Merge pull request #86 from ubermag/precommit_updates

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: 'mumax3c/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

docs/tutorial-standard-problem3.ipynb

@@ -56,7 +56,7 @@
     "\n",
     "# Function for initiaising the flower state.\n",
     "def m_init_flower(pos):\n",
-    "    x, y, z = pos[0] / 1e-9, pos[1] / 1e-9, pos[2] / 1e-9\n",
+    "    _x, y, z = pos[0] / 1e-9, pos[1] / 1e-9, pos[2] / 1e-9\n",
     "    mx = 0\n",
     "    my = 2 * z - 1\n",
     "    mz = -2 * y + 1\n",
@@ -69,7 +69,7 @@
     "\n",
     "# Function for initialising the vortex state.\n",
     "def m_init_vortex(pos):\n",
-    "    x, y, z = pos[0] / 1e-9, pos[1] / 1e-9, pos[2] / 1e-9\n",
+    "    x, _y, _z = pos[0] / 1e-9, pos[1] / 1e-9, pos[2] / 1e-9\n",
     "    mx = 0\n",
     "    my = np.sin(np.pi / 2 * (x - 0.5))\n",
     "    mz = np.cos(np.pi / 2 * (x - 0.5))\n",
@@ -98,7 +98,7 @@
    "outputs": [],
    "source": [
     "def minimise_system_energy(L, m_init):\n",
-    "    print(\"L={:9}, {} \".format(L, m_init.__name__), end=\"\")\n",
+    "    print(f\"L={L:9}, {m_init.__name__} \", end=\"\")\n",
     "    N = 16  # discretisation in one dimension\n",
     "    cubesize = 100e-9  # cube edge length (m)\n",
     "    cellsize = cubesize / N  # discretisation in all three dimensions.\n",
@@ -116,9 +116,9 @@
     "    p2 = (cubesize, cubesize, cubesize)  # Maximum sample coordinate.\n",
     "    cell = (cellsize, cellsize, cellsize)  # Discretisation.\n",
     "    mesh = df.Mesh(\n",
-    "        p1=(0, 0, 0),\n",
-    "        p2=(cubesize, cubesize, cubesize),\n",
-    "        cell=(cellsize, cellsize, cellsize),\n",
+    "        p1=p1,\n",
+    "        p2=p2,\n",
+    "        cell=cell,\n",
     "    )  # Create a mesh object.\n",
     "\n",
     "    system = mm.System(name=\"stdprob3\")\n",
@@ -274,6 +274,8 @@
     }
    ],
    "source": [
+    "import matplotlib.pyplot as plt\n",
+    "\n",
     "L_array = np.linspace(8, 9, 5)  # values of L for which the system is relaxed.\n",
     "\n",
     "vortex_energies = []\n",
@@ -287,8 +289,6 @@
     "    flower_energies.append(flower.table.data.tail(1)[\"E\"][0])\n",
     "\n",
     "# Plot the energy dependences.\n",
-    "import matplotlib.pyplot as plt\n",
-    "\n",
     "plt.plot(L_array, vortex_energies, \"o-\", label=\"vortex\")\n",
     "plt.plot(L_array, flower_energies, \"o-\", label=\"flower\")\n",
     "plt.xlabel(\"L (lex)\")\n",

docs/tutorial-standard-problem4.ipynb

@@ -416,12 +416,10 @@
     }
    ],
    "source": [
-    "print(\"The average magnetisation is {}.\".format(system.m.mean()))\n",
+    "print(f\"The average magnetisation is {system.m.mean()}.\")\n",
     "\n",
     "print(\n",
-    "    \"The magnetisation at the mesh centre {}\\nis {}.\".format(\n",
-    "        system.m.mesh.region.center, system.m(system.m.mesh.region.center)\n",
-    "    )\n",
+    "    f\"The magnetisation at the mesh centre {system.m.mesh.region.center}\\nis {system.m(system.m.mesh.region.center)}.\"\n",
     ")"
    ]
   },
@@ -774,7 +772,7 @@
         -580.7774351392527,
         44.368495675080865,
         249.74999939091504,
-        62.249999986961484,
+        62.24999998696149,
         1.5,
         0,
         0,

