Merge pull request #3 from PhilHem/feature/workshop-updates

Add workshop environment setup and configuration files

Author: Thalla

.github/workflows/test-environment.yml

@@ -0,0 +1,42 @@
+name: Test Environment
+
+on:
+    push:
+        paths:
+            - "pyproject.toml"
+            - "uv.lock"
+    pull_request:
+        paths:
+            - "pyproject.toml"
+            - "uv.lock"
+
+jobs:
+    test-environment:
+        runs-on: ubuntu-latest
+
+        steps:
+            - name: Checkout code
+              uses: actions/checkout@v4
+
+            - name: Install uv
+              uses: astral-sh/setup-uv@v3
+              with:
+                  version: "latest"
+
+            - name: Set up Python
+              run: uv python install 3.8
+
+            - name: Install dependencies
+              run: uv sync
+
+            - name: Test notebook imports
+              run: uv run python scripts/test_environment.py
+
+            - name: Verify notebooks can be parsed
+              run: |
+                  echo "Checking that all notebooks can be parsed..."
+                  for notebook in *.ipynb; do
+                    echo "Parsing $notebook..."
+                    uv run python -c "import nbformat; nbformat.read('$notebook', as_version=4)"
+                  done
+                  echo "✅ All notebooks parsed successfully"

.gitignore

@@ -0,0 +1,58 @@
+# Python
+__pycache__/
+*.py[cod]
+*$py.class
+*.so
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+
+# Virtual environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# uv
+.uv/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+.python-version
+
+# IDE
+.vscode/
+.idea/
+*.swp
+*.swo
+
+# OS
+.DS_Store
+Thumbs.db
+
+# Workshop specific
+test.py  # Created by teaching examples
+worktrees.json
+.history/

README.md

@@ -2,6 +2,39 @@
 
 # Workshop Parallel Jupyter
 
+## Quick Start
+
+This workshop uses a modern Python environment managed with `uv`. To get started:
+
+1. **Install uv** (if not already installed):
+   ```bash
+   curl -LsSf https://astral.sh/uv/install.sh | sh
+   ```
+
+2. **Set up the environment**:
+   ```bash
+   uv sync
+   ```
+
+3. **Test the environment**:
+   ```bash
+   uv run python scripts/test_environment.py
+   ```
+
+4. **Start Jupyter**:
+   ```bash
+   uv run jupyter lab
+   ```
+
+## Environment Testing
+
+The environment is automatically tested via GitHub Actions whenever dependencies change. You can also test locally:
+
+- **Test all imports**: `uv run python scripts/test_environment.py`
+- **Verify notebooks**: All notebooks are automatically validated for syntax
+
+## Prerequisites
+
 Participants must have already completed these basics:
 * Functioning user account on [bwUniCluster](https://wiki.bwhpc.de/e/Category:BwUniCluster_2.0), i.e.
   * bwIDM entitlement 'bwUniCluster' of your home institution

pyproject.toml

@@ -0,0 +1,31 @@
+[project]
+name = "1761731486678-8220ea"
+version = "0.1.0"
+description = "Add your description here"
+readme = "README.md"
+requires-python = ">=3.8,<3.9"
+dependencies = [
+    "bokeh>=2.4.0",
+    "bottleneck>=1.3.0",
+    "dask>=2021.10.0",
+    "dask-jobqueue>=0.8.5",
+    "dask-ml>=2024.4.4",
+    "distributed>=2021.10.0",
+    "graphviz>=0.16.0",
+    "ipykernel>=6.4.0",
+    "ipython>=7.29.0",
+    "jupyter>=1.0.0",
+    "matplotlib>=3.4.0",
+    "mpi4py>=3.0.0",
+    "numba>=0.53.0",
+    "numpy>=1.21.0",
+    "pandas>=1.3.0",
+    "pyarrow>=4.0.0",
+    "s3fs>=2021.7.0",
+    "scikit-learn>=1.0.0",
+    "scipy>=1.7.0",
+    "seaborn>=0.11.0",
+]
+
+[dependency-groups]
+dev = ["nbconvert>=7.16.6", "pytest>=8.3.5", "pytest-html>=4.1.1"]

scripts/test_environment.py

@@ -0,0 +1,54 @@
+#!/usr/bin/env python3
+"""Quick test to verify notebook imports work."""
+
+import sys
+from pathlib import Path
+import nbformat
+
+
+def main():
+    print("🔍 Testing notebook imports...")
+
+    # Get all notebooks
+    notebooks = [f for f in Path(".").glob("*.ipynb") if not f.name.startswith("test_")]
+
+    # Extract and test imports
+    all_imports = set()
+    for nb in notebooks:
+        try:
+            with open(nb, "r") as f:
+                nb_data = nbformat.read(f, as_version=4)
+            for cell in nb_data.cells:
+                if cell.cell_type == "code":
+                    for line in cell.source.split("\n"):
+                        line = line.strip()
+                        if line.startswith(
+                            ("import ", "from ")
+                        ) and not line.startswith("#"):
+                            all_imports.add(line.split("#")[0].strip())
+        except Exception as e:
+            print(f"❌ Error reading {nb.name}: {e}")
+            return False
+
+    # Test imports
+    failed = []
+    for imp in sorted(all_imports):
+        if imp.strip() == "import test":  # Skip teaching example
+            continue
+        try:
+            exec(imp)
+            print(f"✅ {imp}")
+        except Exception as e:
+            print(f"❌ {imp}: {e}")
+            failed.append(imp)
+
+    if failed:
+        print(f"\n❌ {len(failed)} imports failed")
+        return False
+    else:
+        print(f"\n🎉 All {len(all_imports)} imports work!")
+        return True
+
+
+if __name__ == "__main__":
+    sys.exit(0 if main() else 1)