From 04e6b30c5315e240f73b117598475be465aa1e5b Mon Sep 17 00:00:00 2001
From: Ryan Dale <ryan.dale@nih.gov>
Date: Sat, 27 Jan 2024 17:22:35 -0500
Subject: [PATCH 01/21] add a round of comments to GH actions workflows

---
 .github/workflows/base-glibc-busybox-bash.yaml | 15 ++++++++++++++-
 .github/workflows/base-glibc-debian-bash.yaml  | 15 ++++++++++++++-
 2 files changed, 28 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/base-glibc-busybox-bash.yaml b/.github/workflows/base-glibc-busybox-bash.yaml
index 9f76c16d..3ef3ac71 100644
--- a/.github/workflows/base-glibc-busybox-bash.yaml
+++ b/.github/workflows/base-glibc-busybox-bash.yaml
@@ -44,15 +44,19 @@ jobs:
           ${{ env.MAJOR_VERSION }}.${{ env.MINOR_VERSION }}
           latest
         '
+        # Adds image and tags to outputs which can be used in later steps.
         printf %s\\n \
           "image=${image_name}" \
           "tags=$( echo ${tags} )" \
           >> $GITHUB_OUTPUT
 
+        # Create manifest (which is considered arch-independent)
         for tag in ${tags} ; do
           buildah manifest create "${image_name}:${tag}"
         done
 
+        # --iidfile prints the built image ID to the specified file. This is
+        # used so we can refer to the image in later steps.
         iidfile="$( mktemp )"
         buildah bud \
           --iidfile="${iidfile}" \
@@ -71,6 +75,7 @@ jobs:
           image_id="$( cat "${iidfile}" )"
           rm "${iidfile}"
 
+          # Extract various package info and version info to store as labels
           container="$( buildah from "${image_id}" )"
           run() { buildah run "${container}" "${@}" ; }
           deb_list="$( run cat /.deb.lst | tr '\n' '|' | sed 's/|$//' )"
@@ -80,6 +85,7 @@ jobs:
           bash="$( run bash --version | sed '1!d' )"
           buildah rm "${container}"
 
+          # Store package/version info as labels for the image
           container="$( buildah from "${image_id}" )"
           buildah config \
             --label=glibc="${glibc}" \
@@ -89,8 +95,11 @@ jobs:
             --label=pkg-list="${pkg_list}" \
             "${container}"
 
+          # Store the new image (now with labels)
           image_id="$( buildah commit "${container}" )"
           buildah rm "${container}"
+
+          # image tag includes arch; then added to manifest which does not include arch
           for tag in ${tags} ; do
             buildah tag \
               "${image_id}" \
@@ -104,6 +113,8 @@ jobs:
     - name: Test
       run: |
         image='${{ steps.build.outputs.image }}'
+
+        # Extract image ids from manifest to test.
         ids="$(
           for tag in ${{ steps.build.outputs.tags }} ; do
             buildah manifest inspect "${image}:${tag}" \
@@ -114,6 +125,8 @@ jobs:
                 done
           done
           )"
+
+        # See Dockerfile.test for actual tests run
         ids="$( printf %s "${ids}" | sort -u )"
         for id in ${ids} ; do
           podman history "${id}"
@@ -127,7 +140,7 @@ jobs:
     - 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.
+        #               => Try to use the REST API to check for duplicate tags and exit if they exist
         response="$(
           curl -sL \
             'https://quay.io/api/v1/repository/bioconda/${{ steps.build.outputs.image }}/tag/'
diff --git a/.github/workflows/base-glibc-debian-bash.yaml b/.github/workflows/base-glibc-debian-bash.yaml
index 331f44ea..6692f558 100644
--- a/.github/workflows/base-glibc-debian-bash.yaml
+++ b/.github/workflows/base-glibc-debian-bash.yaml
@@ -43,15 +43,19 @@ jobs:
           ${{ env.MAJOR_VERSION }}.${{ env.MINOR_VERSION }}
           latest
         '
+        # Adds image and tags to outputs which can be used in later steps.
         printf %s\\n \
           "image=${image_name}" \
           "tags=$( echo ${tags} )" \
           >> $GITHUB_OUTPUT
 
+        # Create manifest (which is considered arch-independent)
         for tag in ${tags} ; do
           buildah manifest create "${image_name}:${tag}"
         done
 
+        # --iidfile prints the built image ID to the specified file. This is
+        # used so we can refer to the image in later steps.
         for arch in amd64 arm64 ; do
           iidfile="$( mktemp )"
           buildah bud \
@@ -61,6 +65,7 @@ jobs:
           image_id="$( cat "${iidfile}" )"
           rm "${iidfile}"
 
+          # Extract various package info and version info to store as labels
           container="$( buildah from "${image_id}" )"
           run() { buildah run "${container}" "${@}" ; }
           deb_list="$( run cat /.deb.lst | tr '\n' '|' | sed 's/|$//' )"
@@ -70,6 +75,7 @@ jobs:
           bash="$( run bash --version | sed '1!d' )"
           buildah rm "${container}"
 
+          # Store package/version info as labels for the image
           container="$( buildah from "${image_id}" )"
           buildah config \
             --label=glibc="${glibc}" \
@@ -79,8 +85,11 @@ jobs:
             --label=pkg-list="${pkg_list}" \
             "${container}"
 
