Merge pull request #97 from ChristopherMayes/cnsga_write_offspring

xopt/generators/ga/cnsga.py

@@ -125,12 +125,14 @@ def add_data(self, new_data: pd.DataFrame):
             self.population = cnsga_select(
                 candidates, self.n_pop, self.vocs, self.toolbox
             )
-            self.children = []  # reset children
-            self.offspring = None  # reset offspring
 
             if self.options.output_path is not None:
+                self.write_offspring()
                 self.write_population()
 
+            self.children = []  # reset children
+            self.offspring = None  # reset offspring
+
     def generate(self, n_candidates) -> List[Dict]:
         """
         generate `n_candidates` candidates
@@ -143,10 +145,31 @@ def generate(self, n_candidates) -> List[Dict]:
 
         return [self.children.pop() for _ in range(n_candidates)]
 
+    def write_offspring(self, filename=None):
+        """
+        Write the current offspring to a CSV file.
+
+        Similar to write_population
+        """
+        if self.offspring is None:
+            logger.warning("No offspring to write")
+            return
+
+        if filename is None:
+            filename = f"{self.alias}_offspring_{xopt.utils.isotime(include_microseconds=True)}.csv"
+            filename = os.path.join(self.options.output_path, filename)
+
+        self.offspring.to_csv(filename, index_label="xopt_index")
+
     def write_population(self, filename=None):
         """
         Write the current population to a CSV file.
+
+        Similar to write_offspring
         """
+        if self.population is None:
+            logger.warning("No population to write")
+            return
 
         if filename is None:
             filename = f"{self.alias}_population_{xopt.utils.isotime(include_microseconds=True)}.csv"

xopt/utils.py

@@ -148,3 +148,24 @@ def safe_call(func, *args, **kwargs):
 def format_option_descriptions(options_object):
     options_dict = get_descriptions_defaults(options_object)
     return "\n\nGenerator Options\n" + yaml.dump(options_dict)
+
+
+def read_xopt_csv(*files):
+    """
+    Read several Xopt-style CSV files into data
+
+    Parameters
+    ----------
+    file1, file2, ...: path-like
+        One or more Xopt csv files
+
+    Returns
+    -------
+    pd.DataFrame
+        DataFrame with xopt_index as the index column
+    """
+    dfs = []
+    for file in files:
+        df = pd.read_csv(file, index_col="xopt_index")
+        dfs.append(df)
+    return pd.concat(dfs)