Use ruff for code format

00

.pre-commit-config.yaml

@@ -19,41 +19,31 @@ repos:
           - id: yamlfmt
             exclude: tests
 
-    - repo: https://github.com/psf/black
-      rev: 23.12.1
-      hooks:
-          - id: black
-            language_version: python3 # Should be a command that runs python3.6+
-
-    - repo: https://github.com/PyCQA/flake8
-      rev: 6.1.0
-      hooks:
-          - id: flake8
-            args: [--count, --show-source, --statistics]
-            additional_dependencies:
-                - flake8-bugbear==22.7.1
-
-    - repo: https://github.com/pycqa/isort
-      rev: 5.13.2
-      hooks:
-          - id: isort
-            args: [--profile, black, --filter-files]
-
     - repo: https://github.com/sirosen/check-jsonschema
       rev: 0.27.3
       hooks:
           - id: check-github-workflows
 
-    - repo: https://github.com/kynan/nbstripout
-      rev: 0.6.1
-      hooks:
-          - id: nbstripout
-
     - repo: https://github.com/nbQA-dev/nbQA
       rev: 1.7.1
       hooks:
           - id: nbqa-pyupgrade
             args: [--py38-plus]
           - id: nbqa-isort
             args: [--profile=black]
-          - id: nbqa-black
+          - id: nbqa-ruff
+
+    - repo: https://github.com/kynan/nbstripout
+      rev: 0.6.1
+      hooks:
+          - id: nbstripout
+
+    - repo: https://github.com/astral-sh/ruff-pre-commit
+      # Ruff version.
+      rev: v0.1.13
+      hooks:
+        # Run the linter.
+          - id: ruff
+            args: [--fix]
+        # Run the formatter.
+          - id: ruff-format

qe.ipynb

@@ -25,9 +25,27 @@
     "\n",
     "    sys.modules[\"pybel\"] = __import__(\"openbabel\", globals(), locals(), [\"pybel\"]).pybel\n",
     "except Exception:\n",
-    "    pass"
+    "    pass\n",
+    "\n",
+    "import ipywidgets as ipw\n",
+    "from aiidalab_widgets_base.bug_report import (\n",
+    "    install_create_github_issue_exception_handler,\n",
+    ")\n",
+    "from importlib_resources import files\n",
+    "from IPython.display import display\n",
+    "from jinja2 import Environment\n",
+    "\n",
+    "from aiidalab_qe.app import App, static\n",
+    "from aiidalab_qe.version import __version__"
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  },
   {
    "cell_type": "code",
    "execution_count": null,
@@ -45,17 +63,6 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "import ipywidgets as ipw\n",
-    "from aiidalab_widgets_base.bug_report import (\n",
-    "    install_create_github_issue_exception_handler,\n",
-    ")\n",
-    "from importlib_resources import files\n",
-    "from IPython.display import display\n",
-    "from jinja2 import Environment\n",
-    "\n",
-    "from aiidalab_qe.app import App, static\n",
-    "from aiidalab_qe.version import __version__\n",
-    "\n",
     "env = Environment()\n",
     "\n",
     "template = files(static).joinpath(\"welcome.jinja\").read_text()\n",

setup.cfg

@@ -63,12 +63,6 @@ description = Perform Quantum ESPRESSO calculations
 categories =
     quantum
 
-[flake8]
-ignore =
-    E501
-    W503
-    E203
-
 [bumpver]
 current_version = "v23.10.0"
 version_pattern = "v0Y.0M.PATCH[PYTAGNUM]"

src/aiidalab_qe/app/structure/__init__.py

@@ -115,7 +115,7 @@ def __init__(self, description=None, **kwargs):
                 self.message_area,
                 self.confirm_button,
             ],
-            **kwargs
+            **kwargs,
         )
 
     @traitlets.default("state")

src/aiidalab_qe/common/node_view.py

@@ -74,9 +74,7 @@ def _update_displayed_structure(self, change):
     def _update_structure_viewer(self, change):
         """Update the view if displayed_structure trait was modified."""
         with self.hold_trait_notifications():
-            for (
-                comp_id
-            ) in self._viewer._ngl_component_ids:  # pylint: disable=protected-access
+            for comp_id in self._viewer._ngl_component_ids:  # pylint: disable=protected-access
                 self._viewer.remove_component(comp_id)
             self.selection = list()
             if change["new"] is not None:

src/aiidalab_qe/common/setup_pseudos.py

@@ -213,8 +213,9 @@ def install(
 
     except Timeout:
         # Assume that the installation was triggered by a different process.
-        yield "Installation was already started elsewhere, waiting for it to finish...", ProgressBar.AnimationRate(
-            1.0
+        yield (
+            "Installation was already started elsewhere, waiting for it to finish...",
+            ProgressBar.AnimationRate(1.0),
         )
         with FileLock(FN_LOCKFILE, timeout=120):
             if len(pseudos_to_install()) > 0:

src/aiidalab_qe/plugins/bands/workchain.py

@@ -102,8 +102,8 @@ def generate_kpath_2d(structure, kpoints_distance, kpath_2d):
         a2 = reciprocal_cell[1]
         norm_a1 = np.linalg.norm(a1)
         norm_a2 = np.linalg.norm(a2)
-        cos_gamma = a1.dot(a2) / (
-            norm_a1 * norm_a2
+        cos_gamma = (
+            a1.dot(a2) / (norm_a1 * norm_a2)
         )  # Angle between a1 and a2 # like in https://pubs.acs.org/doi/10.1021/acs.jpclett.2c02972
         gamma = np.arccos(cos_gamma)
         eta = (1 - (norm_a1 / norm_a2) * cos_gamma) / (2 * np.power(np.sin(gamma), 2))