Entrypoint

.github/workflows/cdci.yml

@@ -10,7 +10,7 @@ on:
 
 jobs:
   test:
-    name: Test
+    name: Unittests+streamlit
     runs-on: ubuntu-latest
     strategy:
       matrix:
@@ -30,4 +30,59 @@ jobs:
           pip install -e .
       - name: Run tests
         run: python -m pytest tests
+      - name: Execute streamlit report
+        run: |
+          cd docs
+          vuegen --config example_data/MicW2Graph/report_config_micw2graph.yaml
 
+  other-reports:
+    name: Integration tests
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.9", "3.10", "3.11", "3.12", "3.13"]
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+          cache: 'pip' # caching pip dependencies
+          cache-dependency-path: '**/pyproject.toml'
+      - name: Install dependencies
+        run: |
+          pip install --upgrade pip
+          pip install -e ".[quarto]"
+      - name: Execute streamlit report (to check)
+        run: |
+          cd docs
+          vuegen -c example_data/MicW2Graph/report_config_micw2graph.yaml
+      # repeat for easier inspection on GitHub:
+      - name: quarto html report
+        run: |
+          cd docs
+          vuegen -c example_data/MicW2Graph/report_config_micw2graph.yaml -rt html
+      - name: quarto pdf report
+        run: |
+          cd docs
+          vuegen -c example_data/MicW2Graph/report_config_micw2graph.yaml -rt pdf
+      - name: quarto docx report
+        run: |
+          cd docs
+          vuegen -c example_data/MicW2Graph/report_config_micw2graph.yaml -rt docx
+      - name: quarto odt report
+        run: |
+          cd docs
+          vuegen -c example_data/MicW2Graph/report_config_micw2graph.yaml -rt odt
+      - name: quarto revealjs report
+        run: |
+          cd docs
+          vuegen -c example_data/MicW2Graph/report_config_micw2graph.yaml -rt revealjs
+      - name: quarto pptx report
+        run: |
+          cd docs
+          vuegen -c example_data/MicW2Graph/report_config_micw2graph.yaml -rt pptx
+      - name: quarto jupyter report
+        run: |
+          cd docs
+          vuegen -c example_data/MicW2Graph/report_config_micw2graph.yaml -rt jupyter

.gitignore

@@ -123,7 +123,8 @@ quarto_report/
 .DS_Store
 
 # Extra info
-UML_diagrams/
-Graphical_abstract/
+docs/images/UML_diagrams/
+docs/images/Graphical_abstract/
+docs/images/Nfcore_module_figure
 docs/presentations/
 test.py

README.md

@@ -70,15 +70,18 @@ quarto check
 Run VueGen using a configuration file with the following command:
 
 ```bash
-python vuegen/main.py --config docs/example_data/MicW2Graph/report_config_micw2graph.yaml --report_type streamlit
+cd docs
+vuegen --config example_data/MicW2Graph/report_config_micw2graph.yaml --report_type streamlit
 ```
 
+> 💡 If `vuegen` does not work, try `python -m vuegen` instead.
+
 By default, the `streamlit_autorun` argument is set to False, but you can use it in case you want to automatically run the streamlit app.
 
 It's also possible to provide a directory instead of a configuration file:
 
 ```bash
-python vuegen/main.py --directory docs/example_data/MicW2Graph/ --report_type streamlit
+vuegen --directory docs/example_data/MicW2Graph/ --report_type streamlit
 ```
 
 The current report types are streamlit, html, pdf, docx, odt, revealjs, pptx, and jupyter.

pyproject.toml

@@ -27,6 +27,7 @@ kaleido = "0.2.0"
 vl-convert-python = "^1.7.0"
 dataframe-image = "^0.2.6"
 strenum = { version = "^0.4.15", python = "<3.11" }
+
 # optional doc depencencies, follow approach as described here:
 # https://github.com/python-poetry/poetry/issues/2567#issuecomment-646766059
 sphinx = {version="*", optional=true}
@@ -35,13 +36,12 @@ myst-nb = {version="*", optional=true}
 ipywidgets = {version="*", optional=true}
 sphinx-new-tab-link = {version = "!=0.2.2", optional=true}
 jupytext = {version="*", optional=true}
-# quartro
+# quarto
 quarto-cli = {version="*", optional=true}
 
 [tool.poetry.group.dev.dependencies]
 ipykernel = {version="^6.29.5", optional=true}
 
-
 [build-system]
 requires = ["poetry-core"]
 build-backend = "poetry.core.masonry.api"
@@ -52,5 +52,6 @@ streamlit = ["streamlit"]
 quarto = ["quarto-cli", "ipykernel"]
 docs = ["sphinx", "sphinx-book-theme", "myst-nb", "ipywidgets", "sphinx-new-tab-link", "jupytext"]
 
