Merge pull request #134 from DCC-Lab/jlb/linting

Lint project and add check to CI

Author: PyMarc2

.github/workflows/lint.yaml

@@ -0,0 +1,24 @@
+name: Lint
+
+on: [ pull_request, workflow_dispatch ]
+
+jobs:
+  lint:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4
+
+      - name: Set up Python 3.11
+        uses: actions/setup-python@v5
+        with:
+          python-version: 3.11
+
+      - name: Install Ruff
+        run: |
+          python -m pip install --upgrade pip
+          pip install ruff
+
+      - name: Lint check
+        run: ruff check pytissueoptics

pyproject.toml

@@ -59,7 +59,10 @@ line-length = 120
 target-version = "py39"
 
 [tool.ruff.lint]
-select = ["ALL"]
+ignore = [
+  "PT009",  # unittest-style asserts
+  "F405",  # Name defined from star imports
+]
 
 [tool.ruff.format]
 quote-style = "double"

pytissueoptics/__init__.py

@@ -1,5 +1,5 @@
-from .scene import *
-from .rayscattering import *
 from importlib.metadata import version
+from .scene import *  # noqa: F403
+from .rayscattering import *  # noqa: F403
 
 __version__ = version("pytissueoptics")

pytissueoptics/__main__.py

@@ -1,14 +1,15 @@
+import argparse
 import os
 import sys
-import argparse
 
 from pytissueoptics import __version__
 from pytissueoptics.examples import loadExamples
 
 ap = argparse.ArgumentParser(prog="python -m pytissueoptics", description="Run PyTissueOptics examples. ")
 ap.add_argument("-v", "--version", action="version", version=f"PyTissueOptics {__version__}")
-ap.add_argument("-e", "--examples", required=False, default="all",
-                help="Run specific examples by number, e.g. -e 1,2,3. ")
+ap.add_argument(
+    "-e", "--examples", required=False, default="all", help="Run specific examples by number, e.g. -e 1,2,3. "
+)
 ap.add_argument("-l", "--list", required=False, action="store_true", help="List available examples. ")
 ap.add_argument("-t", "--tests", required=False, action="store_true", help="Run unit tests. ")
 

pytissueoptics/examples/__init__.py

@@ -1,13 +1,13 @@
+import importlib
 import os
 import re
 import sys
-import importlib
 from dataclasses import dataclass
 from typing import List
 
 from pygments import highlight
-from pygments.lexers import PythonLexer
 from pygments.formatters import TerminalFormatter
+from pygments.lexers import PythonLexer
 
 EXAMPLE_MODULE = "rayscattering"
 EXAMPLE_FILE_PATTERN = r"^(ex\d+)\.py$"
@@ -32,7 +32,7 @@ def loadExamples() -> List[Example]:
     for file in EXAMPLE_FILES:
         name = re.match(EXAMPLE_FILE_PATTERN, file).group(1)
         module = importlib.import_module(f"pytissueoptics.examples.{EXAMPLE_MODULE}.{name}")
-        with open(os.path.join(EXAMPLE_DIR, file), 'r') as f:
+        with open(os.path.join(EXAMPLE_DIR, file), "r") as f:
             srcCode = f.read()
         pattern = r"def exampleCode\(\):\s*(.*?)\s*if __name__ == \"__main__\":"
         srcCode = re.search(pattern, srcCode, re.DOTALL).group(1)

pytissueoptics/examples/benchmarks/cube60.py

@@ -1,5 +1,5 @@
-import env
-from pytissueoptics import *
+import env  # noqa: F401
+from pytissueoptics import *  # noqa: F403
 
 TITLE = "MCX Homogeneous cube"
 

pytissueoptics/examples/benchmarks/cubesph60b.py

@@ -1,5 +1,5 @@
-import env
-from pytissueoptics import *
+import env  # noqa: F401
+from pytissueoptics import *  # noqa: F403
 
 TITLE = "MCX Sphere"
 

pytissueoptics/examples/benchmarks/env.py

@@ -1,11 +1,7 @@
 # We set up the environment so we do not have to install PyTissueOptics to run the examples.
 # By adjusting the path, we use the current version in development.
 
