edit to run cli as 'evo' not as a file

.gitignore

@@ -24,3 +24,4 @@ docs/_build/
 
 .DS_Store
 .ruff_cache
+.pytest_cache/

MANIFEST.in

@@ -1,2 +1 @@
-include evo/Data/*.txt
-include evo/input/*.yaml
+include evo/data/*.txt

README.md

@@ -11,12 +11,7 @@ Single pressure and decompression can be run for OH, COH, SOH, COHS and COHSN sy
 
 EVo can be set up using either melt volatile contents, or for a set amount of atomic volatile which is preferable for conducting experiments over a wide range of fO2 values.
 
-### Prerequisites
-
-This programme requires Python 3 to run.
-
-Installation/Usage:
-*******************
+## Installation/Usage:
 
 To install locally, EVo must be downloaded from GitHub using
 
@@ -33,16 +28,18 @@ From this point, EVo can either be imported into your python scripts as a regula
 `import evo`
 
 and run using
-`evo.main(<chem_file>, <env_file>, <output_options_file>, folder=<output folder name>)`
+`evo.run_evo(<chem_file>, <env_file>, <output_options_file>, folder=<output folder name>)`
 
-Or EVo can be run directly from the terminal from inside the `evo` directory:
+Or EVo can be run directly from the terminal:
 ```
-cd EVO/evo
-python dgs.py input/chem.yaml input/env.yaml --output-options input/output.yaml
+python evo input_files/chem.yaml input_files/env.yaml --output-options input_files/output.yaml
 ```
 
 The model should run and produce an output file `outputs/dgs_output_*.csv`, and a set of graphs in an 'outputs' folder, if a decompression run has been selected.
 
+The settings are controlled by a set of config files, found in the `input_files` folder.
+You should edit these as described below to set up your decompression experiment.
+
 ### Choosing run options in the env.yaml file
 
 The different run types, model parameters and input values are all set in the env.yaml file. Run types are toggled on or off using True/False, as are the various requirements. You will be warned in the terminal window if the run type you have chosen, and the input parameters selected, do not match. A summary of which parameters are required for which run type will also be given below.

evo/input/chem.yaml → input_files/chem.yaml

@@ -78,4 +78,4 @@ P2O5: 0.51
 # K2O: 0
 # P2O5: 0
 # NIO: 0
-# CR2O3: 0 
+# CR2O3: 0

evo/input/env.yaml → input_files/env.yaml

@@ -32,11 +32,11 @@ LOSS_FRAC: 0.9999
 DENSITY_MODEL: spera2000
 # Relate fo2 to Fe2/Fe3 ratio; pick from kc1991 (Kress & Carmicheal 1991), r2013 (Righter et al., 2013))
 FO2_MODEL: kc1991
-# Rock buffer definitions, options: frost1991; 
+# Rock buffer definitions, options: frost1991;
 FMQ_MODEL: frost1991
 
 # select solubility laws from options. Some options do not include OH-, CO3, CH4 species.
-# OH system models, pick from: burguisser2015 (H2O only); 
+# OH system models, pick from: burguisser2015 (H2O only);
 H2O_MODEL: burguisser2015
 # H2 model, pick from: burguisser2015 (ONLY USE TO COMPARE TO DCOMPRESS; ERROR!); gaillard2003
 H2_MODEL: gaillard2003
@@ -104,4 +104,4 @@ NITROGEN_SET: False
 NITROGEN_START: 0.0001
 
 GRAPHITE_SATURATED: False
-GRAPHITE_START: 0.0001
+GRAPHITE_START: 0.0001

evo/input/output.yaml → input_files/output.yaml

@@ -5,4 +5,4 @@ Plt_gas_species_wt: False
 Plt_gas_species_mol: True
 
 Plt_gas_fraction: True
-Plt_fo2_dFMQ: False
+Plt_fo2_dFMQ: False

pyproject.toml

@@ -3,7 +3,13 @@ requires = ['setuptools>=40.8.0']
 build-backend = 'setuptools.build_meta'
 
