A base Docker image for our modeling needs. Contains the relevant Python packages, e.g., cobra and cameo, as well as chosen solvers, i.e., at the moment GLPK and CPLEX.
Note that the sympy cache is disabled by default (by setting the env var
SYMPY_USE_CACHE=no) as its usage by optlang causes memory leaks.
The following environment variables must be defined in the Travis settings.
| Variable | Description |
|---|---|
REPO_URL |
URL of the private repository storing proprietary solvers. |
GITHUB_TOKEN |
A GitHub access token (which should have repo permissions only) in order to download proprietary solvers. |
GCLOUD_EMAIL |
The Google Cloud e-mail for the Travis service account. |
GCLOUD_KEY |
The Google Cloud key. |
Type make to see frequently used workflow commands. Also take a look at the
.travis.yml configuration to get an idea of the general workflow.
- To test all dependencies for vulnerabilities run
make safety.
Ideas for future improvements:
- Make the installation of various solvers optional.
- Have one base image with the solvers and optlang.
- Layer different images on top of the base image, for example, cobra only, cobra & cameo, add further visualization packages.