From 1402570ab3f280f30bceb4f06735dbd38ca80cfb Mon Sep 17 00:00:00 2001
From: Martin Tzvetanov Grigorov <mgrigorov@apache.org>
Date: Wed, 17 Jan 2024 10:08:00 +0200
Subject: [PATCH 01/98] Use environment variables to set the major and minor
 versions

Use same versions as in the other Docker images:
- major -> 3
- minor -> 0

Suggested-at: https://github.com/bioconda/bioconda-containers/pull/68#issuecomment-1893793704

Signed-off-by: Martin Tzvetanov Grigorov <mgrigorov@apache.org>
---
 .github/workflows/build-env-image.yml | 16 ++++++++++------
 1 file changed, 10 insertions(+), 6 deletions(-)

diff --git a/.github/workflows/build-env-image.yml b/.github/workflows/build-env-image.yml
index 1bad2d18..3e50725d 100644
--- a/.github/workflows/build-env-image.yml
+++ b/.github/workflows/build-env-image.yml
@@ -11,11 +11,19 @@ on:
   push:
     branches:
       - 'main'
+    paths:
+      - 'images/build-env/**'
+      - '.github/workflows/build-env-image.yml'
+
 
 jobs:
   build:
     name: Build image - ${{ matrix.image }}
     runs-on: ubuntu-22.04
+    env:
+      MAJOR_VERSION: 3
+      MINOR_VERSION: 0
+
     strategy:
       matrix:
         include:
@@ -37,11 +45,6 @@ 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: ${{ matrix.arch == 'arm64' }}
       uses: docker/setup-qemu-action@v3
@@ -58,7 +61,8 @@ jobs:
           BASE_IMAGE=${{ matrix.base_image }}
         tags: >-
           latest
-          ${{ steps.get-tag.outputs.tag }}
+          ${{ env.MAJOR_VERSION }}
+          ${{ env.MAJOR_VERSION }}.${{ env.MINOR_VERSION }}
         dockerfiles: |
           ./images/build-env/Dockerfile
 

From 949ac0d9ca1071f7cabe369a050dc0361589db81 Mon Sep 17 00:00:00 2001
From: Martin Tzvetanov Grigorov <mgrigorov@apache.org>
Date: Wed, 24 Jan 2024 09:44:14 +0200
Subject: [PATCH 02/98] Move the environment variables to be workflow level

Install QEMU for all CPU architectures but amd64. At the moment this is
just arm64 but now adding a new arch will not require changes to this
step

Signed-off-by: Martin Tzvetanov Grigorov <mgrigorov@apache.org>
---
 .github/workflows/build-env-image.yml | 15 +++++++--------
 1 file changed, 7 insertions(+), 8 deletions(-)

diff --git a/.github/workflows/build-env-image.yml b/.github/workflows/build-env-image.yml
index 3e50725d..35255aea 100644
--- a/.github/workflows/build-env-image.yml
+++ b/.github/workflows/build-env-image.yml
@@ -15,15 +15,14 @@ on:
       - 'images/build-env/**'
       - '.github/workflows/build-env-image.yml'
 
-
+env:
+  MAJOR_VERSION: 3
+  MINOR_VERSION: 0
+  
 jobs:
   build:
     name: Build image - ${{ matrix.image }}
     runs-on: ubuntu-22.04
-    env:
-      MAJOR_VERSION: 3
-      MINOR_VERSION: 0
-
     strategy:
       matrix:
         include:
@@ -45,11 +44,11 @@ jobs:
         repository: 'bioconda/bioconda-utils'
         path: 'bioconda-utils'
 
-    - name: Install qemu dependency
-      if: ${{ matrix.arch == 'arm64' }}
+    - name: Install QEMU dependency
+      if: ${{ matrix.arch != 'amd64' }}
       uses: docker/setup-qemu-action@v3
       with:
-        platforms: arm64
+        platforms: ${{ matrix.arch }}
 
     - name: Build image
       id: buildah-build

From 450d72e211cdbdd6f83344355c66fd69bff216f0 Mon Sep 17 00:00:00 2001
From: Martin Tzvetanov Grigorov <mgrigorov@apache.org>
Date: Wed, 24 Jan 2024 09:55:36 +0200
Subject: [PATCH 03/98] Build and push manifests for several tags

Signed-off-by: Martin Tzvetanov Grigorov <mgrigorov@apache.org>
---
 .github/workflows/build-env-image.yml | 20 +++++++++++---------
 1 file changed, 11 insertions(+), 9 deletions(-)

diff --git a/.github/workflows/build-env-image.yml b/.github/workflows/build-env-image.yml
index 35255aea..5c9389db 100644
--- a/.github/workflows/build-env-image.yml
+++ b/.github/workflows/build-env-image.yml
@@ -23,6 +23,8 @@ jobs:
   build:
     name: Build image - ${{ matrix.image }}
     runs-on: ubuntu-22.04
+    outputs:
+      tags: ${{ steps.buildah-build.outputs.tags }}
     strategy:
       matrix:
         include:
@@ -85,15 +87,15 @@ jobs:
   build-manifest:
     needs: [build]
     if: github.ref == 'refs/heads/main' && github.repository == 'bioconda/bioconda-containers'
-    name: quay.io/bioconda/${{ matrix.cfg.DOCKER_MANIFEST }}:${{ matrix.cfg.DOCKER_TAG }}
-    runs-on: ubuntu-latest
+    name: Build and push Docker manifest
+    runs-on: ubuntu-22.04
+    env:
+      DOCKER_MANIFEST: bioconda-utils-build-env-cos7
+      DOCKER_IMAGES: "quay.io/<<USER>>/bioconda-utils-build-env-cos7:<<TAG>>,quay.io/<<USER>>/bioconda-utils-build-env-cos7-aarch64:<<TAG>>"
     strategy:
-      fail-fast: false
+      fail-fast: true
       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>>"
+        tag: ${{ fromJson(needs.build.outputs.tags) }}
 
     steps:
       - uses: actions/checkout@v4
@@ -102,7 +104,7 @@ jobs:
         id: interpolate
         run: |
           set -x
-          INTERPOLATED=`echo "${{ matrix.cfg.DOCKER_IMAGES }}" | sed "s#<<USER>>#${{ secrets.QUAY_BIOCONDA_USERNAME }}#g" | sed "s#<<TAG>>#${{ matrix.cfg.DOCKER_TAG }}#g"`
+          INTERPOLATED=`echo "${{ env.DOCKER_IMAGES }}" | sed "s#<<USER>>#${{ secrets.QUAY_BIOCONDA_USERNAME }}#g" | sed "s#<<TAG>>#${{ matrix.tag }}#g"`
           echo "DOCKER_IMAGES=${INTERPOLATED}" >> "$GITHUB_OUTPUT"
 
       - name: Login to Quay.io registry
@@ -115,6 +117,6 @@ jobs:
       - 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 }}:${{ matrix.cfg.DOCKER_TAG }}
+            inputs: quay.io/${{ secrets.QUAY_BIOCONDA_USERNAME }}/${{ env.DOCKER_MANIFEST }}:${{ matrix.tag }}
             images: ${{ steps.interpolate.outputs.DOCKER_IMAGES }}
             push: true

From 5bbfdff99e3befac6ec06c8b9eaccad54d346a38 Mon Sep 17 00:00:00 2001
From: Martin Tzvetanov Grigorov <mgrigorov@apache.org>
Date: Wed, 24 Jan 2024 10:08:57 +0200
Subject: [PATCH 04/98] Temporary enable pushing

Signed-off-by: Martin Tzvetanov Grigorov <mgrigorov@apache.org>
---
 .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 5c9389db..e989db8d 100644
--- a/.github/workflows/build-env-image.yml
+++ b/.github/workflows/build-env-image.yml
@@ -75,7 +75,7 @@ jobs:
         done
 
     - name: Push To Quay
-      if: github.ref == 'refs/heads/main' && github.repository == 'bioconda/bioconda-containers'
+      # if: github.ref == 'refs/heads/main' && github.repository == 'bioconda/bioconda-containers'
       uses: redhat-actions/push-to-registry@v2
       with:
         image: ${{ steps.buildah-build.outputs.image }}
@@ -86,7 +86,7 @@ jobs:
 
   build-manifest:
     needs: [build]
-    if: github.ref == 'refs/heads/main' && github.repository == 'bioconda/bioconda-containers'
+    # if: github.ref == 'refs/heads/main' && github.repository == 'bioconda/bioconda-containers'
     name: Build and push Docker manifest
     runs-on: ubuntu-22.04
     env:

From 958672e5b107d1e1d3fd614c2d9a8ce33389ddd3 Mon Sep 17 00:00:00 2001
From: Martin Tzvetanov Grigorov <mgrigorov@apache.org>
Date: Wed, 24 Jan 2024 10:21:44 +0200
Subject: [PATCH 05/98] Use vars. context for the Quay.io username

Signed-off-by: Martin Tzvetanov Grigorov <mgrigorov@apache.org>
---
 .github/workflows/build-env-image.yml | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/.github/workflows/build-env-image.yml b/.github/workflows/build-env-image.yml
index e989db8d..0901cfa5 100644
--- a/.github/workflows/build-env-image.yml
+++ b/.github/workflows/build-env-image.yml
@@ -29,10 +29,10 @@ jobs:
       matrix:
         include:
           - arch: arm64
-            image: bioconda/bioconda-utils-build-env-cos7-aarch64
+            image: ${{ vars.QUAY_BIOCONDA_USERNAME }}/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
+            image: ${{ vars.QUAY_BIOCONDA_USERNAME }}/bioconda-utils-build-env-cos7-x86_64
             base_image: quay.io/condaforge/linux-anvil-cos7-x86_64
     steps:
     - name: Checkout bioconda-containers
@@ -81,7 +81,7 @@ jobs:
         image: ${{ steps.buildah-build.outputs.image }}
         tags: ${{ steps.buildah-build.outputs.tags }}
         registry: ${{ secrets.QUAY_BIOCONDA_REPO }}
-        username: ${{ secrets.QUAY_BIOCONDA_USERNAME }}
+        username: ${{ vars.QUAY_BIOCONDA_USERNAME }}
         password: ${{ secrets.QUAY_BIOCONDA_TOKEN }}
 
   build-manifest:
@@ -104,19 +104,19 @@ jobs:
         id: interpolate
         run: |
           set -x
-          INTERPOLATED=`echo "${{ env.DOCKER_IMAGES }}" | sed "s#<<USER>>#${{ secrets.QUAY_BIOCONDA_USERNAME }}#g" | sed "s#<<TAG>>#${{ matrix.tag }}#g"`
+          INTERPOLATED=`echo "${{ env.DOCKER_IMAGES }}" | sed "s#<<USER>>#${{ vars.QUAY_BIOCONDA_USERNAME }}#g" | sed "s#<<TAG>>#${{ matrix.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 }}
+          username: ${{ vars.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/${{ secrets.QUAY_BIOCONDA_USERNAME }}/${{ env.DOCKER_MANIFEST }}:${{ matrix.tag }}
+            inputs: quay.io/${{ vars.QUAY_BIOCONDA_USERNAME }}/${{ env.DOCKER_MANIFEST }}:${{ matrix.tag }}
             images: ${{ steps.interpolate.outputs.DOCKER_IMAGES }}
             push: true

From ea80a8eaca0475cda6fcdf72744b854167a3fd17 Mon Sep 17 00:00:00 2001
From: Martin Tzvetanov Grigorov <mgrigorov@apache.org>
Date: Wed, 24 Jan 2024 10:42:36 +0200
Subject: [PATCH 06/98] Convert Bash array 'tags' to JSON array

Signed-off-by: Martin Tzvetanov Grigorov <mgrigorov@apache.org>
---
 .github/workflows/build-env-image.yml | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/build-env-image.yml b/.github/workflows/build-env-image.yml
index 0901cfa5..2b9abfbd 100644
--- a/.github/workflows/build-env-image.yml
+++ b/.github/workflows/build-env-image.yml
@@ -24,7 +24,7 @@ jobs:
     name: Build image - ${{ matrix.image }}
     runs-on: ubuntu-22.04
     outputs:
-      tags: ${{ steps.buildah-build.outputs.tags }}
+      tags: ${{ steps.test.outputs.tags }}
     strategy:
       matrix:
         include:
@@ -68,14 +68,18 @@ jobs:
           ./images/build-env/Dockerfile
 
     - name: Test built image
+      id: test
       run: |
         image='${{ steps.buildah-build.outputs.image }}'
         for tag in ${{ steps.buildah-build.outputs.tags }} ; do
           podman run --rm "${image}:${tag}" bioconda-utils --version
         done
+        tags_json=$(jq --compact-output --null-input '$ARGS.positional' --args -- "${{ steps.buildah-build.outputs.tags }}")
+        echo $tags_json
+        echo "tags=${tags_json}" >> $GITHUB_OUTPUT
 
     - name: Push To Quay
-      # if: github.ref == 'refs/heads/main' && github.repository == 'bioconda/bioconda-containers'
+      if: github.ref == 'refs/heads/main' && github.repository == 'bioconda/bioconda-containers'
       uses: redhat-actions/push-to-registry@v2
       with:
         image: ${{ steps.buildah-build.outputs.image }}

From c1751f93f33a26d6dea7c5be0a1f80b9ec076864 Mon Sep 17 00:00:00 2001
From: Martin Tzvetanov Grigorov <mgrigorov@apache.org>
Date: Wed, 24 Jan 2024 10:51:58 +0200
Subject: [PATCH 07/98] Debug bash array to json array

Signed-off-by: Martin Tzvetanov Grigorov <mgrigorov@apache.org>
---
 .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 2b9abfbd..5e927c7d 100644
--- a/.github/workflows/build-env-image.yml
+++ b/.github/workflows/build-env-image.yml
@@ -70,13 +70,14 @@ jobs:
     - name: Test built image
       id: test
       run: |
+        echo "${{ steps.buildah-build.outputs.tags }}"
         image='${{ steps.buildah-build.outputs.image }}'
         for tag in ${{ steps.buildah-build.outputs.tags }} ; do
           podman run --rm "${image}:${tag}" bioconda-utils --version
         done
         tags_json=$(jq --compact-output --null-input '$ARGS.positional' --args -- "${{ steps.buildah-build.outputs.tags }}")
         echo $tags_json
-        echo "tags=${tags_json}" >> $GITHUB_OUTPUT
+        echo "tags='${tags_json}'" >> $GITHUB_OUTPUT
 
     - name: Push To Quay
       if: github.ref == 'refs/heads/main' && github.repository == 'bioconda/bioconda-containers'

From 13dabbe62b26fb4daaeafbb74bfd0cc65de88ea8 Mon Sep 17 00:00:00 2001
From: Martin Tzvetanov Grigorov <mgrigorov@apache.org>
Date: Wed, 24 Jan 2024 11:03:55 +0200
Subject: [PATCH 08/98] More debug

Signed-off-by: Martin Tzvetanov Grigorov <mgrigorov@apache.org>
---
 .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 5e927c7d..7f3dbbaf 100644
--- a/.github/workflows/build-env-image.yml
+++ b/.github/workflows/build-env-image.yml
@@ -70,6 +70,7 @@ jobs:
     - name: Test built image
       id: test
       run: |
+        jq --version
         echo "${{ steps.buildah-build.outputs.tags }}"
         image='${{ steps.buildah-build.outputs.image }}'
         for tag in ${{ steps.buildah-build.outputs.tags }} ; do
@@ -77,7 +78,7 @@ jobs:
         done
         tags_json=$(jq --compact-output --null-input '$ARGS.positional' --args -- "${{ steps.buildah-build.outputs.tags }}")
         echo $tags_json
-        echo "tags='${tags_json}'" >> $GITHUB_OUTPUT
+        echo "tags=${tags_json}" >> $GITHUB_OUTPUT
 
     - name: Push To Quay
       if: github.ref == 'refs/heads/main' && github.repository == 'bioconda/bioconda-containers'

From 4e4cf3721711ed75438d0e78a2617c39ee99ee65 Mon Sep 17 00:00:00 2001
From: Martin Tzvetanov Grigorov <mgrigorov@apache.org>
Date: Wed, 24 Jan 2024 11:14:32 +0200
Subject: [PATCH 09/98] Convert Bash string to JSON array.

Split by whitespace

Signed-off-by: Martin Tzvetanov Grigorov <mgrigorov@apache.org>
---
 .github/workflows/build-env-image.yml | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/.github/workflows/build-env-image.yml b/.github/workflows/build-env-image.yml
index 7f3dbbaf..c1008cd8 100644
--- a/.github/workflows/build-env-image.yml
+++ b/.github/workflows/build-env-image.yml
@@ -70,13 +70,11 @@ jobs:
     - name: Test built image
       id: test
       run: |
-        jq --version
-        echo "${{ steps.buildah-build.outputs.tags }}"
         image='${{ steps.buildah-build.outputs.image }}'
         for tag in ${{ steps.buildah-build.outputs.tags }} ; do
           podman run --rm "${image}:${tag}" bioconda-utils --version
         done
-        tags_json=$(jq --compact-output --null-input '$ARGS.positional' --args -- "${{ steps.buildah-build.outputs.tags }}")
+        tags_json=$(echo -n "${{ steps.buildah-build.outputs.tags }}" | jq --compact-output --raw-input --slurp 'split(" ")')
         echo $tags_json
         echo "tags=${tags_json}" >> $GITHUB_OUTPUT
 

From 17d313e1d90a50b1243287e33cfa331ffaf20c97 Mon Sep 17 00:00:00 2001
From: Martin Tzvetanov Grigorov <mgrigorov@apache.org>
Date: Wed, 24 Jan 2024 11:39:23 +0200
Subject: [PATCH 10/98] Use `docker manifest` cli instead of
 Noelware/docker-manifest-action

Signed-off-by: Martin Tzvetanov Grigorov <mgrigorov@apache.org>
---
 .github/workflows/build-env-image.yml | 19 ++++++++++++++-----
 1 file changed, 14 insertions(+), 5 deletions(-)

diff --git a/.github/workflows/build-env-image.yml b/.github/workflows/build-env-image.yml
index c1008cd8..a545f687 100644
--- a/.github/workflows/build-env-image.yml
+++ b/.github/workflows/build-env-image.yml
@@ -119,8 +119,17 @@ jobs:
           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/${{ vars.QUAY_BIOCONDA_USERNAME }}/${{ env.DOCKER_MANIFEST }}:${{ matrix.tag }}
-            images: ${{ steps.interpolate.outputs.DOCKER_IMAGES }}
-            push: true
+        run: |
+          PREFIX=${{ secrets.QUAY_BIOCONDA_REPO }}/${{ vars.QUAY_BIOCONDA_USERNAME }}
+          docker manifest create ${PREFIX}/${{ env.DOCKER_MANIFEST }}:${{ matrix.tag }} \
+            --amend ${PREFIX}/bioconda-utils-build-env-cos7-x86_64:${{ matrix.tag }} \
+            --amend ${PREFIX}/bioconda-utils-build-env-cos7-aarch64:${{ matrix.tag }}
+          
+          docker manifest inspect ${PREFIX}/${{ env.DOCKER_MANIFEST }}:${{ matrix.tag }}
+          
+          docker manifest push ${PREFIX}/${{ env.DOCKER_MANIFEST }}:${{ matrix.tag }}
+        # uses: Noelware/docker-manifest-action@v0.3.0
+        # with:
+        #     inputs: quay.io/${{ vars.QUAY_BIOCONDA_USERNAME }}/${{ env.DOCKER_MANIFEST }}:${{ matrix.tag }}
+        #     images: ${{ steps.interpolate.outputs.DOCKER_IMAGES }}
+        #     push: true

From 165af24f6ce5112ce871c0ba6c493e36ffc044bd Mon Sep 17 00:00:00 2001
From: Martin Tzvetanov Grigorov <mgrigorov@apache.org>
Date: Wed, 24 Jan 2024 11:54:20 +0200
Subject: [PATCH 11/98] Go back to `secrets.QUAY_BIOCONDA_USERNAME`

