Try lazy loading; consolidate pylintrc and pyproject

Author: pchlenski

.pylintrc

@@ -2,4 +2,24 @@
 import manify.embedders
 import manify.manifolds
 import manify.predictors
-import manify.utils
+
+# Dynamically check for utils dependencies
+try:
+    import importlib.util
+
+    _utils_deps = ["networkx", "pandas", "matplotlib", "scipy", "anndata", "basemap"]
+    _missing_deps = [dep for dep in _utils_deps if importlib.util.find_spec(dep) is None]
+
+    if not _missing_deps:
+        import manify.utils
+
+        HAS_UTILS = True
+    else:
+        HAS_UTILS = False
+except ImportError:
+    HAS_UTILS = False
+
+# Expose flag for users to check
+__all__ = ["curvature_estimation", "embedders", "manifolds", "predictors"]
+if HAS_UTILS:
+    __all__.append("utils")

manify/__init__.py

@@ -1,5 +1,26 @@
-import manify.utils.benchmarks
-import manify.utils.dataloaders
-import manify.utils.link_prediction
-import manify.utils.preprocessing
-import manify.utils.visualization
+# Lazy loading variant of utils imports - changed to this so that missing imports would be non-breaking for core manify
+
+
+def __getattr__(name):
+    if name == "benchmarks":
+        import manify.utils.benchmarks
+
+        return manify.utils.benchmarks
+    elif name == "dataloaders":
+        import manify.utils.dataloaders
+
+        return manify.utils.dataloaders
+    elif name == "link_prediction":
+        import manify.utils.link_prediction
+
+        return manify.utils.link_prediction
+    elif name == "preprocessing":
+        import manify.utils.preprocessing
+
+        return manify.utils.preprocessing
+    elif name == "visualization":
+        import manify.utils.visualization
+
+        return manify.utils.visualization
+    else:
+        raise AttributeError(f"module 'manify.utils' has no attribute '{name}'")

manify/utils/__init__.py

@@ -17,10 +17,9 @@ dependencies = [
     "tqdm",
     "cvxpy",
     "scikit-learn==1.5.1",
-    "jaxtyping"
 ]
 
-[pyproject.optional_dependencies]
+[project.optional-dependencies]
 dev = [
     "jaxtyping",
 ]
@@ -36,11 +35,31 @@ utils = [
 [tool.setuptools]
 packages = ["manify"]
 
+# Pylint configuration
+[tool.pylint.master]
+init-hook = "import sys; sys.path.append('.')"
+fail-under = 8.0
+ignore = "__pycache__,.git,venv"
+
+[tool.pylint.reports]
+output-format = "colorized"
+
 [tool.pylint.format]
 max-line-length = 120
 
 [tool.pylint."MESSAGES CONTROL"]
 disable = ["invalid-name"]
 
+[tool.pylint.basic]
+good-names = "i,j,k,ex,Run,_,fp"
+argument-rgx = "[a-z_][a-z0-9_]{2,30}$"
+variable-rgx = "[a-z_][a-z0-9_]{2,30}$"
+class-rgx = "[A-Z][a-zA-Z0-9]+$"
+const-rgx = "(([A-Z_][A-Z0-9_]*)|(__.*__))"
+module-rgx = "([a-z_][a-z0-9_]*)"
+
+[tool.pylint.typecheck]
+generated-members = "torch.*,nn.*"
+
 [tool.pytest.ini_options]
-adopts = "--jaxtyping-packages=beartype.beartype"
+adopts = "--jaxtyping-packages=beartype.beartype"