🐛 Fix: Add vuegen logo in the footer of reports from url and add small changes to the demo notebook

Author: sayalaruano

.gitignore

@@ -128,5 +128,5 @@ docs/images/Graphical_abstract/
 docs/images/Nfcore_module_figure
 docs/presentations/
 docs/example_data/Earth_microbiome_vuegen_demo_notebook_test/
-docs/vuegen_case_study_earth_microbiome test.ipynb
+docs/vuegen_case_study_earth_microbiome_test.ipynb
 test.py

docs/vuegen_case_study_earth_microbiome.ipynb

@@ -65,8 +65,18 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "# Install required libraries\n",
-    "%pip install vuegen cartopy seaborn biom-format"
+    "# Vuegen library \n",
+    "%pip install vuegen"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Libraries for the notebook\n",
+    "%pip install cartopy seaborn biom-format"
    ]
   },
   {
@@ -1355,7 +1365,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "### 4.2. HTML report"
+    "### 4.2. Revealjs report"
    ]
   },
   {
@@ -1364,7 +1374,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "report_type = \"html\"\n",
+    "report_type = \"revealjs\"\n",
     "report_name = \"Earth_microbiome_vuegen_demo_notebook_dir\"\n",
     "\n",
     "# Initialize logger\n",
@@ -1540,7 +1550,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "### 5.6. HTML report with the extended configuration file"
+    "### 5.6. Revealjs report with the extended configuration file"
    ]
   },
   {
@@ -1550,7 +1560,7 @@
    "outputs": [],
    "source": [
     "# Test the changes by generarating the report from the modified YAML file\n",
-    "report_type = \"html\"\n",
+    "report_type = \"Revealjs\"\n",
     "report_name = \"Earth_microbiome_vuegen_demo_notebook_config_extended\"\n",
     "\n",
     "# Initialize logger\n",
@@ -1563,7 +1573,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "vuegen",
+   "display_name": "vuegen-IFxaxej_-py3.12",
    "language": "python",
    "name": "python3"
   },
@@ -1577,7 +1587,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.9.21"
+   "version": "3.12.6"
   }
  },
  "nbformat": 4,

src/vuegen/quarto_reportview.py

@@ -172,7 +172,7 @@ def _create_yaml_header(self) -> str:
         <footer class="footer">
             This report was generated with 
             <a href="https://github.com/Multiomics-Analytics-Group/vuegen" target="_blank">
-                <img src="../docs/images/vuegen_logo.svg" alt="VueGen" width="65px">
+                <img src="https://raw.githubusercontent.com/Multiomics-Analytics-Group/vuegen/main/docs/images/vuegen_logo.svg" alt="VueGen" width="65px">
             </a>
             | © 2025 <a href="https://github.com/Multiomics-Analytics-Group" target="_blank">Multiomics Network Analytics Group (MoNA)</a>
         </footer>""",
@@ -218,7 +218,7 @@ def _create_yaml_header(self) -> str:
         <footer class="footer">
             This report was generated with 
             <a href="https://github.com/Multiomics-Analytics-Group/vuegen" target="_blank">
-                <img src="../docs/images/vuegen_logo.svg" alt="VueGen" width="65px">
+                <img src="https://raw.githubusercontent.com/Multiomics-Analytics-Group/vuegen/main/docs/images/vuegen_logo.svg" alt="VueGen" width="65px">
             </a>
             | © 2025 <a href="https://github.com/Multiomics-Analytics-Group" target="_blank">Multiomics Network Analytics Group (MoNA)</a>
         </footer>""",

src/vuegen/utils.py

@@ -738,7 +738,7 @@ def generate_footer() -> str:
 <footer class="footer">
     This report was generated with 
     <a href="https://github.com/Multiomics-Analytics-Group/vuegen" target="_blank">
-        <img src="../../docs/images/vuegen_logo.svg" alt="VueGen" width="65px">
+        <img src="https://raw.githubusercontent.com/Multiomics-Analytics-Group/vuegen/main/docs/images/vuegen_logo.svg" alt="VueGen" width="65px">
     </a>
     | © 2025 <a href="https://github.com/Multiomics-Analytics-Group" target="_blank">
         Multiomics Network Analytics Group (MoNA)