diff --git a/.github/workflows/cibuildwheel.yml b/.github/workflows/cibuildwheel.yml
index 909f2d48..96463f6e 100644
--- a/.github/workflows/cibuildwheel.yml
+++ b/.github/workflows/cibuildwheel.yml
@@ -30,13 +30,6 @@ jobs:
           CIBW_SKIP: "pp* cp36-* cp37-* *musllinux* cp38-macosx_arm64"
           CIBW_TEST_REQUIRES: pytest
           CIBW_TEST_COMMAND: pytest --pyargs nlsam --verbose
-          CIBW_TEST_COMMAND_LINUX: >
-            pytest --pyargs nlsam --verbose &&
-            cd {package}/example &&
-            chmod +x  {package}/nlsam/tests/test_scripts1.sh &&
-            bash {package}/nlsam/tests/test_scripts1.sh &&
-            chmod +x  {package}/nlsam/tests/test_scripts2.sh &&
-            bash {package}/nlsam/tests/test_scripts2.sh
 
       - uses: actions/upload-artifact@v4
         with:
@@ -85,9 +78,9 @@ jobs:
           path=$(python -c "import distributed; print(distributed.__path__[0]);")
           echo "version=v$(python -c "from importlib.metadata import version; print(version('nlsam'));")" >> $GITHUB_ENV
           if [ "$RUNNER_OS" == "Windows" ]; then
-            pyinstaller ./scripts/nlsam_denoising -F --clean --add-data "${path};.\\distributed\\" --noupx
+            pyinstaller ./nlsam/scripts.py -n nlsam_denoising -F --clean --add-data "${path};.\\distributed\\" --noupx
           else
-            pyinstaller ./scripts/nlsam_denoising -F --clean --add-data ${path}:./distributed/ --noupx
+            pyinstaller ./nlsam/scripts.py -n nlsam_denoising -F --clean --add-data ${path}:./distributed/ --noupx
           fi
 
       - uses: actions/upload-artifact@v4
diff --git a/.gitignore b/.gitignore
index 2c919592..06c91ed6 100644
--- a/.gitignore
+++ b/.gitignore
@@ -61,3 +61,7 @@ target/
 
 nlsam.zip
 *.code-workspace
+log
+*.nii
+*.nii.gz
+wheelhouse/*
diff --git a/scripts/nlsam_denoising b/nlsam/scripts.py
old mode 100755
new mode 100644
similarity index 99%
rename from scripts/nlsam_denoising
rename to nlsam/scripts.py
index bc1fc5b1..55634fe4
--- a/scripts/nlsam_denoising
+++ b/nlsam/scripts.py
@@ -1,5 +1,3 @@
-#!/usr/bin/env python
-
 import os
 import argparse
 import logging
diff --git a/nlsam/tests/test_script.py b/nlsam/tests/test_script.py
new file mode 100644
index 00000000..0bc257d1
--- /dev/null
+++ b/nlsam/tests/test_script.py
@@ -0,0 +1,42 @@
+import subprocess
+import pytest
+
+from pathlib import Path
+
+cwd = Path(__file__).parents[2] / Path("example")
+commands_crop = [
+    '''python -c "import nibabel as nib; import numpy as np; d = nib.load('dwi.nii.gz').get_fdata(); nib.save(nib.Nifti1Image(d[40:50, 80:85],np.eye(4)), 'dwi_crop.nii.gz')"''', 
