[MNT] Remove deprecated Nipoppy docs (#224)

* remove Nipoppy pages * add note on Nipoppy to data prep page * remove Nipoppy images * remove custom mlc pattern to ignore Nipoppy links * specify min table-reader plugin ver. to avoid pandas DeprecationWarning
neurobagel · Sep 17, 2024 · 99abb8d · 99abb8d
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diff --git a/docs/data_prep.md b/docs/data_prep.md
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 # Preparing the phenotypic data
 
+!!! tip "Looking for more general guidelines on how to organize your dataset?"
+
+    We recommend also checking out [Nipoppy](https://nipoppy.readthedocs.io/), a protocol for standardized organization and processing of clinical-neuroimaging datasets that extends [BIDS](https://bids-specification.readthedocs.io/en/stable/). 
+    Neurobagel tools are designed to be compatible with data organized according to the Nipoppy specification, although you do not need to use Nipoppy in order to use Neurobagel.
+
 To use the Neurobagel annotation tool, 
 please prepare the tabular data for your dataset as a single, tab-separated file (`.tsv`).
 

diff --git a/docs/imgs/code_org.png b/docs/imgs/code_org.png
diff --git a/docs/imgs/data_org.jpg b/docs/imgs/data_org.jpg
diff --git a/docs/imgs/digest.png b/docs/imgs/digest.png
diff --git a/docs/imgs/nipoppy_org.jpg b/docs/imgs/nipoppy_org.jpg
diff --git a/docs/imgs/steps.jpg b/docs/imgs/steps.jpg
diff --git a/docs/nipoppy/cli_note.md b/docs/nipoppy/cli_note.md
diff --git a/docs/nipoppy/code_org.md b/docs/nipoppy/code_org.md
diff --git a/docs/nipoppy/configs.md b/docs/nipoppy/configs.md
diff --git a/docs/nipoppy/data_org.md b/docs/nipoppy/data_org.md
diff --git a/docs/nipoppy/glossary.md b/docs/nipoppy/glossary.md
diff --git a/docs/nipoppy/installation.md b/docs/nipoppy/installation.md
diff --git a/docs/nipoppy/overview.md b/docs/nipoppy/overview.md