-import sys
 import os
-sys.path.insert(0,
-                os.path.dirname(
-                    os.path.dirname(
-                        os.path.dirname(
-                            os.path.dirname(
-                                os.path.abspath(__file__))))))
+import sys
+
+sys.path.insert(0, os.path.dirname(os.path.dirname(os.path.dirname(os.path.dirname(os.path.abspath(__file__))))))

pytissueoptics/examples/benchmarks/skinvessel.py

@@ -1,5 +1,5 @@
-import env
-from pytissueoptics import *
+import env  # noqa: F401
+from pytissueoptics import *  # noqa: F403
 
 TITLE = "Skin vessel"
 
@@ -13,15 +13,23 @@ def exampleCode():
 
     # Units in mm and mm-1
     waterLayer = Cuboid(1, 0.1, 1, material=ScatteringMaterial(mu_a=0.00004, mu_s=1, g=1, n=1.33), label="water")
-    epidermisLayer = Cuboid(1, 0.06, 1, material=ScatteringMaterial(mu_a=1.65724, mu_s=37.59398, g=0.9, n=1.44), label="epidermis")
-    dermisLayer = Cuboid(1, 0.84, 1, material=ScatteringMaterial(mu_a=0.04585, mu_s=35.65406, g=0.9, n=1.38), label="dermis")
+    epidermisLayer = Cuboid(
+        1, 0.06, 1, material=ScatteringMaterial(mu_a=1.65724, mu_s=37.59398, g=0.9, n=1.44), label="epidermis"
+    )
+    dermisLayer = Cuboid(
+        1, 0.84, 1, material=ScatteringMaterial(mu_a=0.04585, mu_s=35.65406, g=0.9, n=1.38), label="dermis"
+    )
     zStack = waterLayer.stack(epidermisLayer).stack(dermisLayer)
     zStack.translateTo(Vector(0, 0, 0))
-    bloodVessel = Cylinder(0.1, 0.99, material=ScatteringMaterial(mu_a=23.05427, mu_s=9.3985, g=0.9, n=1.361), label="blood")
+    bloodVessel = Cylinder(
+        0.1, 0.99, material=ScatteringMaterial(mu_a=23.05427, mu_s=9.3985, g=0.9, n=1.361), label="blood"
+    )
 
     scene = ScatteringScene([zStack, bloodVessel])
 
-    source = DirectionalSource(position=Vector(0, -0.399, 0), direction=Vector(0, 1, 0), N=N, diameter=0.6, displaySize=0.06)
+    source = DirectionalSource(
+        position=Vector(0, -0.399, 0), direction=Vector(0, 1, 0), N=N, diameter=0.6, displaySize=0.06
+    )
     logger = EnergyLogger(scene, defaultBinSize=0.001)
     source.propagate(scene, logger=logger)
 

pytissueoptics/examples/benchmarks/sphshells.py

@@ -1,5 +1,5 @@
-import env
-from pytissueoptics import *
+import env  # noqa: F401
+from pytissueoptics import *  # noqa: F403
 
 TITLE = "MCX Spherical shells"
 

pytissueoptics/examples/rayscattering/env.py

@@ -1,11 +1,7 @@
 # We set up the environment so we do not have to install PyTissueOptics to run the examples.
 # By adjusting the path, we use the current version in development.
 
