Fix open issues (#355)

* Fix crash in plotly function

* Update pre-commit hooks

* Fix latp cif file (349)

* Add std to mpl plot: jumps vs distance (345)

* Refactor plotting code

* Fix Trajectory.radial_distribution_between_species() error (344)

* Fix formatting

Author: stefsmeets

.pre-commit-config.yaml

@@ -16,23 +16,23 @@ repos:
       - id: debug-statements
       - id: double-quote-string-fixer
   - repo: https://github.com/stefsmeets/nbcheckorder/
-    rev: v0.2.0
+    rev: v0.3.0
     hooks:
       - id: nbcheckorder
   - repo: https://github.com/myint/docformatter
     rev: 06907d0
     hooks:
       - id: docformatter
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.6.9
+    rev: v0.11.0
     hooks:
       - id: ruff
         args: [--fix]
         types_or: [python, pyi, jupyter]
       - id: ruff-format
         types_or: [python, pyi, jupyter]
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.11.2
+    rev: v1.15.0
     hooks:
       - id: mypy
         additional_dependencies: [matplotlib, MDAnalysis, numpy, pymatgen, rich, scikit-image, scipy]

src/gemdat/data/latp.cif

@@ -57,5 +57,5 @@ loop_
  _atom_site_fract_y
  _atom_site_fract_z
  _atom_site_occupancy
-   Li   6b   6  0.00  0.00  0.00
-   Li  18e  18  0.66  0.00  0.25
+   Li   6b   6  0.00  0.00  0.00  1.00
+   Li  18e  18  0.66  0.00  0.25  1.00

src/gemdat/plots/_shared.py

@@ -11,6 +11,7 @@
 from scipy.stats import skewnorm
 
 if TYPE_CHECKING:
+    from gemdat.jumps import Jumps
     from gemdat.orientations import Orientations
     from gemdat.trajectory import Trajectory
 
@@ -127,7 +128,7 @@ def dataframe(self):
 def _get_vibrational_amplitudes_hist(
     *, trajectories: list[Trajectory], bins: int
 ) -> VibrationalAmplitudeHist:
-    """Calculate vabrational amplitudes histogram.
+    """Calculate vibrational amplitudes histogram.
 
     Helper for `vibrational_amplitudes`.
     """
@@ -150,3 +151,38 @@ def _get_vibrational_amplitudes_hist(
     std = np.std(data, axis=0)
 
     return VibrationalAmplitudeHist(amplitudes=amplitudes, counts=mean, std=std)
+
+
+def _jumps_vs_distance(jumps: Jumps, *, resolution: float, n_parts: int) -> pd.DataFrame:
+    """Calculate jumps vs distance histogram.
+
+    Helper for `jumps_vs_distance`.
+    """
+    sites = jumps.sites
+    trajectory = jumps.trajectory
+    lattice = trajectory.get_lattice()
+
+    pdist = lattice.get_all_distances(sites.frac_coords, sites.frac_coords)
+
+    bin_max = (1 + pdist.max() // resolution) * resolution
+    n_bins = int(bin_max / resolution) + 1
+    x = np.linspace(0, bin_max, n_bins)
+
+    bin_idx = np.digitize(pdist, bins=x)
+    data = []
+    for transitions_part in jumps.split(n_parts=n_parts):
+        counts = np.zeros_like(x)
+        for idx, n in zip(bin_idx.flatten(), transitions_part.matrix().flatten()):
+            counts[idx] += n
+        for idx in range(n_bins):
+            if counts[idx] > 0:
+                data.append((x[idx], counts[idx]))
+
+    df = pd.DataFrame(data=data, columns=['Displacement', 'count'])
+
+    grouped = df.groupby(['Displacement'])
+    mean = grouped.mean().reset_index().rename(columns={'count': 'mean'})
+    std = grouped.std().reset_index().rename(columns={'count': 'std'})
+    df = mean.merge(std, how='inner')
+
+    return df

src/gemdat/plots/matplotlib/_energy_along_path.py

@@ -80,7 +80,7 @@ def energy_along_path(
         for idx, path in enumerate(other_paths):
             if path.energy is None:
                 raise ValueError('Pathway does not contain energy data')
-            ax.plot(range(len(path.energy)), path.energy, label=f'Alternative {idx+1}')
+            ax.plot(range(len(path.energy)), path.energy, label=f'Alternative {idx + 1}')
 
