chemparseplot 1.10.1__tar.gz → 1.11.0__tar.gz

{chemparseplot-1.10.1 → chemparseplot-1.11.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: chemparseplot
-Version: 1.10.1
+Version: 1.11.0
 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-1.10.1 → chemparseplot-1.11.0}/_version.py

@@ -18,7 +18,7 @@ version_tuple: tuple[int | str, ...]
 commit_id: str | None
 __commit_id__: str | None
 
-__version__ = version = '1.10.1'
-__version_tuple__ = version_tuple = (1, 10, 1)
+__version__ = version = '1.11.0'
+__version_tuple__ = version_tuple = (1, 11, 0)
 
 __commit_id__ = commit_id = None

{chemparseplot-1.10.1 → chemparseplot-1.11.0}/chemparseplot/plot/disconnectivity.py

@@ -27,9 +27,7 @@ from scipy.sparse.csgraph import connected_components, laplacian
 
 from chemparseplot.plot.theme import RUHI_COLORS
 
-BASIN_PALETTE = [
-    RUHI_COLORS[c] for c in ["teal", "sky", "magenta", "coral", "sunshine"]
-]
+BASIN_PALETTE = [RUHI_COLORS[c] for c in ["teal", "sky", "magenta", "coral", "sunshine"]]
 
 
 def dedup(matrix, energies, tol):
@@ -86,9 +84,7 @@ def bridge_components(adjacency, matrix, weight=0.1):
         for b in range(a + 1, n_comp):
             ia = np.where(labels == a)[0]
             ib = np.where(labels == b)[0]
-            d = np.linalg.norm(
-                matrix[ia][:, None, :] - matrix[ib][None, :, :], axis=-1
-            )
+            d = np.linalg.norm(matrix[ia][:, None, :] - matrix[ib][None, :, :], axis=-1)
             i, j = np.unravel_index(int(np.argmin(d)), d.shape)
             adjacency[ia[i], ib[j]] = weight
             adjacency[ib[j], ia[i]] = weight
@@ -119,9 +115,7 @@ def spectral_basins(adjacency, n_basins, rng, matrix=None):
     first = int(rng.integers(len(x)))
     centers = [x[first]]
     while len(centers) < k:
-        d = np.min(
-            [np.linalg.norm(x - c, axis=1) for c in centers], axis=0
-        )
+        d = np.min([np.linalg.norm(x - c, axis=1) for c in centers], axis=0)
         centers.append(x[int(np.argmax(d))])
     centers = np.array(centers)
     for _ in range(60):
@@ -147,7 +141,7 @@ class Node:
     ```
     """
 
-    __slots__ = ("level", "children", "leaf", "x", "emin", "argmin")
+    __slots__ = ("argmin", "children", "emin", "leaf", "level", "x")
 
     def __init__(self, level, children=None, leaf=None):
         self.level = level
@@ -177,9 +171,7 @@ def merge_tree(adjacency, energies, levels):
         if not mask.any():
             continue
         sub = np.where(mask)[0]
-        _, labels = connected_components(
-            adjacency[sub][:, sub], directed=False
-        )
+        _, labels = connected_components(adjacency[sub][:, sub], directed=False)
         comps = {}
         for local, g in enumerate(sub):
             comps.setdefault(labels[local], []).append(g)
@@ -196,9 +188,7 @@ def merge_tree(adjacency, energies, levels):
             if not merged:
                 node = leaves[extra[0]]
                 for m in extra[1:]:
-                    node = Node(
-                        max(energies[m], node.level), children=[node, leaves[m]]
-                    )
+                    node = Node(max(energies[m], node.level), children=[node, leaves[m]])
             else:
                 node = merged[0] if len(merged) == 1 else Node(lev, children=merged)
                 for m in extra:

{chemparseplot-1.10.1 → chemparseplot-1.11.0}/chemparseplot/plot/landscape.py

@@ -28,7 +28,7 @@ import matplotlib as mpl
 import matplotlib.pyplot as plt
 import numpy as np
 
