chemparseplot 1.9.14__tar.gz → 1.9.16__tar.gz

{chemparseplot-1.9.14 → chemparseplot-1.9.16}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: chemparseplot
-Version: 1.9.14
+Version: 1.9.16
 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-1.9.14 → chemparseplot-1.9.16}/_version.py

@@ -18,7 +18,7 @@ version_tuple: tuple[int | str, ...]
 commit_id: str | None
 __commit_id__: str | None
 
-__version__ = version = '1.9.14'
-__version_tuple__ = version_tuple = (1, 9, 14)
+__version__ = version = '1.9.16'
+__version_tuple__ = version_tuple = (1, 9, 16)
 
 __commit_id__ = commit_id = None

{chemparseplot-1.9.14 → chemparseplot-1.9.16}/chemparseplot/plot/neb.py

@@ -3,7 +3,6 @@ from __future__ import annotations
 import io
 import logging
 import shutil
-import subprocess
 import tempfile
 from dataclasses import dataclass
 from pathlib import Path
@@ -198,20 +197,40 @@ def render_structure_to_image(atoms, zoom, rotation):  # noqa: ARG001
     return img_data
 
 
+def _import_xyzrender():
+    """Import xyzrender via ensure_import (AUTO_DEPS) or a normal import.
+
+    Prefer the Python API over a PATH binary. Matches the suite lazy-dep model
+    (rgpycrumbs ``ensure_import`` / ``RGPYCRUMBS_AUTO_DEPS``).
+    """
+    try:
+        from rgpycrumbs._aux import enable_library_auto_deps, ensure_import
+
+        enable_library_auto_deps()
+        return ensure_import("xyzrender")
+    except ImportError:
+        pass
+    try:
+        import xyzrender
+    except ImportError as exc:
+        msg = (
+            "xyzrender is required for strip_renderer='xyzrender'. "
+            "Install with: pip install 'xyzrender>=0.1.3' "
+            "(or set RGPYCRUMBS_AUTO_DEPS=1 so ensure_import can stage it)"
+        )
+        raise RuntimeError(msg) from exc
+    return xyzrender
+
+
 def _check_xyzrender():
-    """Verify that the ``xyzrender`` binary is on PATH.
+    """Verify xyzrender is importable (package or ensure_import cache).
 
     Raises
     ------
     RuntimeError
-        If xyzrender is not found, with install instructions.
+        If xyzrender cannot be imported, with install instructions.
     """
-    if shutil.which("xyzrender") is None:
-        msg = (
-            "xyzrender binary not found on PATH. "
-            "Install with: pip install 'xyzrender>=0.1.3'"
-        )
-        raise RuntimeError(msg)
+    _import_xyzrender()
 
 
 def _apply_perspective_tilt(atoms, tilt_deg=8.0):
@@ -267,9 +286,8 @@ def _parse_rotation_angles(rotation_str):
 def _render_xyzrender(atoms, rotation="auto", canvas_size=400, config="paton"):
     """Render an ASE Atoms object to a numpy RGBA array via xyzrender.
 
-    Uses the specified config preset (default: ``paton`` for ball-and-stick).
-    Other useful presets: ``bubble`` (space-filling, good for surfaces),
-    ``flat``, ``tube``, ``wire``, ``skeletal``.
+    Uses the **Python API** (``xyzrender.render``), staged through
+    ``ensure_import`` when ``RGPYCRUMBS_AUTO_DEPS=1`` — not a PATH binary.
 
     Parameters
     ----------
@@ -280,15 +298,18 @@ def _render_xyzrender(atoms, rotation="auto", canvas_size=400, config="paton"):
         Any ASE-style string (e.g. ``"0x,90y,0z"``) disables auto-orient
         and pre-rotates the atoms.
     canvas_size : int
-        Output image width/height in pixels (passed as ``-S``).
+        Output image width/height in pixels.
 