-# [project.scripts]
-# my-script = "vuegen.main:main"
+[tool.poetry.scripts]
+# https://python-poetry.org/docs/pyproject/#scripts
+vuegen = "vuegen.__main__:main"

tests/test_module_imports.py

@@ -1,7 +1,7 @@
 
 def test_imports():
     import vuegen
-    import vuegen.main
+    import vuegen.__main__
     import vuegen.quarto_reportview
     import vuegen.report
     import vuegen.report_generator

vuegen/__main__.py

@@ -0,0 +1,49 @@
+import sys
+from pathlib import Path
+
+from vuegen import report_generator
+from vuegen.utils import get_logger, get_parser
+
+
+def main():
+    # Parse command-line arguments
+    parser = get_parser(prog_name="VueGen")
+    args = parser.parse_args()
+
+    # Determine the vuegen arguments
+    config_path = args.config
+    dir_path = args.directory
+    report_type = args.report_type
+    streamlit_autorun = args.streamlit_autorun
+
+    # Determine the report name for logger suffix
+    if config_path:
+        report_name = Path(config_path).stem
+    elif dir_path:
+        report_name = Path(dir_path).name
+    else:
+        print("Please provide a configuration file or directory path:\n")
+        # 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 ?
+
+    # Define logger suffix based on report type and name
+    logger_suffix = f"{report_type}_report_{str(report_name)}"
+
+    # Initialize logger
+    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)
+
+if __name__ == '__main__':
+    main()

vuegen/quarto_reportview.py

@@ -117,6 +117,8 @@ def run_report(self, output_dir: str = BASE_DIR) -> None:
         """
         try:
             subprocess.run(["quarto", "render", os.path.join(output_dir, f"{self.BASE_DIR}.qmd")], check=True)
+            if self.report_type == r.ReportType.JUPYTER:
+                subprocess.run(["quarto", "convert", os.path.join(output_dir, f"{self.BASE_DIR}.qmd")], check=True)
             self.report.logger.info(f"'{self.report.title}' '{self.report_type}' report rendered")
         except subprocess.CalledProcessError as e:
             self.report.logger.error(f"Error running '{self.report.title}' {self.report_type} report: {str(e)}")
@@ -174,8 +176,12 @@ def _create_yaml_header(self) -> str:
     toc: false
     output: true""",
 r.ReportType.JUPYTER: """
-  jupyter:
-    kernel: python3"""
+  html:
+    toc: true
+    toc-location: left
+    toc-depth: 3
+    page-layout: full
+    self-contained: true"""
         }
 
         # Create a key based on the report type and format

vuegen/streamlit_reportview.py

@@ -127,7 +127,13 @@ def run_report(self, output_dir: str = SECTIONS_DIR) -> None:
             # If autorun is False, print instructions for manual execution
             self.report.logger.info(f"All the scripts to build the Streamlit app are available at {output_dir}")
             self.report.logger.info(f"To run the Streamlit app, use the following command:")
-            self.report.logger.info(f"streamlit run {os.path.join(output_dir, self.REPORT_MANAG_SCRIPT)}")             
+            self.report.logger.info(f"streamlit run {os.path.join(output_dir, self.REPORT_MANAG_SCRIPT)}")
+            msg = (
+                f"\nAll the scripts to build the Streamlit app are available at: {output_dir}\n\n"
+                f"To run the Streamlit app, use the following command:\n\n"
+                f"\tstreamlit run {os.path.join(output_dir, self.REPORT_MANAG_SCRIPT)}"
+                )
+            print(msg)
 
     def _format_text(self, text: str, type: str, level: int = 1, color: str = '#000000', text_align: str = 'center') -> str:
         """

vuegen/utils.py

@@ -13,9 +13,9 @@
     from strenum import StrEnum
 
 from io import StringIO
+from pathlib import Path
 from typing import Type
 from urllib.parse import urlparse
-from pathlib import Path
 
 import networkx as nx
 import requests
@@ -145,7 +145,7 @@ def create_folder(directory_path: str, is_nested: bool = False) -> bool:
     except OSError as e:
         raise OSError(f"Error creating directory '{directory_path}': {e}")
 
-def get_args(prog_name: str, others: dict = {}) -> argparse.Namespace:
+def get_parser(prog_name: str, others: dict = {}) -> argparse.Namespace:
     """
     Initiates argparse.ArgumentParser() and adds common arguments.
 
@@ -193,7 +193,7 @@ def get_args(prog_name: str, others: dict = {}) -> argparse.Namespace:
         "-rt",
         "--report_type",
         type = str,
-        default = None, 
+        default = 'streamlit', 
         help = "Type of the report to generate (streamlit, html, pdf, docx, odt, revealjs, pptx, or jupyter)."
     )
     parser.add_argument(
@@ -205,7 +205,7 @@ def get_args(prog_name: str, others: dict = {}) -> argparse.Namespace:
     )
 
     # Parse arguments
-    return parser.parse_args()
+    return parser
 
 def fetch_file_stream(file_path: str) -> StringIO:
     """