+          # Store the new image (now with labels)
           image_id="$( buildah commit "${container}" )"
           buildah rm "${container}"
+
+          # image tag includes arch; then added to manifest which does not include arch
           for tag in ${tags} ; do
             buildah tag \
               "${image_id}" \
@@ -94,6 +103,8 @@ jobs:
     - name: Test
       run: |
         image='${{ steps.build.outputs.image }}'
+
+        # Extract image ids from manifest to test.
         ids="$(
           for tag in ${{ steps.build.outputs.tags }} ; do
             buildah manifest inspect "${image}:${tag}" \
@@ -104,6 +115,8 @@ jobs:
                 done
           done
           )"
+
+        # See Dockerfile.test for actual tests run
         ids="$( printf %s "${ids}" | sort -u )"
         for id in ${ids} ; do
           podman history "${id}"
@@ -117,7 +130,7 @@ jobs:
     - 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.
+        #               => Try to use the REST API to check for duplicate tags and exit if they exist
         response="$(
           curl -sL \
             'https://quay.io/api/v1/repository/bioconda/${{ steps.build.outputs.image }}/tag/'

From 7388860a31e822be20c87b0ad9b5a33f2cb7fa20 Mon Sep 17 00:00:00 2001
From: Ryan Dale <ryan.dale@nih.gov>
Date: Sat, 27 Jan 2024 17:23:13 -0500
Subject: [PATCH 02/21] build build-env images similar to others

---
 .github/workflows/build-env-image.yml | 251 ++++++++++++++++++--------
 images/build-env/Dockerfile           |   7 +-
 images/build-env/Dockerfile.test      |   4 +
 3 files changed, 177 insertions(+), 85 deletions(-)
 create mode 100644 images/build-env/Dockerfile.test

diff --git a/.github/workflows/build-env-image.yml b/.github/workflows/build-env-image.yml
index 1bad2d18..e7300f73 100644
--- a/.github/workflows/build-env-image.yml
+++ b/.github/workflows/build-env-image.yml
@@ -1,8 +1,4 @@
-name: Build image
-concurrency:
-  group: ${{ github.workflow }}-${{ github.ref }}
-  cancel-in-progress: true
-
+name: 'Build & Push: base-glibc-busybox-bash'
 on:
   pull_request:
     paths:
@@ -14,20 +10,18 @@ on:
 
 jobs:
   build:
-    name: Build image - ${{ matrix.image }}
+    name: Build & Push
     runs-on: ubuntu-22.04
-    strategy:
-      matrix:
-        include:
-          - arch: arm64
-            image: bioconda/bioconda-utils-build-env-cos7-aarch64
-            base_image: quay.io/condaforge/linux-anvil-aarch64
-          - arch: amd64
-            image: bioconda/bioconda-utils-build-env-cos7-x86_64
-            base_image: quay.io/condaforge/linux-anvil-cos7-x86_64
+    env:
+      # The base image is not intended to change often and should be used with
+      # version tags or checksum IDs, but not via "latest".
+      MAJOR_VERSION: 3
+      MINOR_VERSION: 0
+      IMAGE_NAME: bioconda-utils-build-env-cos7
+
     steps:
     - name: Checkout bioconda-containers
-      uses: actions/checkout@v4
+    - uses: actions/checkout@v4
       with:
         fetch-depth: 0
     - name: Checkout bioconda-utils
@@ -37,81 +31,178 @@ jobs:
         repository: 'bioconda/bioconda-utils'
         path: 'bioconda-utils'
 
-    - id: get-tag
-      run: |
-        tag=${{ github.event.release && github.event.release.tag_name || github.sha }}
-        printf %s "tag=${tag#v}" >> $GITHUB_OUTPUT
-
-    - name: Install qemu dependency
-      if: ${{ matrix.arch == 'arm64' }}
-      uses: docker/setup-qemu-action@v3
+    - name: Set up QEMU
+      uses: docker/setup-qemu-action@v2
       with:
         platforms: arm64
 
-    - name: Build image
-      id: buildah-build
-      uses: redhat-actions/buildah-build@v2
-      with:
-        image: ${{ matrix.image }}
-        arch: ${{ matrix.arch }}
-        build-args: |
-          BASE_IMAGE=${{ matrix.base_image }}
-        tags: >-
+    - name: Build
+      id: build
+      run: |
+        set -xeu
+        cd 'images/${{ env.IMAGE_NAME }}'
+
+        image_name='${{ env.IMAGE_NAME }}'
+        tags='
+          ${{ env.MAJOR_VERSION }}
+          ${{ env.MAJOR_VERSION }}.${{ env.MINOR_VERSION }}
           latest
-          ${{ steps.get-tag.outputs.tag }}
-        dockerfiles: |
-          ./images/build-env/Dockerfile
+        '
+        # Adds image and tags to outputs which can be used in later steps.
+        printf %s\\n \
+          "image=${image_name}" \
+          "tags=$( echo ${tags} )" \
+          >> $GITHUB_OUTPUT
+
+        # Create manifest (which is considered arch-independent)
+        for tag in ${tags} ; do
+          buildah manifest create "${image_name}:${tag}"
+        done
+
+        # Due to different nomenclature used by conda-forge and buildah, we
+        # need to map archs to base images.
+        for arch_and_image in \
+          "amd64=quay.io/condaforge/linux-anvil-cos7-x86_64" \
+          "arm64=quay.io/condaforge/linux-anvil-aarch64";
+        do
+          # Unpack archs and base images
+          arch=$(cut -f1 -d "=" $arch_and_image)
+          base_image=$(cut -f2 -d "=" $arch_and_image)
+
+          # --iidfile prints the built image ID to the specified file. This is
+          # used so we can refer to the image in later steps.
+          iidfile="$( mktemp )"
+          buildah bud \
+            --arch="${arch}" \
+            --iidfile="${iidfile}" \
+            --build-arg=base_image="$base_image" \
+          image_id="$( cat "${iidfile}" )"
+          rm "${iidfile}"
+
+          # Extract various package info and version info to store as labels
+          container="$( buildah from "${image_id}" )"
+          run() { buildah run "${container}" "${@}" ; }
+          deb_list="$( run cat /.deb.lst | tr '\n' '|' | sed 's/|$//' )"
+          pkg_list="$( run cat /.pkg.lst | tr '\n' '|' | sed 's/|$//' )"
+          glibc="$( run sh -c 'exec "$( find -xdev -name libc.so.6 -print -quit )"' | sed '1!d' )"
+          bash="$( run bash --version | sed '1!d' )"
+          bioconda_utils="$( run bioconda-utils --version )"
+          buildah rm "${container}"
+
+          # Store package/version info as labels for the image
+          container="$( buildah from "${image_id}" )"
+          buildah config \
+            --label=glibc="${glibc}" \
+            --label=bash="${bash}" \
+            --label=deb-list="${deb_list}" \
+            --label=pkg-list="${pkg_list}" \
+            --label=bioconda-utils="${bioconda_utils}" \
+            "${container}"
 
