Ruff (#316)

* add ruff config to pyproject.toml

* migrate existing linter config from setup.cfg to pyproject.toml

* replace isort flake8 pyupgrade autoflake docformatter pre-commit hooks with ruff

* fix auto-fixable ruff errors

* remove flake8 and docformatter from pre-commit.ci skip

* add codespell pre-commit args --ignore-words-list, "nd,te"

since aren't read from pyproject.toml below py3.11 without tomli dep

Author: janosh

.pre-commit-config.yaml

@@ -1,6 +1,6 @@
 ci:
   autoupdate_schedule: quarterly
-  skip: [mypy, flake8, docformatter]
+  skip: [mypy]
 
 default_stages: [commit]
 
@@ -11,29 +11,17 @@ default_install_hook_types: [pre-commit, commit-msg]
 exclude: ^(docs/.+|.*lock.*|jupyterlab-extension/.+|.*\.(svg|js|css))$
 
 repos:
-  - repo: https://github.com/PyCQA/isort
-    rev: 5.12.0
+  - repo: https://github.com/charliermarsh/ruff-pre-commit
+    rev: v0.0.252
     hooks:
-      - id: isort
+      - id: ruff
+        args: [--fix, --ignore, D]
 
   - repo: https://github.com/psf/black
     rev: 23.1.0
     hooks:
       - id: black-jupyter
 
-  - repo: https://github.com/PyCQA/flake8
-    rev: 6.0.0
-    hooks:
-      - id: flake8
-        additional_dependencies: [flake8-bugbear]
-
-  - repo: https://github.com/asottile/pyupgrade
-    rev: v3.3.1
-    hooks:
-      - id: pyupgrade
-        args: [--py38-plus]
-        exclude: ^crystal_toolkit/settings.py$
-
   - repo: https://github.com/pre-commit/mirrors-mypy
     rev: v0.991
     hooks:
@@ -54,29 +42,15 @@ repos:
     hooks:
       - id: codespell
         stages: [commit, commit-msg]
-
-  - repo: https://github.com/PyCQA/autoflake
-    rev: v2.0.1
-    hooks:
-      - id: autoflake
+        args: [--ignore-words-list, "nd,te"]
 
   - repo: https://github.com/nbQA-dev/nbQA
     rev: 1.6.1
     hooks:
-      - id: nbqa-pyupgrade
-        args: [--py38-plus]
-      - id: nbqa-isort
-      - id: nbqa-flake8
-        args: [--ignore=E402]
+      - id: nbqa-ruff
 
   - repo: https://github.com/kynan/nbstripout
     rev: 0.6.1
     hooks:
       - id: nbstripout
         args: [--drop-empty-cells, --keep-output]
-
-  - repo: https://github.com/PyCQA/docformatter
-    rev: v1.6.0.rc1
-    hooks:
-      - id: docformatter
-        args: [--config, setup.cfg]

crystal_toolkit/apps/examples/mpcontribs/catalysis.py

@@ -45,8 +45,7 @@
 class CatalysisApp(MPApp):
     @staticmethod
     def modify_df(dataframe: pd.DataFrame) -> list[pd.DataFrame]:
-        """
-        Filter DataFrame for unary+binary materials visualization.
+        """Filter DataFrame for unary+binary materials visualization.
 
