Added makefile and reformatting

Makefile

@@ -0,0 +1,25 @@
+venv:
+	python -m venv venv
+
+install:
+	python -m pip install .
+
+dev:
+	python -m pip install -e .[dev]
+
+test:
+	pytest tests
+
+coverage:
+	pytest --cov simulatedmicroscopy --cov-report html
+
+clean:
+	rm -rf __pycache__ .pytest_cache htmlcov .coverage
+
+flake:
+	flake8 simulatedmicroscopy tests
+
+black:
+	black simulatedmicroscopy tests
+
+check: black flake test

simulatedmicroscopy/images.py

@@ -168,7 +168,7 @@ def downsample(self, downsample_factor: list[int]) -> type[Image]:
 
         return self
 
-    def convolve(self, other : type[Image]) -> type[Image]:
+    def convolve(self, other: type[Image]) -> type[Image]:
         """Convolve this image with another image (a PSF). The image is overwritten by the result of the convolution.
 
         Parameters
@@ -183,8 +183,8 @@ def convolve(self, other : type[Image]) -> type[Image]:
         """
         if not (self.pixel_sizes == other.pixel_sizes).all():
             raise ValueError("Cannot convolve images with different pixel sizes")
-        
-        self.image = scipy.signal.convolve(self.image, other.image, mode='same')
+
+        self.image = scipy.signal.convolve(self.image, other.image, mode="same")
 
         return self
 

simulatedmicroscopy/psf.py

@@ -35,10 +35,10 @@ def __init__(
         """
         sigmas_nm = np.array(sigmas)
         pixel_sizes_nm = np.round(np.array(pixel_sizes) * 1e9).astype(int)
-        
+
         if not (pixel_sizes_nm < sigmas_nm).all():
             raise ValueError("Pixel sizes should be smaller than given sigmas")
-        
+
         # image size in nm, 4 sigma on all sides of the Gaussian
         image_size_nm = 4 * 2 * sigmas_nm
 

tests/test_image.py

@@ -122,21 +122,22 @@ def test_downsample(downsample_factor):
     "multiplication_factor",
     [
         0.5,
-        1.,
-        2.,
+        1.0,
+        2.0,
     ],
 )
 def test_convolution(multiplication_factor):
-    im = Image(np.ones(shape=(10,10,10)))
-    psf = Image(np.ones(shape=(1,1,1))*multiplication_factor)
+    im = Image(np.ones(shape=(10, 10, 10)))
+    psf = Image(np.ones(shape=(1, 1, 1)) * multiplication_factor)
 
     convolved = im.convolve(psf)
 
     assert im == convolved
 
+
 def test_convolution_wrongpixelsize():
     im = create_demo_image()
-    psf = Image(np.ones(shape=(1,1,1)), pixel_sizes=(10.,10.,10.))
+    psf = Image(np.ones(shape=(1, 1, 1)), pixel_sizes=(10.0, 10.0, 10.0))
 
     with pytest.raises(ValueError):
-        im.convolve(psf)
+        im.convolve(psf)

tests/test_psf.py

@@ -1,11 +1,13 @@
 from simulatedmicroscopy.psf import GaussianPSF
 import pytest
 
+
 def test_can_create_gaussian_psf():
-    psf = GaussianPSF([250.,250.,600.])
+    psf = GaussianPSF([250.0, 250.0, 600.0])
+
+    assert psf.image.sum() > 0.0
 
-    assert psf.image.sum() > 0.
 
 def test_can_gaussian_psf_wrongpixelsize():
     with pytest.raises(ValueError):
-        GaussianPSF([250.,250.,600.], pixel_sizes=[1e-6, 1e-6, 1e-6])
+        GaussianPSF([250.0, 250.0, 600.0], pixel_sizes=[1e-6, 1e-6, 1e-6])