Remove debug statements and commented out code

Signed-off-by: Martin Tzvetanov Grigorov <mgrigorov@apache.org>
---
 .github/workflows/build-env-image.yml | 18 ++++++------------
 1 file changed, 6 insertions(+), 12 deletions(-)

diff --git a/.github/workflows/build-env-image.yml b/.github/workflows/build-env-image.yml
index a545f687..ffde2d61 100644
--- a/.github/workflows/build-env-image.yml
+++ b/.github/workflows/build-env-image.yml
@@ -29,10 +29,10 @@ jobs:
       matrix:
         include:
           - arch: arm64
-            image: ${{ vars.QUAY_BIOCONDA_USERNAME }}/bioconda-utils-build-env-cos7-aarch64
+            image: bioconda/bioconda-utils-build-env-cos7-aarch64
             base_image: quay.io/condaforge/linux-anvil-aarch64
           - arch: amd64
-            image: ${{ vars.QUAY_BIOCONDA_USERNAME }}/bioconda-utils-build-env-cos7-x86_64
+            image: bioconda/bioconda-utils-build-env-cos7-x86_64
             base_image: quay.io/condaforge/linux-anvil-cos7-x86_64
     steps:
     - name: Checkout bioconda-containers
@@ -75,7 +75,6 @@ jobs:
           podman run --rm "${image}:${tag}" bioconda-utils --version
         done
         tags_json=$(echo -n "${{ steps.buildah-build.outputs.tags }}" | jq --compact-output --raw-input --slurp 'split(" ")')
-        echo $tags_json
         echo "tags=${tags_json}" >> $GITHUB_OUTPUT
 
     - name: Push To Quay
@@ -85,7 +84,7 @@ jobs:
         image: ${{ steps.buildah-build.outputs.image }}
         tags: ${{ steps.buildah-build.outputs.tags }}
         registry: ${{ secrets.QUAY_BIOCONDA_REPO }}
-        username: ${{ vars.QUAY_BIOCONDA_USERNAME }}
+        username: ${{ secrets.QUAY_BIOCONDA_USERNAME }}
         password: ${{ secrets.QUAY_BIOCONDA_TOKEN }}
 
   build-manifest:
@@ -108,19 +107,19 @@ jobs:
         id: interpolate
         run: |
           set -x
-          INTERPOLATED=`echo "${{ env.DOCKER_IMAGES }}" | sed "s#<<USER>>#${{ vars.QUAY_BIOCONDA_USERNAME }}#g" | sed "s#<<TAG>>#${{ matrix.tag }}#g"`
+          INTERPOLATED=`echo "${{ env.DOCKER_IMAGES }}" | sed "s#<<USER>>#${{ secrets.QUAY_BIOCONDA_USERNAME }}#g" | sed "s#<<TAG>>#${{ matrix.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: ${{ vars.QUAY_BIOCONDA_USERNAME }}
+          username: ${{ secrets.QUAY_BIOCONDA_USERNAME }}
           password: ${{ secrets.QUAY_BIOCONDA_TOKEN }}
 
       - name: Push Docker manifest list for quay.io/bioconda
         run: |
-          PREFIX=${{ secrets.QUAY_BIOCONDA_REPO }}/${{ vars.QUAY_BIOCONDA_USERNAME }}
+          PREFIX=${{ secrets.QUAY_BIOCONDA_REPO }}/${{ secrets.QUAY_BIOCONDA_USERNAME }}
           docker manifest create ${PREFIX}/${{ env.DOCKER_MANIFEST }}:${{ matrix.tag }} \
             --amend ${PREFIX}/bioconda-utils-build-env-cos7-x86_64:${{ matrix.tag }} \
             --amend ${PREFIX}/bioconda-utils-build-env-cos7-aarch64:${{ matrix.tag }}
@@ -128,8 +127,3 @@ jobs:
           docker manifest inspect ${PREFIX}/${{ env.DOCKER_MANIFEST }}:${{ matrix.tag }}
           
           docker manifest push ${PREFIX}/${{ env.DOCKER_MANIFEST }}:${{ matrix.tag }}
-        # uses: Noelware/docker-manifest-action@v0.3.0
-        # with:
-        #     inputs: quay.io/${{ vars.QUAY_BIOCONDA_USERNAME }}/${{ env.DOCKER_MANIFEST }}:${{ matrix.tag }}
-        #     images: ${{ steps.interpolate.outputs.DOCKER_IMAGES }}
-        #     push: true

From aab49c019f4abc68a0ed8ffd2d4914a985b1afbf Mon Sep 17 00:00:00 2001
From: Martin Tzvetanov Grigorov <mgrigorov@apache.org>
Date: Wed, 24 Jan 2024 13:29:15 +0200
Subject: [PATCH 12/98] Re-enable the check for push to main before pushing the
 manifest

Signed-off-by: Martin Tzvetanov Grigorov <mgrigorov@apache.org>
---
 .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 ffde2d61..cd15f8f8 100644
--- a/.github/workflows/build-env-image.yml
+++ b/.github/workflows/build-env-image.yml
@@ -89,7 +89,7 @@ jobs:
 
   build-manifest:
     needs: [build]
-    # if: github.ref == 'refs/heads/main' && github.repository == 'bioconda/bioconda-containers'
+    if: github.ref == 'refs/heads/main' && github.repository == 'bioconda/bioconda-containers'
     name: Build and push Docker manifest
     runs-on: ubuntu-22.04
     env:

From b22154620699e5766a6f71f860294c11b945582e Mon Sep 17 00:00:00 2001
From: Ryan Dale <ryan.dale@nih.gov>
Date: Sat, 27 Jan 2024 15:58:12 -0500
Subject: [PATCH 13/98] convert to testing targets

---
 .github/workflows/build-env-image.yml | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/build-env-image.yml b/.github/workflows/build-env-image.yml
index cd15f8f8..c4089949 100644
--- a/.github/workflows/build-env-image.yml
+++ b/.github/workflows/build-env-image.yml
@@ -10,7 +10,7 @@ on:
     - '.github/workflows/build-env-image.yml'
   push:
     branches:
-      - 'main'
+      - 'test-push'
     paths:
       - 'images/build-env/**'
       - '.github/workflows/build-env-image.yml'
@@ -29,10 +29,10 @@ jobs:
       matrix:
         include:
           - arch: arm64
-            image: bioconda/bioconda-utils-build-env-cos7-aarch64
+            image: bioconda/tmp-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
+            image: bioconda/tmp-bioconda-utils-build-env-cos7-x86_64
             base_image: quay.io/condaforge/linux-anvil-cos7-x86_64
     steps:
     - name: Checkout bioconda-containers
@@ -78,7 +78,7 @@ jobs:
         echo "tags=${tags_json}" >> $GITHUB_OUTPUT
 
     - name: Push To Quay
-      if: github.ref == 'refs/heads/main' && github.repository == 'bioconda/bioconda-containers'
+      if: github.ref == 'refs/heads/test-push' && github.repository == 'bioconda/bioconda-containers'
       uses: redhat-actions/push-to-registry@v2
       with:
         image: ${{ steps.buildah-build.outputs.image }}

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 14/98] 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 15/98] 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 16/98] 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 17/98] 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 18/98] 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 19/98] 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 20/98] 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 21/98] 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 22/98] 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 23/98] 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 24/98] 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 25/98] 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 26/98] 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 27/98] 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 28/98] 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 29/98] 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 30/98] 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 31/98] 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 32/98] 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 33/98] 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 34/98] 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 }}'

From 1463464d7cb7c7f424f91388898e8754a98525ea Mon Sep 17 00:00:00 2001
From: Ryan Dale <ryan.dale@nih.gov>
Date: Sun, 28 Jan 2024 15:34:42 -0500
Subject: [PATCH 35/98] differentiate between image name and image dir

---
 .../bioconda-utils-build-env-cos7.yml         | 30 ++++++++++++-------
 1 file changed, 20 insertions(+), 10 deletions(-)

diff --git a/.github/workflows/bioconda-utils-build-env-cos7.yml b/.github/workflows/bioconda-utils-build-env-cos7.yml
index a180973d..4e07ca69 100644
--- a/.github/workflows/bioconda-utils-build-env-cos7.yml
+++ b/.github/workflows/bioconda-utils-build-env-cos7.yml
@@ -20,6 +20,10 @@ jobs:
       # version tags or checksum IDs, but not via "latest".
       MAJOR_VERSION: 3
       MINOR_VERSION: 1
+
+      # Used for testing -- set to something like 'tmp-' or 'test-' to prefix
+      # images with this name during testing
+      IMAGE_PREFIX: "tmp-"
       IMAGE_NAME: bioconda-utils-build-env-cos7
 
     steps:
@@ -44,9 +48,9 @@ jobs:
       id: build
       run: |
         set -xeu
-        cd 'images/${{ env.IMAGE_NAME }}'
 
-        image_name='${{ env.IMAGE_NAME }}'
+        image_name='${{ env.IMAGE_PREFIX }}${{ env.IMAGE_NAME }}'
+        image_dir='images/${{ env.IMAGE_NAME }}'
         tags='
           ${{ env.MAJOR_VERSION }}
           ${{ env.MAJOR_VERSION }}.${{ env.MINOR_VERSION }}
@@ -54,10 +58,13 @@ jobs:
         '
         # Adds image and tags to outputs which can be used in later steps.
         printf %s\\n \
-          "image=${image_name}" \
+          "image_dir=${image_dir}" \
+          "image_name=${image_name}" \
           "tags=$( echo ${tags} )" \
           >> $GITHUB_OUTPUT
 
+        cd 'images/${{ env.IMAGE_NAME }}'
+
         # Create manifest (which is considered arch-independent)
         for tag in ${tags} ; do
           buildah manifest create "${image_name}:${tag}"
@@ -120,7 +127,8 @@ jobs:
 
     - name: Test
       run: |
-        image='${{ steps.build.outputs.image }}'
+        image_name='${{ steps.build.outputs.image_name }}'
+        image_dir='${{ steps.build.outputs.image_dir }}'
 
         # Extract image ids from manifest to test.
         ids="$(
@@ -141,7 +149,7 @@ jobs:
           buildah bud \
             --build-arg=base="${id}" \
             --file=Dockerfile.test \
-            "images/${image}"
+            "${image_dir}"
         done
         buildah rmi --prune || true
 
@@ -151,7 +159,7 @@ jobs:
         #               => 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/'
+            'https://quay.io/api/v1/repository/bioconda/${{ steps.build.outputs.image_name }}/tag/'
           )"
 
         existing_tags="$(
@@ -181,7 +189,7 @@ jobs:
       name: Push
       uses: redhat-actions/push-to-registry@v2
       with:
-        image: ${{ steps.build.outputs.image }}
+        image: ${{ steps.build.outputs.image_name }}
         tags: ${{ steps.build.outputs.tags }}
         registry: ${{ secrets.QUAY_BIOCONDA_REPO }}
         username: ${{ secrets.QUAY_BIOCONDA_USERNAME }}
@@ -190,10 +198,12 @@ jobs:
     - if: ${{ github.ref == 'refs/heads/test-push' }}
       name: Test Pushed
       run: |
-        image='${{ env.IMAGE_NAME }}'
+
+        image_name='${{ steps.build.outputs.image_name }}'
+        image_dir='${{ steps.build.outputs.image_dir }}'
         ids="$(
           for tag in ${{ steps.build.outputs.tags }} ; do
-            buildah manifest inspect "${image}:${tag}" \
+            buildah manifest inspect "${image_name}:${tag}" \
               | jq -r '.manifests[]|.digest' \
               | while read id ; do
                   buildah images --format '{{.ID}}{{.Digest}}' \
@@ -207,6 +217,6 @@ jobs:
           buildah bud \
             --build-arg=base="${id}" \
             --file=Dockerfile.test \
-            "images/${image}"
+            "${image_dir}"
         done
         buildah rmi --prune || true

From c035696e9c4a9b1267d865203e36f5ca2c253be4 Mon Sep 17 00:00:00 2001
From: Ryan Dale <ryan.dale@nih.gov>
Date: Sun, 28 Jan 2024 15:53:24 -0500
Subject: [PATCH 36/98] handle cases if image doesn't exist in registry yet

---
 .github/workflows/bioconda-utils-build-env-cos7.yml | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/.github/workflows/bioconda-utils-build-env-cos7.yml b/.github/workflows/bioconda-utils-build-env-cos7.yml
index 4e07ca69..35285a7d 100644
--- a/.github/workflows/bioconda-utils-build-env-cos7.yml
+++ b/.github/workflows/bioconda-utils-build-env-cos7.yml
@@ -162,6 +162,13 @@ jobs:
             'https://quay.io/api/v1/repository/bioconda/${{ steps.build.outputs.image_name }}/tag/'
           )"
 
+        # This might be the first time making this image (e.g., will likely
+        # happen when using a test prefix), in which case there will be no
+        # available images.
+        if [ -z "${response}" ]; then
+          exit 0
+        ]
+
         existing_tags="$(
           printf %s "${response}" \
             | jq -r '.tags[]|select(.end_ts == null or .end_ts >= now)|.name'

From c0c0fb1a58e2e28b524efbd5760bec5667ca44ae Mon Sep 17 00:00:00 2001
From: Ryan Dale <ryan.dale@nih.gov>
Date: Sun, 28 Jan 2024 15:53:44 -0500
Subject: [PATCH 37/98] hard-code repo

---
 .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 35285a7d..c31436b7 100644
--- a/.github/workflows/bioconda-utils-build-env-cos7.yml
+++ b/.github/workflows/bioconda-utils-build-env-cos7.yml
@@ -198,7 +198,7 @@ jobs:
       with:
         image: ${{ steps.build.outputs.image_name }}
         tags: ${{ steps.build.outputs.tags }}
-        registry: ${{ secrets.QUAY_BIOCONDA_REPO }}
+        registry: quay.io/bioconda
         username: ${{ secrets.QUAY_BIOCONDA_USERNAME }}
         password: ${{ secrets.QUAY_BIOCONDA_TOKEN }}
 

From 3bed6b0f0ccd6529d55d4b0e9d9908684e7b2dc1 Mon Sep 17 00:00:00 2001
From: Ryan Dale <ryan.dale@nih.gov>
Date: Sun, 28 Jan 2024 17:05:35 -0500
Subject: [PATCH 38/98] typo

---
 .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 c31436b7..5e06358c 100644
--- a/.github/workflows/bioconda-utils-build-env-cos7.yml
+++ b/.github/workflows/bioconda-utils-build-env-cos7.yml
@@ -167,7 +167,7 @@ jobs:
         # available images.
         if [ -z "${response}" ]; then
           exit 0
-        ]
+        fi
 
         existing_tags="$(
           printf %s "${response}" \

From 3b3df34cd86fd28036cd96985638bb3165265c49 Mon Sep 17 00:00:00 2001
From: Ryan Dale <ryan.dale@nih.gov>
Date: Sun, 28 Jan 2024 17:22:13 -0500
Subject: [PATCH 39/98] debug

---
 .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 5e06358c..8d9322d8 100644
--- a/.github/workflows/bioconda-utils-build-env-cos7.yml
+++ b/.github/workflows/bioconda-utils-build-env-cos7.yml
@@ -165,6 +165,8 @@ jobs:
         # This might be the first time making this image (e.g., will likely
         # happen when using a test prefix), in which case there will be no
         # available images.
+        echo "response:"
+        echo $response
         if [ -z "${response}" ]; then
           exit 0
         fi

From 29f1500609325bae7942a69f6d7529fa6d1a866a Mon Sep 17 00:00:00 2001
From: Ryan Dale <ryan.dale@nih.gov>
Date: Sun, 28 Jan 2024 17:52:19 -0500
Subject: [PATCH 40/98] better check

---
 .github/workflows/bioconda-utils-build-env-cos7.yml | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/.github/workflows/bioconda-utils-build-env-cos7.yml b/.github/workflows/bioconda-utils-build-env-cos7.yml
index 8d9322d8..dfcaf324 100644
--- a/.github/workflows/bioconda-utils-build-env-cos7.yml
+++ b/.github/workflows/bioconda-utils-build-env-cos7.yml
@@ -165,9 +165,7 @@ jobs:
         # This might be the first time making this image (e.g., will likely
         # happen when using a test prefix), in which case there will be no
         # available images.
-        echo "response:"
-        echo $response
-        if [ -z "${response}" ]; then
+        if [ "$(echo "${response}" | jq -r '.error_message')" == "Requires authentication" ]; then
           exit 0
         fi
 

From e4a05408525493f7c4bc84a71e65cccdf1aa9410 Mon Sep 17 00:00:00 2001
From: Ryan Dale <ryan.dale@nih.gov>
Date: Sun, 28 Jan 2024 18:09:34 -0500
Subject: [PATCH 41/98] try pushing an image that has worked before

---
 .github/workflows/base-glibc-debian-bash.yaml | 46 +++++++++++++------
 1 file changed, 31 insertions(+), 15 deletions(-)

diff --git a/.github/workflows/base-glibc-debian-bash.yaml b/.github/workflows/base-glibc-debian-bash.yaml
index 29abe884..da37fcbc 100644
--- a/.github/workflows/base-glibc-debian-bash.yaml
+++ b/.github/workflows/base-glibc-debian-bash.yaml
@@ -2,7 +2,7 @@ name: 'Build & Push: base-glibc-debian-bash'
 on:
   push:
     branches:
-    - main
+    - test-push
     paths:
     - images/base-glibc-debian-bash/*
     - .github/workflows/base-glibc-debian-bash.yaml
@@ -20,8 +20,11 @@ jobs:
       # version tags or checksum IDs, but not via "latest".
       MAJOR_VERSION: 3
       MINOR_VERSION: 1
-      IMAGE_NAME: base-glibc-debian-bash
       DEBIAN_VERSION: '12.2'
+      # Used for testing -- set to something like 'tmp-' or 'test-' to prefix
+      # images with this name during testing
+      IMAGE_PREFIX: "tmp-"
+      IMAGE_NAME: base-glibc-debian-bash
 
     steps:
     - uses: actions/checkout@v4
@@ -35,9 +38,9 @@ jobs:
       id: build
       run: |
         set -xeu
-        cd 'images/${{ env.IMAGE_NAME }}'
 
-        image_name='${{ env.IMAGE_NAME }}'
+        image_name='${{ env.IMAGE_PREFIX }}${{ env.IMAGE_NAME }}'
+        image_dir='images/${{ env.IMAGE_NAME }}'
         tags='
           ${{ env.MAJOR_VERSION }}
           ${{ env.MAJOR_VERSION }}.${{ env.MINOR_VERSION }}
@@ -45,10 +48,13 @@ jobs:
         '
         # Adds image and tags to outputs which can be used in later steps.
         printf %s\\n \
-          "image=${image_name}" \
+          "image_dir=${image_dir}" \
+          "image_name=${image_name}" \
           "tags=$( echo ${tags} )" \
           >> $GITHUB_OUTPUT
 
+        cd 'images/${{ env.IMAGE_NAME }}'
+
         # Create manifest (which is considered arch-independent)
         for tag in ${tags} ; do
           buildah manifest create "${image_name}:${tag}"
@@ -102,7 +108,8 @@ jobs:
 
     - name: Test
       run: |
-        image='${{ steps.build.outputs.image }}'
+        image_name='${{ steps.build.outputs.image_name }}'
+        image_dir='${{ steps.build.outputs.image_dir }}'
 
         # Extract image ids from manifest to test.
         ids="$(
@@ -123,7 +130,7 @@ jobs:
           buildah bud \
             --build-arg=base="${id}" \
             --file=Dockerfile.test \
-            "images/${image}"
+            "${image_dir}"
         done
         buildah rmi --prune || true
 
@@ -133,9 +140,16 @@ jobs:
         #               => 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/'
+            'https://quay.io/api/v1/repository/bioconda/${{ steps.build.outputs.image_name }}/tag/'
           )"
 
