Add pre-commit workflow including ruff

.github/workflows/pre-commit.yml

@@ -0,0 +1,21 @@
+name: Pre-Commit
+
+on:
+  pull_request:
+
+jobs:
+  pre-commit:
+    name: Pre-commit
+    runs-on: ubuntu-latest
+    container:
+      image: ghcr.io/ptb-mr/mrpro_py311:latest
+      options: --user runner
+    steps:
+      - uses: actions/checkout@v4
+      - uses: pre-commit/[email protected]
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
+
+  # Cancel in-progress runs when a new workflow with the same group name is triggered
+  cancel-in-progress: true

.gitignore

@@ -108,3 +108,6 @@ venv.bak/
 
 # PyCharm config folder
 \.idea/
+
+# VS Code config folder
+\.vscode/

.pre-commit-config.yaml

@@ -0,0 +1,28 @@
+default_language_version:
+  python: python3
+
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.6.0
+    hooks:
+      - id: check-added-large-files
+      # - id: check-docstring-first
+      - id: check-merge-conflict
+      - id: check-yaml
+      - id: check-toml
+      - id: check-json
+        exclude: ^.vscode/
+      - id: mixed-line-ending
+
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.6.9
+    hooks:
+      - id: ruff # linter
+        args: [--fix]
+      - id: ruff-format # formatter
+
+  - repo: https://github.com/crate-ci/typos
+    rev: v1.25.0
+    hooks:
+      - id: typos
+        exclude: ^pypulseq/seq_examples/|paper.md

doc/source/conf.py

@@ -12,6 +12,7 @@
 #
 import os
 import sys
+
 sys.path.insert(0, os.path.abspath('../../'))
 
 
@@ -30,9 +31,7 @@
 # Add any Sphinx extension module names here, as strings. They can be
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
-extensions = [
-'sphinx.ext.autodoc', 'sphinx.ext.napoleon', 'recommonmark'
-]
+extensions = ['sphinx.ext.autodoc', 'sphinx.ext.napoleon', 'recommonmark']
 
 source_suffix = {
     '.rst': 'restructuredtext',

doc/walkthrough/gre_walkthrough.ipynb

@@ -48,18 +48,25 @@
    "outputs": [],
    "source": [
     "seq = Sequence()\n",
-    "fov = 256e-3 # field of view\n",
-    "Nx = 256 # number of frequency encodes\n",
-    "Ny = 256 # number of phase encodes\n",
-    "alpha = 10 # RF flip\n",
+    "fov = 256e-3  # field of view\n",
+    "Nx = 256  # number of frequency encodes\n",
+    "Ny = 256  # number of phase encodes\n",
+    "alpha = 10  # RF flip\n",
     "slice_thickness = 3e-3\n",
-    "TE = 7.38e-3 # echo time\n",
-    "TR = 100e-3 # repetition time\n",
+    "TE = 7.38e-3  # echo time\n",
+    "TR = 100e-3  # repetition time\n",
     "\n",
     "rf_spoiling_inc = 117\n",
     "\n",
-    "sys = Opts(max_grad=28, grad_unit='mT/m', max_slew=150, slew_unit='T/m/s', rf_ringdown_time=20e-6, rf_dead_time=100e-6,\n",
-    "           adc_dead_time=10e-6)"
+    "sys = Opts(\n",
+    "    max_grad=28,\n",
+    "    grad_unit='mT/m',\n",
+    "    max_slew=150,\n",
+    "    slew_unit='T/m/s',\n",
+    "    rf_ringdown_time=20e-6,\n",
+    "    rf_dead_time=100e-6,\n",
+    "    adc_dead_time=10e-6,\n",
+    ")"
    ]
   },
   {
@@ -88,23 +95,36 @@
     }
    ],
    "source": [
-    "rf, gz, gzr = make_sinc_pulse(flip_angle=alpha * math.pi / 180, duration=4e-3, slice_thickness=slice_thickness,\n",
-    "                              apodization=0.5, time_bw_product=4, system=sys, return_gz=True)\n",
+    "rf, gz, gzr = make_sinc_pulse(\n",
+    "    flip_angle=alpha * math.pi / 180,\n",
+    "    duration=4e-3,\n",
+    "    slice_thickness=slice_thickness,\n",
+    "    apodization=0.5,\n",
+    "    time_bw_product=4,\n",
+    "    system=sys,\n",
+    "    return_gz=True,\n",
+    ")\n",
     "\n",
     "delta_k = 1 / fov\n",
     "gx = make_trapezoid(channel='x', flat_area=Nx * delta_k, flat_time=6.4e-3, system=sys)\n",
     "adc = make_adc(num_samples=Nx, duration=gx.flat_time, delay=gx.rise_time, system=sys)\n",
     "gx_pre = make_trapezoid(channel='x', area=-gx.area / 2, duration=2e-3, system=sys)\n",
     "gz_reph = make_trapezoid(channel='z', area=-gz.area / 2, duration=2e-3, system=sys)\n",
-    "phase_areas = (np.arange(Ny) - Ny / 2) * delta_k\n",
+    "phase_areas = (np.arrange(Ny) - Ny / 2) * delta_k\n",
     "\n",
     "gx_spoil = make_trapezoid(channel='x', area=2 * Nx * delta_k, system=sys)\n",
     "gz_spoil = make_trapezoid(channel='z', area=4 / slice_thickness, system=sys)\n",
     "\n",
-    "delay_TE = math.ceil((TE - calc_duration(gx_pre) - gz.fall_time - gz.flat_time / 2 - calc_duration(\n",
-    "    gx) / 2) / seq.grad_raster_time) * seq.grad_raster_time\n",
-    "delay_TR = math.ceil((TR - calc_duration(gx_pre) - calc_duration(gz) - calc_duration(\n",
-    "    gx) - delay_TE) / seq.grad_raster_time) * seq.grad_raster_time\n",
+    "delay_TE = (\n",
+    "    math.ceil(\n",
+    "        (TE - calc_duration(gx_pre) - gz.fall_time - gz.flat_time / 2 - calc_duration(gx) / 2) / seq.grad_raster_time\n",
+    "    )\n",
+    "    * seq.grad_raster_time\n",
+    ")\n",
+    "delay_TR = (\n",
+    "    math.ceil((TR - calc_duration(gx_pre) - calc_duration(gz) - calc_duration(gx) - delay_TE) / seq.grad_raster_time)\n",
+    "    * seq.grad_raster_time\n",
+    ")\n",
     "\n",
     "assert np.all(delay_TR >= calc_duration(gx_spoil, gz_spoil))"
    ]
@@ -128,7 +148,7 @@
     "rf_phase = 0\n",
     "rf_inc = 0\n",
     "\n",
-    "for i in range(Ny): # We have Ny phase encodes\n",
+    "for i in range(Ny):  # We have Ny phase encodes\n",
     "    rf.phase_offset = rf_phase / 180 * np.pi\n",
     "    adc.phase_offset = rf_phase / 180 * np.pi\n",
     "    rf_inc = divmod(rf_inc + rf_spoiling_inc, 360.0)[1]\n",
@@ -148,7 +168,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "5. Visualise the constructed pulse sequence by calling the `plot()` command. The `plot()` command visualises the ADC and RF events in one window, and the gradient events in another window. For GRE, the `plot()` command should display two plots that look like this:\n",
+    "5. Visualize the constructed pulse sequence by calling the `plot()` command. The `plot()` command visualizes the ADC and RF events in one window, and the gradient events in another window. For GRE, the `plot()` command should display two plots that look like this:\n",
     "\n",
     "![GRE Plot 1](./gre_1.png)\n",
     "![GRE Plot 2](./gre_2.png)"