 [tool.setuptools]
-packages = ["evo"]
+
+  [tool.setuptools.packages.find]
+    where = ["src"]
+    include = ["evo*"]
+
+  [tool.setuptools.package-data]
+    "evo" = ["data/*.txt"]
 
 [project]
 name = "EVo"
@@ -14,6 +20,7 @@ license = {file = "LICENSE"}
 classifiers = ["License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)",
     "Programming Language :: Python :: 3"]
 requires-python = ">=3.9"
+scripts = { evo = "evo:main" }
 
 dependencies = ["numpy>=1.21.0",
   "scipy>=1.7.0",

evo/__init__.py → src/evo/__init__.py

@@ -4,4 +4,6 @@
 method.
 """
 
-from .dgs import main as main
+from evo.dgs import run_evo as run_evo
+
+__all__ = ["run_evo"]

src/evo/__main__.py

@@ -0,0 +1,42 @@
+import argparse
+
+from evo.dgs import run_evo
+
+
+def main(argv=None):
+    my_parser = argparse.ArgumentParser(
+        prog="dgs", description="Run EVo: a thermodynamic magma degassing model"
+    )
+
+    # Add the arguments
+    my_parser.add_argument("chem", metavar="chem.yaml", help="the magma chemistry file")
+
+    my_parser.add_argument(
+        "env", metavar="env.yaml", help="the run environment settings file"
+    )
+
+    my_parser.add_argument(
+        "--output-options",
+        help="use selected output options from output.yaml file",
+    )
+
+    my_parser.add_argument(
+        "-o", "--output", help="the folder location to write the results to"
+    )
+
+    # Parse in files
+    args = my_parser.parse_args(argv)
+
+    f_chem = args.chem  # set chemical compositions file
+    f_env = args.env  # set environment file
+
+    if args.output_options:
+        f_out = args.output_options  # set output file as an optional input
+        run_evo(f_chem, f_env, f_out, folder=args.output)
+    else:
+        f_out = None
+        run_evo(f_chem, f_env, f_out, folder=args.output)
+
+
+if __name__ == "__main__":
+    main()

evo/dgs.py → src/evo/dgs.py

@@ -57,7 +57,6 @@
 # ------------------------------------------------------------------------
 
 # python main [ ensure these are on your system ]
-import argparse
 import time
 from pathlib import Path
 
@@ -75,7 +74,7 @@
 # ------------------------------------------------------------------------
 
 
-def main(f_chem, f_env, f_out, folder="outputs"):
+def run_evo(f_chem, f_env, f_out, folder="outputs"):
     """Main function for EVo.
 
     Call to run the model.
@@ -212,43 +211,3 @@ def main(f_chem, f_env, f_out, folder="outputs"):
         writeout_figs(sys, melt, gas, out, sys.P_track)
 
         return df
-
-
-if __name__ == "__main__":
-    # -------------------------------------------------------------------
-    # SYSTEM SETUP ------------------------------------------------------
-    # -------------------------------------------------------------------
-
-    # Create the parser
-    my_parser = argparse.ArgumentParser(
-        prog="dgs", description="Run EVo: a thermodynamic magma degassing model"
-    )
-
-    # Add the arguments
-    my_parser.add_argument("chem", metavar="chem.yaml", help="the magma chemistry file")
-
-    my_parser.add_argument(
-        "env", metavar="env.yaml", help="the run environment settings file"
-    )
-
-    my_parser.add_argument(
-        "--output-options",
-        help="use selected output options from output.yaml file",
-    )
-
-    my_parser.add_argument(
-        "-o", "--output", help="the folder location to write the results to"
-    )
-
-    # Parse in files
-    args = my_parser.parse_args()
-
-    f_chem = args.chem  # set chemical compositions file
-    f_env = args.env  # set environment file
-
-    if args.output_options:
-        f_out = args.output_options  # set output file as an optional input
-        main(f_chem, f_env, f_out, folder=args.output)
-    else:
-        f_out = None
-        main(f_chem, f_env, f_out, folder=args.output)

evo/dgs_classes.py → src/evo/dgs_classes.py

@@ -1,11 +1,11 @@
 # dgs_classes
 
 import copy
+import importlib.resources
 import inspect
 import itertools
 import re
 import sys
-from pathlib import Path
 
 import numpy as np
 
@@ -812,7 +812,7 @@ def get_G(self, T):
 