+        # This might be the first time making this image (e.g., will likely
+        # happen when using a test prefix), in which case there will be no
+        # available images.
+        if [ "$(echo "${response}" | jq -r '.error_message')" == "Requires authentication" ]; then
+          exit 0
+        fi
+
         existing_tags="$(
           printf %s "${response}" \
             | jq -r '.tags[]|select(.end_ts == null or .end_ts >= now)|.name'
@@ -159,23 +173,25 @@ 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:
-        image: ${{ steps.build.outputs.image }}
+        image: ${{ steps.build.outputs.image_name }}
         tags: ${{ steps.build.outputs.tags }}
-        registry: ${{ secrets.QUAY_BIOCONDA_REPO }}
+        registry: quay.io/bioconda
         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 }}'
+
+        image_name='${{ steps.build.outputs.image_name }}'
+        image_dir='${{ steps.build.outputs.image_dir }}'
         ids="$(
           for tag in ${{ steps.build.outputs.tags }} ; do
-            buildah manifest inspect "${image}:${tag}" \
+            buildah manifest inspect "${image_name}:${tag}" \
               | jq -r '.manifests[]|.digest' \
               | while read id ; do
                   buildah images --format '{{.ID}}{{.Digest}}' \
@@ -189,6 +205,6 @@ jobs:
           buildah bud \
             --build-arg=base="${id}" \
             --file=Dockerfile.test \
-            "images/${image}"
+            "${image_dir}"
         done
         buildah rmi --prune || true

From 1164bfbe8aa09c26c5628587ef7d88360323bcf4 Mon Sep 17 00:00:00 2001
From: Ryan Dale <ryan.dale@nih.gov>
Date: Sun, 28 Jan 2024 18:23:31 -0500
Subject: [PATCH 42/98] port recent changes to busybox

---
 .../workflows/base-glibc-busybox-bash.yaml    | 44 +++++++++++++------
 1 file changed, 30 insertions(+), 14 deletions(-)

diff --git a/.github/workflows/base-glibc-busybox-bash.yaml b/.github/workflows/base-glibc-busybox-bash.yaml
index 300702a8..9629acd3 100644
--- a/.github/workflows/base-glibc-busybox-bash.yaml
+++ b/.github/workflows/base-glibc-busybox-bash.yaml
@@ -20,9 +20,12 @@ jobs:
       # version tags or checksum IDs, but not via "latest".
       MAJOR_VERSION: 3
       MINOR_VERSION: 1
-      IMAGE_NAME: base-glibc-busybox-bash
       BUSYBOX_VERSION: '1.36.1'
       DEBIAN_VERSION: '12.2'
+      # Used for testing -- set to something like 'tmp-' or 'test-' to prefix
+      # images with this name during testing
+      IMAGE_PREFIX: "tmp-"
+      IMAGE_NAME: base-glibc-busybox-bash
 
     steps:
     - uses: actions/checkout@v4
@@ -36,9 +39,9 @@ jobs:
       id: build
       run: |
         set -xeu
-        cd 'images/${{ env.IMAGE_NAME }}'
 
-        image_name='${{ env.IMAGE_NAME }}'
+        image_name='${{ env.IMAGE_PREFIX }}${{ env.IMAGE_NAME }}'
+        image_dir='images/${{ env.IMAGE_NAME }}'
         tags='
           ${{ env.MAJOR_VERSION }}
           ${{ env.MAJOR_VERSION }}.${{ env.MINOR_VERSION }}
@@ -46,10 +49,13 @@ jobs:
         '
         # Adds image and tags to outputs which can be used in later steps.
         printf %s\\n \
-          "image=${image_name}" \
+          "image_dir=${image_dir}" \
+          "image_name=${image_name}" \
           "tags=$( echo ${tags} )" \
           >> $GITHUB_OUTPUT
 
+        cd 'images/${{ env.IMAGE_NAME }}'
+
         # Create manifest (which is considered arch-independent)
         for tag in ${tags} ; do
           buildah manifest create "${image_name}:${tag}"
@@ -112,7 +118,8 @@ jobs:
 
     - name: Test
       run: |
-        image='${{ steps.build.outputs.image }}'
+        image_name='${{ steps.build.outputs.image_name }}'
+        image_dir='${{ steps.build.outputs.image_dir }}'
 
         # Extract image ids from manifest to test.
         ids="$(
@@ -133,7 +140,7 @@ jobs:
           buildah bud \
             --build-arg=base="${id}" \
             --file=Dockerfile.test \
-            "images/${image}"
+            "${image_dir}"
         done
         buildah rmi --prune || true
 
@@ -143,9 +150,16 @@ jobs:
         #               => 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/'
+            'https://quay.io/api/v1/repository/bioconda/${{ steps.build.outputs.image_name }}/tag/'
           )"
 
+        # This might be the first time making this image (e.g., will likely
+        # happen when using a test prefix), in which case there will be no
+        # available images.
+        if [ "$(echo "${response}" | jq -r '.error_message')" == "Requires authentication" ]; then
+          exit 0
+        fi
+
         existing_tags="$(
           printf %s "${response}" \
             | jq -r '.tags[]|select(.end_ts == null or .end_ts >= now)|.name'
@@ -169,23 +183,25 @@ 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:
-        image: ${{ steps.build.outputs.image }}
+        image: ${{ steps.build.outputs.image_name }}
         tags: ${{ steps.build.outputs.tags }}
-        registry: ${{ secrets.QUAY_BIOCONDA_REPO }}
+        registry: quay.io/bioconda
         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 }}'
+
+        image_name='${{ steps.build.outputs.image_name }}'
+        image_dir='${{ steps.build.outputs.image_dir }}'
         ids="$(
           for tag in ${{ steps.build.outputs.tags }} ; do
-            buildah manifest inspect "${image}:${tag}" \
+            buildah manifest inspect "${image_name}:${tag}" \
               | jq -r '.manifests[]|.digest' \
               | while read id ; do
                   buildah images --format '{{.ID}}{{.Digest}}' \
@@ -199,6 +215,6 @@ jobs:
           buildah bud \
             --build-arg=base="${id}" \
             --file=Dockerfile.test \
-            "images/${image}"
+            "${image_dir}"
         done
         buildah rmi --prune || true

From 5fec03600aba98b6c27bd411b781d3d3dcb7e2ba Mon Sep 17 00:00:00 2001
From: Ryan Dale <ryan.dale@nih.gov>
Date: Mon, 29 Jan 2024 15:10:50 -0500
Subject: [PATCH 43/98] comment out push

---
 .github/workflows/bioconda-utils-build-env-cos7.yml | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/.github/workflows/bioconda-utils-build-env-cos7.yml b/.github/workflows/bioconda-utils-build-env-cos7.yml
index dfcaf324..a96dc41d 100644
--- a/.github/workflows/bioconda-utils-build-env-cos7.yml
+++ b/.github/workflows/bioconda-utils-build-env-cos7.yml
@@ -1,11 +1,11 @@
 name: 'Build & Push: bioconda-utils-build-env-cos7'
 on:
   push:
-    branches:
-    - test-push
-    paths:
-    - images/bioconda-utils-build-env-cos7/**
-    - .github/workflows/bioconda-utils-build-env-cos7.yml
+    # branches:
+    # - test-push
+    # paths:
+    # - images/bioconda-utils-build-env-cos7/**
+    # - .github/workflows/bioconda-utils-build-env-cos7.yml
   pull_request:
     paths:
     - images/bioconda-utils-build-env-cos7/**

From ed9a1f936aa0f554918aceb336ad560f7b4ca1c5 Mon Sep 17 00:00:00 2001
From: Ryan Dale <ryan.dale@nih.gov>
Date: Mon, 29 Jan 2024 15:26:52 -0500
Subject: [PATCH 44/98] try new credentials

---
 .github/workflows/bioconda-utils-build-env-cos7.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/bioconda-utils-build-env-cos7.yml b/.github/workflows/bioconda-utils-build-env-cos7.yml
index a96dc41d..832aa1ee 100644
--- a/.github/workflows/bioconda-utils-build-env-cos7.yml
+++ b/.github/workflows/bioconda-utils-build-env-cos7.yml
@@ -199,8 +199,8 @@ jobs:
         image: ${{ steps.build.outputs.image_name }}
         tags: ${{ steps.build.outputs.tags }}
         registry: quay.io/bioconda
-        username: ${{ secrets.QUAY_BIOCONDA_USERNAME }}
-        password: ${{ secrets.QUAY_BIOCONDA_TOKEN }}
+        username: ${{ secrets.QUAY_BIOCONDA_USERNAME_2024 }}
+        password: ${{ secrets.QUAY_BIOCONDA_TOKEN_2024}}
 
     - if: ${{ github.ref == 'refs/heads/test-push' }}
       name: Test Pushed

From 319b352334a2478075ddc91c07830824c93d9bb1 Mon Sep 17 00:00:00 2001
From: Ryan Dale <ryan.dale@nih.gov>
Date: Mon, 29 Jan 2024 15:46:10 -0500
Subject: [PATCH 45/98] whitespace to trigger

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

diff --git a/.github/workflows/bioconda-utils-build-env-cos7.yml b/.github/workflows/bioconda-utils-build-env-cos7.yml
index 832aa1ee..b04855f0 100644
--- a/.github/workflows/bioconda-utils-build-env-cos7.yml
+++ b/.github/workflows/bioconda-utils-build-env-cos7.yml
@@ -1,3 +1,4 @@
+
 name: 'Build & Push: bioconda-utils-build-env-cos7'
 on:
   push:

From 1387d2da8d534a90f1ebb14c1f2098fc9cd20dcf Mon Sep 17 00:00:00 2001
From: Ryan Dale <ryan.dale@nih.gov>
Date: Mon, 29 Jan 2024 15:46:45 -0500
Subject: [PATCH 46/98] disable push for now

---
 .github/workflows/bioconda-utils-build-env-cos7.yml | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/.github/workflows/bioconda-utils-build-env-cos7.yml b/.github/workflows/bioconda-utils-build-env-cos7.yml
index b04855f0..bd2ebf60 100644
--- a/.github/workflows/bioconda-utils-build-env-cos7.yml
+++ b/.github/workflows/bioconda-utils-build-env-cos7.yml
@@ -1,7 +1,6 @@
-
 name: 'Build & Push: bioconda-utils-build-env-cos7'
 on:
-  push:
+  # push:
     # branches:
     # - test-push
     # paths:

From 8e89ac24652dd8c6954f8ad905b68520d602ac22 Mon Sep 17 00:00:00 2001
From: Ryan Dale <ryan.dale@nih.gov>
Date: Mon, 29 Jan 2024 16:04:05 -0500
Subject: [PATCH 47/98] re-enable push

---
 .github/workflows/bioconda-utils-build-env-cos7.yml | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/.github/workflows/bioconda-utils-build-env-cos7.yml b/.github/workflows/bioconda-utils-build-env-cos7.yml
index bd2ebf60..1684fca6 100644
--- a/.github/workflows/bioconda-utils-build-env-cos7.yml
+++ b/.github/workflows/bioconda-utils-build-env-cos7.yml
@@ -1,11 +1,11 @@
 name: 'Build & Push: bioconda-utils-build-env-cos7'
 on:
-  # push:
-    # branches:
-    # - test-push
-    # paths:
-    # - images/bioconda-utils-build-env-cos7/**
-    # - .github/workflows/bioconda-utils-build-env-cos7.yml
+  push:
+    branches:
+    - test-push
+    paths:
+    - images/bioconda-utils-build-env-cos7/**
+    - .github/workflows/bioconda-utils-build-env-cos7.yml
   pull_request:
     paths:
     - images/bioconda-utils-build-env-cos7/**

From f2c528c34e9d0fd5f6dbe1bfbd8e0e0f3f804e92 Mon Sep 17 00:00:00 2001
From: Ryan Dale <ryan.dale@nih.gov>
Date: Mon, 29 Jan 2024 16:53:02 -0500
Subject: [PATCH 48/98] back to original credentials

---
 .github/workflows/bioconda-utils-build-env-cos7.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/bioconda-utils-build-env-cos7.yml b/.github/workflows/bioconda-utils-build-env-cos7.yml
index 1684fca6..dfcaf324 100644
--- a/.github/workflows/bioconda-utils-build-env-cos7.yml
+++ b/.github/workflows/bioconda-utils-build-env-cos7.yml
@@ -199,8 +199,8 @@ jobs:
         image: ${{ steps.build.outputs.image_name }}
         tags: ${{ steps.build.outputs.tags }}
         registry: quay.io/bioconda
-        username: ${{ secrets.QUAY_BIOCONDA_USERNAME_2024 }}
-        password: ${{ secrets.QUAY_BIOCONDA_TOKEN_2024}}
+        username: ${{ secrets.QUAY_BIOCONDA_USERNAME }}
+        password: ${{ secrets.QUAY_BIOCONDA_TOKEN }}
 
     - if: ${{ github.ref == 'refs/heads/test-push' }}
       name: Test Pushed

From a4d6bc16327918d20383fbb09fa186e6a0227654 Mon Sep 17 00:00:00 2001
From: Ryan Dale <ryan.dale@nih.gov>
Date: Tue, 30 Jan 2024 14:19:26 -0500
Subject: [PATCH 49/98] rm existing workflows for testing

---
 .../workflows/base-glibc-busybox-bash.yaml    | 220 -----------------
 .github/workflows/base-glibc-debian-bash.yaml | 210 ----------------
 .../bioconda-recipes-issue-responder.yaml     | 112 ---------
 .../bioconda-utils-build-env-cos7.yml         | 229 ------------------
 .github/workflows/bot.yaml                    | 123 ----------
 .github/workflows/create-env.yaml             | 145 -----------
 6 files changed, 1039 deletions(-)
 delete mode 100644 .github/workflows/base-glibc-busybox-bash.yaml
 delete mode 100644 .github/workflows/base-glibc-debian-bash.yaml
 delete mode 100644 .github/workflows/bioconda-recipes-issue-responder.yaml
 delete mode 100644 .github/workflows/bioconda-utils-build-env-cos7.yml
 delete mode 100644 .github/workflows/bot.yaml
 delete mode 100644 .github/workflows/create-env.yaml

