Merge pull request #189 from jhlegarreta/ApplyIsortToPackageImports

STYLE: Apply `isort` to package imports

.github/workflows/check_format.yml

@@ -0,0 +1,25 @@
+name: code format
+
+on: [push]
+
+jobs:
+  pre-commit:
+
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ubuntu-latest]
+        python-version: ['3.10']
+        requires: ['latest']
+
+    steps:
+    - name: Check out repository
+      uses: actions/checkout@v4
+
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v4
+      with:
+        python-version: ${{ matrix.python-version }}
+
+    - name: Install and run pre-commit hooks
+      uses: pre-commit/[email protected]

.github/workflows/test_package.yaml

@@ -29,6 +29,7 @@ jobs:
       if: matrix.requires == 'minimal'
       run: |
         python -c "req = open('requirements.txt').read().replace(' >= ', ' == ') ; open('requirements.txt', 'w').write(req)"
+        python -c "req = open('requirements_dev.txt').read().replace(' >= ', ' == ') ; open('requirements_dev.txt', 'w').write(req)"
         python -c "req = open('setup.py').read().replace(' >= ', ' == ') ; open('setup.py', 'w').write(req)"
 
     # - name: Cache pip
@@ -45,6 +46,7 @@ jobs:
       # if: steps.cache.outputs.cache-hit != 'true'
       run: |
         python -m pip install --upgrade --user pip setuptools pytest-cov
+        pip install -r requirements_dev.txt
         python --version
         pip --version
         pip list

.pre-commit-config.yaml

@@ -0,0 +1,10 @@
+default_language_version:
+  python: python3.10
+
+repos:
+  - repo: https://github.com/timothycrosley/isort
+    rev: 5.11.5
+    hooks:
+      - id: isort
+        name: isort
+        types: [python]

README.md

@@ -3,6 +3,8 @@ whitematteranalysis
 
 [![test, package](https://github.com/SlicerDMRI/whitematteranalysis/actions/workflows/test_package.yaml/badge.svg?branch=master)](https://github.com/SlicerDMRI/whitematteranalysis/actions/workflows/test_package.yaml?query=branch%3Amaster)
 [![Documentation Status](https://readthedocs.org/projects/whitematteranalysis/badge/?version=latest)](https://whitematteranalysis.readthedocs.io/en/latest/?badge=latest)
+[![Imports: isort](https://img.shields.io/badge/%20imports-isort-%231674b1?style=flat&labelColor=ef8336)](https://pycqa.github.io/isort/)
+
 
 # Synopsis
 

bin/harden_transform_with_slicer.py

@@ -2,11 +2,13 @@
 # -*- coding: utf-8 -*-
 
 import argparse
-import slicer
-import os
 import glob
+import os
 import shutil
 
+import slicer
+
+
 def harden_transform(polydata, transform, inverse, outdir):
 
     polydata_base_path, polydata_name = os.path.split(polydata)

bin/wm_append_clusters.py

@@ -1,8 +1,9 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 
-import os
 import argparse
+import os
+
 import vtk
 
 import whitematteranalysis as wma

bin/wm_append_clusters_to_anatomical_tracts.py

@@ -1,10 +1,11 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 
-import os
 import argparse
-import vtk
 import glob
+import os
+
+import vtk
 
 import whitematteranalysis as wma
 

bin/wm_append_diffusion_measures_across_subjects.py

@@ -1,11 +1,12 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 
-import numpy
 import argparse
-import pandas
-import os
 import glob
+import os
+
+import numpy
+import pandas
 
 
 def _build_arg_parser():

bin/wm_assess_cluster_location_by_hemisphere.py

@@ -1,6 +1,12 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 
+import argparse
+import glob
+import os
+import shutil
+import warnings
+
 # If the cluster was created in bilateral clustering and is not commissural, separate into separate directories
 # output should be a right_hem and a left_hem directory
 # copy MRML files from toplevel directory into this one
@@ -12,12 +18,7 @@
 # For running this per-subject, the alignment should be performed to handle the tracts near the midline better.
 # That should be added as an option.
 import numpy
-import argparse
-import os
-import shutil
 import vtk
-import glob
-import warnings
 
 import whitematteranalysis as wma
 

bin/wm_average_tract_measures.py

@@ -1,12 +1,13 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 
-import numpy
 import argparse
-import pandas
 import os
 import re
 
