Merge pull request #71 from lagru/prep-euroscipy22

Prepare tooling and lectures for EuroSciPy 2022

Author: emmanuelle

.github/workflows/deploy.yml

@@ -50,7 +50,7 @@ jobs:
             -screen 0 1920x1200x24 -ac +extension GLX
           # Install Python dependencies
           pip install --upgrade pip
-          pip install -r requirements.txt
+          pip install -r requirements.txt -r requirements_dev.txt
           # Install Node.js dependencies
           # TODO Uncomment when skimage theme is ready
           # npm install -g npm

check_setup.py

@@ -1,6 +1,12 @@
+"""Check if runtime dependencies are installed.
+
+The script currently does not check for specified optional requirements, e.g.
+'scikit-image[data]'.
+"""
+
 import sys
 import os
-from distutils.version import LooseVersion
+from packaging.version import parse
 
 if sys.version_info.major < 3:
     print('[!] You are running an old version of Python. '
@@ -15,6 +21,7 @@
         (req.split() for req in reqs if req.strip())]
 
 pkg_names = {
+    'scikit-image[data]': 'skimage',
     'scikit-image': 'skimage',
     'scikit-learn': 'sklearn'
 }
@@ -23,7 +30,11 @@
     module_name = pkg_names.get(pkg, pkg)
     try:
         m = __import__(module_name)
-        status = '✓'
+        version_installed = m.__version__
+        if parse(version_wanted) > parse(version_installed):
+            status = 'X'
+        else:
+            status = '✓'
     except ImportError as e:
         m = None
         if (pkg != 'numpy' and 'numpy' in str(e)):
@@ -32,11 +43,6 @@
         else:
             version_installed = 'Not installed'
             status = 'X'
-
-    if m is not None:
-        version_installed = m.__version__
-        if LooseVersion(version_wanted) > LooseVersion(version_installed):
-            status = 'X'
-    print('[{}] {:<11} {}'.format(
-        status, pkg.ljust(13), version_installed)
-        )
+    print(
+        '[{}] {:<20} {}'.format(status, pkg.ljust(13), version_installed)
+    )

lectures/4_segmentation.ipynb

@@ -21,7 +21,7 @@
    "source": [
     "# Segmentation\n",
     "\n",
-    "--------------\n",
+    "\n",
     "\n",
     "## Separating an image into one or more regions of interest.\n",
     "\n",
@@ -259,13 +259,13 @@
     "    \"\"\"Generate points defining a circle on an image.\"\"\"\n",
     "    radians = np.linspace(0, 2*np.pi, resolution)\n",
     "\n",
-    "    c = center[1] + radius*np.cos(radians)\n",
     "    r = center[0] + radius*np.sin(radians)\n",
+    "    c = center[1] + radius*np.cos(radians)\n",
     "    \n",
-    "    return np.array([c, r]).T\n",
+    "    return np.array([r, c]).T\n",
     "\n",
     "# Exclude last point because a closed path should not have duplicate points\n",
-    "points = circle_points(200, [100, 220], 100)[:-1]"
+    "points = circle_points(resolution=200, center=[100, 220], radius=100)[:-1]"
    ]
   },
   {
@@ -284,8 +284,8 @@
    "outputs": [],
    "source": [
     "fig, ax = image_show(astronaut)\n",
-    "ax.plot(points[:, 0], points[:, 1], '--r', lw=3)\n",
-    "ax.plot(snake[:, 0], snake[:, 1], '-b', lw=3);"
+    "ax.plot(points[:, 1], points[:, 0], '--r', lw=3)\n",
+    "ax.plot(snake[:, 1], snake[:, 0], '-b', lw=3);"
    ]
   },
   {
@@ -338,7 +338,7 @@
     "indices = draw.circle_perimeter(100, 220, 25)\n",
     "\n",
     "astronaut_labels[indices] = 1\n",
-    "astronaut_labels[points[:, 1].astype(int), points[:, 0].astype(int)] = 2\n",
+    "astronaut_labels[points[:, 0].astype(int), points[:, 1].astype(int)] = 2\n",
     "\n",
     "image_show(astronaut_labels);"
    ]

