Merge pull request #270 from materialsproject/numba-optional-dep

Make `dscribe` an optional dependency

Author: mkhorton

crystal_toolkit/components/localenv.py

@@ -1,16 +1,12 @@
 import itertools
 from multiprocessing import cpu_count
+from warnings import warn
 
-from dash import dcc
-from dash import html
 import plotly.express as px
-from dash import callback_context
+from dash import callback_context, dcc, html
 from dash.dependencies import Input, Output
 from dash.exceptions import PreventUpdate
-from dash_mp_components import GraphComponent
-from dscribe.descriptors import SOAP
-from dscribe.kernels import REMatchKernel
-from pymatgen.ext.matproj import MPRester
+import dash_mp_components as mpc
 from pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies import (
     SimplestChemenvStrategy,
 )
@@ -23,29 +19,40 @@
 from pymatgen.analysis.chemenv.coordination_environments.structure_environments import (
     LightStructureEnvironments,
 )
-from pymatgen.analysis.graphs import MoleculeGraph
-from pymatgen.analysis.graphs import StructureGraph
-from pymatgen.analysis.local_env import cn_opt_params, LocalStructOrderParams
+from pymatgen.analysis.graphs import MoleculeGraph, StructureGraph
+from pymatgen.analysis.local_env import LocalStructOrderParams, cn_opt_params
 from pymatgen.core.structure import Molecule, Structure
+from pymatgen.ext.matproj import MPRester
 from pymatgen.io.ase import AseAtomsAdaptor
 from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
-from pymatgen.util.string import unicodeify_species, unicodeify
+from pymatgen.util.string import unicodeify, unicodeify_species
 from sklearn.preprocessing import normalize
 
 from crystal_toolkit.components.structure import StructureMoleculeComponent
 from crystal_toolkit.core.legend import Legend
 from crystal_toolkit.core.panelcomponent import PanelComponent
 from crystal_toolkit.helpers.layouts import (
-    get_data_list,
-    Columns,
-    Column,
-    get_tooltip,
-    cite_me,
-    Loading,
     H5,
+    Column,
+    Columns,
     Label,
+    Loading,
+    cite_me,
+    get_data_list,
+    get_tooltip,
 )
 
+try:
+    from dscribe.descriptors import SOAP
+    from dscribe.kernels import REMatchKernel
+except ImportError:
+    warn(
+        "Using dscribe SOAP and REMatchKernel requires the dscribe package "
+        "which was made optional since it in turn requires numba and numba "
+        "was a common source of installation issues."
+    )
+    SOAP = None
+
 
 def _get_local_order_parameters(structure_graph, n):
     """
@@ -530,6 +537,9 @@ def update_soap_analysis(struct, all_kwargs):
 
             if not struct:
                 raise PreventUpdate
+                
+            if not SOAP:
+                return mpc.Markdown("This feature will not work unless `dscribe` is installed on the server.")
 
             struct = self.from_data(struct)
             kwargs = self.reconstruct_kwargs_from_state(callback_context.inputs)
@@ -563,7 +573,7 @@ def _get_all_structs_from_elements(elements):
 
             with MPRester() as mpr:
                 docs = mpr.query(
-                    {"chemsys": {"$in": all_chemsyses}}, ["task_id", "structure"],
+                    {"chemsys": {"$in": all_chemsyses}}, ["task_id", "structure"]
                 )
             structs.update({d["task_id"]: d["structure"] for d in docs})
             return structs
@@ -577,6 +587,10 @@ def update_soap_similarities(struct, all_kwargs):
             if not struct:
                 raise PreventUpdate
 
+            if not SOAP:
+                return mpc.Markdown("This feature will not work unless `dscribe` is installed on the server.")
+
+
             structs = {"input": self.from_data(struct)}
             kwargs = self.reconstruct_kwargs_from_state(callback_context.inputs)
 
@@ -706,7 +720,7 @@ def update_bondinggraph_analysis(graph, display_options):
             }
 
             return html.Div(
-                [GraphComponent(graph=graph_data, options=options)],
+                [mpc.GraphComponent(graph=graph_data, options=options)],
                 style={"width": "65vmin", "height": "65vmin"},
             )