fix: enable LaTeX rendering and update test reference data

.github/workflows/tests.yml

@@ -23,6 +23,11 @@ jobs:
         python-version: ${{ matrix.python-version }}
         allow-prereleases: true
 
+    - name: Install LaTeX
+      run: |
+        sudo apt-get update
+        sudo apt-get install -y --no-install-recommends texlive texlive-latex-extra cm-super lmodern dvipng
+
     - name: Install dependencies
       env:
         BEZIER_IGNORE_VERSION_CHECK: "1"

src/MPP/graph/kinetic_network.py

@@ -13,6 +13,7 @@
 from .._style import FONT_FAMILY
 
 pplt.use_style(figsize=1.8, figratio=1)
+plt.rcParams["text.usetex"] = True
 plt.rcParams["font.family"] = [FONT_FAMILY]
 
 USE_FA2 = True

src/MPP/plot.py

@@ -32,8 +32,9 @@
 
 
 def _apply_style(**kwargs):
-    """Call pplt.use_style and enforce the package font family."""
+    """Call pplt.use_style and enforce LaTeX rendering with the package font family."""
     pplt.use_style(**kwargs)
+    plt.rcParams["text.usetex"] = True
     plt.rcParams["font.family"] = [FONT_FAMILY]
 
 
@@ -255,9 +256,7 @@ def implied_timescales(
     if first_ref:
         ref_trajectory = trajectories.pop(0)
     x, y = utils.get_grid_format(len(trajectories))
-    _apply_style(
-        figsize=(2.7 * scale, 2.7 * scale), latex=False, colors="pastel_autumn"
-    )
+    _apply_style(figsize=(2.7 * scale, 2.7 * scale), colors="pastel_autumn")
     fig, axs = plt.subplots(y, x, sharex=True, sharey=True)
     plt.grid(False)
     if not isinstance(axs, np.ndarray):
@@ -381,7 +380,7 @@ def relative_implied_timescales(cl, out):
     out : str
         Path to save the output figure.
     """
-    _apply_style(figsize=(8, 2.5), latex=False, colors="pastel_autumn")
+    _apply_style(figsize=(8, 2.5), colors="pastel_autumn")
 
     ref = cl.reference
     its = cl.timescales / ref.timescales
@@ -838,7 +837,6 @@ def contact_rep(contacts, cluster_file, state_trajectory, output, grid, scale=1)
         figsize=1.2 * scale,
         colors="pastel_autumn",
         true_black=True,
-        latex=False,
     )
 
     # load files
@@ -912,7 +910,7 @@ def contact_rep(contacts, cluster_file, state_trajectory, output, grid, scale=1)
             pplt.text(
                 0.5,
                 0.95,
-                rf"S{state + 1} {pop_state:.1%}",
+                rf"S{state + 1} {100 * pop_state:.1f}\%",
                 ha="center",
                 va="top",
                 ax=ax,
@@ -1066,7 +1064,6 @@ def rmsd(rmsds, pops, helices=None, filename=None):
         figsize=(w, h),
         colors="pastel_autumn",
         true_black=True,
-        latex=False,
     )
     fig, axs = plt.subplots(
         n_plots,
@@ -1259,7 +1256,6 @@ def delta_rmsd(rmsds, pops, helices=None, filename=None):
         figsize=(w, h),
         colors="pastel_autumn",
         true_black=True,
-        latex=False,
     )
     fig, axs = plt.subplots(
         n_plots,
@@ -1443,6 +1439,9 @@ def state_trajectory(trajectory, filename, row_length=0.2, frame_length=0.2):
         Duration of each frame in ns. Used to scale the x-axis label in μs.
         (default 0.2)
     """
+    plt.rcParams["text.usetex"] = True
+    plt.rcParams["font.family"] = [FONT_FAMILY]
+
     if row_length > 1:
         x_max = int(row_length)
     elif row_length > 0:
@@ -1570,7 +1569,6 @@ def chapman_kolmogorov(mpt, out, frame_length=0.2):
         figsize=4.8,
         colors="pastel_autumn",
         true_black=True,
-        latex=False,
     )
 
     nrows, ncols = utils.get_grid_format(mpt.n_macrostates[mpt.run_index])

tests/test_plots.py

@@ -259,12 +259,15 @@ def _assert_font_family(self, dataset, kind, d, g, stochastic=False):
             / f"Z{'_stochastic' if stochastic else ''}.npy"
         )
 
-        observed_fonts = []
+        observed = []
 
         original_savefig = matplotlib.figure.Figure.savefig
 
         def capturing_savefig(fig_self, fname, *args, **kwargs):
-            observed_fonts.append(list(plt.rcParams.get("font.family", [])))
+            observed.append({
+                "usetex": plt.rcParams.get("text.usetex"),
+                "font.family": list(plt.rcParams.get("font.family", [])),
+            })
             return original_savefig(fig_self, fname, *args, **kwargs)
 
         with tempfile.TemporaryDirectory() as tmpdir:
@@ -276,14 +279,18 @@ def capturing_savefig(fig_self, fname, *args, **kwargs):
                 _run_main_with_args(args)
 
         self.assertTrue(
-            len(observed_fonts) > 0,
+            len(observed) > 0,
             f"savefig was never called for plot kind '{kind}'",
         )
-        for fonts in observed_fonts:
+        for snapshot in observed:
+            self.assertTrue(
+                snapshot["usetex"],
+                f"text.usetex is not True for plot kind '{kind}': {snapshot}",
+            )
             self.assertIn(
                 FONT_FAMILY,
-                fonts,
-                f"Font family '{FONT_FAMILY}' not found in {fonts} for plot kind '{kind}'",
+                snapshot["font.family"],
+                f"Font family '{FONT_FAMILY}' not set for plot kind '{kind}': {snapshot}",
             )
 
     def test_font_dendrogram(self):