Update pre-commits and pytest configuration

.pre-commit-config.yaml

@@ -1,37 +1,23 @@
-default_language_version:
-  python: python3.8
+exclude: 'dev'
 
 repos:
 - repo: https://github.com/pre-commit/pre-commit-hooks
-  rev: v4.4.0
+  rev: v4.5.0
   hooks:
   - id: check-merge-conflict  # checks for files that contain merge conflict strings
   - id: check-toml  # checks toml files for parseable syntax
   - id: debug-statements  # checks for debugger imports and py37+ `breakpoint()` calls in python source
-#  - id: trailing-whitespace   # needs more checks
-#    args: [--markdown-linebreak-ext=md]
-#    exclude: 'oommfc/tests/test_sample/.*'
 
-- repo: https://github.com/pycqa/isort
-  rev: 5.12.0
+- repo: https://github.com/astral-sh/ruff-pre-commit
+  rev: v0.4.4
   hooks:
-  - id: isort
-
-- repo: https://github.com/nbQA-dev/nbQA
-  rev: 1.7.0
-  hooks:
-  - id: nbqa-isort  # isort inside Jupyter notebooks
-
-- repo: https://github.com/PyCQA/flake8
-  rev: 6.1.0
-  hooks:
-  - id: flake8
-    additional_dependencies: [flake8-rst-docstrings]  #, flake8-docstrings]
-
-- repo: https://github.com/psf/black
-  rev: 23.9.1
-  hooks:
-  - id: black-jupyter
+    # Run the linter.
+    - id: ruff
+      types_or: [python, pyi, jupyter]
+      args: [--fix, --exit-non-zero-on-fix]
+    # Run the formatter.
+    - id: ruff-format
+      types_or: [python, pyi, jupyter]
 
 # - repo: https://github.com/codespell-project/codespell
 #   rev: v2.1.0

oommfc/__init__.py

@@ -1,11 +1,11 @@
 """OOMMF calculator."""
+
 import importlib.metadata
 
 import pytest
 
 import oommfc.oommf
 import oommfc.scripts
-
 from .compute import compute
 from .delete import delete
 from .drivers import Driver, HysteresisDriver, MinDriver, TimeDriver

oommfc/compute.py

@@ -39,7 +39,7 @@ def schedule_script(func, system):
         msg = f"Computing the value of {func} is not supported."
         raise ValueError(msg)
 
-    return 'Schedule "{}" archive Step 1\n'.format(output)
+    return f'Schedule "{output}" archive Step 1\n'
 
 
 def compute(

oommfc/drivers/driver.py

@@ -188,7 +188,7 @@ def write_mif(
                 compute=compute,
                 **kwargs,
             )
-            with open(self._miffilename(system), "wt", encoding="utf-8") as miffile:
+            with open(self._miffilename(system), "w", encoding="utf-8") as miffile:
                 miffile.write(mif)
 
             # Generate and save json info file for a drive (not compute).

oommfc/oommf/__init__.py

@@ -1,4 +1,5 @@
 """OOMMF driving utility"""
+
 from .oommf import (
     DockerOOMMFRunner,
     ExeOOMMFRunner,

oommfc/oommf/oommf.py

@@ -158,7 +158,7 @@ def status(self):
             td.drive(system, t=1e-12, n=1, runner=self)
             print("OOMMF found and running.")
             return 0
-        except (EnvironmentError, RuntimeError):
+        except (OSError, RuntimeError):
             print("Cannot find OOMMF.")
             return 1
 
@@ -250,7 +250,7 @@ def __init__(self, oommf_tcl):
 
     def errors(self):
         errors_file = os.path.join(os.path.dirname(self.oommf_tcl), "boxsi.errors")
-        with open(errors_file, "r") as f:
+        with open(errors_file) as f:
             errors = f.read()
 
         return errors
@@ -285,13 +285,13 @@ def errors(self):
                 "oommf",
                 "boxsi.errors",
             )
-            with open(errors_file, "r") as f:
+            with open(errors_file) as f:
                 errors = f.read()
             return errors
 
         except FileNotFoundError:
             msg = "boxsi.errors cannot be retrieved."
-            raise EnvironmentError(msg)
+            raise OSError(msg) from None
 
     def __repr__(self):
         return f"ExeOOMMFRunner({self.oommf_exe})"
@@ -357,7 +357,7 @@ def _kill(self, targets=("all",), dry_run=False):
 
     def errors(self):
         msg = "boxsi.errors cannot be retrieved from Docker container."
-        raise EnvironmentError(msg)
+        raise OSError(msg)
 
     def __repr__(self):
         return f"DockerOOMMFRunner(docker_exe={self.docker_exe}, image={self.image})"
@@ -569,7 +569,7 @@ def autoselect_runner(self):
 