pyproject.toml

@@ -28,7 +28,7 @@ dependencies = [
 
 [project.optional-dependencies]
 sigpy = ["sigpy>=0.1.26"]
-test = ["pytest"]
+test = ["pytest", "pre-commit"]
 
 [project.urls]
 Homepage = "https://github.com/imr-framework/pypulseq"
@@ -41,6 +41,79 @@ SAR = ["QGlobal.mat"]
 [tool.setuptools.dynamic]
 version = { attr = "version.__version__" }
 
+[tool.ruff]
+line-length = 120
+extend-exclude = ["__init__.py"]
+exclude = ["doc/**", "pypulseq/seq_examples/**"]
+
+# RUFF section
+[tool.ruff.lint]
+select = [
+  "A",   # flake8-builtins
+  "ARG", # flake8-unused-arguments
+  "B",   # flake8-bugbear
+  "C4",  # flake8-comprehensions
+  "COM", # flake8-commas
+  # "D",   # pydocstyle
+  # "E",   # pycodestyle errors
+  "F", # Pyflakes
+  # "FA", # flake8-future-annotations
+  "I", # isort
+  # "N",   # pep8-naming
+  "NPY", # NumPy-specific rules
+  "RUF", # Ruff-specific rules
+  "S",   # flake8-bandit
+  "SIM", # flake8-simplify
+  # "UP",  # pyupgrade
+  "PIE", # flake8-pie
+  "PTH", # flake8-use-pathlib
+  "Q",   # flake8-quotes
+  "W",   # pycodestyle warnings
+  "YTT", # flake8-2020
+  # "ERA", # flake8-eradicate
+]
+
+extend-select = [
+  # "ANN001", #  type annotation for function argument
+  # # "ANN201", #  return type annonation public function
+  # # "ANN205", #  return type annonation static method
+  # # "ANN401", #  any type annotation
+  # # "BLE001", #  blind exception
+  # # "D107",   #  missing docstring in __init__
+  # # "D417",   #  undocumented-parameter
+]
+
+ignore = [
+  "B028",   #  explicit "stacklevel" arg in warnings
+  "COM812", #  missing-trailing-comma (conflict with formatter)
+  "PTH123", #  use of Path.open
+  "S101",   #  use of assert
+  "S307",   #  use of possibly insecure eval function
+  "S311",   #  standard pseudo-random generators
+  "S324",   #  insecure hash function
+  "SIM108", #  if-else-block-instead-of-if-exp
+  "SIM115", #  use of context manager
+]
+
+[tool.ruff.lint.isort]
+force-single-line = false
+split-on-trailing-comma = false
+
+[tool.ruff.lint.flake8-quotes]
+docstring-quotes = "double"
+inline-quotes = "single"
+
+[tool.ruff.lint.pydocstyle]
+convention = "numpy"
+
+[tool.ruff.format]
+quote-style = "single"
+skip-magic-trailing-comma = false
+
+[tool.typos.default]
+locale = "en-us"
+exclude = ["pypulseq/seq_examples/**"]
+
 # PyTest section
 [tool.pytest.ini_options]
 testpaths = ["pypulseq/tests"]