diff --git a/.github/workflows/base-glibc-busybox-bash.yaml b/.github/workflows/base-glibc-busybox-bash.yaml
deleted file mode 100644
index 9629acd3..00000000
--- a/.github/workflows/base-glibc-busybox-bash.yaml
+++ /dev/null
@@ -1,220 +0,0 @@
-name: 'Build & Push: base-glibc-busybox-bash'
-on:
-  push:
-    branches:
-    - main
-    paths:
-    - images/base-glibc-busybox-bash/*
-    - .github/workflows/base-glibc-busybox-bash.yaml
-  pull_request:
-    paths:
-    - images/base-glibc-busybox-bash/*
-    - .github/workflows/base-glibc-busybox-bash.yaml
-
-jobs:
-  build:
-    name: Build & Push
-    runs-on: ubuntu-22.04
-    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: 1
-      BUSYBOX_VERSION: '1.36.1'
-      DEBIAN_VERSION: '12.2'
-      # Used for testing -- set to something like 'tmp-' or 'test-' to prefix
-      # images with this name during testing
-      IMAGE_PREFIX: "tmp-"
-      IMAGE_NAME: base-glibc-busybox-bash
-
-    steps:
-    - uses: actions/checkout@v4
-
-    - name: Set up QEMU
-      uses: docker/setup-qemu-action@v3
-      with:
-        platforms: arm64
-
-    - name: Build
-      id: build
-      run: |
-        set -xeu
-
-        image_name='${{ env.IMAGE_PREFIX }}${{ env.IMAGE_NAME }}'
-        image_dir='images/${{ env.IMAGE_NAME }}'
-        tags='
-          ${{ env.MAJOR_VERSION }}
-          ${{ env.MAJOR_VERSION }}.${{ env.MINOR_VERSION }}
-          latest
-        '
-        # Adds image and tags to outputs which can be used in later steps.
-        printf %s\\n \
-          "image_dir=${image_dir}" \
-          "image_name=${image_name}" \
-          "tags=$( echo ${tags} )" \
-          >> $GITHUB_OUTPUT
-
-        cd 'images/${{ env.IMAGE_NAME }}'
-
-        # 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="${iidfile}" \
-          --build-arg=busybox_version='${{ env.BUSYBOX_VERSION }}' \
-          --file=Dockerfile.busybox
-        busybox_image="$( cat "${iidfile}" )"
-        rm "${iidfile}"
-
-        for arch in amd64 arm64 ; do
-          iidfile="$( mktemp )"
-          buildah bud \
-            --arch="${arch}" \
-            --iidfile="${iidfile}" \
-            --build-arg=busybox_image="${busybox_image}" \
-            --build-arg=debian_version='${{ env.DEBIAN_VERSION }}'
-          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 "$( find -xdev -name libc.so.6 -print -quit )"' | sed '1!d' )"
-          busybox="$( run busybox | sed '1!d' )"
-          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="${glibc}" \
-            --label=busybox="${busybox}" \
-            --label=bash="${bash}" \
-            --label=deb-list="${deb_list}" \
-            --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}" \
-              "${image_name}:${tag}-${arch}"
-            buildah manifest add \
-              "${image_name}:${tag}" \
-              "${image_id}"
-          done
-        done
-
-    - name: Test
-      run: |
-        image_name='${{ steps.build.outputs.image_name }}'
-        image_dir='${{ steps.build.outputs.image_dir }}'
-
-        # 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="${id}" \
-            --file=Dockerfile.test \
-            "${image_dir}"
-        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_name }}/tag/'
-          )"
-
-        # This might be the first time making this image (e.g., will likely
-        # happen when using a test prefix), in which case there will be no
-        # available images.
-        if [ "$(echo "${response}" | jq -r '.error_message')" == "Requires authentication" ]; then
-          exit 0
-        fi
-
-        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/test-push' }}
-      name: Push
-      uses: redhat-actions/push-to-registry@v2
-      with:
-        image: ${{ steps.build.outputs.image_name }}
-        tags: ${{ steps.build.outputs.tags }}
-        registry: quay.io/bioconda
-        username: ${{ secrets.QUAY_BIOCONDA_USERNAME }}
-        password: ${{ secrets.QUAY_BIOCONDA_TOKEN }}
-
-    - if: ${{ github.ref == 'refs/heads/test-push' }}
-      name: Test Pushed
-      run: |
-
-        image_name='${{ steps.build.outputs.image_name }}'
-        image_dir='${{ steps.build.outputs.image_dir }}'
-        ids="$(
-          for tag in ${{ steps.build.outputs.tags }} ; do
-            buildah manifest inspect "${image_name}:${tag}" \
-              | jq -r '.manifests[]|.digest' \
-              | while read id ; do
-                  buildah images --format '{{.ID}}{{.Digest}}' \
-                  | sed -n "s/${id}//p"
-                done
-          done
-          )"
-        ids="$( printf %s "${ids}" | sort -u )"
-        for id in ${ids} ; do
-          podman history "${id}"
-          buildah bud \
-            --build-arg=base="${id}" \
-            --file=Dockerfile.test \
-            "${image_dir}"
-        done
-        buildah rmi --prune || true
diff --git a/.github/workflows/base-glibc-debian-bash.yaml b/.github/workflows/base-glibc-debian-bash.yaml
deleted file mode 100644
index da37fcbc..00000000
--- a/.github/workflows/base-glibc-debian-bash.yaml
+++ /dev/null
@@ -1,210 +0,0 @@
-name: 'Build & Push: base-glibc-debian-bash'
-on:
-  push:
-    branches:
-    - test-push
-    paths:
-    - images/base-glibc-debian-bash/*
-    - .github/workflows/base-glibc-debian-bash.yaml
-  pull_request:
-    paths:
-    - images/base-glibc-debian-bash/*
-    - .github/workflows/base-glibc-debian-bash.yaml
-
-jobs:
-  build:
-    name: Build & Push
-    runs-on: ubuntu-22.04
-    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: 1
-      DEBIAN_VERSION: '12.2'
-      # Used for testing -- set to something like 'tmp-' or 'test-' to prefix
-      # images with this name during testing
-      IMAGE_PREFIX: "tmp-"
-      IMAGE_NAME: base-glibc-debian-bash
-
-    steps:
-    - uses: actions/checkout@v4
-
-    - name: Set up QEMU
-      uses: docker/setup-qemu-action@v3
-      with:
-        platforms: arm64
-
-    - name: Build
-      id: build
-      run: |
-        set -xeu
-
-        image_name='${{ env.IMAGE_PREFIX }}${{ env.IMAGE_NAME }}'
-        image_dir='images/${{ env.IMAGE_NAME }}'
-        tags='
-          ${{ env.MAJOR_VERSION }}
-          ${{ env.MAJOR_VERSION }}.${{ env.MINOR_VERSION }}
-          latest
-        '
-        # Adds image and tags to outputs which can be used in later steps.
-        printf %s\\n \
-          "image_dir=${image_dir}" \
-          "image_name=${image_name}" \
-          "tags=$( echo ${tags} )" \
-          >> $GITHUB_OUTPUT
-
-        cd 'images/${{ env.IMAGE_NAME }}'
-
-        # 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 \
-            --arch="${arch}" \
-            --iidfile="${iidfile}" \
-            --build-arg=debian_version='${{ env.DEBIAN_VERSION }}'
-          image_id="$( 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' )"
-          debian="$( run cat /etc/debian_version | sed '1!d' )"
-          bash="$( 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}" \
-            --label=debian="${debian}" \
-            --label=bash="${bash}" \
-            --label=deb-list="${deb_list}" \
-            --label=pkg-list="${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}" \
-              "${image_name}:${tag}-${arch}"
-            buildah manifest add \
-              "${image_name}:${tag}" \
-              "${image_id}"
-          done
-        done
-
-    - name: Test
-      run: |
-        image_name='${{ steps.build.outputs.image_name }}'
-        image_dir='${{ steps.build.outputs.image_dir }}'
-
-        # 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="${id}" \
-            --file=Dockerfile.test \
-            "${image_dir}"
-        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_name }}/tag/'
-          )"
-
-        # This might be the first time making this image (e.g., will likely
-        # happen when using a test prefix), in which case there will be no
-        # available images.
-        if [ "$(echo "${response}" | jq -r '.error_message')" == "Requires authentication" ]; then
-          exit 0
-        fi
-
-        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/test-push' }}
-      name: Push
-      uses: redhat-actions/push-to-registry@v2
-      with:
-        image: ${{ steps.build.outputs.image_name }}
-        tags: ${{ steps.build.outputs.tags }}
-        registry: quay.io/bioconda
-        username: ${{ secrets.QUAY_BIOCONDA_USERNAME }}
-        password: ${{ secrets.QUAY_BIOCONDA_TOKEN }}
-
-    - if: ${{ github.ref == 'refs/heads/test-push' }}
-      name: Test Pushed
-      run: |
-
-        image_name='${{ steps.build.outputs.image_name }}'
-        image_dir='${{ steps.build.outputs.image_dir }}'
-        ids="$(
-          for tag in ${{ steps.build.outputs.tags }} ; do
-            buildah manifest inspect "${image_name}:${tag}" \
-              | jq -r '.manifests[]|.digest' \
-              | while read id ; do
-                  buildah images --format '{{.ID}}{{.Digest}}' \
-                  | sed -n "s/${id}//p"
-                done
-          done
-          )"
-        ids="$( printf %s "${ids}" | sort -u )"
-        for id in ${ids} ; do
-          podman history "${id}"
-          buildah bud \
-            --build-arg=base="${id}" \
-            --file=Dockerfile.test \
-            "${image_dir}"
-        done
-        buildah rmi --prune || true
diff --git a/.github/workflows/bioconda-recipes-issue-responder.yaml b/.github/workflows/bioconda-recipes-issue-responder.yaml
deleted file mode 100644
index 7218a752..00000000
--- a/.github/workflows/bioconda-recipes-issue-responder.yaml
+++ /dev/null
@@ -1,112 +0,0 @@
-name: 'Build & Push: bioconda-recipes-issue-responder'
-on:
-  push:
-    branches:
-    - main
-    paths:
-    - images/bioconda-recipes-issue-responder/*
-    - .github/workflows/bioconda-recipes-issue-responder.yaml
-  pull_request:
-    paths:
-    - images/bioconda-recipes-issue-responder/*
-    - .github/workflows/bioconda-recipes-issue-responder.yaml
-
-jobs:
-  build:
-    name: Build & Push
-    runs-on: ubuntu-22.04
-    env:
-      IMAGE_NAME: bioconda-recipes-issue-responder
-      IMAGE_VERSION: '1.1.1'
-
-    steps:
-    - uses: actions/checkout@v2
-
-    - name: Build
-      id: buildah-build
-      uses: redhat-actions/buildah-build@v2
-      with:
-        image: ${{ env.IMAGE_NAME }}
-        tags: >-
-          latest
-          ${{ env.IMAGE_VERSION }}
-        context: ./images/${{ env.IMAGE_NAME }}
-        dockerfiles: |
-          ./images/${{ env.IMAGE_NAME }}/Dockerfile
-
-    - name: Test
-      run: |
-        image='${{ steps.buildah-build.outputs.image }}'
-        ids="$(
-          for tag in ${{ steps.buildah-build.outputs.tags }} ; do
-            buildah images --quiet --no-trunc "${image}:${tag}"
-          done
-          )"
-        ids="$( 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
-
-    - 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.
-        respone="$(
-          curl -sL \
-            'https://quay.io/api/v1/repository/bioconda/${{ steps.buildah-build.outputs.image }}/image'
-          )"
-
-        existing_tags="$(
-          printf %s "${respone}" \
-            | jq -r '.images[].tags[]'
-          )" \
-          || {
-            printf %s\\n \
-              'Could not get list of image tags.' \
-              'Does the repository exist on Quay.io?' \
-              'Quay.io REST API response was:' \
-              "${respone}"
-            exit 1
-          }
-        for tag in ${{ steps.buildah-build.outputs.tags }} ; do
-          if [ \! "${tag}" = latest ] ; then
-            if printf %s "${existing_tags}" | grep -qxF "${tag}" ; then
-              printf 'Tag %s already exists!\n' "${tag}"
-              exit 1
-            fi
-          fi
-        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 }}
-        registry: ${{ secrets.QUAY_BIOCONDA_REPO }}
-        username: ${{ secrets.QUAY_BIOCONDA_USERNAME }}
-        password: ${{ secrets.QUAY_BIOCONDA_TOKEN }}
-
-    - if: ${{ github.ref == 'refs/heads/main' }}
-      name: Test Pushed
-      run: |
-        image='${{ steps.buildah-build.outputs.image }}'
-        ids="$(
-          for tag in ${{ steps.buildah-build.outputs.tags }} ; do
-            buildah images --quiet --no-trunc "${image}:${tag}"
-          done
-          )"
-        ids="$( 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/.github/workflows/bioconda-utils-build-env-cos7.yml b/.github/workflows/bioconda-utils-build-env-cos7.yml
deleted file mode 100644
index dfcaf324..00000000
--- a/.github/workflows/bioconda-utils-build-env-cos7.yml
+++ /dev/null
@@ -1,229 +0,0 @@
-name: 'Build & Push: bioconda-utils-build-env-cos7'
-on:
-  push:
-    branches:
-    - test-push
-    paths:
-    - images/bioconda-utils-build-env-cos7/**
-    - .github/workflows/bioconda-utils-build-env-cos7.yml
-  pull_request:
-    paths:
-    - images/bioconda-utils-build-env-cos7/**
-    - .github/workflows/bioconda-utils-build-env-cos7.yml
-
-jobs:
-  build:
-    name: Build & Push
-    runs-on: ubuntu-22.04
-    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: 1
-
-      # Used for testing -- set to something like 'tmp-' or 'test-' to prefix
-      # images with this name during testing
-      IMAGE_PREFIX: "tmp-"
-      IMAGE_NAME: bioconda-utils-build-env-cos7
-
-    steps:
-    - name: Checkout bioconda-containers
-      uses: actions/checkout@v4
-      with:
-        fetch-depth: 0
-
-    - name: Checkout bioconda-utils
-      uses: actions/checkout@v4
-      with:
-        fetch-depth: 0
-        repository: 'bioconda/bioconda-utils'
-        path: 'images/bioconda-utils-build-env-cos7/bioconda-utils'
-
-    - name: Set up QEMU
-      uses: docker/setup-qemu-action@v3
-      with:
-        platforms: arm64
-
-    - name: Build
-      id: build
-      run: |
-        set -xeu
-
-        image_name='${{ env.IMAGE_PREFIX }}${{ env.IMAGE_NAME }}'
-        image_dir='images/${{ env.IMAGE_NAME }}'
-        tags='
-          ${{ env.MAJOR_VERSION }}
-          ${{ env.MAJOR_VERSION }}.${{ env.MINOR_VERSION }}
-          latest
-        '
-        # Adds image and tags to outputs which can be used in later steps.
-        printf %s\\n \
-          "image_dir=${image_dir}" \
-          "image_name=${image_name}" \
-          "tags=$( echo ${tags} )" \
-          >> $GITHUB_OUTPUT
-
-        cd 'images/${{ env.IMAGE_NAME }}'
-
-        # Create manifest (which is considered arch-independent)
-        for tag in ${tags} ; do
-          buildah manifest create "${image_name}:${tag}"
-        done
-
-        # Due to different nomenclature used by conda-forge and buildah, we
-        # need to map archs to base images.
-        for arch_and_image in \
-          "amd64=quay.io/condaforge/linux-anvil-cos7-x86_64" \
-          "arm64=quay.io/condaforge/linux-anvil-aarch64";
-        do
-          # Unpack archs and base images
-          arch=$(echo $arch_and_image | cut -f1 -d "=")
-          base_image=$(echo $arch_and_image | cut -f2 -d "=")
-
-          # --iidfile prints the built image ID to the specified file. This is
-          # used so we can refer to the image in later steps.
-          iidfile="$( 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 sh -c '. /opt/conda/etc/profile.d/conda.sh && conda activate base && bioconda-utils --version' | rev | cut -f1 -d " " | rev )"
-          buildah rm "${container}"
-
-          # Store package/version info as labels for the image
-          container="$( 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}" \
-            "${container}"
-
-          # Store the new image (now with labels)
-          image_id="$( 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_name='${{ steps.build.outputs.image_name }}'
-        image_dir='${{ steps.build.outputs.image_dir }}'
-
-        # 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="${id}" \
-            --file=Dockerfile.test \
-            "${image_dir}"
-        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_name }}/tag/'
-          )"
-
-        # This might be the first time making this image (e.g., will likely
-        # happen when using a test prefix), in which case there will be no
-        # available images.
-        if [ "$(echo "${response}" | jq -r '.error_message')" == "Requires authentication" ]; then
-          exit 0
-        fi
-
-        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/test-push' }}
-      name: Push
-      uses: redhat-actions/push-to-registry@v2
-      with:
-        image: ${{ steps.build.outputs.image_name }}
-        tags: ${{ steps.build.outputs.tags }}
-        registry: quay.io/bioconda
-        username: ${{ secrets.QUAY_BIOCONDA_USERNAME }}
-        password: ${{ secrets.QUAY_BIOCONDA_TOKEN }}
-
-    - if: ${{ github.ref == 'refs/heads/test-push' }}
-      name: Test Pushed
-      run: |
-
-        image_name='${{ steps.build.outputs.image_name }}'
-        image_dir='${{ steps.build.outputs.image_dir }}'
-        ids="$(
-          for tag in ${{ steps.build.outputs.tags }} ; do
-            buildah manifest inspect "${image_name}:${tag}" \
-              | jq -r '.manifests[]|.digest' \
-              | while read id ; do
-                  buildah images --format '{{.ID}}{{.Digest}}' \
-                  | sed -n "s/${id}//p"
-                done
-          done
-          )"
-        ids="$( printf %s "${ids}" | sort -u )"
-        for id in ${ids} ; do
-          podman history "${id}"
-          buildah bud \
-            --build-arg=base="${id}" \
-            --file=Dockerfile.test \
-            "${image_dir}"
-        done
-        buildah rmi --prune || true
diff --git a/.github/workflows/bot.yaml b/.github/workflows/bot.yaml
deleted file mode 100644
index 3b6371db..00000000
--- a/.github/workflows/bot.yaml
+++ /dev/null
@@ -1,123 +0,0 @@
-name: 'Build & Push: bot'
-on:
-  push:
-    branches:
-    - main
-    paths:
-    - images/bot/**
-    - .github/workflows/bot.yaml
-  pull_request:
-    paths:
-    - images/bot/**
-    - .github/workflows/bot.yaml
-
-jobs:
-  build:
-    name: Build & Push
-    strategy:
-      matrix:
-        include:
-        - tag: comment
-          packages: ""
-        - tag: merge
-          packages: "anaconda-client skopeo"
-        - tag: update
-          packages: "git openssh"
-    runs-on: ubuntu-22.04
-    env:
-      IMAGE_NAME: bot
-      IMAGE_VERSION: '1.1.23'
-
-    steps:
-    - uses: actions/checkout@v2
-
-    - name: Build
-      id: buildah-build
-      uses: redhat-actions/buildah-build@v2
-      with:
-        image: ${{ env.IMAGE_NAME }}
-        tags: >-
-          ${{ matrix.tag }}
-          ${{ matrix.tag }}-${{ env.IMAGE_VERSION }}
-        context: ./images/${{ env.IMAGE_NAME }}
-        dockerfiles: |
-          ./images/${{ env.IMAGE_NAME }}/Dockerfile
-        build-args: |
-          packages=${{ matrix.packages }}
-
-    - name: Test
-      run: |
-        image='${{ steps.buildah-build.outputs.image }}'
-        ids="$(
-          for tag in ${{ steps.buildah-build.outputs.tags }} ; do
-            buildah images --quiet --no-trunc "${image}:${tag}"
-          done
-          )"
-        ids="$( printf %s "${ids}" | sort -u )"
-        for id in ${ids} ; do
-          podman history "${id}"
-          buildah bud \
-            --build-arg=base="${id}" \
-            --file=Dockerfile.test \
-            'images/${{ env.IMAGE_NAME }}'
-        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.
-    #    respone="$(
-    #      curl -sL \
-    #        'https://quay.io/api/v1/repository/bioconda/${{ steps.buildah-build.outputs.image }}/image'
-    #      )"
-
-    #    existing_tags="$(
-    #      printf %s "${respone}" \
-    #        | jq -r '.images[].tags[]'
-    #      )" \
-    #      || {
-    #        printf %s\\n \
-    #          'Could not get list of image tags.' \
-    #          'Does the repository exist on Quay.io?' \
-    #          'Quay.io REST API response was:' \
-    #          "${respone}"
-    #        exit 1
-    #      }
-    #    for tag in ${{ steps.buildah-build.outputs.tags }} ; do
-    #      if [ \! "${tag}" = '${{ matrix.tag }}' ] ; then
-    #        if printf %s "${existing_tags}" | grep -qxF "${tag}" ; then
-    #          printf 'Tag %s already exists!\n' "${tag}"
-    #          exit 1
-    #        fi
-    #      fi
-    #    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 }}
-        registry: ${{ secrets.QUAY_BIOCONDA_REPO }}
-        username: ${{ secrets.QUAY_BIOCONDA_USERNAME }}
-        password: ${{ secrets.QUAY_BIOCONDA_TOKEN }}
-
-    - if: ${{ github.ref == 'refs/heads/main' }}
-      name: Test Pushed
-      run: |
-        image='${{ steps.buildah-build.outputs.image }}'
-        ids="$(
-          for tag in ${{ steps.buildah-build.outputs.tags }} ; do
-            buildah images --quiet --no-trunc "${image}:${tag}"
-          done
-          )"
-        ids="$( printf %s "${ids}" | sort -u )"
-        for id in ${ids} ; do
-          podman history "${id}"
-          buildah bud \
-            --build-arg=base="${id}" \
-            --file=Dockerfile.test \
-            'images/${{ env.IMAGE_NAME }}'
-        done
-        buildah rmi --prune || true
diff --git a/.github/workflows/create-env.yaml b/.github/workflows/create-env.yaml
deleted file mode 100644
index 811cb643..00000000
--- a/.github/workflows/create-env.yaml
+++ /dev/null
@@ -1,145 +0,0 @@
-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@v3
-      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

From 73f1d828f5ea7d53ec969cb529e0e5f4dca6af39 Mon Sep 17 00:00:00 2001
From: Ryan Dale <ryan.dale@nih.gov>
Date: Tue, 30 Jan 2024 14:19:45 -0500
Subject: [PATCH 50/98] add test caller and called workflow

---
 .github/workflows/caller.yml        | 11 ++++++++
 .github/workflows/generic_build.yml | 40 +++++++++++++++++++++++++++++
 2 files changed, 51 insertions(+)
 create mode 100644 .github/workflows/caller.yml
 create mode 100644 .github/workflows/generic_build.yml

diff --git a/.github/workflows/caller.yml b/.github/workflows/caller.yml
new file mode 100644
index 00000000..c0a09c92
--- /dev/null
+++ b/.github/workflows/caller.yml
@@ -0,0 +1,11 @@
+name: "Generic caller test"
+on:
+  pull_request:
+
+jobs:
+  call-generic-build:
+    uses: bioconda/bioconda-containers/.github/workflows/generic_build.yml
+    with:
+      image_name: example-image
+      tags: 'major.minor latest'
+
diff --git a/.github/workflows/generic_build.yml b/.github/workflows/generic_build.yml
new file mode 100644
index 00000000..444cff5c
--- /dev/null
+++ b/.github/workflows/generic_build.yml
@@ -0,0 +1,40 @@
+on:
+  workflow_call:
+    inputs:
+      image_name:
+        required: true
+        type: string
+      image_dir:
+        required: true
+        type: string
+      tags:
+        required: true
+        type: string
+      busybox_version:
+        required: false
+        type: string
+      debian_version:
+        required: false
+        type: string
+      image_prefix:
+        required: false
+        type: string
+
+jobs:
+  build:
+    runs-on: ubuntu-22.04
+  steps:
+  - uses: actions/checkout@v4
+  
+  - name: Set up QEMU
+    uses: docker/setup-qemu-action@v3
+    with:
+      platforms: arm64
+
+  - name: Build
+    id: build
+    run: |
+      set -xeu
+      image_name='${{ inputs.image_name }}${{ inputs.image_prefix }}'
+      image_dir='images/${{ inputs.image_name }}'
+

From b2d6b7e4f2fe129ef29aad4673f8b5c7f458e482 Mon Sep 17 00:00:00 2001
From: Ryan Dale <ryan.dale@nih.gov>
Date: Tue, 30 Jan 2024 14:21:10 -0500
Subject: [PATCH 51/98] bump

---
 .github/workflows/caller.yml        | 2 ++
 .github/workflows/generic_build.yml | 5 +----
 2 files changed, 3 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/caller.yml b/.github/workflows/caller.yml
index c0a09c92..67ef0a3b 100644
--- a/.github/workflows/caller.yml
+++ b/.github/workflows/caller.yml
@@ -1,6 +1,8 @@
 name: "Generic caller test"
 on:
   pull_request:
+    paths:
+    - .github/workflows/caller.yml
 
 jobs:
   call-generic-build:
diff --git a/.github/workflows/generic_build.yml b/.github/workflows/generic_build.yml
index 444cff5c..84d9e28a 100644
--- a/.github/workflows/generic_build.yml
+++ b/.github/workflows/generic_build.yml
@@ -4,9 +4,6 @@ on:
       image_name:
         required: true
         type: string
-      image_dir:
-        required: true
-        type: string
       tags:
         required: true
         type: string
@@ -37,4 +34,4 @@ jobs:
       set -xeu
       image_name='${{ inputs.image_name }}${{ inputs.image_prefix }}'
       image_dir='images/${{ inputs.image_name }}'
-
+      

From 99550cdc2faaa3445d99e235582eaabe012a9c6a Mon Sep 17 00:00:00 2001
From: Ryan Dale <ryan.dale@nih.gov>
Date: Tue, 30 Jan 2024 14:22:36 -0500
Subject: [PATCH 52/98] bump

