Set up GitLab/Travis CI

[dzhoshkun]

Related to https://cmiclab.cs.ucl.ac.uk/CMIC/NiftyNet/issues/269

We should set up CPU-only CI tests on Travis until a long-term solution for GPU testing has been found.

[dzhoshkun]

• would the Travis matrix work for the different scripts currently available?

[dzhoshkun]

https://docs.travis-ci.com/user/languages/python

[tomdoel]

For the ImageSplit project, I wanted to avoid different testing paths for travis, gitlab-ci and local testing. So I set up tox.ini to do most of the CI steps using virtualenvs, and then configured .travis.yml and .gitlab-ci.yml to run the tests using the tox command. Another advantage is I can run any of the CI stages locally; e.g. tox will run all the tests; tox -e lint will run the linting etc.

[dzhoshkun]

@tomdoel Thanks for letting me know! This looks quite useful for avoiding duplication. Do you have any failing tests? I'd like to see what the log looks like. In the past I had difficulties tracing problems in failing CI builds when running the CI commands e.g. off a shell script. I wonder whether tox provides more useful output in such cases.

[tomdoel]

A failing test example with tox: https://cmiclab.cs.ucl.ac.uk/GIFT-Surg/ImageSplit/-/jobs/42111

[dzhoshkun]

• configure tox: sample only!
• set up Travis to use tox script
• consider opening a new issue for translating the existing CI scripts to tox (or maybe multiple issues, with one for each part)

[dzhoshkun]

• testenv:lint not run

[dzhoshkun]

• revert above commit (tox-lint)

[dzhoshkun]

redefined-variable-type was deprecated already in 2017, might have just been removed by now.

[dzhoshkun]

redefined-variable-type became an extension (unavailable by default) as of pylint 1.7

[dzhoshkun]

@wyli As of bdc6655, Travis CI is set up and the pylintjob and quicktest sections of GitLab CI have been translated to Travis CI. You can actually click the red cross next to the commit hash above and see the result for yourself 😄

There are two issues, though:

• I haven't been able to get pylint to run, mainly due to version incompatibilities (current version: 1.9.1, on Adelie we have 1.5.2)
• But the actual problem is that it takes about 30 mins to run even the quicktest section, due to the absence of GPU computing on Travis.

[wyli]

@dzhoshkun Looks nice! I'll send you a merge request to fix the pylint tests (we could take this opportunity to disucss/test the new workflow for contributors #98 ).

[dzhoshkun]

There seems to be another, (given the current setup) possibly easier, way to continue testing with our custom hardware (since GitLab v10.6 on 22 March as far as I can see).

[dzhoshkun]

• finalise the GitLab CI/CD for GitHub test: https://gitlab.com/dzhoshkun/cpp-py-example/services/github/edit (imported from https://github.com/dzhoshkun/cpp-py-example)

[dzhoshkun]

@wyli @tomdoel I've managed to set up GitLab CI for one of my personal projects on GitHub, running its CI pipelines on Adelie. For the result, please see this commit (click the green tick!) and also this PR showing "All checks passed".

For the record, this feature has been around for a while, but involved a manual setup, and did not transmit the CI pipeline result back to GitHub.

Also for the record, I've imported the project not from CmicLab to GitLab, but from GitHub to GitLab. Mentioning this explicitly, as currently there seems to be an issue exporting projects from CmicLab.

[wyli]

Cool, looks like a feasible solution for GPU tests.

[wyli]

Sometimes CI runner couldn't find pylint command (https://gitlab.com/NifTK/NiftyNet/-/jobs/80703023) any idea?