-from chemparseplot.plot.theme import RUHI_COLORS, RUHI_THEME
+from chemparseplot.plot.theme import RUHI_THEME
 
 ARM_MARKERS = ["o", "^", "s", "P", "X"]
 
@@ -170,9 +170,16 @@ def run_sketchmap(
         for line in lm_raw.splitlines()
         if line.strip() and not line.startswith("#")
     ]
-    idx = np.array([int(r[0]) for r in rows])
+    idx = [int(r[0]) for r in rows]
+    # Guarantee the pinned rows: dimlandmark's -ifirst only seeds the greedy
+    # walk, and farthest-point sampling skips anything near an already-kept
+    # point, which is exactly where a pinned reference's twin sits.
+    selected = [i for i in idx if i >= n_pinned]
+    keep = list(range(n_pinned)) + selected
+    keep = keep[: max(n_landmark, n_pinned)]
+    idx = np.array(keep)
     (workdir / "landmarks.dat").write_text(
-        "\n".join(" ".join(r[1:]) for r in rows) + "\n"
+        "\n".join(" ".join(f"{v:.8f}" for v in matrix[i]) for i in keep) + "\n"
     )
     proj = subprocess.run(  # noqa: S603
         [
@@ -232,14 +239,12 @@ def plot_landscape_surface(ax, coords, energies, cmap=None, levels=20):
         np.linspace(coords[:, 0].min(), coords[:, 0].max(), 240),
         np.linspace(coords[:, 1].min(), coords[:, 1].max(), 240),
     )
-    surface = griddata(
-        coords, np.clip(energies, vmin, vmax), (gx, gy), method="linear"
-    )
+    surface = griddata(coords, np.clip(energies, vmin, vmax), (gx, gy), method="linear")
     lv = np.linspace(vmin, vmax, levels)
-    cf = ax.contourf(gx, gy, surface, levels=lv, cmap=cmap, vmin=vmin, vmax=vmax,
-                     alpha=0.85)
-    ax.contour(gx, gy, surface, levels=lv, colors="black", linewidths=0.3,
-               alpha=0.45)
+    cf = ax.contourf(
+        gx, gy, surface, levels=lv, cmap=cmap, vmin=vmin, vmax=vmax, alpha=0.85
+    )
+    ax.contour(gx, gy, surface, levels=lv, colors="black", linewidths=0.3, alpha=0.45)
     ax.set_facecolor(RUHI_THEME.gridcolor)
     return cf
 
@@ -250,8 +255,14 @@ def margin_inset_slots(n):
     ```{versionadded} 1.10.0
     ```
     """
-    slots = [(-0.26, 0.82), (-0.26, 0.22), (1.30, 0.82), (1.30, 0.22),
-             (-0.26, 0.52), (1.30, 0.52)]
+    slots = [
+        (-0.26, 0.82),
+        (-0.26, 0.22),
+        (1.30, 0.82),
+        (1.30, 0.22),
+        (-0.26, 0.52),
+        (1.30, 0.52),
+    ]
     return slots[:n]
 
 
@@ -296,8 +307,16 @@ def place_margin_insets(fig, ax, entries, zoom=0.14, renderer="xyzrender"):
             renderer=renderer,
             xyzrender_config="paton",
         )
-        ax.scatter([x], [y], marker="o", s=120, facecolors="none",
-                   edgecolors="black", linewidths=1.4, zorder=7)
+        ax.scatter(
+            [x],
+            [y],
+            marker="o",
+            s=120,
+            facecolors="none",
+            edgecolors="black",
+            linewidths=1.4,
+            zorder=7,
+        )
         if entry.get("label"):
             ax.annotate(
                 entry["label"],

{chemparseplot-1.10.1 → chemparseplot-1.11.0}/chemparseplot/plot/neb.py

@@ -560,6 +560,7 @@ def plot_structure_strip(
     max_display_height_px: float | None = None,
     width_fill_fraction=0.82,
     prefer_single_row: bool = True,
+    label_ax=None,
 ) -> Any:
     """Renders a horizontal gallery of atomic structures.
 
