Scripts (#16)

.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

docs/conf.py

@@ -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.
 #

docs/requirements.txt

@@ -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

dpr/register.py

@@ -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 = []

scripts/dpr → dpr/scripts/dpr.py

@@ -1,5 +1,3 @@
-#!/usr/bin/env python
-
 import numpy as np
 import matplotlib.pyplot as plt
 
@@ -153,7 +151,3 @@ def main():
 
     with open(args.output, 'w') as file:
         np.savetxt(file, resampled, delimiter=delimiter, fmt='%s')
-
-
-if __name__ == "__main__":
-    main()

scripts/dpr_make_fancy_graph → dpr/scripts/dpr_make_fancy_graph.py

@@ -1,5 +1,3 @@
-#!/usr/bin/env python
-
 import numpy as np
 
 import argparse
@@ -123,7 +121,3 @@ def main():
                                  coord1_label=args.labelx, coord2_label=args.labely, title=args.title)
 
     fig.savefig(args.output, dpi=args.dpi, bbox_inches='tight')
-
-
-if __name__ == "__main__":
-    main()

dpr/tests/test_scripts.py

@@ -0,0 +1,23 @@
+import subprocess
+import pytest
+
+from pathlib import Path
+
+cwd = Path(__file__).parents[2] / Path("datasets")
+commands_dpr = [
+    ('dpr', 'af_left_AFD.txt', 'af_left_AFD_realigned.txt', '--exploredti', '--do_graph', '-f', '-v', '--points', '75'),
+    ('dpr', 'af_left_AFD.txt', 'af_left_AFD_realigned.csv', '--exploredti', '-f')
+]
+
+commands_dpr_graph = [
+    ('dpr_make_fancy_graph', 'af_left_pval_unaligned.txt', 'af_left_coordinates.txt', 'af_left_truncated_coordinates.txt', 'af_left_average_coordinates.txt', '0,2', 'pvals_unaligned.png', '--title', "p-values before realignment", '-f'),
+    ('dpr_make_fancy_graph', 'af_left_pval_realigned.txt', 'af_left_coordinates.txt', 'af_left_truncated_coordinates.txt', 'af_left_average_coordinates.txt', '0,2', 'pvals_realigned.png', '-f', '-v', '--labelx', '"label X"', '--labely', 'Label Y', '--dpi', '100')
+]
+
+@pytest.mark.parametrize("command", commands_dpr)
+def test_script_dpr(command):
+    subprocess.run(command, cwd=cwd, check=True)
+
+@pytest.mark.parametrize("command", commands_dpr_graph)
+def test_script_dpr_graph(command):
+    subprocess.run(command, cwd=cwd, check=True)

dpr/utils.py

@@ -69,41 +69,38 @@ def draw_fancy_graph(pval, coords1, coords2, truncated_coords1, truncated_coords
     if title is None:
         title = 'p-values after realignment'
 
-    # This is to draw on a white background
-    with plt.style.context('seaborn-whitegrid'):
+    fig, ax = plt.subplots(1, 1, sharex='col', sharey='row', figsize=(8, 8))
 
-        fig, ax = plt.subplots(1, 1, sharex='col', sharey='row', figsize=(8, 8))
+    # Draw the full length shadow bundle
+    for x, y in zip(coords1, coords2):
+        ax.plot(x, y, color=shadow_cmap, alpha=0.1, zorder=1)
 
-        # Draw the full length shadow bundle
-        for x, y in zip(coords1, coords2):
-            ax.plot(x, y, color=shadow_cmap, alpha=0.1, zorder=1)
+    # Draw the original coord, but truncated between rois
+    for x, y in zip(truncated_coords1, truncated_coords2):
+        ax.plot(x, y, color=bundle_cmap, alpha=0.3, zorder=2)
 
