🎨 format docs as they were adapted

- api changes needed to be reflected in docs.
- format docs
- enforce using action

Author: enryH

.github/workflows/cdci.yml

@@ -18,6 +18,8 @@ jobs:
     steps:
       - uses: actions/checkout@v4
       - uses: psf/black@stable
+        with:
+          jupyter: true
       - uses: isort/isort-action@v1
       - name: Set up Python ${{ matrix.python-version }}
         uses: actions/setup-python@v5

docs/vuegen_basic_case_study.ipynb

@@ -67,7 +67,7 @@
    },
    "outputs": [],
    "source": [
-    "# Vuegen library \n",
+    "# Vuegen library\n",
     "%pip install vuegen"
    ]
   },
@@ -78,6 +78,7 @@
    "outputs": [],
    "source": [
     "import os\n",
+    "\n",
     "IN_COLAB = \"COLAB_GPU\" in os.environ"
    ]
   },
@@ -181,14 +182,20 @@
     "# run_streamlit = True # uncomment line to run the streamlit report\n",
     "# Launch the Streamlit report depneding on the platform\n",
     "if not IN_COLAB and run_streamlit:\n",
-    "   !streamlit run streamlit_report/sections/report_manager.py\n",
+    "    !streamlit run streamlit_report/sections/report_manager.py\n",
     "elif run_streamlit:\n",
-    "   # see: https://discuss.streamlit.io/t/how-to-launch-streamlit-app-from-google-colab-notebook/42399\n",
-    "   print(\"Password/Enpoint IP for localtunnel is:\",urllib.request.urlopen('https://ipv4.icanhazip.com').read().decode('utf8').strip(\"\\n\"))\n",
-    "   # Run the Streamlit app in the background\n",
-    "   !streamlit run streamlit_report/sections/report_manager.py --server.address=localhost &>/content/logs.txt &\n",
-    "   # Expose the Streamlit app on port 8501\n",
-    "   !npx localtunnel --port 8501 --subdomain vuegen-demo\n",
+    "    # see: https://discuss.streamlit.io/t/how-to-launch-streamlit-app-from-google-colab-notebook/42399\n",
+    "    print(\n",
+    "        \"Password/Enpoint IP for localtunnel is:\",\n",
+    "        urllib.request.urlopen(\"https://ipv4.icanhazip.com\")\n",
+    "        .read()\n",
+    "        .decode(\"utf8\")\n",
+    "        .strip(\"\\n\"),\n",
+    "    )\n",
+    "    # Run the Streamlit app in the background\n",
+    "    !streamlit run streamlit_report/sections/report_manager.py --server.address=localhost &>/content/logs.txt &\n",
+    "    # Expose the Streamlit app on port 8501\n",
+    "    !npx localtunnel --port 8501 --subdomain vuegen-demo\n",
     "else:\n",
     "    print(\"Streamlit report not executed, set run_streamlit to True to run the report\")"
    ]
@@ -208,7 +215,9 @@
    "source": [
     "# Generate the report\n",
     "report_type = \"html\"\n",
-    "report_dir, config_path = report_generator.get_report(dir_path = base_output_dir, report_type = report_type, logger = None)\n",
+    "report_dir, config_path = report_generator.get_report(\n",
+    "    dir_path=base_output_dir, report_type=report_type, logger=None\n",
+    ")\n",
     "print(f\"Report generated at: {report_dir}\")"
    ]
   },
@@ -236,11 +245,15 @@
     "vuegen_logo_path = \"https://raw.githubusercontent.com/Multiomics-Analytics-Group/vuegen/main/docs/images/vuegen_logo.svg\"\n",
     "\n",
     "# Load the YAML file\n",
-    "print(f\"Loading the YAML config file from: {config_path}\") # generated based on directory path above\n",
+    "print(\n",
+    "    f\"Loading the YAML config file from: {config_path}\"\n",
+    ")  # generated based on directory path above\n",
     "config = load_yaml_config(config_path)\n",
     "\n",
     "# Update the logo and graphical abstract with the URL\n",
-    "config[\"report\"].update({\"logo\": vuegen_logo_path, \"graphical_abstract\": vuegen_logo_path})"
+    "config[\"report\"].update(\n",
+    "    {\"logo\": vuegen_logo_path, \"graphical_abstract\": vuegen_logo_path}\n",
+    ")"
    ]
   },
   {
@@ -258,15 +271,17 @@
    "source": [
     "# Update the description for the EDA section\n",
     "for section in config[\"sections\"]:\n",
-    "    if section[\"title\"] == \"Plots\":  \n",
+    "    if section[\"title\"] == \"Plots\":\n",
     "        section[\"description\"] = \"This section contains example plots\"\n",
     "\n",
     "# Update the description for the alpha diversity subsection from the Metagenomics section\n",
     "for section in config[\"sections\"]:\n",
     "    if section[\"title\"] == \"Dataframes\":\n",
