refactor(run_gr): renamed batch to multiprocess

examples/run_gr.py

@@ -14,11 +14,11 @@ datasets = [
 
 # 1. It is better to run dataloader first to generate a tsv file.
 # Alternatively, to run directly on h5 files, add use_tsv=False.
-# 2. First run with run_GP = True, batch=False, and max_no_cells = 20
+# 2. First run with run_GP = True, multiprocess=False, and max_no_cells = 20
 # to check visually the results.
-# 3. Then run with max_no_cells=None and batch=True for multiprocessing.
+# 3. Then run with max_no_cells=None and multiprocess=True for multiprocessing.
 # The results are saved in a pkl file.
-# No figures are produced unless batch=False.
+# No figures are produced unless multiprocess=False.
 # Any figures are saved in a pdf file.
 # 4. Finally run with run_GP = False.
 # This load the pkl file and integrates into dataloader's data frame.
@@ -32,7 +32,7 @@ for dataname in datasets:
             dataname,
             max_no_cells=20,
             wdir=wdir,
-            batch=False,
+            multiprocess=False,
             convert_to_hours=False,
             mother_bounds={1: (1, 6), 2: (-1, 4)},
         )

growth_rate.py

@@ -20,7 +20,7 @@ def find_all_grs(
     use_tsv=True,
     bud_bounds=None,
     mother_bounds=None,
-    batch=False,
+    multiprocess=False,
     convert_to_hours=True,
 ):
     """
@@ -45,7 +45,7 @@ def find_all_grs(
     mother_bounds: dict, optional
         To change bounds on the hyperparameters for the Gaussian process
         applied to mothers.
-    batch: boolean, optional
+    multiprocess: boolean, optional
         If True, use multiprocessing, but no plots are then produced.
     convert_to_hours: boolean
         If True, divide time values by 60.
@@ -78,7 +78,7 @@ def find_all_grs(
         buddings,
         max_no_cells=max_no_cells,
         bounds=bud_bounds,
-        batch=batch,
+        multiprocess=multiprocess,
         convert_to_hours=convert_to_hours,
     )
     if save:
@@ -91,7 +91,7 @@ def find_all_grs(
         m_vol,
         max_no_cells=max_no_cells,
         bounds=mother_bounds,
-        batch=batch,
+        multiprocess=multiprocess,
         convert_to_hours=convert_to_hours,
     )
     if save:
@@ -107,7 +107,7 @@ def find_gr(
     bounds=None,
     noruns=10,
     verbose=True,
-    batch=False,
+    multiprocess=False,
     max_no_cells=None,
     convert_to_hours=True,
 ):
@@ -158,9 +158,9 @@ def find_gr(
     else:
         no_cells = volume.shape[0]
     # loop over cells
-    if batch:
+    if multiprocess:
         config["verbose"] = False
-        res = run_batch(t, volume, buddings_df, buddings, no_cells, config)
+        res = run_parallel(t, volume, buddings_df, buddings, no_cells, config)
     else:
         res = run_series(t, volume, buddings_df, buddings, no_cells, config)
     # convert results into dataframes
@@ -215,7 +215,7 @@ def run_series(t, volume, buddings_df, buddings, no_cells, config):
     return res
 
 
-def run_batch(t, volume, buddings_df, buddings, no_cells, config):
+def run_parallel(t, volume, buddings_df, buddings, no_cells, config):
     """
     Use multiprocessing to speed GPs.