test: isolated tests of functionality

.github/workflows/GithubActionTests.yml

@@ -6,6 +6,7 @@ concurrency:
 
 jobs:
   test-linux:
+    if: false
     name: Linux tests
     runs-on: ubuntu-latest
     strategy:
@@ -33,13 +34,6 @@ jobs:
           conda activate bioconda
           python setup.py install
 
-      - name: Build docker container
-        run: |
-          docker build -t quay.io/bioconda/bioconda-utils-build-env-cos7:latest ./
-          docker history quay.io/bioconda/bioconda-utils-build-env-cos7:latest
-          docker run --rm -t quay.io/bioconda/bioconda-utils-build-env-cos7:latest sh -lec 'type -t conda && conda info -a && conda list'
-          docker build -t quay.io/bioconda/bioconda-utils-test-env-cos7:latest -f ./Dockerfile.test ./
-
       - name: Run tests '${{ matrix.py_test_marker }}'
         run: |
           eval "$(conda shell.bash hook)"
@@ -50,6 +44,7 @@ jobs:
               echo "Skipping pytest - only docs modified"
           fi
   test-macosx:
+    if: false
     name: OSX tests
     runs-on: macos-latest
     steps:
@@ -81,6 +76,7 @@ jobs:
           fi
 
   autobump-test:
+    if: false
     name: autobump test
     runs-on: ubuntu-latest
     steps:

.github/workflows/build-images.yml

@@ -0,0 +1,68 @@
+# Build all container images.
+#
+# Most of the work is done in generic_build.bash, so see that file for details.
+
+name: Build images
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+on:
+  pull_request:
+    paths-ignore:
+    - '.circleci/**'
+    - 'docs/**'
+    - 'test/**'
+
+env:
+  BIOCONDA_UTILS_VERSION: ${{ github.event.release && github.event.release.tag_name || github.head_ref || github.ref_name }}
+  tags: "0.1 latest"
+
+jobs:
+
+  build-image:
+    runs-on: ubuntu-20.04
+    steps:
+    - name: build
+      run: |
+        set -x
+        echo $BIOCONDA_UTILS_VERSION
+        echo '${{ secrets.GITHUB_TOKEN }}' | podman login ghcr.io -u '${{ github.actor }}' --password-stdin
+        mkdir img
+        cd img
+        echo "FROM debian:12.1-slim" > Dockerfile
+
+        for tag in $tags; do
+          buildah manifest create "test:$tag"
+        done
+
+        for arch in amd64 arm64; do
+          buildah bud --arch $arch --file Dockerfile --iidfile=$arch.id
+          image_id="$(cat $arch.id)"
+          container="$( buildah from ${image_id} )"
+          buildah config --label=org.opencontainers.image.source=https://github.com/bioconda/bioconda-utils "${container}"
+          image_id="$( buildah commit "${container}" )"
+          buildah rm "${container}"
+
+          for tag in $tags; do
+            buildah tag "${image_id}" "test:$tag-$arch"
+            buildah manifest add "test:$tag" "${image_id}"
+          done
+
+        done
+
+        for tag in $tags; do
+          podman push "localhost/test:$tag" "ghcr.io/bioconda/test:$tag"
+        done
+
+
+  pull-image:
+    runs-on: ubuntu-20.04
+    needs: [build-image]
+    steps:
+    - name: pull
+      run: |
+        for tag in $tags; do
+          podman pull "ghcr.io/bioconda/test:$tag"
+          docker pull "ghcr.io/bioconda/test:$tag"
+        done

