Automate validation.py as an integration test

[nelse003]

Aim: Run validation code* at least at every code change/ daily.

Validation code: Minimal:

• Validation of a single dataset that the minima is within 2 step distance (i.e 0.02, with 0.01 step) with fixed B and set occupancy

Enhancements:

• Validation with multiple input datasets
• Validation with
• Email results to Elliot
• Check all expected files are output

Consider closed if minimal condition met, then move enhancements to new issues.

Questions:

• How to run test code given the difficulties of how code uses cctbx and phenix, and can only be run by ccp4-python.

[nelse003]

How:

• [x] Setup a test

• What does this need to be written in?

• [x] Setup a Docker image

• Needs CCP4 & Phenix

• Copy setup from https://github.com/reskyner/ccp4_docker

• Use nelse003/ccp4_phenix_docker (forked from: https://github.com/reskyner/ccp4_docker)

• Dockerfile: This contains the instructions for setting up the base install, i.e

• Use Ubuntu

• Get ccp4

• ccp4.setup-sh script to be stored in repo to allow setup of program before testing

• pandda update script is stored in repo to allow setup of program before testing

Needed:

• How to install phenix using a command line tool, CCP4 can be installed via wget.

Dockerfile : Like that in XCE repo- to be in exhaustive_search repo

• Gets docker image from other file
• Adds ./run_tests
• Adds ./compile_test.py
• Creates directory XChemExplorer - why?
• Adds to that dir? why?

./run_tests

Bash script that just shows that docker is ok... Assuming placholder for further tests?

compile_test.py

Changes enbvironment variables and and imports all xce components. this is considered a "Build/ compile test"?

• [x] Setup Travis CI

Travis CI needs:

• GitHub login
• Project hosted as a repository on GitHub
• Working code in your project
• Working build or test script

Read: https://docs.travis-ci.com/user/getting-started/

.travis.yml (XCE version)

• Used to provide information to travis CI

• sudo: required

• services: docker

• Lines needed for docker to run (See for more info: https://docs.travis-ci.com/user/docker/)

- install: docker build -t reskyner/xce Builds the version of docker

Not sure where this is pointing to, but should be getting the docker build? Thought his would be at rskyner/ccp4_docker

script: docker run reskyner/xce /bin/bash -c "/ccp4/bin/ccp4-python /XChemExplorer/compile_test.py"

This runs the compile_test.py script using docker image

[nelse003]

https://medium.com/mobileforgood/coding-tips-patterns-for-continuous-integration-with-docker-on-travis-ci-9cedb8348a62 https://docs.travis-ci.com/user/environment-variables/#Defining-Variables-in-Repository-Settings

[nelse003]

Need to:

• [ ] Get phenix in docker image

• [ ] Reduce docker images size if possible, reducing cache build time

Apply more tests:

• [ ] Validation: Does it run? Output check with 2 steps?

• [ ] Exhaustive search: Does it run?