build: migrate package to src layout

- Move package modules from pepsy/ to src/pepsy/
- Update setuptools package discovery to use src/
- Point Sphinx docs path insertion to src/
- Add tests/conftest.py to include src in local test runs
- Validate editable install and test execution

Author: rezaquant

docs/conf.py

@@ -5,7 +5,7 @@
 import sys
 
 ROOT = Path(__file__).resolve().parents[1]
-sys.path.insert(0, str(ROOT))
+sys.path.insert(0, str(ROOT / "src"))
 
 # Avoid numba cache-path issues when importing quimb-dependent modules in docs builds.
 os.environ.setdefault("NUMBA_CACHE_DIR", "/tmp")

pyproject.toml

@@ -27,8 +27,11 @@ dev = ["pytest", "nbclient", "nbconvert"]
 [tool.setuptools]
 include-package-data = true
 
+[tool.setuptools.package-dir]
+"" = "src"
+
 [tool.setuptools.packages.find]
-where = ["."]
+where = ["src"]
 include = ["pepsy*"]
 
 [tool.pytest.ini_options]