Create new Half life and error columns with units of seconds

.github/workflows/tests.yml

@@ -7,7 +7,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ['3.10', '3.11', '3.12', '3.13']
+        python-version: ['3.11', '3.12', '3.13']
 
     steps:
     - name: Checkout repository

README.md

@@ -124,21 +124,8 @@ isort . && ruff format && ruff check && mypy nuclearmasses
 
 ## Known issues
 
-- [#5](https://github.com/php1ic/nuclearmasses/issues/5) The half life from the NUBASE data is stored as the individual elements, a column with the value in seconds would be useful
-```python
->>> df[(df['A'] == 14) & (df['Symbol'] == 'C')][['HalfLifeValue', 'HalfLifeUnit', 'HalfLifeError']]
-           HalfLifeValue HalfLifeUnit  HalfLifeError
-TableYear
-1983                 NaN         <NA>            NaN
-1993                 NaN         <NA>            NaN
-1995                5.73           ky           0.04
-2003                5.70           ky           0.03
-2012                5.70           ky           0.03
-2016                5.70           ky           0.03
-2020                5.70           ky           0.03
-```
 - [#6](https://github.com/php1ic/nuclearmasses/issues/6) The decay mode field from the NUBASE data is stored 'as-is' from the file.
 It looks like it can be split on the ';' character for isotopes where there is more than one mode.
 A dictionary of {decay mode: fraction} may be the best way to store all of this information.
-- [#7](https://github.com/php1ic/nuclearmasses/issues/7) Information from anything other than the ground state of an isotope is ignored when parsing the NUABSE file.
+- [#7](https://github.com/php1ic/nuclearmasses/issues/7) Information from anything other than the ground state of an isotope is ignored when parsing the NUBASE file.
 The selection of what is and what is not included appears random to me which is why I simply ignored for the moment.

nuclearmasses/element_converter.py

@@ -1,3 +1,8 @@
+import astropy  # type: ignore[import-untyped]
+import numpy as np
+import pandas as pd
+
+
 class ElementConverter:
     """A utility class for converting between symbol and Z value
 
@@ -29,3 +34,11 @@ def __init__(self) -> None:
 
         # Switch the keys and values of the z_to_symbol dictionary so a user can access the Z value using the symbol
         self.symbol_to_z: dict[str, int] = {val: key for key, val in self.z_to_symbol.items()}
+
+    def unit_to_seconds(self, unit_str: str) -> float:
+        if pd.isna(unit_str):
+            return np.nan
+        try:
+            return float(astropy.units.Unit(unit_str).to(astropy.units.s))
+        except Exception:
+            return np.nan

nuclearmasses/nubase_parse.py

@@ -17,9 +17,13 @@ class NUBASEParser(NUBASEFile):
 
     def __init__(self, filename: pathlib.Path, year: int):
         """Set the file to read and the table year."""
-        self.filename = filename
-        self.year = year
-        super().__init__(self.year)
+        super().__init__(year)
+        self.filename: pathlib.Path = filename
+        self.year: int = year
+        self.unit_replacements: dict[str, str] = {
+            r"y$": "yr",
+            r"^m$": "min",
+        }
         logging.info(f"Reading {self.filename} from {self.year}")
 
     def _column_names(self) -> list[str]:
@@ -75,6 +79,8 @@ def _data_types(self) -> dict:
                     "HalfLifeValue": "float64",
                     "HalfLifeUnit": "string",
                     "HalfLifeError": "float64",
+                    "HalfLifeSeconds": "float64",
+                    "HalfLifeErrorSeconds": "float64",
                     "Spin": "string",
                     "DecayModes": "string",
                 }
@@ -93,6 +99,8 @@ def _data_types(self) -> dict:
                     "HalfLifeValue": "float64",
                     "HalfLifeUnit": "string",
                     "HalfLifeError": "float64",
+                    "HalfLifeSeconds": "float64",
+                    "HalfLifeErrorSeconds": "float64",
                     "Spin": "string",
                     "DiscoveryYear": "Int64",
                     "DecayModes": "string",
@@ -157,11 +165,25 @@ def read_file(self) -> pd.DataFrame:
 