docs/tutorial-standard-problem5.ipynb

@@ -185,7 +185,7 @@
    ],
    "source": [
     "def m_vortex(pos):\n",
-    "    x, y, z = pos[0] / 1e-9 - 50, pos[1] / 1e-9 - 50, pos[2] / 1e-9\n",
+    "    x, y, _z = pos[0] / 1e-9 - 50, pos[1] / 1e-9 - 50, pos[2] / 1e-9\n",
     "\n",
     "    return (-y, x, 10)\n",
     "\n",

mumax3c/__init__.py

@@ -1,4 +1,5 @@
 """Mumax3 calculator."""
+
 import importlib.metadata
 
 import pytest
@@ -7,8 +8,10 @@
 import mumax3c.scripts
 
 # from .compute import compute  # compute is not yet supported
-from .delete import delete
-from .drivers import MinDriver, RelaxDriver, TimeDriver
+from .delete import delete as delete
+from .drivers import MinDriver as MinDriver
+from .drivers import RelaxDriver as RelaxDriver
+from .drivers import TimeDriver as TimeDriver
 
 runner = mumax3c.mumax3.Runner()
 """Controls the default runner.

mumax3c/drivers/__init__.py

@@ -1,4 +1,4 @@
-from .driver import Driver
-from .mindriver import MinDriver
-from .relaxdriver import RelaxDriver
-from .timedriver import TimeDriver
+from .driver import Driver as Driver
+from .mindriver import MinDriver as MinDriver
+from .relaxdriver import RelaxDriver as RelaxDriver
+from .timedriver import TimeDriver as TimeDriver

mumax3c/drivers/driver.py

@@ -127,7 +127,7 @@ def write_mx3(self, system, dirname=".", ovf_format="bin8", abspath=True, **kwar
                 ovf_format=ovf_format,
                 **kwargs,
             )
-            with open(self._mx3filename(system), "wt", encoding="utf-8") as mx3file:
+            with open(self._mx3filename(system), "w", encoding="utf-8") as mx3file:
                 mx3file.write(mx3)
 
             # Generate and save json info file for a drive (not compute).

mumax3c/mumax3/__init__.py

@@ -1 +1,4 @@
-from .mumax3 import ExeMumax3Runner, Mumax3Runner, Runner, overhead
+from .mumax3 import ExeMumax3Runner as ExeMumax3Runner
+from .mumax3 import Mumax3Runner as Mumax3Runner
+from .mumax3 import Runner as Runner
+from .mumax3 import overhead as overhead

mumax3c/mumax3/mumax3.py

@@ -56,7 +56,7 @@ def status(self):
             td.drive(system, t=1e-12, n=1, runner=self)
             print("mumax3 found and running.")
             return 0
-        except (EnvironmentError, RuntimeError):
+        except (OSError, RuntimeError):
             print("Cannot find mumax3.")
             return 1
 
@@ -210,7 +210,7 @@ def autoselect_runner(self):
                 " Ubermag. Make sure it is properly installed and can be found on the"
                 " command line."
             )
-            raise EnvironmentError(msg)
+            raise OSError(msg)
 
