Merge pull request #65 from anissa111/main

Embed README in index.rst

.gitignore

@@ -15,4 +15,5 @@ cupid.egg-info
 externals/
 
 # Documentation
-/docs/_build/
+/docs/_build/
+/docs/README.md

README.md

@@ -1,4 +1,5 @@
 # <img src="images/logo.png" alt="CUPiD Logo" width=100 /> CUPiD: CESM Unified Postprocessing and Diagnostics
+
 Python Framework for Generating Diagnostics from CESM
 
 ## Project Vision
@@ -21,15 +22,15 @@ The initial examples have hard-coded paths that require you to be on `casper`.
 The code relies on submodules to install `manage_externals` and then uses `manage_externals` for a few packages that are still being developed,
 so the `git clone` process is a little more complicated than usual:
 
-```
+``` bash
 $ git clone --recurse-submodules https://github.com/NCAR/CUPiD.git
 $ cd CUPiD
 $ ./manage_externals/checkout_externals
 ```
 
 Then build the necessary conda environments with
 
-```
+``` bash
 $ mamba env create -f environments/dev-environment.yml
 $ conda activate cupid-dev
 $ which cupid-run
@@ -45,7 +46,7 @@ If you do not have `mamba` installed, you can still use `conda`... it will just
 1. If `./manage_externals/checkout_externals` is not found, run `git submodule update --init` to clone the submodule.
 1. If `which cupid-run` returned the error `which: no cupid-run in ($PATH)`, then please run the following:
 
-```
+``` bash
 $ conda activate cupid-dev
 $ pip install -e .  # installs cupid
 ```
@@ -55,7 +56,7 @@ $ pip install -e .  # installs cupid
 CUPiD currently provides two examples for generating diagnostics.
 To test the package out, try to run `examples/coupled-model`:
 
-```
+``` bash
 $ conda activate cupid-dev
 $ cd examples/coupled_model
 $ cupid-run config.yml
@@ -68,7 +69,7 @@ directory to your local machine and look at `index.html` in a web browser.
 
 ### Looking at Output
 
-For users running on the NCAR super computers (derecho or casper), you can visualize the web page in a browser using the FastX service. FastX requires you to be on the internal NCAR network (either on-site or via the VPN, and can be accessed via the following steps:
+For users running on the NCAR super computers (derecho or casper), you can visualize the web page in a browser using the FastX service. FastX requires you to be on the internal NCAR network (either on-site or via the VPN), and can be accessed via the following steps:
 
 1. Open a new browser window that points to https://fastx.ucar.edu:3300/session/
 1. Open a default desktop icon.

docs/conf.py

@@ -12,10 +12,27 @@
 import os
 import sys
 import datetime
+import re
+
 sys.path.insert(0, os.path.abspath('../..'))
 
 print("sys.path:", sys.path)
 
+# Copy README into docs
+# This is to allow us to remove the header image from the docs copy of README
+# without affecting the original README, but still pull the source README
+# into the docs build fresh each time.
+os.system('cp ../README.md ./README.md')
+
+# Remove any images from the first line of the README
+with open('README.md', 'r') as f:
+    readme1 = f.readline()
+    readme1 = re.sub('<img.*?> ', '', readme1)
+    readme = f.read()
+
+with open('README.md', 'w') as f:
+    f.write(readme1+readme)
+
 # -- Project information -----------------------------------------------------
 
 project = 'CUPiD'

docs/index.rst

@@ -5,6 +5,5 @@ CUPiD Documentation
    :maxdepth: 2
    :hidden:
 
-    Installation Guide <install.rst>
-
-More details can be found in the main repository `README <https://github.com/TeaganKing/CUPiD/blob/main/README.md>`_ .
+.. include:: README.md
+   :parser: myst