chemparseplot 1.9.0__tar.gz → 1.9.2__tar.gz

{chemparseplot-1.9.0 → chemparseplot-1.9.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: chemparseplot
-Version: 1.9.0
+Version: 1.9.2
 Summary: Parsers and plotting tools for computational chemistry
 Project-URL: Documentation, https://chemparseplot.rgoswami.me
 Project-URL: Issues, https://github.com/HaoZeke/chemparseplot/issues

{chemparseplot-1.9.0 → chemparseplot-1.9.2}/_version.py

@@ -18,7 +18,7 @@ version_tuple: tuple[int | str, ...]
 commit_id: str | None
 __commit_id__: str | None
 
-__version__ = version = '1.9.0'
-__version_tuple__ = version_tuple = (1, 9, 0)
+__version__ = version = '1.9.2'
+__version_tuple__ = version_tuple = (1, 9, 2)
 
 __commit_id__ = commit_id = None

{chemparseplot-1.9.0 → chemparseplot-1.9.2}/chemparseplot/parse/eon/neb.py

@@ -69,7 +69,7 @@ def load_or_compute_data(
     ```{versionadded} 0.1.0
     ```
     """
-    if cache_file and cache_file.exists() and not force_recompute:
+    if cache_file and Path(cache_file).exists() and not force_recompute:
         log.info(f"Loading cached {context_name} data from {cache_file}...")
         try:
             df = pl.read_parquet(cache_file)
@@ -111,7 +111,7 @@ def load_structures_and_calculate_additional_rmsd(
     sp_data = None
     ira_instance = ira_mod.IRA() if ira_mod else None
 
-    if sp_file and sp_file.exists():
+    if sp_file and Path(sp_file).exists():
         log.info(f"Loading explicit saddle point from {sp_file}")
         sp_atoms = ase_read(sp_file)
         sp_rmsd_r = calculate_rmsd_from_ref(

{chemparseplot-1.9.0 → chemparseplot-1.9.2}/chemparseplot/plot/neb.py

@@ -584,11 +584,14 @@ def plot_structure_strip(
 
     ax.axis("off")
     n_plot = len(atoms_list)
-    n_cols = min(n_plot, max_cols)
-    n_rows = (n_plot + max_cols - 1) // max_cols
+    # Prefer a single row when everything fits; multi-row with a shared label
+    # baseline previously stacked numbers on top of each other.
+    effective_max_cols = max(max_cols, n_plot) if n_plot <= 16 else max_cols
+    n_cols = min(n_plot, effective_max_cols)
+    n_rows = (n_plot + effective_max_cols - 1) // effective_max_cols
 
     # Adaptive font size: shrink for many items
-    label_fontsize = min(11, max(7, 14 - n_plot))
+    label_fontsize = min(11, max(7, 14 - n_plot // 2))
 
     fig = ax.figure
     fig.canvas.draw()
@@ -599,7 +602,6 @@ def plot_structure_strip(
     ax.set_xlim(0, ax_w_px)
     ax.set_ylim(0, ax_h_px)
 
-    per_row_px = ax_h_px / max(n_rows, 1)
     per_col_px = ax_w_px / max(n_cols, 1)
     label_band_px = label_fontsize * fig.dpi / 72 * 1.8
     top_padding_px = 6.0
@@ -607,7 +609,7 @@ def plot_structure_strip(
     row_gap_px = 10.0
     usable_total_height_px = max(
         24.0,
-        ax_h_px - label_band_px - top_padding_px - bottom_padding_px,
+        ax_h_px - label_band_px * n_rows - top_padding_px - bottom_padding_px,
     )
     slot_height_px = usable_total_height_px / max(n_rows, 1)
     slot_width_px = per_col_px
@@ -615,7 +617,7 @@ def plot_structure_strip(
     target_width_px = max(
         20, int(round((slot_width_px - col_gap_px) * width_fill_fraction))
     )
-    available_height_px = max(20.0, slot_height_px - row_gap_px)
+    available_height_px = max(20.0, slot_height_px - row_gap_px - label_band_px * 0.35)
     target_height_px = max(
         20,
         int(
@@ -626,14 +628,14 @@ def plot_structure_strip(
             )
         ),
     )
-    label_y_px = 4.0
     canvas = np.zeros((ax_h_px, ax_w_px, 4), dtype=np.float32)
 
     for i, atoms in enumerate(atoms_list):
-        col = i % max_cols
-        row = i // max_cols
+        col = i % effective_max_cols
+        row = i // effective_max_cols
         slot_center_x = (col + 0.5) * slot_width_px
         slot_top_y = ax_h_px - top_padding_px - row * slot_height_px
+        slot_bottom_y = slot_top_y - slot_height_px
         img_top_y = (
             slot_top_y - (slot_height_px - target_height_px) / 2 - target_height_px
         )
@@ -661,15 +663,20 @@ def plot_structure_strip(
         _alpha_blit_rgba(canvas, resized, x0, y0)
 
         if labels and i < len(labels):
+            # Label under *this* cell (not a shared strip baseline). Multi-row
+            # layouts previously wrote every label at y=4, so column mates from
+            # different rows stacked on top of each other.
+            cell_label_y = max(2.0, slot_bottom_y + 3.0)
             ax.text(
                 x=slot_center_x,
-                y=label_y_px,
+                y=cell_label_y,
                 s=labels[i],
                 ha="center",
                 va="bottom",
                 fontsize=label_fontsize,
                 color=theme_color,
                 fontweight="bold",
+                clip_on=False,
             )
 
     ax.imshow(
@@ -1585,12 +1592,19 @@ def landscape_half_span(x_limits, final_r, final_p, additional_atoms_data, globa
 
 
 def save_plot(output_file, dpi, *, has_strip):
-    """Save plots without tight-bbox strip overflow."""
-
-    save_kwargs = {"transparent": False, "pad_inches": 0.1, "dpi": dpi}
-    if not has_strip:
-        save_kwargs["bbox_inches"] = "tight"
-    plt.savefig(output_file, **save_kwargs)
+    """Save plots, cropping unused figure canvas (including strip layouts)."""
+
+    # Strips use imshow+Text (not unclipped AnnotationBbox growth), so tight
+    # bbox is safe and removes the large whitespace left by equal-aspect
+    # landscape axes inside a tall/wide figure.
+    del has_strip  # kept for API compatibility with callers
+    plt.savefig(
+        output_file,
+        transparent=False,
+        dpi=dpi,
+        bbox_inches="tight",
+        pad_inches=0.12,
+    )
 
 
 def profile_structure_indices(atoms_list, y_values, plot_structures, plot_mode):
@@ -1610,15 +1624,22 @@ def profile_strip_payload(atoms_list, x_values, y_values, plot_structures, plot_
     """Build an ordered strip payload for profile plots."""
 
     payload = []
+    saddle_idx = (
+        int(np.argmax(y_values[1:-1]) + 1)
+        if plot_mode == "energy" and len(y_values) > 2
+        else int(np.argmin(y_values))
+    )
     for index in profile_structure_indices(
         atoms_list, y_values, plot_structures, plot_mode
     ):
-        if plot_structures == "all":
-            label = str(index)
-        elif index == 0:
+        if index == 0:
             label = "R"
         elif index == len(atoms_list) - 1:
             label = "P"
+        elif index == saddle_idx:
+            label = "SP"
+        elif plot_structures == "all":
+            label = str(index)
         else:
             label = "SP"
         payload.append(