Initial commit

Author: php1ic

.github/workflows/tests.yml

@@ -0,0 +1,24 @@
+name: Unit Tests
+
+on: [push, pull_request]
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ['3.10', '3.11', '3.12', '3.13']
+
+    steps:
+    - name: Checkout repository
+    - uses: actions/checkout@v4
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v5
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install -e .
+    - name: Test with pytest
+      run: pytest -v

.gitignore

@@ -0,0 +1,21 @@
+# Files and directories created by python
+**/__pycache__/
+**/.pytest_cache
+
+# A catch all for virtual env directories
+.venv*/
+venv*/
+
+# PyCharm settings directory
+.idea/
+
+# Jupyter related files and directories
+*.ipynb
+.ipynb_checkpoints/
+
+# Test coverage related files and directories
+.coverage
+coverage_html_report
+
+# Package build files and folders
+*.egg-info/

LICENSE

@@ -0,0 +1,19 @@
+MIT License
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

nuclearmasses/__init__.py

@@ -0,0 +1,56 @@
+"""Storage for variable line positions."""
+from nuclearmasses.parse import Parse
+
+
+class AMEMassFile(Parse):
+    """Easy access to where the variables are in the AME mass file."""
+
+    def __init__(self, year: int):
+        """Setup up the values."""
+        super().__init__()
+        if year < 2020:
+            self.HEADER = 39
+            self.FOOTER = None
+            self.START_A = 16
+            self.END_A = 19
+            self.START_Z = 11
+            self.END_Z = 14
+            self.START_ME = 29
+            self.END_ME = 41
+            self.START_DME = 42
+            self.END_DME = 53
+            self.START_BE_PER_A = 54
+            self.END_BE_PER_A = 64
+            self.START_DBE_PER_A = 65
+            self.END_DBE_PER_A = 72
+            self.START_BETA_DECAY_ENERGY = 76
+            self.END_BETA_DECAY_ENERGY = 86
+            self.START_DBETA_DECAY_ENERGY = 87
+            self.END_DBETA_DECAY_ENERGY = 95
+            self.START_MICRO_U = 100
+            self.END_MICRO_U = 112
+            self.START_MICRO_DU = 113
+            self.END_MICRO_DU = 125
+        else:
+            self.HEADER = 36
+            self.FOOTER = None
+            self.START_A = 16
+            self.END_A = 19
+            self.START_Z = 11
+            self.END_Z = 14
+            self.START_ME = 29
+            self.END_ME = 42
+            self.START_DME = 43
+            self.END_DME = 53
+            self.START_BE_PER_A = 56
+            self.END_BE_PER_A = 66
+            self.START_DBE_PER_A = 69
+            self.END_DBE_PER_A = 77
+            self.START_BETA_DECAY_ENERGY = 82
+            self.END_BETA_DECAY_ENERGY = 93
+            self.START_DBETA_DECAY_ENERGY = 95
+            self.END_DBETA_DECAY_ENERGY = 104
+            self.START_MICRO_U = 110
+            self.END_MICRO_U = 120
+            self.START_MICRO_DU = 124
+            self.END_MICRO_DU = 135

nuclearmasses/ame_mass_file.py

@@ -0,0 +1,55 @@
+"""Extract the data from the AME mass file."""
+import logging
+import pathlib
+
+import pandas as pd
+
+from nuclearmasses.ame_mass_file import AMEMassFile
+
+
+class AMEMassParser(AMEMassFile):
+    """Parse the AME mass file.
+
+    The format is known but I don't think python can easily parse it.
+    """
+
+    def __init__(self, filename: pathlib.Path, year: int):
+        """Set the file to read and table year."""
+        self.filename = filename
+        self.year = year
+        super().__init__(self.year)
+        logging.info(f"Reading {self.filename} from {self.year}")
+
+    def _read_line(self, line: str) -> dict:
+        """Read a line from the file."""
+        if line.find("#") != -1:
+            line = line.replace("#", " ")
+
+        data = {
+            "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),
+            "AMEMassExcess": self._read_as_float(line, self.START_ME, self.END_ME),
+            "AMEMassExcessError": self._read_as_float(line, self.START_DME, self.END_DME),
+            "BindingEnergyPerA": self._read_as_float(line, self.START_BE_PER_A, self.END_BE_PER_A),
+            "BindingEnergyPerAError": self._read_as_float(line, self.START_DBE_PER_A, self.END_DBE_PER_A),
+            "BetaDecayEnergy": self._read_as_float(line, self.START_BETA_DECAY_ENERGY, self.END_BETA_DECAY_ENERGY),
+            "BetaDecayEnergyError": self._read_as_float(line, self.START_DBETA_DECAY_ENERGY, self.END_DBETA_DECAY_ENERGY),
+            "AtomicMass": self._read_as_float(line, self.START_MICRO_U, self.END_MICRO_U),
+            "AtomicMassError": self._read_as_float(line, self.START_MICRO_DU, self.END_MICRO_DU),
+        }
+
+        data["N"] = data["A"] - data["Z"]
+        data["Symbol"] = self.z_to_symbol[data["Z"]]
+
+        return data
+
+    def read_file(self) -> pd.DataFrame:
+        """Read the file."""
+        with open(self.filename, "r") as f:
+            lines = [line.rstrip() for line in f]
+
+        # Remove the header lines
+        lines = lines[self.HEADER: self.FOOTER]
+
+        return pd.DataFrame([self._read_line(line) for line in lines])