---
 .github/workflows/generic_build.yml | 30 +++++++++++++++--------------
 1 file changed, 16 insertions(+), 14 deletions(-)

diff --git a/.github/workflows/generic_build.yml b/.github/workflows/generic_build.yml
index 84d9e28a..b18a47ff 100644
--- a/.github/workflows/generic_build.yml
+++ b/.github/workflows/generic_build.yml
@@ -19,19 +19,21 @@ on:
 
 jobs:
   build:
+    name: building
     runs-on: ubuntu-22.04
-  steps:
-  - uses: actions/checkout@v4
-  
-  - name: Set up QEMU
-    uses: docker/setup-qemu-action@v3
-    with:
-      platforms: arm64
 
-  - name: Build
-    id: build
-    run: |
-      set -xeu
-      image_name='${{ inputs.image_name }}${{ inputs.image_prefix }}'
-      image_dir='images/${{ inputs.image_name }}'
-      
+    steps:
+    - uses: actions/checkout@v4
+
+    - name: Set up QEMU
+      uses: docker/setup-qemu-action@v3
+      with:
+        platforms: arm64
+
+    - name: Build
+      id: build
+      run: |
+        set -xeu
+        image_name='${{ inputs.image_name }}${{ inputs.image_prefix }}'
+        image_dir='images/${{ inputs.image_name }}'
+

From 7efe5174813faa1414013d0ce0b2680c77cdc8f9 Mon Sep 17 00:00:00 2001
From: Ryan Dale <ryan.dale@nih.gov>
Date: Tue, 30 Jan 2024 14:23:22 -0500
Subject: [PATCH 53/98] add version

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

diff --git a/.github/workflows/caller.yml b/.github/workflows/caller.yml
index 67ef0a3b..aff1445b 100644
--- a/.github/workflows/caller.yml
+++ b/.github/workflows/caller.yml
@@ -6,7 +6,7 @@ on:
 
 jobs:
   call-generic-build:
-    uses: bioconda/bioconda-containers/.github/workflows/generic_build.yml
+    uses: bioconda/bioconda-containers/.github/workflows/generic_build.yml@reusable-workflow-testing
     with:
       image_name: example-image
       tags: 'major.minor latest'

From a135954e8c64a1b378a93c87bdb9062f6812949c Mon Sep 17 00:00:00 2001
From: Ryan Dale <ryan.dale@nih.gov>
Date: Tue, 30 Jan 2024 14:24:22 -0500
Subject: [PATCH 54/98] bump

---
 .github/workflows/generic_build.yml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/.github/workflows/generic_build.yml b/.github/workflows/generic_build.yml
index b18a47ff..227e8172 100644
--- a/.github/workflows/generic_build.yml
+++ b/.github/workflows/generic_build.yml
@@ -36,4 +36,6 @@ jobs:
         set -xeu
         image_name='${{ inputs.image_name }}${{ inputs.image_prefix }}'
         image_dir='images/${{ inputs.image_name }}'
+        echo $image_name
+        echo $image_dir
 

From a420a4fd02c64414ab63de4e33de727e470b4fee Mon Sep 17 00:00:00 2001
From: Ryan Dale <ryan.dale@nih.gov>
Date: Tue, 30 Jan 2024 14:25:48 -0500
Subject: [PATCH 55/98] bump

---
 .github/workflows/caller.yml        | 4 +++-
 .github/workflows/generic_build.yml | 2 +-
 2 files changed, 4 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/caller.yml b/.github/workflows/caller.yml
index aff1445b..112d0378 100644
--- a/.github/workflows/caller.yml
+++ b/.github/workflows/caller.yml
@@ -6,8 +6,10 @@ on:
 
 jobs:
   call-generic-build:
+    env:
+      image_name: example-image
     uses: bioconda/bioconda-containers/.github/workflows/generic_build.yml@reusable-workflow-testing
     with:
-      image_name: example-image
+      image_name: ${{ env.image_name }}
       tags: 'major.minor latest'
 
diff --git a/.github/workflows/generic_build.yml b/.github/workflows/generic_build.yml
index 227e8172..49c3557e 100644
--- a/.github/workflows/generic_build.yml
+++ b/.github/workflows/generic_build.yml
@@ -19,7 +19,7 @@ on:
 
 jobs:
   build:
-    name: building
+    name: Generic build
     runs-on: ubuntu-22.04
 
     steps:

From 02847d6095de182cfab6f24ca0f9f15f016f7b55 Mon Sep 17 00:00:00 2001
From: Ryan Dale <ryan.dale@nih.gov>
Date: Tue, 30 Jan 2024 14:30:41 -0500
Subject: [PATCH 56/98] bump

---
 .github/workflows/caller.yml | 11 +++++++----
 1 file changed, 7 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/caller.yml b/.github/workflows/caller.yml
index 112d0378..811fb196 100644
--- a/.github/workflows/caller.yml
+++ b/.github/workflows/caller.yml
@@ -5,11 +5,14 @@ on:
     - .github/workflows/caller.yml
 
 jobs:
-  call-generic-build:
-    env:
-      image_name: example-image
+  build-image-1:
     uses: bioconda/bioconda-containers/.github/workflows/generic_build.yml@reusable-workflow-testing
     with:
-      image_name: ${{ env.image_name }}
+      image_name: image-1
       tags: 'major.minor latest'
 
+build-image-2:
+    uses: bioconda/bioconda-containers/.github/workflows/generic_build.yml@reusable-workflow-testing
+    with:
+      image_name: image-2
+      tags: 'major.minor latest'

From 5f45578efdaeb274f7129be099b9f32c07e4680a Mon Sep 17 00:00:00 2001
From: Ryan Dale <ryan.dale@nih.gov>
Date: Tue, 30 Jan 2024 14:31:07 -0500
Subject: [PATCH 57/98] bump

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

diff --git a/.github/workflows/caller.yml b/.github/workflows/caller.yml
index 811fb196..3c8f5d22 100644
--- a/.github/workflows/caller.yml
+++ b/.github/workflows/caller.yml
@@ -11,7 +11,7 @@ jobs:
       image_name: image-1
       tags: 'major.minor latest'
 
-build-image-2:
+  build-image-2:
     uses: bioconda/bioconda-containers/.github/workflows/generic_build.yml@reusable-workflow-testing
     with:
       image_name: image-2

From 2b029c4d23048c57c9ffe72a2dd4c486a1e807a1 Mon Sep 17 00:00:00 2001
From: Ryan Dale <ryan.dale@nih.gov>
Date: Tue, 30 Jan 2024 14:36:42 -0500
Subject: [PATCH 58/98] bump

---
 .github/workflows/caller.yml        | 13 ++++---------
 .github/workflows/generic_build.yml | 25 +++++++++++++++++++++++++
 2 files changed, 29 insertions(+), 9 deletions(-)

diff --git a/.github/workflows/caller.yml b/.github/workflows/caller.yml
index 3c8f5d22..5bb94c4e 100644
--- a/.github/workflows/caller.yml
+++ b/.github/workflows/caller.yml
@@ -5,14 +5,9 @@ on:
     - .github/workflows/caller.yml
 
 jobs:
-  build-image-1:
+  create-env:
     uses: bioconda/bioconda-containers/.github/workflows/generic_build.yml@reusable-workflow-testing
     with:
-      image_name: image-1
-      tags: 'major.minor latest'
-
-  build-image-2:
-    uses: bioconda/bioconda-containers/.github/workflows/generic_build.yml@reusable-workflow-testing
-    with:
-      image_name: image-2
-      tags: 'major.minor latest'
+      image_name: base-glibc-debian-bash
+      tags: '3.1 3 latest'
+      debian_version: '12.2'
diff --git a/.github/workflows/generic_build.yml b/.github/workflows/generic_build.yml
index 49c3557e..f13a8c0c 100644
--- a/.github/workflows/generic_build.yml
+++ b/.github/workflows/generic_build.yml
@@ -36,6 +36,31 @@ jobs:
         set -xeu
         image_name='${{ inputs.image_name }}${{ inputs.image_prefix }}'
         image_dir='images/${{ inputs.image_name }}'
+        tags='${{ inputs.tags }}'
         echo $image_name
         echo $image_dir
+        echo $tags
+
+        # Adds image and tags to outputs which can be used in later steps.
+        printf %s\\n \
+          "image_dir=${image_dir}" \
+          "image_name=${image_name}" \
+          "tags=$( echo ${tags} )" \
+          >> $GITHUB_OUTPUT
+
+        cd $image_dir
+        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 \
+            --arch="${arch}" \
+            --iidfile="${iidfile}" \
+            --build-arg=debian_version='${{ env.DEBIAN_VERSION }}'
+          image_id="$( cat "${iidfile}" )"
+          rm "${iidfile}"
 

From 082cf5bf3405abb0d4d871f5c8dd57dc1e577592 Mon Sep 17 00:00:00 2001
From: Ryan Dale <ryan.dale@nih.gov>
Date: Tue, 30 Jan 2024 14:38:09 -0500
Subject: [PATCH 59/98] bump

---
 .github/workflows/generic_build.yml | 34 +++++++++++++++++++++++++++++
 1 file changed, 34 insertions(+)

diff --git a/.github/workflows/generic_build.yml b/.github/workflows/generic_build.yml
index f13a8c0c..f448e50b 100644
--- a/.github/workflows/generic_build.yml
+++ b/.github/workflows/generic_build.yml
@@ -64,3 +64,37 @@ 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="$( run cat /.deb.lst | tr '\n' '|' | sed 's/|$//' )"
+          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' )"
+          debian="$( run cat /etc/debian_version | sed '1!d' )"
+          bash="$( 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}" \
+            --label=debian="${debian}" \
+            --label=bash="${bash}" \
+            --label=deb-list="${deb_list}" \
+            --label=pkg-list="${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}" \
+              "${image_name}:${tag}-${arch}"
+            buildah manifest add \
+              "${image_name}:${tag}" \
+              "${image_id}"
+          done
+        done

From a250b8f2e645912ffa6d4d9445705716a6c2267a Mon Sep 17 00:00:00 2001
From: Ryan Dale <ryan.dale@nih.gov>
Date: Tue, 30 Jan 2024 14:40:55 -0500
Subject: [PATCH 60/98] bump

---
 .github/workflows/generic_build.yml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/.github/workflows/generic_build.yml b/.github/workflows/generic_build.yml
index f448e50b..77f8f89d 100644
--- a/.github/workflows/generic_build.yml
+++ b/.github/workflows/generic_build.yml
@@ -37,6 +37,7 @@ jobs:
         image_name='${{ inputs.image_name }}${{ inputs.image_prefix }}'
         image_dir='images/${{ inputs.image_name }}'
         tags='${{ inputs.tags }}'
+        debian_version='${{ inputs.debian_version }}'
         echo $image_name
         echo $image_dir
         echo $tags
@@ -98,3 +99,4 @@ jobs:
               "${image_id}"
           done
         done
+

From 3f7ff8811f87186085e5c0912681c8115ecddc77 Mon Sep 17 00:00:00 2001
From: Ryan Dale <ryan.dale@nih.gov>
Date: Tue, 30 Jan 2024 14:42:23 -0500
Subject: [PATCH 61/98] bump

---
 .github/workflows/generic_build.yml | 30 +++++++++++++++++++++++++++--
 1 file changed, 28 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/generic_build.yml b/.github/workflows/generic_build.yml
index 77f8f89d..e427e794 100644
--- a/.github/workflows/generic_build.yml
+++ b/.github/workflows/generic_build.yml
@@ -37,7 +37,6 @@ jobs:
         image_name='${{ inputs.image_name }}${{ inputs.image_prefix }}'
         image_dir='images/${{ inputs.image_name }}'
         tags='${{ inputs.tags }}'
-        debian_version='${{ inputs.debian_version }}'
         echo $image_name
         echo $image_dir
         echo $tags
@@ -61,7 +60,7 @@ jobs:
           buildah bud \
             --arch="${arch}" \
             --iidfile="${iidfile}" \
-            --build-arg=debian_version='${{ env.DEBIAN_VERSION }}'
+            --build-arg=debian_version='${{ inputs.debian_version }}'
           image_id="$( cat "${iidfile}" )"
           rm "${iidfile}"
 
@@ -100,3 +99,30 @@ jobs:
           done
         done
 
+    - name: Test
+      run: |
+        image_name='${{ inputs.image_name }}'
+        image_dir='${{ inputs.image_dir }}'
+
+        # Extract image ids from manifest to test.
+        ids="$(
+          for tag in ${{ inputs.tags }} ; do
+            buildah manifest inspect "${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="${id}" \
+            --file=Dockerfile.test \
+            "${image_dir}"
+        done
+        buildah rmi --prune || true

From 4f3e455f878e8cc76f65c6445c0c02c811f1aa57 Mon Sep 17 00:00:00 2001
From: Ryan Dale <ryan.dale@nih.gov>
Date: Tue, 30 Jan 2024 14:47:09 -0500
Subject: [PATCH 62/98] bump

---
 .github/workflows/generic_build.yml | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/generic_build.yml b/.github/workflows/generic_build.yml
index e427e794..b3589f17 100644
--- a/.github/workflows/generic_build.yml
+++ b/.github/workflows/generic_build.yml
@@ -53,6 +53,9 @@ jobs:
           buildah manifest create "${image_name}:${tag}"
         done
 
+        if '${{ inputs.debian_version }}'; then
+          BUILD_ARGS="--build"'${{ inputs_debian_version }}'
+
         # --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
@@ -101,13 +104,14 @@ jobs:
 
     - name: Test
       run: |
+        set -xeu
         image_name='${{ inputs.image_name }}'
         image_dir='${{ inputs.image_dir }}'
 
         # Extract image ids from manifest to test.
         ids="$(
           for tag in ${{ inputs.tags }} ; do
-            buildah manifest inspect "${image}:${tag}" \
+            buildah manifest inspect "${image_name}:${tag}" \
               | jq -r '.manifests[]|.digest' \
               | while read id ; do
                   buildah images --format '{{.ID}}{{.Digest}}' \

From 6105f7b5f62176493175b4175ff2e489c0811ed3 Mon Sep 17 00:00:00 2001
From: Ryan Dale <ryan.dale@nih.gov>
Date: Tue, 30 Jan 2024 15:26:23 -0500
Subject: [PATCH 63/98] bump

---
 .github/workflows/generic_build.yml | 12 ++++++++----
 1 file changed, 8 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/generic_build.yml b/.github/workflows/generic_build.yml
index b3589f17..1b14d34b 100644
--- a/.github/workflows/generic_build.yml
+++ b/.github/workflows/generic_build.yml
@@ -52,9 +52,13 @@ jobs:
         for tag in ${tags} ; do
           buildah manifest create "${image_name}:${tag}"
         done
-
-        if '${{ inputs.debian_version }}'; then
-          BUILD_ARGS="--build"'${{ inputs_debian_version }}'
+        debian_version='${{ inputs.debian_version }}'
+        busybox_version='${{ inputs.busybox_version }}'
+        echo "Busybox: $busybox_version"
+        BUILD_ARGS=""
+        if [ ! -z "${debian_version}" ]; then
+          BUILD_ARGS="--build=$debian_version"
+        fi
 
         # --iidfile prints the built image ID to the specified file. This is
         # used so we can refer to the image in later steps.
@@ -63,7 +67,7 @@ jobs:
           buildah bud \
             --arch="${arch}" \
             --iidfile="${iidfile}" \
-            --build-arg=debian_version='${{ inputs.debian_version }}'
+            $BUILD_ARGS
           image_id="$( cat "${iidfile}" )"
           rm "${iidfile}"
 

From 4a4d66ef06f0103e3f397b1d562f4301aec68321 Mon Sep 17 00:00:00 2001
From: Ryan Dale <ryan.dale@nih.gov>
Date: Tue, 30 Jan 2024 15:28:39 -0500
Subject: [PATCH 64/98] bump

---
 .github/workflows/generic_build.yml | 16 +++++++++-------
 1 file changed, 9 insertions(+), 7 deletions(-)

diff --git a/.github/workflows/generic_build.yml b/.github/workflows/generic_build.yml
index 1b14d34b..d2a3c77e 100644
--- a/.github/workflows/generic_build.yml
+++ b/.github/workflows/generic_build.yml
@@ -34,12 +34,16 @@ jobs:
       id: build
       run: |
         set -xeu
+
+        # Store provided inputs as local vars
         image_name='${{ inputs.image_name }}${{ inputs.image_prefix }}'
         image_dir='images/${{ inputs.image_name }}'
         tags='${{ inputs.tags }}'
-        echo $image_name
-        echo $image_dir
-        echo $tags
+        debian_version='${{ inputs.debian_version }}'
+        busybox_version='${{ inputs.busybox_version }}'
+
+        # FIXME: just used for testing to see if we get default values
+        echo "Busybox: $busybox_version"
 
         # Adds image and tags to outputs which can be used in later steps.
         printf %s\\n \
@@ -52,12 +56,10 @@ jobs:
         for tag in ${tags} ; do
           buildah manifest create "${image_name}:${tag}"
         done
-        debian_version='${{ inputs.debian_version }}'
-        busybox_version='${{ inputs.busybox_version }}'
-        echo "Busybox: $busybox_version"
+
         BUILD_ARGS=""
         if [ ! -z "${debian_version}" ]; then
-          BUILD_ARGS="--build=$debian_version"
+          BUILD_ARGS="--build-arg=debian_version=$debian_version"
         fi
 
         # --iidfile prints the built image ID to the specified file. This is

From 9cdbcec6a91fa4ec70a44c6bc6ad7f976fe7500e Mon Sep 17 00:00:00 2001
From: Ryan Dale <ryan.dale@nih.gov>
Date: Tue, 30 Jan 2024 15:43:48 -0500
Subject: [PATCH 65/98] bump

---
 .github/workflows/caller.yml        | 11 ++++++++--
 .github/workflows/generic_build.yml | 34 ++++++++++++++---------------
 2 files changed, 25 insertions(+), 20 deletions(-)

diff --git a/.github/workflows/caller.yml b/.github/workflows/caller.yml
index 5bb94c4e..6dd3bdaa 100644
--- a/.github/workflows/caller.yml
+++ b/.github/workflows/caller.yml
@@ -5,9 +5,16 @@ on:
     - .github/workflows/caller.yml
 
 jobs:
-  create-env:
+  base-glibc-debian-bash:
     uses: bioconda/bioconda-containers/.github/workflows/generic_build.yml@reusable-workflow-testing
     with:
       image_name: base-glibc-debian-bash
       tags: '3.1 3 latest'
-      debian_version: '12.2'
+      build_args: '--build-arg=debian_version=12.2'
+
+  base-glibc-debian-bash:
+    uses: bioconda/bioconda-containers/.github/workflows/generic_build.yml@reusable-workflow-testing
+    with:
+      image_name: base-glibc-busybox-bash
+      tags: '3.1 3 latest'
+      build_args: '--build-arg=debian_version=12.2 --build-arg=busybox_version=1.36.1'
diff --git a/.github/workflows/generic_build.yml b/.github/workflows/generic_build.yml
index d2a3c77e..ed810f73 100644
--- a/.github/workflows/generic_build.yml
+++ b/.github/workflows/generic_build.yml
@@ -7,15 +7,15 @@ on:
       tags:
         required: true
         type: string
-      busybox_version:
-        required: false
-        type: string
-      debian_version:
+      build_args:
         required: false
         type: string
       image_prefix:
         required: false
         type: string
+      archs:  # space-separated list of architectures, e.g., "arm64 amd64"
+        required: true
+        type: string
 
 jobs:
   build:
@@ -39,11 +39,8 @@ jobs:
         image_name='${{ inputs.image_name }}${{ inputs.image_prefix }}'
         image_dir='images/${{ inputs.image_name }}'
         tags='${{ inputs.tags }}'
-        debian_version='${{ inputs.debian_version }}'
-        busybox_version='${{ inputs.busybox_version }}'
-
-        # FIXME: just used for testing to see if we get default values
-        echo "Busybox: $busybox_version"
+        archs='${{ inputs.archs }}'
+        build_args='${{ inputs.build_args }}'
 
         # Adds image and tags to outputs which can be used in later steps.
         printf %s\\n \
@@ -52,24 +49,22 @@ jobs:
           "tags=$( echo ${tags} )" \
           >> $GITHUB_OUTPUT
 
