Move CI to GitHub Actions

[samuell]

Description

This PR moves the CI workflow configuration from the previous Travis CI one to GitHub actions, as suggested in #174

Some more details of changes done:

• The install script uses micromamba instead of conda if inside GitHub actions
• Some dependency specs were adjusted to make the installation go through
• A pointer to a folder ${CONDA_PREFIX}/testproject was changed to ${CONDA_PREFIX}/testdata instead, since the former does not exist in the repo.
• Two smaller bugs identified by flake8 was fixed, along with a typo

You can check the output of the converted code on the actions tab of this repo.

Primary function of PR

• Hotfix
• Patch
• Minor functionality improvement
• New type of analysis
• Backward-breaking functionality improvement
• This change requires internal documents to be updated
• This change requires another repository to be updated

Testing

If the update is a hotfix, it is sufficient to rely on the development testing along with the Travis self-test automatically applied to the PR.

Test routine to verify the stability of the PR:

• bash /home/proj/production/servers/resources/hasta.scilifelab.se/install-microsalt-stage.sh BRANCHNAME
• us
• conda activate S_microSALT
• (SITUATIONAL) export MICROSALT_CONFIG=/home/proj/dropbox/microSALT.json
• Select a relevant subset of the following:
• microSALT analyse project MIC3109
• microSALT analyse project MIC4107
• microSALT analyse project MIC4109
• microSALT analyse project ACC5551

Verify that the results for projects MIC3109, MIC4107, MIC4109 & ACC5551 are consistent with the results attached to AMSystem doc 1490, Microbial_WGS.xlsx

Test results

These are the results of the tests, and necessary conclusions, that prove the stability of the PR.

Sign-offs

• Code tested by @octocat
• Approved to run at Clinical-Genomics by @sylvinite

[samuell]

I haven't successfully tested the installation on Hasta Stage yet, since it seems to break on some unrelated things (can not find databases etc).

I might need to discuss with some of you on how to best test this on Hasta.

[Vince-janv]

Nice 👍