Move test_notebooks script from CIL-Demos

env/cil_demos.yml

@@ -4,7 +4,7 @@ channels:
   - https://software.repos.intel.com/python/conda
 dependencies:
   - python=3.12
-  - ccpi::cil=24.3.0
+  - ccpi::cil=25.0.0
   - numpy=1.26
   - astra-toolbox=2.1=cuda*
   - ccpi::tigre=2.6

env/cil_test_demos.yml

@@ -0,0 +1,43 @@
+name: cil_test_demos
+channels:
+  - conda-forge
+  - nvidia
+  - https://software.repos.intel.com/python/conda
+dependencies:
+  # base (vis. recipe/conda_build_config.yaml)
+  - python >=3.10,<3.13
+  - numpy >=1.23,<2
+  - libgomp      # [linux]
+  - ccpi::cil=24.3.0
+  - ccpi::cil-data >=22
+  - ccpi::tigre 2.6
+  - ccpi::ccpi-regulariser 24.0.1
+  - ccpi::tomophantom 2.0.0
+  - astra-toolbox 2.1 cuda*
+  - cvxpy
+  - python-wget
+  - ipykernel 
+  - scikit-image
+  - packaging
+  - cmake >=3.16
+  - setuptools >=64
+  - ipp-include 2021.12
+  - ipp-devel 2021.12
+  - ipp 2021.12
+  - ipywidgets
+  - scipy >=1.4
+  - matplotlib-base >=3.3
+  - h5py
+  - pillow
+  - dxchange
+  - olefile >=0.46
+  - pywavelets
+  - numba
+  - tqdm
+  - zenodo_get >=1.6
+  - pytest
+  - nbmake
+  - tectonic
+  - pip
+  - pip:
+    - unittest-parametrize

