Update README with new instructions

README.adoc

@@ -12,7 +12,7 @@ The following steps from the setup have to be followed every time before running
 
 === Launch Julia
 
-To activate the environment, navigate to the main directory `/ReCo.jl` and then run the following to launch Julia:
+To activate the environment, navigate to the main directory `ReCo.jl` and then run the following to launch Julia:
 
 [source,bash]
 ----
@@ -22,7 +22,7 @@ julia --threads auto
 
 `auto` automatically sets the number of threads to use. If you want to use a specific number `N` of threads, replace `auto` with `N`.
 
-=== Activating environment
+=== Activating environments
 
 After launching Julia, the package environment has to be activated by running the following in the REPL:
 
@@ -32,6 +32,16 @@ using Pkg
 Pkg.activate(".")
 ----
 
+`"."` stands for the current path which has to be the path of the package directory `ReCo.jl`.
+
+If specified otherwise, an environment in a subdirectory has to be activated instead of the package environment. To activate an environment of a subdirectory `SUBDIRECTORY`, run the following:
+
+[source,julia]
+----
+using Pkg
+Pkg.activate("SUBDIRECTORY")
+----
+
 === Install/update dependencies
 
 After activating the package environment, run the following to install/update the package dependencies:
@@ -77,6 +87,7 @@ 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, see the documentation of `init_sim` or `run_sim`.
 
 == Simulation visualization
+For visualization, the environment of the subdirectory `visualization` has to be activated.
 
 === Animation
 
@@ -84,6 +95,7 @@ To generate an animation of a simulation, run the following:
 
 [source,julia]
 ----
+using Animation
 animate(sim_dir)
 ----
 
@@ -95,6 +107,7 @@ To plot only one snapshot of a simulation, run the following:
 
 [source,julia]
 ----
+using SnapshotPlot
 plot_snapshot(sim_dir)
 ----
 
@@ -102,13 +115,14 @@ This will ask for the number of the snapshot to plot out of the total number of
 
 == Run a reinforcement learning process
 
-Run a reinforcement learning process and return the environment helper and the the path of the process directory relative to the directory `ReCo.jl`:
+Run a reinforcement learning process and return the environment helper and the the relative path of the process directory:
+
 [source,julia]
 ----
 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 short description of an environment is included at the beginning of the corresponding file.
+`ENVTYPE` has to be replaced by one of the environments named after the file names in the directory `RL/Envs`, for example: `LocalCOMEnv`. A short description of an environment is included at the beginning of the corresponding file.
 
 The documentation of `run_rl` includes all possible optional arguments.
 
@@ -121,11 +135,11 @@ The documentation of `run_rl` includes all possible optional arguments.
 env_helper.shared.agent.policy.learner.approximator.table
 ----
 
-To generate a LaTeX table with the states and actions combintation names for the Q-matrix, run the following after activating the environment in `ReCo.jl/analysis`:
+To generate a LaTeX table with the states and actions combintation names for the Q-matrix, activate the environment of the subdirectory `analysis` and run the following:
 
 [source,julia]
 ----
-include("Q_matrix_latex_export.jl")
+include("analysis/Q_matrix_latex_export.jl")
 export_q_matrix(env_helper, FILENAME_WITHOUT_EXTENSION)
 ----
 
@@ -147,10 +161,11 @@ To access the rewards, run the following:
 env_helper.shared.hook.rewards
 ----
 
-To plot the rewards, run the following:
+To plot the rewards, activate the environment of the subdirectory `visualization` and run the following:
 
 [source,julia]
 ----
+using RewardsPlot
 plot_rewards(rl_dir)
 ----
 
@@ -158,11 +173,11 @@ The function's documentation explains where the output is placed.
 
 === Mean kappa
 
-To plot the mean of kappa as the ratio of the eigenvalues of the gyration tensor, run the following after activating the environment in `ReCo.jl/analysis`:
+To plot the mean of kappa as the ratio of the eigenvalues of the gyration tensor, activate the environment of the subdirectory `analysis` and run the following:
 
 [source,julia]
 ----
-include("mean_kappa.jl")
+include("analysis/mean_kappa.jl")
 plot_mean_κ(; rl_dir=rl_dir, n_last_episodes=N_LAST_EPISODES)
 ----
 
@@ -170,39 +185,39 @@ plot_mean_κ(; rl_dir=rl_dir, n_last_episodes=N_LAST_EPISODES)
 
 == Run analysis
 
-First, `cd` into and activate the environment in `ReCo.jl/analysis`.
+First, activate the environment of the subdirectory `analysis`.
 
 === Mean squared displacement and random walk
 
 [source,julia]
 ----
-include("mean_squared_displacement.jl")
+include("analysis/mean_squared_displacement.jl")
 run_msd_analysis()
 run_random_walk()
 ----
 
-The output is `ReCo.jl/exports/graphics/mean_squared_displacement.pdf` and `ReCo.jl/exports/graphics/random_walk.pdf`.
+The output is `exports/graphics/mean_squared_displacement.pdf` and `exports/graphics/random_walk.pdf`.
 
 === Radial distribution function
 
 [source,julia]
 ----
-include("radial_distribution_function/radial_distribution_function.jl")
+include("analysis/radial_distribution_function/radial_distribution_function.jl")
 run_radial_distribution_analysis()
 ----
 
-The output is `ReCo.jl/exports/graphics/radial_distribution.pdf` and `ReCo.jl/exports/graphics/radial_distribution_all_vs.pdf`.
+The output is `exports/graphics/radial_distribution.pdf` and `exports/graphics/radial_distribution_all_vs.pdf`.
 
 === Reward discount analysis
 
 [source,julia]
 ----
-include("reward_discount_analysis.jl")
+include("analysis/reward_discount_analysis.jl")
 run_reward_discount_analysis()
 ----
 
-The output is `ReCo.jl/exports/graphics/reward_discount_analysis.pdf`.
+The output is `exports/graphics/reward_discount_analysis.pdf`.
 
 == Graphics
 
-The directory `ReCo.jl/graphics` has some Julia files that generate graphics related to this package. The function in every file that has to be run to generate the corresponding graphics starts with `plot_` or `gen_`. The output is placed in `ReCo.jl/exports/graphics`.
+The subdirectory `graphics` has some Julia files that generate graphics related to this package. The function in every file that has to be run to generate the corresponding graphics starts with `plot_` or `gen_`. The output is placed in `exports/graphics`. The subdirectory of a file has an environment that has to be activated first.