chemparseplot 1.6.1__tar.gz → 1.7.0__tar.gz

{chemparseplot-1.6.1 → chemparseplot-1.7.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: chemparseplot
-Version: 1.6.1
+Version: 1.7.0
 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-1.6.1 → chemparseplot-1.7.0}/_version.py

@@ -18,7 +18,7 @@ version_tuple: tuple[int | str, ...]
 commit_id: str | None
 __commit_id__: str | None
 
-__version__ = version = '1.6.1'
-__version_tuple__ = version_tuple = (1, 6, 1)
+__version__ = version = '1.7.0'
+__version_tuple__ = version_tuple = (1, 7, 0)
 
 __commit_id__ = commit_id = None

{chemparseplot-1.6.1 → chemparseplot-1.7.0}/chemparseplot/__init__.py

@@ -3,3 +3,5 @@
 # SPDX-License-Identifier: MIT
 
 from chemparseplot import parse, units
+
+__all__ = ["parse", "units"]

{chemparseplot-1.6.1 → chemparseplot-1.7.0}/chemparseplot/parse/__init__.py

@@ -4,6 +4,8 @@
 
 from chemparseplot.parse import eon, orca, patterns
 
+__all__ = ["eon", "orca", "patterns"]
+
 # Lazy imports for modules with optional heavy deps (h5py, pandas)
 # Import directly: from chemparseplot.parse.chemgp_hdf5 import read_h5_table
 # Or: from chemparseplot.parse import plumed, projection

{chemparseplot-1.6.1 → chemparseplot-1.7.0}/chemparseplot/parse/eon/dimer_trajectory.py

@@ -140,7 +140,9 @@ def load_dimer_trajectory(job_dir: Path) -> DimerTrajectoryData:
         initial = atoms_list[0]
 
     saddle_path = job_dir / "saddle.con"
-    saddle = readcon.read_con_as_ase(str(saddle_path))[0] if saddle_path.exists() else None
+    saddle = (
+        readcon.read_con_as_ase(str(saddle_path))[0] if saddle_path.exists() else None
+    )
 
     mode = _load_mode_dat(job_dir / "mode.dat")
 

{chemparseplot-1.6.1 → chemparseplot-1.7.0}/chemparseplot/parse/eon/saddle_search.py

@@ -7,10 +7,15 @@ from enum import Enum
 from pathlib import Path
 
 import numpy as np
-from rgpycrumbs.basetypes import DimerOpt, MolGeom, SaddleMeasure, SpinID
-from rgpycrumbs.parsers.bless import BLESS_LOG
-from rgpycrumbs.parsers.common import _NUM
-from rgpycrumbs.search.helpers import tail
+
+try:
+    from rgpycrumbs.basetypes import DimerOpt, MolGeom, SaddleMeasure, SpinID
+    from rgpycrumbs.parsers.bless import BLESS_LOG
+    from rgpycrumbs.parsers.common import _NUM
+    from rgpycrumbs.search.helpers import tail
+except ImportError:
+    DimerOpt = MolGeom = SaddleMeasure = SpinID = None
+    BLESS_LOG = _NUM = tail = None
 
 log = logging.getLogger(__name__)
 

{chemparseplot-1.6.1 → chemparseplot-1.7.0}/chemparseplot/parse/orca/__init__.py

@@ -3,3 +3,5 @@
 # SPDX-License-Identifier: MIT
 
 from chemparseplot.parse.orca import geomscan
+
+__all__ = ["geomscan"]

{chemparseplot-1.6.1 → chemparseplot-1.7.0}/chemparseplot/parse/orca/neb/interp.py

@@ -17,8 +17,6 @@ end
 
 import re
 
-from rgpycrumbs.basetypes import nebiter, nebpath
-
 import chemparseplot.parse.converter as conv
 import chemparseplot.parse.patterns as pat
 from chemparseplot.units import Q_
@@ -38,6 +36,8 @@ def extract_interp_points(text: str) -> list[int, Q_, Q_]:
     ```{versionadded} 0.0.2
     ```
     """
+    from rgpycrumbs.basetypes import nebiter, nebpath
+
     data = []
     for match in re.finditer(INTERP_PAT, text, re.DOTALL):
         iteration = int(match.group("iteration"))

{chemparseplot-1.6.1 → chemparseplot-1.7.0}/chemparseplot/parse/orca/neb/opi_parser.py

@@ -17,7 +17,6 @@ from pathlib import Path
 from typing import Any
 
 import numpy as np
-from rgpycrumbs._aux import ensure_import
 
 # Lazy import - will be loaded on first use
 _opi_output = None
@@ -27,6 +26,8 @@ def _get_opi_output():
     """Get OPI Output class, installing if needed."""
     global _opi_output
     if _opi_output is None:
+        from rgpycrumbs._aux import ensure_import
+
         _opi_output = ensure_import("opi.output.core").Output
     return _opi_output
 

{chemparseplot-1.6.1 → chemparseplot-1.7.0}/chemparseplot/parse/sella/saddle_search.py

