move script to entrypoint

.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

.gitignore

@@ -61,3 +61,7 @@ target/
 
 nlsam.zip
 *.code-workspace
+log
+*.nii
+*.nii.gz
+wheelhouse/*

scripts/nlsam_denoising → nlsam/scripts.py

@@ -1,5 +1,3 @@
-#!/usr/bin/env python
-
 import os
 import argparse
 import logging

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)

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"

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)