Merge branch 'main' into os_installers

Author: enryH

.github/workflows/cdci.yml

@@ -17,6 +17,8 @@ jobs:
         python-version: ["3.9", "3.10", "3.11", "3.12", "3.13"]
     steps:
       - uses: actions/checkout@v4
+      - uses: psf/black@stable 
+      - uses: isort/isort-action@v1
       - name: Set up Python ${{ matrix.python-version }}
         uses: actions/setup-python@v5
         with:

.github/workflows/docs.yml

@@ -57,6 +57,7 @@ jobs:
         run: |
           find docs/streamlit_report/sections -type f -name "*.py" -exec sed -i 's|/home/runner/work/vuegen/vuegen/docs/||g' {} +
       - name: Publish Streamlit report to streamlit-example branch
+        if: startsWith(github.ref, 'refs/tags')
         uses: peaceiris/actions-gh-pages@v4
         with:
           github_token: ${{ secrets.GITHUB_TOKEN }}

docs/conf.py

@@ -17,7 +17,9 @@
 
 project = "vuegen"
 copyright = "2024, Multiomics-Analytics-Group"
-author = "Multiomics-Analytics-Group, Sebastián Ayala Ruano, Henry Webel, Alberto Santos"
+author = (
+    "Multiomics-Analytics-Group, Sebastián Ayala Ruano, Henry Webel, Alberto Santos"
+)
 PACKAGE_VERSION = metadata.version("vuegen")
 version = PACKAGE_VERSION
 release = PACKAGE_VERSION
@@ -54,6 +56,8 @@
 nb_execution_raise_on_error = True
 # Rendering
 nb_merge_streams = True
+# maximum execution time per cell in seconds
+nb_execution_timeout = 120
 
 # https://myst-nb.readthedocs.io/en/latest/authoring/custom-formats.html#write-custom-formats
 # ! if you use it, then you cannot directly execute the notebook in the browser in colab

pyproject.toml

@@ -60,3 +60,6 @@ docs = ["sphinx", "sphinx-book-theme", "myst-nb", "ipywidgets", "sphinx-new-tab-
 [tool.poetry.scripts]
 # https://python-poetry.org/docs/pyproject/#scripts
 vuegen = "vuegen.__main__:main"
+
+[tool.isort]
+profile = "black"

src/vuegen/__init__.py

@@ -1 +1 @@
-__version__ = "1.0.0"
+__version__ = "1.0.0"

src/vuegen/__main__.py

@@ -26,11 +26,11 @@ def main():
         # https://docs.python.org/3/library/argparse.html#printing-help
         parser.print_help()
         sys.exit(1)
-        
+
     if config_path and dir_path:
         print("Please provide only one of configuration file or directory path:\n")
         parser.print_help()
-        sys.exit(1) # otherwise could resort to either or ?
+        sys.exit(1)  # otherwise could resort to either or ?
 
     # Define logger suffix based on report type and name
     logger_suffix = f"{report_type}_report_{str(report_name)}"
@@ -39,11 +39,14 @@ def main():
     logger = get_logger(f"{logger_suffix}")
 
     # Generate the report
-    report_generator.get_report(report_type=report_type,
-                                logger=logger,
-                                config_path=config_path,
-                                dir_path=dir_path,
-                                streamlit_autorun=streamlit_autorun)
+    report_generator.get_report(
+        report_type=report_type,
+        logger=logger,
+        config_path=config_path,
+        dir_path=dir_path,
+        streamlit_autorun=streamlit_autorun,
+    )
+
 
-if __name__ == '__main__':
+if __name__ == "__main__":
     main()