+        # Dockerfile lives here
         cd $image_dir
+
         for tag in ${tags} ; do
           buildah manifest create "${image_name}:${tag}"
         done
 
-        BUILD_ARGS=""
-        if [ ! -z "${debian_version}" ]; then
-          BUILD_ARGS="--build-arg=debian_version=$debian_version"
-        fi
 
         # --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
+        for arch in $archs ; do
           iidfile="$( mktemp )"
           buildah bud \
             --arch="${arch}" \
             --iidfile="${iidfile}" \
-            $BUILD_ARGS
+            $build_args
           image_id="$( cat "${iidfile}" )"
           rm "${iidfile}"
 
@@ -111,10 +106,12 @@ jobs:
     - name: Test
       run: |
         set -xeu
+
+        # Store inputs as local variables
         image_name='${{ inputs.image_name }}'
-        image_dir='${{ inputs.image_dir }}'
+        image_dir="images/${image_name}"
 
-        # Extract image ids from manifest to test.
+        # Extract image IDs from the manifest built in the last step
         ids="$(
           for tag in ${{ inputs.tags }} ; do
             buildah manifest inspect "${image_name}:${tag}" \
@@ -126,7 +123,8 @@ jobs:
           done
           )"
 
-        # See Dockerfile.test for actual tests run
+        # Run the tests; see Dockerfile.test in the relevant image dir for the
+        # actual tests run
         ids="$( printf %s "${ids}" | sort -u )"
         for id in ${ids} ; do
           podman history "${id}"

From ae59451b55bca7213bb00e2e42f4590f49e1a03d Mon Sep 17 00:00:00 2001
From: Ryan Dale <ryan.dale@nih.gov>
Date: Tue, 30 Jan 2024 15:44:19 -0500
Subject: [PATCH 66/98] bump

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

diff --git a/.github/workflows/caller.yml b/.github/workflows/caller.yml
index 6dd3bdaa..60abb751 100644
--- a/.github/workflows/caller.yml
+++ b/.github/workflows/caller.yml
@@ -12,7 +12,7 @@ jobs:
       tags: '3.1 3 latest'
       build_args: '--build-arg=debian_version=12.2'
 
-  base-glibc-debian-bash:
+  base-glibc-busybox-bash:
     uses: bioconda/bioconda-containers/.github/workflows/generic_build.yml@reusable-workflow-testing
     with:
       image_name: base-glibc-busybox-bash

From d3f9140a61a98152013a6e9ee844a3628700432c Mon Sep 17 00:00:00 2001
From: Ryan Dale <ryan.dale@nih.gov>
Date: Tue, 30 Jan 2024 15:44:57 -0500
Subject: [PATCH 67/98] bump

---
 .github/workflows/caller.yml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/.github/workflows/caller.yml b/.github/workflows/caller.yml
index 60abb751..83495beb 100644
--- a/.github/workflows/caller.yml
+++ b/.github/workflows/caller.yml
@@ -11,6 +11,7 @@ jobs:
       image_name: base-glibc-debian-bash
       tags: '3.1 3 latest'
       build_args: '--build-arg=debian_version=12.2'
+      archs: 'amd64'
 
   base-glibc-busybox-bash:
     uses: bioconda/bioconda-containers/.github/workflows/generic_build.yml@reusable-workflow-testing
@@ -18,3 +19,4 @@ jobs:
       image_name: base-glibc-busybox-bash
       tags: '3.1 3 latest'
       build_args: '--build-arg=debian_version=12.2 --build-arg=busybox_version=1.36.1'
+      archs: 'amd64'

From 855a94ca78c64b73a2b92355b0c3de545d33446f Mon Sep 17 00:00:00 2001
From: Ryan Dale <ryan.dale@nih.gov>
Date: Tue, 30 Jan 2024 15:53:21 -0500
Subject: [PATCH 68/98] bump

---
 .github/workflows/generic_build.yml | 36 +++++++++++++++++++++++++----
 1 file changed, 31 insertions(+), 5 deletions(-)

diff --git a/.github/workflows/generic_build.yml b/.github/workflows/generic_build.yml
index ed810f73..aac8f681 100644
--- a/.github/workflows/generic_build.yml
+++ b/.github/workflows/generic_build.yml
@@ -7,7 +7,10 @@ on:
       tags:
         required: true
         type: string
-      build_args:
+      busybox_version:
+        required: false
+        type: string
+      debian_version:
         required: false
         type: string
       image_prefix:
@@ -39,8 +42,9 @@ jobs:
         image_name='${{ inputs.image_name }}${{ inputs.image_prefix }}'
         image_dir='images/${{ inputs.image_name }}'
         tags='${{ inputs.tags }}'
+        debian_version='${{ inputs.debian_version }}'
+        busybox_version='${{ inputs.busybox_version }}'
         archs='${{ inputs.archs }}'
-        build_args='${{ inputs.build_args }}'
 
         # Adds image and tags to outputs which can be used in later steps.
         printf %s\\n \
@@ -56,15 +60,37 @@ jobs:
           buildah manifest create "${image_name}:${tag}"
         done
 
+        # Incrementally compose build args. Using this 
+        BUILD_ARGS=""
+        if [ ! -z "${debian_version}" ]; then
+          BUILD_ARGS=$(echo $BUILD_ARGS "--build-arg=debian_version=$debian_version")
+        fi
+
+        # If busybox_version was specified, assume we are making a busybox image.
+        if [ ! -z "${busybox_version}" ]; then
+          BUILD_ARGS=$(echo $BUILD_ARGS "--build-arg=busybox_version=$busybox_version")
+
+          # Make a busybox image that we'll use further below.
+          # --iidfile prints the built image ID to the specified file so we can
+          # refer to the image later
+          iidfile="$( mktemp )"
+          buildah bud \
+            --iidfile="${iidfile}" \
+            --file=Dockerfile.busybox \
+            $BUILD_ARGS
+          busybox_image="$( cat "${iidfile}" )"
+          rm "${iidfile}"
+
+          # And then extend the build args with this image.
+          BUILD_ARGS=$(echo $BUILD_ARGS "--build-arg=busybox_image=${busybox_image}")
+        fi
 
-        # --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 $archs ; do
           iidfile="$( mktemp )"
           buildah bud \
             --arch="${arch}" \
             --iidfile="${iidfile}" \
-            $build_args
+            $BUILD_ARGS
           image_id="$( cat "${iidfile}" )"
           rm "${iidfile}"
 

From 447d5d42093785735e052e63d2441cc806004790 Mon Sep 17 00:00:00 2001
From: Ryan Dale <ryan.dale@nih.gov>
Date: Tue, 30 Jan 2024 15:54:01 -0500
Subject: [PATCH 69/98] bump

---
 .github/workflows/caller.yml | 9 +++++----
 1 file changed, 5 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/caller.yml b/.github/workflows/caller.yml
index 83495beb..54cb2b02 100644
--- a/.github/workflows/caller.yml
+++ b/.github/workflows/caller.yml
@@ -10,13 +10,14 @@ jobs:
     with:
       image_name: base-glibc-debian-bash
       tags: '3.1 3 latest'
-      build_args: '--build-arg=debian_version=12.2'
-      archs: 'amd64'
+      debian_version: '12.2'
+      archs: 'arm64'
 
-  base-glibc-busybox-bash:
+  base-glibc-debian-bash:
     uses: bioconda/bioconda-containers/.github/workflows/generic_build.yml@reusable-workflow-testing
     with:
       image_name: base-glibc-busybox-bash
       tags: '3.1 3 latest'
-      build_args: '--build-arg=debian_version=12.2 --build-arg=busybox_version=1.36.1'
+      debian_version: '12.2'
+      busybox_version: '1.36.1'
       archs: 'amd64'

From 2372f15e1f99d38c660f07dfadcbc8c8844e7faa Mon Sep 17 00:00:00 2001
From: Ryan Dale <ryan.dale@nih.gov>
Date: Tue, 30 Jan 2024 15:55:17 -0500
Subject: [PATCH 70/98] bump

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

diff --git a/.github/workflows/caller.yml b/.github/workflows/caller.yml
index 54cb2b02..3f77a463 100644
--- a/.github/workflows/caller.yml
+++ b/.github/workflows/caller.yml
@@ -13,7 +13,7 @@ jobs:
       debian_version: '12.2'
       archs: 'arm64'
 
-  base-glibc-debian-bash:
+  base-glibc-busybox-bash:
     uses: bioconda/bioconda-containers/.github/workflows/generic_build.yml@reusable-workflow-testing
     with:
       image_name: base-glibc-busybox-bash

From 000e9469822f1aef6e98f0ae228717185a2539e4 Mon Sep 17 00:00:00 2001
From: Ryan Dale <ryan.dale@nih.gov>
Date: Tue, 30 Jan 2024 17:50:07 -0500
Subject: [PATCH 71/98] bump

---
 .github/workflows/base-glibc-busybox-bash.yml | 16 +++++++++++++
 .github/workflows/base-glibc-debian-bash.yml  | 15 ++++++++++++
 .github/workflows/caller.yml                  | 23 -------------------
 3 files changed, 31 insertions(+), 23 deletions(-)
 create mode 100644 .github/workflows/base-glibc-busybox-bash.yml
 create mode 100644 .github/workflows/base-glibc-debian-bash.yml
 delete mode 100644 .github/workflows/caller.yml

diff --git a/.github/workflows/base-glibc-busybox-bash.yml b/.github/workflows/base-glibc-busybox-bash.yml
new file mode 100644
index 00000000..e5ea9d9d
--- /dev/null
+++ b/.github/workflows/base-glibc-busybox-bash.yml
@@ -0,0 +1,16 @@
+name: "base-glibc-busybox-bash"
+on:
+  pull_request:
+    paths:
+    - .github/workflows/base-glibc-busybox-bash.yml
+    - .github/workflows/generic_build.yml
+
+jobs:
+  base-glibc-busybox-bash:
+    uses: bioconda/bioconda-containers/.github/workflows/generic_build.yml@reusable-workflow-testing
+    with:
+      image_name: base-glibc-busybox-bash
+      tags: '3.1 3 latest'
+      busybox_version: '1.36.1'
+      debian_version: '12.2'
+      archs: 'arm64 amd64'
diff --git a/.github/workflows/base-glibc-debian-bash.yml b/.github/workflows/base-glibc-debian-bash.yml
new file mode 100644
index 00000000..217a69e3
--- /dev/null
+++ b/.github/workflows/base-glibc-debian-bash.yml
@@ -0,0 +1,15 @@
+name: "base-glibc-debian-bash"
+on:
+  pull_request:
+    paths:
+    - .github/workflows/base-glibc-debian-bash.yml
+    - .github/workflows/generic_build.yml
+
+jobs:
+  base-glibc-debian-bash:
+    uses: bioconda/bioconda-containers/.github/workflows/generic_build.yml@reusable-workflow-testing
+    with:
+      image_name: base-glibc-debian-bash
+      tags: '3.1 3 latest'
+      debian_version: '12.2'
+      archs: 'arm64 amd64'
diff --git a/.github/workflows/caller.yml b/.github/workflows/caller.yml
deleted file mode 100644
index 3f77a463..00000000
--- a/.github/workflows/caller.yml
+++ /dev/null
@@ -1,23 +0,0 @@
-name: "Generic caller test"
-on:
-  pull_request:
-    paths:
-    - .github/workflows/caller.yml
-
-jobs:
-  base-glibc-debian-bash:
-    uses: bioconda/bioconda-containers/.github/workflows/generic_build.yml@reusable-workflow-testing
-    with:
-      image_name: base-glibc-debian-bash
-      tags: '3.1 3 latest'
-      debian_version: '12.2'
-      archs: 'arm64'
-
-  base-glibc-busybox-bash:
-    uses: bioconda/bioconda-containers/.github/workflows/generic_build.yml@reusable-workflow-testing
-    with:
-      image_name: base-glibc-busybox-bash
-      tags: '3.1 3 latest'
-      debian_version: '12.2'
-      busybox_version: '1.36.1'
-      archs: 'amd64'

From dedefebf66bb355d439eeda1c3b608b4fb48534a Mon Sep 17 00:00:00 2001
From: Ryan Dale <ryan.dale@nih.gov>
Date: Thu, 1 Feb 2024 13:25:25 -0500
Subject: [PATCH 72/98] now try bioconda-utils image

---
 .../bioconda-utils-build-env-cos7.yml         | 15 ++++
 .github/workflows/generic_build.yml           | 74 +++++++++++++++----
 2 files changed, 73 insertions(+), 16 deletions(-)
 create mode 100644 .github/workflows/bioconda-utils-build-env-cos7.yml

diff --git a/.github/workflows/bioconda-utils-build-env-cos7.yml b/.github/workflows/bioconda-utils-build-env-cos7.yml
new file mode 100644
index 00000000..d96f59e9
--- /dev/null
+++ b/.github/workflows/bioconda-utils-build-env-cos7.yml
@@ -0,0 +1,15 @@
+name: "bioconda-utils-build-env-cos7"
+on:
+  pull_request:
+    paths:
+    - .github/workflows/bioconda-utils-build-env-cos7.yml
+    - .github/workflows/generic_build.yml
+
+jobs:
+  bioconda-utils-build-env-cos7:
+    uses: bioconda/bioconda-containers/.github/workflows/generic_build.yml@reusable-workflow-testing
+    with:
+      image_name: bioconda-utils-build-env-cos7
+      tags: '3.1 3 latest'
+      debian_version: '12.2'
+      archs: 'arm64 amd64'
diff --git a/.github/workflows/generic_build.yml b/.github/workflows/generic_build.yml
index aac8f681..db85ff11 100644
--- a/.github/workflows/generic_build.yml
+++ b/.github/workflows/generic_build.yml
@@ -1,12 +1,17 @@
 on:
   workflow_call:
     inputs:
+      # target image name to build
       image_name:
         required: true
         type: string
+
+      # target tags to build (space-separated)
       tags:
         required: true
         type: string
+
+      # will be passed as a build-arg to Docker
       busybox_version:
         required: false
         type: string
@@ -16,10 +21,16 @@ on:
       image_prefix:
         required: false
         type: string
-      archs:  # space-separated list of architectures, e.g., "arm64 amd64"
+
+      # space-separated list of architectures, e.g., "arm64 amd64"
+      archs: 
         required: true
         type: string
 
+      bioconda_utils:
+        required: false
+        type: boolean
+
 jobs:
   build:
     name: Generic build
@@ -60,15 +71,27 @@ jobs:
           buildah manifest create "${image_name}:${tag}"
         done
 
-        # Incrementally compose build args. Using this 
+        archs_and_images=$archs
+        # ----------------------------------------------------------------------
+        # Incrementally compose build args, depending on which inputs were
+        # provided.
         BUILD_ARGS=""
         if [ ! -z "${debian_version}" ]; then
-          BUILD_ARGS=$(echo $BUILD_ARGS "--build-arg=debian_version=$debian_version")
+          BUILD_ARGS+="--build-arg=debian_version=$debian_version"
+        fi
+
+        if [ '${{ inputs.bioconda_utils }}' ]; then
+        # Due to different nomenclature used by conda-forge and buildah, we
+        # need to map archs to base images.
+          archs_and_images='
+            amd64=quay.io/condaforge/linux-anvil-cos7-x86_64
+            arm64=quay.io/condaforge/linux-anvil-aarch64
+          '
         fi
 
         # If busybox_version was specified, assume we are making a busybox image.
         if [ ! -z "${busybox_version}" ]; then
-          BUILD_ARGS=$(echo $BUILD_ARGS "--build-arg=busybox_version=$busybox_version")
+          BUILD_ARGS+="--build-arg=busybox_version=$busybox_version"
 
           # Make a busybox image that we'll use further below.
           # --iidfile prints the built image ID to the specified file so we can
@@ -82,43 +105,62 @@ jobs:
           rm "${iidfile}"
 
           # And then extend the build args with this image.
-          BUILD_ARGS=$(echo $BUILD_ARGS "--build-arg=busybox_image=${busybox_image}")
+          BUILD_ARGS+="--build-arg=busybox_image=${busybox_image}"
         fi
 
-        for arch in $archs ; do
+        # ----------------------------------------------------------------------
+
+        # Build each arch's image
+        for arch in $arch_and_image ; do
+          arch=$(echo $arch_and_image | cut -f1 -d "=")
+          base_image=$(echo $arch_and_image | cut -f2 -d "=")
           iidfile="$( mktemp )"
           buildah bud \
             --arch="${arch}" \
             --iidfile="${iidfile}" \
+            --build_arg=base_image="${base_image}" \
             $BUILD_ARGS
           image_id="$( cat "${iidfile}" )"
           rm "${iidfile}"
 
-          # Extract various package info and version info to store as labels
+          # Extract various package info and version info...
           container="$( buildah from "${image_id}" )"
           run() { buildah run "${container}" "${@}" ; }
+
+          # Incrementally make labels
+
           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' )"
           debian="$( run cat /etc/debian_version | sed '1!d' )"
           bash="$( run bash --version | sed '1!d' )"
+
           buildah rm "${container}"
 
-          # Store package/version info as labels for the image
+          LABELS=""
+          LABELS+="--label=deb-list=${deb_list} "
+          LABELS+="--label=pkg-list=${pkg_list} "
+          LABELS+="--label=glibc=${glibc} "
+          LABELS+="--label=debian=${debian} "
+          LABELS+="--label=bash=${bash} "
+          if [ '${{ inputs.bioconda_utils }}' ]; then
+            bioconda_utils="$(
+              run sh -c '. /opt/conda/etc/profile.d/conda.sh && conda activate base && bioconda-utils --version' \
+              | rev | cut -f1 -d " " | rev 
+            )"
+            LABELS+="--label=bioconda-utils=${bioconda_utils} "
+          fi
+
+          # ...then store that info as labels for the image
           container="$( buildah from "${image_id}" )"
-          buildah config \
-            --label=glibc="${glibc}" \
-            --label=debian="${debian}" \
-            --label=bash="${bash}" \
-            --label=deb-list="${deb_list}" \
-            --label=pkg-list="${pkg_list}" \
-            "${container}"
+          buildah config $LABELS "${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
+          # Add images to manifest. Individual image tags include arch; manifest does not.
           for tag in ${tags} ; do
             buildah tag \
               "${image_id}" \

From bc1f53dcf5fec731a0aeaf7c3ee5e0c4a66aa94b Mon Sep 17 00:00:00 2001
From: Ryan Dale <ryan.dale@nih.gov>
Date: Thu, 1 Feb 2024 22:28:16 -0500
Subject: [PATCH 73/98] varname

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

diff --git a/.github/workflows/generic_build.yml b/.github/workflows/generic_build.yml
index db85ff11..281fbf81 100644
--- a/.github/workflows/generic_build.yml
+++ b/.github/workflows/generic_build.yml
@@ -111,7 +111,7 @@ jobs:
         # ----------------------------------------------------------------------
 
         # Build each arch's image
-        for arch in $arch_and_image ; do
+        for arch in $archs_and_images ; do
           arch=$(echo $arch_and_image | cut -f1 -d "=")
           base_image=$(echo $arch_and_image | cut -f2 -d "=")
           iidfile="$( mktemp )"

From 2321455976487596acda98f2eac24f09ec22a223 Mon Sep 17 00:00:00 2001
From: Ryan Dale <ryan.dale@nih.gov>
Date: Thu, 1 Feb 2024 22:34:09 -0500
Subject: [PATCH 74/98] separate build arg for image

---
 .github/workflows/generic_build.yml | 9 +++++++--
 1 file changed, 7 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/generic_build.yml b/.github/workflows/generic_build.yml
index 281fbf81..8bba1ad4 100644
--- a/.github/workflows/generic_build.yml
+++ b/.github/workflows/generic_build.yml
@@ -114,12 +114,17 @@ jobs:
         for arch in $archs_and_images ; do
           arch=$(echo $arch_and_image | cut -f1 -d "=")
           base_image=$(echo $arch_and_image | cut -f2 -d "=")
+          BASE_IMAGE_BUILD_ARG=""
+          if [ ! -z "$base_image" ]; then
+            BASE_IMAGE_BUILD_ARG="--build_arg=base_image="${base_image}""
+          fi
+
           iidfile="$( mktemp )"
           buildah bud \
             --arch="${arch}" \
             --iidfile="${iidfile}" \
-            --build_arg=base_image="${base_image}" \
-            $BUILD_ARGS
+            $BUILD_ARGS \
+            $BASE_IMAGE_BUILD_ARG
           image_id="$( cat "${iidfile}" )"
           rm "${iidfile}"
 