         # If OOMMFRunner was not returned up to this point, we raise an
         # exception.
-        raise EnvironmentError("Cannot find OOMMF.")
+        raise OSError("Cannot find OOMMF.")
 
     def __repr__(self):
         # avoid selecting a runner when calling __repr__
@@ -600,22 +600,21 @@ def overhead():
     True
 
     """
-    with tempfile.TemporaryDirectory() as workingdir:
-        with uu.changedir(workingdir):
-            # Running OOMMF through oommfc.
-            system = mm.examples.macrospin()
-            td = oc.TimeDriver()
-            oommfc_start = time.time()
-            td.drive(system, t=1e-12, n=1)
-            oommfc_stop = time.time()
-            oommfc_time = oommfc_stop - oommfc_start
-
-            # Running OOMMF directly.
-            oommf_runner = oc.runner.runner
-            mifpath = pathlib.Path(f"{system.name}/drive-0/macrospin.mif").resolve()
-            oommf_start = time.time()
-            oommf_runner.call(str(mifpath))
-            oommf_stop = time.time()
-            oommf_time = oommf_stop - oommf_start
+    with tempfile.TemporaryDirectory() as workingdir, uu.changedir(workingdir):
+        # Running OOMMF through oommfc.
+        system = mm.examples.macrospin()
+        td = oc.TimeDriver()
+        oommfc_start = time.time()
+        td.drive(system, t=1e-12, n=1)
+        oommfc_stop = time.time()
+        oommfc_time = oommfc_stop - oommfc_start
+
+        # Running OOMMF directly.
+        oommf_runner = oc.runner.runner
+        mifpath = pathlib.Path(f"{system.name}/drive-0/macrospin.mif").resolve()
+        oommf_start = time.time()
+        oommf_runner.call(str(mifpath))
+        oommf_stop = time.time()
+        oommf_time = oommf_stop - oommf_start
 
     return oommfc_time - oommf_time

oommfc/scripts/driver.py

@@ -75,10 +75,7 @@ def driver_script(
             driver.evolver.fixed_spins = resstr
 
         # What is saved in output?
-        if output_step:
-            output_str = "Step"
-        else:
-            output_str = "Stage"
+        output_str = "Step" if output_step else "Stage"
 
         mif += oc.scripts.evolver_script(driver.evolver)
 

oommfc/scripts/energy.py

@@ -1,3 +1,4 @@
+import contextlib
 import numbers
 import warnings
 
@@ -22,10 +23,7 @@ def exchange_script(term, system):
         mif += "}\n\n"
 
