Update Nubase to NUBASE

To align with AME, always refer to NUBASE in all capital letters.

Author: php1ic

README.md

@@ -40,8 +40,8 @@ For example, track how the accuracy of the mass excess of 18B changes once it is
 ```python
 >>> import pynch.mass_table as mt
 >>> df = mt.MassTable().full_data
->>> df[(df['A'] == 18) & (df['Z'] == 5)][['Experimental', 'NubaseMassExcess', 'NubaseMassExcessError', 'NubaseRelativeError', 'DiscoveryYear']]
-           Experimental  NubaseMassExcess  NubaseMassExcessError  NubaseRelativeError  DiscoveryYear
+>>> df[(df['A'] == 18) & (df['Z'] == 5)][['Experimental', 'NUBASEMassExcess', 'NUBASEMassExcessError', 'NUBASERelativeError', 'DiscoveryYear']]
+           Experimental  NUBASEMassExcess  NUBASEMassExcessError  NUBASERelativeError  DiscoveryYear
 TableYear
 2003              False           52320.0                  800.0             0.015291           1900
 2012               True           51850.0                  170.0             0.003279           2010
@@ -52,7 +52,7 @@ Or for all of the A=100 isotopes from the 2012 table that have a mass-excess err
 ```python
 >>> import pynch.mass_table as mt
 >>> df = mt.MassTable().full_data
->>> df.query('TableYear == 2012 and A == 100 and NubaseMassExcessError < 10.0')[['A', 'Z', 'Symbol', 'DiscoveryYear']]
+>>> df.query('TableYear == 2012 and A == 100 and NUBASEMassExcessError < 10.0')[['A', 'Z', 'Symbol', 'DiscoveryYear']]
              A   Z Symbol  DiscoveryYear
 TableYear
 2012       100  40     Zr           1970
@@ -68,12 +68,12 @@ Or how does the NUBASE mass-excess compare with the AME value for experimentally
 >>> import pynch.mass_table as mt
 >>> df = mt.MassTable().full_data
 >>> # Create a new column comparing the measured values
->>> df['NUBASE-AME'] = df['NubaseMassExcess'] - df['AMEMassExcess']
+>>> df['NUBASE-AME'] = df['NUBASEMassExcess'] - df['AMEMassExcess']
 >>> # Extract the data for measured isotopes and from the latest table
 >>> df_comparison = df.query('TableYear == 2020 and Experimental == True')
 >>> # Sort the difference in measured data by absolute value and print the columns we are interested in
->>> df_comparison.sort_values(by=['NUBASE-AME'], key=abs, ascending=False)[['A', 'Z', 'Symbol', 'NubaseMassExcess', 'AMEMassExcess', 'NUBASE-AME']].head(n=10)
-             A   Z Symbol  NubaseMassExcess  AMEMassExcess  NUBASE-AME
+>>> df_comparison.sort_values(by=['NUBASE-AME'], key=abs, ascending=False)[['A', 'Z', 'Symbol', 'NUBASEMassExcess', 'AMEMassExcess', 'NUBASE-AME']].head(n=10)
+             A   Z Symbol  NUBASEMassExcess  AMEMassExcess  NUBASE-AME
 TableYear
 2020       221  91     Pa           20370.0      20374.937      -4.937
 2020        57  23      V          -44440.0     -44435.063      -4.937

pynch/mass_table.py

@@ -9,7 +9,7 @@
 from pynch.ame_mass_parse import AMEMassParser
 from pynch.ame_reaction_1_parse import AMEReactionParserOne
 from pynch.ame_reaction_2_parse import AMEReactionParserTwo
-from pynch.nubase_parse import NubaseParser
+from pynch.nubase_parse import NUBASEParser
 
 
 class MassTable:
@@ -79,7 +79,7 @@ def _validate_year(self, year: int) -> int:
     def _parse_nubase_data(self, year: int) -> pd.DataFrame:
         """Get the nubase for the given year as a pandas.DataFrame."""
         year = self._validate_year(year)
-        return NubaseParser(self._get_nubase_datafile(year), year).read_file()
+        return NUBASEParser(self._get_nubase_datafile(year), year).read_file()
 
     def _parse_ame_data(self, year: int) -> pd.DataFrame:
         """Combine all the AME files from the given year into a pandas.DataFrame."""
@@ -98,14 +98,14 @@ def _combine_all_data(self) -> pd.DataFrame:
         common_columns = ['A', 'Z', 'N', 'TableYear', 'Symbol']
         df = self.nubase.merge(self.ame, on=common_columns)
 
-        df["NubaseRelativeError"] = abs(
-            df["NubaseMassExcessError"] / df["NubaseMassExcess"]
+        df["NUBASERelativeError"] = abs(
+            df["NUBASEMassExcessError"] / df["NUBASEMassExcess"]
         )
         df["AMERelativeError"] = abs(df["AMEMassExcessError"] / df["AMEMassExcess"])
 
         # 12C has a 0.0 +/ 0.0 mass excess by definition so calculating relative error -> NaN
         # Set the value to 0.0 as that's what it is
-        df.loc[(df.Symbol == "C") & (df.A == 12), "NubaseRelativeError"] = 0.0
+        df.loc[(df.Symbol == "C") & (df.A == 12), "NUBASERelativeError"] = 0.0
         df.loc[(df.Symbol == "C") & (df.A == 12), "AMERelativeError"] = 0.0
 
         # 198Au has a typo in it's decay mode in the 2012 table. It is recorded as '-'

pynch/nubase_file.py

@@ -2,7 +2,7 @@
 from pynch.parse import Parse
 
 
-class NubaseFile(Parse):
+class NUBASEFile(Parse):
     """Easy access to where variables are in the NUBASE file.
 