.gitignore

@@ -15,3 +15,5 @@ docs/source/developer/_autosummary
 
 # Mac OS Files
 .DS_Store
+env
+recipes/

build.sh

@@ -0,0 +1,124 @@
+#!/bin/bash
+
+# create-env depends on base-busybox and build-env (which in turn also depends
+# on base-busybox). base-debian is independent.
+#
+# This can be run locally for testing, and can be used as a template for CI.
+#
+#  base-busybox    base-debian
+#   |        |
+# build-env  |
+#   \        |
+#    \       |
+#    create-env
+
+set -euo
+
+# Used for build-env.
+# bioconda-utils will be cloned to this folder inside the image dir (where the
+# Dockerfile is) and the version will be checked out.
+export BIOCONDA_UTILS_FOLDER=bioconda-utils
+export BIOCONDA_UTILS_VERSION=v2.11.1
+
+export DEBIAN_VERSION="12.2"
+export BUSYBOX_VERSION="1.36.1"
+
+# Use same tags for base-busybox and base-debian
+export BASE_TAG="0.1"
+
+# If the repository doesn't already exist on quay.io, by default this is
+# considered an error. Set to false to avoid this (e.g., when building images
+# with new names, or local test ones).
+export ERROR_IF_MISSING=false
+
+# Architectures to build for (under emulation)
+export ARCHS="arm64 amd64"
+
+# Store as separate vars so we can use these for dependencies.
+BUILD_ENV_IMAGE_NAME=tmp-build-env
+CREATE_ENV_IMAGE_NAME=tmp-create-env
+BASE_DEBIAN_IMAGE_NAME=tmp-debian
+BASE_BUSYBOX_IMAGE_NAME=tmp-busybox
+
+BUILD_BUSYBOX=false # build busybox image?
+BUILD_DEBIAN=true # build debian image?
+BUILD_BUILD_ENV=false # build build-env image?
+BUILD_CREATE_ENV=false  # build create-env image?
+
+# # Build base-busybox------------------------------------------------------------
+if [ $BUILD_BUSYBOX == "true" ]; then
+
+  buildah manifest rm "${BASE_BUSYBOX_IMAGE_NAME}:${BASE_TAG}" || true
+  buildah manifest rm "${BASE_BUSYBOX_IMAGE_NAME}:latest" || true
+
+  IMAGE_NAME=$BASE_BUSYBOX_IMAGE_NAME \
+  IMAGE_DIR=images/base-glibc-busybox-bash \
+  ARCHS=$ARCHS \
+  TYPE="base-busybox" \
+  TAG=$BASE_TAG \
+  ./generic_build.bash
+fi
+
+# Build base-debian-------------------------------------------------------------
+if [ $BUILD_DEBIAN == "true" ]; then
+
+  buildah manifest rm "${BASE_DEBIAN_IMAGE_NAME}:${BASE_TAG}" || true
+  buildah manifest rm "${BASE_DEBIAN_IMAGE_NAME}:latest" || true
+
+  IMAGE_NAME=$BASE_DEBIAN_IMAGE_NAME \
+  IMAGE_DIR=images/base-glibc-debian-bash \
+  ARCHS=$ARCHS \
+  TYPE="base-debian" \
+  TAG=$BASE_TAG \
+  ./generic_build.bash
+fi
+
+# Build build-env---------------------------------------------------------------
+
+if [ $BUILD_BUILD_ENV == "true" ]; then 
+  # Clone bioconda-utils into same directory as Dockerfile
+  if [ ! -e "images/bioconda-utils-build-env-cos7/bioconda-utils" ]; then
+    git clone https://github.com/bioconda/bioconda-utils images/bioconda-utils-build-env-cos7/bioconda-utils
+  else
+    (cd images/bioconda-utils-build-env-cos7/bioconda-utils && git fetch)
+  fi
+
+  buildah manifest rm "${BUILD_ENV_IMAGE_NAME}:${BIOCONDA_UTILS_VERSION}-base${BASE_TAG}" || true
+  buildah manifest rm "${BUILD_ENV_IMAGE_NAME}:latest" || true
+
+  IMAGE_NAME=$BUILD_ENV_IMAGE_NAME \
+  IMAGE_DIR=images/bioconda-utils-build-env-cos7 \
+  ARCHS=$ARCHS \
+  TYPE="build-env" \
+  TAG=$BASE_TAG \
+  BUSYBOX_IMAGE=localhost/$BASE_BUSYBOX_IMAGE_NAME \
+  ./generic_build.bash
+fi
+# # Build create-env--------------------------------------------------------------
+
+if [ $BUILD_CREATE_ENV == "true" ]; then 
+
+  buildah manifest rm "${CREATE_ENV_IMAGE_NAME}:${BIOCONDA_UTILS_VERSION}-base${BASE_TAG}" || true
+  buildah manifest rm "${CREATE_ENV_IMAGE_NAME}:latest" || true
+
+  # Get the exact versions of mamba and conda that were installed in build-env.
+  CONDA_VERSION=$(
+          podman run -t localhost/${BUILD_ENV_IMAGE_NAME}:${BIOCONDA_UTILS_VERSION} \
+          bash -c "/opt/conda/bin/conda list --export '^conda$'| sed -n 's/=[^=]*$//p'"
+  )
+  MAMBA_VERSION=$(
+          podman run -t localhost/${BUILD_ENV_IMAGE_NAME}:${BIOCONDA_UTILS_VERSION} \
+          bash -c "/opt/conda/bin/conda list --export '^mamba$'| sed -n 's/=[^=]*$//p'"
+  )
+  # Remove trailing \r with parameter expansion
+  export CONDA_VERSION=${CONDA_VERSION%$'\r'}
+  export MAMBA_VERSION=${MAMBA_VERSION%$'\r'}
+
+  IMAGE_NAME=$CREATE_ENV_IMAGE_NAME \
+  IMAGE_DIR=images/create-env \
+  ARCHS=$ARCHS \
+  TYPE="create-env" \
+  TAG=$BASE_TAG \
+  BUSYBOX_IMAGE=localhost/$BASE_BUSYBOX_IMAGE_NAME \
+  ./generic_build.bash
+fi