From 5989f1b071d12e1812fa0a5990779850393ea611 Mon Sep 17 00:00:00 2001
From: Ryan Dale <ryan.dale@nih.gov>
Date: Fri, 2 Feb 2024 09:23:09 -0500
Subject: [PATCH 75/98] label fixes

---
 .../bioconda-utils-build-env-cos7.yml         |  1 +
 .github/workflows/generic_build.yml           | 44 +++++++++++--------
 2 files changed, 26 insertions(+), 19 deletions(-)

diff --git a/.github/workflows/bioconda-utils-build-env-cos7.yml b/.github/workflows/bioconda-utils-build-env-cos7.yml
index d96f59e9..af548485 100644
--- a/.github/workflows/bioconda-utils-build-env-cos7.yml
+++ b/.github/workflows/bioconda-utils-build-env-cos7.yml
@@ -13,3 +13,4 @@ jobs:
       tags: '3.1 3 latest'
       debian_version: '12.2'
       archs: 'arm64 amd64'
+      bioconda_utils: 'master'
diff --git a/.github/workflows/generic_build.yml b/.github/workflows/generic_build.yml
index 8bba1ad4..12a2f6c7 100644
--- a/.github/workflows/generic_build.yml
+++ b/.github/workflows/generic_build.yml
@@ -56,6 +56,7 @@ jobs:
         debian_version='${{ inputs.debian_version }}'
         busybox_version='${{ inputs.busybox_version }}'
         archs='${{ inputs.archs }}'
+        bioconda_utils='${{ inputs.bioconda_utils }}'
 
         # Adds image and tags to outputs which can be used in later steps.
         printf %s\\n \
@@ -80,7 +81,7 @@ jobs:
           BUILD_ARGS+="--build-arg=debian_version=$debian_version"
         fi
 
-        if [ '${{ inputs.bioconda_utils }}' ]; then
+        if [ ! -z "${bioconda_utils}" ]; then
         # Due to different nomenclature used by conda-forge and buildah, we
         # need to map archs to base images.
           archs_and_images='
@@ -93,7 +94,10 @@ jobs:
         if [ ! -z "${busybox_version}" ]; then
           BUILD_ARGS+="--build-arg=busybox_version=$busybox_version"
 
-          # Make a busybox image that we'll use further below.
+          # Make a busybox image that we'll use further below. As shown in the
+          # Dockerfile.busybox, this uses the build-busybox script which in turn
+          # cross-compiles for x86_64 and aarch64, and these are later copied
+          # into an arch-specific container.
           # --iidfile prints the built image ID to the specified file so we can
           # refer to the image later
           iidfile="$( mktemp )"
@@ -128,38 +132,37 @@ jobs:
           image_id="$( cat "${iidfile}" )"
           rm "${iidfile}"
 
-          # Extract various package info and version info...
+          # Extract various package info and version info, then store that info as labels
           container="$( buildah from "${image_id}" )"
           run() { buildah run "${container}" "${@}" ; }
-
-          # Incrementally make labels
-
           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' )"
           debian="$( run cat /etc/debian_version | sed '1!d' )"
           bash="$( run bash --version | sed '1!d' )"
 
-          buildah rm "${container}"
-
-          LABELS=""
-          LABELS+="--label=deb-list=${deb_list} "
-          LABELS+="--label=pkg-list=${pkg_list} "
-          LABELS+="--label=glibc=${glibc} "
-          LABELS+="--label=debian=${debian} "
-          LABELS+="--label=bash=${bash} "
-          if [ '${{ inputs.bioconda_utils }}' ]; then
+          if [ ! -z "${bioconda_utils}" ]; then
             bioconda_utils="$(
               run sh -c '. /opt/conda/etc/profile.d/conda.sh && conda activate base && bioconda-utils --version' \
               | rev | cut -f1 -d " " | rev 
             )"
-            LABELS+="--label=bioconda-utils=${bioconda_utils} "
+            buildah config --label=bioconda-utils="${bioconda_utils}" ${container}
           fi
 
-          # ...then store that info as labels for the image
+          if [ ! -z "${busybox_version}" ]; then
+            buildah config --label=busybox-version="${busybox_version}"
+          fi
+
+
+          buildah rm "${container}"
           container="$( buildah from "${image_id}" )"
-          buildah config $LABELS "${container}"
+          buildah config \
+            --label=glibc="${glibc}" \
+            --label=debian="${debian}" \
+            --label=bash="${bash}" \
+            --label=deb-list="${deb_list}" \
+            --label=pkg-list="${pkg_list}" \
+            "${container}"
 
           # Store the new image (now with labels)
           image_id="$( buildah commit "${container}" )"
@@ -173,8 +176,11 @@ jobs:
             buildah manifest add \
               "${image_name}:${tag}" \
               "${image_id}"
+
+            buildah inspect -t image ${image_name}:${tag}
           done
         done
+        buidah_inspect -t manifest ${image_name}
 
     - name: Test
       run: |

From 033f85057c31451d61c878c802c893dac6edf78d Mon Sep 17 00:00:00 2001
From: Ryan Dale <ryan.dale@nih.gov>
Date: Fri, 2 Feb 2024 09:30:54 -0500
Subject: [PATCH 76/98] bump

---
 .github/workflows/generic_build.yml | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/.github/workflows/generic_build.yml b/.github/workflows/generic_build.yml
index 12a2f6c7..ed76cfa1 100644
--- a/.github/workflows/generic_build.yml
+++ b/.github/workflows/generic_build.yml
@@ -76,9 +76,9 @@ jobs:
         # ----------------------------------------------------------------------
         # Incrementally compose build args, depending on which inputs were
         # provided.
-        BUILD_ARGS=""
+        BUILD_ARGS=()
         if [ ! -z "${debian_version}" ]; then
-          BUILD_ARGS+="--build-arg=debian_version=$debian_version"
+          BUILD_ARGS+=("--build-arg=debian_version=$debian_version")
         fi
 
         if [ ! -z "${bioconda_utils}" ]; then
@@ -92,7 +92,7 @@ jobs:
 
         # If busybox_version was specified, assume we are making a busybox image.
         if [ ! -z "${busybox_version}" ]; then
-          BUILD_ARGS+="--build-arg=busybox_version=$busybox_version"
+          BUILD_ARGS+=("--build-arg=busybox_version=$busybox_version")
 
           # Make a busybox image that we'll use further below. As shown in the
           # Dockerfile.busybox, this uses the build-busybox script which in turn
@@ -104,12 +104,12 @@ jobs:
           buildah bud \
             --iidfile="${iidfile}" \
             --file=Dockerfile.busybox \
-            $BUILD_ARGS
+            ${BUILD_ARGS[@]}
           busybox_image="$( cat "${iidfile}" )"
           rm "${iidfile}"
 
           # And then extend the build args with this image.
-          BUILD_ARGS+="--build-arg=busybox_image=${busybox_image}"
+          BUILD_ARGS+=("--build-arg=busybox_image=${busybox_image}")
         fi
 
         # ----------------------------------------------------------------------
@@ -127,7 +127,7 @@ jobs:
           buildah bud \
             --arch="${arch}" \
             --iidfile="${iidfile}" \
-            $BUILD_ARGS \
+            ${BUILD_ARGS[@]} \
             $BASE_IMAGE_BUILD_ARG
           image_id="$( cat "${iidfile}" )"
           rm "${iidfile}"

From 88ecc6f03fbeacb1a1803ecec1eb7d3e4227a411 Mon Sep 17 00:00:00 2001
From: Ryan Dale <ryan.dale@nih.gov>
Date: Fri, 2 Feb 2024 09:33:01 -0500
Subject: [PATCH 77/98] bump

---
 .github/workflows/bioconda-utils-build-env-cos7.yml | 2 +-
 .github/workflows/generic_build.yml                 | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/bioconda-utils-build-env-cos7.yml b/.github/workflows/bioconda-utils-build-env-cos7.yml
index af548485..2ec5767f 100644
--- a/.github/workflows/bioconda-utils-build-env-cos7.yml
+++ b/.github/workflows/bioconda-utils-build-env-cos7.yml
@@ -13,4 +13,4 @@ jobs:
       tags: '3.1 3 latest'
       debian_version: '12.2'
       archs: 'arm64 amd64'
-      bioconda_utils: 'master'
+      bioconda_utils: true
diff --git a/.github/workflows/generic_build.yml b/.github/workflows/generic_build.yml
index ed76cfa1..a39101e8 100644
--- a/.github/workflows/generic_build.yml
+++ b/.github/workflows/generic_build.yml
@@ -141,7 +141,7 @@ jobs:
           debian="$( run cat /etc/debian_version | sed '1!d' )"
           bash="$( run bash --version | sed '1!d' )"
 
-          if [ ! -z "${bioconda_utils}" ]; then
+          if [ "${bioconda_utils}" ]; then
             bioconda_utils="$(
               run sh -c '. /opt/conda/etc/profile.d/conda.sh && conda activate base && bioconda-utils --version' \
               | rev | cut -f1 -d " " | rev 

From 07c54d3d3e37b292c5dcce293c2bbeef17c2987f Mon Sep 17 00:00:00 2001
From: Ryan Dale <ryan.dale@nih.gov>
Date: Fri, 2 Feb 2024 09:34:56 -0500
Subject: [PATCH 78/98] bump

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

diff --git a/.github/workflows/generic_build.yml b/.github/workflows/generic_build.yml
index a39101e8..5cf6b97d 100644
--- a/.github/workflows/generic_build.yml
+++ b/.github/workflows/generic_build.yml
@@ -177,10 +177,10 @@ jobs:
               "${image_name}:${tag}" \
               "${image_id}"
 
-            buildah inspect -t image ${image_name}:${tag}
+            # buildah inspect -t image ${image_name}:${tag}
           done
         done
-        buidah_inspect -t manifest ${image_name}
+        # buidah_inspect -t manifest ${image_name}
 
     - name: Test
       run: |

From 5d5e9f1197d3d66713a6b9264dc197c09dadc601 Mon Sep 17 00:00:00 2001
From: Ryan Dale <ryan.dale@nih.gov>
Date: Fri, 2 Feb 2024 09:35:52 -0500
Subject: [PATCH 79/98] bump

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

diff --git a/.github/workflows/generic_build.yml b/.github/workflows/generic_build.yml
index 5cf6b97d..13da4752 100644
--- a/.github/workflows/generic_build.yml
+++ b/.github/workflows/generic_build.yml
@@ -116,8 +116,8 @@ jobs:
 
         # Build each arch's image
         for arch in $archs_and_images ; do
-          arch=$(echo $arch_and_image | cut -f1 -d "=")
-          base_image=$(echo $arch_and_image | cut -f2 -d "=")
+          arch=$(echo $archs_and_images | cut -f1 -d "=")
+          base_image=$(echo $archs_and_images | cut -f2 -d "=")
           BASE_IMAGE_BUILD_ARG=""
           if [ ! -z "$base_image" ]; then
             BASE_IMAGE_BUILD_ARG="--build_arg=base_image="${base_image}""

From 432b9a6fd4617fa991d75d98384d6ae24a822c18 Mon Sep 17 00:00:00 2001
From: Ryan Dale <ryan.dale@nih.gov>
Date: Fri, 2 Feb 2024 09:39:34 -0500
Subject: [PATCH 80/98] bump

---
 .github/workflows/generic_build.yml | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/generic_build.yml b/.github/workflows/generic_build.yml
index 13da4752..e8918a2e 100644
--- a/.github/workflows/generic_build.yml
+++ b/.github/workflows/generic_build.yml
@@ -84,10 +84,10 @@ jobs:
         if [ ! -z "${bioconda_utils}" ]; then
         # Due to different nomenclature used by conda-forge and buildah, we
         # need to map archs to base images.
-          archs_and_images='
-            amd64=quay.io/condaforge/linux-anvil-cos7-x86_64
-            arm64=quay.io/condaforge/linux-anvil-aarch64
-          '
+          archs_and_images=(
+            "amd64=quay.io/condaforge/linux-anvil-cos7-x86_64",
+            "arm64=quay.io/condaforge/linux-anvil-aarch64"
+          )
         fi
 
         # If busybox_version was specified, assume we are making a busybox image.

From 8ef2c10c931c77c0a92dcef68dea017aa2c66efd Mon Sep 17 00:00:00 2001
From: Ryan Dale <ryan.dale@nih.gov>
Date: Fri, 2 Feb 2024 10:49:54 -0500
Subject: [PATCH 81/98] bump

---
 .github/workflows/generic_build.yml | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/generic_build.yml b/.github/workflows/generic_build.yml
index e8918a2e..b50deddf 100644
--- a/.github/workflows/generic_build.yml
+++ b/.github/workflows/generic_build.yml
@@ -15,9 +15,11 @@ on:
       busybox_version:
         required: false
         type: string
+
       debian_version:
         required: false
         type: string
+
       image_prefix:
         required: false
         type: string
@@ -50,7 +52,7 @@ jobs:
         set -xeu
 
         # Store provided inputs as local vars
-        image_name='${{ inputs.image_name }}${{ inputs.image_prefix }}'
+        image_name='${{ inputs.image_prefix }}${{ inputs.image_name }}'
         image_dir='images/${{ inputs.image_name }}'
         tags='${{ inputs.tags }}'
         debian_version='${{ inputs.debian_version }}'
@@ -85,7 +87,7 @@ jobs:
         # Due to different nomenclature used by conda-forge and buildah, we
         # need to map archs to base images.
           archs_and_images=(
-            "amd64=quay.io/condaforge/linux-anvil-cos7-x86_64",
+            "amd64=quay.io/condaforge/linux-anvil-cos7-x86_64"
             "arm64=quay.io/condaforge/linux-anvil-aarch64"
           )
         fi

From 8544b9a4f1c23227074bf1d9513a7806914d626e Mon Sep 17 00:00:00 2001
From: Ryan Dale <ryan.dale@nih.gov>
Date: Fri, 2 Feb 2024 11:04:34 -0500
Subject: [PATCH 82/98] bump

---
 .github/workflows/generic_build.yml | 10 ++++++----
 1 file changed, 6 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/generic_build.yml b/.github/workflows/generic_build.yml
index b50deddf..5dbb8744 100644
--- a/.github/workflows/generic_build.yml
+++ b/.github/workflows/generic_build.yml
@@ -154,9 +154,11 @@ jobs:
           if [ ! -z "${busybox_version}" ]; then
             buildah config --label=busybox-version="${busybox_version}"
           fi
-
-
           buildah rm "${container}"
+
+          # TODO: use array for labels, and make sure this next container is
+        # the one getting the labels (above, bioconda-utils is added to the
+        # first container which is then rmed)
           container="$( buildah from "${image_id}" )"
           buildah config \
             --label=glibc="${glibc}" \
@@ -179,10 +181,10 @@ jobs:
               "${image_name}:${tag}" \
               "${image_id}"
 
-            # buildah inspect -t image ${image_name}:${tag}
+            buildah inspect -t image ${image_name}:${tag}
           done
         done
-        # buidah_inspect -t manifest ${image_name}
+        buidah inspect -t manifest ${image_name}
 
     - name: Test
       run: |

From 5bdc847be8a5ea6cdedc0b842a1a7069c0f2571d Mon Sep 17 00:00:00 2001
From: Ryan Dale <ryan.dale@nih.gov>
Date: Fri, 2 Feb 2024 11:05:30 -0500
Subject: [PATCH 83/98] bump

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

diff --git a/.github/workflows/generic_build.yml b/.github/workflows/generic_build.yml
index 5dbb8744..e03003c4 100644
--- a/.github/workflows/generic_build.yml
+++ b/.github/workflows/generic_build.yml
@@ -122,7 +122,7 @@ jobs:
           base_image=$(echo $archs_and_images | cut -f2 -d "=")
           BASE_IMAGE_BUILD_ARG=""
           if [ ! -z "$base_image" ]; then
-            BASE_IMAGE_BUILD_ARG="--build_arg=base_image="${base_image}""
+            BASE_IMAGE_BUILD_ARG="--build-arg=base_image="${base_image}""
           fi
 
           iidfile="$( mktemp )"

From befacb87b22dddc0c060c77d0188f67fd128b250 Mon Sep 17 00:00:00 2001
From: Ryan Dale <ryan.dale@nih.gov>
Date: Fri, 2 Feb 2024 11:26:56 -0500
Subject: [PATCH 84/98] bump

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

diff --git a/.github/workflows/generic_build.yml b/.github/workflows/generic_build.yml
index e03003c4..04b733da 100644
--- a/.github/workflows/generic_build.yml
+++ b/.github/workflows/generic_build.yml
@@ -184,7 +184,7 @@ jobs:
             buildah inspect -t image ${image_name}:${tag}
           done
         done
-        buidah inspect -t manifest ${image_name}
+        buildah inspect -t manifest ${image_name}
 
     - name: Test
       run: |

From a1fd5d2c84723570927911de432e107f6c2afb72 Mon Sep 17 00:00:00 2001
From: Ryan Dale <ryan.dale@nih.gov>
Date: Fri, 2 Feb 2024 11:38:14 -0500
Subject: [PATCH 85/98] bump

---
 .github/workflows/generic_build.yml | 36 +++++++++++++----------------
 1 file changed, 16 insertions(+), 20 deletions(-)

diff --git a/.github/workflows/generic_build.yml b/.github/workflows/generic_build.yml
index 04b733da..7603ac80 100644
--- a/.github/workflows/generic_build.yml
+++ b/.github/workflows/generic_build.yml
@@ -134,41 +134,37 @@ jobs:
           image_id="$( cat "${iidfile}" )"
           rm "${iidfile}"
 
-          # Extract various package info and version info, then store that info as labels
+          # Extract various package info and version info, then store that info
+          # as labels. Container is removed at the end to avoid e.g. having these
+          # commands in the history of the container.
           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' )"
-          debian="$( run cat /etc/debian_version | sed '1!d' )"
-          bash="$( run bash --version | sed '1!d' )"
+          LABELS=()
+          LABELS+=("--label=deb-list=\"$( run cat /.deb.lst | tr '\n' '|' | sed 's/|$//' )\"")
+          LABELS+=("--label=pkg-list=\"$( run cat /.pkg.lst | tr '\n' '|' | sed 's/|$//' )\"")
+          LABELS+=("--label=glibc=\"$( run sh -c 'exec "$( find -xdev -name libc.so.6 -print -quit )"' | sed '1!d' )\"")
+          LABELS+=("--label=debian=\"$( run cat /etc/debian_version | sed '1!d' )\"")
+          LABELS+=("--label=bash=\"$( run bash --version | sed '1!d' )\"")
 
           if [ "${bioconda_utils}" ]; then
             bioconda_utils="$(
               run sh -c '. /opt/conda/etc/profile.d/conda.sh && conda activate base && bioconda-utils --version' \
               | rev | cut -f1 -d " " | rev 
             )"
-            buildah config --label=bioconda-utils="${bioconda_utils}" ${container}
+            LABELS+=("--label=\"${bioconda_utils}\"")
           fi
 
           if [ ! -z "${busybox_version}" ]; then
-            buildah config --label=busybox-version="${busybox_version}"
+            LABELS+=("--label=busybox-version=\"${busybox_version}\"")
           fi
           buildah rm "${container}"
 
-          # TODO: use array for labels, and make sure this next container is
-        # the one getting the labels (above, bioconda-utils is added to the
-        # first container which is then rmed)
+          # Add labels to a new container...
           container="$( buildah from "${image_id}" )"
-          buildah config \
-            --label=glibc="${glibc}" \
-            --label=debian="${debian}" \
-            --label=bash="${bash}" \
-            --label=deb-list="${deb_list}" \
-            --label=pkg-list="${pkg_list}" \
-            "${container}"
-
-          # Store the new image (now with labels)
+          buildah config ${LABELS[@]} "${container}"
+
+          # ...then store the container (now with labels) as a new image. This
+          # is what we'll use to upload.
           image_id="$( buildah commit "${container}" )"
           buildah rm "${container}"
 

