Merge branch 'doc' into PR-JupyterKernel

doc/InSituPythonAnalysis/JupyterNotebookAccess/JupyterNotebook.md

@@ -115,4 +115,3 @@ We can press "Restart" button (:arrows_counterclockwise:) to reconnect to libyt
 - The functionality is limited to taking Python inputs and printing outputs from all the MPI processes only. `libyt` hasn't done implementing Jupyter's full feature, like data streaming, supporting `ipwidgets` yet.
 - See [Limitations in MPI Related Python Tasks]({% link InSituPythonAnalysis/Limitations.md %}#limitations-in-mpi-related-python-tasks).
 
-## FAQs

doc/InSituPythonAnalysis/UsingYT.md

@@ -17,7 +17,7 @@ nav_order: 2
 ---
 
 ## Requirements
-- Python package [`yt`](https://yt-project.org/) and [`yt_libyt`](https://github.com/data-exp-lab/yt_libyt).
+- Python package [`yt`](https://yt-project.org/) and [`yt_libyt`]({% link HowToInstall.md %}#yt_libyt).
 
 ## Use yt for In Situ Python Analysis under Parallel Computation
 `libyt` directly borrows parallel computation feature in `yt` using `mpi4py`. You can also refer to [**Parallel Computation With yt**](https://yt-project.org/doc/analyzing/parallel_computation.html#parallel-computation-with-yt).

doc/libytAPI/ActivateJupyterKernel.md

@@ -30,7 +30,9 @@ int yt_run_JupyterKernel(const char* flag_file_name, bool use_connection_file);
 > :information_source: The API only launches a Jupyter kernel that exposes simulation data. For how to connect to the kernel, please go to [Jupyter Notebook Access]({% link InSituPythonAnalysis/JupyterNotebookAccess/JupyterNotebook.md %}#jupyter-notebook-access). 
 
 ## Connection File
-The connection file name must be `libyt_kernel_connection.json`. This is the same connection file used in Jupyter but with different file name. `libyt` use this connection file to bind to ports and construct kernel.
+The connection file name must be `libyt_kernel_connection.json`. This is the same connection file used in Jupyter but with different file name.
+(Please refer to [Jupyter Client -- Connection files](https://jupyter-client.readthedocs.io/en/stable/kernels.html#connection-files))
+`libyt` use this connection file to bind to ports and construct kernel.
 
 For example:
 ```json

doc/libytAPI/index.md

@@ -8,22 +8,16 @@ has_toc: false
 ---
 
 # libyt API
-{: .no_toc }
-<details open markdown="block">
-  <summary>
-    Table of contents
-  </summary>
-  {: .text-delta }
-- TOC
-{:toc}
-</details>
----
 
 ## Procedure
-It can break down into three stages, initialization, loading simulation data into Python and do in situ analysis during the iterative process in simulation, 
-and finalization.
+It can break down into five stages: 
+  - initialization, 
+  - loading simulation data into Python[^1], 
+  - do in situ analysis, 
+  - reset, 
+  - and finalization.
 
-Currently, `libyt` only supports loading simulation data with adaptive mesh refinement grid structure (AMR grid) to Python.[^1]
+## libyt API
 
 <table>
   <thead>
@@ -40,7 +34,7 @@ Currently, `libyt` only supports loading simulation data with adaptive mesh refi
       <td>Initialize embedded Python and import inline Python script.</td>
     </tr>
     <tr>
-      <td rowspan=6><strong>Iteration</strong></td>
+      <td rowspan=3><strong>Loading data</strong></td>
       <td><code>yt_set_Parameters</code>, <code>yt_set_UserParameter*</code></td>
       <td>Set yt parameters and user specific parameters.</td>
     </tr>
@@ -53,6 +47,7 @@ Currently, `libyt` only supports loading simulation data with adaptive mesh refi
       <td>Tell libyt you're done.</td>
     </tr>
     <tr>
+      <td rowspan=3><strong>In situ analysis</strong></td>
       <td><code>yt_run_Function</code>, <code>yt_run_FunctionArguments</code></td>
       <td>Run Python functions.</td>
     </tr>
@@ -65,6 +60,7 @@ Currently, `libyt` only supports loading simulation data with adaptive mesh refi
       <td>Activate interactive prompt. This is only available in Jupyter kernel mode.</td>
     </tr>
     <tr>
+      <td rowspan=1><strong>Reset</strong></td>
       <td><code>yt_free</code></td>
       <td>Free resources for in situ analysis.</td>
     </tr>
@@ -78,6 +74,7 @@ Currently, `libyt` only supports loading simulation data with adaptive mesh refi
 
 
 ----
-[^1]: :lizard: Even though we can still activate Python prompt and run in situ Python script with no data loaded ahead in non-AMR grid simulation with just `yt_initialize`, `yt_run_Function`, `yt_run_FunctionArguments`, `yt_run_InteractiveMode`, and `yt_finalize`. We are trying to make `libyt` works with more data structure.
+[^1]: :lizard: Currently, `libyt` only supports loading simulation data with adaptive mesh refinement grid structure (AMR grid) to Python. We are trying to make `libyt` works with more data structure.
+