/Ensembl mapping
+]
+
+[project.optional-dependencies]
+dev = [
+    "pytest>=8.0",
+    "ruff>=0.5",
+]
+
+[tool.setuptools.packages.find]
+where = ["."]
+include = ["src*"]
+
+[tool.ruff]
+line-length = 100
+target-version = "py311"
+
+[tool.pytest.ini_options]
+testpaths = ["tests"]