Improve and document notebook test script

README.md

@@ -4,3 +4,61 @@ Static hosting:
 
 - Source: https://github.com/TomographicImaging/scripts
 - Rendered: https://tomographicimaging.github.io/scripts
+
+## Environment files for installing software
+
+### CIL-Demos
+`cil_demos.yml` - for installing the latest release of CIL-Demos on a system with a GPU.
+`cil_demos_cpu.yml` - for installing the latest release of CIL-Demos on a system without a GPU.
+
+### CIL
+`cil.yml` - for installing the latest release of CIL.
+`cil_test.yml` - for installing the latest release of CIL with the requirements for running the tests.
+
+### CILViewer
+`cilviewer_ui` - for installing the latest release of CILViewer, with packages needed to run the GUI.
+
+
+## Script for Testing CIL demos
+
+`test_notebooks_sequential.py` is a script for testing the CIL-Demos
+
+To use it:
+1. Clone [CIL-Demos](https://github.com/TomographicImaging/CIL-Demos), if you haven't already, and move to the branch of CIL-Demos you would like to test.
+2. Clone [scripts](https://github.com/TomographicImaging/scripts)
+3. Download all datasets used by the [CIL-Demos](https://github.com/TomographicImaging/CIL-Demos) notebooks you would like to test.
+4. Create an environment using: 
+    ```sh
+    conda env create -f https://tomographicimaging.github.io/scripts/env/cil_test_demos.yml
+    ```
+5. Clone [CIL](https://github.com/TomographicImaging/CIL), if you haven't already, and move to the branch of CIL you would like to test the demos with.
+6. Activate the environment you created:
+    ```sh
+    conda activate cil_test_demos
+    ```
+7. Navigate into the CIL directory and install CIL into this environment:
+    ```sh
+    pip install -e .
+    ```
+8. The script uses `nbmake` and needs to point to the kernel to run the notebooks with. We need to make sure our conda environment is registered with the correct jupyter kernel name. Run:
+    ```sh
+    jupyter kernelspec list
+    ```
+    If there is a kernel with name `cil_test_demos` then move to step 9. If not, run:
+    ```sh
+    python -m ipykernel install --user --name cil_test_demos --display-name "cil_test_demos"
+    ```
+9. At the top of the `test_notebooks_sequential.py` file, update these variables:
+    `CIL_DEMOS_DIR` - should point to your clone of CIL-Demos
+    `DATA_PATH` and `DATA_PATH_ALT` should point to directories where the CIL-Demos data is saved.
+10. Run `test_notebooks_sequential.py`. This is likely to take quite a long time. It will create the following inside the `scripts` directory:
+
+    `test_notebooks_*.log` log file (with name including date and time of run)
+        This shows which notebooks have run and whether they have passed or failed.
+
+    `tmp_notebooks` directory
+        This contains the run and rendered `.ipynb` notebook files.
+
+    `html_outputs` directory
+        This contains run and rendered notebooks as `html` files.
+

test_notebooks_sequential.py

@@ -25,15 +25,42 @@
 
 LOG_NAME = "test_notebooks_" + datetime.now().strftime("%Y%m%d_%H%M%S") + ".log"
 
-def preprocess_notebook(original_path):
-    rel_path = os.path.relpath(original_path, CIL_DEMOS_DIR)
-    rel_path = rel_path.replace("..", "_")
-    tmp_path = os.path.join(TMP_OUTPUT_DIR, rel_path)
-    tmp_dir = os.path.dirname(tmp_path)
-    os.makedirs(tmp_dir, exist_ok=True)
-    tmp_path = tmp_path.replace('.ipynb', '_tmp.ipynb')
+def copy_all_files():
+    """
+    Copy all *.ipynb and *.py files from `folders` into TMP_OUTPUT_DIR,
+    preserving relative directory structure.
+    Renames any *.ipynb files to *_tmp.ipynb
+
+    Returns a list of tuples: (original_path, copied_path) for all notebooks.
+    """
+    notebook_paths = []
+    for folder in folders:
+        for root, _, files in os.walk(folder):
+            for file in files:
+                if file.endswith('.ipynb') or file.endswith('.py'):
+                    original_path = os.path.join(root, file)
+
+                    rel_path = os.path.relpath(original_path, CIL_DEMOS_DIR)
+                    rel_path = rel_path.replace("..", "_")
+                    tmp_path = os.path.join(TMP_OUTPUT_DIR, rel_path)
+                    tmp_dir = os.path.dirname(tmp_path)
+                    os.makedirs(tmp_dir, exist_ok=True)
+                    if file.endswith('.ipynb') and not file.endswith('_tmp.ipynb'):
+                        tmp_path = tmp_path.replace('.ipynb', '_tmp.ipynb')
+                        if os.path.exists(tmp_path):
+                            with open(LOG_NAME, "a") as log_file:
+                                log_file.write(f"Skipping (tmp exists): {original_path}\n")
+
+                    if not os.path.exists(tmp_path):
+                        shutil.copy(original_path, tmp_path)
+
+                        if file.endswith('.ipynb'):
+                            notebook_paths.append((original_path, tmp_path))
+    return notebook_paths
+
 
-    shutil.copy(original_path, tmp_path)
+
+def preprocess_notebook(original_path, tmp_path):
 
     with open(tmp_path, 'r') as f:
         notebook = nbformat.read(f, as_version=4)
@@ -183,25 +210,19 @@ def cleanup_notebook_files(tmp_path):
 def main():
     results = {}
     all_warnings = {}
-    for folder in folders:
-        for root, _, files in os.walk(folder):
-            for file in files:
-                if file.endswith('.ipynb') and not file.endswith('_tmp.ipynb'):
-                    original_path = os.path.join(root, file)
-                    rel_path = os.path.relpath(original_path, CIL_DEMOS_DIR)
-                    rel_path = rel_path.replace("..", "_")
-                    tmp_path = os.path.join(TMP_OUTPUT_DIR, rel_path).replace('.ipynb', '_tmp.ipynb')
+    with open(LOG_NAME, "a") as log:
+        log.write("=== Copying Files ===\n")
 
-                    if os.path.exists(tmp_path):
-                        with open(LOG_NAME, "a") as log_file:
-                            log_file.write(f"Skipping (tmp exists): {original_path}\n")
-                        continue
+    notebooks = copy_all_files()
 
-                    with open(LOG_NAME, "a") as log_file:
-                        log_file.write(f"\n=== Processing notebook: {original_path} ===\n")
-                    tmp_path = preprocess_notebook(original_path)
-                    passed = run_notebook_test(tmp_path, original_path, all_warnings)
-                    results[original_path] = 'passed' if passed else 'failed'
+    for original_path, copied_path in notebooks:
+
+
+        with open(LOG_NAME, "a") as log_file:
+            log_file.write(f"\n=== Processing notebook: {original_path} ===\n")
+        tmp_path = preprocess_notebook(original_path, copied_path)
+        passed = run_notebook_test(tmp_path, original_path, all_warnings)
+        results[original_path] = 'passed' if passed else 'failed'
 
     with open(LOG_NAME, "a") as log_file:
         log_file.write("\n======== Notebook Test Summary =========\n")