-        # Draw the original coord, but truncated between rois
-        for x, y in zip(truncated_coords1, truncated_coords2):
-            ax.plot(x, y, color=bundle_cmap, alpha=0.3, zorder=2)
+    # Draw the mean coord
+    x = average1
+    y = average2
+    ax.plot(x, y, color=mean_fiber_cmap, zorder=5)
 
-        # Draw the mean coord
-        x = average1
-        y = average2
-        ax.plot(x, y, color=mean_fiber_cmap, zorder=5)
+    # We resample the pvals because the coords may be at the tracking stepsize and the final results at the voxel resolution
+    old = np.arange(len(pval)) / len(pval)
+    new = np.arange(len(x)) / len(x)
+    pval_resampled = np.interp(new, old, pval)
 
-        # We resample the pvals because the coords may be at the tracking stepsize and the final results at the voxel resolution
-        old = np.arange(len(pval)) / len(pval)
-        new = np.arange(len(x)) / len(x)
-        pval_resampled = np.interp(new, old, pval)
+    # This makes everything above the threshold invisible on the final graph
+    pval_resampled[pval_resampled > pval_threshold] = np.nan
+    cmap_axis = ax.scatter(x, y, c=pval_resampled, cmap=pval_cmap, zorder=10, marker='.', vmin=0, vmax=pval_threshold)
 
-        # This makes everything above the threshold invisible on the final graph
-        pval_resampled[pval_resampled > pval_threshold] = np.nan
-        cmap_axis = ax.scatter(x, y, c=pval_resampled, cmap=pval_cmap, zorder=10, marker='.', vmin=0, vmax=pval_threshold)
+    if draw_colorbar:
+        colorbar(cmap_axis)
 
-        if draw_colorbar:
-            colorbar(cmap_axis)
+    ax.axis('equal')
+    ax.set_xlabel(f"{coord1_label} coordinates (mm)", fontsize=12)
+    ax.set_ylabel(f"{coord2_label} coordinates (mm)", fontsize=12)
 
-        ax.axis('equal')
-        ax.set_xlabel("{} coordinates (mm)".format(coord1_label), fontsize=12)
-        ax.set_ylabel("{} coordinates (mm)".format(coord2_label), fontsize=12)
-
-        ax.set_title(title, fontsize=20)
-        fig.tight_layout()
+    ax.set_title(title, fontsize=20)
+    fig.tight_layout()
 
     return fig, ax

pyproject.toml

@@ -4,19 +4,25 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "dpr"
-version = '0.2.1'
-requires-python = ">=3.7"
-dependencies = ['numpy>=1.10',
-                'scipy>=0.19',
-                'matplotlib>=2.0']
+version = '0.2.2'
+requires-python = ">=3.9"
+dependencies = ['numpy>=1.15', 
+                'scipy>=1.2', 
+                'matplotlib>=3.0']
 description = 'Implementation of "Reducing variability in along-tract analysis with diffusion profile realignment".'
 readme = "README.md"
-license = {text = "MIT License"}
-authors = [
-  {name = "Samuel St-Jean", email = "[email protected]"}
-]
+license = { text = "MIT License" }
+authors = [{ name = "Samuel St-Jean", email = "[email protected]" }]
+
+[project.scripts]
+dpr = "dpr.scripts.dpr:main"
+dpr_make_fancy_graph = "dpr.scripts.dpr_make_fancy_graph:main"
 
 [project.urls]
 Homepage = "https://github.com/samuelstjean/dpr"
 Documentation = "https://dpr.readthedocs.io/en/latest/"
 Changelog = "https://github.com/samuelstjean/dpr/blob/master/CHANGELOG.md"
+
+[tool.setuptools]
+packages = ["dpr", 
+            "dpr.scripts"]

setup.py

@@ -1,7 +1,3 @@
-from setuptools import setup, find_packages
+from setuptools import setup
 
-scripts=['scripts/dpr',
-         'scripts/dpr_make_fancy_graph']
-
-setup(scripts=scripts,
-      packages=find_packages())
+setup()