[Bioc-devel] Add dockerhub push to github repository

[Murphy, Alan E]

Hey Nuno,

Thanks so much, see below.

Kind regards,
Alan.

name: R GitHub Actions

on:
  push:
    branches:
      - main
      - master
      - dev-am
  pull_request:
    branches:
      - main
      - master

jobs:
  R-CMD-check:
    name: R-CMD-check
    runs-on: ubuntu-latest
    container: almurphy/scfdev:latest
    env:
      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
      RGL_USE_NULL: TRUE
    steps:
      - uses: actions/checkout using v2
      - name: Setup R
        uses: r-lib/actions/setup-r using v1
        with:
          install-r: false

      - name: Install dependencies
        run: |
          install.packages(c("remotes", "rcmdcheck"))
          remotes::install_deps(dependencies = TRUE)
        shell: Rscript {0}
      - name: Check
        run: rcmdcheck::rcmdcheck(args = "--no-manual", error_on = "error")
        shell: Rscript {0}

      - name: Get R package version
        run: |
          version=$(grep Version DESCRIPTION | grep -o "[0-9.]\+")
          echo "packageVersion=${version}" >> $GITHUB_ENV
        shell: bash {0}

      - name: Build and push
        uses: docker/build-push-action using v2
        with:
          push: true
          username: ${{ secrets.DOCKER_USERNAME }}
          password: ${{ secrets.DOCKER_TOKEN }}
          repository: almurphy/scfdev
          tag_with_ref: true
          tag_with_sha: true
          tags: ${{ github.repository }}:${{ env.packageVersion }}
________________________________
From: Nuno Agostinho <nunodanielagostinho using gmail.com>
Sent: 03 June 2021 20:15
To: Murphy, Alan E <a.murphy using imperial.ac.uk>
Cc: bioc-devel using r-project.org <bioc-devel using r-project.org>
Subject: Re: [Bioc-devel] Add dockerhub push to github repository

Hey Alan,

is that installing the master branch or the current branch that has been pushed to?

It is based on the current branch.

Building image [***/scfdev:combiz/scFlow:0.7.1 ***/scfdev:dev-am ***/scfdev:sha-658a6af]
invalid argument "***/scfdev:combiz/scFlow:0.7.1" for "-t, --tag" flag: invalid reference format

I don't think the problem is the Dockerfile, but the GitHub Actions workflow itself (specifically, the issue seems to be related with the tag of the image). Could you show me your GitHub Actions workflow file to check what is going on?

Cheers,
Nuno

On 3 Jun 2021, at 20:05, Murphy, Alan E <a.murphy using imperial.ac.uk<mailto:a.murphy using imperial.ac.uk>> wrote:

Hey Nuno,

Thank you very much for your comprehensive explanation!

I have a question regarding the `remotes::install_local()` approach in the dockerfile, is that installing the master branch or the current branch that has been pushed to? I ask as I'm working on 'dev-am' branch and I got the following error:

Building image [***/scfdev:combiz/scFlow:0.7.1 ***/scfdev:dev-am ***/scfdev:sha-658a6af]
invalid argument "***/scfdev:combiz/scFlow:0.7.1" for "-t, --tag" flag: invalid reference format
See 'docker build --help'.
Error: Error: exit status 125
Usage:
  github-actions build-push [flags]

Flags:
  -h, --help   help for build-push

exit status 125

Obviously, this may not be down to this but I'm just trying to rule things out since this was the only change I made to the dockerfile. The docker file has this added following your dockerfile:

## Install scFlow package
# Copy description
WORKDIR scFlow
ADD . .

# Install R package from source
RUN Rscript -e "remotes::install_local()"
RUN rm -rf *

Cheers,
Alan.
________________________________
From: Nuno Agostinho <nunodanielagostinho using gmail.com<mailto:nunodanielagostinho using gmail.com>>
Sent: 03 June 2021 11:57
To: Murphy, Alan E <a.murphy using imperial.ac.uk<mailto:a.murphy using imperial.ac.uk>>
Cc: bioc-devel using r-project.org<mailto:bioc-devel using r-project.org> <bioc-devel using r-project.org<mailto:bioc-devel using r-project.org>>
Subject: Re: [Bioc-devel] Add dockerhub push to github repository

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Hey Alan,

I would like to automatically create a new image and push to dockerhub with github actions when I push changes to the github repository. Does anyone have an example of this process in their repositories?

Well, I use GitHub actions to build a Docker image and push it to GitHub Container Registry, maybe this could help somehow: https://github.com/nuno-agostinho/psichomics/blob/master/.github/workflows/docker.yml

I use GitHub releases to release a new package version and, every time I release a new version, a new Docker image is built (this image also gets automatically tagged with the latest tag). I also build Docker images every time I push changes to the dev branch.

Regarding DockerHub, I have DockerHub set up to automatically build Docker images every time I push to master (to create the latest tag) and dev branches in GitHub, as well as every time I create a new tag (which I do when creating new releases). I could put this in the GitHub actions, but I didn't bother yet.

I would ideally like the tag of this dockerhub push to be the R package version (from the DESCRIPTION) to differentiate between images, is this possible?

I think you can run some bash script in your GitHub Actions based on your DESCRIPTION file. I would have to test but maybe something like:

    - name: Get R package version
      run: |
        version=$(grep Version DESCRIPTION | grep -o "[0-9.]\+")
        echo "packageVersion=${version}" >> $GITHUB_ENV
      shell:
        bash {0}

You can then access this variable in other steps via ${{ env.packageVersion }} like so:

    - name: Build and push
      uses: docker/build-push-action using v2
      with:
        push: true
        tags: ${{ github.repository }}:${{ env.packageVersion }}

Is there a way to tell the Dockerfile to install the R package in the current repository?

To build the image, I use ADD . . to put the GitHub repository content in the Docker image and then install the package using remotes::install_local(), as you can see from my Dockerfile: https://github.com/nuno-agostinho/psichomics/blob/master/Dockerfile

I hope I was clear and helpful. Please tell me if you need help with anything else! :)

Best,
Nuno Agostinho

On 3 Jun 2021, at 07:52, Murphy, Alan E <a.murphy using imperial.ac.uk<mailto:a.murphy using imperial.ac.uk>> wrote:

Hi all,

I'm working on developing an R package with the aim to eventually submit to Bioconductor. I would like to automatically create a new image and push to dockerhub with github actions when I push changes to the github repository. Does anyone have an example of this process in their repositories?

Two things to also consider, I would ideally like the tag of this dockerhub push to be the R package version (from the DESCRIPTION) to differentiate between images, is this possible? Secondly, I currently have the dockerfile created but, since my R package repository is private I have been building the R package and using the tar.gz file in the dockerfile to install the package (rather than using devtools::install_github()). Is there a way to tell the Dockerfile to install the R package in the current repository?

Kind regards,
Alan.

Alan Murphy
Bioinformatician
Neurogenomics lab
UK Dementia Research Institute
Imperial College London

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