nuclearmasses/ame_mass_parse.py

@@ -0,0 +1,72 @@
+"""Storage for the variable line positions."""
+from nuclearmasses.parse import Parse
+
+
+class AMEReactionFileOne(Parse):
+    """Easy access to where the variables are in the first AME reaction file."""
+
+    def __init__(self, year: int):
+        """Setup the values that locate the variable."""
+        super().__init__()
+        if year < 2020:
+            self.HEADER = 39
+            self.FOOTER = None
+            self.START_R1_A = 1
+            self.END_R1_A = 4
+            self.START_R1_Z = 8
+            self.END_R1_Z = 11
+            self.START_S2N = 14
+            self.END_S2N = 22
+            self.START_DS2N = 23
+            self.END_DS2N = 30
+            self.START_S2P = 32
+            self.END_S2P = 40
+            self.START_DS2P = 41
+            self.END_DS2P = 48
+            self.START_QA = 50
+            self.END_QA = 58
+            self.START_DQA = 59
+            self.END_DQA = 66
+            self.START_Q2B = 67
+            self.END_Q2B = 76
+            self.START_DQ2B = 77
+            self.END_DQ2B = 84
+            self.START_QEP = 85
+            self.END_QEP = 94
+            self.START_DQEP = 95
+            self.END_DQEP = 102
+            self.START_QBN = 103
+            self.END_QBN = 112
+            self.START_DQBN = 113
+            self.END_DQBN = 125
+        else:
+            self.HEADER = 35
+            self.FOOTER = None
+            self.START_R1_A = 1
+            self.END_R1_A = 4
+            self.START_R1_Z = 8
+            self.END_R1_Z = 11
+            self.START_S2N = 14
+            self.END_S2N = 24
+            self.START_DS2N = 25
+            self.END_DS2N = 34
+            self.START_S2P = 36
+            self.END_S2P = 46
+            self.START_DS2P = 47
+            self.END_DS2P = 56
+            self.START_QA = 58
+            self.END_QA = 68
+            self.START_DQA = 69
+            self.END_DQA = 78
+            self.START_Q2B = 79
+            self.END_Q2B = 90
+            self.START_DQ2B = 91
+            self.END_DQ2B = 100
+            self.START_QEP = 101
+            self.END_QEP = 112
+            self.START_DQEP = 113
+            self.END_DQEP = 122
+            self.START_QBN = 123
+            self.END_QBN = 134
+            self.START_DQBN = 135
+            self.END_DQBN = 144