+    '''python -c "import nibabel as nib; import numpy as np; d = nib.load('mask.nii.gz').get_fdata(); nib.save(nib.Nifti1Image(d[40:50, 80:85],np.eye(4)), 'mask_crop.nii.gz')"''', 
+    '''python -c "import nibabel as nib; import numpy as np; d = nib.load('mask.nii.gz').get_fdata(); nib.save(nib.Nifti1Image(np.random.rayleigh(10, d[40:50, 80:85].shape),np.eye(4)), 'noise.nii.gz')"''',
+]
+
+commands_nlsam = [
+    # Test on example dataset
+    'nlsam_denoising dwi_crop.nii.gz dwi_nlsam.nii.gz bvals bvecs -f -N 1 --noise_est local_std --sh_order 0 --log log --cores 1 -m mask_crop.nii.gz',
+    'nlsam_denoising dwi_crop.nii.gz dwi_nlsam.nii.gz bvals bvecs -m mask_crop.nii.gz -f -N 1 --noise_est local_std --sh_order 6 --iterations 5 --verbose --save_sigma sigma.nii.gz',
+    'nlsam_denoising dwi_crop.nii.gz dwi_nlsam.nii.gz bvals bvecs -m mask_crop.nii.gz -f --noise_est auto --sh_order 6 --iterations 5 --verbose --save_sigma sigma.nii.gz --save_N N.nii.gz',
+    'nlsam_denoising dwi_crop.nii.gz dwi_nlsam.nii.gz bvals bvecs -m mask_crop.nii.gz -f --verbose --sh_order 0 --b0_threshold 10 --noise_mask pmask.nii.gz',
+    # Test on niftis
+    "gunzip dwi_crop.nii.gz mask_crop.nii.gz sigma.nii.gz"
+    "nlsam_denoising dwi_crop.nii dwi_nlsam.nii bvals bvecs -m mask_crop.nii -f --verbose --sh_order 0 -N 1 --no_stabilization --load_sigma sigma.nii --is_symmetric --use_threading --save_difference diff.nii",
+    "nlsam_denoising dwi_crop.nii dwi_nlsam.nii bvals bvecs -m mask_crop.nii -f --verbose --sh_order 0 --no_denoising --save_sigma sigma.nii --save_stab stab.nii --load_mhat dwi_crop.nii --save_eta eta.nii",
+    # Test on example dataset
+    "nlsam_denoising dwi_crop.nii.gz dwi_nlsam.nii.gz bvals bvecs -m mask_crop.nii.gz -f --verbose -N 1 --noise_est local_std --sh_order 0 --block_size 2,2,2 --save_sigma sigma.nii.gz --cores 1",
+    "nlsam_denoising dwi_crop.nii.gz dwi_nlsam.nii.gz bvals bvecs -m mask_crop.nii.gz -f --verbose --sh_order 0 -N 1 --load_sigma sigma.nii.gz --no_subsample --fix_implausible --no_clip_eta",
+    "nlsam_denoising dwi_crop.nii.gz dwi_nlsam.nii.gz bvals bvecs -m mask_crop.nii.gz -f --verbose --sh_order 0 --noise_map noise.nii.gz --noise_mask pmask.nii.gz --use_f32",
+    "nlsam_denoising dwi_crop.nii.gz dwi_nlsam.nii.gz bvals bvecs -m mask_crop.nii.gz -f --verbose --sh_order 0 -N 1 --load_sigma sigma.nii.gz --no_stabilization --no_denoising",
+    "nlsam_denoising dwi_crop.nii.gz dwi_nlsam.nii.gz bvals bvecs -m mask_crop.nii.gz -f --verbose --sh_order 0 -N 1 --load_sigma sigma.nii.gz --no_denoising --no_clip_eta",
+    "nlsam_denoising dwi_crop.nii.gz dwi_nlsam.nii.gz bvals bvecs -m mask_crop.nii.gz -f --verbose --sh_order 0 -N 1 --noise_est local_std --no_denoising",