     elif isinstance(term.A, dict):
-        if "default" in term.A.keys():
-            default_value = term.A["default"]
-        else:
-            default_value = 0
+        default_value = term.A.get("default", 0)
         mif = "# Exchange6Ngbr\n"
         mif += f"Specify Oxs_Exchange6Ngbr:{term.name} {{\n"
         mif += f"  default_A {default_value}\n"
@@ -61,7 +59,9 @@ def zeeman_script(term, system):
     if isinstance(term.wave, str) or isinstance(term.func, str):
         if isinstance(term.wave, str):
             warnings.warn(
-                "Parameter `wave` is deprecated; use `func` instead.", FutureWarning
+                "Parameter `wave` is deprecated; use `func` instead.",
+                FutureWarning,
+                stacklevel=2,
             )
         if isinstance(term.H, (df.Field, dict)):
             if term.wave == "sin" or term.func == "sin":
@@ -220,10 +220,8 @@ def zeeman_script(term, system):
         mif += f'Specify {term.tcl_strings["energy"]}:{term.name} {{\n'
         mif += f'  script {term.tcl_strings["script_name"]}\n'
         for key in ["type", "script_args"]:
-            try:
+            with contextlib.suppress(KeyError):
                 mif += f"  {key} {term.tcl_strings[key]}\n"
-            except KeyError:
-                pass
         if term.tcl_strings["energy"] == "Oxs_TransformZeeman":
             mif += f"  field {Hname}\n"
         mif += "}\n\n"
@@ -264,14 +262,16 @@ def dmi_script(term, system):
     elif (tcc := term.crystalclass) in ["D2d_x", "D2d_y", "D2d_z", "D2d"]:
         if tcc == "D2d":
             warnings.warn(
-                "Use of `D2d` is deprecated; use `D2d_z` instead.", FutureWarning
+                "Use of `D2d` is deprecated; use `D2d_z` instead.",
+                FutureWarning,
+                stacklevel=2,
             )
             tcc = "D2d_z"
         oxs = f"Oxs_DMI_{tcc}"
     elif (tcc := term.crystalclass) in ["Cnv_x", "Cnv_y", "Cnv_z", "Cnv"]:
         if tcc == "Cnv":
             msg = "Use of `Cnv` is deprecated; use `Cnv_z` instead."
-            warnings.warn(msg, FutureWarning)
+            warnings.warn(msg, FutureWarning, stacklevel=2)
             tcc = "Cnv_z"
         oxs = f"Oxs_DMI_{tcc}"
 
@@ -290,10 +290,7 @@ def dmi_script(term, system):
         mif += "}\n\n"
 
     elif isinstance(term.D, dict):
-        if "default" in term.D.keys():
-            default_value = term.D["default"]
-        else:
-            default_value = 0
+        default_value = term.D.get("default", 0)
         mif += f"  default_D {default_value}\n"
         mif += "  atlas :main_atlas\n"
         mif += "  D {\n"

oommfc/scripts/evolver.py

@@ -70,20 +70,20 @@ def evolver_script(evolver, **kwargs):
         mif += "}\n\n"
 
         if isinstance(evolver, (oc.SpinXferEvolver, oc.Xf_ThermSpinXferEvolver)):
-            setattr(evolver, "J_profile", "TimeFunction")
-            setattr(evolver, "J_profile_args", "total_time")
+            evolver.J_profile = "TimeFunction"
+            evolver.J_profile_args = "total_time"
         elif isinstance(evolver, oc.SpinTEvolver):
-            setattr(evolver, "u_profile", "TimeFunction")
-            setattr(evolver, "u_profile_args", "total_time")
+            evolver.u_profile = "TimeFunction"
+            evolver.u_profile_args = "total_time"
     if hasattr(evolver, "tcl_strings") and isinstance(evolver.tcl_strings, dict):
         print(evolver.tcl_strings)
         mif += evolver.tcl_strings["script"]
         if isinstance(evolver, (oc.SpinXferEvolver, oc.Xf_ThermSpinXferEvolver)):
-            setattr(evolver, "J_profile", evolver.tcl_strings["script_name"])
-            setattr(evolver, "J_profile_args", evolver.tcl_strings["script_args"])
+            evolver.J_profile = evolver.tcl_strings["script_name"]
+            evolver.J_profile_args = evolver.tcl_strings["script_args"]
         elif isinstance(evolver, oc.SpinTEvolver):
-            setattr(evolver, "u_profile", evolver.tcl_strings["script_name"])
-            setattr(evolver, "u_profile_args", evolver.tcl_strings["script_args"])
+            evolver.u_profile = evolver.tcl_strings["script_name"]
+            evolver.u_profile_args = evolver.tcl_strings["script_args"]
 
