Merge pull request #28 from TeaganKing/example_run

Update quickstart instructions

README.md

@@ -18,8 +18,7 @@ CUPiD is a collaborative effort that unifies all CESM component diagnostics and
 To install CUPiD, you need to check out the code and then set up a few environments.
 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 one more package,
-so the `git clone` process is a little more complicated than usual:
+The code relies on submodules to install `manage_externals` and then uses `manage_externals` for one more package, so the `git clone` process is a little more complicated than usual:
 
 ```
 $ git clone --recurse-submodules https://github.com/NCAR/CUPiD.git
@@ -31,25 +30,33 @@ Then build the necessary conda environments with
 
 ```
 $ conda env create -f nbscuid/dev-environment.yml
+$ which nbscuid-run
 $ conda env create -f mom6-environment.yml
 ```
 
-Note that `conda` now defaults to using `mamba` to solve environments;
-the `mom6-environment.yml` environment is complicated,
-so older versions of `conda` should be updated (`conda update -n base conda`) or you should use `mamba` instead.
+Notes:
+
+1. `conda` now defaults to using `mamba` to solve environments; the `mom6-environment.yml` environment is complicated, so older versions of `conda` should be updated (`conda update -n base conda`) or you should use `mamba` instead.
+
+2. IF `which nbscuid-run` returned the error `which: no nbscuid-run in ($PATH)`, then please run the following:
+
+```
+$ conda activate nbscuid-dev
+$ pip install -e .  # installs nbscuid
+```
 
 ## Running
 
 CUPiD currently provides two examples for generating diagnostics.
 To test the package out, try to run `examples/adf-mom6`:
 
 ```
-$ cd examples/adf-mom6
 $ conda activate nbscuid-dev
+$ cd examples/adf-mom6
 $ nbscuid-run config.yml
 $ nbscuid-build config.yml # Will build HTML from Jupyter Book
 ```
 
 After the last step is finished, you can use Jupyter to view generated notebooks in `${CUPID_ROOT}/examples/adf-mom6/computed_notebooks/adf-quick-run`
 or you can copy the entire `${CUPID_ROOT}/examples/adf-mom6/computed_notebooks/adf-quick-run/_build/html`
-directory to your local machine and look at `index.html` in a web browser.
+directory to your local machine and look at `index.html` in a web browser.