+    "nlsam_denoising dwi_crop.nii.gz dwi_nlsam.nii.gz bvals bvecs -m mask_crop.nii.gz -f --verbose --sh_order 0 --noise_est auto --no_denoising --cores 4",
+    "nlsam_denoising dwi_crop.nii.gz dwi_nlsam.nii.gz bvals bvecs -m mask_crop.nii.gz -f --verbose --sh_order 0 --no_denoising",
+]
+
+
+@pytest.mark.parametrize("command", commands_crop)
+def test_crop(command):
+    subprocess.run([command], shell=True, cwd=cwd, check=True)
+
+
+@pytest.mark.parametrize("command", commands_nlsam)
+def test_script_nlsam(command):
+    subprocess.run([command], shell=True, cwd=cwd, check=True)
diff --git a/nlsam/tests/test_scripts1.sh b/nlsam/tests/test_scripts1.sh
deleted file mode 100755
index a7039bb4..00000000
--- a/nlsam/tests/test_scripts1.sh
+++ /dev/null
@@ -1,36 +0,0 @@
-check_return_code ()
-{
-    if [ $1 -ne 0 ]; then
-        echo 'Something failed in python apparently'
-        exit 1
-    fi
-
-    echo 'stuff finished'
-}
-
-# Crop example dataset
-python -c 'import nibabel as nib; import numpy as np; d = nib.load("dwi.nii.gz").get_fdata(); nib.save(nib.Nifti1Image(d[40:50, 80:85],np.eye(4)), "dwi_crop.nii.gz")'
-python -c 'import nibabel as nib; import numpy as np; d = nib.load("mask.nii.gz").get_fdata(); nib.save(nib.Nifti1Image(d[40:50, 80:85],np.eye(4)), "mask_crop.nii.gz")'
-python -c 'import nibabel as nib; import numpy as np; d = nib.load("mask.nii.gz").get_fdata(); nib.save(nib.Nifti1Image(np.random.rayleigh(10, d[40:50, 80:85].shape),np.eye(4)), "noise.nii.gz")'
-
-# Test on example dataset
-nlsam_denoising dwi_crop.nii.gz dwi_nlsam.nii.gz bvals bvecs -f -N 1 --noise_est local_std --sh_order 0 --log log --cores 1 -m mask_crop.nii.gz
-check_return_code $?
-
-nlsam_denoising dwi_crop.nii.gz dwi_nlsam.nii.gz bvals bvecs -m mask_crop.nii.gz -f -N 1 --noise_est local_std --sh_order 6 --iterations 5 --verbose --save_sigma sigma.nii.gz
-check_return_code $?
-
-nlsam_denoising dwi_crop.nii.gz dwi_nlsam.nii.gz bvals bvecs -m mask_crop.nii.gz -f --noise_est auto --sh_order 6 --iterations 5 --verbose --save_sigma sigma.nii.gz --save_N N.nii.gz
-check_return_code $?
-
-nlsam_denoising dwi_crop.nii.gz dwi_nlsam.nii.gz bvals bvecs -m mask_crop.nii.gz -f --verbose --sh_order 0 --b0_threshold 10 --noise_mask pmask.nii.gz
-check_return_code $?
-
-# Test on niftis
-gunzip dwi_crop.nii.gz mask_crop.nii.gz sigma.nii.gz
-
-nlsam_denoising dwi_crop.nii dwi_nlsam.nii bvals bvecs -m mask_crop.nii -f --verbose --sh_order 0 -N 1 --no_stabilization --load_sigma sigma.nii --is_symmetric --use_threading --save_difference diff.nii
-check_return_code $?
-
-nlsam_denoising dwi_crop.nii dwi_nlsam.nii bvals bvecs -m mask_crop.nii -f --verbose --sh_order 0 --no_denoising --save_sigma sigma.nii --save_stab stab.nii --load_mhat dwi_crop.nii --save_eta eta.nii
-check_return_code $?
