Converted utils.autoconvert and utils.get_subplot_dimension into inte…

…rnal functions

ensemble_md/analysis/analyze_traj.py

@@ -390,7 +390,7 @@ def plot_state_trajs(trajs, state_ranges, fig_name, dt=None, stride=1, title_pre
     x_range = [np.min(x), np.max(x)]
     y_range = [-0.2, np.max(trajs) + 0.2]
     n_configs = len(trajs)
-    n_rows, n_cols = utils.get_subplot_dimension(n_configs)
+    n_rows, n_cols = utils._get_subplot_dimension(n_configs)
     _, ax = plt.subplots(nrows=n_rows, ncols=n_cols, figsize=(2.5 * n_cols, 2.5 * n_rows))
     for i in range(n_configs):
         plt.subplot(n_rows, n_cols, i + 1)
@@ -537,7 +537,7 @@ def plot_state_hist(trajs, state_ranges, fig_name, stack=True, figsize=None, pre
         plt.tight_layout()
         plt.savefig(f'{fig_name}', dpi=600)
     else:
-        n_rows, n_cols = utils.get_subplot_dimension(n_configs)
+        n_rows, n_cols = utils._get_subplot_dimension(n_configs)
         _, ax = plt.subplots(nrows=n_rows, ncols=n_cols, figsize=(4 * n_cols, 3 * n_rows))
         for i in range(n_configs):
             plt.subplot(n_rows, n_cols, i + 1)

ensemble_md/tests/test_utils.py

@@ -55,31 +55,31 @@ def test_format_time():
 
 def test_autoconvert():
     # Test non-string input
-    assert utils.autoconvert(42) == 42
+    assert utils._autoconvert(42) == 42
 
     # Test string input that can be converted to int
-    assert utils.autoconvert("42") == 42
+    assert utils._autoconvert("42") == 42
 
     # Test string input that can be converted to float
-    assert utils.autoconvert("3.14159") == 3.14159
+    assert utils._autoconvert("3.14159") == 3.14159
 
     # Test string input that can be converted to a numpy array of ints
-    assert utils.autoconvert("1 2 3") == [1, 2, 3]
+    assert utils._autoconvert("1 2 3") == [1, 2, 3]
 
     # Test string input that can be converted to a numpy array of floats
-    assert utils.autoconvert("1.0 2.0 3.0") == [1.0, 2.0, 3.0]
+    assert utils._autoconvert("1.0 2.0 3.0") == [1.0, 2.0, 3.0]
 
 
 def test_get_subplot_dimension():
-    assert utils.get_subplot_dimension(1) == (1, 1)
-    assert utils.get_subplot_dimension(2) == (1, 2)
-    assert utils.get_subplot_dimension(3) == (2, 2)
-    assert utils.get_subplot_dimension(4) == (2, 2)
-    assert utils.get_subplot_dimension(5) == (2, 3)
-    assert utils.get_subplot_dimension(6) == (2, 3)
-    assert utils.get_subplot_dimension(7) == (3, 3)
-    assert utils.get_subplot_dimension(8) == (3, 3)
-    assert utils.get_subplot_dimension(9) == (3, 3)
+    assert utils._get_subplot_dimension(1) == (1, 1)
+    assert utils._get_subplot_dimension(2) == (1, 2)
+    assert utils._get_subplot_dimension(3) == (2, 2)
+    assert utils._get_subplot_dimension(4) == (2, 2)
+    assert utils._get_subplot_dimension(5) == (2, 3)
+    assert utils._get_subplot_dimension(6) == (2, 3)
+    assert utils._get_subplot_dimension(7) == (3, 3)
+    assert utils._get_subplot_dimension(8) == (3, 3)
+    assert utils._get_subplot_dimension(9) == (3, 3)
 
 
 def test_weighted_mean():

ensemble_md/utils/gmx_parser.py

@@ -312,7 +312,7 @@ def __eq__(self, other):
 
     def _transform(self, value):
         if self.autoconvert:
-            return utils.autoconvert(value)
+            return utils._autoconvert(value)
         else:
             return value.rstrip()
 

ensemble_md/utils/utils.py

@@ -133,7 +133,7 @@ def format_time(t):
     return t_str
 
 
-def autoconvert(s):
+def _autoconvert(s):
     """
     Converts input to a numerical type if possible. Used for the MDP parser.
     Modified from `utilities.py in GromacsWrapper <https://github.com/Becksteinlab/GromacsWrapper>`_.
@@ -179,7 +179,7 @@ def autoconvert(s):
     raise ValueError("Failed to autoconvert {0!r}".format(s))
 
 
-def get_subplot_dimension(n_panels):
+def _get_subplot_dimension(n_panels):
     """
     Gets the numbers of rows and columns in a subplot such that
     the arrangement of the .