Use Ruff instead of flake8, black, isort, pyupgrade (#566)

* Enable linter on docs/
* Fix collection-literal-concatenation

.pre-commit-config.yaml

@@ -12,49 +12,24 @@ repos:
           - id: trailing-whitespace
             exclude: miscellaneous/structures
 
+    - repo: https://github.com/astral-sh/ruff-pre-commit
+      rev: v0.2.2
+      hooks:
+          - id: ruff-format
+            exclude: ^docs/.*
+          - id: ruff
+            args: [--fix, --exit-non-zero-on-fix, --show-fixes]
+
     - repo: https://github.com/jumanjihouse/pre-commit-hook-yamlfmt
       rev: 0.2.3
       hooks:
           - id: yamlfmt
 
-    - 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==23.2.13
-                - flake8-builtins==2.1.0
-                - flake8-comprehensions==3.10.1
-                - flake8-debugger==4.1.2
-                - flake8-logging-format==0.9.0
-                - pep8-naming==0.13.3
-                - pyflakes==3.1.0
-                - tryceratops==1.1.0
-
-    - 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/asottile/pyupgrade
-      rev: v3.15.0
-      hooks:
-          - id: pyupgrade
-            args: [--py39-plus]
-
     - repo: https://github.com/kynan/nbstripout
       rev: 0.6.1
       hooks:

aiidalab_widgets_base/bug_report.py

@@ -28,6 +28,7 @@ def find_installed_packages(python_bin: str | None = None) -> dict[str, str]:
         [python_bin, "-m", "pip", "list", "--format=json"],
         encoding="utf-8",
         capture_output=True,
+        check=True,
     ).stdout
 
     return {package["name"]: package["version"] for package in json.loads(output)}
@@ -160,7 +161,7 @@ def install_create_github_issue_exception_handler(output, url, labels=None):
             display(welcome_message, app_with_work_chain_selector, footer)
 
     """
-    global _ORIGINAL_EXCEPTION_HANDLER
+    global _ORIGINAL_EXCEPTION_HANDLER  # noqa
 
     if labels is None:
         labels = []

aiidalab_widgets_base/computational_resources.py

@@ -376,7 +376,7 @@ def _ssh_keygen(self):
             "",
         ]
         if not fpath.exists():
-            subprocess.run(keygen_cmd, capture_output=True)
+            subprocess.run(keygen_cmd, capture_output=True, check=True)
 
     def _can_login(self):
         """Check if it is possible to login into the remote host."""
@@ -1028,6 +1028,7 @@ def test(self, _=None):
         process_result = subprocess.run(
             ["verdi", "computer", "test", "--print-traceback", self.label.value],
             capture_output=True,
+            check=False,
         )
 
         if process_result.returncode == 0:
@@ -1602,7 +1603,7 @@ def __init__(
         enable_detailed_setup=True,
     ):
         if not any((enable_detailed_setup, enable_quick_setup)):
-            raise ValueError(  # noqa
+            raise ValueError(
                 "At least one of `enable_quick_setup` and `enable_detailed_setup` should be True."
             )
 

aiidalab_widgets_base/databases.py

@@ -152,8 +152,8 @@ class :class:`aiidalab_widgets_base.structures.StructureManagerWidget`.
 
     def __init__(
         self,
-        embedded: bool = True,
-        title: str = None,
+        embedded=True,
+        title=None,
         **kwargs,
     ) -> None:
         try:

aiidalab_widgets_base/elns.py

@@ -249,9 +249,7 @@ def update_list_of_elns(self):
             self.write_to_config(config)
             default_eln = None
 
-        self.eln_instance.options = [("Setup new ELN", {})] + [
-            (k, v) for k, v in config.items()
-        ]
+        self.eln_instance.options = [("Setup new ELN", {}), *list(config.items())]
         if default_eln:
             self.eln_instance.label = default_eln
 

aiidalab_widgets_base/export.py

@@ -40,8 +40,6 @@ def export_aiida_subgraph(self, change=None):  # pylint: disable=unused-argument
             document.body.appendChild(link);
             link.click();
             document.body.removeChild(link);
-            """.format(
-                payload=payload, filename=f"export_{self.process.id}.aiida"
-            )
+            """.format(payload=payload, filename=f"export_{self.process.id}.aiida")
         )
         display(javas)

aiidalab_widgets_base/misc.py

@@ -20,7 +20,7 @@ def copy_to_clipboard(self, change=None):  # pylint:disable=unused-argument
         from IPython.display import Javascript, display
 
         javas = Javascript(
-            """
+            f"""
            function copyStringToClipboard (str) {{
                // Create new element
                var el = document.createElement('textarea');
@@ -37,10 +37,8 @@ def copy_to_clipboard(self, change=None):  # pylint:disable=unused-argument
                // Remove temporary element
                document.body.removeChild(el);
             }}
-            copyStringToClipboard("{selection}");
-       """.format(
-                selection=self.value
-            )
+            copyStringToClipboard("{self.value}");
+        """
         )  # For the moment works for Chrome, but doesn't work for Firefox.
         if self.value:  # If no value provided - do nothing.
             display(javas)

