miscellaneous doc enhancements (#813)

* update submodule * update submodule * update submodule to docs/adjust-docs PR branch * include new external notebook * new icon * update submodule * zulip instead of github discussions * usage -> api * new logo * u. sm.
theislab · Oct 31, 2024 · 90cb1d6 · 90cb1d6
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diff --git a/docs/_static/tutorials/patient_trajectory.png b/docs/_static/tutorials/patient_trajectory.png
diff --git a/docs/conf.py b/docs/conf.py
@@ -179,4 +179,5 @@
     "tutorials/notebooks/cohort_tracking": "_static/tutorials/cohort_tracking.png",
     "tutorials/notebooks/bias": "_static/tutorials/bias.png",
     "tutorials/notebooks/out_of_core": "_static/tutorials/out_of_core.png",
+    "tutorials/notebooks/patient_trajectory": "_static/tutorials/patient_trajectory.png",
 }
diff --git a/docs/tutorials/index.md b/docs/tutorials/index.md
@@ -8,7 +8,7 @@ The easiest way to get familiar with ehrapy is to follow along with our tutorial
 Many are also designed to work seamlessly in Binder, a free cloud computing platform.
 
 :::{note}
-For questions about the usage of ehrapy use [Github Discussions].
+For questions about the usage of ehrapy use the [zulip forum](https://scverse.zulipchat.com/#narrow/channel/465075-ehrapy).
 :::
 
 ## Quick start
@@ -28,6 +28,7 @@ For questions about the usage of ehrapy use [Github Discussions].
    notebooks/cohort_tracking
    notebooks/bias
    notebooks/out_of_core
+   notebooks/patient_trajectory
 
 ```
 
@@ -52,4 +53,4 @@ For questions about the usage of ehrapy use [Github Discussions].
         For a more in depth introduction please read the `Scanpy paper <https://genomebiology.biomedcentral.com/articles/10.1186/s13059-017-1382-0>`_.
 ```
 
-[github discussions]: https://github.com/theislab/ehrapy/discussions
+[zulip forum]: https://scverse.zulipchat.com/#narrow/channel/465075-ehrapy
diff --git a/docs/tutorials/notebooks b/docs/tutorials/notebooks
diff --git a/docs/usage/usage.md b/docs/usage/usage.md
@@ -1,4 +1,4 @@
-# Usage
+# API
 
 Import the ehrapy API as follows:
+10 −95		ehrapy_introduction.ipynb
+1 −1		mimic_2_causal_inference.ipynb
+8 −8		mimic_2_fate.ipynb
+1 −1		mimic_2_survival_analysis.ipynb
+9 −87		out_of_core.ipynb
+24 −0		patient_trajectory.ipynb
-Original file line number
+Diff line change
@@ -1,4 +1,4 @@
-    # Usage
+    # API
     Import the ehrapy API as follows:
@@ Expand Down @@