-import sys
 import os
-sys.path.insert(0,
-                os.path.dirname(
-                    os.path.dirname(
-                        os.path.dirname(
-                            os.path.dirname(
-                                os.path.abspath(__file__))))))
+import sys
+
+sys.path.insert(0, os.path.dirname(os.path.dirname(os.path.dirname(os.path.dirname(os.path.abspath(__file__))))))

pytissueoptics/examples/rayscattering/ex01.py

@@ -1,5 +1,5 @@
-import env
-from pytissueoptics import *    
+import env  # noqa: F401
+from pytissueoptics import *  # noqa: F403
 
 TITLE = "Divergent source propagation through a multi-layered tissue"
 
@@ -12,8 +12,9 @@ def exampleCode():
 
     tissue = samples.PhantomTissue()
     logger = EnergyLogger(tissue)
-    source = DivergentSource(position=Vector(0, 0, -0.2), direction=Vector(0, 0, 1), N=N,
-                             diameter=0.1, divergence=0.4, displaySize=0.2)
+    source = DivergentSource(
+        position=Vector(0, 0, -0.2), direction=Vector(0, 0, 1), N=N, diameter=0.1, divergence=0.4, displaySize=0.2
+    )
 
     tissue.show(source=source)
 

pytissueoptics/examples/rayscattering/ex02.py

@@ -1,5 +1,5 @@
-import env
-from pytissueoptics import *
+import env  # noqa: F401
+from pytissueoptics import *  # noqa: F403
 
 TITLE = "Propagation in an Infinite Medium"
 
@@ -10,14 +10,16 @@
 
 def exampleCode():
     import math
+
     N = 10000 if hardwareAccelerationIsAvailable() else 25
 
     myMaterial = ScatteringMaterial(mu_s=30.0, mu_a=0.1, g=0.9)
     tissue = samples.InfiniteTissue(myMaterial)
 
     logger = EnergyLogger(tissue)
-    source = DivergentSource(position=Vector(0, 0, 0), direction=Vector(0, 0, 1), N=N,
-                             diameter=0.2, divergence=math.pi/4)
+    source = DivergentSource(
+        position=Vector(0, 0, 0), direction=Vector(0, 0, 1), N=N, diameter=0.2, divergence=math.pi / 4
+    )
 
     source.propagate(tissue, logger=logger)
 

pytissueoptics/examples/rayscattering/ex03.py

@@ -1,8 +1,10 @@
-import env
-from pytissueoptics import *
+import env  # noqa: F401
+from pytissueoptics import *  # noqa: F403
 
-TITLE = "Propagate in a in a non-scattering custom scene with an optical lens." \
-        "Learn to save and load your data so you don't have to simulate again."
+TITLE = (
+    "Propagate in a in a non-scattering custom scene with an optical lens."
+    "Learn to save and load your data so you don't have to simulate again."
+)
 
 DESCRIPTION = """  
 Thin Cuboid solids are used as screens for visualization, and a SymmetricLens() as a lens. They all go into a 

pytissueoptics/examples/rayscattering/ex04.py

@@ -1,5 +1,5 @@
-import env
-from pytissueoptics import *
+import env  # noqa: F401
+from pytissueoptics import *  # noqa: F403
 
 TITLE = "Custom layer stack"
 

pytissueoptics/examples/rayscattering/ex05.py

@@ -1,5 +1,5 @@
-import env
-from pytissueoptics import *
+import env  # noqa: F401
+from pytissueoptics import *  # noqa: F403
 
 TITLE = "Sphere inside a cube"
 
@@ -14,12 +14,13 @@ def exampleCode():
     material2 = ScatteringMaterial(mu_s=30, mu_a=0.2, g=0.9, n=1.7)
 
     cube = Cuboid(a=3, b=3, c=3, position=Vector(0, 0, 0), material=material1, label="cube")
-    sphere = Sphere(radius=1, order=3, position=Vector(0, 0, 0), material=material2, label="sphere",
-                    smooth=True)
+    sphere = Sphere(radius=1, order=3, position=Vector(0, 0, 0), material=material2, label="sphere", smooth=True)
     scene = ScatteringScene([cube, sphere])
 
     logger = EnergyLogger(scene)
-    source = DirectionalSource(position=Vector(0, 0, -2), direction=Vector(0, 0, 1), N=N, diameter=0.5, displaySize=0.25)
+    source = DirectionalSource(
+        position=Vector(0, 0, -2), direction=Vector(0, 0, 1), N=N, diameter=0.5, displaySize=0.25
+    )
 
     source.propagate(scene, logger)
 

pytissueoptics/examples/scene/env.py

@@ -1,11 +1,7 @@
 # We set up the environment so we do not have to install PyTissueOptics to run the examples.
 # By adjusting the path, we use the current version in development.
 