From 37b6e47295a37e1fcc7345161a5b5bccf11c007e Mon Sep 17 00:00:00 2001
From: Ryan Dale <ryan.dale@nih.gov>
Date: Fri, 2 Feb 2024 11:40:48 -0500
Subject: [PATCH 86/98] bump

---
 .github/workflows/generic_build.yml | 8 ++++++++
 1 file changed, 8 insertions(+)

diff --git a/.github/workflows/generic_build.yml b/.github/workflows/generic_build.yml
index 7603ac80..c981810e 100644
--- a/.github/workflows/generic_build.yml
+++ b/.github/workflows/generic_build.yml
@@ -46,6 +46,14 @@ jobs:
       with:
         platforms: arm64
 
+    - name: Checkout bioconda-utils
+      uses: actions/checkout@v4
+      if: '${{ inputs.bioconda_utils }}'
+      with:
+        fetch-depth: 0
+        repository: 'bioconda/bioconda-utils'
+        path: 'images/bioconda-utils-build-env-cos7/bioconda-utils'
+
     - name: Build
       id: build
       run: |

From f72e4a7139ae9b1e2b5e2bad2e8cb1f68bd00a21 Mon Sep 17 00:00:00 2001
From: Ryan Dale <ryan.dale@nih.gov>
Date: Fri, 2 Feb 2024 11:46:25 -0500
Subject: [PATCH 87/98] bump

---
 .github/workflows/generic_build.yml | 10 ++++++++--
 1 file changed, 8 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/generic_build.yml b/.github/workflows/generic_build.yml
index c981810e..50162745 100644
--- a/.github/workflows/generic_build.yml
+++ b/.github/workflows/generic_build.yml
@@ -91,7 +91,7 @@ jobs:
           BUILD_ARGS+=("--build-arg=debian_version=$debian_version")
         fi
 
-        if [ ! -z "${bioconda_utils}" ]; then
+        if [ "${bioconda_utils}" == "true" ]; then
         # Due to different nomenclature used by conda-forge and buildah, we
         # need to map archs to base images.
           archs_and_images=(
@@ -150,7 +150,13 @@ jobs:
           LABELS=()
           LABELS+=("--label=deb-list=\"$( run cat /.deb.lst | tr '\n' '|' | sed 's/|$//' )\"")
           LABELS+=("--label=pkg-list=\"$( run cat /.pkg.lst | tr '\n' '|' | sed 's/|$//' )\"")
-          LABELS+=("--label=glibc=\"$( run sh -c 'exec "$( find -xdev -name libc.so.6 -print -quit )"' | sed '1!d' )\"")
+          LABELS+=("--label=glibc=\"$( 
+            run sh -c 'exec "$( find -xdev -name libc.so.6 -print -quit )"'
+            | sed '1!d'
+            | sed "s/ /_/g" 
+            | sed "s/\"//g" 
+            | sed "s/\'//g")\""
+          )
           LABELS+=("--label=debian=\"$( run cat /etc/debian_version | sed '1!d' )\"")
           LABELS+=("--label=bash=\"$( run bash --version | sed '1!d' )\"")
 

From 1d6be82978f6728c6912a1b1433c9685bf5ebf01 Mon Sep 17 00:00:00 2001
From: Ryan Dale <ryan.dale@nih.gov>
Date: Fri, 2 Feb 2024 11:51:39 -0500
Subject: [PATCH 88/98] bump

---
 .github/workflows/generic_build.yml | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/generic_build.yml b/.github/workflows/generic_build.yml
index 50162745..a39ab3e8 100644
--- a/.github/workflows/generic_build.yml
+++ b/.github/workflows/generic_build.yml
@@ -82,7 +82,9 @@ jobs:
           buildah manifest create "${image_name}:${tag}"
         done
 
-        archs_and_images=$archs
+        # get space-separated archs input string into an array
+        read -r -a archs_and_images <<<"$archs"
+
         # ----------------------------------------------------------------------
         # Incrementally compose build args, depending on which inputs were
         # provided.

From c4034c6c8c4574f7c845b92feed9a4c9df3388f5 Mon Sep 17 00:00:00 2001
From: Ryan Dale <ryan.dale@nih.gov>
Date: Fri, 2 Feb 2024 11:57:32 -0500
Subject: [PATCH 89/98] bump

---
 .github/workflows/generic_build.yml | 8 +-------
 1 file changed, 1 insertion(+), 7 deletions(-)

diff --git a/.github/workflows/generic_build.yml b/.github/workflows/generic_build.yml
index a39ab3e8..55da99a4 100644
--- a/.github/workflows/generic_build.yml
+++ b/.github/workflows/generic_build.yml
@@ -152,13 +152,7 @@ jobs:
           LABELS=()
           LABELS+=("--label=deb-list=\"$( run cat /.deb.lst | tr '\n' '|' | sed 's/|$//' )\"")
           LABELS+=("--label=pkg-list=\"$( run cat /.pkg.lst | tr '\n' '|' | sed 's/|$//' )\"")
-          LABELS+=("--label=glibc=\"$( 
-            run sh -c 'exec "$( find -xdev -name libc.so.6 -print -quit )"'
-            | sed '1!d'
-            | sed "s/ /_/g" 
-            | sed "s/\"//g" 
-            | sed "s/\'//g")\""
-          )
+          # LABELS+=("--labels=glibc=\"$( run sh -c 'exec "$( find -xdev -name libc.so.6 -print -quit )"' | sed '1!d' )\"")
           LABELS+=("--label=debian=\"$( run cat /etc/debian_version | sed '1!d' )\"")
           LABELS+=("--label=bash=\"$( run bash --version | sed '1!d' )\"")
 

From 1766609b0456bb972be496cb7270cc19dbbd69e3 Mon Sep 17 00:00:00 2001
From: Ryan Dale <ryan.dale@nih.gov>
Date: Mon, 5 Feb 2024 09:15:13 -0500
Subject: [PATCH 90/98] bump

---
 .github/workflows/generic_build.yml | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/generic_build.yml b/.github/workflows/generic_build.yml
index 55da99a4..957a558e 100644
--- a/.github/workflows/generic_build.yml
+++ b/.github/workflows/generic_build.yml
@@ -152,7 +152,7 @@ jobs:
           LABELS=()
           LABELS+=("--label=deb-list=\"$( run cat /.deb.lst | tr '\n' '|' | sed 's/|$//' )\"")
           LABELS+=("--label=pkg-list=\"$( run cat /.pkg.lst | tr '\n' '|' | sed 's/|$//' )\"")
-          # LABELS+=("--labels=glibc=\"$( run sh -c 'exec "$( find -xdev -name libc.so.6 -print -quit )"' | sed '1!d' )\"")
+          LABELS+=("--labels=glibc=\"$( run sh -c 'exec "$( find -xdev -name libc.so.6 -print -quit )"' | sed '1!d' )\"")
           LABELS+=("--label=debian=\"$( run cat /etc/debian_version | sed '1!d' )\"")
           LABELS+=("--label=bash=\"$( run bash --version | sed '1!d' )\"")
 
@@ -171,7 +171,10 @@ jobs:
 
           # Add labels to a new container...
           container="$( buildah from "${image_id}" )"
-          buildah config ${LABELS[@]} "${container}"
+
+          # FIXME: can't quite get the quoting right for args in array, so
+          # disabling for now to get other things working.
+          # buildah config ${LABELS[@]} "${container}"
 
           # ...then store the container (now with labels) as a new image. This
           # is what we'll use to upload.

From cc61158135358f704d9acabf982941f9166ed9cb Mon Sep 17 00:00:00 2001
From: Ryan Dale <ryan.dale@nih.gov>
Date: Mon, 5 Feb 2024 09:39:36 -0500
Subject: [PATCH 91/98] bump

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

diff --git a/.github/workflows/generic_build.yml b/.github/workflows/generic_build.yml
index 957a558e..0ac77eb2 100644
--- a/.github/workflows/generic_build.yml
+++ b/.github/workflows/generic_build.yml
@@ -190,7 +190,7 @@ jobs:
               "${image_name}:${tag}" \
               "${image_id}"
 
-            buildah inspect -t image ${image_name}:${tag}
+            buildah inspect -t image ${image_name}:${tag}-${arch}
           done
         done
         buildah inspect -t manifest ${image_name}

From 1398b8f2c7ba66785b05f66b4ac9c658dbddee9a Mon Sep 17 00:00:00 2001
From: Ryan Dale <ryan.dale@nih.gov>
Date: Mon, 5 Feb 2024 11:39:40 -0500
Subject: [PATCH 92/98] bump

---
 .github/workflows/generic_build.yml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/generic_build.yml b/.github/workflows/generic_build.yml
index 0ac77eb2..ab37aece 100644
--- a/.github/workflows/generic_build.yml
+++ b/.github/workflows/generic_build.yml
@@ -127,9 +127,9 @@ jobs:
         # ----------------------------------------------------------------------
 
         # Build each arch's image
-        for arch in $archs_and_images ; do
-          arch=$(echo $archs_and_images | cut -f1 -d "=")
-          base_image=$(echo $archs_and_images | cut -f2 -d "=")
+        for arch_and_image in "${archs_and_images[@]}" ; do
+          arch=$(echo $arch_and_image | cut -f1 -d "=")
+          base_image=$(echo $arch_and_image | cut -f2 -d "=")
           BASE_IMAGE_BUILD_ARG=""
           if [ ! -z "$base_image" ]; then
             BASE_IMAGE_BUILD_ARG="--build-arg=base_image="${base_image}""

From c739426f07ff14c2ee0d8787196bb602385a15e1 Mon Sep 17 00:00:00 2001
From: Ryan Dale <ryan.dale@nih.gov>
Date: Mon, 5 Feb 2024 12:00:59 -0500
Subject: [PATCH 93/98] try label fix

---
 .github/workflows/generic_build.yml | 7 ++-----
 1 file changed, 2 insertions(+), 5 deletions(-)

diff --git a/.github/workflows/generic_build.yml b/.github/workflows/generic_build.yml
index ab37aece..baec7e5a 100644
--- a/.github/workflows/generic_build.yml
+++ b/.github/workflows/generic_build.yml
@@ -161,7 +161,7 @@ jobs:
               run sh -c '. /opt/conda/etc/profile.d/conda.sh && conda activate base && bioconda-utils --version' \
               | rev | cut -f1 -d " " | rev 
             )"
-            LABELS+=("--label=\"${bioconda_utils}\"")
+            LABELS+=("--label=bioconda-utils=\"${bioconda_utils}\"")
           fi
 
           if [ ! -z "${busybox_version}" ]; then
@@ -171,10 +171,7 @@ jobs:
 
           # Add labels to a new container...
           container="$( buildah from "${image_id}" )"
-
-          # FIXME: can't quite get the quoting right for args in array, so
-          # disabling for now to get other things working.
-          # buildah config ${LABELS[@]} "${container}"
+          buildah config ${LABELS[@]} "${container}"
 
           # ...then store the container (now with labels) as a new image. This
           # is what we'll use to upload.

From d85af0c99648ec767e37065a49cfda7bf65eb801 Mon Sep 17 00:00:00 2001
From: Ryan Dale <ryan.dale@nih.gov>
Date: Mon, 5 Feb 2024 12:10:34 -0500
Subject: [PATCH 94/98] bump

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

diff --git a/.github/workflows/generic_build.yml b/.github/workflows/generic_build.yml
index baec7e5a..a2e81161 100644
--- a/.github/workflows/generic_build.yml
+++ b/.github/workflows/generic_build.yml
@@ -152,7 +152,7 @@ jobs:
           LABELS=()
           LABELS+=("--label=deb-list=\"$( run cat /.deb.lst | tr '\n' '|' | sed 's/|$//' )\"")
           LABELS+=("--label=pkg-list=\"$( run cat /.pkg.lst | tr '\n' '|' | sed 's/|$//' )\"")
-          LABELS+=("--labels=glibc=\"$( run sh -c 'exec "$( find -xdev -name libc.so.6 -print -quit )"' | sed '1!d' )\"")
+          LABELS+=("--label=glibc=\"$( run sh -c 'exec "$( find -xdev -name libc.so.6 -print -quit )"' | sed '1!d' )\"")
           LABELS+=("--label=debian=\"$( run cat /etc/debian_version | sed '1!d' )\"")
           LABELS+=("--label=bash=\"$( run bash --version | sed '1!d' )\"")
 

From 5c0dc83de9c5e8012c5ceeb48e4956eab29d495d Mon Sep 17 00:00:00 2001
From: Ryan Dale <ryan.dale@nih.gov>
Date: Mon, 5 Feb 2024 14:08:11 -0500
Subject: [PATCH 95/98] back to disabling labels

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

diff --git a/.github/workflows/generic_build.yml b/.github/workflows/generic_build.yml
index a2e81161..437dd697 100644
--- a/.github/workflows/generic_build.yml
+++ b/.github/workflows/generic_build.yml
@@ -156,7 +156,7 @@ jobs:
           LABELS+=("--label=debian=\"$( run cat /etc/debian_version | sed '1!d' )\"")
           LABELS+=("--label=bash=\"$( run bash --version | sed '1!d' )\"")
 
-          if [ "${bioconda_utils}" ]; then
+          if [ "${bioconda_utils}" == "true" ]; then
             bioconda_utils="$(
               run sh -c '. /opt/conda/etc/profile.d/conda.sh && conda activate base && bioconda-utils --version' \
               | rev | cut -f1 -d " " | rev 
@@ -171,7 +171,7 @@ jobs:
 
           # Add labels to a new container...
           container="$( buildah from "${image_id}" )"
-          buildah config ${LABELS[@]} "${container}"
+          # buildah config ${LABELS[@]} "${container}"
 
           # ...then store the container (now with labels) as a new image. This
           # is what we'll use to upload.

From 823ff050e577fc59ac90b6e41313b354e5711721 Mon Sep 17 00:00:00 2001
From: aliciaaevans <alicia.evans@nih.gov>
Date: Mon, 5 Feb 2024 16:08:48 -0500
Subject: [PATCH 96/98] test a few label quoting things

---
 .github/workflows/generic_build.yml | 10 +++++++++-
 1 file changed, 9 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/generic_build.yml b/.github/workflows/generic_build.yml
index 437dd697..ace2e7d4 100644
--- a/.github/workflows/generic_build.yml
+++ b/.github/workflows/generic_build.yml
@@ -171,7 +171,15 @@ jobs:
 
           # Add labels to a new container...
           container="$( buildah from "${image_id}" )"
-          # buildah config ${LABELS[@]} "${container}"
+
+          # FIXME: Test out different options
+          declare -a mycmd=( buildah config ${LABELS[@]} "${container}" )
+          echo "Label args: " "${LABELS[@]}"
+          echo "Label args with @Q: " "${LABELS[@]@Q}"
+          echo "Label command: " "${mycmd[@]}"
+          echo "Label command with @Q: " "${mycmd[@]@Q}"
+
+          buildah config "${LABELS[@]}" "${container}"
 
           # ...then store the container (now with labels) as a new image. This
           # is what we'll use to upload.

From 4e130a7d2347bda25acd2541c057466e99ddbf90 Mon Sep 17 00:00:00 2001
From: aliciaaevans <alicia.evans@nih.gov>
Date: Mon, 5 Feb 2024 16:40:14 -0500
Subject: [PATCH 97/98] remove extra double quotes

---
 .github/workflows/generic_build.yml | 26 +++++++++++++-------------
 1 file changed, 13 insertions(+), 13 deletions(-)

diff --git a/.github/workflows/generic_build.yml b/.github/workflows/generic_build.yml
index ace2e7d4..62621ffc 100644
--- a/.github/workflows/generic_build.yml
+++ b/.github/workflows/generic_build.yml
@@ -150,34 +150,34 @@ jobs:
           container="$( buildah from "${image_id}" )"
           run() { buildah run "${container}" "${@}" ; }
           LABELS=()
-          LABELS+=("--label=deb-list=\"$( run cat /.deb.lst | tr '\n' '|' | sed 's/|$//' )\"")
-          LABELS+=("--label=pkg-list=\"$( run cat /.pkg.lst | tr '\n' '|' | sed 's/|$//' )\"")
-          LABELS+=("--label=glibc=\"$( run sh -c 'exec "$( find -xdev -name libc.so.6 -print -quit )"' | sed '1!d' )\"")
-          LABELS+=("--label=debian=\"$( run cat /etc/debian_version | sed '1!d' )\"")
-          LABELS+=("--label=bash=\"$( run bash --version | sed '1!d' )\"")
+          LABELS+=("--label=deb-list=$( run cat /.deb.lst | tr '\n' '|' | sed 's/|$//' )")
+          LABELS+=("--label=pkg-list=$( run cat /.pkg.lst | tr '\n' '|' | sed 's/|$//' )")
+          LABELS+=("--label=glibc=$( run sh -c 'exec "$( find -xdev -name libc.so.6 -print -quit )"' | sed '1!d' )")
+          LABELS+=("--label=debian=$( run cat /etc/debian_version | sed '1!d' )")
+          LABELS+=("--label=bash=$( run bash --version | sed '1!d' )")
 
           if [ "${bioconda_utils}" == "true" ]; then
             bioconda_utils="$(
               run sh -c '. /opt/conda/etc/profile.d/conda.sh && conda activate base && bioconda-utils --version' \
               | rev | cut -f1 -d " " | rev 
             )"
-            LABELS+=("--label=bioconda-utils=\"${bioconda_utils}\"")
+            LABELS+=("--label=bioconda-utils=${bioconda_utils}")
           fi
 
           if [ ! -z "${busybox_version}" ]; then
-            LABELS+=("--label=busybox-version=\"${busybox_version}\"")
+            LABELS+=("--label=busybox-version=${busybox_version}")
           fi
           buildah rm "${container}"
 
           # Add labels to a new container...
           container="$( buildah from "${image_id}" )"
 
-          # FIXME: Test out different options
-          declare -a mycmd=( buildah config ${LABELS[@]} "${container}" )
-          echo "Label args: " "${LABELS[@]}"
-          echo "Label args with @Q: " "${LABELS[@]@Q}"
-          echo "Label command: " "${mycmd[@]}"
-          echo "Label command with @Q: " "${mycmd[@]@Q}"
+          # # FIXME: Test out different options
+          # declare -a mycmd=( buildah config ${LABELS[@]} "${container}" )
+          # echo "Label args: " "${LABELS[@]}"
+          # echo "Label args with @Q: " "${LABELS[@]@Q}"
+          # echo "Label command: " "${mycmd[@]}"
+          # echo "Label command with @Q: " "${mycmd[@]@Q}"
 
           buildah config "${LABELS[@]}" "${container}"
 

From c3bd6749909bffb2cbc4a969b0f3bb37442595cd Mon Sep 17 00:00:00 2001
From: aliciaaevans <alicia.evans@nih.gov>
Date: Mon, 5 Feb 2024 16:48:04 -0500
Subject: [PATCH 98/98] remove extra logging

---
 .github/workflows/generic_build.yml | 8 --------
 1 file changed, 8 deletions(-)

diff --git a/.github/workflows/generic_build.yml b/.github/workflows/generic_build.yml
index 62621ffc..548ea51f 100644
--- a/.github/workflows/generic_build.yml
+++ b/.github/workflows/generic_build.yml
@@ -171,14 +171,6 @@ jobs:
 
           # Add labels to a new container...
           container="$( buildah from "${image_id}" )"
-
-          # # FIXME: Test out different options
-          # declare -a mycmd=( buildah config ${LABELS[@]} "${container}" )
-          # echo "Label args: " "${LABELS[@]}"
-          # echo "Label args with @Q: " "${LABELS[@]@Q}"
-          # echo "Label command: " "${mycmd[@]}"
-          # echo "Label command with @Q: " "${mycmd[@]@Q}"
-
           buildah config "${LABELS[@]}" "${container}"
 
           # ...then store the container (now with labels) as a new image. This