Add notebooks folder and actions

.github/scripts/render_and_screenshot.py

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+import os
+import subprocess
+import nbformat
+from nbconvert import HTMLExporter
+from selenium import webdriver
+from webdriver_manager.chrome import ChromeDriverManager
+from selenium.webdriver.chrome.options import Options
+import time
+import re
+
+# Directories
+notebooks_dir = "notebooks"
+screenshots_dir = os.path.join(notebooks_dir, "screenshots")
+
+# Ensure screenshots directory exists
+os.makedirs(screenshots_dir, exist_ok=True)
+
+# Function to render Jupyter Notebook or Quarto file
+def render_file(file_path):
+    if file_path.endswith(".ipynb"):
+        html_exporter = HTMLExporter()
+        with open(file_path, "r", encoding="utf-8") as f:
+            notebook_content = nbformat.read(f, as_version=4) 
+        body, _ = html_exporter.from_notebook_node(notebook_content)
+        return body
+    elif file_path.endswith(".qmd"):
+        subprocess.run(["quarto", "render", file_path, "--no-execute"])
+        #subprocess.run(["quarto", "render", file_path])
+        html_path = file_path.replace(".qmd", ".html")
+        with open(html_path, "r", encoding="utf-8") as f:
+            body = f.read()
+        os.remove(html_path)  # Clean up
+        return body
+
+# Function to capture screenshot of HTML content
+def capture_screenshot(html_content, output_path):
+    # options = webdriver.ChromeOptions()
+    # options.add_argument("--headless")
+    # options.add_argument("--no-sandbox")
+    # options.add_argument("--disable-dev-shm-usage")
+
+    # driver = webdriver.Chrome(ChromeDriverManager().install(), options=options)
+     # Set up Chrome options
+    chrome_options = Options()
+    chrome_options.add_argument("--headless")
+    chrome_options.add_argument("--no-sandbox")
+    chrome_options.add_argument("--disable-dev-shm-usage")
+
+    # Ensure the WebDriver is passed the options only once
+    driver = webdriver.Chrome(options=chrome_options)
+
+    with open("temp.html", "w") as f:
+        f.write(html_content)
+
+    driver.get(f"file://{os.path.abspath('temp.html')}")
+    time.sleep(2)  # Allow time for rendering
+    driver.set_window_size(1200, 2000)
+    driver.save_screenshot(output_path)
+    driver.quit()
+    os.remove("temp.html")
+
+# Function to update README.md
+def update_readme(section, file_name, file_path, screenshot_path):
+    readme_path = os.path.join(notebooks_dir, "README.md")
+    title = file_name.split(".")[0]  # Get title from file name
+    title = title.replace("_", " ").title()  # Replace underscores with spaces and capitalize
+    screenshot_rel_path = os.path.relpath(screenshot_path, notebooks_dir)
+    file_rel_path = os.path.relpath(file_path, notebooks_dir)
+
+    # Load the README.md content
+    with open(readme_path, "r") as f:
+        content = f.read()
+
+    # Define the pattern to match an existing entry
+    pattern = re.compile(rf"(## {title}\n\[.*\]\({re.escape(file_rel_path)}\)\n!\[.*\]\(.*\))", re.MULTILINE)
+
+    # Create the new entry text
+    new_entry = f"## {title}\n[{file_name}]({file_rel_path})\n![{title}]({screenshot_rel_path})\n"
+
+    if pattern.search(content):
+        # If the entry exists, update it with the new screenshot path
+        content = pattern.sub(new_entry, content)
+    else:
+        # If no entry exists, add a new one under the correct section
+        if section == "Python":
+            content = re.sub(r"(# Python\n)", rf"\1{new_entry}\n", content)
+        elif section == "R":
+            content = re.sub(r"(# R\n)", rf"\1{new_entry}\n", content)
+
+    # Write the updated content back to README.md
+    with open(readme_path, "w") as f:
+        f.write(content)
+
+# Main function to process all new files
+def process_notebooks():
+    for root, _, files in os.walk(notebooks_dir):
+        for file in files:
+            if file.endswith(".ipynb") or file.endswith(".qmd"):
+                file_path = os.path.join(root, file)
+                section = "Python" if "Python" in root else "R"
+
+                print(f"Processing {file_path}...")
+
+                # Render file to HTML
+                html_content = render_file(file_path)
+
+                # Capture screenshot
+                screenshot_name = file.replace(".ipynb", ".png").replace(".qmd", ".png")
+                screenshot_path = os.path.join(screenshots_dir, screenshot_name)
+                capture_screenshot(html_content, screenshot_path)
+
+                # Update README
+                update_readme(section, file, file_path, screenshot_path)
+
+# Run the process
+process_notebooks()

.github/workflows/render_and_update_readme.yml

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+name: Render Notebooks and Update README
+
+on:
+  push:
+    paths:
+      - 'notebooks/R/**'
+      - 'notebooks/Python/**'
+  pull_request:
+    paths:
+      - 'notebooks/R/**'
+      - 'notebooks/Python/**'
+
+jobs:
+  render_and_update:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v3
+
+      # Install necessary dependencies
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: '3.x'
+
+      - name: Install dependencies
+        run: |
+          pip install nbconvert selenium webdriver-manager quarto-cli
+
+      # Render the added/changed files
+      - name: Render and take screenshots
+        run: |
+          python .github/scripts/render_and_screenshot.py
+
+      # Commit changes (screenshots and updated README)
+      - name: Commit and push changes
+        run: |
+          git config --global user.name "GitHub Actions"
+          git config --global user.email "[email protected]"
+          git add notebooks/screenshots README.md
+          git commit -m "Auto update README with new files and screenshots"
+          git push

.gitignore

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+.DS_Store
+.Rhistory
+*.Rproj
+shapes
+.Rproj.user
+*_storr
+shapes_errors
+*.sqlite
+*.sqlite-journal
+*.rds
+dev.R
+protectedseas.zip
+data/
+.venv/

notebooks/README.md

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+# Notebooks
+
+Here we present some notebooks covering several topics as OBIS data access, data cleaning, environmental information extraction, and data visualization.
+
+# R
+
+
+
+# Python
+
+
+
+------
+_Created by the OBIS secretariat_