@@ -8,8 +8,13 @@ from pathlib import Path
 import ase
 import numpy as np
 from ase.io import read
-from rgpycrumbs.basetypes import SaddleMeasure, SpinID
-from rgpycrumbs.time.helpers import one_day_tdelta
+
+try:
+    from rgpycrumbs.basetypes import SaddleMeasure, SpinID
+    from rgpycrumbs.time.helpers import one_day_tdelta
+except ImportError:
+    SaddleMeasure = SpinID = None
+    one_day_tdelta = None
 
 log = logging.getLogger(__name__)
 

{chemparseplot-1.6.1 → chemparseplot-1.7.0}/chemparseplot/parse/trajectory/__init__.py

@@ -3,3 +3,5 @@
 # SPDX-License-Identifier: MIT
 
 from chemparseplot.parse.trajectory import hdf5, neb
+
+__all__ = ["hdf5", "neb"]

{chemparseplot-1.6.1 → chemparseplot-1.7.0}/chemparseplot/plot/__init__.py

@@ -11,6 +11,15 @@ from chemparseplot.plot.theme import (
     setup_publication_theme,
 )
 
+__all__ = [
+    "RUHI_COLORS",
+    "RUHI_THEME",
+    "PlotTheme",
+    "get_theme",
+    "setup_global_theme",
+    "setup_publication_theme",
+]
+
 
 # Lazy imports for submodules with heavy deps (cmcrameri, pint, etc.)
 def __getattr__(name):

{chemparseplot-1.6.1 → chemparseplot-1.7.0}/chemparseplot/plot/chemgp.py

@@ -1,5 +1,3 @@
-from functools import lru_cache
-
 """ChemGP visualization functions.
 
 Mixed plotnine (for 1D line charts) and matplotlib (for 2D
@@ -15,6 +13,7 @@ for ggplot2 grammar.
 """
 
 import logging
+from functools import lru_cache
 
 import matplotlib.patheffects as mpe
 import matplotlib.pyplot as plt

{chemparseplot-1.6.1 → chemparseplot-1.7.0}/chemparseplot/plot/geomscan.py

@@ -1,7 +1,6 @@
 from typing import Any
 
 import matplotlib.pyplot as plt
-from rgpycrumbs.interpolation import spline_interp
 
 from chemparseplot.plot.structs import BasePlotter
 
@@ -24,6 +23,8 @@ def plot_energy_paths(
         distance_values = path.distance.to(units["distance"])
         energy_values = path.energy.to(units["energy"])
 
+        from rgpycrumbs.interpolation import spline_interp
+
         distance_fine, energy_fine = spline_interp(distance_values.m, energy_values.m)
 
         # Determine the color for each path using the colormap

{chemparseplot-1.6.1 → chemparseplot-1.7.0}/chemparseplot/plot/neb.py

@@ -8,7 +8,6 @@ from dataclasses import dataclass
 from pathlib import Path
 from typing import Any
 
-import matplotlib.patheffects as path_effects
 import matplotlib.pyplot as plt
 import numpy as np
 from ase.io import write as ase_write
@@ -16,12 +15,6 @@ from matplotlib import tri
 from matplotlib.collections import LineCollection
 from matplotlib.offsetbox import AnnotationBbox, OffsetImage
 from matplotlib.patches import ArrowStyle
-from rgpycrumbs.surfaces import (
-    NYSTROM_N_INDUCING_DEFAULT,
-    NYSTROM_THRESHOLD,
-    get_surface_model,
-    nystrom_paths_needed,
-)
 from scipy import ndimage
 from scipy.interpolate import (
     CubicHermiteSpline,
@@ -813,6 +806,13 @@ def plot_landscape_surface(
     Added the *project_path* parameter for reaction-valley coordinate projection.
     ```
     """
+    from rgpycrumbs.surfaces import (
+        NYSTROM_N_INDUCING_DEFAULT,
+        NYSTROM_THRESHOLD,
+        get_surface_model,
+        nystrom_paths_needed,
+    )
+
     log.info(f"Generating 2D surface using {method} (Projected: {project_path})...")
 
     if basis is None and project_path:

{chemparseplot-1.6.1 → chemparseplot-1.7.0}/chemparseplot/plot/structs.py

@@ -2,7 +2,6 @@ from collections import namedtuple
 
 import matplotlib.pyplot as plt
 from cmcrameri import cm
-from rgpycrumbs.interpolation import spline_interp
 
 # Define a namedtuple for energy paths
 EnergyPath = namedtuple("EnergyPath", ["label", "distance", "energy"])
@@ -77,6 +76,8 @@ class TwoDimPlot(BasePlotter):
         for idx, xy_data in enumerate(self.data):
             x_values = xy_data.x.to(self.x_unit).m
             y_values = xy_data.y.to(self.y_unit).m
+            from rgpycrumbs.interpolation import spline_interp
+
             distance_fine, y_fine = spline_interp(x_values, y_values)
 
             color = self.colormap(idx / len(self.data))