     Returns
     -------
     numpy.ndarray
         RGBA image array with shape ``(H, W, 4)`` and float dtype.
     """
+    import os
+
     from ase.io import write as _ase_write
 
+    xr = _import_xyzrender()
     with tempfile.NamedTemporaryFile(suffix=".xyz", delete=False) as xyz_fh:
         xyz_path = xyz_fh.name
     png_path = xyz_path.rsplit(".", 1)[0] + ".png"
@@ -299,31 +320,23 @@ def _render_xyzrender(atoms, rotation="auto", canvas_size=400, config="paton"):
 
         if has_custom_rotation:
             rx, ry, rz = _parse_rotation_angles(rotation)
-            # Pre-rotate and disable auto-orient
             atoms.rotate(rx, "x", center="COP")
             atoms.rotate(ry, "y", center="COP")
             atoms.rotate(rz, "z", center="COP")
 
         _ase_write(xyz_path, atoms, format="xyz")
-        cmd = [
-            "xyzrender",
+        # Python API: same knobs as CLI --hy -t -S --config
+        xr.render(
             xyz_path,
-            "-o",
-            png_path,
-            "-S",
-            str(canvas_size),
-            "--config",
-            config,
-            "--hy",
-            "-t",
-        ]
-        if has_custom_rotation:
-            cmd.append("--no-orient")
-        subprocess.run(cmd, check=True, capture_output=True)  # noqa: S603
+            config=config,
+            canvas_size=canvas_size,
+            hy=True,
+            transparent=True,
+            orient=not has_custom_rotation,
+            output=png_path,
+        )
         img_data = plt.imread(png_path)
     finally:
-        import os
-
         for p in (xyz_path, png_path):
             try:
                 os.unlink(p)

chemparseplot-1.9.16/tests/plot/test_neb_renderers.py

@@ -0,0 +1,146 @@
+# SPDX-FileCopyrightText: 2023-present Rohit Goswami <rog32@hi.is>
+#
+# SPDX-License-Identifier: MIT
+import shutil
+from unittest.mock import patch
+
+import numpy as np
+import pytest
+
+from tests.conftest import skip_if_not_env
+
+skip_if_not_env("neb")
+
+import matplotlib.pyplot as plt
+from ase import Atoms
+
+from chemparseplot.plot.neb import (
+    _check_xyzrender,
+    _render_xyzrender,
+    plot_structure_strip,
+    render_structure_to_image,
+)
+
+pytestmark = pytest.mark.neb
+
+
+@pytest.fixture()
+def water():
+    return Atoms(
+        "H2O",
+        positions=[[0, 0, 0], [0.76, 0.59, 0], [-0.76, 0.59, 0]],
+    )
+
+
+class TestRenderStructureToImage:
+    """ASE renderer contract."""
+
+    def test_returns_rgba(self, water):
+        img = render_structure_to_image(water, zoom=0.3, rotation="0x,90y,0z")
+        assert isinstance(img, np.ndarray)
+        assert img.ndim == 3
+        assert img.shape[2] == 4
+        assert img.dtype in (np.float32, np.float64)
+
+
+class TestCheckXyzrender:
+    """Package importability (ensure_import / site-packages), not PATH binary."""
+
+    def test_missing_package_raises(self):
+        import builtins
+        real_import = builtins.__import__
+
+        def fake_import(name, *a, **k):
+            if name == "xyzrender" or name.startswith("xyzrender."):
+                raise ImportError("blocked")
+            if name == "rgpycrumbs" or name.startswith("rgpycrumbs."):
+                raise ImportError("blocked")
+            return real_import(name, *a, **k)
+
+        with patch.object(builtins, "__import__", side_effect=fake_import):
+            with pytest.raises(RuntimeError, match="xyzrender is required"):
+                _check_xyzrender()
+
+    def test_present_package_passes(self):
+        pytest.importorskip("xyzrender")
+        _check_xyzrender()
+
+
+class TestRenderXyzrender:
+    """xyzrender Python API renderer."""
+
+    def test_produces_image(self, water):
+        pytest.importorskip("xyzrender")
+        img = _render_xyzrender(water, canvas_size=200)
+        assert isinstance(img, np.ndarray)
+        assert img.ndim == 3
+        assert img.shape[2] in (3, 4)
+
+
+class TestPlotStructureStripRendererParam:
+    """Renderer dispatch in plot_structure_strip."""
+
+    def test_ase_renderer_called(self, water):
+        _, ax = plt.subplots()
+        atoms_list = [water, water]
+        labels = ["A", "B"]
+
+        with patch("chemparseplot.plot.neb.render_structure_to_image") as mock_render:
+            mock_render.return_value = np.zeros((10, 10, 4), dtype=np.float32)
+            plot_structure_strip(ax, atoms_list, labels, renderer="ase")
+            assert mock_render.call_count == len(atoms_list)
+
+        plt.close("all")
+
+
+class TestXyzrenderCliApiParity:
+    """CLI and Python API must match for the same xyzrender version."""
+
+    def test_cli_python_api_parity(self, water, tmp_path):
+        import importlib.util
+        import subprocess
+
+        pytest.importorskip("xyzrender")
+        cli = shutil.which("xyzrender")
+        if cli is None:
+            pytest.skip("xyzrender console script not on PATH")
+        # same package as importable xyzrender
+        import xyzrender
+
+        # write shared geometry
+        from ase.io import write as ase_write
+
+        xyz = tmp_path / "w.xyz"
+        png_cli = tmp_path / "cli.png"
+        ase_write(str(xyz), water, format="xyz")
+        subprocess.run(
+            [
+                cli,
+                str(xyz),
+                "-o",
+                str(png_cli),
+                "-S",
+                "200",
+                "--config",
+                "paton",
+                "--hy",
+                "-t",
+            ],
+            check=True,
+            capture_output=True,
+        )
+        img_cli = plt.imread(png_cli)
+        img_api = _render_xyzrender(water, canvas_size=200, config="paton")
+        a = np.asarray(img_cli, dtype=float)
+        b = np.asarray(img_api, dtype=float)
+        if a.max() > 1.5:
+            a = a / 255.0
+        if b.max() > 1.5:
+            b = b / 255.0
+        if a.shape[-1] == 3:
+            a = np.concatenate([a, np.ones(a.shape[:2] + (1,))], axis=-1)
+        if b.shape[-1] == 3:
+            b = np.concatenate([b, np.ones(b.shape[:2] + (1,))], axis=-1)
+        assert a.shape == b.shape, (a.shape, b.shape)
+        # bit-identical for same xyzrender version
+        np.testing.assert_allclose(a, b, atol=1e-5, rtol=0)

