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| -rw-r--r-- | README.md | 10 | ||||
| -rw-r--r-- | doc/docker-container.org | 86 |
2 files changed, 95 insertions, 1 deletions
@@ -42,9 +42,17 @@ Also mariadb and redis need to be running, see ## Testing To have tests pass, the redis and mariadb instance should be running, because of -asserts sprinkled in the code base(these will be removed in due time). +asserts sprinkled in the code base. + +Right now, the only tests running in CI are unittests. Please make +sure the existing unittests are green when submitting a PR. + +See +[./bin/genenetwork2](https://github.com/genenetwork/genenetwork2/blob/testing/doc/docker-container.org) +for more details. #### Mechanical Rob + We are building 'Mechanical Rob' automated testing using Python [requests](https://github.com/genenetwork/genenetwork2/tree/testing/test/requests) which can be run with: diff --git a/doc/docker-container.org b/doc/docker-container.org new file mode 100644 index 00000000..3c9864c5 --- /dev/null +++ b/doc/docker-container.org @@ -0,0 +1,86 @@ +#+TITLE: Genenetwork2 Dockerized + +* Table of Contents :TOC: +- [[#introduction][Introduction]] +- [[#creating-the-docker-images][Creating the Docker Images]] +- [[#pushing-to-dockerhub][Pushing to DockerHub]] + +* Introduction + +The CI(Continuous Integration) system for Genenetwork2 uses [[https://github.com/features/actions][Github +Actions]]. As such, it's important to have a way to run tests using +facilities provided by GUIX in a reproducible way. This project +leverages GUIX to generate a docker container from which the unittests +are ran from. + +Find instructions on how to set docker up inside GUIX [[https://github.com/pjotrp/guix-notes/blob/master/CONTAINERS.org#run-docker][here]]. This +document will not get into that. It's assumed that you have a working +dockec setup. + +The rest of this document outlines how the docker container used in +the CI builds were created. + +* Creating the Docker Images + +First create the image by running: + +#+begin_src sh +# For the Python 2 version: +env GUIX_PACKAGE_PATH="/home/bonface/projects/guix-bioinformatics::/home/bonface/projects/guix-past/modules" \ + ./pre-inst-env guix pack -f docker --no-grafts \ + -S /usr/bin=/bin -S /etc/profile=/etc/profile \ + -S /share/genenetwork2=/share/genenetwork2 \ + -S /share/javascript=/share/javascript \ + -S /lib=/lib \ + -S /usr/gn2-profile=/ \ + coreutils bash genenetwork2 + +# For the Python 3 version: +env GUIX_PACKAGE_PATH="/home/bonface/projects/guix-bioinformatics::/home/bonface/projects/guix-past/modules" \ + ./pre-inst-env guix pack -f docker --no-grafts \ + -S /usr/bin=/bin -S /etc/profile=/etc/profile \ + -S /share/genenetwork2=/share/genenetwork2 \ + -S /share/javascript=/share/javascript \ + -S /lib=/lib \ + -S /usr/gn2-profile=/ \ + coreutils bash python3-genenetwork2 + #+end_src + +The output will look something similar to: + +: /gnu/store/dj1xh19jq1l9vwq24w3nay2954x0wabb-docker-pack.tar.gz + +Load the docker image by running: + +: docker load --input /gnu/store/dj1xh19jq1l9vwq24w3nay2954x0wabb-docker-pack.tar.gz + +Results look something similar to: + +#+begin_export ascii +a93f52b7f565: Loading layer 3.174GB/3.174GB +Loaded image: coreutils-genenetwork2:latest +#+end_export + +Assuming you have a docker instance running, you could always run +commands in it e.g: + +: docker run "coreutils-genenetwork2:latest" python --version + + +* Pushing to DockerHub + +We use DockerHub to store the docker images from which we use on our +CI environment using Github Actions. + +To push to dockerhub, first get the image name by running =docker +images=. Push to dockerhub using a command similar to: + +: docker push bonfacekilz/python2-genenetwork2:latest + +Right now, we have 2 images on DockerHub: + +- https://hub.docker.com/repository/docker/bonfacekilz/python2-genenetwork2: + Contains the python2 version of gn2. Don't use this. Please use the + python3 image! +- https://hub.docker.com/repository/docker/bonfacekilz/python3-genenetwork2: + Contains the python3 version of gn2. |