         Calculates the GfF for a given temperature, to use in calculations
         of equilibrium constants. Reads in critical data for the species
-        from the Data folder, linearly interpolating between temperatures.
+        from the 'data' folder, linearly interpolating between temperatures.
 
         Parameters
         ----------
@@ -825,37 +825,37 @@ def get_G(self, T):
             Gibbs free energy of formation
         """
 
-        # Open the file for data for the molecule
-        file_path = Path(__file__).parent / f"Data/{self.Mol}.txt"
-
-        path = open(file_path)  # Opens the file for data for the molecule
-
-        Temp_ref = []  # To store temperatures which need to be interpolated
-        del_G_ref = []  # To store values of G which need to be interpolated
-        inter_count = 0
-
-        # iterate through file to find correct values according to T provided.
-        for aRow in path:
-            values = aRow.split("\t")
-            if not aRow.startswith("#"):  # takes out descriptive headers
-                if T - float(values[0]) == 0:
-                    # can find K with values in table, no interpolation needed
-                    # adds name of mol. and delG. of form. to the del_G dictionary
-                    self.delG = float(values[6])
-                    break
-                elif inter_count == 1:
-                    # adds in the upper table values for interpolation
-                    Temp_ref.append(float(values[0]))
-                    del_G_ref.append(float(values[6]))
-                    break
-                elif T - float(values[0]) <= 99:
-                    Temp_ref.append(float(values[0]))
-                    del_G_ref.append(float(values[6]))
-                    inter_count += 1
+        filename = f"{self.Mol}.txt"
+
+        data_file = importlib.resources.files("evo") / "data" / filename
+
+        with data_file.open("r", encoding="utf-8") as path:
+            Temp_ref = []  # To store temperatures for interpolation
+            del_G_ref = []  # To store values of G for interpolation
+            inter_count = 0
+
+            # Iterate through file to find correct values according to T provided.
+            for aRow in path:
+                values = aRow.split("\t")
+                if not aRow.startswith("#"):  # Skips descriptive headers
+                    if T - float(values[0]) == 0:
+                        # Exact match found, no interpolation needed
+                        self.delG = float(values[6])
+                        return self.delG
+                    elif inter_count == 1:
+                        # Adds in the upper table values for interpolation
+                        Temp_ref.append(float(values[0]))
+                        del_G_ref.append(float(values[6]))
+                        break
+                    elif T - float(values[0]) <= 99:
+                        Temp_ref.append(float(values[0]))
+                        del_G_ref.append(float(values[6]))
+                        inter_count += 1
+
+        # Perform interpolation if needed
         if len(Temp_ref) == 2:
-            # interpolate between 2 and returns value for Gf.
             self.delG = np.interp(T, Temp_ref, del_G_ref)
-        path.close()
+
         return self.delG
 
 

evo/multirun.py → src/evo/multirun.py

@@ -5,7 +5,7 @@
 import numpy as np
 import yaml
 
-from evo.dgs import main
+from evo.dgs import run_evo
 
 
 def amend_env(file, **kwargs):
@@ -72,7 +72,7 @@ def multirun(**kwargs):
         onerun = {}
 
         # Runs EVo
-        main("chem.yaml", "multirun.yaml", None)
+        run_evo("chem.yaml", "multirun.yaml", None)
 
         # Copies the dgs_output file into a separate file ready to be run again.
         copyfile("Output/dgs_output.csv", f"Output/output_{run_name}.csv")

testing_file.py

@@ -0,0 +1,3 @@
+import evo
+
+evo.main("input_files/chem.yaml", "input_files/env.yaml", None, folder="testing_things")