Create .pre-commit-config.yaml (#1793)

Closes #1771.

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

.deepsource.toml

@@ -10,12 +10,3 @@ name = "python"
 
   [analyzers.meta]
   runtime_version = "3.x.x"
-
-[[transformers]]
-name = "prettier"
-
-[[transformers]]
-name = "isort"
-
-[[transformers]]
-name = "black"

.github/PULL_REQUEST_TEMPLATE.md

@@ -6,7 +6,6 @@
 
 - [ ] I have read the ["Guidelines" section](https://quantum-accelerators.github.io/quacc/dev/contributing.html#guidelines) of the contributing guide. Don't lie! 😉
 - [ ] My PR is on a custom branch and is _not_ named `main`.
-- [ ] I have used `black`, `isort`, and `ruff` as described in the [style guide](https://quantum-accelerators.github.io/quacc/dev/contributing.html#style).
 - [ ] I have added relevant, comprehensive [unit tests](https://quantum-accelerators.github.io/quacc/dev/contributing.html#unit-tests).
 
 ### Notes

.gitignore

@@ -12,7 +12,7 @@ package.json
 *parsl.log
 runinfo
 
-# Docs 
+# Docs
 .cache/
 docs/reference/*
 *doctrees*

.pre-commit-config.yaml

@@ -0,0 +1,23 @@
+ci:
+  autoupdate_schedule: monthly
+  autofix_commit_msg: pre-commit auto-fixes
+  autoupdate_commit_msg: pre-commit autoupdate
+
+repos:
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.3.0
+    hooks:
+      - id: ruff
+        args: [--fix]
+      - id: ruff-format
+
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.5.0
+    hooks:
+      - id: end-of-file-fixer
+      - id: trailing-whitespace
+
+  - repo: https://github.com/adamchainz/blacken-docs
+    rev: 1.16.0
+    hooks:
+      - id: blacken-docs

README.md

@@ -21,7 +21,7 @@
 ## Documentation 📖
 
 <p align="center">
-     <a href="https://quantum-accelerators.github.io/quacc/"><b><i>Learn More Here!</i></b></a> 
+     <a href="https://quantum-accelerators.github.io/quacc/"><b><i>Learn More Here!</i></b></a>
 </p>
 
 ... or skip straight to one of the following sections:

docs/dev/contributing.md

@@ -58,7 +58,7 @@ In general, please try to keep the code style consistent when possible, particul
 
 2. Address any relevant issues raised by the GitHub Actions test suite.
 
-3. All Python code should be formatted with [isort](https://github.com/PyCQA/isort) (`isort .`), [black](https://github.com/psf/black) (`black .`), and [ruff](https://github.com/astral-sh/ruff) (`ruff . --fix`).
+3. All Python code should be formatted with [ruff](https://github.com/astral-sh/ruff) (`ruff format . --fix`).
 
 ## Unit Tests
 

docs/dev/recipes/flows.md

@@ -44,14 +44,17 @@ quacc fully supports complex, dynamic flows where the number of jobs is not know
     from random import randint
     from quacc import flow, job, subflow
 
+
     @job
     def add(a, b):
         return a + b
 
+
     @job
     def make_list(val):
         return [val] * randint(2, 5)
 
+
     @subflow
     def add_distributed(vals, c):
         outputs = []
@@ -60,6 +63,7 @@ quacc fully supports complex, dynamic flows where the number of jobs is not know
             outputs.append(output)
         return outputs
 
+
     @flow
     def workflow(a, b, c):
         output1 = add(a, b)

docs/maintainers/internal.md

@@ -16,7 +16,7 @@ For a pull request opened by a contributor not on the whitelist, [@buildbot-prin
 
 To upload to PyPI manually in the case of a GitHub Actions failure:
 
-```python
+```bash
 pip install -e .
 python -m build
 twine check dist/*

docs/user/advanced/vasp_hpc.md

@@ -75,7 +75,9 @@ First, prepare your `QUACC_VASP_PP_PATH` environment variable in the `~/.bashrc`
     concurrent_jobs = 2
     nodes_per_job = 1
     cores_per_node = 128
-    vasp_parallel_cmd = f"srun -N {nodes_per_job} --ntasks-per-node={cores_per_node} --cpu_bind=cores"
+    vasp_parallel_cmd = (
+        f"srun -N {nodes_per_job} --ntasks-per-node={cores_per_node} --cpu_bind=cores"
+    )
     min_slurm_allocations = 0
     max_slurm_allocations = 1
 

docs/user/recipes/recipes_intro.md

@@ -39,7 +39,7 @@ print(result)
 
