Add mypy and fix related errors.

Author: bbremer

doc/Makefile

@@ -20,9 +20,8 @@ doc:
 	sphinx-build source/ build/
 
 clean:
-	rm -r build/generated/
+	rm -r build/
 	rm -r source/generated/
-	rm build/*.html
 
 # Catch-all target: route all unknown targets to Sphinx using the new
 # "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).

doc/source/conf.py

@@ -37,30 +37,31 @@
 ]
 napoleon_use_ivar = True
 
+# Add any paths that contain custom static files (such as style sheets) here,
+# relative to this directory. They are copied after the builtin static files,
+# so a file named "default.css" will overwrite the builtin "default.css".
+html_static_path = ['static']
+html_css_files = ['functions.css']
+
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ['templates']
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
 # This pattern also affects html_static_path and html_extra_path.
-exclude_patterns = ['templates']
+# exclude_patterns = ['templates']
 
 autodoc_typehints = 'description'
 autodoc_typehints_description_target = 'documented'
 autodoc_default_options = {"members": True, "inherited-members": True}
-
+autodoc_member_order = 'bysource'
 
 # -- Options for HTML output -------------------------------------------------
 
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
 #
-# html_theme = 'alabaster'
-
-# Add any paths that contain custom static files (such as style sheets) here,
-# relative to this directory. They are copied after the builtin static files,
-# so a file named "default.css" will overwrite the builtin "default.css".
-html_static_path = []
+html_theme = 'alabaster'
 
 
 # Changes autoclass "variables" to "attributes".

doc/source/reference.rst

@@ -11,4 +11,5 @@ Reference Manual
    :toctree: generated/
    :template: class.rst
 
-   ggrecomb.ParentAlignment
+   ParentAlignment
+   PDBStructure

doc/source/static/functions.css

@@ -0,0 +1,10 @@
+.function {
+    padding-bottom: 10pt;
+    padding-top: 10pt;
+}
+
+.method {
+    border-top: 3px solid #d0d0d0;
+    padding-bottom: 10pt;
+    padding-top: 10pt;
+}

doc/source/templates/class.rst

@@ -4,6 +4,7 @@
 .. currentmodule:: {{ module }}
 
 .. autoclass:: {{ objname }}
+   :no-undoc-members:
 
 .. raw:: html
 

mypy.ini

@@ -1,4 +1,4 @@
 [mypy]
 
-[mypy-Bio.*]
+[mypy-Bio.*,matplotlib.*,scipy.*]
 ignore_missing_imports = True

src/ggrecomb/__init__.py

@@ -1,4 +1,2 @@
 from .parent_alignment.pdb_structure import PDBStructure
-
-# Must come second because it imports PDBStructure.
 from .parent_alignment.parent_alignment import ParentAlignment

src/ggrecomb/energy_functions.py

@@ -2,11 +2,13 @@
 
 import numpy as np
 
-from ggrecomb.parent_alignment import ParentAlignment
+from ggrecomb import ParentAlignment
 
 
 class EnergyFunction:
-    pass
+    # TODO: Implement general energy function.
+    def __init__(self, pa: ParentAlignment):
+        raise NotImplementedError
 
 
 class SCHEMA(EnergyFunction):

src/ggrecomb/library.py

@@ -10,7 +10,7 @@
 from functools import cached_property
 from itertools import combinations
 
-from ggrecomb.parent_alignment import ParentAlignment
+from ggrecomb import ParentAlignment
 
 
 # @dataclass(repr=False)
@@ -21,7 +21,7 @@ def __init__(
         breakpoints: dict[int, list[tuple[int, str]]],
         parent_alignment: ParentAlignment,
         bp_to_group: dict[int, int] = None,
-        group_bp_cache: dict[tuple[int], float] = None,
+        group_bp_cache: dict[tuple[int, ...], float] = None,
     ):
         self.energy = energy
         self.breakpoints = breakpoints