Replace isort and flake8 with ruff, upgrade hooks (#272)

* Replace isort and flake8 with ruff, upgrade hooks

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* Remove 82 line length config

* Run pre-commit on all

* Rm commented out isort config

---------

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

.pre-commit-config.yaml

@@ -10,19 +10,15 @@ repos:
   - id: check-added-large-files
 
 - repo: https://github.com/psf/black
-  rev: 22.12.0
+  rev: 23.1.0
   hooks:
   - id: black
-- repo: https://github.com/PyCQA/isort
-  rev: 5.12.0
+- repo: https://github.com/charliermarsh/ruff-pre-commit
+  rev: v0.0.241
   hooks:
-  - id: isort
-- repo: https://github.com/PyCQA/flake8
-  rev: 6.0.0
-  hooks:
-  - id: flake8
+  - id: ruff
 - repo: https://github.com/snakemake/snakefmt
-  rev: v0.8.0
+  rev: v0.8.1
   hooks:
   - id: snakefmt
 - repo: https://github.com/executablebooks/mdformat

docs/debug/gh-163-snakemake-resources/run.py

@@ -3,7 +3,10 @@
 from snakemake import snakemake
 
 make = partial(
-    snakemake, snakefile="Snakefile", targets=("earth", "space"), printshellcmds=True
+    snakemake,
+    snakefile="Snakefile",
+    targets=("earth", "space"),
+    printshellcmds=True,
 )
 
 

docs/examples/snek5000-canonical/src/snek5000_canonical/output.py

@@ -5,7 +5,6 @@
 
 
 class OutputCanonical(OutputBase):
-
     template_box = box
     template_makefile_usr = makefile_usr
     template_size = size

docs/examples/snek5000-tgv/src/snek5000_tgv/solver.py

@@ -48,7 +48,8 @@ def create_default_params(cls):
 
         # Read defaults for `params.nek` from `tgv.par.cfg` (original code)
         complete_params_from_par_file(
-            params, Path(__file__).parent / f"{cls.info_solver.short_name}.par.cfg"
+            params,
+            Path(__file__).parent / f"{cls.info_solver.short_name}.par.cfg",
         )
 
         # Boundary conditions

noxfile.py

@@ -301,7 +301,8 @@ def ctags(session):
         )
     )
     run_ext(
-        session, f"ctags -f {output} --language-force=Fortran -R {sources['nek5000']}"
+        session,
+        f"ctags -f {output} --language-force=Fortran -R {sources['nek5000']}",
     )
     run_ext(session, f"ctags -f {output} {excludes} --append -R {sources['snek5000']}")
 
@@ -382,7 +383,13 @@ def release_tests(session, dist_type):
         ), "Poetry local configuration exists. Please remove to continue"
         session.install("poetry")
         session.run(
-            "python", "-m", "poetry", "config", "--local", "virtualenvs.create", "false"
+            "python",
+            "-m",
+            "poetry",
+            "config",
+            "--local",
+            "virtualenvs.create",
+            "false",
         )
         pytest_cmd = install_with_tests(session, ["--no-root"])
     else:

pyproject.toml

@@ -9,11 +9,11 @@ build-backend = "setuptools.build_meta"
 [tool.setuptools_scm]
 write_to = "src/snek5000/_version.py"
 
-[tool.isort]
-known_first_party = ["fluiddyn", "fluidsim_core", "snek5000"]
-# multi_line_output = 3
-profile = "black"
-line_length = 82
+[tool.ruff]
+ignore = ["E501", "W505"]
+
+[tool.ruff.isort]
+known-first-party = ["fluiddyn", "fluidsim_core", "snek5000"]
 
 [tool.coverage.run]
 source = ["snek5000", "snek5000_canonical", "./tests"]

src/snek5000/info.py

@@ -53,7 +53,10 @@ def _init_root(self):
         self._set_child("classes")
         self.classes._set_child(
             "Oper",
-            attribs={"module_name": "snek5000.operators", "class_name": "Operators"},
+            attribs={
+                "module_name": "snek5000.operators",
+                "class_name": "Operators",
+            },
         )
 
 
@@ -64,7 +67,10 @@ def _init_root(self):
         super()._init_root()
         self.classes._set_child(
             "Output",
-            attribs={"module_name": "snek5000.output.base", "class_name": "Output"},
+            attribs={
+                "module_name": "snek5000.output.base",
+                "class_name": "Output",
+            },
         )
         self.classes._set_child(
             "Make", attribs={"module_name": "snek5000.make", "class_name": "Make"}

src/snek5000/make.py

@@ -30,7 +30,6 @@ class Make:
     """
 
     def __init__(self, sim=None, path_run=None):
-
         if (sim is None and path_run is None) or (
             sim is not None and path_run is not None
         ):

src/snek5000/output/base.py

@@ -146,7 +146,8 @@ def _set_info_solver_classes(cls, classes):
         classes._set_child(
             "HistoryPoints",
             dict(
-                module_name="snek5000.output.history_points", class_name="HistoryPoints"
+                module_name="snek5000.output.history_points",
+                class_name="HistoryPoints",
             ),
         )
 

src/snek5000/output/history_points.py

@@ -129,7 +129,6 @@ def load(self):
             return self.coords, self._data
 
     def _load_full(self):
-
         with open(self.path_file) as file:
             nb_points = int(file.readline().split(" ", 1)[0])
             coords = np.loadtxt(file, max_rows=nb_points)
@@ -148,7 +147,6 @@ def _load_full(self):
         return self.coords, df
 
     def _create_df_from_lines(self, lines, nb_points):
-
         columns = ["time", "ux", "uy"]
 
         sim = self.output.sim

src/snek5000/output/remaining_clock_time.py

@@ -23,7 +23,6 @@ def _load_times(self):
         return data
 
     def load(self):
-
         if not self.path_file.exists():
             raise IOError(
                 f"No file {self.path_file}. "

src/snek5000/params.py

@@ -85,7 +85,8 @@ def load_params(path_dir="."):
     Simul = import_cls_simul(short_name)
 
     return Simul.load_params_from_file(
-        path_xml=path_dir / "params_simul.xml", path_par=path_dir / f"{short_name}.par"
+        path_xml=path_dir / "params_simul.xml",
+        path_par=path_dir / f"{short_name}.par",
     )
 
 

src/snek5000/util/console.py

@@ -8,7 +8,6 @@
 
 
 def print_versions():
-
     import pymech
     import snakemake
 

tests/conftest.py

@@ -264,7 +264,6 @@ def sim_tgv_executed():
 
 
 def create_fake_nek_files(path_dir, name_solver, nb_files=1):
-
     nx = 2
     ny = 4
     nz = 6

tests/test_params.py

@@ -143,7 +143,6 @@ def format_par(text):
 
 
 def test_user_params():
-
     tmp_dir = Path(tempfile.mkdtemp("snek5000", __name__))
 
     def complete_create_default_params(p):