Merge branch 'main' of github.com:michael-petersen/LinearResponse.jl

Author: michael-petersen

README.md

@@ -12,20 +12,22 @@ To fully use **LinearResponse.jl**, you will need **OrbitalElements.jl**, **Fini
 
 The libraries under the JuliaStellarDynamics organisation are currently unregistered[^1]. To add them to your julia[^2] registry, follow these steps:
 
-You may add all the packages[^3][^4] at once with this command:
+You may add all the packages[^3] at once with this command:
     ```
-    julia -e 'using Pkg; Pkg.add(url="https://github.com/JuliaStellarDynamics/OrbitalElements.jl.git"); Pkg.add(url="https://github.com/JuliaStellarDynamics/AstroBasis.jl.git"); Pkg.add(url="https://github.com/JuliaStellarDynamics/FiniteHilbertTransform.jl.git"); Pkg.add(url="https://github.com/JuliaStellarDynamics/LinearResponse.jl.git")'
+    julia -e 'using Pkg; Pkg.add(url="https://github.com/JuliaStellarDynamics/FiniteHilbertTransform.jl.git");
+    Pkg.add(url="https://github.com/JuliaStellarDynamics/OrbitalElements.jl.git");
+    Pkg.add(url="https://github.com/JuliaStellarDynamics/AstroBasis.jl.git");
+    Pkg.add(url="https://github.com/JuliaStellarDynamics/LinearResponse.jl.git")'
     ```
 
 You can confirm the current version with `status LinearResponse` in the julia package manager.
 
-
 ---
 ## Quickstart
 
 To reproduce the Plummer radial orbit instability calculation, see the example script in `examples/PlummerE/runExamplePlummer.jl`. Download the file by running:
 ```
-wget ttps://github.com/JuliaStellarDynamics/LinearResponse.jl/blob/main/examples/PlummerE/runExamplePlummer.jl
+wget https://github.com/JuliaStellarDynamics/LinearResponse.jl/blob/main/examples/PlummerE/runExamplePlummer.jl
 ```
 This script will compute the location of the unstable radial orbit instability mode, using a simplified version of the calculation from [Petersen et al. (2024)](https://ui.adsabs.harvard.edu/abs/2023arXiv231110630P/abstract) (`n1max=1` instead of `n1max=10`, which results in a factor of 10 speedup). The outputs will all be cached (appearing as several files with the `.h5` extension in the folder where the script is run), so re-running the example is inexpensive. This script will take approximately one minute to run.
 
@@ -48,6 +50,7 @@ In this image and test, we are highlighting two key results:
 
 An extension of this script, where the growth rate is computed for a range of radial anisotropy parameters, is Figure 1 in [Petersen et al. (2024)](https://ui.adsabs.harvard.edu/abs/2023arXiv231110630P/abstract).
 
+---
 ### Other examples
 
 The `examples` directory also includes several other basic calculations for the Isochrone, Plummer, and Zang disc models. For example, to (very nearly) reproduce the Isochrone damped dipole mode calculation from Fouvry & Prunet (2022), see the example driver script in `examples/IsochroneE/runlinearresponseIsochroneISO.jl`. Note that this mode is not converged: adjusting parameters (in particular `n1max`) will result in different pole locations. The example `examples/IsochroneA/runlinearresponseIsochroneISO.jl` is precisely the calculation performed by [Fouvry & Prunet (2022)](https://ui.adsabs.harvard.edu/abs/2022MNRAS.509.2443F/abstract) -- that is, with the analytic isochrone relations. This example will take substantially more computational effort, and can take up to twenty minutes to complete.
@@ -60,15 +63,31 @@ If you prefer interactive Jupyter notebooks, you will need to install `IJulia` f
 The interactive introduction example is then given in `examples/PlummerE/runExamplePlummer.ipynb`.
 
 
+---
+## Uninstall
+
+
+First start by removing the packages from the environment by running
+```
+julia -e 'using Pkg; Pkg.rm("OrbitalElements"); Pkg.rm("AstroBasis");Pkg.rm("FiniteHilbertTransform");Pkg.rm("LinearResponse");'
+```
 
+If you worked in a test environment (that you do not want to keep) you can also simply erase the folder using `rm -r /path/to/my_env`.
+
+Then to fully erase the package (installed in ~/.julia), run
+```
+julia -e 'using Pkg; using Dates; Pkg.gc(collect_delay=Day(0));'
+```
+
+It will erase all the packages which are not known in any of your "active" (i.e., for which the Manifest.toml file is reachable) project/environments, in particular `LinearResponse`.
 
 ---
 
 ## Authors
 
-Mathieu Roule - @MathieuRoule - [email protected]
+Mike Petersen -  [@michael-petersen](https://github.com/michael-petersen) - [email protected]
 
-Mike Petersen -  @michael-petersen - [email protected]
+Mathieu Roule -  [@MathieuRoule](https://github.com/MathieuRoule) - [email protected]
 
 ---
 
@@ -77,9 +96,4 @@ Mike Petersen -  @michael-petersen - [email protected]
 [^2]: If you are new to `julia`, install by following the instructions at [julialang.org/downloads/](https://julialang.org/downloads/). To invoke Julia in the Terminal, you need to make sure that the `julia` command-line program is in your `PATH`. 
 See [here](https://julialang.org/downloads/platform/#optional_add_julia_to_path) for detailed instructions.
 
-[^3]: **Note on working with environments.** By default packages are added to the default environment at ~/.julia/environments/v1.#. It is however easy to create other, independent, projects. If you want to install the `LinearResponse` package in a different/test environment, first create a folder to host the environment files (Project.toml and Manifest.toml which will be created later on). Then, for every command line invoking Julia, use `julia --project=/path/to/my_env` instead of `julia` alone. Note that packages will always be cloned in ~/.julia/packages but only accessible in your project's context.
-
-[^4]: You may also uninstall the libraries by removing the packages, by running
-```
-julia -e 'using Pkg; Pkg.rm("OrbitalElements"); Pkg.rm("AstroBasis");Pkg.rm("FiniteHilbertTransform");Pkg.rm("LinearResponse");'
-```
+[^3]: **Note on working with environments.** By default packages are added to the default environment at ~/.julia/environments/v1.#. It is however easy to create other, independent, projects. If you want to install the packages in a different/test environment, first create a folder to host the environment files (Project.toml and Manifest.toml which will be created later on). Then, for every command line invoking Julia, use `julia --project=/path/to/my_env` instead of `julia` alone. Note that packages will always be cloned in ~/.julia/packages but only accessible in your project's context.