aiidalab_widgets_base/process.py

@@ -156,10 +156,10 @@ def __init__(self, process=None, **kwargs):
         self.info = ipw.HTML()
 
         self.flat_mapping = self.generate_flat_mapping(process=process) or {}
-        inputs_list = [(key, value) for key, value in self.flat_mapping.items()]
+        inputs_list = list(self.flat_mapping.items())
 
         self._inputs = ipw.Dropdown(
-            options=[("Select input", "")] + inputs_list,
+            options=[("Select input", ""), *inputs_list],
             description="Select input:",
             style={"description_width": "initial"},
             disabled=False,
@@ -230,7 +230,7 @@ def __init__(self, process=None, **kwargs):
             else []
         )
         outputs = ipw.Dropdown(
-            options=[("Select output", "")] + outputs_list,
+            options=[("Select output", ""), *outputs_list],
             label="Select output",
             description="Select outputs:",
             style={"description_width": "initial"},
@@ -285,7 +285,7 @@ def __init__(
                     )
                 )
         self.output = ipw.HTML()
-        super().__init__(children=[self.output] + self.followers, **kwargs)
+        super().__init__(children=[self.output, *self.followers], **kwargs)
         self.update()
 
     def update(self):

aiidalab_widgets_base/structures.py

@@ -118,8 +118,11 @@ def __init__(
             self._structure_importers(importers),
             self.viewer,
             ipw.HBox(
-                store_and_description
-                + [self.structure_label, self.structure_description]
+                [
+                    *store_and_description,
+                    self.structure_label,
+                    self.structure_description,
+                ]
             ),
         ]
 
@@ -131,7 +134,7 @@ def __init__(
             accordion.set_title(0, "Edit Structure")
             children += [accordion]
 
-        super().__init__(children=children + [self.output], **kwargs)
+        super().__init__(children=[*children, self.output], **kwargs)
 
     def _structure_importers(self, importers):
         """Preparing structure importers."""
@@ -217,7 +220,7 @@ def store_structure(self, _=None):
         ):
             # Make a link between self.input_structure and self.structure_node
             @engine.calcfunction
-            def user_modifications(source_structure):
+            def user_modifications(_source_structure):
                 return self.structure_node
 
             structure_node = user_modifications(self.input_structure)
@@ -469,7 +472,7 @@ class StructureExamplesWidget(ipw.VBox):
 
     def __init__(self, examples, title="", **kwargs):
         self.title = title
-        self.on_structure_selection = lambda structure_ase, name: None
+        self.on_structure_selection = lambda _structure_ase, _name: None
         self._select_structure = ipw.Dropdown(
             options=self.get_example_structures(examples)
         )
@@ -483,7 +486,7 @@ def get_example_structures(examples):
             raise TypeError(
                 f"parameter examples should be of type list, {type(examples)} given"
             )
-        return [("Select structure", False)] + examples
+        return [("Select structure", False), *examples]
 
     def _on_select_structure(self, change=None):
         """When structure is selected."""
@@ -687,7 +690,7 @@ class SmilesWidget(ipw.VBox):
 
     def __init__(self, title=""):
         self.title = title
-        try:  # noqa: TC101
+        try:
             from rdkit import Chem  # noqa: F401
             from rdkit.Chem import AllChem  # noqa: F401
         except ImportError:
@@ -1065,13 +1068,11 @@ def _apply_cell_transformation(self, _=None, atoms=None):
             try:
                 atoms = make_supercell(atoms, mat)
             except Exception as e:
-                self._status_message.message = """
+                self._status_message.message = f"""
             <div class="alert alert-info">
-            <strong>The transformation matrix is wrong! {}</strong>
+            <strong>The transformation matrix is wrong! {e}</strong>
             </div>
-            """.format(
-                    e
-                )
+            """
                 return
             # translate
             atoms.translate(-atoms.cell.array.dot(translate))
@@ -1546,8 +1547,9 @@ def copy_sel(self, _=None, atoms=None, selection=None):
         add_atoms.translate([1.0, 0, 0])
         atoms += add_atoms
 
-        self.structure, self.input_selection = atoms, list(
-            range(last_atom, last_atom + len(selection))
+        self.structure, self.input_selection = (
+            atoms,
+            list(range(last_atom, last_atom + len(selection))),
         )
 
     @_register_structure

aiidalab_widgets_base/utils/__init__.py

@@ -52,8 +52,8 @@ def get_ase_from_file(fname, file_format=None):  # pylint: disable=redefined-bui
 
 def find_ranges(iterable):
     """Yield range of consecutive numbers."""
-    for group in mit.consecutive_groups(iterable):
-        group = list(group)
+    for grp in mit.consecutive_groups(iterable):
+        group = list(grp)
         if len(group) == 1:
             yield group[0]
         else: