Convert GenX submodule to a subtree (macroenergy#194)

* Remove submodule

* Squashed 'src/GenX/' content from commit 23819da4

git-subtree-dir: src/GenX
git-subtree-split: 23819da459be7e4769ccad6a541124343f510cc7

* Removed .gitmodules

* Update submodule instructions -> subtree instructions

* Update Project.toml

Added compat lower limits. These may be too strict, so we can revise them in the future. In particular, some of these might not be valid for Julia 1.6.7

* Update Project.toml

* Update package name

* Rename DOLPHYN.jl to Dolphyn.jl

* Revert "Update package name"

This reverts commit dc0646d.

* Revert "Update Project.toml"

This reverts commit 8fa6501.

* Revert "Rename DOLPHYN.jl to Dolphyn.jl"

This reverts commit 2ae1d3a.

* Revert "Update Project.toml"

This reverts commit 10b786c.

* Update README.md

README.md

@@ -1,4 +1,5 @@
 # DOLPHYN
+
 ## Overview
 DOLPHYN is a configurable, [open source](https://github.com/macroenergy/DOLPHYN/blob/README_Doc_Update/LICENSE) energy system optimization model developed to explore interactions between multiple energy vectors and emerging technologies across their supply chains as part of a future integrated low-carbon energy system.
 
@@ -37,15 +38,13 @@ Use the File -> Clone Respository -> URL dropdown menu to clone the DOLPHYN repo
 
 In the top-level folder where you want to place DOLPHYN, run:
 
-- <code>git clone --recurse-submodules https://github.com/macroenergy/DOLPHYN</code>
+- <code>git clone https://github.com/macroenergy/DOLPHYN</code>
 
 ### If you are working from an existing project
 
 #### Existing Project Using GitHub Desktop
 
-Pull the latest version of DOLPHYN from the main branch. Sometimes the GenX submodule in the src/GenX folder will not update correctly and remain empty.
-
-If this happens, either use the command line arguments below to init and update the submodule, or delete the entire DOLPHYN folder from your computer and re-clone the repository.
+Pull the latest version of DOLPHYN from the main branch. If you previously used the verison of DOLPHYN where GenX was a submodule (as opposed to ordinary folder as it is now) then some of the submodule config files may remain in your project. The easiest solution is to delete your entire DOLPHYN folder from your computer and re-clone the repository.
 
 #### Existing Project Using GitHub via your terminal / command line
 
@@ -54,8 +53,6 @@ In your top-level folder (generally DOLPHYN or DOLPHYN-DEV), run:
 -	<code>git pull</code>
 -	<code>git checkout main</code>
 -	<code>cd src/GenX</code>
--	<code>git submodule init</code>
--	<code>git submodule update</code>
 
 ## Install the Gurobi and / or HiGHS solvers
 
@@ -118,4 +115,4 @@ Once the model has completed running, results will be written into the "Results"
 **NorthSea_2030** is a combined power and hydrogen model for the EU for the year 2030. It contains a power model with hourly resolution, contains zones representing Belgium, Germany, Denmark, France, Great Britain, the Netherlands, Sweden, and Norway. The model also includes a CO2 constraint representing 30% of 2015 power sector CO2 emissions applied to the hydrogen and power sector jointly. Expect a run time of ~10 minutes.
 
 ## DOLPHYN Team
-The model was originally [developed](https://pubs.rsc.org/en/content/articlehtml/2021/ee/d1ee00627d) by [Guannan He](https://www.guannanhe.com/) while at the MIT Energy Initiative, and is now maintained by a team contributors at [MITEI](https://energy.mit.edu/) led by [Dharik Mallapragada](http://mallapragada.mit.edu/) and Ruaridh Macdonald as well as Guannan He's research group at Peking University. Key contributors include Dharik S. Mallapragada, Ruaridh Macdonald, Guannan He, Mary Bennett, Shantanu Chakraborty, Anna Cybulsky, Michael Giovanniello, Jun Wen Law, Youssef Shaker, Nicole Shi and Yuheng Zhang.
+The model was originally [developed](https://pubs.rsc.org/en/content/articlehtml/2021/ee/d1ee00627d) by [Guannan He](https://www.guannanhe.com/) while at the MIT Energy Initiative, and is now maintained by a team contributors at [MITEI](https://energy.mit.edu/) led by [Dharik Mallapragada](http://mallapragada.mit.edu/) and Ruaridh Macdonald as well as Guannan He's research group at Peking University. Key contributors include Dharik S. Mallapragada, Ruaridh Macdonald, Guannan He, Mary Bennett, Shantanu Chakraborty, Anna Cybulsky, Michael Giovanniello, Jun Wen Law, Youssef Shaker, Nicole Shi and Yuheng Zhang.

docs/src/index.md

@@ -42,15 +42,13 @@ Use the File -> Clone Respository -> URL dropdown menu to clone the DOLPHYN repo
 
 In the top-level folder where you want to place DOLPHYN, run:
 
-- <code>git clone --recurse-submodules https://github.com/macroenergy/DOLPHYN</code>
+- <code>git clone https://github.com/macroenergy/DOLPHYN</code>
 
 ### If you are working from an existing project
 
 #### Existing Project Using GitHub Desktop
 
-Pull the latest version of DOLPHYN from the main branch. Sometimes the GenX submodule in the src/GenX folder will not update correctly and remain empty.
-
-If this happens, either use the command line arguments below to init and update the submodule, or delete the entire DOLPHYN folder from your computer and re-clone the repository.
+Pull the latest version of DOLPHYN from the main branch. If you previously used the verison of DOLPHYN where GenX was a submodule (as opposed to ordinary folder as it is now) then some of the submodule config files may remain in your project. The easiest solution is to delete your entire DOLPHYN folder from your computer and re-clone the repository.
 
 #### Existing Project Using GitHub via your terminal / command line
 
@@ -59,8 +57,6 @@ In your top-level folder (generally DOLPHYN or DOLPHYN-DEV), run:
 -	<code>git pull</code>
 -	<code>git checkout main</code>
 -	<code>cd src/GenX</code>
--	<code>git submodule init</code>
--	<code>git submodule update</code>
 
 ## Install the Gurobi and / or HiGHS solvers
 

src/GenX/.gitignore

@@ -0,0 +1,44 @@
+*.jl.cov
+*.jl.*.cov
+*.jl.mem
+*.DS_Store
+Manifest.toml
+.Rhistory
+deps/deps.jl
+.vscode/
+GenXJulEnv/
+output_data/
+MGAResults_min/
+MGAResults_max/
+YourModel.lp
+time_domain_reduction/PreCluster_Plots.jl
+time_domain_reduction/TSC_Plots.jl
+time_domain_reduction/TSC.jl
+
+gurobi.log
+cplex.log
+Highs.log
+
+/docs/build/
+
+# Microsoft office temporary files
+~$*
+
+# Never include output folders
+**/Results*/
+**/TDR_Results/
+
+# Example systems which may be or have been under development
+Example_Systems/NYISO*
+Example_Systems/RealSystemExample/PG_Test_2030_p1/
+Example_Systems/RealSystemExample/Inputs/
+Example_Systems/SmallNewEngland/ThreeZones_full*
+Example_Systems/SmallNewEngland/Test_Up_Time/
+Example_Systems/SmallNewEngland/Test_Down_Time/
+2050/
+
+Example_Systems/SmallNewEngland/ThreeZones_full.zip
+Example_Systems/SmallNewEngland/ThreeZones_full/*
+
+Example_Systems/SmallNewEngland/ThreeZones_MultiStage/Inputs/*
+test_get_retirement_period.jl