wtsi-npg / npg_ranger

NGS data streaming (sam, bam, cram, vcf) - pre-production
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Add GitHub actions #238

Closed ghost closed 2 years ago

ghost commented 2 years ago

Adds a GitHub action which does the same as TravisCI. Miniconda was upgraded to a recent release to allow it to find dependencies.

Tests were disabled in two separate commits to allow a successful CI run:

Link to the most recent CI run: https://github.com/absanger/npg_ranger/actions/runs/1717456988

jmtcsngr commented 2 years ago

I think because everything is moving to actions, there is no good reason to keep the travis part.

.travis.yml can go .travis/install.sh can be relocated to .github folder or to a scripts folder to follow what happened in other projects like npg_conda

I like the idea of testing with ubuntu latest, but I guess it will resolve to >20 and we still have some need to test with bionic.

So I propose:

jobs:
  build:
    strategy:
      fail-fast: false
      matrix:
        os: [ubuntu-18.04, ubuntu-latest]
        node-version: ["10.16.3", "10.18.1", "12.14.1", "14", "16"]
    runs-on: ${{ matrix.os }}

We can probably remove the node 10x things very soon to reduce number of jobs.

What do you think?

ghost commented 2 years ago

I'll go with a scripts folder to remove all the travis bits and add bionic. As for node versions, could we already drop the 10.x versions already? A few updated dependencies require node >=12 now, such as the mongodb driver and commander. (Though upgrading commander passes tests on node 10, and mongodb has a node 10-compatible version supported until this summer...)

jmtcsngr commented 2 years ago

We both agree about the scripts folder, please go ahead.

Happy to dump 10x node as we need to keep things moving anyway. Better to focus your efforts on the versions we will most likely use. We may need to update the package.json to say we are dropping the support (something similar for npm).

You can also update the contributors list in package json with your name.