lectures/solutions/4_segmentation.ipynb

@@ -343,18 +343,16 @@
    "outputs": [],
    "source": [
     "def circle_points(resolution, center, radius):\n",
-    "    \"\"\"\n",
-    "    Generate points defining a circle on an image.\n",
-    "    \"\"\"\n",
+    "    \"\"\"Generate points defining a circle on an image.\"\"\"\n",
     "    radians = np.linspace(0, 2*np.pi, resolution)\n",
     "\n",
-    "    c = center[1] + radius*np.cos(radians)\n",
     "    r = center[0] + radius*np.sin(radians)\n",
+    "    c = center[1] + radius*np.cos(radians)\n",
     "    \n",
-    "    return np.array([c, r]).T\n",
+    "    return np.array([r, c]).T\n",
     "\n",
     "# Exclude last point because a closed path should not have duplicate points\n",
-    "points = circle_points(200, [100, 220], 100)[:-1]"
+    "points = circle_points(resolution=200, center=[100, 220], radius=100)[:-1]"
    ]
   },
   {
@@ -363,7 +361,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "snake = seg.active_contour(astronaut_gray, points, alpha=0.1, w_edge=1.3)"
+    "snake = seg.active_contour(astronaut_gray, points, alpha=0.1)"
    ]
   },
   {
@@ -390,8 +388,8 @@
    ],
    "source": [
     "fig, ax = image_show(astronaut)\n",
-    "ax.plot(points[:, 0], points[:, 1], '--r', lw=3)\n",
-    "ax.plot(snake[:, 0], snake[:, 1], '-b', lw=3);"
+    "ax.plot(points[:, 1], points[:, 0], '--r', lw=3)\n",
+    "ax.plot(snake[:, 1], snake[:, 0], '-b', lw=3);"
    ]
   },
   {
@@ -461,7 +459,7 @@
     "indices = draw.circle_perimeter(100, 220, 25)\n",
     "\n",
     "astronaut_labels[indices] = 1\n",
-    "astronaut_labels[points[:, 1].astype(np.int), points[:, 0].astype(np.int)] = 2\n",
+    "astronaut_labels[points[:, 0].astype(int), points[:, 1].astype(int)] = 2\n",
     "\n",
     "image_show(astronaut_labels);"
    ]

preparation.md

@@ -16,11 +16,12 @@ required packages installed in order to participate fully.
   Everyone else, feel free to use your favorite distribution, but
   please ensure the requirements below are met:
 
-  - `numpy` >= 1.12
-  - `scipy` >= 1.0
-  - `matplotlib` >= 2.1
-  - `scikit-image` >= 0.15
-  - `scikit-learn` >= 0.18
+  - `numpy` >= 1.21
+  - `scipy` >= 1.7
+  - `matplotlib` >= 3.5
+  - `scikit-image` >= 0.19
+  - `scikit-learn` >= 1.0
+  - `notebook` >= 6.4 (or `jupyterlab` >= 3.3) 
 
   Please see "Test your setup" below.
 

requirements.txt

@@ -1,15 +1,7 @@
 scikit-image[data] >= 0.19
-numpy >= 1.12
-scipy >= 1.0
-matplotlib >= 2.1
-notebook >= 4.0
-scikit-learn >= 0.18
-jupyter-book >= 0.10.2
-napari[all]
-jupytext >=1.10.3
-sphinx_autodoc_typehints>=1.11.0
-ghp-import
-pytest
-pytest-qt
-pooch
-furo
+numpy >= 1.21
+scipy >= 1.7
+matplotlib >= 3.5
+notebook >= 6.4
+scikit-learn >= 1.0
+packaging >= 21.3

requirements_dev.txt

@@ -0,0 +1,9 @@
+jupyter-book >= 0.10.2
+napari[all]
+jupytext >=1.10.3
+sphinx_autodoc_typehints>=1.11.0
+ghp-import
+pytest
+pytest-qt
+pooch
+furo