-    - name: Test built image
+          # Store the new image (now with labels)
+          image_id="$( buildah commit "${container}" )"
+          buildah rm "${container}"
+
+          # image tag includes arch; then added to manifest which does not include arch
+          for tag in ${tags} ; do
+            buildah tag \
+              "${image_id}" \
+              "${image_name}:${tag}-${arch}"
+            buildah manifest add \
+              "${image_name}:${tag}" \
+              "${image_id}"
+          done
+        done
+
+    - name: Test
       run: |
-        image='${{ steps.buildah-build.outputs.image }}'
-        for tag in ${{ steps.buildah-build.outputs.tags }} ; do
-          podman run --rm "${image}:${tag}" bioconda-utils --version
+        image='${{ steps.build.outputs.image }}'
+
+        # Extract image ids from manifest to test.
+        ids="$(
+          for tag in ${{ steps.build.outputs.tags }} ; do
+            buildah manifest inspect "${image}:${tag}" \
+              | jq -r '.manifests[]|.digest' \
+              | while read id ; do
+                  buildah images --format '{{.ID}}{{.Digest}}' \
+                  | sed -n "s/${id}//p"
+                done
+          done
+          )"
+
+        # See Dockerfile.test for actual tests run
+        ids="$( printf %s "${ids}" | sort -u )"
+        for id in ${ids} ; do
+          podman history "${id}"
+          buildah bud \
+            --build-arg=base="${id}" \
+            --file=Dockerfile.test \
+            "images/${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 and exit if they exist
+        response="$(
+          curl -sL \
+            'https://quay.io/api/v1/repository/bioconda/${{ steps.build.outputs.image }}/tag/'
+          )"
 
-    - name: Push To Quay
-      if: github.ref == 'refs/heads/main' && github.repository == 'bioconda/bioconda-containers'
+        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.buildah-build.outputs.image }}
-        tags: ${{ steps.buildah-build.outputs.tags }}
+        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 }}
 
-  build-manifest:
-    needs: [build]
-    if: github.ref == 'refs/heads/main' && github.repository == 'bioconda/bioconda-containers'
-    name: quay.io/bioconda/${{ matrix.cfg.DOCKER_MANIFEST }}:${{ matrix.cfg.DOCKER_TAG }}
-    runs-on: ubuntu-latest
-    strategy:
-      fail-fast: false
-      matrix:
-        cfg:
-          - DOCKER_MANIFEST: bioconda-utils-build-env-cos7
-            DOCKER_TAG: "latest"
-            DOCKER_IMAGES: "quay.io/<<USER>>/bioconda-utils-build-env-cos7:<<TAG>>,quay.io/<<USER>>/bioconda-utils-build-env-cos7-aarch64:<<TAG>>"
-
-    steps:
-      - uses: actions/checkout@v4
-
-      - name: Interpolate placeholders
-        id: interpolate
-        run: |
-          set -x
-          INTERPOLATED=`echo "${{ matrix.cfg.DOCKER_IMAGES }}" | sed "s#<<USER>>#${{ secrets.QUAY_BIOCONDA_USERNAME }}#g" | sed "s#<<TAG>>#${{ matrix.cfg.DOCKER_TAG }}#g"`
-          echo "DOCKER_IMAGES=${INTERPOLATED}" >> "$GITHUB_OUTPUT"
-
-      - name: Login to Quay.io registry
-        uses: docker/login-action@v2
-        with:
-          registry: ${{ secrets.QUAY_BIOCONDA_REPO }}
-          username: ${{ secrets.QUAY_BIOCONDA_USERNAME }}
-          password: ${{ secrets.QUAY_BIOCONDA_TOKEN }}
-
-      - name: Push Docker manifest list for quay.io/bioconda
-        uses: Noelware/docker-manifest-action@v0.3.0
-        with:
-            inputs: quay.io/${{ secrets.QUAY_BIOCONDA_USERNAME }}/${{ matrix.cfg.DOCKER_MANIFEST }}:${{ matrix.cfg.DOCKER_TAG }}
-            images: ${{ steps.interpolate.outputs.DOCKER_IMAGES }}
-            push: true
+    - if: ${{ github.ref == 'refs/heads/main' }}
+      name: Test Pushed
+      run: |
+        image='${{ env.IMAGE_NAME }}'
+        ids="$(
+          for tag in ${{ steps.build.outputs.tags }} ; do
+            buildah manifest inspect "${image}:${tag}" \
+              | jq -r '.manifests[]|.digest' \
+              | while read id ; do
+                  buildah images --format '{{.ID}}{{.Digest}}' \
+                  | sed -n "s/${id}//p"
+                done
+          done
+          )"
+        ids="$( printf %s "${ids}" | sort -u )"
+        for id in ${ids} ; do
+          podman history "${id}"
+          buildah bud \
+            --build-arg=base="${id}" \
+            --file=Dockerfile.test \
+            "images/${image}"
+        done
+        buildah rmi --prune || true
diff --git a/images/build-env/Dockerfile b/images/build-env/Dockerfile
index 6573054b..f90b0a69 100644
--- a/images/build-env/Dockerfile
+++ b/images/build-env/Dockerfile
@@ -1,9 +1,6 @@
-# Specify the base image to support multi-arch images, such as
-# - 'quay.io/condaforge/linux-anvil-aarch64' for Linux aarch64
-# - 'quay.io/condaforge/linux-anvil-cos7-x86_64' for Linux x86_64
-ARG BASE_IMAGE=quay.io/condaforge/linux-anvil-cos7-x86_64
+ARG base_image
 
