Scripts (#16)

Author: samuelstjean

.github/workflows/python-package.yml

@@ -18,9 +18,9 @@ jobs:
 
     runs-on: ${{ matrix.os }}
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
     - name: Install dependencies
@@ -36,4 +36,4 @@ jobs:
         flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
     - name: Test with pytest
       run: |
-        pytest
+        pytest .

.github/workflows/pythonpublish.yml

@@ -8,15 +8,15 @@ jobs:
   deploy:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - name: Set up Python
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: '3.x'
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
-        pip install setuptools wheel twine build
+        pip install twine build
     - name: Build and publish
       env:
         TWINE_USERNAME: ${{ secrets.PYPI_USERNAME }}

.gitignore

@@ -1,3 +1,6 @@
+*.png 
+*.csv
+
 # Byte-compiled / optimized / DLL files
 __pycache__/
 *.py[cod]
@@ -149,10 +152,8 @@ octave-workspace
 # Local History for Visual Studio Code
 .history/
 
-
 ## Sublime text
 
-
 # Cache files for Sublime Text
 *.tmlanguage.cache
 *.tmPreferences.cache

CHANGELOG.md

@@ -1,5 +1,10 @@
 # Changelog
 
+## [v0.2.2]
+
+- Moved the scripts to a proper entrypoint instead of an added file
+    - This changes nothing in the way each script is called but just makes it more robust on Windows
+
 ## [v0.2.1] - 2023-06-01
 
 - Support for csv files input and output

datasets/af_left_AFD_realigned.png

@@ -24,7 +24,7 @@
 language = 'en'
 
 # The full version, including alpha/beta/rc tags
-release = 'v0.2.1'
+release = 'v0.2.2'
 
 # If your documentation needs a minimal Sphinx version, state it here.
 #

datasets/pvals_realigned.png

@@ -1,6 +1,5 @@
 sphinx >= 5.3.0
 sphinx_rtd_theme >= 1.1.1
 readthedocs-sphinx-search >= 0.3.2
-sphinx-rtd-theme
 sphinx-autoapi
 myst-parser

datasets/pvals_unaligned.png

@@ -106,7 +106,7 @@ def align_bundles(bundles, percent=15, padding=0., order=1, eps=1e-5, mode='full
             shifts[outliers] = 0.
             shifts[:, outliers] = 0.
 
-        warn('Possible outliers found {}'.format(outliers))
+        warn(f'Possible outliers found {outliers}')
 
     # use the custom shift patterns
     ys = apply_shift(bundles, shifts[original_templater])
@@ -123,7 +123,7 @@ def resample_bundles_to_same(bundles, num_points=None):
         bundles = bundles[None, :]
 
     if bundles.ndim != 2:
-        error = 'bundles needs to be a 2D array, but is {}D'.format(bundles.ndim)
+        error = f'bundles needs to be a 2D array, but is {bundles.ndim}D'
         raise ValueError(error)
 
     if num_points is None:
@@ -176,7 +176,7 @@ def flip_fibers(bundles, coordinates, padding=np.nan, template=None):
     '''
 
     if coordinates[0].shape[1] != 3:
-        raise ValueError('coordinates should be Nx3 but is {}'.format(coordinates[0].shape))
+        raise ValueError(f'coordinates should be Nx3 but is {coordinates[0].shape}')
 
     new_bundles = np.zeros_like(bundles)
 
@@ -201,7 +201,7 @@ def flip_fibers(bundles, coordinates, padding=np.nan, template=None):
 def truncate(bundles, mode='shortest', trimval=np.nan, axis=0):
 
     if bundles.ndim > 2:
-        error = 'Number of dimension must be lower than 2, but was {}'.format(bundles.ndim)
+        error = f'Number of dimension must be lower than 2, but was {bundles.ndim}'
         raise ValueError(error)
 
     if mode == 'shortest':
@@ -211,11 +211,11 @@ def truncate(bundles, mode='shortest', trimval=np.nan, axis=0):
     elif isinstance(mode, int):
 
         if mode > 100 or mode < 1:
-            raise ValueError('mode must be between 1 and 100 {}'.format(mode))
+            raise ValueError(f'mode must be between 1 and 100 {mode}')
 
         threshold = np.floor(mode * bundles.shape[0] / 100)
     else:
-        raise ValueError('Unrecognized truncation mode {}'.format(mode))
+        raise ValueError(f'Unrecognized truncation mode {mode}')
 
     if np.isnan(trimval):
         indexes = np.isfinite(bundles).sum(axis=axis) >= threshold
@@ -246,7 +246,7 @@ def filter_pairs(allpairs, mode):
     elif mode == 'everything':
         func = lambda *_: True  # this always return True
     else:
-        error = 'String mismatch, mode was {} of type {}'.format(mode, type(mode))
+        error = f'String mismatch, mode was {mode} of type {type(mode)}'
         raise ValueError(error)
 
     output = []