documentation progress using documenter

Author: Barbie

.gitignore

@@ -1 +1,3 @@
 .DS_Store
+
+docs/build

README.md

@@ -1,24 +1,23 @@
 # Dar_One
-a zero-D environment in julia powered by Darwin and MITgcm
 
 Built off of Gael Forget's MITgcmTools! (https://github.com/gaelforget/MITgcmTools.jl)
 
-# Setup
-
-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 
+- [Dar_One](https://github.com/barbara42/Dar_One) - Julia 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))
 
+
+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
+
 # Setting up with docker
 
 (1) Download and install [docker desktop](https://www.docker.com/).
@@ -37,22 +36,17 @@ Dar_One is a Julia interface for using the [MITgcm](https://mitgcm.org/) with a
 - 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)!
+You're now ready for the [beginner tutorial](beginner_tutorial)!
 # Setting up on local machine
 
 If you have a windows machine, abandon all hope or dual boot linux 
 
-TODO! 
+TODO
 
 # Contributing 
 
-We have three main branches
-- main
-- test
-- dev 
-
-All other branches are feature branches. Once a feature has been implemented, tested, and documented you can make a pull request to merge it into the `dev` branch. From there, it will be deployed (hopefully in the future). If the deploy passes, it will automatically get merged into the `test` branch. 
+We have three main branches: `main`, `test`, and `dev`.
 
-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`. 
+All other branches are feature branches. Once a feature has been implemented, tested, and documented you can make a pull request to merge it into the `dev` branch. 
 
-`main` is the most recent and stable version of the code. This branch is used for the docker image. 
+`main` is the most stable version of the code. This branch is used for the docker image. 

beginner_tutorial/README.md

@@ -9,4 +9,10 @@ for [local machine setup](../README.md/#setting-up-on-local-machine). (HIGHLY re
 
 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 
+- the executable is called `mitgcmuv` and lives in the `darwin3/verification/dar_one_config/build` directory 
+
+If you're doing it locally... 
+- run `julia how-to-build.jl`
+- TODO: more info and troubleshooting to come
+
+## Running 

src/DarOneTools.jl

@@ -10,6 +10,8 @@ include("ReadFiles.jl")
 include("ModelSteps.jl")
 include("NamelistHelpers.jl")
 
+export MITgcm_path, base_configuration, filexe
+
 # Types 
 export MITgcm_config, MITgcm_namelist
 
@@ -23,9 +25,6 @@ export update_param, update_tracers, update_tracer, update_temperature, update_d
 export create_MITgcm_config, dar_one_run
 export tracer_name_to_id, tracer_id_to_name
 
-
-export MITgcm_path, base_configuration, filexe
-
 #export pause, stop, clock, monitor, train, help
 export verification_experiments, read_namelist, write_namelist
 export read_mdsio, read_meta, read_available_diagnostics

src/NamelistHelpers.jl

@@ -9,7 +9,14 @@ using NCDatasets
 # export tracer_name_to_id
 # export update_diagnostic_freq
 # export update_temperature
+"""
+    update_param(file_name, group_name, param_name, new_param_value, config_obj)  
+
+Speficy a parameter to update  
 
+Arguments:
+- TODO
+"""
 function update_param(file_name, group_name, param_name, new_param_value, config_obj)
     rundir = joinpath(config_obj.folder, config_obj.ID, "run")
     # read the contents of the data file into a namelist 
@@ -87,7 +94,7 @@ end
 """
     tracer_name_to_id(name)
     
-Return the int in the tracer name. i.e. tracer_name_to_id("TRAC21") will return 21      
+Return the int in the tracer name. i.e. `tracer_name_to_id("TRAC21")` will return 21      
 """
 function tracer_name_to_id(name)
     return parse(Int64, name[5:6])