diff --git a/nlsam/tests/test_scripts2.sh b/nlsam/tests/test_scripts2.sh
deleted file mode 100755
index 2b7f589d..00000000
--- a/nlsam/tests/test_scripts2.sh
+++ /dev/null
@@ -1,39 +0,0 @@
-check_return_code ()
-{
-    if [ $1 -ne 0 ]; then
-        echo 'Something failed in python apparently'
-        exit 1
-    fi
-
-    echo 'stuff finished'
-}
-
-# Crop example dataset
-python -c 'import nibabel as nib; import numpy as np; d = nib.load("dwi.nii.gz").get_fdata(); nib.save(nib.Nifti1Image(d[40:50, 80:85],np.eye(4)), "dwi_crop.nii.gz")'
-python -c 'import nibabel as nib; import numpy as np; d = nib.load("mask.nii.gz").get_fdata(); nib.save(nib.Nifti1Image(d[40:50, 80:85],np.eye(4)), "mask_crop.nii.gz")'
-python -c 'import nibabel as nib; import numpy as np; d = nib.load("mask.nii.gz").get_fdata(); nib.save(nib.Nifti1Image(np.random.rayleigh(10, d[40:50, 80:85].shape),np.eye(4)), "noise.nii.gz")'
-
-# Test on example dataset
-nlsam_denoising dwi_crop.nii.gz dwi_nlsam.nii.gz bvals bvecs -m mask_crop.nii.gz -f --verbose -N 1 --noise_est local_std --sh_order 0 --block_size 2,2,2 --save_sigma sigma.nii.gz --cores 1
-check_return_code $?
-
-nlsam_denoising dwi_crop.nii.gz dwi_nlsam.nii.gz bvals bvecs -m mask_crop.nii.gz -f --verbose --sh_order 0 -N 1 --load_sigma sigma.nii.gz --no_subsample --fix_implausible --no_clip_eta
-check_return_code $?
-
-nlsam_denoising dwi_crop.nii.gz dwi_nlsam.nii.gz bvals bvecs -m mask_crop.nii.gz -f --verbose --sh_order 0 --noise_map noise.nii.gz --noise_mask pmask.nii.gz --use_f32
-check_return_code $?
-
-nlsam_denoising dwi_crop.nii.gz dwi_nlsam.nii.gz bvals bvecs -m mask_crop.nii.gz -f --verbose --sh_order 0 -N 1 --load_sigma sigma.nii.gz --no_stabilization --no_denoising
-check_return_code $?
-
-nlsam_denoising dwi_crop.nii.gz dwi_nlsam.nii.gz bvals bvecs -m mask_crop.nii.gz -f --verbose --sh_order 0 -N 1 --load_sigma sigma.nii.gz --no_denoising --no_clip_eta
-check_return_code $?
-
-nlsam_denoising dwi_crop.nii.gz dwi_nlsam.nii.gz bvals bvecs -m mask_crop.nii.gz -f --verbose --sh_order 0 -N 1 --noise_est local_std --no_denoising
-check_return_code $?
-
-nlsam_denoising dwi_crop.nii.gz dwi_nlsam.nii.gz bvals bvecs -m mask_crop.nii.gz -f --verbose --sh_order 0 --noise_est auto --no_denoising --cores 4
-check_return_code $?
-
-nlsam_denoising dwi_crop.nii.gz dwi_nlsam.nii.gz bvals bvecs -m mask_crop.nii.gz -f --verbose --sh_order 0 --no_denoising
-check_return_code $?
diff --git a/pyproject.toml b/pyproject.toml
index 27085c20..18d75584 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -2,11 +2,10 @@
 requires = ["Cython>=0.29.33",
             "scipy>=1.5",
             "oldest-supported-numpy",
-            "setuptools",
+            "setuptools>=60",
             "wheel"]
 build-backend = "setuptools.build_meta"
 
-
 [project]
 name = "nlsam"
 version = '0.7.1'
@@ -32,3 +31,7 @@ dependencies = [
 homepage = "https://github.com/samuelstjean/nlsam"
 documentation = "https://nlsam.readthedocs.io/en/latest/"
 changelog = "https://github.com/samuelstjean/nlsam/blob/master/CHANGELOG.md"
+
+
+[project.scripts]
+nlsam_denoising = "nlsam.scripts:main"
diff --git a/setup.py b/setup.py
index 59160b6f..b1d2d725 100644
--- a/setup.py
+++ b/setup.py
@@ -5,10 +5,8 @@
 
 ext_modules = cythonize("nlsam/*.pyx")
 include_dirs = [numpy.get_include()]
-scripts = ['scripts/nlsam_denoising']
 
 setup(
-    scripts=scripts,
-    packages=find_packages(),
     include_dirs=include_dirs,
+    packages=find_packages(),
     ext_modules=ext_modules)