         ax.legend(fontsize=8)
 

src/gemdat/plots/matplotlib/_jumps_vs_distance.py

@@ -3,18 +3,20 @@
 from typing import TYPE_CHECKING
 
 import matplotlib.pyplot as plt
-import numpy as np
+
+from .._shared import _jumps_vs_distance
 
 if TYPE_CHECKING:
     import matplotlib.figure
 
-    from gemdat import Jumps
+    from gemdat.jumps import Jumps
 
 
 def jumps_vs_distance(
     *,
     jumps: Jumps,
     jump_res: float = 0.1,
+    n_parts: int = 1,
 ) -> matplotlib.figure.Figure:
     """Plot jumps vs. distance histogram.
 
@@ -24,32 +26,27 @@ def jumps_vs_distance(
         Input data
     jump_res : float, optional
         Resolution of the bins in Angstrom
+    n_parts : int
+        Number of parts for error analysis
 
     Returns
     -------
     fig : matplotlib.figure.Figure
         Output figure
     """
-    sites = jumps.sites
-
-    trajectory = jumps.trajectory
-    lattice = trajectory.get_lattice()
-
-    pdist = lattice.get_all_distances(sites.frac_coords, sites.frac_coords)
-
-    bin_max = (1 + pdist.max() // jump_res) * jump_res
-    n_bins = int(bin_max / jump_res) + 1
-    x = np.linspace(0, bin_max, n_bins)
-    counts = np.zeros_like(x)
-
-    bin_idx = np.digitize(pdist, bins=x)
-    for idx, n in zip(bin_idx.flatten(), jumps.matrix().flatten()):
-        counts[idx] += n
+    df = _jumps_vs_distance(jumps=jumps, resolution=jump_res, n_parts=n_parts)
 
     fig, ax = plt.subplots()
 
-    ax.bar(x, counts, width=(jump_res * 0.8))
+    if n_parts == 1:
+        ax.bar('Displacement', 'mean', data=df, width=(jump_res * 0.8))
+    else:
+        ax.bar('Displacement', 'mean', yerr='std', data=df, width=(jump_res * 0.8))
 
-    ax.set(title='Jumps vs. Distance', xlabel='Distance (Å)', ylabel='Number of jumps')
+    ax.set(
+        title='Jumps vs. Distance',
+        xlabel='Distance (Å)',
+        ylabel='Number of jumps',
+    )
 
     return fig

src/gemdat/plots/plotly/_displacement_histogram.py

@@ -87,7 +87,7 @@ def displacement_histogram(trajectory: Trajectory, n_parts: int = 1) -> go.Figur
 
         fig.update_layout(
             title=(
-                'Displacement per element after ' f'{int(interval[1]-interval[0])} timesteps'
+                f'Displacement per element after {int(interval[1] - interval[0])} timesteps'
             ),
             xaxis_title='Displacement (Å)',
             yaxis_title='Nr. of atoms',

src/gemdat/plots/plotly/_energy_along_path.py

@@ -88,7 +88,7 @@ def energy_along_path(
                 go.Scatter(
                     x=np.arange(len(path.energy)),
                     y=path.energy,
-                    name=f'Alternative {idx+1}',
+                    name=f'Alternative {idx + 1}',
                     mode='lines',
                     line={'width': 1},
                 )

src/gemdat/plots/plotly/_jumps_vs_distance.py

@@ -2,16 +2,21 @@
 
 from typing import TYPE_CHECKING
 
-import numpy as np
-import pandas as pd
 import plotly.express as px
 import plotly.graph_objects as go
 
+from .._shared import _jumps_vs_distance
+
 if TYPE_CHECKING:
     from gemdat import Jumps
 
 
-def jumps_vs_distance(*, jumps: Jumps, jump_res: float = 0.1, n_parts: int = 1) -> go.Figure:
+def jumps_vs_distance(
+    *,
+    jumps: Jumps,
+    jump_res: float = 0.1,
+    n_parts: int = 1,
+) -> go.Figure:
     """Plot jumps vs. distance histogram.
 
