From e4343133b62fd6800cfa1d08b50812e9745793e4 Mon Sep 17 00:00:00 2001
From: Iain Emsley <iain.emsley@warwick.ac.uk>
Date: Fri, 11 Jul 2025 10:04:10 +0100
Subject: [PATCH 001/109] Update build-and-publish-image.yml for two images

---
 .github/workflows/build-and-publish-image.yml | 20 +++++++++++++++----
 1 file changed, 16 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/build-and-publish-image.yml b/.github/workflows/build-and-publish-image.yml
index 7d0014dc2..7aabc3a4d 100644
--- a/.github/workflows/build-and-publish-image.yml
+++ b/.github/workflows/build-and-publish-image.yml
@@ -41,7 +41,17 @@ jobs:
     steps:
       - name: Checkout repository
         uses: actions/checkout@v4
-
+      - name: Set up QEMU
+        uses: docker/setup-qemu-action@v1
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v1
+      - name: Cache Docker layers
+        uses: actions/cache@v2
+        with:
+          path: /tmp/.buildx-cache
+          key: ${{ runner.os }}-buildx-${{ github.sha }}
+          restore-keys: |
+            ${{ runner.os }}-buildx-
       - name: Extract version number
         run: |
           VER=$(cat VERSION)
@@ -50,9 +60,11 @@ jobs:
       - name: Log in to the Container registry
         uses: docker/login-action@v3
         with:
-          registry: ${{ env.REGISTRY }}
-          username: ${{ github.actor }}
-          password: ${{ secrets.GITHUB_TOKEN }}
+          username: ${{ secrets.DOCKERHUB_USERNAME }}
+          password: ${{ secrets.DOCKERHUB_TOKEN }}
+          #registry: ${{ env.REGISTRY }}
+          #username: ${{ github.actor }}
+          #password: ${{ secrets.GITHUB_TOKEN }}
 
       - name: Extract metadata (tags, labels) for Docker
         id: meta

From d7f099864c714b276a64be9aa8469e5f4d9da325 Mon Sep 17 00:00:00 2001
From: Iain Emsley <iain.emsley@warwick.ac.uk>
Date: Fri, 11 Jul 2025 10:26:36 +0100
Subject: [PATCH 002/109] Update cache

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

diff --git a/.github/workflows/build-and-publish-image.yml b/.github/workflows/build-and-publish-image.yml
index 7aabc3a4d..3fe0e1367 100644
--- a/.github/workflows/build-and-publish-image.yml
+++ b/.github/workflows/build-and-publish-image.yml
@@ -46,7 +46,7 @@ jobs:
       - name: Set up Docker Buildx
         uses: docker/setup-buildx-action@v1
       - name: Cache Docker layers
-        uses: actions/cache@v2
+        uses: actions/cache@v4
         with:
           path: /tmp/.buildx-cache
           key: ${{ runner.os }}-buildx-${{ github.sha }}

From 38e53862f6fbdbe3bd781121fc97d5c66134c5af Mon Sep 17 00:00:00 2001
From: Iain Emsley <iain.emsley@warwick.ac.uk>
Date: Fri, 11 Jul 2025 10:36:15 +0100
Subject: [PATCH 003/109] Update build-and-publish-image.yml

---
 .github/workflows/build-and-publish-image.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/build-and-publish-image.yml b/.github/workflows/build-and-publish-image.yml
index 3fe0e1367..ef632af36 100644
--- a/.github/workflows/build-and-publish-image.yml
+++ b/.github/workflows/build-and-publish-image.yml
@@ -3,6 +3,7 @@
 # separate terms of service, privacy policy, and support
 # documentation.
 
+
 name: Build and publish Docker image
 
 on:

From 69fe2056190aef0284d13d9748630c02f4a08033 Mon Sep 17 00:00:00 2001
From: Iain Emsley <iain.emsley@warwick.ac.uk>
Date: Fri, 11 Jul 2025 10:47:22 +0100
Subject: [PATCH 004/109] Update build-and-publish-image.yml

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

diff --git a/.github/workflows/build-and-publish-image.yml b/.github/workflows/build-and-publish-image.yml
index ef632af36..c3bf93ca6 100644
--- a/.github/workflows/build-and-publish-image.yml
+++ b/.github/workflows/build-and-publish-image.yml
@@ -71,7 +71,8 @@ jobs:
         id: meta
         uses: docker/metadata-action@v5
         with:
-          images: ${{ env.REGISTRY }}/${{ github.repository }}
+          images: ${{ secrets.DOCKERHUB_USERNAME }}
+          #images: ${{ env.REGISTRY }}/${{ github.repository }}
           tags: |
             type=ref,event=branch
             type=ref,event=pr

