Fix pydantic error due to future type annotation (#310)

* pre-commit autoupdate to fix isort error in CI

* remove pipe for type union in pydantic Settings model

* pre-commit run black --all-files

* exclude crystal_toolkit/settings.py from auto-upgrading

* fix flake8 errors and skip docformatter in pre-commit.ci

Author: janosh

.pre-commit-config.yaml

@@ -1,6 +1,6 @@
 ci:
   autoupdate_schedule: quarterly
-  skip: [mypy, flake8]
+  skip: [mypy, flake8, docformatter]
 
 default_stages: [commit]
 
@@ -12,12 +12,12 @@ exclude: ^(docs/.+|.*lock.*|jupyterlab-extension/.+|.*\.(svg|js|css))$
 
 repos:
   - repo: https://github.com/PyCQA/isort
-    rev: 5.11.4
+    rev: 5.12.0
     hooks:
       - id: isort
 
   - repo: https://github.com/psf/black
-    rev: 22.12.0
+    rev: 23.1.0
     hooks:
       - id: black-jupyter
 
@@ -32,6 +32,7 @@ repos:
     hooks:
       - id: pyupgrade
         args: [--py38-plus]
+        exclude: ^crystal_toolkit/settings.py$
 
   - repo: https://github.com/pre-commit/mirrors-mypy
     rev: v0.991
@@ -55,12 +56,12 @@ repos:
         stages: [commit, commit-msg]
 
   - repo: https://github.com/PyCQA/autoflake
-    rev: v2.0.0
+    rev: v2.0.1
     hooks:
       - id: autoflake
 
   - repo: https://github.com/nbQA-dev/nbQA
-    rev: 1.6.0
+    rev: 1.6.1
     hooks:
       - id: nbqa-pyupgrade
         args: [--py38-plus]
@@ -75,7 +76,7 @@ repos:
         args: [--drop-empty-cells, --keep-output]
 
   - repo: https://github.com/PyCQA/docformatter
-    rev: v1.5.1
+    rev: v1.6.0.rc1
     hooks:
       - id: docformatter
         args: [--config, setup.cfg]

crystal_toolkit/_version.py

@@ -1 +1,3 @@
-__version__ = "2023.01.31"
+from __future__ import annotations
+
+__version__ = "2023.01.31"

crystal_toolkit/apps/examples/mpcontribs/catalysis.py

@@ -230,7 +230,6 @@ def get_plot_data(smile: str) -> pd.DataFrame:
         )
         @cache.memoize(timeout=60 * 60 * 24)
         def update_figure(smile, mid_E, range_E, active_tab):
-
             # guard statement to ensure callback is not triggered unless viewing visualization
             if active_tab != "visualization":
                 raise PreventUpdate
@@ -302,7 +301,6 @@ def get_visualization(self, structure):
         ).layout()
 
     def get_layout(self, payload=None):
-
         tabs = dcc.Tabs(
             [
                 dcc.Tab(
@@ -413,7 +411,6 @@ def get_visualization_layout(self, payload=None):
         return viz_div
 
     def get_search_layout(self, payload=None):
-
         if not payload:
             return self.get_catalysis_explorer()
 

crystal_toolkit/apps/examples/tests/test_fermi_surface.py

@@ -5,7 +5,6 @@
 
 
 def test_diffraction(dash_duo: DashDuo) -> None:
-
     dash_duo.start_server(app)
     dash_duo.clear_storage()
 

crystal_toolkit/apps/main.py

@@ -184,7 +184,6 @@
 if SETTINGS.MP_EMBED_MODE:
     mp_section: tuple[Any, ...] = (html.Div(),)
 else:
-
     # bsdos_component = ctc.BandstructureAndDosPanelComponent(
     #     origin_component=search_component
     # )
@@ -527,7 +526,6 @@ def master_update_structure(
     upload_data = upload_data or {}
 
     if load_by == "mpid":
-
         if search_mpid is None:
             raise PreventUpdate
 
@@ -540,7 +538,6 @@ def master_update_structure(
                 struct = mpr.get_structure_by_material_id(search_mpid)
                 print("Struct from material.")
     else:
-
         struct = MPComponent.from_data(upload_data["data"])
 
     return struct

crystal_toolkit/components/bandstructure.py

@@ -50,7 +50,6 @@ def __init__(
         id: str = None,
         **kwargs,
     ) -> None:
-
         # this is a compound component, can be fed by mpid or
         # by the BandStructure itself
         super().__init__(
@@ -65,7 +64,6 @@ def __init__(
 
     @property
     def _sub_layouts(self) -> dict[str, Component]:
-
         # defaults
         state = {"label-select": "lm", "dos-select": "ap"}
 