chemparseplot-1.9.14/tests/plot/test_neb_renderers.py

@@ -1,86 +0,0 @@
-# SPDX-FileCopyrightText: 2023-present Rohit Goswami <rog32@hi.is>
-#
-# SPDX-License-Identifier: MIT
-import shutil
-from unittest.mock import patch
-
-import numpy as np
-import pytest
-
-from tests.conftest import skip_if_not_env
-
-skip_if_not_env("neb")
-
-import matplotlib.pyplot as plt
-from ase import Atoms
-
-from chemparseplot.plot.neb import (
-    _check_xyzrender,
-    _render_xyzrender,
-    plot_structure_strip,
-    render_structure_to_image,
-)
-
-pytestmark = pytest.mark.neb
-
-
-@pytest.fixture()
-def water():
-    return Atoms(
-        "H2O",
-        positions=[[0, 0, 0], [0.76, 0.59, 0], [-0.76, 0.59, 0]],
-    )
-
-
-class TestRenderStructureToImage:
-    """ASE renderer contract."""
-
-    def test_returns_rgba(self, water):
-        img = render_structure_to_image(water, zoom=0.3, rotation="0x,90y,0z")
-        assert isinstance(img, np.ndarray)
-        assert img.ndim == 3
-        assert img.shape[2] == 4
-        assert img.dtype in (np.float32, np.float64)
-
-
-class TestCheckXyzrender:
-    """Binary availability check."""
-
-    def test_missing_binary_raises(self):
-        with patch.object(shutil, "which", return_value=None):
-            with pytest.raises(RuntimeError, match="xyzrender binary not found"):
-                _check_xyzrender()
-
-    def test_present_binary_passes(self):
-        with patch.object(shutil, "which", return_value="/usr/bin/xyzrender"):
-            _check_xyzrender()
-
-
-class TestRenderXyzrender:
-    """xyzrender subprocess renderer."""
-
-    @pytest.mark.skipif(
-        shutil.which("xyzrender") is None,
-        reason="xyzrender not installed",
-    )
-    def test_produces_image(self, water):
-        img = _render_xyzrender(water, canvas_size=200)
-        assert isinstance(img, np.ndarray)
-        assert img.ndim == 3
-        assert img.shape[2] in (3, 4)
-
-
-class TestPlotStructureStripRendererParam:
-    """Renderer dispatch in plot_structure_strip."""
-
-    def test_ase_renderer_called(self, water):
-        _, ax = plt.subplots()
-        atoms_list = [water, water]
-        labels = ["A", "B"]
-
-        with patch("chemparseplot.plot.neb.render_structure_to_image") as mock_render:
-            mock_render.return_value = np.zeros((10, 10, 4), dtype=np.float32)
-            plot_structure_strip(ax, atoms_list, labels, renderer="ase")
-            assert mock_render.call_count == len(atoms_list)
-
-        plt.close("all")