separated setup and tutorial readmes

Author: Barbie

README.md

@@ -5,7 +5,44 @@ Built off of Gael Forget's MITgcmTools! (https://github.com/gaelforget/MITgcmToo
 
 # Setup
 
-# Example
+Dar_One can be run in one of two ways. 
+1) In a **docker container** using the dar_one_docker image, where all dependencies are handled for you 
+2) On your local machine, where you have to set up the environment, download dependencies, etc 
+    - this is more time consuming, and I strongly recommend using the docker image
+    - instructions for local setup are below
+
+##  Overview of program structure 
+
+Dar_One is a Julia interface for using the [MITgcm](https://mitgcm.org/) with a [Darwin](https://darwinproject.mit.edu/) configuration to include biogeochemical forcing for marine microbes. This means it's composed of two main parts
+- [Dar_One Julia](https://github.com/barbara42/Dar_One) - interface for organizing experiments and setting up parameters for model runs 
+    - `MITgcm_path` variable should point to darwin3
+- [darwin3](https://github.com/darwinproject/darwin3) - MITgcm source code set up to include all things Darwin 
+    - `dar_one_config` - folder for the base configuration files for Dar_One, which lives in the darwin3/verification/ folder. ([dar_one_config github](https://github.com/barbara42/dar_one_config))
+
+# Setting up with docker
+
+(1) Download and install [docker desktop](https://www.docker.com/).
+
+(2) Get the [dar_one_docker image](https://hub.docker.com/repository/docker/birdy1123/dar_one_docker).
+- using the command line, run 
+
+    `docker pull birdy1123/dar_one_docker`
+
+- If you go to the "Images" tab in the docker desktop UI, you should see "birdy1123/dar_one_docker"
+
+(3) Run a container based on the dar_one_docker image
+- using the command line, run 
+
+    `docker run -it birdy1123/dar_one_docker` 
+- this runs the container in interactive mode (`-i`) with terminal access (`-t`) 
+- you should see the prompt change to `root@some-number:/dar_one_docker#`
+
+You're now ready for the [beginner tutorial](beginner_tutorial/README.md)!
+# Setting up on local machine
+
+If you have a windows machine, abandon all hope or dual boot linux 
+
+TODO! 
 
 # Contributing 
 
@@ -18,4 +55,4 @@ All other branches are feature branches. Once a feature has been implemented, te
 
 This branch is for people who deeply understand the code and want to beta test new features. Once apropriate testing and tutorials have been created, there will be a merge planned for `main`. 
 
-`main` is the most recent and stable version of the code. This branch will be deployed to cloud computing resources and publically available. 
+`main` is the most recent and stable version of the code. This branch is used for the docker image. 

beginner_tutorial/README.md

@@ -1,72 +1,12 @@
 # Dar_One Beginner Tutorial
 
-This tutorial is meant to be run in one of two ways. 
-1) In a **docker container** using the dar_one_docker image, where all dependencies are handled for you 
-2) On your local machine, where you have to set up the environment, download dependencies, etc 
-    - this is more time consuming, and I strongly recommend using the docker image
-    - instructions for local setup are below
+BEFORE YOU START:
 
-##  Overview of program structure 
+Follow the setup guide for using the [dar_one_docker image](../README.md/#setting-up-with-docker) or  
+for [local machine setup](../README.md/#setting-up-on-local-machine). (HIGHLY recommend using docker over setting up your own machine) 
 
-Dar_One is a Julia interface for using the [MITgcm](https://mitgcm.org/) with a [Darwin](https://darwinproject.mit.edu/) configuration to include biogeochemical forcing for marine microbes. This means it's composed of two main parts
-- [Dar_One Julia](https://github.com/barbara42/Dar_One) - interface for organizing experiments and setting up parameters for model runs 
-    - `MITgcm_path` variable should point to darwin3
-- [darwin3](https://github.com/darwinproject/darwin3) - MITgcm source code set up to include all things Darwin 
-    - `dar_one_config` - folder for the base configuration files for Dar_One, which lives in the darwin3/verification/ folder 
+## Building
 
-# Setting up with docker
-
-(1) Download and install [docker desktop](https://www.docker.com/). If you're new to docker, here's some tutorials to learn more
-- put
-- links
-- here
-
-Building
+If you're using dar_one_docker...
 - you don't have to do anything! I already built the mitgcm executable for the docker container
-- the executable is called `mitgcmuv` and lives in the `darwin3/verification/dar_one_config/build` directory 
-
-# Setting up on local machine
-
-If you have a windows machine, abandon all hope or dual boot linux 
-
-
-Building 
-
-
-
-
-
-
-# OLD TUTORIAL 
-The overall workflow of this tutorial is to run
-- `darwin-setup.jl` (which creates the executable and sets up the proper folders on your machine)
-- `darwin-run.jl` (where you modify runtime parameters, and then run the model)
-- `darwin-plot.jl` (where we look at output)
-
-**Note:** for the plots to show up, darwin-plot.jl must be run from a REPL or notebook. For example, I use VSCode and choose the "Execute active file in REPL" option in the run config. 
-
-## darwin-setup.jl
-
-
-To run on your local machine, make the following changes
-- change `MITgcm_path[1]` to point to the root directory of your local version of the darwin MITgcm
-- **note**: BUILD DOES NOT WORK FOR ME
-- run darwin-setup
-- copy down the `config_id` that is printed out in the terminal 
-
-## darwin-run.jl
-
-Make the following changes
-- update `MITgcm_path[1]` to be the root directory of your local version of the darwin MITgcm
-- update `config_id` to be the config_id that was output from running darwin-setup
-- modifying runtime parameters
-    - TODO
-
-## darwin-plot.jl
-
-Update 
-- `config_id`
-- `data_folder` (TODO: more info)
-- `folder`
-
-To see the plots this **MUST** be run from a REPL! 
+- the executable is called `mitgcmuv` and lives in the `darwin3/verification/dar_one_config/build` directory