             # Convert stable isotopes into ones with enormous lifetimes with zero error so we can cast
             mask = df["HalfLifeValue"] == "stbl"
-            df.loc[mask, ["HalfLifeValue", "HalfLifeUnit", "HalfLifeError"]] = (99.99, "Zy", 0.0)
+            df.loc[mask, ["HalfLifeValue", "HalfLifeUnit", "HalfLifeError"]] = (99.99, "Zyr", 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)
+
+            # Use the 3 half-life columns to create 2 new columns with units of seconds
+            df["HalfLifeUnit"] = df["HalfLifeUnit"].astype("string")
+            for pattern, replacement in self.unit_replacements.items():
+                df["HalfLifeUnit"] = df["HalfLifeUnit"].str.replace(pattern, replacement, regex=True)
+
+            # Ensure numeric values
+            for col in ["HalfLifeValue", "HalfLifeError"]:
+                df[col] = pd.to_numeric(df[col], errors="coerce")
+            # Pre-compute unit -> second conversions
+            unit_map = df["HalfLifeUnit"].map(self.unit_to_seconds)
+
+            df["HalfLifeSeconds"] = df["HalfLifeValue"] * unit_map
+            df["HalfLifeErrorSeconds"] = df["HalfLifeError"] * unit_map
         except ValueError as e:
             print(f"Parsing error: {e}")
 

pyproject.toml

@@ -11,7 +11,7 @@ authors = [
 description = "A python package to parse and store the various files published by AME and NUBASE"
 version = "0.0.1"
 readme = "README.md"
-requires-python = ">=3.10"
+requires-python = ">=3.11"
 classifiers = [
   "Development Status :: 4 - Beta",
   "Intended Audience :: Education",
@@ -20,7 +20,6 @@ classifiers = [
   "Programming Language :: Python",
   "Programming Language :: Python :: 3",
   "Programming Language :: Python :: 3 :: Only",
-  "Programming Language :: Python :: 3.10",
   "Programming Language :: Python :: 3.11",
   "Programming Language :: Python :: 3.12",
   "Programming Language :: Python :: 3.13",
@@ -30,6 +29,8 @@ classifiers = [
   "Topic :: Scientific/Engineering :: Physics",
 ]
 dependencies = [
+  "astropy",
+  "numpy",
   "pandas",
   "pytest",
 ]

tests/test_nubase_parse.py

@@ -24,8 +24,10 @@ def test_1995_nubase():
             "NUBASEMassExcess": [-60085],
             "NUBASEMassExcessError": [29],
             "HalfLifeValue": [2.99],
-            "HalfLifeUnit": ["m"],
+            "HalfLifeUnit": ["min"],
             "HalfLifeError": [0.07],
+            "HalfLifeSeconds": [179.4],
+            "HalfLifeErrorSeconds": [4.2],
             "Spin": ["3+"],
             "DecayModes": ["B-=100"],
         }
@@ -54,8 +56,10 @@ def test_2003_nubase():
             "NUBASEMassExcess": [-60070],
             "NUBASEMassExcessError": [30],
             "HalfLifeValue": [2.99],
-            "HalfLifeUnit": ["m"],
+            "HalfLifeUnit": ["min"],
             "HalfLifeError": [0.07],
+            "HalfLifeSeconds": [179.4],
+            "HalfLifeErrorSeconds": [4.2],
             "Spin": ["3+"],
             "DecayModes": ["B-=100"],
         }
@@ -84,8 +88,10 @@ def test_2012_nubase():
             "NUBASEMassExcess": [-60060],
             "NUBASEMassExcessError": [30],
             "HalfLifeValue": [2.99],
-            "HalfLifeUnit": ["m"],
+            "HalfLifeUnit": ["min"],
             "HalfLifeError": [0.07],
+            "HalfLifeSeconds": [179.4],
+            "HalfLifeErrorSeconds": [4.2],
             "Spin": ["3+"],
             "DiscoveryYear": [1960],
             "DecayModes": ["B-=100"],
@@ -115,8 +121,10 @@ def test_2016_nubase():
             "NUBASEMassExcess": [-60060],
             "NUBASEMassExcessError": [30],
             "HalfLifeValue": [2.99],
-            "HalfLifeUnit": ["m"],
+            "HalfLifeUnit": ["min"],
             "HalfLifeError": [0.07],
+            "HalfLifeSeconds": [179.4],
+            "HalfLifeErrorSeconds": [4.2],
             "Spin": ["3+"],
             "DiscoveryYear": [1960],
             "DecayModes": ["B-=100"],
@@ -147,8 +155,10 @@ def test_2020_nubase():
             "NUBASEMassExcess": [-60060],
             "NUBASEMassExcessError": [30],
             "HalfLifeValue": [2.99],
-            "HalfLifeUnit": ["m"],
+            "HalfLifeUnit": ["min"],
             "HalfLifeError": [0.07],
+            "HalfLifeSeconds": [179.4],
+            "HalfLifeErrorSeconds": [4.2],
             "Spin": ["3+"],
             "DiscoveryYear": [1960],
             "DecayModes": ["B-=100"],