 
 def overhead():
@@ -235,22 +235,21 @@ def overhead():
     True
 
     """
-    with tempfile.TemporaryDirectory() as workingdir:
-        with uu.changedir(workingdir):
-            # Running mumax3 through mumax3c.
-            system = mm.examples.macrospin()
-            td = mc.TimeDriver()
-            mumax3c_start = time.time()
-            td.drive(system, t=1e-12, n=1)
-            mumax3c_stop = time.time()
-            mumax3c_time = mumax3c_stop - mumax3c_start
-
-            # Running mumax3 directly.
-            mumax3_runner = mc.runner.runner
-            mx3path = pathlib.Path(f"{system.name}/drive-0/macrospin.mx3").resolve()
-            mumax3_start = time.time()
-            mumax3_runner.call(str(mx3path))
-            mumax3_stop = time.time()
-            mumax3_time = mumax3_stop - mumax3_start
+    with tempfile.TemporaryDirectory() as workingdir, uu.changedir(workingdir):
+        # Running mumax3 through mumax3c.
+        system = mm.examples.macrospin()
+        td = mc.TimeDriver()
+        mumax3c_start = time.time()
+        td.drive(system, t=1e-12, n=1)
+        mumax3c_stop = time.time()
+        mumax3c_time = mumax3c_stop - mumax3c_start
+
+        # Running mumax3 directly.
+        mumax3_runner = mc.runner.runner
+        mx3path = pathlib.Path(f"{system.name}/drive-0/macrospin.mx3").resolve()
+        mumax3_start = time.time()
+        mumax3_runner.call(str(mx3path))
+        mumax3_stop = time.time()
+        mumax3_time = mumax3_stop - mumax3_start
 
     return mumax3c_time - mumax3_time

mumax3c/scripts/__init__.py

@@ -1,6 +1,7 @@
-from .driver import driver_script
-from .energy import energy_script
-from .magnetisation import magnetisation_script
-from .mesh import mesh_script
-from .system import system_script
-from .util import mumax3_regions, set_parameter
+from .driver import driver_script as driver_script
+from .energy import energy_script as energy_script
+from .magnetisation import magnetisation_script as magnetisation_script
+from .mesh import mesh_script as mesh_script
+from .system import system_script as system_script
+from .util import mumax3_regions as mumax3_regions
+from .util import set_parameter as set_parameter

mumax3c/scripts/util.py

@@ -55,9 +55,9 @@ def mumax3_regions(system, ovf_format="bin4", abspath=True):
                 continue
             unique_index += 1
             mx3 += f"Msat.setregion({unique_index}, {ms})\n"
-            region_indices[
-                (sr_indices == sr_index) & np.isclose(Ms_array, ms)
-            ] = unique_index
+            region_indices[(sr_indices == sr_index) & np.isclose(Ms_array, ms)] = (
+                unique_index
+            )
             region_relator[sr_name].append(unique_index)
 
     if unique_index > max_index:

mumax3c/tests/conftest.py

@@ -8,6 +8,7 @@
     "TestExchange.test_field",
     "test_simple_hysteresis_loop",
     "test_stepped_hysteresis_loop",
+    "test_hysteresis_check_for_energy",
     "TestMinDriver.test_evolver_nodriver",
     "TestMinDriver.test_evolver_driver",
     "TestMinDriver.test_wrong_evolver",

pyproject.toml

@@ -26,7 +26,7 @@ authors = [
 ]
 
 classifiers = [
-    "Development Status :: 4 - Beta",
+    "Development Status :: 5 - Production/Stable",
     "Intended Audience :: Education",
     "Intended Audience :: Developers",
     "Intended Audience :: Science/Research",
@@ -66,15 +66,49 @@ repository = "https://github.com/ubermag/mumax3c"
 
 
 
-[tool.black]
-experimental-string-processing = true
 
 [tool.coverage.run]
 omit = ["mumax3c/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 = ["mumax3c"]
+
+[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 = ["mumax3c*"]

setup.cfg

@@ -1,30 +1,2 @@
-[flake8]
-exclude =
-  .git,
-  __pycache__,
-  build,
-  dev,
-  dist,
-  setup.py
-# black has a longer default line length
-max-line-length = 88
-# D107: missing docstring in __init__
-# E203: withespace before ':', required for black
-# RST210: Inline strong start-string without end-string.  # complains about "**kwargs" in docstrings
-extend-ignore = D107,RST210,E203
-per-file-ignores =
-  # imported but unused
-  __init__.py: F401
-  # ignore missing docstrings in tests
-  test_*.py: D100,D101,D102,D103
-docstring-convention: numpy
-# flake8-rst-docstrings:
-rst-roles =
-  py:class,
-  py:func,
-rst-directives =
-  seealso,
-  plot,
-
 [codespell]
 skip = .*,build/*,dev/*,dist/*

tasks.py

@@ -1,4 +1,5 @@
 """Tasks to release the package."""
+
 import os
 import shutil