From c954803afbcb2fb7ceccc1ace10a8f32286127ed Mon Sep 17 00:00:00 2001
From: Sean Colby <seanmcolby@gmail.com>
Date: Wed, 8 Jan 2025 17:06:31 -0800
Subject: [PATCH] Separate `finish` and `parse` functionality

---
 isicle/mobility.py | 24 +++++++++++++---
 isicle/parse.py    | 72 ++++------------------------------------------
 2 files changed, 26 insertions(+), 70 deletions(-)

diff --git a/isicle/mobility.py b/isicle/mobility.py
index d5e20a7..7d4cec7 100644
--- a/isicle/mobility.py
+++ b/isicle/mobility.py
@@ -1,3 +1,4 @@
+import glob
 import os
 import shutil
 import subprocess
@@ -116,10 +117,10 @@ def _configure_mobcal(self, i2=5013489, buffer_gas='helium',
              'IMP': imp,
              'NUM_THREADS': processes}
 
-        self.mobcal_params = os.path.join(self.temp_dir,
+        self._mobcal_params = os.path.join(self.temp_dir,
                                           'mobcal.params')
 
-        with open(self.mobcal_params, 'w') as f:
+        with open(self._mobcal_params, 'w') as f:
             f.write('\n'.join(['{} {}'.format(k, v) for k, v in d.items()]))
             f.write('\n')
 
@@ -175,13 +176,28 @@ def finish(self):
         # Result container
         result = {}
 
+        # Enumerate output files
+        for outfile in outfiles:
+            # Split name and extension
+            basename, ext = os.path.basename(outfile).rsplit('.', 1)
+
+            # Read output content
+            with open(outfile, 'rb') as f:
+                contents = f.read()
+
+            # Attempt utf-8 decode
+            try:
+                result[ext] = contents.decode('utf-8')
+            except UnicodeDecodeError:
+                result[ext] = contents
+
         # Assign to attribute
         self.result = result
         return self.result
     
     def parse(self):
         """
-        Parse ORCA simulation results.
+        Parse Mobcal simulation results.
 
         Returns
         -------
@@ -191,7 +207,7 @@ def parse(self):
         """
 
         if self.result is None:
-            raise RuntimeError("Must complete ORCA simulation.")
+            raise RuntimeError("Must complete Mobcal simulation.")
 
         parser = isicle.parse.MobcalParser(data=self.result)
 
diff --git a/isicle/parse.py b/isicle/parse.py
index 01d21d5..2f88926 100644
--- a/isicle/parse.py
+++ b/isicle/parse.py
@@ -353,9 +353,6 @@ def parse(self):
 
         return result
 
-    def save(self, path):
-        isicle.io.save_pickle(path, self.result)
-
 
 class NWChemParser(FileParserInterface):
     """Extract information from NWChem simulation output files."""
@@ -748,9 +745,6 @@ def parse(self):
 
         return result
 
-    def save(self, path):
-        isicle.io.save_pickle(path, self.result)
-
 
 class ImpactParser(FileParserInterface):
     """
@@ -812,41 +806,26 @@ def parse(self):
         self.result = result
         return result  # TODO: return CCS?
 
-    def save(self, path: str, sep="\t"):
-        """
-        Write parsed object to file
-        """
-        pd.DataFrame(self.result).to_csv(path, sep=sep, index=False)
-        return
-
 
 class MobcalParser(FileParserInterface):
     """
     Extract text from a MOBCAL mobility calculation output file.
     """
 
-    def __init__(self):
-        """
-        Add docstring
-        """
-        self.contents = None
-        self.result = {}
+    def __init__(self, data=None):
+        self.data = data
 
-    def load(self, path: str):
-        """
-        Load in the data file
-        """
-        with open(path, "r") as f:
-            self.contents = f.readlines()
+        self.result = {}
 
-        return self.contents
+    def load(self, path):
+        self.data = isicle.io.load_pickle(path)
 
     def parse(self):
         """
         Extract relevant information from data
         """
         done = False
-        for line in self.contents:
+        for line in self.data["out"]:
             # if "average (second order) TM mobility" in line:
             #     m_mn = float(line.split('=')[-1])
             if "average TM cross section" in line:
@@ -860,37 +839,6 @@ def parse(self):
 
         return self.result
 
-    def save(self, path: str, sep="\t"):
-        """
-        Write parsed object to file
-        """
-        pd.DataFrame(self.result).to_csv(path, sep=sep, index=False)
-        return
-
-
-class SanderParser(FileParserInterface):
-    """
-    Extract text from an Sander simulated annealing simulation output file.
-    """
-
-    def load(self, path: str):
-        """
-        Load in the data file
-        """
-        raise NotImplementedError
-
-    def parse(self):
-        """
-        Extract relevant information from data
-        """
-        raise NotImplementedError
-
-    def save(self, path: str):
-        """
-        Write parsed object to file
-        """
-        raise NotImplementedError
-
 
 class XTBParser(FileParserInterface):
     """
@@ -1160,11 +1108,3 @@ def parse(self):
                 result["energy"] = self._crest_energy()
 
         return result
-
-    def save(self, path):
-        """
-        Add docstring
-        """
-        with open(path, "wb") as f:
-            pickle.dump(self, f)
-        return