Merge branch 'main' into new_deploy_docs

neurobagel · May 8, 2024 · 39c5686 · 39c5686
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diff --git a/docs/nipoppy/cli_note.md b/docs/nipoppy/cli_note.md
@@ -0,0 +1,10 @@
+!!! note "Nipoppy docs are moving"
+
+    Nipoppy is undergoing a major refactor to move from scripts to a 
+    command-line interface (CLI) and Python API. The new documentation website
+    (work in progress) can be found at
+    [https://nipoppy.readthedocs.io/](https://nipoppy.readthedocs.io/).
+
+    If you are using the (soon-to-be legacy) scripts from Nipoppy 0.1.0, this is
+    still the correct place to be. But we encourage you to check out the new
+    website!
diff --git a/docs/nipoppy/code_org.md b/docs/nipoppy/code_org.md
@@ -1,3 +1,7 @@
+{%
+    include-markdown "nipoppy/cli_note.md"
+%}
+
 ## Code organization
 
 ---

diff --git a/docs/nipoppy/configs.md b/docs/nipoppy/configs.md
@@ -1,3 +1,7 @@
+{%
+    include-markdown "nipoppy/cli_note.md"
+%}
+
 ## Global files
 
 ---

diff --git a/docs/nipoppy/data_org.md b/docs/nipoppy/data_org.md
@@ -1,3 +1,7 @@
+{%
+    include-markdown "nipoppy/cli_note.md"
+%}
+
 ## Data organization
 
 ---

diff --git a/docs/nipoppy/glossary.md b/docs/nipoppy/glossary.md
@@ -1,3 +1,7 @@
+{%
+    include-markdown "nipoppy/cli_note.md"
+%}
+
 ## Glossary
 
 This page lists some definitions for important/recurring terms used in the Nipoppy framework.

diff --git a/docs/nipoppy/installation.md b/docs/nipoppy/installation.md
@@ -1,3 +1,7 @@
+{%
+    include-markdown "nipoppy/cli_note.md"
+%}
+
 ## Code installation and dataset setup
 
 ---

diff --git a/docs/nipoppy/overview.md b/docs/nipoppy/overview.md
@@ -1,3 +1,7 @@
+{%
+    include-markdown "nipoppy/cli_note.md"
+%}
+
 ## What is Nipoppy? 
 
 [Nipoppy](https://github.com/neurodatascience/nipoppy) is a lightweight framework for analyzing (neuro)imaging and clinical data. It is designed to help users do the following:

diff --git a/docs/nipoppy/trackers.md b/docs/nipoppy/trackers.md
@@ -1,3 +1,7 @@
+{%
+    include-markdown "nipoppy/cli_note.md"
+%}
+
 ## Track data availability status
 
 ---

diff --git a/docs/nipoppy/workflow/bids_conv.md b/docs/nipoppy/workflow/bids_conv.md
@@ -1,3 +1,7 @@
+{%
+    include-markdown "nipoppy/cli_note.md"
+%}
+
 ## Objective
 
 ---

diff --git a/docs/nipoppy/workflow/dicom_org.md b/docs/nipoppy/workflow/dicom_org.md
@@ -1,3 +1,7 @@
+{%
+    include-markdown "nipoppy/cli_note.md"
+%}
+
 ## Objective
 
 ---

diff --git a/docs/nipoppy/workflow/proc_pipe/fmriprep.md b/docs/nipoppy/workflow/proc_pipe/fmriprep.md
@@ -1,3 +1,7 @@
+{%
+    include-markdown "nipoppy/cli_note.md"
+%}
+
 ## Objective
 
 ---

diff --git a/docs/nipoppy/workflow/proc_pipe/mriqc.md b/docs/nipoppy/workflow/proc_pipe/mriqc.md
@@ -1,3 +1,7 @@
+{%
+    include-markdown "nipoppy/cli_note.md"
+%}
+
 ## MRIQC image processing pipeline
 
 ---