1. Installation

Currently there are the following options for installing the package:

1.1. Conda

This is currently only available for Linux.

  1. Install Latex on your system. E.g., see the provided bindep.txt file for which TeX Live packages are needed for a selection of popular Linux distribuions.

  2. conda install -c jakobandersen -c conda-forge mod

  3. (Optional, but recommended) Install a pre-compiled Latex format file. During figure generation by PostMØD (mod_post) a Latex format file is needed. It depends on your Latex installation and can therefore not be provided in the Conda package. It will then be compiled at each invocation. To check, try running, e.g., mod -e "smiles('O').print()". If the post-processor output has a line with compileFmt, the format file is not installed.

    Run mod_post --install-format to install the format file (or mod_post --install-format-sudo if you don’t own the folder with the Conda installation).

1.2. Docker

A Docker image with an installation is available at Docker Hub, so getting started can be done simply via

docker run -it jakobandersen/mod

It will put you into an empty folder /workDir. The image is build with a copy of the Examples in /examples.

In order to exchange data with the container it may be convient to start the container with a local folder mounted, for example the current folder

docker run -it -v $(pwd):/workdir jakobandersen/mod

However, the user running inside the container is root so all files you create inside the shared folder will have root as owner and group. Therefore, it may be better to tell Docker to run with your own user and group inside

docker run -it -v $(pwd):/workdir -u $(id -u):$(id -g) jakobandersen/mod

Note though, that your user/group probably doesn’t exist in the container so you may get some warnings about the group not existing and that the user does not have a name. This is however usually not a problem.

As a final optimization, every time you execute the command above, you create a new container. You can use docker container prune to delete stopped containers. Assuming you only work within the shared /workdir there is no particular reason for the container to hang around once you exit, so you can add --rm to the command to let Docker automatically delete it once you exit. We thus arrive at the following full command

docker run -it --rm -v $(pwd):/workdir -u $(id -u):$(id -g) jakobandersen/mod

As a quick test, you can try running mod -e "smiles('O').print() inside the container. When it’s done, then outside the container you should now be able to open the printed summary summary/summary.pdf. You can thus use the mod command inside the container, but otherwise do all file manipulation outside the container.