🔧 Replace black/isort/pyupgrade/flake8 with ruff

.pre-commit-config.yaml

@@ -8,25 +8,16 @@ exclude: >
 
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.1.0
+    rev: v4.5.0
     hooks:
       - id: check-json
       - id: check-yaml
       - id: end-of-file-fixer
       - id: trailing-whitespace
 
-  - repo: https://github.com/asottile/pyupgrade
-    rev: v2.31.1
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.1.6
     hooks:
-      - id: pyupgrade
-        args: [--py38-plus]
-
-  - repo: https://github.com/pycqa/isort
-    rev: 5.12.0
-    hooks:
-      - id: isort
-
-  - repo: https://github.com/psf/black
-    rev: 22.3.0
-    hooks:
-      - id: black
+    - id: ruff
+      args: [--fix]
+    - id: ruff-format

README.md

@@ -107,11 +107,10 @@ pytest --lammps-workdir "test_workdir"
 
 ### Pre-commit
 
-The code is formatted and linted using [pre-commit](https://pre-commit.com/), so that the code conform to the standard. One must simply install the repository with the `pre-commit` extra dependencies:
+The code is formatted and linted using [pre-commit](https://pre-commit.com/), so that the code conform to the standard:
 
 ```shell
 cd aiida-lammps
-pip install -e .[pre-commit]
 pre-commit run --all
 ```
 or to automate runs, triggered before each commit:
@@ -120,11 +119,6 @@ or to automate runs, triggered before each commit:
 pre-commit install
 ```
 
-The pre-commit can also be run in an isolated environment via `tox` with:
-
-```shell
-tox -e pre-commit
-```
-
 ## License
-The `aiida-lammps` plugin package is released under the MIT license. See the `LICENSE.txt` file for more details.
+
+The `aiida-lammps` plugin package is released under the MIT license. See the `LICENSE` file for more details.

aiida_lammps/calculations/base.py

@@ -7,7 +7,7 @@
 the input structure and whether or not a restart file is provided.
 """
 import os
-from typing import Union
+from typing import ClassVar, Dict, Union
 
 from aiida import orm
 from aiida.common import datastructures
@@ -30,7 +30,7 @@ class LammpsBaseCalculation(CalcJob):
     the input structure and whether or not a restart file is provided.
     """
 
-    _DEFAULT_VARIABLES = {
+    _DEFAULT_VARIABLES: ClassVar[Dict[str, str]] = {
         "input_filename": "input.in",
         "structure_filename": "structure.dat",
         "output_filename": "lammps.out",
@@ -325,10 +325,7 @@ def prepare_for_submission(self, folder):
         else:
             _parameters = {}
 
-        if "settings" in self.inputs:
-            settings = self.inputs.settings.get_dict()
-        else:
-            settings = {}
+        settings = self.inputs.settings.get_dict() if "settings" in self.inputs else {}
 
         # Set the remote copy list and the symlink so that if one needs to use restartfiles from
         # a previous calculations one can do so without problems

aiida_lammps/calculations/raw.py

@@ -131,9 +131,8 @@ def prepare_for_submission(self, folder: Folder) -> CalcInfo:
             # namespace, falling back to the filename of the ``SinglefileData`` node if not defined.
             filename = filenames.get(key, node.filename)
 
-            with folder.open(filename, "wb") as target:
-                with node.open(mode="rb") as source:
-                    shutil.copyfileobj(source, target)
+            with folder.open(filename, "wb") as target, node.open(mode="rb") as source:
+                shutil.copyfileobj(source, target)
 
             provenance_exclude_list.append(filename)
 

aiida_lammps/data/potential.py

@@ -23,7 +23,7 @@ class written by Sebastiaan Huber.
 import json
 import os
 import pathlib
-from typing import BinaryIO, List, Optional, Union
+from typing import Any, BinaryIO, ClassVar, Dict, List, Optional, Union
 import warnings
 
 from aiida import orm, plugins
@@ -164,7 +164,7 @@ class written by Sebaastian Huber.
         "lammps_potentials.json",
     )
 
-    _extra_keys = {
+    _extra_keys: ClassVar[Dict[str, Any]] = {
         "title": {"validator": _validate_string},
         "developer": {"validator": _validate_string_list},
         "publication_year": {"validator": _validate_datetime},
@@ -190,12 +190,12 @@ class written by Sebaastian Huber.
     def get_or_create(
         cls,
         source: Union[str, pathlib.Path, BinaryIO],
-        filename: str = None,
-        pair_style: str = None,
-        species: list = None,
-        atom_style: str = None,
-        units: str = None,
-        extra_tags: dict = None,
+        filename: Optional[str] = None,
+        pair_style: Optional[str] = None,
+        species: Optional[list] = None,
+        atom_style: Optional[str] = None,
+        units: Optional[str] = None,
+        extra_tags: Optional[dict] = None,
     ):
         """
         Get lammps potential data node from database or create a new one.
@@ -290,7 +290,7 @@ def prepare_source(cls, source: Union[str, pathlib.Path, BinaryIO]) -> BinaryIO:
         ) and not cls.is_readable_byte_stream(source):
             raise TypeError(
                 "`source` should be a `str` or `pathlib.Path` filepath on "
-                + f"disk or a stream of bytes, got: {source}"
+                f"disk or a stream of bytes, got: {source}"
             )
 
         if isinstance(source, (str, pathlib.Path)):
@@ -328,7 +328,7 @@ def validate_pair_style(self, pair_style: str):
         """
         if pair_style is None:
             raise TypeError("The pair_style of the potential must be provided.")