{chemparseplot-1.6.1 → chemparseplot-1.7.0}/pyproject.toml

@@ -182,6 +182,8 @@ ban-relative-imports = "all"
   "FBT002",
   "PLW2901",
 ]
+"chemparseplot/plot/structs.py" = ["PLC0415"]
+"chemparseplot/plot/geomscan.py" = ["PLC0415"]
 "chemparseplot/plot/neb.py" = ["PLR2004", "PLC0415", "C408"]
 "chemparseplot/parse/orca/neb/opi_parser.py" = [
   "PLC0415", # late imports for optional deps (ase)

{chemparseplot-1.6.1 → chemparseplot-1.7.0}/tests/conftest.py

@@ -8,7 +8,7 @@ import pytest
 # Define the requirements for each suite/marker
 ENVIRONMENT_REQUIREMENTS = {
     "pure": ["numpy"],
-    "neb": ["numpy", "polars", "ase", "h5py", "scipy", "matplotlib"],
+    "neb": ["numpy", "polars", "ase", "h5py", "scipy", "matplotlib", "rgpycrumbs"],
 }
 
 

{chemparseplot-1.6.1 → chemparseplot-1.7.0}/tests/parse/orca/test_interp.py

@@ -1,11 +1,19 @@
 # SPDX-FileCopyrightText: 2023-present Rohit Goswami <rog32@hi.is>
 #
 # SPDX-License-Identifier: MIT
+import pytest
+
+from tests.conftest import skip_if_not_env
+
+skip_if_not_env("neb")
+
 from rgpycrumbs.basetypes import nebiter
 
 from chemparseplot.parse.orca.neb.interp import extract_interp_points
 from chemparseplot.units import ureg
 
+pytestmark = pytest.mark.neb
+
 
 def test_extract_interp_points_valid_input():
     # Example valid text input

{chemparseplot-1.6.1 → chemparseplot-1.7.0}/tests/test_coverage_batch.py

@@ -191,6 +191,10 @@ class TestPlotLazyImports:
 # ============================================================
 # chemparseplot.parse.neb_utils (calculate_landscape_coords)
 # ============================================================
+@pytest.mark.skipif(
+    importlib.util.find_spec("rgpycrumbs") is None,
+    reason="rgpycrumbs not installed",
+)
 class TestCalculateLandscapeCoords:
     def test_with_mock_ira(self):
         """Test with a mock IRA that returns identity RMSD."""

{chemparseplot-1.6.1 → chemparseplot-1.7.0}/tests/test_full_coverage.py

@@ -32,6 +32,8 @@ try:
 except ImportError:
     _HAS_CMCRAMERI = False
 
+_HAS_RGPYCRUMBS = importlib.util.find_spec("rgpycrumbs") is not None
+
 
 # ============================================================
 # chemparseplot.parse.chemgp_hdf5
@@ -773,7 +775,8 @@ _PY310 = sys.version_info < (3, 11)
 
 
 @pytest.mark.skipif(
-    not _HAS_CMCRAMERI or _PY310, reason="cmcrameri required, py3.10 has recursion issue"
+    not _HAS_CMCRAMERI or _PY310 or not _HAS_RGPYCRUMBS,
+    reason="cmcrameri + rgpycrumbs required, py3.10 has recursion issue",
 )
 class TestGeomscanPlot:
     def test_plot_energy_paths(self):
@@ -794,7 +797,7 @@ class TestGeomscanPlot:
         units = {"distance": "angstrom", "energy": "eV"}
 
         with patch(
-            "chemparseplot.plot.geomscan.spline_interp",
+            "rgpycrumbs.interpolation.spline_interp",
             return_value=(np.linspace(0, 3, 100), np.sin(np.linspace(0, 3, 100))),
         ):
             from chemparseplot.plot.geomscan import plot_energy_paths
@@ -1274,6 +1277,7 @@ class TestNebPlotSurface:
 # ============================================================
 # chemparseplot.parse.trajectory.hdf5 (lines 253-294)
 # ============================================================
+@pytest.mark.skipif(not _HAS_RGPYCRUMBS, reason="rgpycrumbs required")
 class TestTrajectoryHdf5:
     def _make_h5_result(self, tmp_path, n_images=5, n_atoms=3):
         """Create a minimal neb_result.h5 file."""
@@ -1414,6 +1418,7 @@ class TestTrajectoryHdf5:
 # ============================================================
 # chemparseplot.parse.trajectory.neb (fallback paths)
 # ============================================================
+@pytest.mark.skipif(not _HAS_RGPYCRUMBS, reason="rgpycrumbs required")
 class TestTrajectoryNeb:
     def test_get_energy_from_calc(self):
         from ase import Atoms

{chemparseplot-1.6.1 → chemparseplot-1.7.0}/tests/tutorials/test_chemparseplot.py

@@ -6,6 +6,12 @@ Verifies that tutorial code examples work correctly.
 Run with: cd chemparseplot && uv run python tests/tutorials/test_chemparseplot.py
 """
 
+import pytest
+
+from tests.conftest import skip_if_not_env
+
+skip_if_not_env("neb")
+
 import sys
 from pathlib import Path