-import sys
 import os
-sys.path.insert(0,
-                os.path.dirname(
-                    os.path.dirname(
-                        os.path.dirname(
-                            os.path.dirname(
-                                os.path.abspath(__file__))))))
+import sys
+
+sys.path.insert(0, os.path.dirname(os.path.dirname(os.path.dirname(os.path.dirname(os.path.abspath(__file__))))))

pytissueoptics/examples/scene/example0.py

@@ -1,4 +1,4 @@
-import env
+import env  # noqa: F401
 
 TITLE = "Explore different Shapes"
 
@@ -10,7 +10,7 @@
 
 
 def exampleCode():
-    from pytissueoptics.scene import Vector, Cuboid, Sphere, Ellipsoid, MayaviViewer
+    from pytissueoptics.scene import Cuboid, Ellipsoid, MayaviViewer, Sphere, Vector
 
     cuboid = Cuboid(a=1, b=3, c=1, position=Vector(1, 0, 0))
     sphere = Sphere(radius=0.5, position=Vector(0, 0, 0))

pytissueoptics/examples/scene/example1.py

@@ -1,4 +1,4 @@
-import env
+import env  # noqa: F401
 
 TITLE = "Transforms on a Solid"
 
@@ -8,7 +8,7 @@
 
 
 def exampleCode():
-    from pytissueoptics.scene import Vector, Cuboid, MayaviViewer
+    from pytissueoptics.scene import Cuboid, MayaviViewer, Vector
 
     centerCube = Cuboid(a=1, b=1, c=1, position=Vector(0, 0, 0))
     topCube = Cuboid(a=1, b=1, c=1, position=Vector(0, 2, 0))

pytissueoptics/examples/scene/example2.py

@@ -1,4 +1,4 @@
-import env
+import env  # noqa: F401
 
 TITLE = "Stacking Cuboids"
 
@@ -7,7 +7,7 @@
 
 
 def exampleCode():
-    from pytissueoptics.scene import Cuboid, Vector, MayaviViewer
+    from pytissueoptics.scene import Cuboid, MayaviViewer, Vector
 
     cuboid1 = Cuboid(1, 1, 1, position=Vector(2, 0, 0))
     cuboid2 = Cuboid(2, 1, 1, position=Vector(0, 2, 0))
@@ -26,4 +26,4 @@ def exampleCode():
 
 
 if __name__ == "__main__":
-    exampleCode() 
+    exampleCode()

pytissueoptics/examples/scene/example3.py

@@ -1,12 +1,12 @@
-import env
+import env  # noqa: F401
 
 TITLE = "Load a .obj wavefront file"
 
 DESCRIPTION = """ """
 
 
 def exampleCode():
-    from pytissueoptics.scene import loadSolid, MayaviViewer
+    from pytissueoptics.scene import MayaviViewer, loadSolid
 
     solid = loadSolid("pytissueoptics/examples/scene/droid.obj")
 

pytissueoptics/examples/scene/example4.py

@@ -1,12 +1,20 @@
-import env
+import env  # noqa: F401
 
 TITLE = "Lenses"
 
 DESCRIPTION = """Explore different types of lens-shaped solids."""
 
 
 def exampleCode():
-    from pytissueoptics.scene import Vector, MayaviViewer, RefractiveMaterial, ThickLens, SymmetricLens, PlanoConvexLens, PlanoConcaveLens
+    from pytissueoptics.scene import (
+        MayaviViewer,
+        PlanoConcaveLens,
+        PlanoConvexLens,
+        RefractiveMaterial,
+        SymmetricLens,
+        ThickLens,
+        Vector,
+    )
 
     material = RefractiveMaterial(refractiveIndex=1.44)
     lens1 = ThickLens(30, 60, diameter=25.4, thickness=4, material=material, position=Vector(0, 0, 0))