         Args:
           dataframe (pd.DataFrame): the dataframe that you want to modify
@@ -93,7 +92,6 @@ def get_plot(
         :param user_options: Not implemented.
         :return: 2D plot
         """
-
         # Create a list of unique elements for use as axis labels
         element_list = df_min_E.element_tup.tolist()
         flat_element_list = [item for sublist in element_list for item in sublist]
@@ -108,14 +106,11 @@ def construct_grid(df, labels):
             el_combos = list(lookup_dict["energy"])
             for i in range(len(labels)):
                 for k in range(len(labels)):
-                    if i == k:
-                        els_now = tuple(
-                            [
-                                labels[i],
-                            ]
-                        )
-                    else:
-                        els_now = tuple(np.sort([labels[i], labels[k]]))
+                    els_now = (
+                        (labels[i],)
+                        if i == k
+                        else tuple(np.sort([labels[i], labels[k]]))
+                    )
                     if els_now in el_combos:
                         grid[i, k] = lookup_dict["energy"][els_now]
                         random_ids = df_all_data[
@@ -261,10 +256,7 @@ def display_click_data(clickData):
             else:
                 el1 = str(clickData["points"][0]["x"])
                 el2 = str(clickData["points"][0]["y"])
-                if el1 == el2:
-                    el_combo = el1
-                else:
-                    el_combo = el1 + ", " + el2
+                el_combo = el1 if el1 == el2 else el1 + ", " + el2
                 randids = clickData["points"][0]["text"].split("-")
                 num_calcs = str(len(randids) - 1)
                 table = ctl.get_data_list(

crystal_toolkit/apps/main.py

@@ -303,7 +303,7 @@
 panel_choices = dcc.Dropdown(
     options=[{"label": panel.title, "value": idx} for idx, panel in enumerate(panels)],
     multi=True,
-    value=[idx for idx in range(len(panels))],
+    value=list(range(len(panels))),
     id="panel-choices",
 )
 
@@ -506,19 +506,18 @@ def master_update_structure(
 
     Returns: an encoded Structure
     """
-
     if not search_mpid and not upload_data:
         raise PreventUpdate
 
     if not dash.callback_context.triggered:
         raise PreventUpdate
 
-    if len(dash.callback_context.triggered) > 1:
-        # triggered by both on initial load
-        load_by = "mpid"
-    elif (
-        dash.callback_context.triggered[0]["prop_id"] == f"{search_component.id()}.data"
+    if (
+        len(dash.callback_context.triggered) > 1
+        or dash.callback_context.triggered[0]["prop_id"]
+        == f"{search_component.id()}.data"
     ):
+        # triggered by both on initial load
         load_by = "mpid"
     else:
         load_by = "uploaded"

crystal_toolkit/components/bandstructure.py

@@ -601,7 +601,7 @@ def get_figure(
         xaxis_style_dos = {}
         yaxis_style_dos = {}
 
-        y_title = dict(text="E−E<sub>fermi</sub> (eV)", font=dict(size=16))
+        y_title = dict(text="E-E<sub>fermi</sub> (eV)", font=dict(size=16))
         if bs:
             bs_traces, bs_data = BandstructureAndDosComponent.get_bandstructure_traces(
                 bs, path_convention=path_convention, energy_window=energy_window
@@ -752,10 +752,9 @@ def get_figure(
             dos_domain = dos_domain or [1.0, 1.0]
         elif dos:
             bs_domain = bs_domain or [0, 0]
-            if horizontal_dos:
-                dos_domain = dos_domain or [0, 1.0]
-            else:
-                dos_domain = dos_domain or [0, 0.3]
+            dos_domain = (
+                dos_domain or [0, 1.0] if horizontal_dos else dos_domain or [0, 0.3]
+            )
 
         figure["layout"]["xaxis1"]["domain"] = bs_domain
         figure["layout"]["xaxis2"]["domain"] = dos_domain

crystal_toolkit/components/diffraction.py

@@ -136,7 +136,8 @@ def two_theta_to_q(two_theta: float, xray_wavelength: float) -> float:
     def grain_to_hwhm(
         tau: float, two_theta: float, K: float = 0.9, wavelength: float | str = "CuKa"
     ) -> float:
-        """_summary_
+        """Calculate the half-width half-max (alpha or gamma) for a given grain size and
+        angle.
 
