Remove Manifest

README.adoc

@@ -39,15 +39,19 @@ After activating the package environment, run the follwing to install the packag
 Pkg.instantiate()
 ----
 
-== Run simulation
+=== Import the package
 
-Import the package:
+You can import the package by running:
 
 [source, julia]
 ----
 using ReCo
 ----
 
+This will export the package methods that are intended to be used by the end user.
+
+== Run simulation
+
 Initialize a simulation with 100 particles having a self-propulsion velocity of 40.0 and return the relative path to the simulation directory:
 
 [source, julia]
@@ -64,13 +68,17 @@ run_sim(sim_dir, duration=20.0)
 
 The values for the number of particles, self-propulsion velocity and simulation duration are used here as an example. For more information about possible values and other optional arguments, press `?` in the REPL after running `using ReCo`. Then type `init_sim` or `run_sim` followed by pressing enter. This will show the method's documention.
 
-== Run reinforcement learning
+== Simulation visualization
-Import the package:
 
-[source, julia]
+=== Animation
-----
+
-using ReCo
+//TODO
-----
+
+=== Snapshot plot
+
+//TODO
+
+== Run reinforcement learning
 
 Run a reinforcement learning process and return the environment helper and the the path of the process directory relative to the directory `ReCo.jl`:
 [source, julia]
@@ -79,6 +87,7 @@ env_helper, rl_dir = run_rl(ENVTYPE)
 ----
 
 ENVTYPE has to be replaced by one of the environments named after the file names in the directory `ReCo.jl/RL/Envs`, for example: `LocalCOMEnv`. A description of an environment is included at the beginning of the corresponding file.
+//TODO: Descriptions of envs
 
 For more information about all possible optional arguments, press `?` in the REPL after running `using ReCo`. Then type `run_rl` followed by pressing enter.
 
@@ -142,4 +151,12 @@ run_random_walk()
 ----
 include("analysis/radial_distribution_function/radial_distribution_function.jl")
 run_radial_distribution_analysis()
-----
+----
+
+=== Reward discount analysis
+
+//TODO
+
+== Graphics
+
+//TODO

test/Manifest.toml

@@ -1,68 +0,0 @@
-# This file is machine-generated - editing it directly is not advised
-
-julia_version = "1.7.1"
-manifest_format = "2.0"
-
-[[deps.Artifacts]]
-uuid = "56f22d72-fd6d-98f1-02f0-08ddc0907c33"
-
-[[deps.Base64]]
-uuid = "2a0f44e3-6c83-55bd-87e4-b1978d98bd5f"
-
-[[deps.CompilerSupportLibraries_jll]]
-deps = ["Artifacts", "Libdl"]
-uuid = "e66e0078-7015-5450-92f7-15fbd957f2ae"
-
-[[deps.InteractiveUtils]]
-deps = ["Markdown"]
-uuid = "b77e0a4c-d291-57a0-90e8-8db25a27a240"
-
-[[deps.Libdl]]
-uuid = "8f399da3-3557-5675-b5ff-fb832c97cbdb"
-
-[[deps.LinearAlgebra]]
-deps = ["Libdl", "libblastrampoline_jll"]
-uuid = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
-
-[[deps.Logging]]
-uuid = "56ddb016-857b-54e1-b83d-db4d58db5568"
-
-[[deps.Markdown]]
-deps = ["Base64"]
-uuid = "d6f4376e-aef5-505a-96c1-9c027394607a"
-
-[[deps.OpenBLAS_jll]]
-deps = ["Artifacts", "CompilerSupportLibraries_jll", "Libdl"]
-uuid = "4536629a-c528-5b80-bd46-f80d51c5b363"
-
-[[deps.Random]]
-deps = ["SHA", "Serialization"]
-uuid = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
-
-[[deps.SHA]]
-uuid = "ea8e919c-243c-51af-8825-aaa63cd721ce"
-
-[[deps.Serialization]]
-uuid = "9e88b42a-f829-5b0c-bbe9-9e923198166b"
-
-[[deps.SparseArrays]]
-deps = ["LinearAlgebra", "Random"]
-uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
-
-[[deps.StaticArrays]]
-deps = ["LinearAlgebra", "Random", "Statistics"]
-git-tree-sha1 = "2884859916598f974858ff01df7dfc6c708dd895"
-uuid = "90137ffa-7385-5640-81b9-e52037218182"
-version = "1.3.3"
-
-[[deps.Statistics]]
-deps = ["LinearAlgebra", "SparseArrays"]
-uuid = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
-
-[[deps.Test]]
-deps = ["InteractiveUtils", "Logging", "Random", "Serialization"]
-uuid = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
-
-[[deps.libblastrampoline_jll]]
-deps = ["Artifacts", "Libdl", "OpenBLAS_jll"]
-uuid = "8e850b90-86db-534c-a0d3-1478176c7d93"