nuclearmasses/ame_reaction_1_file.py

@@ -0,0 +1,61 @@
+"""Extract the data from the first reaction file."""
+import logging
+import pathlib
+
+import pandas as pd
+
+from nuclearmasses.ame_reaction_1_file import AMEReactionFileOne
+
+
+class AMEReactionParserOne(AMEReactionFileOne):
+    """Parse the first AME reaction file.
+
+    The format is known but I don't think python can easily parse it.
+    """
+
+    def __init__(self, filename: pathlib.Path, year: int):
+        """Set the file to read and table year."""
+        self.filename = filename
+        self.year = year
+        super().__init__(self.year)
+        logging.info(f"Reading {self.filename} from {self.year}")
+
+    def _read_line(self, line: str) -> dict:
+        """Read a line from the file."""
+        # Don't use a '#' as an experimental marker in this file
+        # but still need to remove it
+        if line.find("#") != -1:
+            line = line.replace("#", " ")
+
+        data = {
+            "TableYear": self.year,
+            "A": self._read_as_int(line, self.START_R1_A, self.END_R1_A),
+            "Z": self._read_as_int(line, self.START_R1_Z, self.END_R1_Z),
+            "TwoNeutronSeparationEnergy": self._read_as_float(line, self.START_S2N, self.END_S2N),
+            "TwoNeutronSeparationEnergyError": self._read_as_float(line, self.START_DS2N, self.END_DS2N),
+            "TwoProtonSeparationEnergy": self._read_as_float(line, self.START_S2P, self.END_S2P),
+            "TwoProtonSeparationEnergyError": self._read_as_float(line, self.START_DS2P, self.END_DS2P),
+            "QAlpha": self._read_as_float(line, self.START_QA, self.END_QA),
+            "QAlphaError": self._read_as_float(line, self.START_DQA, self.END_DQA),
+            "QTwoBeta": self._read_as_float(line, self.START_Q2B, self.END_Q2B),
+            "QTwoBetaError": self._read_as_float(line, self.START_DQ2B, self.END_DQ2B),
+            "QEpsilon": self._read_as_float(line, self.START_QEP, self.END_QEP),
+            "QEpsilonError": self._read_as_float(line, self.START_DQEP, self.END_DQEP),
+            "QBetaNeutron": self._read_as_float(line, self.START_QBN, self.END_QBN),
+            "QBetaNeutronError": self._read_as_float(line, self.START_DQBN, self.END_DQBN),
+        }
+
+        data["N"] = data["A"] - data["Z"]
+        data["Symbol"] = self.z_to_symbol[data["Z"]]
+
+        return data
+
+    def read_file(self) -> pd.DataFrame:
+        """Read the file."""
+        with open(self.filename, "r") as f:
+            lines = [line.rstrip() for line in f]
+
+        # Remove the header lines
+        lines = lines[self.HEADER: self.FOOTER]
+
+        return pd.DataFrame([self._read_line(line) for line in lines])

nuclearmasses/ame_reaction_1_parse.py

@@ -0,0 +1,72 @@
+"""Storage for the variable line positions."""
+from nuclearmasses.parse import Parse
+
+
+class AMEReactionFileTwo(Parse):
+    """Easy access to where the variables are in the second AME reaction file."""
+
+    def __init__(self, year: int):
+        """Setup the values that locate the variables."""
+        super().__init__()
+        if year < 2020:
+            self.HEADER = 39
+            self.FOOTER = None
+            self.START_R2_A = 1
+            self.END_R2_A = 4
+            self.START_R2_Z = 8
+            self.END_R2_Z = 11
+            self.START_SN = 14
+            self.END_SN = 22
+            self.START_DSN = 23
+            self.END_DSN = 30
+            self.START_SP = 32
+            self.END_SP = 40
+            self.START_DSP = 41
+            self.END_DSP = 48
+            self.START_Q4B = 49
+            self.END_Q4B = 58
+            self.START_DQ4B = 59
+            self.END_DQ4B = 66
+            self.START_QDA = 67
+            self.END_QDA = 76
+            self.START_DQDA = 77
+            self.END_DQDA = 84
+            self.START_QPA = 85
+            self.END_QPA = 94
+            self.START_DQPA = 95
+            self.END_DQPA = 102
+            self.START_QNA = 103
+            self.END_QNA = 112
+            self.START_DQNA = 113
+            self.END_DQNA = 125
+        else:
+            self.HEADER = 37
+            self.FOOTER = 3645
+            self.START_R2_A = 1
+            self.END_R2_A = 4
+            self.START_R2_Z = 8
+            self.END_R2_Z = 11
+            self.START_SN = 14
+            self.END_SN = 24
+            self.START_DSN = 25
+            self.END_DSN = 34
+            self.START_SP = 36
+            self.END_SP = 46
+            self.START_DSP = 47
+            self.END_DSP = 56
+            self.START_Q4B = 57
+            self.END_Q4B = 68
+            self.START_DQ4B = 69
+            self.END_DQ4B = 78
+            self.START_QDA = 79
+            self.END_QDA = 90
+            self.START_DQDA = 91
+            self.END_DQDA = 100
+            self.START_QPA = 101
+            self.END_QPA = 112
+            self.START_DQPA = 113
+            self.END_DQPA = 122
+            self.START_QNA = 123
+            self.END_QNA = 134
+            self.START_DQNA = 135
+            self.END_DQNA = 144