-        if pair_style not in self.default_potential_info.keys():
+        if pair_style not in self.default_potential_info:
             raise KeyError(f'The pair_style "{pair_style}" is not valid')
         self.base.attributes.set("pair_style", pair_style)
 
@@ -440,12 +440,12 @@ def validate_extra_tags(self, extra_tags: dict):
     def set_file(
         self,
         source: Union[str, pathlib.Path, BinaryIO],
-        filename: str = None,
-        pair_style: str = None,
-        species: list = None,
-        atom_style: str = None,
-        units: str = None,
-        extra_tags: dict = None,
+        filename: Optional[str] = None,
+        pair_style: Optional[str] = None,
+        species: Optional[list] = None,
+        atom_style: Optional[str] = None,
+        units: Optional[str] = None,
+        extra_tags: Optional[dict] = None,
         **kwargs,
     ):
         """Set the file content.

aiida_lammps/data/trajectory.py

@@ -90,7 +90,6 @@ def set_from_fileobj(self, fileobj, aliases=None):
                 self._compression_method,
             ) as zip_file:
                 for step_id, trajectory_step in enumerate(iter_trajectories(fileobj)):
-
                     # extract data to store in attributes
                     time_steps.append(trajectory_step.timestep)
                     if number_atoms is None:
@@ -135,13 +134,13 @@ def set_from_fileobj(self, fileobj, aliases=None):
 
         self.base.attributes.set("number_steps", len(time_steps))
         self.base.attributes.set("number_atoms", number_atoms)
-        self.base.attributes.set("field_names", list(sorted(field_names)))
+        self.base.attributes.set("field_names", sorted(field_names))
         self.base.attributes.set("trajectory_filename", self._trajectory_filename)
         self.base.attributes.set("timestep_filename", self._timestep_filename)
         self.base.attributes.set("zip_prefix", self._zip_prefix)
         self.base.attributes.set("compression_method", self._compression_method)
         self.base.attributes.set("aliases", aliases)
-        self.base.attributes.set("elements", list(sorted(elements)))
+        self.base.attributes.set("elements", sorted(elements))
 
     @property
     def number_steps(self):
@@ -199,14 +198,12 @@ def get_step_string(self, step_idx):
         with self.base.repository.open(
             self.base.attributes.get("trajectory_filename"),
             mode="rb",
-        ) as handle:
-            with ZipFile(
-                handle,
-                "r",
-                self.base.attributes.get("compression_method"),
-            ) as zip_file:
-                with zip_file.open(zip_name, "r") as step_file:
-                    content = step_file.read()
+        ) as handle, ZipFile(
+            handle,
+            "r",
+            self.base.attributes.get("compression_method"),
+        ) as zip_file, zip_file.open(zip_name, "r") as step_file:
+            content = step_file.read()
         return content.decode("utf8")
 
     def get_step_data(self, step_idx):
@@ -224,17 +221,16 @@ def iter_step_strings(self, steps=None):
         with self.base.repository.open(
             self.base.attributes.get("trajectory_filename"),
             mode="rb",
-        ) as handle:
-            with ZipFile(
-                handle,
-                "r",
-                self.base.attributes.get("compression_method"),
-            ) as zip_file:
-                for step_idx in steps:
-                    zip_name = f'{self.base.attributes.get("zip_prefix")}{step_idx}'
-                    with zip_file.open(zip_name) as step_file:
-                        content = step_file.read()
-                        yield content
+        ) as handle, ZipFile(
+            handle,
+            "r",
+            self.base.attributes.get("compression_method"),
+        ) as zip_file:
+            for step_idx in steps:
+                zip_name = f'{self.base.attributes.get("zip_prefix")}{step_idx}'
+                with zip_file.open(zip_name) as step_file:
+                    content = step_file.read()
+                    yield content
 
     def get_step_structure(
         self,

aiida_lammps/parsers/base.py

@@ -208,16 +208,18 @@ def parse_restartfile(
 
         restart_filename = ""
 
-        if parameters.get("restart", {}).get("print_final", False):
-            if input_restart_filename in list_of_files:
-                with self.node.outputs.retrieved.base.repository.open(
-                    input_restart_filename,
-                    mode="rb",
-                ) as handle:
-                    restart_file = orm.SinglefileData(handle)
-                self.out("restartfile", restart_file)
-                restart_found = True
-                restart_filename = input_restart_filename
+        if (
+            parameters.get("restart", {}).get("print_final", False)
+            and input_restart_filename in list_of_files
+        ):
+            with self.node.outputs.retrieved.base.repository.open(
+                input_restart_filename,
+                mode="rb",
+            ) as handle:
+                restart_file = orm.SinglefileData(handle)
+            self.out("restartfile", restart_file)
+            restart_found = True
+            restart_filename = input_restart_filename
 
         if (
             parameters.get("restart", {}).get("print_intermediate", False)