Improve type annotations for core.structure (materialsproject#3837)

* remove a lot of ignore tags * first go: quick look and comment/type tweaks * remove ALL type: ignore[reportPossiblyUnboundVariable] * a quick look * tweak module docstring * fix/supress PossiblyUnboundVariable * pre-commit fix * add debug tag * fix some mypy errors * fix some mypy errors * suppress errors in `__setitem__` * fix typos * fix union * revert change to md * tweaks --------- Co-authored-by: Janosh Riebesell <[email protected]>
ab5424 · May 25, 2024 · d0ad785 · d0ad785
1 parent 74e692b
commit d0ad785
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diff --git a/.github/code_of_conduct.md b/.github/code_of_conduct.md
@@ -6,7 +6,7 @@ In the interest of fostering an open and welcoming environment, we as
 contributors and maintainers pledge to make participation in our project and
 our community a harassment-free experience for everyone, regardless of age, body
 size, disability, ethnicity, sex characteristics, gender identity and expression,
-level of experience, education, socio-economic status, nationality, personal
+level of experience, education, socioeconomic status, nationality, personal
 appearance, race, religion, or sexual identity and orientation.
 
 ## Our Standards

diff --git a/pymatgen/analysis/chemenv/utils/scripts_utils.py b/pymatgen/analysis/chemenv/utils/scripts_utils.py
@@ -213,6 +213,7 @@ def compute_environments(chemenv_configuration):
     default_strategy.setup_options(chemenv_configuration.package_options["default_strategy"]["strategy_options"])
     max_dist_factor = chemenv_configuration.package_options["default_max_distance_factor"]
     first_time = True
+    test = None
     while True:
         if len(questions) > 1:
             found = False
@@ -240,7 +241,7 @@ def compute_environments(chemenv_configuration):
 
         input_source = ""
         if found and len(questions) > 1:
-            input_source = test  # type: ignore[reportPossiblyUnboundVariable]
+            input_source = test
 
         structure = None
         if source_type == "cif":

diff --git a/pymatgen/analysis/local_env.py b/pymatgen/analysis/local_env.py
@@ -828,7 +828,7 @@ def get_all_voronoi_polyhedra(self, structure: Structure):
         del indices  # Save memory (tessellations can be costly)
 
         # Run the tessellation
-        qvoronoi_input = [s.coords for s in sites]
+        qvoronoi_input = [s.coords for s in sites if s is not None]
         voro = Voronoi(qvoronoi_input)
 
         # Get the information for each neighbor

diff --git a/pymatgen/analysis/solar/__init__.py b/pymatgen/analysis/solar/__init__.py
@@ -1 +1 @@
-"""Modules for prediciting theoretical solar-cell efficiency."""
+"""Module for predicting theoretical solar-cell efficiency."""
diff --git a/pymatgen/analysis/topological/__init__.py b/pymatgen/analysis/topological/__init__.py
@@ -1 +1 @@
-"""Modules for prediciting topological properties."""
+"""Module for predicting topological properties."""
diff --git a/pymatgen/core/interface.py b/pymatgen/core/interface.py
@@ -761,7 +761,7 @@ def gb_from_parameters(
                 sites_away_gb.append(site)
         if len(sites_near_gb) >= 1:
             s_near_gb = Structure.from_sites(sites_near_gb)
-            s_near_gb.merge_sites(tol=bond_length * rm_ratio, mode="d")
+            s_near_gb.merge_sites(tol=bond_length * rm_ratio, mode="delete")
             all_sites = sites_away_gb + s_near_gb.sites  # type: ignore
             gb_with_vac = Structure.from_sites(all_sites)