     "        for subsection in section[\"subsections\"]:\n",
     "            if subsection[\"title\"] == \"All Formats\":\n",
-    "                subsection[\"description\"] = \"This subsection contains example dataframes.\"\n"
+    "                subsection[\"description\"] = (\n",
+    "                    \"This subsection contains example dataframes.\"\n",
+    "                )"
    ]
   },
   {
@@ -285,11 +300,11 @@
     "# Define new plot with a URL as the file path\n",
     "vuegen_abst_fig = {\n",
     "    \"title\": \"Graphical overview of VueGen’s workflow and components\",\n",
-    "    \"file_path\": \"https://raw.githubusercontent.com/Multiomics-Analytics-Group/vuegen/main/docs/images/vuegen_graph_abstract.png\", \n",
+    "    \"file_path\": \"https://raw.githubusercontent.com/Multiomics-Analytics-Group/vuegen/main/docs/images/vuegen_graph_abstract.png\",\n",
     "    \"description\": \"\",\n",
     "    \"caption\": \"The diagram illustrates the processing pipeline of VueGen, starting from either a directory or a YAML configuration file. Reports consist of hierarchical sections and subsections, each containing various components such as plots, dataframes, Markdown, HTML, and data retrieved via API calls.\",\n",
     "    \"component_type\": \"plot\",\n",
-    "    \"plot_type\": \"static\"\n",
+    "    \"plot_type\": \"static\",\n",
     "}\n",
     "\n",
     "# Add the plot to the Sample Provenance subsection in the EDA section\n",
@@ -321,7 +336,9 @@
    "source": [
     "# Test the changes by generarating the report from the modified YAML file\n",
     "report_type = \"streamlit\"\n",
-    "_ = report_generator.get_report(config_path = config_path, report_type = report_type, logger = None)"
+    "_ = report_generator.get_report(\n",
+    "    config_path=config_path, report_type=report_type, logger=None\n",
+    ")"
    ]
   },
   {
@@ -334,14 +351,20 @@
     "# run_streamlit = True # uncomment line to run the streamlit report\n",
     "# Launch the Streamlit report depneding on the platform\n",
     "if not IN_COLAB and run_streamlit:\n",
-    "   !streamlit run streamlit_report/sections/report_manager.py\n",
+    "    !streamlit run streamlit_report/sections/report_manager.py\n",
     "elif run_streamlit:\n",
-    "   # see: https://discuss.streamlit.io/t/how-to-launch-streamlit-app-from-google-colab-notebook/42399\n",
-    "   print(\"Password/Enpoint IP for localtunnel is:\",urllib.request.urlopen('https://ipv4.icanhazip.com').read().decode('utf8').strip(\"\\n\"))\n",
-    "   # Run the Streamlit app in the background\n",
-    "   !streamlit run streamlit_report/sections/report_manager.py --server.address=localhost &>/content/logs.txt &\n",
-    "   # Expose the Streamlit app on port 8501\n",
-    "   !npx localtunnel --port 8501 --subdomain vuegen-demo\n",
+    "    # see: https://discuss.streamlit.io/t/how-to-launch-streamlit-app-from-google-colab-notebook/42399\n",
+    "    print(\n",
+    "        \"Password/Enpoint IP for localtunnel is:\",\n",
+    "        urllib.request.urlopen(\"https://ipv4.icanhazip.com\")\n",
+    "        .read()\n",
+    "        .decode(\"utf8\")\n",
+    "        .strip(\"\\n\"),\n",
+    "    )\n",
+    "    # Run the Streamlit app in the background\n",
+    "    !streamlit run streamlit_report/sections/report_manager.py --server.address=localhost &>/content/logs.txt &\n",
+    "    # Expose the Streamlit app on port 8501\n",
+    "    !npx localtunnel --port 8501 --subdomain vuegen-demo\n",
     "else:\n",
     "    print(\"Streamlit report not executed, set run_streamlit to True to run the report\")"
    ]
@@ -361,13 +384,15 @@
    "source": [
     "# Test the changes by generarating the report from the modified YAML file\n",
     "report_type = \"html\"\n",
-    "_ = report_generator.get_report(config_path = config_path, report_type = report_type, logger = None)"
+    "_ = report_generator.get_report(\n",
+    "    config_path=config_path, report_type=report_type, logger=None\n",
+    ")"
    ]
   }
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "vuegen",
+   "display_name": "vuegen_py312",
    "language": "python",
    "name": "python3"
   },
@@ -381,7 +406,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.9.21"
+   "version": "3.12.9"
   }
  },
  "nbformat": 4,