Docker

In order to implement a GitHub Actions workflow in which Armadillo, nlohmann_json, NetCDF and their dependencies can be linked or included in the compiled model, Docker can be used to create an image on which these dependencies can be kept.

The NetCDF documentation suggests using a package management tool to install NetCDF.

“The easiest way to get netCDF is through a package management program, such as rpm, yum, homebrew, macports, adept, and others.”

This document describes how to use Conda to install NetCDF and Armadillo and how to create a Docker image that can be activated by GitHub Actions in order to run automated tests when pull requests are made to a specified branch.

Conda

The conda package manager can quickly install the dependencies needed by Aether.

If you don’t have conda installed on your system, it merely requires downloading and running a shell script. For more information, see conda’s installation guide.

If you would like to install the dependencies on your local machine without using a Docker image, the following commands create and activate a virtual environment named aether-armadillo-json-netcdf in which the armadillo and nlohmann_json header files and the netcdf-cxx4 library are installed.

conda create --name netcdf-armadillo-json --channel conda-forge netcdf-cxx4 armadillo nlohmann_json
conda activate netcdf-armadillo-json

Building a Docker image

Since conda was used to install the dependencies, it’s necessary to activate conda in a Docker file in order to create the Docker image. This post by Itamar Turner-Trauring describes the difficulty of getting conda activate to run in the bash shell

The bash shell started by Docker isn’t configured to activate a conda environment.

Building a Docker image

can be linked into the source code, it is useful to

Aether’s source code relies on a few dependencies in order to run properly:

Armadillo
NetCDF
nlohmann JSON library

Aether manages these dependencies using git’s submodule capability. Submodules are their own repositories that are contained within a larger repository. Submodules can nest within other submodules and their contents can be edited and updated.

Verify your version of git

In order to get started, you will need to verify which version of git you have installed because git’s support for submodules has changed throughout its various releases. These instructions will work for releases equal to or newer than git 2.7. In order to verify which version of git you are using, type:

git --version

Adding a submodule to a repository

mkdir external
git submodule add https://github.com/nlohmann/json external/json

Modifying your git config to show the status of submodules

git config --global status.submoduleSummary true

Organization of the .gitmodules file

The submodules are defined in a dot file stored in the root directory of the repository, .gitmodules.

cat .gitsubmodules
[submodule "external/json"]
    path = external/json
    url = https://github.com/nlohmann/json

Cloning a repository and its submodules

git clone https://github.com/AetherModel/Aether.git
cd Aether
git submodule init
git submodule update

Removing a submodule from a repository

Temporary removal

git submodule deinit external/json

Permament removal

git submodule deinit external/json
git rm external/json
git commit -m "Removed json submodule"