Make mypy a dev dependency and fix any issues it found

Author: php1ic

nuclearmasses/ame_mass_parse.py

@@ -114,16 +114,17 @@ def read_file(self) -> pd.DataFrame:
             df["Symbol"] = pd.to_numeric(df["Z"]).map(self.z_to_symbol)
 
             # Combine the two columns to create the atomic mass then drop the redundant column
+            # Pandas is happy to use '+' for any type, but mypy doesn't like it, hence the use of str.cat()
             df["AtomicMass"] = (
-                df["AtomicNumber"].astype("string")
-                + "."
-                + df["AtomicMass"].astype("string").str.replace(".", "", regex=False)
+                df["AtomicNumber"]
+                .astype("string")
+                .str.cat(df["AtomicMass"].astype("string").str.replace(".", "", regex=False), sep=".")
             )
             df = df.drop(columns=["AtomicNumber"])
 
             # We need to rescale the error value because we combined the two columns above
             df = df.assign(AtomicMassError=df["AtomicMassError"].astype(float) / 1.0e6)
-
-            return df.astype(self._data_types())
         except ValueError as e:
             print(f"Parsing error: {e}")
+
+        return df.astype(self._data_types())

nuclearmasses/ame_reaction_1_parse.py

@@ -117,7 +117,7 @@ def read_file(self) -> pd.DataFrame:
             df["TableYear"] = self.year
             df["N"] = pd.to_numeric(df["A"]) - pd.to_numeric(df["Z"])
             df["Symbol"] = pd.to_numeric(df["Z"]).map(self.z_to_symbol)
-
-            return df.astype(self._data_types())
         except ValueError as e:
             print(f"Parsing error: {e}")
+
+        return df.astype(self._data_types())

nuclearmasses/ame_reaction_2_parse.py

@@ -121,7 +121,7 @@ def read_file(self) -> pd.DataFrame:
             df["TableYear"] = self.year
             df["N"] = pd.to_numeric(df["A"]) - pd.to_numeric(df["Z"])
             df["Symbol"] = pd.to_numeric(df["Z"]).map(self.z_to_symbol)
-
-            return df.astype(self._data_types())
         except ValueError as e:
             print(f"Parsing error: {e}")
+
+        return df.astype(self._data_types())

nuclearmasses/element_converter.py

@@ -7,7 +7,7 @@ class ElementConverter:
     TODO: Create accessor function that do some argument validation
     """
 
-    def __init__(self):
+    def __init__(self) -> None:
         """Construct the symbol -> Z and Z -> symbol dictionaries."""
         # fmt: off
         # Fromatter wants to put each item on it's own line, I don't

nuclearmasses/nubase_parse.py

@@ -2,6 +2,7 @@
 
 import logging
 import pathlib
+import typing
 
 import pandas as pd
 
@@ -133,7 +134,7 @@ def read_file(self) -> pd.DataFrame:
         try:
             df = pd.read_fwf(
                 self.filename,
-                colspecs=self.column_limits,
+                colspecs=typing.cast(typing.Sequence[tuple[int, int]], self.column_limits),  # appease mypy
                 names=self._column_names(),
                 na_values=self._na_values(),
                 keep_default_na=False,
@@ -155,16 +156,13 @@ def read_file(self) -> pd.DataFrame:
             df = df.drop(columns=["State", "IsomerEnergy", "IsomerEnergyError"])
 
             # Convert stable isotopes into ones with enormous lifetimes with zero error so we can cast
-            df.loc[df["HalfLifeValue"] == "stbl", ["HalfLifeValue", "HalfLifeUnit", "HalfLifeError"]] = [
-                99.99,
-                "Zy",
-                0.0,
-            ]
+            mask = df["HalfLifeValue"] == "stbl"
+            df.loc[mask, ["HalfLifeValue", "HalfLifeUnit", "HalfLifeError"]] = (99.99, "Zy", 0.0)
 
             df["HalfLifeValue"] = df["HalfLifeValue"].astype("string").str.replace(r"[<>?~]", "", regex=True)
             # We'll be lazy here and remove any characters in this column. Future us will parse this properly
             df["HalfLifeError"] = df["HalfLifeError"].astype("string").str.replace(r"[<>?~a-z]", "", regex=True)
-
-            return df.astype(self._data_types())
         except ValueError as e:
             print(f"Parsing error: {e}")
+
+        return df.astype(self._data_types())

pyproject.toml

@@ -44,6 +44,8 @@ keywords = [
 [project.optional-dependencies]
 dev = [
   "coverage",
+  "mypy",
+  "pandas-stubs",
 ]
 
 [project.urls]