Currently there are the following options for installing the package:
Installing via Conda.
Running via a pre-compiled Docker image.
This is currently only available for Linux.
Install Latex on your system. E.g., see the provided
bindep.txtfile for which TeX Live packages are needed for a selection of popular Linux distribuions.
conda install -c jakobandersen -c conda-forge mod
(Optional, but recommended) Install a pre-compiled Latex format file. During figure generation by PostMØD 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.
mod_post --install-formatto install the format file (or
mod_post --install-format-sudoif you don’t own the folder with the Conda installation).
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
The image is build with a copy of the Examples in
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
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
You can thus use the
mod command inside the container, but otherwise
do all file manipulation outside the container.