     # temperature cannot spacially vary
 

oommfc/scripts/mesh.py

@@ -12,7 +12,7 @@ def mesh_script(mesh):
         mif += oc.scripts.box_atlas(mesh.region.pmin, mesh.region.pmax, name="entire")
         mif += "# MultiAtlas\n"
         mif += "Specify Oxs_MultiAtlas:main_atlas {\n"
-        for name in mesh.subregions.keys():
+        for name in mesh.subregions:
             mif += f"  atlas :{name}_atlas\n"
         mif += "  atlas :entire_atlas\n"
         mif += f"  xrange {{ {mesh.region.pmin[0]} {mesh.region.pmax[0]} }}\n"

oommfc/scripts/util.py

@@ -86,7 +86,7 @@ def setup_scalar_parameter(parameter, name):
         # to avoid changing the dictionary used in the respective term
         # in the system (from micromagneticmodel)
         param = parameter.copy()
-        if "default" not in param.keys():
+        if "default" not in param:
             param["default"] = 0
         mif = atlas_scalar_field(param, f"{name}")
         return mif, f"{name}"
@@ -102,7 +102,7 @@ def setup_vector_parameter(parameter, name):
         return mif, f"{name}"
 
     elif isinstance(parameter, dict):
-        if "default" not in parameter.keys():
+        if "default" not in parameter:
             parameter["default"] = (0, 0, 0)
         mif = atlas_vector_field(parameter, f"{name}")
         return mif, f"{name}"

oommfc/tests/test_oommf.py

@@ -27,9 +27,7 @@ def check_runner(runner):
 
     # Cleanup created files.
     for f in os.listdir(dirname):
-        if f.endswith(".odt"):
-            os.remove(os.path.join(dirname, f))
-        elif f.endswith(".omf") and f.startswith("test_oommf-Oxs"):
+        if f.endswith(".odt") or f.endswith(".omf") and f.startswith("test_oommf-Oxs"):
             os.remove(os.path.join(dirname, f))
 
 
@@ -120,7 +118,7 @@ def test_missing_oommf():
     oc.runner.oommf_exe = "wrong_name"
     oc.runner.docker_exe = "wrong_name"
     with pytest.raises(EnvironmentError):
-        oc.runner.runner
+        oc.runner.runner  # noqa: B018
 
 
 def test_get_cached_runner(reset_runner, monkeypatch):
@@ -138,7 +136,7 @@ def test_get_cached_runner(reset_runner, monkeypatch):
     oc.runner.cache_runner = False
     oc.runner.docker_exe = "wrong_name"  # ensure that we do not find docker
     with pytest.raises(EnvironmentError):
-        oc.runner.runner
+        oc.runner.runner  # noqa: B018
 
     oc.runner.envvar = "OOMMFTCL"
     if oommf_tcl_path():

pyproject.toml

@@ -61,15 +61,49 @@ repository = "https://github.com/ubermag/oommfc"
 
 
 
-[tool.black]
-experimental-string-processing = true
 
 [tool.coverage.run]
 omit = ["oommfc/tests/*"]
 
-[tool.isort]
-profile = "black"
-skip_gitignore = true  # ignores files listed in .gitignore
+[tool.ruff.lint]
+ignore-init-module-imports = true  # do not remove unused imports in __init__ and warn instead
+select = [
+    "B",   # flake8-bugbear
+    "E",   # pycodestyle
+    "F",   # Pyflakes
+    "I",   # isort
+    "SIM", # flake8-simplify
+    "UP",  # pyupgrade
+]
+ignore = [
+    # conflict with other rules
+    "D203",  # one-blank-line-before-class (conflicts with D204)
+    "D212",  # multi-line-summary-first-line (conflicts with D213)
+    # conflict with formatter
+    "D206",  # indent-with-spaces
+    "D300",  # triple-single-quotes
+    "E111",  # indentation-with-invalid-multiple
+    "E114",  # indentation-with-invalid-multiple-comment
+    "E117",  # over-indented
+    # conflict with Python 3.6 compatibility
+    "UP022", # replace-stdout-stderr
+]
+
+[tool.ruff.lint.isort]
+known-local-folder = ["oommfc"]
+
+[tool.ruff.lint.per-file-ignores]
+"*.ipynb" = [
+    "B018",  # "Found useless expression. Either assign it to a variable or remove it."; false positives when using implicit __repr__ in the notebook
+    "E501",  # line too long
+    "F811",  # 'redefined-while-unused'; many false positives in notebooks because ipywidgets decorated functions are not recognised
+]
+
+[tool.pytest.ini_options]
+filterwarnings = [
+    "error",
+    "ignore:((.|\n)*)Sentinel is not a public part of the traitlets API((.|\n)*)",  # dependency of k3d
+]
 
 [tool.setuptools.packages.find]
 include = ["oommfc*"]