-FROM ${BASE_IMAGE} as base
+FROM ${base_image} as base
 
 # Copy over C.UTF-8 locale from our base image to make it consistently available during build.
 COPY --from=quay.io/bioconda/base-glibc-busybox-bash /usr/lib/locale/C.utf8 /usr/lib/locale/C.utf8
diff --git a/images/build-env/Dockerfile.test b/images/build-env/Dockerfile.test
new file mode 100644
index 00000000..2232c7c8
--- /dev/null
+++ b/images/build-env/Dockerfile.test
@@ -0,0 +1,4 @@
+ARG base
+FROM "${base}"
+RUN bioconda-utils --version
+RUN bioconda-utils --help

From 3938cd154e746824531a197871fad0edc2dbfa33 Mon Sep 17 00:00:00 2001
From: Ryan Dale <ryan.dale@nih.gov>
Date: Sat, 27 Jan 2024 17:38:49 -0500
Subject: [PATCH 03/21] fix name

---
 .github/workflows/build-env-image.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/build-env-image.yml b/.github/workflows/build-env-image.yml
index e7300f73..dc84040d 100644
--- a/.github/workflows/build-env-image.yml
+++ b/.github/workflows/build-env-image.yml
@@ -1,4 +1,4 @@
-name: 'Build & Push: base-glibc-busybox-bash'
+name: 'Build & Push: bioconda-utils-build-env-cos7'
 on:
   pull_request:
     paths:

From 66efe129b40085a456143286e25065a66ab4d539 Mon Sep 17 00:00:00 2001
From: Ryan Dale <ryan.dale@nih.gov>
Date: Sat, 27 Jan 2024 17:39:37 -0500
Subject: [PATCH 04/21] version bumps

---
 .github/workflows/base-glibc-busybox-bash.yaml | 2 +-
 .github/workflows/base-glibc-debian-bash.yaml  | 2 +-
 .github/workflows/build-env-image.yml          | 2 +-
 3 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/base-glibc-busybox-bash.yaml b/.github/workflows/base-glibc-busybox-bash.yaml
index 3ef3ac71..e86b7df2 100644
--- a/.github/workflows/base-glibc-busybox-bash.yaml
+++ b/.github/workflows/base-glibc-busybox-bash.yaml
@@ -19,7 +19,7 @@ jobs:
       # The base image is not intended to change often and should be used with
       # version tags or checksum IDs, but not via "latest".
       MAJOR_VERSION: 3
-      MINOR_VERSION: 0
+      MINOR_VERSION: 1
       IMAGE_NAME: base-glibc-busybox-bash
       BUSYBOX_VERSION: '1.36.1'
       DEBIAN_VERSION: '12.2'
diff --git a/.github/workflows/base-glibc-debian-bash.yaml b/.github/workflows/base-glibc-debian-bash.yaml
index 6692f558..6f264521 100644
--- a/.github/workflows/base-glibc-debian-bash.yaml
+++ b/.github/workflows/base-glibc-debian-bash.yaml
@@ -19,7 +19,7 @@ jobs:
       # The base image is not intended to change often and should be used with
       # version tags or checksum IDs, but not via "latest".
       MAJOR_VERSION: 3
-      MINOR_VERSION: 0
+      MINOR_VERSION: 1
       IMAGE_NAME: base-glibc-debian-bash
       DEBIAN_VERSION: '12.2'
 
diff --git a/.github/workflows/build-env-image.yml b/.github/workflows/build-env-image.yml
index dc84040d..9bb9afef 100644
--- a/.github/workflows/build-env-image.yml
+++ b/.github/workflows/build-env-image.yml
@@ -16,7 +16,7 @@ jobs:
       # The base image is not intended to change often and should be used with
       # version tags or checksum IDs, but not via "latest".
       MAJOR_VERSION: 3
-      MINOR_VERSION: 0
+      MINOR_VERSION: 1
       IMAGE_NAME: bioconda-utils-build-env-cos7
 
     steps:

From d257763a76d9d73d079fc1ac1802fa52d38db573 Mon Sep 17 00:00:00 2001
From: Ryan Dale <ryan.dale@nih.gov>
Date: Sat, 27 Jan 2024 17:42:54 -0500
Subject: [PATCH 05/21] match format of others

---
 .github/workflows/build-env-image.yml | 14 +++++++++-----
 1 file changed, 9 insertions(+), 5 deletions(-)

diff --git a/.github/workflows/build-env-image.yml b/.github/workflows/build-env-image.yml
index 9bb9afef..3ab77c05 100644
--- a/.github/workflows/build-env-image.yml
+++ b/.github/workflows/build-env-image.yml
@@ -1,12 +1,16 @@
 name: 'Build & Push: bioconda-utils-build-env-cos7'
 on:
-  pull_request:
-    paths:
-    - 'images/build-env/**'
-    - '.github/workflows/build-env-image.yml'
   push:
     branches:
-      - 'main'
+      - main
+    paths:
+    - images/build-env/**
+    - .github/workflows/build-env-image.yml
+  pull_request:
+    paths:
+    - images/build-env/**
+    - .github/workflows/build-env-image.yml
+
 
 jobs:
   build:

From 82bd178331959e70b221341e0aabaa36b4eb134c Mon Sep 17 00:00:00 2001
From: Ryan Dale <ryan.dale@nih.gov>
Date: Sat, 27 Jan 2024 17:46:08 -0500
Subject: [PATCH 06/21] syntax

---
 .github/workflows/build-env-image.yml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/build-env-image.yml b/.github/workflows/build-env-image.yml
index 3ab77c05..91892419 100644
--- a/.github/workflows/build-env-image.yml
+++ b/.github/workflows/build-env-image.yml
@@ -2,7 +2,7 @@ name: 'Build & Push: bioconda-utils-build-env-cos7'
 on:
   push:
     branches:
-      - main
+    - main
     paths:
     - images/build-env/**
     - .github/workflows/build-env-image.yml
@@ -12,6 +12,7 @@ on:
     - .github/workflows/build-env-image.yml
 
 
+
 jobs:
   build:
     name: Build & Push

From e9d5cf63a2b753be1fb9590e1512d81aab72e926 Mon Sep 17 00:00:00 2001
From: Ryan Dale <ryan.dale@nih.gov>
Date: Sat, 27 Jan 2024 17:48:31 -0500
Subject: [PATCH 07/21] syntax

---
 .github/workflows/build-env-image.yml | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/.github/workflows/build-env-image.yml b/.github/workflows/build-env-image.yml
index 91892419..aaea6185 100644
--- a/.github/workflows/build-env-image.yml
+++ b/.github/workflows/build-env-image.yml
@@ -11,8 +11,6 @@ on:
     - images/build-env/**
     - .github/workflows/build-env-image.yml
 
-
-
 jobs:
   build:
     name: Build & Push
@@ -29,6 +27,7 @@ jobs:
     - uses: actions/checkout@v4
       with:
         fetch-depth: 0
+
     - name: Checkout bioconda-utils
       uses: actions/checkout@v4
       with:

From cfdcde2e647ec2e7b24e32b0dde5eabbc3316efc Mon Sep 17 00:00:00 2001
From: Ryan Dale <ryan.dale@nih.gov>
Date: Sat, 27 Jan 2024 21:31:16 -0500
Subject: [PATCH 08/21] syntax

---
 .github/workflows/build-env-image.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/build-env-image.yml b/.github/workflows/build-env-image.yml
index aaea6185..cb769807 100644
--- a/.github/workflows/build-env-image.yml
+++ b/.github/workflows/build-env-image.yml
@@ -29,7 +29,7 @@ jobs:
         fetch-depth: 0
 
     - name: Checkout bioconda-utils
-      uses: actions/checkout@v4
+    - uses: actions/checkout@v4
       with:
         fetch-depth: 0
         repository: 'bioconda/bioconda-utils'

From 5d0aceb7ef40547006e36c761c727f0e0578b037 Mon Sep 17 00:00:00 2001
From: Ryan Dale <ryan.dale@nih.gov>
Date: Sat, 27 Jan 2024 21:32:19 -0500
Subject: [PATCH 09/21] syntax

---
 .github/workflows/build-env-image.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/build-env-image.yml b/.github/workflows/build-env-image.yml
index cb769807..78489804 100644
--- a/.github/workflows/build-env-image.yml
+++ b/.github/workflows/build-env-image.yml
@@ -24,12 +24,12 @@ jobs:
 
     steps:
     - name: Checkout bioconda-containers
-    - uses: actions/checkout@v4
+      uses: actions/checkout@v4
       with:
         fetch-depth: 0
 
     - name: Checkout bioconda-utils
-    - uses: actions/checkout@v4
+      uses: actions/checkout@v4
       with:
         fetch-depth: 0
         repository: 'bioconda/bioconda-utils'

From db02883b5c8fae1c4fe46dc5eb7f74900f0d7a66 Mon Sep 17 00:00:00 2001
From: Ryan Dale <ryan.dale@nih.gov>
Date: Sat, 27 Jan 2024 21:38:40 -0500
Subject: [PATCH 10/21] move dockerfiles to dir named after image

---
 images/{build-env => bioconda-utils-build-env-cos7}/Dockerfile    | 0
 .../{build-env => bioconda-utils-build-env-cos7}/Dockerfile.test  | 0
 2 files changed, 0 insertions(+), 0 deletions(-)
 rename images/{build-env => bioconda-utils-build-env-cos7}/Dockerfile (100%)
 rename images/{build-env => bioconda-utils-build-env-cos7}/Dockerfile.test (100%)

diff --git a/images/build-env/Dockerfile b/images/bioconda-utils-build-env-cos7/Dockerfile
similarity index 100%
rename from images/build-env/Dockerfile
rename to images/bioconda-utils-build-env-cos7/Dockerfile
diff --git a/images/build-env/Dockerfile.test b/images/bioconda-utils-build-env-cos7/Dockerfile.test
similarity index 100%
rename from images/build-env/Dockerfile.test
rename to images/bioconda-utils-build-env-cos7/Dockerfile.test

From de684e66b4bc1c24e24984ef17e3d218905bdb46 Mon Sep 17 00:00:00 2001
From: Ryan Dale <ryan.dale@nih.gov>
Date: Sat, 27 Jan 2024 21:42:46 -0500
Subject: [PATCH 11/21] echo

---
 .github/workflows/build-env-image.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/build-env-image.yml b/.github/workflows/build-env-image.yml
index 78489804..30653cbf 100644
--- a/.github/workflows/build-env-image.yml
+++ b/.github/workflows/build-env-image.yml
@@ -70,8 +70,8 @@ jobs:
           "arm64=quay.io/condaforge/linux-anvil-aarch64";
         do
           # Unpack archs and base images
-          arch=$(cut -f1 -d "=" $arch_and_image)
-          base_image=$(cut -f2 -d "=" $arch_and_image)
+          arch=$(echo $arch_and_image | cut -f1 -d "=")
+          base_image=$(echo $arch_and_image | cut -f2 -d "=")
 
           # --iidfile prints the built image ID to the specified file. This is
           # used so we can refer to the image in later steps.

From 690e42a612a56f124858514d6f2bd62281d285ff Mon Sep 17 00:00:00 2001
From: Ryan Dale <ryan.dale@nih.gov>
Date: Sat, 27 Jan 2024 21:44:49 -0500
Subject: [PATCH 12/21] separate command

---
 .github/workflows/build-env-image.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/build-env-image.yml b/.github/workflows/build-env-image.yml
index 30653cbf..dc34c583 100644
--- a/.github/workflows/build-env-image.yml
+++ b/.github/workflows/build-env-image.yml
@@ -79,7 +79,7 @@ jobs:
           buildah bud \
             --arch="${arch}" \
             --iidfile="${iidfile}" \
-            --build-arg=base_image="$base_image" \
+            --build-arg=base_image="$base_image"
           image_id="$( cat "${iidfile}" )"
           rm "${iidfile}"
 

From 2dd87a36be38e6870dd329f416332c90ab0f9675 Mon Sep 17 00:00:00 2001
From: Ryan Dale <ryan.dale@nih.gov>
Date: Sat, 27 Jan 2024 22:14:58 -0500
Subject: [PATCH 13/21] clone bioconda-utils inside image dir

---
 .github/workflows/build-env-image.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/build-env-image.yml b/.github/workflows/build-env-image.yml
index dc34c583..2e96e7dc 100644
--- a/.github/workflows/build-env-image.yml
+++ b/.github/workflows/build-env-image.yml
@@ -33,7 +33,7 @@ jobs:
       with:
         fetch-depth: 0
         repository: 'bioconda/bioconda-utils'
-        path: 'bioconda-utils'
+        path: 'images/bioconda-utils-build-env-cos7/bioconda-utils'
 
     - name: Set up QEMU
       uses: docker/setup-qemu-action@v2

From cee51474c39c289acdcc392a599fd89c09d4dd97 Mon Sep 17 00:00:00 2001
From: Ryan Dale <ryan.dale@nih.gov>
Date: Sat, 27 Jan 2024 22:18:21 -0500
Subject: [PATCH 14/21] bump qemu action version

---
 .github/workflows/base-glibc-busybox-bash.yaml | 2 +-
 .github/workflows/base-glibc-debian-bash.yaml  | 2 +-
 .github/workflows/build-env-image.yml          | 2 +-
 .github/workflows/create-env.yaml              | 2 +-
 4 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/base-glibc-busybox-bash.yaml b/.github/workflows/base-glibc-busybox-bash.yaml
index e86b7df2..300702a8 100644
--- a/.github/workflows/base-glibc-busybox-bash.yaml
+++ b/.github/workflows/base-glibc-busybox-bash.yaml
@@ -28,7 +28,7 @@ jobs:
     - uses: actions/checkout@v4
 
     - name: Set up QEMU
-      uses: docker/setup-qemu-action@v2
+      uses: docker/setup-qemu-action@v3
       with:
         platforms: arm64
 
diff --git a/.github/workflows/base-glibc-debian-bash.yaml b/.github/workflows/base-glibc-debian-bash.yaml
index 6f264521..29abe884 100644
--- a/.github/workflows/base-glibc-debian-bash.yaml
+++ b/.github/workflows/base-glibc-debian-bash.yaml
@@ -27,7 +27,7 @@ jobs:
     - uses: actions/checkout@v4
 
     - name: Set up QEMU
-      uses: docker/setup-qemu-action@v2
+      uses: docker/setup-qemu-action@v3
       with:
         platforms: arm64
 
diff --git a/.github/workflows/build-env-image.yml b/.github/workflows/build-env-image.yml
index 2e96e7dc..e6969c3e 100644
--- a/.github/workflows/build-env-image.yml
+++ b/.github/workflows/build-env-image.yml
@@ -36,7 +36,7 @@ jobs:
         path: 'images/bioconda-utils-build-env-cos7/bioconda-utils'
 
     - name: Set up QEMU
-      uses: docker/setup-qemu-action@v2
+      uses: docker/setup-qemu-action@v3
       with:
         platforms: arm64
 
diff --git a/.github/workflows/create-env.yaml b/.github/workflows/create-env.yaml
index 21162b41..faefe0bb 100644
--- a/.github/workflows/create-env.yaml
+++ b/.github/workflows/create-env.yaml
@@ -24,7 +24,7 @@ jobs:
     - uses: actions/checkout@v4
 
     - name: Set up QEMU
-      uses: docker/setup-qemu-action@v2
+      uses: docker/setup-qemu-action@v3
       with:
         platforms: arm64
 

From 03f6fb70b0e3ce34cd938ed9b1049dc76b098a5c Mon Sep 17 00:00:00 2001
From: Ryan Dale <ryan.dale@nih.gov>
Date: Sat, 27 Jan 2024 22:25:22 -0500
Subject: [PATCH 15/21] activate env for testing

---
 images/bioconda-utils-build-env-cos7/Dockerfile.test | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/images/bioconda-utils-build-env-cos7/Dockerfile.test b/images/bioconda-utils-build-env-cos7/Dockerfile.test
index 2232c7c8..1c9b9830 100644
--- a/images/bioconda-utils-build-env-cos7/Dockerfile.test
+++ b/images/bioconda-utils-build-env-cos7/Dockerfile.test
@@ -1,4 +1,6 @@
 ARG base
 FROM "${base}"
-RUN bioconda-utils --version
-RUN bioconda-utils --help
+RUN . /opt/conda/etc/profile.d/conda.sh \
+  && conda activate base \
+  && bioconda-utils --version \
+  && bioconda-utils --help

From dd004ce83fd1d105eb0cf159f154028812c30645 Mon Sep 17 00:00:00 2001
From: Ryan Dale <ryan.dale@nih.gov>
Date: Sat, 27 Jan 2024 22:28:34 -0500
Subject: [PATCH 16/21] version bump create-env

---
 .github/workflows/create-env.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/create-env.yaml b/.github/workflows/create-env.yaml
index faefe0bb..811cb643 100644
--- a/.github/workflows/create-env.yaml
+++ b/.github/workflows/create-env.yaml
@@ -17,7 +17,7 @@ jobs:
     runs-on: ubuntu-22.04
     env:
       MAJOR_VERSION: 3
-      MINOR_VERSION: 0
+      MINOR_VERSION: 1
       IMAGE_NAME: create-env
 
     steps:

From 1ea327067563edbb36c2e9db81c1dd9b96092421 Mon Sep 17 00:00:00 2001
From: Ryan Dale <ryan.dale@nih.gov>
Date: Sat, 27 Jan 2024 22:28:45 -0500
Subject: [PATCH 17/21] rename yaml to be consistent with image name

---
 ...ld-env-image.yml => bioconda-utils-build-env-cos7.yml} | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)
 rename .github/workflows/{build-env-image.yml => bioconda-utils-build-env-cos7.yml} (97%)

diff --git a/.github/workflows/build-env-image.yml b/.github/workflows/bioconda-utils-build-env-cos7.yml
similarity index 97%
rename from .github/workflows/build-env-image.yml
rename to .github/workflows/bioconda-utils-build-env-cos7.yml
index e6969c3e..5c655556 100644
--- a/.github/workflows/build-env-image.yml
+++ b/.github/workflows/bioconda-utils-build-env-cos7.yml
@@ -4,12 +4,12 @@ on:
     branches:
     - main
     paths:
-    - images/build-env/**
-    - .github/workflows/build-env-image.yml
+    - images/bioconda-utils-build-env-cos7/**
+    - .github/workflows/bioconda-utils-build-env-cos7.yml
   pull_request:
     paths:
-    - images/build-env/**
-    - .github/workflows/build-env-image.yml
+    - images/bioconda-utils-build-env-cos7/**
+    - .github/workflows/bioconda-utils-build-env-cos7.yml
 
 jobs:
   build:

From ce01478f20a705222bc4fd0c28de259ca83661ef Mon Sep 17 00:00:00 2001
From: Ryan Dale <ryan.dale@nih.gov>
Date: Sun, 28 Jan 2024 10:24:58 -0500
Subject: [PATCH 18/21] fix getting bioconda-utils version

---
 .github/workflows/bioconda-utils-build-env-cos7.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/bioconda-utils-build-env-cos7.yml b/.github/workflows/bioconda-utils-build-env-cos7.yml
index 5c655556..bce71516 100644
--- a/.github/workflows/bioconda-utils-build-env-cos7.yml
+++ b/.github/workflows/bioconda-utils-build-env-cos7.yml
@@ -90,7 +90,7 @@ jobs:
           pkg_list="$( run cat /.pkg.lst | tr '\n' '|' | sed 's/|$//' )"
           glibc="$( run sh -c 'exec "$( find -xdev -name libc.so.6 -print -quit )"' | sed '1!d' )"
           bash="$( run bash --version | sed '1!d' )"
-          bioconda_utils="$( run bioconda-utils --version )"
+          bioconda_utils="$( run ". /opt/conda/etc/profile.d/conda.sh && conda activate base && bioconda-utils --version" )"
           buildah rm "${container}"
 
           # Store package/version info as labels for the image

From 2ef2354b9f8d6c760646ff2ef84ca7bf7d5f90ea Mon Sep 17 00:00:00 2001
From: Ryan Dale <ryan.dale@nih.gov>
Date: Sun, 28 Jan 2024 10:37:05 -0500
Subject: [PATCH 19/21] rm labeling using bioconda-utils for now

---
 .github/workflows/bioconda-utils-build-env-cos7.yml | 2 --
 1 file changed, 2 deletions(-)

diff --git a/.github/workflows/bioconda-utils-build-env-cos7.yml b/.github/workflows/bioconda-utils-build-env-cos7.yml
index bce71516..d01bdba0 100644
--- a/.github/workflows/bioconda-utils-build-env-cos7.yml
+++ b/.github/workflows/bioconda-utils-build-env-cos7.yml
@@ -90,7 +90,6 @@ jobs:
           pkg_list="$( run cat /.pkg.lst | tr '\n' '|' | sed 's/|$//' )"
           glibc="$( run sh -c 'exec "$( find -xdev -name libc.so.6 -print -quit )"' | sed '1!d' )"
           bash="$( run bash --version | sed '1!d' )"
-          bioconda_utils="$( run ". /opt/conda/etc/profile.d/conda.sh && conda activate base && bioconda-utils --version" )"
           buildah rm "${container}"
 
           # Store package/version info as labels for the image
@@ -100,7 +99,6 @@ jobs:
             --label=bash="${bash}" \
             --label=deb-list="${deb_list}" \
             --label=pkg-list="${pkg_list}" \
-            --label=bioconda-utils="${bioconda_utils}" \
             "${container}"
 
           # Store the new image (now with labels)

From fbff2c834c0d1cc2f0abc8869afb9f632a0d62b7 Mon Sep 17 00:00:00 2001
From: Ryan Dale <ryan.dale@nih.gov>
Date: Sun, 28 Jan 2024 10:57:57 -0500
Subject: [PATCH 20/21] add back bioconda-utils label

---
 .github/workflows/bioconda-utils-build-env-cos7.yml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/.github/workflows/bioconda-utils-build-env-cos7.yml b/.github/workflows/bioconda-utils-build-env-cos7.yml
index d01bdba0..f66dd9af 100644
--- a/.github/workflows/bioconda-utils-build-env-cos7.yml
+++ b/.github/workflows/bioconda-utils-build-env-cos7.yml
@@ -90,6 +90,7 @@ jobs:
           pkg_list="$( run cat /.pkg.lst | tr '\n' '|' | sed 's/|$//' )"
           glibc="$( run sh -c 'exec "$( find -xdev -name libc.so.6 -print -quit )"' | sed '1!d' )"
           bash="$( run bash --version | sed '1!d' )"
+          bioconda_utils="$( run sh -c '. /opt/conda/etc/profile.d/conda.sh && conda activate base && bioconda-utils --version' | rev | cut -f1 -d " " | rev )"
           buildah rm "${container}"
 
           # Store package/version info as labels for the image
@@ -99,6 +100,7 @@ jobs:
             --label=bash="${bash}" \
             --label=deb-list="${deb_list}" \
             --label=pkg-list="${pkg_list}" \
+            --label=bioconda-utils="${bioconda_utils}" \
             "${container}"
 
           # Store the new image (now with labels)

From 19aba6bf29f42840741263c11b140a21e8342ae5 Mon Sep 17 00:00:00 2001
From: Ryan Dale <ryan.dale@nih.gov>
Date: Sun, 28 Jan 2024 14:29:36 -0500
Subject: [PATCH 21/21] target test-push branch

---
 .github/workflows/bioconda-utils-build-env-cos7.yml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/bioconda-utils-build-env-cos7.yml b/.github/workflows/bioconda-utils-build-env-cos7.yml
index f66dd9af..a180973d 100644
--- a/.github/workflows/bioconda-utils-build-env-cos7.yml
+++ b/.github/workflows/bioconda-utils-build-env-cos7.yml
@@ -2,7 +2,7 @@ name: 'Build & Push: bioconda-utils-build-env-cos7'
 on:
   push:
     branches:
-    - main
+    - test-push
     paths:
     - images/bioconda-utils-build-env-cos7/**
     - .github/workflows/bioconda-utils-build-env-cos7.yml
@@ -177,7 +177,7 @@ jobs:
           esac
         done
 
-    - if: ${{ github.ref == 'refs/heads/main' }}
+    - if: ${{ github.ref == 'refs/heads/test-push' }}
       name: Push
       uses: redhat-actions/push-to-registry@v2
       with:
@@ -187,7 +187,7 @@ jobs:
         username: ${{ secrets.QUAY_BIOCONDA_USERNAME }}
         password: ${{ secrets.QUAY_BIOCONDA_TOKEN }}
 
-    - if: ${{ github.ref == 'refs/heads/main' }}
+    - if: ${{ github.ref == 'refs/heads/test-push' }}
       name: Test Pushed
       run: |
         image='${{ env.IMAGE_NAME }}'