From 65e41cd95d305c86bb549282caa41cd556a631f6 Mon Sep 17 00:00:00 2001
From: Iain Emsley <iain.emsley@warwick.ac.uk>
Date: Fri, 11 Jul 2025 10:57:43 +0100
Subject: [PATCH 005/109] Update registry and added platform tags

---
 .github/workflows/build-and-publish-image.yml | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/.github/workflows/build-and-publish-image.yml b/.github/workflows/build-and-publish-image.yml
index c3bf93ca6..2ea7c7a7f 100644
--- a/.github/workflows/build-and-publish-image.yml
+++ b/.github/workflows/build-and-publish-image.yml
@@ -63,6 +63,7 @@ jobs:
         with:
           username: ${{ secrets.DOCKERHUB_USERNAME }}
           password: ${{ secrets.DOCKERHUB_TOKEN }}
+          registry: ${{ secrets.DOCKERHUB_USERNAME }}
           #registry: ${{ env.REGISTRY }}
           #username: ${{ github.actor }}
           #password: ${{ secrets.GITHUB_TOKEN }}
@@ -88,3 +89,6 @@ jobs:
           build-args: |
             CONTAINER_VERSION=${{ env.VERSION }}
           labels: ${{ steps.meta.outputs.labels }}
+          platforms: linux/amd64,linux/arm64/v8
+          cache-from: type=local,src=/tmp/.buildx-cache
+          cache-to: type=local,dest=/tmp/.buildx-cache

From a7f491e395ccd6e2da1d0505751423ecc94010d7 Mon Sep 17 00:00:00 2001
From: Iain Emsley <iain.emsley@warwick.ac.uk>
Date: Fri, 11 Jul 2025 11:02:44 +0100
Subject: [PATCH 006/109] Update build-and-publish-image.yml

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

diff --git a/.github/workflows/build-and-publish-image.yml b/.github/workflows/build-and-publish-image.yml
index 2ea7c7a7f..01389d9a9 100644
--- a/.github/workflows/build-and-publish-image.yml
+++ b/.github/workflows/build-and-publish-image.yml
@@ -63,8 +63,8 @@ jobs:
         with:
           username: ${{ secrets.DOCKERHUB_USERNAME }}
           password: ${{ secrets.DOCKERHUB_TOKEN }}
-          registry: ${{ secrets.DOCKERHUB_USERNAME }}
-          #registry: ${{ env.REGISTRY }}
+          #registry: ${{ secrets.DOCKERHUB_USERNAME }}
+          registry: ${{ env.REGISTRY }}
           #username: ${{ github.actor }}
           #password: ${{ secrets.GITHUB_TOKEN }}
 

From 70cddd6ff5f9950ef0b46dd5b08ac943032b9553 Mon Sep 17 00:00:00 2001
From: Iain Emsley <iain.emsley@warwick.ac.uk>
Date: Fri, 11 Jul 2025 11:04:42 +0100
Subject: [PATCH 007/109] Update build-and-publish-image.yml

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

diff --git a/.github/workflows/build-and-publish-image.yml b/.github/workflows/build-and-publish-image.yml
index 01389d9a9..9447c0ddd 100644
--- a/.github/workflows/build-and-publish-image.yml
+++ b/.github/workflows/build-and-publish-image.yml
@@ -61,10 +61,9 @@ jobs:
       - name: Log in to the Container registry
         uses: docker/login-action@v3
         with:
+          registry: ${{ env.REGISTRY }}
           username: ${{ secrets.DOCKERHUB_USERNAME }}
           password: ${{ secrets.DOCKERHUB_TOKEN }}
-          #registry: ${{ secrets.DOCKERHUB_USERNAME }}
-          registry: ${{ env.REGISTRY }}
           #username: ${{ github.actor }}
           #password: ${{ secrets.GITHUB_TOKEN }}
 

From c450b56d6cbfcf9e79159152049b90bb0bb19854 Mon Sep 17 00:00:00 2001
From: Iain Emsley <iain.emsley@warwick.ac.uk>
Date: Fri, 11 Jul 2025 11:24:23 +0100
Subject: [PATCH 008/109] Update build-and-publish-image.yml