+import numpy
+import pandas
+
 
 def _build_arg_parser():
 

bin/wm_change_nrrd_dir.py

@@ -1,17 +1,17 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 
-import glob
-import os
 import argparse
+import glob
 import multiprocessing
+import os
+
 import numpy
 import vtk
+from joblib import Parallel, delayed
 
 import whitematteranalysis as wma
 
-from joblib import Parallel, delayed
-
 
 def _build_arg_parser():
 

bin/wm_cluster_atlas.py

@@ -1,16 +1,17 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 
-import numpy
 import argparse
-import os
 import multiprocessing
-import vtk
+import os
 import time
 
+import matplotlib.pyplot as plt
+import numpy
+import vtk
+
 import whitematteranalysis as wma
 
-import matplotlib.pyplot as plt
 
 def main():
     #-----------------

bin/wm_cluster_from_atlas.py

@@ -1,11 +1,12 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 
-import numpy
 import argparse
-import os
 import multiprocessing
+import os
 import time
+
+import numpy
 import vtk
 
 import whitematteranalysis as wma

bin/wm_cluster_remove_outliers.py

@@ -1,12 +1,12 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 
-import numpy
 import argparse
-import os
 import glob
+import os
 import shutil
 
+import numpy
 import vtk
 
 import whitematteranalysis as wma

bin/wm_cluster_volumetric_measurements.py

@@ -3,9 +3,10 @@
 
 import argparse
 import os
+
 import nibabel
-import vtk
 import numpy
+import vtk
 from nibabel.affines import apply_affine
 
 import whitematteranalysis as wma

bin/wm_compare_vtks.py

@@ -3,14 +3,14 @@
 
 import argparse
 import os
+import time
+
 import numpy
 import vtk
-import time
 
 import whitematteranalysis as wma
 
 
-
 def _build_arg_parser():
 
     parser = argparse.ArgumentParser(

bin/wm_create_mrml_file.py

@@ -3,14 +3,14 @@
 
 import argparse
 import os
+import time
+
 import numpy
 import vtk
-import time
 
 import whitematteranalysis as wma
 
 
-
 def _build_arg_parser():
 
     parser = argparse.ArgumentParser(

bin/wm_diffusion_measurements.py

@@ -8,7 +8,6 @@
 import whitematteranalysis as wma
 
 
-
 def _build_arg_parser():
 
     parser = argparse.ArgumentParser(

bin/wm_download_anatomically_curated_atlas.py

@@ -1,14 +1,15 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 
+import argparse
 import enum
 import os
-import argparse
-import urllib.request, urllib.error, urllib.parse
-import zipfile
-import sys
 import ssl
-
+import sys
+import urllib.error
+import urllib.parse
+import urllib.request
+import zipfile
 
 ZENODO_RECORD_ROOT_URL = "https://zenodo.org/record/"
 ZENODO_API_RECORD_ROOT_URL = "https://zenodo.org/api/records/"

bin/wm_harden_transform.py

@@ -3,12 +3,12 @@
 
 import argparse
 import os
+
 from joblib import Parallel, delayed
 
 import whitematteranalysis as wma
 
 
-
 def _build_arg_parser():
 
     parser = argparse.ArgumentParser(

bin/wm_preprocess_all.py

@@ -1,16 +1,15 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 
-import glob
-import os
 import argparse
+import glob
 import multiprocessing
+import os
 from pathlib import Path
 
-import whitematteranalysis as wma
-
 from joblib import Parallel, delayed
 
+import whitematteranalysis as wma
 
 
 def _build_arg_parser():

bin/wm_quality_control_after_clustering.py

@@ -2,15 +2,17 @@
 # -*- coding: utf-8 -*-
 
 import argparse
+import glob
 import os
+
 import numpy
-import glob
 
 import whitematteranalysis as wma
 
 HAVE_PLT = 1
 try:
     import matplotlib
+
     # Force matplotlib to not use any Xwindows backend.
     matplotlib.use('Agg')
     import matplotlib.pyplot as plt

bin/wm_quality_control_cluster_measurements.py

@@ -3,6 +3,7 @@
 
 import argparse
 import os
+
 import numpy
 import scipy.stats
 

bin/wm_quality_control_tract_overlap.py

@@ -4,13 +4,13 @@
 
 import argparse
 import os
+import time
+
 import numpy
 import vtk
-import time
 
 import whitematteranalysis as wma
 
-
 HAVE_PLT = 1
 
 try: