build and publish containers to quay.io (#1485)

* Modernize Dockerfile

Use non-MUSL based container image so we can benefit from manylinux1
wheels

* build and publish containers to quay.io

Author: mr-c

.github/workflows/quay-publish.yml

@@ -0,0 +1,36 @@
+name: publish-quay
+on:
+  push:
+    branches:
+      - main
+    tags:
+      - '*'
+  workflow_dispatch: {}
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@master
+      - name: Get image tags
+        id: image_tags
+        run: |
+          echo -n ::set-output name=IMAGE_TAGS::$(git describe --tags)
+      - name: Build and publish cwltool_module image to Quay
+        uses: docker/build-push-action@v1
+        with:
+          file: cwltool.Dockerfile
+          registry: ${{ secrets.REGISTRY_SERVER }}
+          repository: ${{ secrets.REGISTRY_NAMESPACE }}/cwltool_module
+          username: ${{ secrets.REGISTRY_USERNAME }}
+          password: ${{ secrets.REGISTRY_PASSWORD }}
+          tags: "${{ steps.image_tags.outputs.IMAGE_TAGS }}"
+          target: module
+      - name: Build and publish cwltool image to Quay
+        uses: docker/build-push-action@v1
+        with:
+          file: cwltool.Dockerfile
+          registry: ${{ secrets.REGISTRY_SERVER }}
+          repository: ${{ secrets.REGISTRY_NAMESPACE }}/cwltool
+          username: ${{ secrets.REGISTRY_USERNAME }}
+          password: ${{ secrets.REGISTRY_PASSWORD }}
+          tags: "${{ steps.image_tags.outputs.IMAGE_TAGS }}"

README.rst

@@ -10,6 +10,8 @@ Conda: |Conda Version| |Conda Installs|
 
 Debian: |Debian Testing package| |Debian Stable package|
 
+Quay.io (Docker): |Quay.io Container|
+
 .. |Linux Status| image:: https://github.com/common-workflow-language/cwltool/actions/workflows/ci-tests.yml/badge.svg?branch=main
    :target: https://github.com/common-workflow-language/cwltool/actions/workflows/ci-tests.yml
 
@@ -37,6 +39,9 @@ Debian: |Debian Testing package| |Debian Stable package|
 .. |Conda Installs| image:: https://anaconda.org/conda-forge/cwltool/badges/downloads.svg
    :target: https://anaconda.org/conda-forge/cwltool
 
+.. |Quay.io Container| image:: https://quay.io/repository/commonwl/cwltool/status
+   :target https://quay.io/repository/commonwl/cwltool
+
 This is the reference implementation of the Common Workflow Language.  It is
 intended to be feature complete and provide comprehensive validation of CWL
 files as well as provide other tools related to working with CWL.

build-cwl-docker.sh

@@ -1,10 +1,10 @@
 #!/bin/bash
-set -e
-docker build --file=cwltool.Dockerfile --tag=commonworkflowlanguage/cwltool_module --target module .
-docker build --file=cwltool.Dockerfile --tag=commonworkflowlanguage/cwltool .
+set -ex
+docker build --file=cwltool.Dockerfile --tag=quay.io/commonwl/cwltool_module --target module .
+docker build --file=cwltool.Dockerfile --tag=quay.io/commonwl/cwltool .
 
 version=$(git describe --tags)
 if echo "$version" | grep -vq '\-' >& /dev/null ; then
-    docker tag commonworkflowlanguage/cwltool_module commonworkflowlanguage/cwltool_module:"$version"
-    docker tag commonworkflowlanguage/cwltool commonworkflowlanguage/cwltool:"$version"
+    docker tag quay.io/commonwl/cwltool_module quay.io/commonwl/cwltool_module:"$version"
+    docker tag quay.io/commonwl/cwltool quay.io/commonwl/cwltool:"$version"
 fi

cwltool.Dockerfile

@@ -1,6 +1,14 @@
-FROM python:3.8-alpine as builder
-
-RUN apk add --no-cache git gcc python3-dev libxml2-dev libxslt-dev libc-dev linux-headers
+FROM python:3.9-slim as builder
+
+RUN apt-get update && apt-get install -y \
+	gcc \
+	git \
+	libc-dev \
+	libxml2-dev \
+	libxslt1-dev \
+	python3-dev \
+  && rm -rf /var/lib/apt/lists/*
+#	linux-headers \
 
 WORKDIR /cwltool
 COPY . .
@@ -9,16 +17,28 @@ RUN python setup.py bdist_wheel --dist-dir=/wheels
 RUN pip wheel -r requirements.txt --wheel-dir=/wheels
 RUN pip install --no-index --no-warn-script-location --root=/pythonroot/ /wheels/*.whl
 
-FROM python:3.8-alpine as module
-LABEL maintainer peter.amstutz@curoverse.com
+FROM python:3.9-slim as module
+LABEL maintainer peter.amstutz@curii.com
 
-RUN apk add --no-cache docker nodejs graphviz libxml2 libxslt
+RUN apt-get update && apt-get install -y \
+	docker.io \
+	graphviz \
+	libxml2 \
+	libxslt1.1 \
+	nodejs \
+  && rm -rf /var/lib/apt/lists/*
 COPY --from=builder /pythonroot/ /
 
-FROM python:3.8-alpine
-LABEL maintainer peter.amstutz@curoverse.com
+FROM python:3.9-slim
+LABEL maintainer peter.amstutz@curii.com
 
-RUN apk add --no-cache docker nodejs graphviz libxml2 libxslt
+RUN apt-get update && apt-get install -y \
+	docker.io \
+	graphviz \
+	libxml2 \
+	libxslt1.1 \
+	nodejs \
+  && rm -rf /var/lib/apt/lists/*
 COPY --from=builder /pythonroot/ /
 COPY cwltool-in-docker.sh /cwltool-in-docker.sh