 ??? Info "Printed Output"
 
-    ```python
+    ```
     {'atoms': Atoms(symbols='Cu', pbc=True, cell=[[0.0, 1.805, 1.805], [1.805, 0.0, 1.805], [1.805, 1.805, 0.0]], initial_magmoms=...),
     'atoms_info': {'\_id': 'f8d53f110f524872f30a5cc20e8befb1'},
     'builder_meta': {'build_date': datetime.datetime(2024, 1, 22, 6, 53, 30, 342389),
@@ -150,7 +150,7 @@ print(result2)
 
 ??? Info "Printed Output"
 
-    ```python
+    ```
     {'atoms': Atoms(symbols='Cu', pbc=True, cell=[[0.0, 1.805, 1.805], [1.805, 0.0, 1.805], [1.805, 1.805, 0.0]], initial_magmoms=...),
      'atoms_info': {'_id': 'f8d53f110f524872f30a5cc20e8befb1',
       '_old_ids': ['f8d53f110f524872f30a5cc20e8befb1']},

pyproject.toml

@@ -18,7 +18,7 @@ classifiers = [
     "Programming Language :: Python :: 3.9",
     "Programming Language :: Python :: 3.10",
     "Programming Language :: Python :: 3.11",
-    "Programming Language :: Python :: 3.12", 
+    "Programming Language :: Python :: 3.12",
     "Intended Audience :: Science/Research",
     "Topic :: Scientific/Engineering",
     "Operating System :: Microsoft :: Windows",
@@ -54,7 +54,7 @@ prefect = ["prefect>=2.14.14", "prefect-dask>=0.2.6", "dask-jobqueue>=0.8.2"]
 redun = ["redun>=0.16.2"]
 sella = ["sella>=2.3.2", "jax<=0.4.24", "jaxlib<=0.4.24"]
 tblite = ["tblite[ase]>=0.3.0; platform_system=='Linux'"]
-dev = ["black>=23.7.0", "codecov-cli>=0.4.1", "isort>=5.12.0", "pytest>=7.4.0", "pytest-cov>=3.0.0", "ruff>=0.0.285"]
+dev = ["codecov-cli>=0.4.1", "pytest>=7.4.0", "pytest-cov>=3.0.0", "ruff>=0.0.285"]
 docs = [
     "blacken-docs>=1.16.0",
     "mkdocs-material>=9.1.21",

src/quacc/_cli/quacc.py

@@ -45,7 +45,7 @@ def main(
         help="Show the application's version and exit.",
         callback=callback,
         is_eager=True,
-    )
+    ),
 ) -> None:
     """
     The main CLI interface, with an option to return the version.

src/quacc/atoms/defects.py

@@ -167,7 +167,8 @@ def _get_defect_entry_from_defect(
     defect_supercell.remove(dummy_site)
 
     computed_structure_entry = ComputedStructureEntry(
-        structure=defect_supercell, energy=0.0  # needs to be set, so set to 0.0
+        structure=defect_supercell,
+        energy=0.0,  # needs to be set, so set to 0.0
     )
 
     return DefectEntry(

src/quacc/atoms/slabs.py

@@ -9,6 +9,7 @@
 import numpy as np
 from ase import Atoms
 from pymatgen.analysis.adsorption import AdsorbateSiteFinder
+from pymatgen.core.structure import Structure
 from pymatgen.core.surface import Slab, center_slab, generate_all_slabs
 from pymatgen.io.ase import AseAtomsAdaptor
 
@@ -18,7 +19,6 @@
     from typing import Literal, TypedDict
 
     from numpy.typing import ArrayLike
-    from pymatgen.core.structure import Structure
 
     class AdsSiteFinderKwargs(TypedDict, total=False):
         """
@@ -67,10 +67,9 @@ def flip_atoms(
         Inverted slab
     """
 
-    if isinstance(atoms, Atoms):
-        new_atoms = copy_atoms(atoms)
-    else:
-        new_atoms = atoms.to_ase_atoms()
+    new_atoms = (
+        atoms.to_ase_atoms() if isinstance(atoms, Structure) else copy_atoms(atoms)
+    )
 
     new_atoms.rotate(180, "x")
     new_atoms.wrap()

