Added pyproject.toml

README.md

@@ -26,7 +26,7 @@ pip install --user -r requirements.txt
 
 With all of the necessary requirements installed, the below will start the app
 ```bash
-python3 app.py
+python3 src/app.py
 ```
 The console will tell you where to point your browser - likely http://127.0.0.1:8050/.
 
@@ -43,7 +43,7 @@ No comparison or validation is done on common values.
 
 ## Additional uses
 
-If you want to do your own thing with the data, you could import this module, access `MassTable().full_data`, then sort, slice and filter the resultant dataframe to your heart's content.
+If you want to do your own thing with the data, you could install this package, import this module, access `MassTable().full_data`, then sort, slice and filter the resultant dataframe to your heart's content. You can install this package with `pip install git+<package-repo>` where `<package-repo>` is the git repository of this package.
 
 For example, track how the accuracy of the mass excess of 18B changes once it is experimentally measured
 ```python

pyproject.toml

@@ -0,0 +1,16 @@
+[build-system]
+requires = ["setuptools>=64", "setuptools_scm>=8"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "pynch"
+dynamic = ["dependencies", "version"]
+
+[tool.setuptools]
+include-package-data = true
+
+[tool.setuptools.packages.find]
+where = ["src"]
+
+[tool.setuptools.dynamic]
+dependencies = {file = ["requirements.txt"]}

app.py → src/app.py

@@ -53,7 +53,7 @@ def update_graph(y_var, x_value, year):
 
     logit = (
         True
-        if y_var in ["HalfLife", "NubaseRelativeError", "AMERelativeError"]
+        if y_var in ["HalfLife", "NUBASERelativeError", "AMERelativeError"]
         else False
     )
 

pynch/mass_table.py → src/pynch/mass_table.py

@@ -1,4 +1,5 @@
 """Functionality to parse all data file into a single object."""
+import importlib.resources
 import logging
 import pathlib
 import typing
@@ -8,7 +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:
@@ -20,7 +21,7 @@ class MassTable:
     def __init__(self):
         """Do all of the work at construction."""
         # Assume this file is some/path/pynch/pynch/mass_table.py
-        self.data_path = pathlib.Path(__file__) / ".." / ".." / "data"
+        self.data_path = "data"
         self.existing_years = [2003, 2012, 2016, 2020]
         self.nubase = pd.concat([self._parse_nubase_data(y) for y in self.existing_years], ignore_index=True)
         self.ame = pd.concat([self._parse_ame_data(y) for y in self.existing_years], ignore_index=True)
@@ -29,8 +30,9 @@ def __init__(self):
 
     def _get_nubase_datafile(self, year: int) -> pathlib.Path:
         """Use the given year to locate the nubase mass table file and return the absolute path."""
-        nubase_mass = self.data_path / pathlib.Path(str(year))
-        nubase_mass = nubase_mass.resolve()
+        with importlib.resources.path("pynch", self.data_path) as p:
+            nubase_mass = p / pathlib.Path(str(year))
+            nubase_mass = nubase_mass.resolve()
 
         if year == 2003:
             nubase_mass = nubase_mass / "nubtab03.asc"
@@ -45,8 +47,9 @@ def _get_nubase_datafile(self, year: int) -> pathlib.Path:
 
     def _get_ame_datafiles(self, year: int) -> typing.Tuple[pathlib.Path, pathlib.Path, pathlib.Path]:
         """Use the given year to locate the 3 AME data file and return the absolute path."""
-        data_dir = self.data_path / pathlib.Path(str(year))
-        data_dir = data_dir.resolve()
+        with importlib.resources.path("pynch", self.data_path) as p:
+            data_dir = p / pathlib.Path(str(year))
+            data_dir = data_dir.resolve()
 
         if year == 2003:
             ame_mass = data_dir / "mass.mas03"
@@ -78,7 +81,7 @@ 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."""
@@ -97,14 +100,14 @@ 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 → src/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 → src/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
             # )