How to contribute to/develop COBREXA

If you want to contribute to the COBREXA package, please fork the present repository by following these instructions.

Step 1: Retrieve a local version of COBREXA

There are two ways that you can retrieve a local copy of the package: one is to manually clone the forked repository, and the second one is to use the integrated Julia package manager.

Option 1: Manually clone your fork

Warning

Please make sure you have forked the repository, as described above.

You can do this as follows from the command line:

$ git clone git@github.com:yourUsername/COBREXA.jl.git COBREXA.jl
$ cd COBREXA.jl
$ git checkout -b yourNewBranch origin/develop

where yourUsername is your Github username and yourNewBranch is the name of a new branch.

Then, in order to develop the package, you can install your cloned version as follows (make sure you are in the COBREXA.jl directory):

(v1.1) pkg> add .

(press ] to get into the packaging environment)

This adds the COBREXA.jl package and all its dependencies. You can verify that the installation worked by typing:

(v1.1) pkg> status

If everything went smoothly, this should print something similar to:

(v1.1) pkg> status
    Status `~/.julia/environments/v1.1/Project.toml`
    [babc4406] COBREXA v0.1.0 #yourNewBranch (.)

Now, you can readily start using the COBREXA module:

julia> using COBREXA

Option 2: Use the Julia package manager

When you are used to using the Julia package manager for developing or contributing to packages, you can type:

(v1.1) pkg> dev COBREXA

This will install the COBREXA package locally and check it out for development. You can check the location of the package with:

(v1.1) pkg> status
    Status `~/.julia/environments/v1.4/Project.toml`
  [a03a9c34] COBREXA v0.0.5 [`~/.julia/dev/COBREXA`]

The default location of the package is ~/.julia/dev/COBREXA.

You can then set your remote by executing these commands in a regular shell:

$ cd ~/.julia/dev/COBREXA
$ git remote rename origin upstream # renames the origin as upstream
$ git remote add origin git@github.com:yourUsername/COBREXA.jl.git
$ git fetch origin

where yourUsername is your Github username.

Warning

Make sure that your fork is located at github.com/yourUsername/COBREXA.jl.

Then, checkout a branch yourNewBranch:

$ cd ~/.julia/dev/COBREXA
$ git checkout -b yourNewBranch origin/develop

Then, you can readily use the COBREXA package:

julia> using COBREXA

After making changes, precompile the package:

(v1.1) pkg> precompile

Step 2: Activate COBREXA

Warning

Please note that you cannot use the dependencies of COBREXA directly, unless they are installed separately or the environment has been activated:

(v1.1) pkg> activate .
(COBREXA) pkg> instantiate

Now, the environment is activated (you can see it with the prompt change (COBREXA) pkg>). Now, you can use the dependency. For instance:

julia> using JuMP
Warning

If you do not activate the environment before using any of the dependencies, you will see a red error messages prompting you to install the dependency explicitly.

Step 3: Contribute!

Tip

Adding [skip ci] in your commit message will skip CI from automatically testing that commit.