     The NUBASE data file is formatted by location in the line, values exist

pynch/nubase_parse.py

@@ -6,10 +6,10 @@
 
 import pandas as pd
 
-from pynch.nubase_file import NubaseFile
+from pynch.nubase_file import NUBASEFile
 
 
-class NubaseParser(NubaseFile):
+class NUBASEParser(NUBASEFile):
     """Parse the NUBASE data file.
 
     A collection of functions to parse the weird format of the NUBASE file.
@@ -96,8 +96,8 @@ def _read_line(self, line: str) -> dict:
             "TableYear": self.year,
             "A": self._read_as_int(line, self.START_A, self.END_A),
             "Z": self._read_as_int(line, self.START_Z, self.END_Z),
-            "NubaseMassExcess": self._read_as_float(line, self.START_ME, self.END_ME),
-            "NubaseMassExcessError": self._read_as_float(line, self.START_DME, self.END_DME),
+            "NUBASEMassExcess": self._read_as_float(line, self.START_ME, self.END_ME),
+            "NUBASEMassExcessError": self._read_as_float(line, self.START_DME, self.END_DME),
             # "LevelEnergy" : self._read_as_float(,
             #     line, self.START_ISOMER, self.END_ISOMER
             # )

tests/test_nubase_parse.py

@@ -4,7 +4,7 @@
 
 
 def test_read_halflife_value():
-    parser = nbp.NubaseParser(pathlib.Path("."), 2003)
+    parser = nbp.NUBASEParser(pathlib.Path("."), 2003)
 
     line_01 = "232 0950   232Am   43400#     300#                             1.31   m 0.04                 91           B+=?;A=2#;B+SF=0.069 10"
     assert parser._read_halflife_value(line_01) == 1.31
@@ -14,7 +14,7 @@ def test_read_halflife_value():
 
 
 def test_read_halflife_error():
-    parser = nbp.NubaseParser(pathlib.Path("."), 2003)
+    parser = nbp.NUBASEParser(pathlib.Path("."), 2003)
 
     line_01 = "113 0500   113Sn  -88333        4                            115.09   d 0.03   1/2+          00           B+=100"
     assert parser._read_halflife_error(line_01) == 0.03
@@ -24,14 +24,14 @@ def test_read_halflife_error():
 
 
 def test_no_decay_mode():
-    parser = nbp.NubaseParser(pathlib.Path("."), 2012)
+    parser = nbp.NUBASEParser(pathlib.Path("."), 2012)
 
     no_decay = "044 0212   44Scn  -37669.9      1.8     146.224   0.022       50.4   us 0.7    0-            99"
     assert parser._read_decay_string(no_decay) == "UNKNOWN"
 
 
 def test_readable_line():
-    parser = nbp.NubaseParser(pathlib.Path("."), 2003)
+    parser = nbp.NUBASEParser(pathlib.Path("."), 2003)
 
     bad_line01 = "003 0030   3Li     28670#    2000#                      RN   p-unst                          98           p ?"
     bad_line02 = "130 0556   130Csx -86873       17        27      15         R=.2~~~.1          fsmix"
@@ -47,7 +47,7 @@ def test_readable_line():
 
 
 def test_read_line():
-    parser = nbp.NubaseParser(pathlib.Path("."), 2003)
+    parser = nbp.NUBASEParser(pathlib.Path("."), 2003)
 
     iso_line = "183 0791   183Aum -30114       10        73.3     0.4         >1     us        (1/2)+        99           IT=100"
     assert parser._read_line(iso_line) == dict()
@@ -59,8 +59,8 @@ def test_read_line():
     assert d['Z'] == 29
     assert d['N'] == 28
     assert d['Experimental'] is True
-    assert d['NubaseMassExcess'] == -47310.0
-    assert d['NubaseMassExcessError'] == 16.0
+    assert d['NUBASEMassExcess'] == -47310.0
+    assert d['NUBASEMassExcessError'] == 16.0
     assert d['HalfLifeValue'] == 196.3
     assert d['HalfLifeUnit'] == "ms"
     assert d['HalfLifeError'] == 0.7
@@ -75,8 +75,8 @@ def test_read_line():
     assert d['Z'] == 53
     assert d['N'] == 57
     assert d['Experimental'] is False
-    assert d['NubaseMassExcess'] == -60320
-    assert d['NubaseMassExcessError'] == 310
+    assert d['NUBASEMassExcess'] == -60320
+    assert d['NUBASEMassExcessError'] == 310
     assert d['HalfLifeValue'] == 650
     assert d['HalfLifeUnit'] == "ms"
     assert d['HalfLifeError'] == 20
@@ -85,7 +85,7 @@ def test_read_line():
     assert d['Decay'] == "B+"
 
     # 2020 table has a new format
-    parser = nbp.NubaseParser(pathlib.Path("."), 2020)
+    parser = nbp.NUBASEParser(pathlib.Path("."), 2020)
 
     # Use the same isotope as previously tested
     gs_line = "057 0290   57Cu   -47309.0        0.5                                 196.4   ms 0.7    3/2-*         98          1976 B+=100"
@@ -95,8 +95,8 @@ def test_read_line():
     assert d['Z'] == 29
     assert d['N'] == 28
     assert d['Experimental'] is True
-    assert d['NubaseMassExcess'] == -47309.0
-    assert d['NubaseMassExcessError'] == 0.5
+    assert d['NUBASEMassExcess'] == -47309.0
+    assert d['NUBASEMassExcessError'] == 0.5
     assert d['HalfLifeValue'] == 196.4
     assert d['HalfLifeUnit'] == "ms"
     assert d['HalfLifeError'] == 0.7