         Args:
             tau (float): grain size in nm
@@ -197,7 +198,7 @@ def _sub_layouts(self) -> dict[str, Component]:
             help_str="This defines the wavelength of the incident X-ray radiation.",
             options=[
                 {
-                    "label": f'{name.replace("a", "α").replace("b", "β")} ({wavelength:.3f} Å)',
+                    "label": f'{name.replace("a", "α").replace("b", "β")} ({wavelength:.3f} Å)',  # noqa: RUF001
                     "value": name,
                 }
                 for name, wavelength in WAVELENGTHS.items()
@@ -243,7 +244,7 @@ def _sub_layouts(self) -> dict[str, Component]:
                 self.get_choice_input(
                     kwarg_label="x_axis",
                     state=state,
-                    label="Choice of 𝑥 axis",
+                    label="Choice of x axis",
                     help_str="Can choose between 2𝜃 or Q, where Q is the magnitude of the reciprocal lattice and "
                     "independent of radiation source.",  # TODO: improve
                     options=[
@@ -293,10 +294,7 @@ def layout(self, static_image: bool = False) -> Columns:
             Columns: from crystal_toolkit.helpers.layouts
         """
         sub_layouts = self._sub_layouts
-        if static_image:
-            inner = sub_layouts["static_image"]
-        else:
-            inner = sub_layouts["graph"]
+        inner = sub_layouts["static_image"] if static_image else sub_layouts["graph"]
 
         return Columns(
             [
@@ -355,11 +353,8 @@ def get_figure(
         num_sigma = {"G": 5, "L": 12, "V": 12}[peak_profile]
 
         # optimal number of points per degree determined through usage experiments
-        if grain_size > 10:
-            # scaled to log size to the 4th power
-            N_density = 150 * (math.log10(grain_size) ** 4)
-        else:
-            N_density = 150
+        # scaled to log size to the 4th power
+        N_density = 150 * (math.log10(grain_size) ** 4) if grain_size > 10 else 150
 
         N = int(N_density * domain)  # num total points
 

crystal_toolkit/components/localenv.py

@@ -64,6 +64,7 @@ def _get_local_order_parameters(structure_graph, n):
     underlying motif (e.g., CN=4, then calculate the
     square planar, tetrahedral, see-saw-like,
     rectangular see-saw-like order parameters).
+
     Args:
         structure_graph: StructureGraph object
         n (int): site index.
@@ -77,7 +78,7 @@ def _get_local_order_parameters(structure_graph, n):
     # import, also makes sense to have this as a general NN method
     cn = structure_graph.get_coordination_of_site(n)
     if cn in [int(k_cn) for k_cn in cn_opt_params]:
-        names = [k for k in cn_opt_params[cn]]
+        names = list(cn_opt_params[cn])
         types = []
         params = []
         for name in names:
@@ -92,7 +93,7 @@ def _get_local_order_parameters(structure_graph, n):
             for connected_site in structure_graph.get_connected_sites(n)
         ]
         lostop_vals = lostops.get_order_parameters(
-            sites, 0, indices_neighs=[i for i in range(1, cn + 1)]
+            sites, 0, indices_neighs=list(range(1, cn + 1))
         )
         d = {}
         for i, lostop in enumerate(lostop_vals):
@@ -436,7 +437,7 @@ def run_algorithm(algorithm):
                     style={"width": "16rem"},  # TODO: remove in-line style
                 )
 
-                normalize_kernel = self.get_bool_input(
+                _normalize_kernel = self.get_bool_input(
                     label="Normalize",
                     kwarg_label="normalize_kernel",
                     state=state,
@@ -797,7 +798,7 @@ def get_valences(struct):
 
                 # represent the local environment as a molecule
                 mol = Molecule.from_sites(
-                    [struct[index]] + lse.neighbors_sets[index][0].neighb_sites
+                    [struct[index], *lse.neighbors_sets[index][0].neighb_sites]
                 )
                 mol = mol.get_centered_molecule()
                 mg = MoleculeGraph.with_empty_graph(molecule=mol)

crystal_toolkit/components/phase_diagram.py

@@ -416,7 +416,6 @@ def ternary_plot(plot_data):
 