@@ -191,9 +189,7 @@ def _get_bs_dos(
             return None, None
 
         if mpid:
-
             with MPRester() as mpr:
-
                 try:
                     bandstructure_symm_line = mpr.get_bandstructure_by_material_id(mpid)
                 except Exception as exc:
@@ -207,7 +203,6 @@ def _get_bs_dos(
                     density_of_states = None
 
         else:
-
             if bandstructure_symm_line and isinstance(bandstructure_symm_line, dict):
                 bandstructure_symm_line = BandStructureSymmLine.from_dict(
                     bandstructure_symm_line
@@ -224,7 +219,6 @@ def get_ifermi_scene(bs: BandStructure) -> Scene:
 
     @staticmethod
     def get_brillouin_zone_scene(bs: BandStructureSymmLine) -> Scene:
-
         if not bs:
             return Scene(name="brillouin_zone", contents=[])
 
@@ -281,7 +275,6 @@ def get_brillouin_zone_scene(bs: BandStructureSymmLine) -> Scene:
         vbm = bs.get_vbm()["kpoint"]
 
         if cbm and vbm:
-
             if cbm.label:
                 cbm_label = cbm.label
                 for orig, new in pretty_labels.items():
@@ -325,7 +318,6 @@ def get_brillouin_zone_scene(bs: BandStructureSymmLine) -> Scene:
     def get_bandstructure_traces(
         bs, path_convention: str, energy_window: tuple[float, float] = (-6.0, 10.0)
     ) -> tuple:
-
         if path_convention == "lm":
             bs = HighSymmKpath.get_continuous_path(bs)
 
@@ -350,7 +342,6 @@ def get_bandstructure_traces(
         vbm_new = bs_data["vbm"]
 
         for d, dist_val in enumerate(bs_data["distances"]):
-
             x_dat = dist_val
 
             traces_for_segment = []
@@ -474,7 +465,6 @@ def get_dos_traces(
         energy_window: tuple[float, float] = (-6.0, 10.0),
         horizontal: bool = False,
     ) -> list:
-
         if horizontal:
             dos_axis, en_axis = "y", "x"
         else:
@@ -548,7 +538,6 @@ def get_dos_traces(
         ]
 
         for label in proj_data:
-
             if spin_polarized:
                 trace = {
                     dos_axis: -1.0
@@ -594,9 +583,7 @@ def get_figure(
         bs_domain=None,
         dos_domain=None,
     ) -> go.Figure:
-
         if (not dos) and (not bs):
-
             empty_plot_style = {
                 "xaxis": {"visible": False},
                 "yaxis": {"visible": False},
@@ -777,7 +764,6 @@ def get_figure(
 
     @staticmethod
     def _get_data_list_dict(bs, dos):
-
         return {
             "Band Gap": "... eV",
             "Direct Gap": "...",
@@ -791,7 +777,6 @@ def generate_callbacks(self, app, cache):
             Output(self.id("bsdos-div"), "children"), [Input(self.id("traces"), "data")]
         )
         def update_graph(traces):
-
             if traces == "error":
                 body = MessageBody(
                     dcc.Markdown(
@@ -822,7 +807,6 @@ def update_label_select(mpid, path_convention):
             if not mpid:
                 raise PreventUpdate
             else:
-
                 label_value = path_convention
                 label_style = {"maxWidth": "200"}
 
@@ -887,7 +871,6 @@ def update_select(elements, mpid):
             Input(self.id("label-select"), "value"),
         )
         def bs_dos_data(data, path_convention, dos_select, label_select):
-
             # Obtain bands to plot over and generate traces for bs data:
             energy_window = (-6.0, 10.0)
 

crystal_toolkit/components/diffraction.py

@@ -155,7 +155,6 @@ def grain_to_hwhm(
 
     @property
     def _sub_layouts(self) -> dict[str, Component]:
-
         state = {
             "peak_profile": "G",
             "shape_factor": 0.94,
@@ -339,7 +338,6 @@ def get_figure(
         x_axis,
         broadening=True,
     ) -> go.Figure:
-
         hkl_list = [hkl[0]["hkl"] for hkl in hkls]
         # convert to (h k l) format
         hkls = [f"hkl: ({' '.join(map(str, hkl))})" for hkl in hkl_list]
@@ -434,7 +432,6 @@ def generate_callbacks(self, app, cache):
             ],
         )
         def update_graph(data, logsize, rad_source, peak_profile, K, x_axis, structure):
-
             if not data:
                 raise PreventUpdate
 
@@ -480,7 +477,6 @@ def update_graph(data, logsize, rad_source, peak_profile, K, x_axis, structure):
             ],
         )
         def pattern_from_struct(struct, rad_source):
-
             if struct is None or not rad_source:
                 raise PreventUpdate
 

crystal_toolkit/components/diffraction_tem.py

@@ -188,7 +188,6 @@ def generate_callbacks(self, app, cache):
             ],
         )
         def generate_diffraction_pattern(structure, *args):
-
             structure = self.from_data(structure)
             kwargs = self.reconstruct_kwargs_from_state()