@@ -580,6 +581,10 @@ def plot_structure_strip(
         If True (default), pack up to 16 structures in one row. If False,
         honour ``max_cols`` so e.g. 12 images with ``max_cols=6`` become two
         rows of larger molecules.
+    label_ax : matplotlib.axes.Axes or None
+        Optional caption-only axis. When supplied, structure images use the
+        full height of ``ax`` and labels are placed in ``label_ax`` at matching
+        normalized column and row positions.
 
     ```{versionadded} 0.1.0
     ```
@@ -601,6 +606,8 @@ def plot_structure_strip(
         labels = []
 
     ax.axis("off")
+    if label_ax is not None:
+        label_ax.axis("off")
     n_plot = len(atoms_list)
     # Single-row packing is optional: landscape strips with many images often
     # want max_cols=6 → two rows of larger structures.
@@ -623,13 +630,26 @@ def plot_structure_strip(
     ax.set_xlim(0, ax_w_px)
     ax.set_ylim(0, ax_h_px)
 
+    label_w_px = 0
+    label_h_px = 0
+    if label_ax is not None:
+        label_bbox = label_ax.get_window_extent(mpl_renderer)
+        label_w_px = max(1, int(round(label_bbox.width)))
+        label_h_px = max(1, int(round(label_bbox.height)))
+        label_ax.set_xlim(0, label_w_px)
+        label_ax.set_ylim(0, label_h_px)
+
     per_col_px = ax_w_px / max(n_cols, 1)
     # The band must hold the tallest label: multiline labels previously
     # overflowed a fixed 1.8-line reservation into the structure images.
-    max_label_lines = max(
-        (str(lbl).count("\n") + 1 for lbl in labels), default=1
-    ) if labels else 1
-    label_band_px = label_fontsize * fig.dpi / 72 * (0.9 + 1.35 * max_label_lines)
+    max_label_lines = (
+        max((str(lbl).count("\n") + 1 for lbl in labels), default=1) if labels else 1
+    )
+    label_band_px = (
+        0.0
+        if label_ax is not None
+        else label_fontsize * fig.dpi / 72 * (0.9 + 1.35 * max_label_lines)
+    )
     top_padding_px = 6.0
     bottom_padding_px = 6.0
     row_gap_px = 10.0
@@ -689,16 +709,25 @@ 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=cell_label_y,
+            text_ax = label_ax if label_ax is not None else ax
+            if label_ax is not None:
+                label_slot_width = label_w_px / max(n_cols, 1)
+                label_row_height = label_h_px / max(n_rows, 1)
+                label_x = (col + 0.5) * label_slot_width
+                label_y = label_h_px - (row + 0.5) * label_row_height
+                label_va = "center"
+            else:
+                # Each row owns its caption baseline so column mates cannot
+                # occupy the same text position.
+                label_x = slot_center_x
+                label_y = max(2.0, slot_bottom_y + 3.0)
+                label_va = "bottom"
+            text_ax.text(
+                x=label_x,
+                y=label_y,
                 s=labels[i],
                 ha="center",
-                va="bottom",
+                va=label_va,
                 fontsize=label_fontsize,
                 color=theme_color,
                 fontweight="bold",

{chemparseplot-1.10.1 → chemparseplot-1.11.0}/pyproject.toml

@@ -211,6 +211,7 @@ ban-relative-imports = "all"
   "PLW2901",
 ]
 "chemparseplot/plot/geomscan.py" = ["PLC0415"]
+"chemparseplot/plot/landscape.py" = ["PLC0415"] # optional plotting deps stay lazy
 "chemparseplot/units.py" = [
   "F822",    # lazy Q_/ureg via __getattr__
   "EM102",

{chemparseplot-1.10.1 → chemparseplot-1.11.0}/tests/plot/test_landscape_disconnectivity.py

