ensure CI works with versions of nim not available in ubuntu repos

[davidhwyllie]

The catwalk software used by findneighbour4 relies on nim. At present, the nim version pulled by apt-get is old (1.06) wherease the latest nim (requirement for the latest catwalk) is 1.4.0. Need to adjust the CI script to allow the latest nim in the CI environment.

[davidhwyllie]

A recipe for github actions using the latest nim is available: https://github.com/marketplace/actions/setup-nim-environment

[davidhwyllie]

See branch issue93. Unable so far to find a github action which allows this. Tried the following:

https://github.com/alaviss/setup-nim https://github.com/marketplace/actions/setup-nim-environment https://github.com/iffy/install-nim

These approaches fail with various errors, which are shown in the github action and various commits to issue93 branch.

[davidhwyllie]

Used direct cloning and installation in local directory:

        mkdir external_software
        cd external_software
        wget https://nim-lang.org/download/nim-1.4.8-linux_x64.tar.xz
        tar -xf nim-1.4.8-linux_x64.tar.xz
        ./nim-1.4.8/bin/nimble --version

        # clone catwalk relatedness engine
        git clone https://gitea.mmmoxford.uk/dvolk/catwalk.git
        cd catwalk
        ../nim-1.4.8/bin/nimble -y build -d:release -d:danger -d:no_serialisation --nimbleDir:../nim-1.4.8/bin

Note that this works locally but when installed as part of a github action

# This workflow will build the latest version of nim
# and test catwalk

name: Test catwalk with latest nim

on: 
  workflow_dispatch:
    inputs:
      tags:
        description: 'Test catwalk with latest nim'
  push:
    branches:
    - '*'

jobs:
  build:

    runs-on: ubuntu-latest
    strategy:
      matrix:
        python-version: ["3.8"]
        mongodb-version: ["4.4.4"]

    steps:
    - uses: actions/checkout@v2

    - name: Setup Nim environment and catwalk
      run: |
        mkdir external_software
        cd external_software
        wget https://nim-lang.org/download/nim-1.4.8-linux_x64.tar.xz
        tar -xf nim-1.4.8-linux_x64.tar.xz
        ./nim-1.4.8/bin/nimble --version

        # clone catwalk relatedness engine
        git clone https://gitea.mmmoxford.uk/dvolk/catwalk.git
        cd catwalk
        ../nim-1.4.8/bin/nimble -y build -d:release -d:danger -d:no_serialisation --nimbleDir:../nim-1.4.8/bin

this fails reporting

dependency nim > 1.4.0 not present. Presumably the nimble package manager is checking some central location for nimble.

[davidhwyllie]

-- filed bug report

Please note that the step prepending the directory to the system PATH variable cannot itself access the updated path variable. This is documented below:

https://docs.github.com/en/actions/learn-github-actions/workflow-commands-for-github-actions#adding-a-system-path You'll be able to access the updated path in subsequent steps. I was able to successfully test this out with the following workflow

# This workflow will use the latest version of nim

name: Test latest nim

on: 
  workflow_dispatch:
    inputs:
      tags:
        description: 'Test latest nim'

jobs:
  build:

    runs-on: ubuntu-latest

    steps:
    - uses: actions/checkout@v2

    - name: Setup Nim 
      run: |
        mkdir external_software
        cd external_software
        wget https://nim-lang.org/download/nim-1.4.8-linux_x64.tar.xz
        tar -xf nim-1.4.8-linux_x64.tar.xz
        echo "Checking nimble works when relative path applied"
        ./nim-1.4.8/bin/nimble --version
        # show what is on the path
        echo "Current path"
        sed 's/:/\n/g' <<< "$PATH"
        NIMDIR="`pwd`/nim-1.4.8/bin"
        echo "Nim directory:"
        echo "$NIMDIR"
        echo "Checking nimble works when computed NIMDIR path applied"
        ${NIMDIR}/nimble --version
        echo "Appending to PATH"
        echo "$NIMDIR" >> $GITHUB_PATH

    - name: updated
      run: |
          echo "Updated path"       
          # show what is on the path
          sed 's/:/\n/g' <<< "$PATH"

          # is nimble accessible on path
          echo "Nimble version:"
          nimble --version

[davidhwyllie]

Issue resolved. CI scripts updated.