test_notebooks_sequential.py

@@ -0,0 +1,218 @@
+import pytest
+import nbformat
+import os
+import re
+import shutil
+import subprocess
+from datetime import datetime
+
+DATA_PATH = '/mnt/share/materials/SIRF/Fully3D/CIL/'
+DATA_PATH_ALT = '/mnt/share/materials/CIL/'
+
+SCRIPT_DIR = os.path.dirname(os.path.abspath(__file__))
+CIL_DEMOS_DIR = os.path.expanduser(os.path.join('~', 'CIL-Demos'))
+
+PDF_OUTPUT_DIR = os.path.join(SCRIPT_DIR, 'html_outputs')
+TMP_OUTPUT_DIR = os.path.join(SCRIPT_DIR, 'tmp_notebooks')
+
+os.makedirs(TMP_OUTPUT_DIR, exist_ok=True)
+os.makedirs(PDF_OUTPUT_DIR, exist_ok=True)
+
+folders = [
+    os.path.join(CIL_DEMOS_DIR, 'demos'),
+    os.path.join(CIL_DEMOS_DIR, 'how-to')
+]
+
+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')
+
+    shutil.copy(original_path, tmp_path)
+
+    with open(tmp_path, 'r') as f:
+        notebook = nbformat.read(f, as_version=4)
+
+    warning_cell = nbformat.v4.new_code_cell(
+    source="""import warnings
+notebook_warnings = []
+def warning_collector(message, category, filename, lineno, file=None, line=None):
+    notebook_warnings.append(f"{category.__name__}: {message} (File {filename}, line {lineno})")
+warnings.showwarning = warning_collector
+"""
+    )
+
+    notebook.cells.insert(0, warning_cell)
+
+    for cell in notebook.cells:
+        if cell.cell_type == 'code':
+            cell.source = re.sub(r'/mnt/materials/SIRF/Fully3D/CIL/', DATA_PATH, cell.source)
+            cell.source = re.sub(r'/mnt/materials/CIL/', DATA_PATH_ALT, cell.source)
+            if '# %load' in cell.source:
+                try:
+                    snippet_file = cell.source.split('snippets/')[1].split('\'')[0]
+                    snippet_path = os.path.join(os.path.dirname(original_path), 'snippets', snippet_file)
+                    with open(snippet_path, 'r') as sf:
+                        cell.source = sf.read()
+                except Exception as e:
+                    with open(LOG_NAME, "a") as log_file:
+                        log_file.write(f"Snippet load failed for {original_path}: {e}\n")
+            if '...' in cell.source:
+                cell.source = ""
+
+    with open(tmp_path, 'w') as f:
+        nbformat.write(notebook, f)
+
+    return tmp_path
+
+def run_notebook_test(tmp_path, original_path, all_warnings):
+    original_folder = os.path.dirname(os.path.abspath(original_path))
+    tmp_abs_path = os.path.abspath(tmp_path)
+    with open(LOG_NAME, "a") as log_file:
+        result = subprocess.run(
+            [
+                'pytest',
+                '--nbmake',
+                '--nbmake-kernel=cil_test_demos',
+                '--nbmake-timeout=900',
+                '--overwrite',
+                tmp_abs_path
+            ],
+            cwd=original_folder,
+            stdout=log_file,
+            stderr=subprocess.STDOUT,
+            text=True,
+            env={**os.environ, 'PYTHONPATH': original_folder}
+        )
+
+    try:
+        with open(tmp_path, 'r') as f:
+            nb = nbformat.read(f, as_version=4)
+
+        for cell in nb.cells:
+            if cell.cell_type == 'code' and 'notebook_warnings' not in cell.source:
+                for out in cell.get('outputs', []):
+                    if out.output_type == 'stream':
+                        text = out.get('text', '')
+                        for line in text.splitlines():
+                            if 'Warning' in line or 'Error' in line:
+                                all_warnings.setdefault(tmp_path, []).append(line)
+
+        if tmp_path in all_warnings:
+            with open(LOG_NAME, "a") as log_file:
+                log_file.write(f"\n=== Warnings in {tmp_path} ===\n")
+                for w in all_warnings[tmp_path]:
+                    log_file.write(w + "\n")
+
+    except Exception:
+        pass
+
+    return result.returncode == 0
+
+def convert_notebook_to_html(tmp_path):
+    parent_dir_name = os.path.basename(os.path.dirname(tmp_path))
+    subfolder_path = os.path.join(PDF_OUTPUT_DIR, parent_dir_name)
+    os.makedirs(subfolder_path, exist_ok=True)
+    html_output_path = os.path.join(subfolder_path, os.path.basename(tmp_path).replace('.ipynb', '.html'))
+    subprocess.run(
+        [
+            'jupyter', 'nbconvert',
+            '--to', 'html',
+            '--template', 'lab',
+            '--HTMLExporter.embed_mathjax=True',
+            '--HTMLExporter.mathjax_url=nbextensions/mathjax/MathJax.js?config=TeX-AMS_HTML',
+            '--output', os.path.basename(html_output_path),
+            '--output-dir', subfolder_path,
+            tmp_path
+        ],
+        cwd=os.path.dirname(tmp_path),
+        stdout=subprocess.DEVNULL,
+        stderr=subprocess.DEVNULL,
+        check=True
+    )
+    with open(LOG_NAME, "a") as log_file:
+        log_file.write(f"Saved HTML to: {html_output_path}\n")
+
+def convert_notebook_to_pdf(tmp_path):
+    subprocess.run(
+        ['jupyter', 'nbconvert', '--to', 'latex', tmp_path],
+        cwd=os.path.dirname(tmp_path),
+        stdout=subprocess.DEVNULL,
+        stderr=subprocess.DEVNULL,
+        check=True
+    )
+    tex_file = tmp_path.replace('.ipynb', '.tex')
+    parent_dir_name = os.path.basename(os.path.dirname(tmp_path))
+    subfolder_path = os.path.join(PDF_OUTPUT_DIR, parent_dir_name)
+    os.makedirs(subfolder_path, exist_ok=True)
+    subprocess.run(
+        ['tectonic', tex_file, '--print', '--outdir', subfolder_path],
+        cwd=os.path.dirname(tmp_path),
+        stdout=subprocess.DEVNULL,
+        stderr=subprocess.DEVNULL,
+        check=True
+    )
+    pdf_name = os.path.basename(tex_file).replace('.tex', '.pdf')
+    subfolder_pdf_path = os.path.join(subfolder_path, pdf_name)
+    with open(LOG_NAME, "a") as log_file:
+        log_file.write(f"Saved PDF to: {subfolder_pdf_path}\n")
+
+def cleanup_notebook_files(tmp_path):
+    try:
+        os.remove(tmp_path)
+    except Exception:
+        pass
+    tex_file = tmp_path.replace('.ipynb', '.tex')
+    if os.path.exists(tex_file):
+        try:
+            os.remove(tex_file)
+        except Exception:
+            pass
+    files_dir = tmp_path.replace('.ipynb', '_files')
+    if os.path.exists(files_dir):
+        try:
+            shutil.rmtree(files_dir)
+        except Exception:
+            pass
+
+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')
+
+                    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
+
+                    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'
+
+    with open(LOG_NAME, "a") as log_file:
+        log_file.write("\n======== Notebook Test Summary =========\n")
+        for nb, status in results.items():
+            log_file.write(f"{nb}: {status}\n")
+
+        log_file.write("\n======== All Warnings Summary =========\n")
+        for nb, warns in all_warnings.items():
+            log_file.write(f"\n{nb}:\n")
+            for w in warns:
+                log_file.write(f"  {w}\n")
+
+if __name__ == "__main__":
+    main()