From 67c7722d69acfa8f0be34092b401fd0618e28f6a Mon Sep 17 00:00:00 2001
From: jdeschamps <6367888+jdeschamps@users.noreply.github.com>
Date: Fri, 8 Nov 2024 12:41:19 +0100
Subject: [PATCH] Fix paths

---
 .../configuration/convenience_functions.md          |  8 ++++----
 docs/guides/careamist_api/usage/datasets.md         |  2 +-
 docs/guides/dev_resources/CI.md                     |  0
 docs/guides/dev_resources/tooling.md                |  0
 docs/guides/lightning_api/training.md               |  0
 mkdocs.yml                                          |  2 +-
 scripts/gen_jupyter_nav.py                          | 13 ++++++++++---
 7 files changed, 16 insertions(+), 9 deletions(-)
 delete mode 100644 docs/guides/dev_resources/CI.md
 delete mode 100644 docs/guides/dev_resources/tooling.md
 delete mode 100644 docs/guides/lightning_api/training.md

diff --git a/docs/guides/careamist_api/configuration/convenience_functions.md b/docs/guides/careamist_api/configuration/convenience_functions.md
index 072890ec3..a77f9e4ef 100644
--- a/docs/guides/careamist_api/configuration/convenience_functions.md
+++ b/docs/guides/careamist_api/configuration/convenience_functions.md
@@ -12,8 +12,8 @@ to create configurations with a only few parameters related to the algorithm use
 want to train.
 
 All convenience methods can be found in the `careamics.config` modules. CAREamics 
-currently supports [Noise2Void](../../algorithms/n2v/index.md) and its variants, 
-[CARE](../../algorithms/care/index.md) and [Noise2Noise](../../algorithms/n2n/index.md). 
+currently supports [Noise2Void](../../../algorithms/Noise2Void) and its variants, 
+[CARE](../../../algorithms/CARE) and [Noise2Noise](../../../algorithms/Noise2Noise). 
 
 ``` python title="Import convenience functions"
 --8<-- "careamics-examples/guides/careamist_api/configuration/convenience_functions.py:imports"
@@ -278,7 +278,7 @@ variants [N2V2](../../../algorithms/n2v2/) and [structN2V](../../../algorithms/s
 !!! note "Understanding Noise2Void and its variants"
 
     Before deciding which variant to use, and how to modify the parameters, we recommend
-    to die a little a bit on [how each algorithm works](../../algorithms/index.md)!
+    to die a little a bit on [how each algorithm works](../../../algorithms/index.md)!
 
 
 ### Noise2Void parameters
@@ -325,7 +325,7 @@ StructN2V has two parameters that can be set:
 
 ### Using another loss function
 
-As opposed to Noise2Void, [CARE](../../../algorithms/care/) and [Noise2Noise](../../../algorithms/n2n) 
+As opposed to Noise2Void, [CARE](../../../algorithms/CARE) and [Noise2Noise](../../../algorithms/Noise2Noise) 
 can be trained with different loss functions. This can be set using the `loss` parameter 
 (surprise, surprise!).
 
diff --git a/docs/guides/careamist_api/usage/datasets.md b/docs/guides/careamist_api/usage/datasets.md
index df7f0df9e..7662567a5 100644
--- a/docs/guides/careamist_api/usage/datasets.md
+++ b/docs/guides/careamist_api/usage/datasets.md
@@ -130,7 +130,7 @@ into the network. CAREamics supports the following transforms (see
 
 
 The `Normalize` transform is always applied, and the rest are optional. The exception is
-`N2VManipulateModel`, which is only applied when training with N2V (see [Noise2Void](../../../algorithms/n2v/index.md)).
+`N2VManipulateModel`, which is only applied when training with N2V (see [Noise2Void](../../../algorithms/Noise2Void)).
 
 !!! note "When to turn off transforms?"
 
diff --git a/docs/guides/dev_resources/CI.md b/docs/guides/dev_resources/CI.md
deleted file mode 100644
index e69de29bb..000000000
diff --git a/docs/guides/dev_resources/tooling.md b/docs/guides/dev_resources/tooling.md
deleted file mode 100644
index e69de29bb..000000000
diff --git a/docs/guides/lightning_api/training.md b/docs/guides/lightning_api/training.md
deleted file mode 100644
index e69de29bb..000000000
diff --git a/mkdocs.yml b/mkdocs.yml
index a345c8c93..e3bbe45f2 100644
--- a/mkdocs.yml
+++ b/mkdocs.yml
@@ -33,7 +33,7 @@ nav:
       - napari plugins:
           - guides/napari_plugin/index.md
       - Tutorials:
-          - guides/turotials/index.md
+          - guides/tutorials/index.md
       - Lightning API:
           - guides/lightning_api/index.md
           - guides/lightning_api/lightning_module.md
diff --git a/scripts/gen_jupyter_nav.py b/scripts/gen_jupyter_nav.py
index 223ec016f..1df120a14 100644
--- a/scripts/gen_jupyter_nav.py
+++ b/scripts/gen_jupyter_nav.py
@@ -51,11 +51,18 @@ def bottom_text() -> str:
         "[the guide](../../guides/dev_resources/website.md#jupyter-notebook-applications)."
     )
 
-def open_section(title: str) -> str:
+def open_section(title: str, skip_algo: bool = False) -> str:
     """Open the tags of a new card grid section."""
+
+    if skip_algo:
+        algo = ""
+    else:
+        algo = f"For more details on the algorithm, check out its [description](../../algorithms/{title}).\n\n"
+
+
     return (
         f"# {title}\n\n"
-        f"For more details on the algorithm, check out its [description](../../algorithms/{title.lower()}).\n\n"
+        f"{algo}"
         f"<div class=\"md-container secondary-section\">\n"
         f"  <div class=\"g\">\n"
         f"      <div class=\"section\">\n"
@@ -217,7 +224,7 @@ class Card:
     with mkdocs_gen_files.open(index_file, "a") as index_md:
         
         # open section
-        index_md.write(open_section(cat))
+        index_md.write(open_section(cat, skip_algo = cat == "Lightning_API"))
 
         # write rows
         count = 0