Fancier note styling in installation instructions

Author: rutgerkok

manuals/INSTALLATION.md

@@ -2,11 +2,11 @@
 =========================
 [← Back to main page](./index.md)
 
-> ### Notice
-> This current verstion of OrganoidTracker is different from the version published in [our most recent paper](https://doi.org/10.1038/s41592-025-02845-6). The main change is that the Tensorflow library has been replaced with PyTorch. We have converted our trained neural networks to be compatible with PyTorch. Should you need any assistance upgrading to this version from the old published version, feel free to contact us. In case you still need access to the old version, it is still available.
-> 
-> **Old links**: [Old manual](https://github.com/jvzonlab/OrganoidTracker/blob/v2/manuals/index.md) | [Old ZIP download](https://github.com/jvzonlab/OrganoidTracker/archive/refs/heads/v2.zip) | [Old source code](https://github.com/jvzonlab/OrganoidTracker/tree/v2)
+:::{note}
+This current version of OrganoidTracker is different from the version published in [our most recent paper](https://doi.org/10.1038/s41592-025-02845-6). The main change is that the Tensorflow library has been replaced with PyTorch. We have converted our trained neural networks to be compatible with PyTorch. Should you need any assistance upgrading to this version from the old published version, feel free to contact us. In case you still need access to the old version, it is still available.
 
+**Old links**: [Old manual](https://github.com/jvzonlab/OrganoidTracker/blob/v2/manuals/index.md) | [Old ZIP download](https://github.com/jvzonlab/OrganoidTracker/archive/refs/heads/v2.zip) | [Old source code](https://github.com/jvzonlab/OrganoidTracker/tree/v2)
+:::
 
 ## Windows
 **System requirements:**

organoid_tracker/text_popup/help_popup.py

@@ -40,11 +40,15 @@ def navigate(self, url: str) -> Optional[str]:
             raise UserError("File not found", url + " does not exist")
         markdown_str =  _file_get_contents(file)
 
+        # Replace :::{note} style blocks with a block using horizontal lines
+        markdown_str = markdown_str.replace(":::{note}", "\n----------------\n### Note:")
+        markdown_str = markdown_str.replace(":::", "\n-----------------\n")
+
         # Cut off everything after :::{eval-rst}  (that is metadata for the Sphinx documentation builder)
         try:
             remove_start_index = markdown_str.index(":::{eval-rst}")
             markdown_str = markdown_str[0:remove_start_index]
         except ValueError:
-            pass  # There's not metadata
+            pass  # There's no metadata
 
         return markdown_str