@@ -48,9 +48,7 @@ def test_cn_matrix_species_restriction():
     pos = np.zeros((4, 3))
     pos[:, 0] = [0.0, 1.0, 5.0, 6.0]
     full = cn_matrix([pos.ravel()], ["O", "H", "O", "H"], cutoff=1.5)
-    only_o = cn_matrix(
-        [pos.ravel()], ["O", "H", "O", "H"], cutoff=1.5, cn_species="O"
-    )
+    only_o = cn_matrix([pos.ravel()], ["O", "H", "O", "H"], cutoff=1.5, cn_species="O")
     assert full.shape[1] == 4
     assert only_o.shape[1] == 2
 
@@ -106,9 +104,7 @@ def test_merge_tree_deep_chain_no_recursion():
 
 def test_spectral_basins_shapes():
     rng = np.random.default_rng(7)
-    m = np.vstack(
-        [rng.normal(0, 0.1, size=(10, 2)), rng.normal(5, 0.1, size=(10, 2))]
-    )
+    m = np.vstack([rng.normal(0, 0.1, size=(10, 2)), rng.normal(5, 0.1, size=(10, 2))])
     adjacency = knn_graph(m, k=3)
     assign = spectral_basins(adjacency, 2, rng, matrix=m)
     assert assign.shape == (20,)
@@ -119,12 +115,8 @@ def test_spectral_basins_shapes():
 
 def test_plot_disconnectivity_end_to_end():
     rng = np.random.default_rng(9)
-    m = np.vstack(
-        [rng.normal(0, 0.2, size=(15, 3)), rng.normal(4, 0.2, size=(15, 3))]
-    )
-    es = np.concatenate(
-        [rng.uniform(-10, -8, size=15), rng.uniform(-9, -7, size=15)]
-    )
+    m = np.vstack([rng.normal(0, 0.2, size=(15, 3)), rng.normal(4, 0.2, size=(15, 3))])
+    es = np.concatenate([rng.uniform(-10, -8, size=15), rng.uniform(-9, -7, size=15)])
     fig, ax = plt.subplots()
     reps, root = plot_disconnectivity(ax, m, es, dedup_tol=0.01, knn=3)
     assert len(reps) <= 30

{chemparseplot-1.10.1 → chemparseplot-1.11.0}/tests/plot/test_strip_rendering.py

@@ -197,6 +197,43 @@ class TestPlotStructureStrip:
         assert len(ax.artists) == 0
         plt.close(fig)
 
+    def test_separate_label_axis_keeps_text_out_of_image_band(
+        self, monkeypatch, small_molecules
+    ):
+        fig = plt.figure(figsize=(6, 2.4))
+        grid = fig.add_gridspec(2, 1, height_ratios=(4, 1), hspace=0.08)
+        image_ax = fig.add_subplot(grid[0])
+        label_ax = fig.add_subplot(grid[1])
+
+        def _fake_render(*_args, **_kwargs):
+            img = np.zeros((60, 80, 4), dtype=np.float32)
+            img[10:50, 20:60, :3] = 1.0
+            img[10:50, 20:60, 3] = 1.0
+            return img
+
+        labels = ["Cage\n0.00 eV", "Prism\n0.10 eV", "Book\n0.20 eV"]
+        monkeypatch.setattr("chemparseplot.plot.neb._render_atoms", _fake_render)
+        plot_structure_strip(
+            image_ax,
+            small_molecules,
+            labels,
+            label_ax=label_ax,
+        )
+
+        fig.canvas.draw()
+        mpl_renderer = fig.canvas.get_renderer()
+        image_bbox = image_ax.get_window_extent(mpl_renderer)
+        label_bbox = label_ax.get_window_extent(mpl_renderer)
+
+        assert len(image_ax.texts) == 0
+        assert [text.get_text() for text in label_ax.texts] == labels
+        for text in label_ax.texts:
+            text_bbox = text.get_window_extent(mpl_renderer)
+            assert label_bbox.contains(text_bbox.x0, text_bbox.y0)
+            assert label_bbox.contains(text_bbox.x1, text_bbox.y1)
+            assert text_bbox.y1 <= image_bbox.y0
+        plt.close(fig)
+
 
 class TestPlotStructureInset:
     def test_basic_inset(self, h2o):