src/quacc/settings.py

@@ -52,7 +52,7 @@ class QuaccSettings(BaseSettings):
         _DEFAULT_CONFIG_FILE_PATH,
         description=(
             """
-            Path to the YAML file to load alternative quacc configuration 
+            Path to the YAML file to load alternative quacc configuration
             defaults from.
             """
         ),
@@ -76,7 +76,7 @@ class QuaccSettings(BaseSettings):
         Path.cwd(),
         description=(
             """
-            Directory to permanently store I/O-based calculation results in. 
+            Directory to permanently store I/O-based calculation results in.
             Note that this behavior may be modified by the chosen workflow engine.
             """
         ),
@@ -85,10 +85,10 @@ class QuaccSettings(BaseSettings):
         None,
         description=(
             """
-            The base directory where calculations are run. If set to None, calculations will be run in a 
-            temporary directory within `RESULTS_DIR`. If a `Path` is supplied, calculations will 
-            be run in a temporary directory within `SCRATCH_DIR`. Files are always moved back 
-            to `RESULTS_DIR` after the calculation is complete, and the temporary directory 
+            The base directory where calculations are run. If set to None, calculations will be run in a
+            temporary directory within `RESULTS_DIR`. If a `Path` is supplied, calculations will
+            be run in a temporary directory within `SCRATCH_DIR`. Files are always moved back
+            to `RESULTS_DIR` after the calculation is complete, and the temporary directory
             in `SCRATCH_DIR` is removed.
             """
         ),
@@ -97,8 +97,8 @@ class QuaccSettings(BaseSettings):
         True,
         description=(
             """
-            Whether to have a unique directory in RESULTS_DIR for each job. 
-            Some workflow engines have an option to do this for you already, 
+            Whether to have a unique directory in RESULTS_DIR for each job.
+            Some workflow engines have an option to do this for you already,
             in which case you should set this to False.
             """
         ),
@@ -132,10 +132,10 @@ class QuaccSettings(BaseSettings):
         None,
         description=(
             """
-            The desired Maggma data store where calculation results will be stored. All data stores listed in 
-            `maggma.stores.__init__.py` are supported. If a dictionary is provided, the first key must be set 
+            The desired Maggma data store where calculation results will be stored. All data stores listed in
+            `maggma.stores.__init__.py` are supported. If a dictionary is provided, the first key must be set
             to the desired store type. The sub-parameters are the keyword arguments accepted by the Store.
-            An example is shown below: 
+            An example is shown below:
 
             ```yaml
             STORE:
@@ -165,7 +165,7 @@ class QuaccSettings(BaseSettings):
         Path(which("orca") or "orca"),
         description=(
             """
-            Path to the ORCA executable. This must be the full, absolute path 
+            Path to the ORCA executable. This must be the full, absolute path
             for parallel calculations to work.
             """
         ),
@@ -298,7 +298,7 @@ class QuaccSettings(BaseSettings):
         1.0,
         description=(
             """
-            Default initial magmom to use for a given element if a preset 
+            Default initial magmom to use for a given element if a preset
             with magmoms is provided but an element is missing from the list.
             """
         ),
@@ -307,7 +307,7 @@ class QuaccSettings(BaseSettings):
         0.05,
         description=(
             """
-            If the absolute value of all magnetic moments are below this value, 
+            If the absolute value of all magnetic moments are below this value,
             they will be set to 0 such that a spin-unpolarized calculation will be performed.
             """
         ),
@@ -316,7 +316,7 @@ class QuaccSettings(BaseSettings):
         True,
         description=(
             """
-            If True, any pre-existing atoms.get_magnetic_moments() will be set 
+            If True, any pre-existing atoms.get_magnetic_moments() will be set
             in atoms.set_initial_magnetic_moments().
             """
         ),
@@ -334,7 +334,7 @@ class QuaccSettings(BaseSettings):
         False,
         description=(
             """
-            If VTST-related input swaps should be used when running Custodian. 
+            If VTST-related input swaps should be used when running Custodian.
             Requires VASP to be compiled with VTST
             """
         ),
@@ -365,7 +365,7 @@ class QuaccSettings(BaseSettings):
         None,
         description=(
             """
-            After this many seconds, Custodian will stop running 
+            After this many seconds, Custodian will stop running
             and ensure that VASP writes a STOPCAR
             """
         ),
@@ -421,7 +421,7 @@ class QuaccSettings(BaseSettings):
         False,
         description=(
             """
-            Whether to run in debug mode. This will set the logging level to DEBUG, 
+            Whether to run in debug mode. This will set the logging level to DEBUG,
             ASE logs (e.g. optimizations, vibrations, thermo) are printed to stdout.
             """
         ),

src/quacc/utils/files.py

@@ -150,7 +150,7 @@ def copy_decompress_files(
 
             if source_filepath.is_symlink():
                 continue
-            elif source_filepath.is_file():
+            if source_filepath.is_file():
                 copy(source_filepath, destination_filepath)
                 decompress_file(destination_filepath)
             elif source_filepath.is_dir():