fix typing, fix 2D plotting issues (#896)

* fix typing, fix 2D plotting issues

* Update plotting.py

* Ignore extra flatten calls

* Add smoke tests

* Add changelog

* ignore one more flatten call

---------

Co-authored-by: Mike Henry <[email protected]>

news/pr_896.rst

@@ -0,0 +1,25 @@
+**Added:**
+
+* <news item>
+
+**Changed:**
+
+* <news item>
+
+**Deprecated:**
+
+* <news item>
+
+**Removed:**
+
+* <news item>
+
+**Fixed:**
+
+* 2D RMSD plotting now allows for fewer than 5 states (PR #896).
+* 2D RMSD plotting no longer draws empty axes when
+  the number of states - 1 is not divisible by 4 (PR #896).
+
+**Security:**
+
+* <news item>

openfe/analysis/plotting.py

@@ -82,24 +82,40 @@ def plot_lambda_transition_matrix(matrix: npt.NDArray) -> Axes:
             )
 
         # anotate axes
-        base_settings = {
+        base_settings: dict[str, Union[str, int]] = {
             'size': 10, 'va': 'center', 'ha': 'center', 'color': 'k',
             'family': 'sans-serif'
         }
         for i in range(num_states):
             ax.annotate(
-                i, xy=(i + 0.5, 1), xytext=(i + 0.5, num_states + 0.5),
+                text=f"{i}",
+                xy=(i + 0.5, 1),
+                xytext=(i + 0.5, num_states + 0.5),
+                xycoords='data',
+                textcoords=None,
+                arrowprops=None,
+                annotation_clip=None,
                 **base_settings,
             )
             ax.annotate(
-                i, xy=(-0.5, num_states - (num_states - 0.5)),
+                text=f"{i}",
+                xy=(-0.5, num_states - (num_states - 0.5)),
                 xytext=(-0.5, num_states - (i + 0.5)),
+                xycoords='data',
+                textcoords=None,
+                arrowprops=None,
+                annotation_clip=None,
                 **base_settings,
             )
 
         ax.annotate(
-            r"$\lambda$", xy=(-0.5, num_states - (num_states - 0.5)),
+            r"$\lambda$",
+            xy=(-0.5, num_states - (num_states - 0.5)),
             xytext=(-0.5, num_states + 0.5),
+            xycoords='data',
+            textcoords=None,
+            arrowprops=None,
+            annotation_clip=None,
             **base_settings,
         )
 
@@ -278,15 +294,21 @@ def plot_2D_rmsd(data: list[list[float]],
     fig, axes = plt.subplots(nrows, 4)
 
     for i, (arr, ax) in enumerate(
-            zip(twod_rmsd_arrs, chain.from_iterable(axes))):
+            zip(twod_rmsd_arrs, axes.flatten())):   # type: ignore
         ax.imshow(arr,
                   vmin=0, vmax=vmax,
                   cmap=plt.get_cmap('cividis'))
         ax.axis('off')  # turn off ticks/labels
         ax.set_title(f'State {i}')
 
-    plt.colorbar(axes[0][0].images[0],
-                 cax=axes[-1][-1],
+    # if we have any leftover plots then we turn them off
+    # except the last one!
+    overage = len(axes.flatten()) - len(twod_rmsd_arrs)  # type: ignore
+    for i in range(overage, len(axes.flatten())-1):  # type: ignore
+        axes.flatten()[i].set_axis_off()  # type: ignore
+
+    plt.colorbar(axes.flatten()[0].images[0],  # type: ignore
+                 cax=axes.flatten()[-1],  # type: ignore
                  label="RMSD scale (A)",
                  orientation="horizontal")
 

openfe/tests/analysis/test_plotting.py

@@ -1,8 +1,10 @@
 import numpy as np
 import matplotlib
+import matplotlib.pyplot as plt
 import pytest
 from openfe.analysis.plotting import (
     plot_lambda_transition_matrix,
+    plot_2D_rmsd,
 )
 
 
@@ -150,3 +152,15 @@ def test_mbar_overlap_plot_high_warn(matrix):
 def test_mbar_overlap_plot():
     ax = plot_lambda_transition_matrix(MBAR_OVERLAP_NORMAL)
     assert isinstance(ax, matplotlib.axes.Axes)
+
+
+@pytest.mark.parametrize('num', [i for i in range(1, 30)])
+def test_plot_2D_rmsd(num):
+    """
+    Smoke test:
+      Loop through and test plotting fictitious 2D data
+    """
+    points = num * (num-1) // 2
+    data = [[0.5 for x in range(points)] for i in range(num)]
+    fig = plot_2D_rmsd(data)
+    plt.close(fig)

openfe/tests/protocols/test_openmm_equil_rfe_protocols.py

@@ -1633,7 +1633,7 @@ def test_filenotfound_replica_states(self, protocolresult):
 def test_get_charge_difference(mapping_name, result, request):
     mapping = request.getfixturevalue(mapping_name)
     if result != 0:
-        ion = 'Na\+' if result == -1 else 'Cl\-'
+        ion = r'Na\+' if result == -1 else r'Cl\-'
         wmsg = (f"A charge difference of {result} is observed "
                 "between the end states. This will be addressed by "
                 f"transforming a water into a {ion} ion")