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Replace /bin/sh with a wrapper to /bin/bash #136

Replace /bin/sh with a wrapper to /bin/bash

Replace /bin/sh with a wrapper to /bin/bash #136

Workflow file for this run

name: 'Build & Push: create-env'
on:
push:
branches:
- main
paths:
- images/create-env/*
- .github/workflows/create-env.yaml
pull_request:
paths:
- images/create-env/*
- .github/workflows/create-env.yaml
jobs:
build:
name: Build & Push
runs-on: ubuntu-22.04
env:
MAJOR_VERSION: 3
MINOR_VERSION: 1
IMAGE_NAME: create-env
steps:
- uses: actions/checkout@v4
- name: Set up QEMU
uses: docker/setup-qemu-action@v2
with:
platforms: arm64
- name: Prepare
id: prepare
run: |
curl -sSL \
'https://raw.githubusercontent.com/bioconda/bioconda-common/master/common.sh' \
| sed -n \
's/BIOCONDA_UTILS_TAG=v/bioconda_utils_version=/p' \
>> $GITHUB_OUTPUT
- name: Build
id: build
uses: redhat-actions/buildah-build@v2
with:
image: ${{ env.IMAGE_NAME }}
tags: >-
latest
${{ env.MAJOR_VERSION }}
${{ env.MAJOR_VERSION }}.${{ env.MINOR_VERSION }}
archs: amd64,arm64
context: ./images/${{ env.IMAGE_NAME }}
containerfiles: |
./images/${{ env.IMAGE_NAME }}/Dockerfile
build-args: |
bioconda_utils_version=${{ steps.prepare.outputs.bioconda_utils_version }}
- name: Test
run: |
set -x
image='${{ steps.build.outputs.image }}'
for tag in ${{ steps.build.outputs.tags }} ; do
buildah manifest inspect \
"${image}:${tag}" \
| jq '.manifests|{([.[].digest]|sort|join("+")): [.[]|["'"${tag}"'", .platform.architecture, .digest]|join(" ")]}'
done \
| jq -rs 'add|add[]' \
| while read tag arch digest ; do
podman images --format='{{.ID}}|{{.Digest}}|{{.RepoDigests}}' \
| sed -n "/${digest}/{s/|.*//p;q}" \
| xargs -n1 -- \
sh -xc \
'podman history "${1}" ; podman inspect "${1}"' --
buildah bud \
--arch="${arch}" \
--build-arg=base="${image}:${tag}" \
--file=Dockerfile.test \
"images/${image}"
done
buildah rmi --prune || true
- name: Check Tags
run: |
# FIX upstream: Quay.io does not support immutable images currently.
# => Try to use the REST API to check for duplicate tags.
response="$(
curl -sL \
'https://quay.io/api/v1/repository/bioconda/${{ steps.build.outputs.image }}/tag/'
)"
existing_tags="$(
printf %s "${response}" \
| jq -r '.tags[]|select(.end_ts == null or .end_ts >= now)|.name'
)" \
|| {
printf %s\\n \
'Could not get list of image tags.' \
'Does the repository exist on Quay.io?' \
'Quay.io REST API response was:' \
"${response}"
exit 1
}
for tag in ${{ steps.build.outputs.tags }} ; do
case "${tag}" in
latest | '${{ env.MAJOR_VERSION }}' ) ;;
* )
if printf %s "${existing_tags}" | grep -qxF "${tag}" ; then
printf 'Tag %s already exists!\n' "${tag}"
exit 1
fi
esac
done
- if: ${{ github.ref == 'refs/heads/main' }}
name: Push
uses: redhat-actions/push-to-registry@v2
with:
image: ${{ steps.build.outputs.image }}
tags: ${{ steps.build.outputs.tags }}
registry: ${{ secrets.QUAY_BIOCONDA_REPO }}
username: ${{ secrets.QUAY_BIOCONDA_USERNAME }}
password: ${{ secrets.QUAY_BIOCONDA_TOKEN }}
- if: ${{ github.ref == 'refs/heads/main' }}
name: Test Pushed
run: |
set -x
image='${{ steps.build.outputs.image }}'
for tag in ${{ steps.build.outputs.tags }} ; do
buildah manifest inspect \
"${image}:${tag}" \
| jq '.manifests|{([.[].digest]|sort|join("+")): [.[]|["'"${tag}"'", .platform.architecture, .digest]|join(" ")]}'
done \
| jq -rs 'add|add[]' \
| while read tag arch digest ; do
podman images --format='{{.ID}}|{{.Digest}}|{{.RepoDigests}}' \
| sed -n "/${digest}/{s/|.*//p;q}" \
| xargs -n1 -- \
sh -xc \
'podman history "${1}" ; podman inspect "${1}"' --
buildah bud \
--arch="${arch}" \
--build-arg=base="${image}:${tag}" \
--file=Dockerfile.test \
"images/${image}"
done
buildah rmi --prune || true