         Returns: go.Figure
         """
-
         go.Scatterternary(
             {
                 "mode": "markers",
@@ -656,10 +655,11 @@ def update_entries_store(rows):
                 try:
                     comp = Composition(row["Formula"])
                     energy = row["Formation Energy (eV/atom)"]
-                    if row["Material ID"] is None:
-                        attribute = "Custom Entry"
-                    else:
-                        attribute = row["Material ID"]
+                    attribute = (
+                        "Custom Entry"
+                        if row["Material ID"] is None
+                        else row["Material ID"]
+                    )
                     # create new entry object containing mpid as attribute (to combine with custom entries)
                     entry = PDEntry(
                         comp, float(energy) * comp.num_atoms, attribute=attribute
@@ -693,10 +693,13 @@ def create_table(chemsys, pd_time, n_clicks, pd, rows):
             if trigger["prop_id"] == f"{self.id()}.modified_timestamp":
                 table_content = self.create_table_content(self.from_data(pd))
                 return table_content
-            elif trigger["prop_id"] == f"{self.id('editing-rows-button')}.n_clicks":
-                if n_clicks > 0 and rows:
-                    rows.append(self.empty_row)
-                    return rows
+            elif (
+                trigger["prop_id"] == f"{self.id('editing-rows-button')}.n_clicks"
+                and n_clicks > 0
+                and rows
+            ):
+                rows.append(self.empty_row)
+                return rows
 
             with MPRester() as mpr:
                 entries = mpr.get_entries_in_chemsys(chemsys)

crystal_toolkit/components/phonon.py

@@ -705,7 +705,6 @@ def highlight_bz_on_hover_bs(hover_data, click_data, label_select):
             """Highlight the corresponding point/edge of the Brillouin Zone when hovering the band
             structure plot.
             """
-
             # TODO: figure out what to return (CSS?) to highlight BZ edge/point
             return
 

crystal_toolkit/components/pourbaix.py

@@ -356,7 +356,7 @@ def get_figure(
                     marker={"color": "Black"},
                     line={"color": "Black", "width": 0},
                     mode="lines",
-                    showlegend=True if legend_entry not in include_legend else False,
+                    showlegend=legend_entry not in include_legend,
                 )
             )
 
@@ -374,10 +374,11 @@ def get_figure(
 
             # stable entries are black with default color scheme,
             # so use white lines instead
-            if heatmap_entry:
-                line = {"color": "White", "width": 4}
-            else:
-                line = {"color": "Black", "width": 1}
+            line = (
+                {"color": "White", "width": 4}
+                if heatmap_entry
+                else {"color": "Black", "width": 1}
+            )
 
             shape = go.layout.Shape(
                 type="path", path=path, fillcolor="rgba(0,0,0,0)", opacity=1, line=line
@@ -550,7 +551,7 @@ def _sub_layouts(self) -> dict[str, Component]:
                     help_str="Whether to filter solid phases by stability on the compositional phase diagram. "
                     "The practical consequence of this is that highly oxidized or reduced phases that "
                     "might show up in experiments due to kinetic limitations on oxygen/hydrogen evolution "
-                    "won’t appear in the diagram, but they are not actually “stable” (and are frequently "
+                    "won't appear in the diagram, but they are not actually “stable” (and are frequently "
                     "overstabilized from DFT errors). Hence, including only the stable solid phases generally "
                     "leads to the most accurate Pourbaix diagrams.",
                 ),
@@ -789,7 +790,7 @@ def make_figure(pourbaix_entries, *args) -> go.Figure:
                 conc_dict=conc_dict,
                 filter_solids=kwargs["filter_solids"],
             )
-            self.logger.debug(
+            self.logger.debug(  # noqa: PLE1205
                 "Generated pourbaix diagram",
                 len(pourbaix_entries),
                 heatmap_entry,

crystal_toolkit/components/robocrys.py

@@ -49,5 +49,5 @@ def run_robocrys_analysis(new_store_contents):
                 style={"white-space": "nowrap"},
             )
             return MessageContainer(
-                MessageBody([f"{description} – ", repo_link]), kind="dark"
+                MessageBody([f"{description} - ", repo_link]), kind="dark"
             )