Allow to give settings to chemiscope.explore

python/chemiscope/explore/__init__.py

@@ -5,7 +5,14 @@
 __all__ = ["explore", "metatensor_featurizer"]
 
 
-def explore(frames, featurize=None, properties=None, environments=None, mode="default"):
+def explore(
+    frames,
+    featurize=None,
+    properties=None,
+    environments=None,
+    settings=None,
+    mode="default",
+):
     """
     Automatically explore a dataset containing all structures in ``frames``.
 
@@ -32,11 +39,14 @@ def explore(frames, featurize=None, properties=None, environments=None, mode="de
         with the atomic structures. Properties can be extracted from frames with
         :py:func:`extract_properties` or manually defined by the user.
 
-    :param environments: optional. List of environments (described as
-        ``(structure id, center id, cutoff)``) to include when extracting the
-        atomic properties. Can be extracted from frames with
-        :py:func:`all_atomic_environments`.
-        or manually defined.
+    :param environments: optional. List of environments (described as ``(structure id,
+        center id, cutoff)``) to include when extracting the atomic properties. Can be
+        extracted from frames with :py:func:`all_atomic_environments`. or manually
+        defined.
+
+    :param dict settings: optional dictionary of settings to use when displaying the
+        data. Possible entries for the ``settings`` dictionary are documented in the
+        chemiscope input file reference.
 
     :param str mode: optional. Visualization mode for the chemiscope widget. Can be one
         of "default", "structure", or "map". The default mode is "default".
@@ -121,6 +131,8 @@ def soap_kpca_featurize(frames, environments):
     return show(
         frames=frames,
         properties=properties,
+        shapes=None,
         environments=environments,
+        settings=settings,
         mode=mode,
     )

python/chemiscope/jupyter.py

@@ -176,28 +176,26 @@ def show(
     mode="default",
 ):
     """
-    Show the dataset defined by the given ``frames`` and ``properties``
-    (optionally ``meta``, ``environments`` and ``shapes`` as well) using an embedded
-    chemiscope visualizer inside a Jupyter notebook. These parameters have the same
-    meaning as in the :py:func:`chemiscope.create_input` function.
-
-    The ``mode`` keyword also allows overriding the default two-panels
-    visualization to show only a structure panel (``mode = "structure"``) or the
-    map panel (``mode = "map"``). These modes also make it possible to view a
-    dataset for which properties (or frames) are not available.
-
-    When inside a jupyter notebook, the returned object will create a new
-    chemiscope visualizer displaying the dataset. The object exposes a
-    `settings` traitlet, that allows to modify the visualization options
-    (possibly even linking the parameters to another widget). Printing the value
-    of the `settings` property is also a good way to see a full list of the
-    available options.
-
-    The returned object also have a ``save`` function that can be used to save
-    the dataset to a ``.json`` or ``.json.gz`` file to load it in the main website
-    later. The visualization options will be those used in the active widget, so
-    this is also a good way to tweak the appearence of the visualization before
-    saving it.
+    Show the dataset defined by the given ``frames`` and ``properties`` (optionally
+    ``meta``, ``environments`` and ``shapes`` as well) using an embedded chemiscope
+    visualizer inside a Jupyter notebook. These parameters have the same meaning as in
+    the :py:func:`chemiscope.create_input` function.
+
+    The ``mode`` keyword also allows overriding the default two-panels visualization to
+    show only a structure panel (``mode = "structure"``) or the map panel (``mode =
+    "map"``). These modes also make it possible to view a dataset for which properties
+    (or frames) are not available.
+
+    When inside a jupyter notebook, the returned object will create a new chemiscope
+    visualizer displaying the dataset. The object exposes a ``settings`` traitlet, that
+    allows to modify the visualization options (possibly even linking the parameters to
+    another widget). Printing the value of the ``settings`` property is also a good way
+    to see a full list of the available options.
+
+    The returned object also have a ``save`` function that can be used to save the
+    dataset to a ``.json`` or ``.json.gz`` file to load it in the main website later.
+    The visualization options will be those used in the active widget, so this is also a
+    good way to tweak the appearance of the visualization before saving it.
 
     .. code-block:: python