     Parameters
@@ -28,32 +33,7 @@ def jumps_vs_distance(*, jumps: Jumps, jump_res: float = 0.1, n_parts: int = 1)
     fig : plotly.graph_objects.Figure
         Output figure
     """
-    sites = jumps.sites
-    trajectory = jumps.trajectory
-    lattice = trajectory.get_lattice()
-
-    pdist = lattice.get_all_distances(sites.frac_coords, sites.frac_coords)
-
-    bin_max = (1 + pdist.max() // jump_res) * jump_res
-    n_bins = int(bin_max / jump_res) + 1
-    x = np.linspace(0, bin_max, n_bins)
-
-    bin_idx = np.digitize(pdist, bins=x)
-    data = []
-    for transitions_part in jumps.split(n_parts=n_parts):
-        counts = np.zeros_like(x)
-        for idx, n in zip(bin_idx.flatten(), transitions_part.matrix().flatten()):
-            counts[idx] += n
-        for idx in range(n_bins):
-            if counts[idx] > 0:
-                data.append((x[idx], counts[idx]))
-
-    df = pd.DataFrame(data=data, columns=['Displacement', 'count'])
-
-    grouped = df.groupby(['Displacement'])
-    mean = grouped.mean().reset_index().rename(columns={'count': 'mean'})
-    std = grouped.std().reset_index().rename(columns={'count': 'std'})
-    df = mean.merge(std, how='inner')
+    df = _jumps_vs_distance(jumps=jumps, resolution=jump_res, n_parts=n_parts)
 
     if n_parts == 1:
         fig = px.bar(df, x='Displacement', y='mean', barmode='stack')

src/gemdat/plots/plotly/_plot3d.py

@@ -212,7 +212,7 @@ def plot_paths(
             size = 6
             color = 'teal'
         else:
-            name = f'Alternative {idx+1}'
+            name = f'Alternative {idx + 1}'
             size = 5
             color = None
 

src/gemdat/plots/plotly/_rectilinear.py

@@ -58,7 +58,7 @@ def rectilinear(
             z=hist,
             colorbar={
                 'title': 'Areal probability',
-                'titleside': 'right',
+                'title_side': 'right',
             },
         )
     )

src/gemdat/shape.py

@@ -129,8 +129,8 @@ def to_str(x):
             'Spacegroup',
             f'    {symbol} ({self.spacegroup.int_number})',
             'Lattice',
-            f"    abc   : {' '.join(to_str(val) for val in self.lattice.abc)}",
-            f"    angles: {' '.join(to_str(val) for val in self.lattice.angles)}",
+            f'    abc   : {" ".join(to_str(val) for val in self.lattice.abc)}',
+            f'    angles: {" ".join(to_str(val) for val in self.lattice.angles)}',
             f'Unique sites ({len(self.sites)})',
         ]
         for site in self.sites:

src/gemdat/trajectory.py

@@ -749,6 +749,7 @@ def metrics(self) -> TrajectoryMetrics:
 
         return TrajectoryMetrics(trajectory=self)
 
+    @plot_backend
     def radial_distribution_between_species(self, *, module, **kwargs) -> RDFData:
         """See [gemdat.rdf.radial_distribution_between_species][] for more
         info."""

src/gemdat/transitions.py

@@ -465,7 +465,7 @@ def _compute_site_radius(
 
             raise ValueError(
                 'Crystallographic sites are too close together '
-                f'(expected: >{site_radius*2:.4f}, '
+                f'(expected: >{site_radius * 2:.4f}, '
                 f'got: {min_dist:.4f} for {msg}'
             )
 

src/gemdat/utils.py

@@ -202,7 +202,7 @@ def warn_lattice_not_close(a: Lattice, b: Lattice):
     """Raises a userwarning if lattices are not close."""
     if not is_lattice_similar(a, b):
         warnings.warn(
-            'Lattices are not similar.' f'a: {a.parameters}, b: {b.parameters}',
+            f'Lattices are not similar.a: {a.parameters}, b: {b.parameters}',
             UserWarning,
         )
 

tests/helpers/__init__.py

@@ -55,7 +55,8 @@ def assert_figures_similar(fig, *, name: str, ext: str = 'png', rms: float = 0.0
             err[key] = Path(err[key]).relative_to('.')
         raise AssertionError(
             (
-                'images not close (RMS {rms:.3f}):'
-                '\n\t{actual}\n\t{expected}\n\t{diff}'.format(**err)
+                'images not close (RMS {rms:.3f}):\n\t{actual}\n\t{expected}\n\t{diff}'.format(
+                    **err
+                )
             )
         )