---
 .github/workflows/build-and-publish-image.yml | 6 ++----
 1 file changed, 2 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/build-and-publish-image.yml b/.github/workflows/build-and-publish-image.yml
index 9447c0ddd..6956d5d35 100644
--- a/.github/workflows/build-and-publish-image.yml
+++ b/.github/workflows/build-and-publish-image.yml
@@ -62,10 +62,8 @@ jobs:
         uses: docker/login-action@v3
         with:
           registry: ${{ env.REGISTRY }}
-          username: ${{ secrets.DOCKERHUB_USERNAME }}
-          password: ${{ secrets.DOCKERHUB_TOKEN }}
-          #username: ${{ github.actor }}
-          #password: ${{ secrets.GITHUB_TOKEN }}
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
 
       - name: Extract metadata (tags, labels) for Docker
         id: meta

From aed15157d6283d227232c46a2b2bcd870a942002 Mon Sep 17 00:00:00 2001
From: Iain Emsley <iain.emsley@warwick.ac.uk>
Date: Fri, 11 Jul 2025 16:08:52 +0100
Subject: [PATCH 009/109] Update build-and-publish-image.yml

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

diff --git a/.github/workflows/build-and-publish-image.yml b/.github/workflows/build-and-publish-image.yml
index 6956d5d35..6c340e19e 100644
--- a/.github/workflows/build-and-publish-image.yml
+++ b/.github/workflows/build-and-publish-image.yml
@@ -69,8 +69,7 @@ jobs:
         id: meta
         uses: docker/metadata-action@v5
         with:
-          images: ${{ secrets.DOCKERHUB_USERNAME }}
-          #images: ${{ env.REGISTRY }}/${{ github.repository }}
+          images: ${{ env.REGISTRY }}/${{ github.repository }}
           tags: |
             type=ref,event=branch
             type=ref,event=pr

From d068c982e6fba71952169a044270dbc57f3b3efc Mon Sep 17 00:00:00 2001
From: Iain Emsley <iain.emsley@warwick.ac.uk>
Date: Fri, 25 Jul 2025 09:35:42 +0100
Subject: [PATCH 010/109] Initial reusable flow

---
 .github/workflows/call_jobs.yml               |  24 ++++
 .github/workflows/reuse-build-and-publish.yml | 109 ++++++++++++++++++
 2 files changed, 133 insertions(+)
 create mode 100644 .github/workflows/call_jobs.yml
 create mode 100644 .github/workflows/reuse-build-and-publish.yml

diff --git a/.github/workflows/call_jobs.yml b/.github/workflows/call_jobs.yml
new file mode 100644
index 000000000..b5e00d312
--- /dev/null
+++ b/.github/workflows/call_jobs.yml
@@ -0,0 +1,24 @@
+name: Call reusable workflows
+
+on:
+  pull_request:
+    branches:
+      - ["main","devel"]
+
+jobs:
+  call-workflow-amd64:
+    permissions:
+      contents: read
+      pull-requests: write
+    uses: r-devel/r-devel/.github/workflows/reuse-build-and-publish.yml@v1
+    with:
+      config-path: .github/labeler.yml
+      event_name: ${{ github.event_name }}
+      pull_request: ${{ github.pull_request.merged }}
+      repository: ${{ github.event_name }}
+      version: ${{ github.event_name }}
+      image_name: ${{ github.repository }}
+      ref_name: ${{ github.branch }}
+      actor: ${{ github.actor }}
+    secrets:
+      personal_access_token: ${{ secrets.GITHUB_TOKEN }}
diff --git a/.github/workflows/reuse-build-and-publish.yml b/.github/workflows/reuse-build-and-publish.yml
new file mode 100644
index 000000000..966260f6c
--- /dev/null
+++ b/.github/workflows/reuse-build-and-publish.yml
@@ -0,0 +1,109 @@
+# This workflow uses actions that are not certified by GitHub.
+# They are provided by a third-party and are governed by
+# separate terms of service, privacy policy, and support
+# documentation.
+
+#https://github.com/r-devel/r-dev-env/issues/252
+
+name: Build and publish Docker image
+
+env:
+  REGISTRY: ghcr.io
+
+on:
+  workflow_call:
+    inputs:
+      event_name: 
+        description: event name
+        required: true
+        type: string
+      pull_request: 
+        description: pull request
+        required: false
+        type: string
+      repository: 
+        description: repository name
+        required: true
+        type: string
+      version: 
+        description: container version
+        required: true
+        type: number
+      image_name:
+        description: image name
+        required: true
+        type: string
+      ref_name: 
+        description: ref name
+        required: true
+        type: string
+      actor: 
+        description: github actor 
+        required: true
+        type: string
+    secrets:
+      github_token:
+        required: true
+  push:
+    branches: ["main","devel"]
+    paths:
+      - '.github/workflows/reuse-build-and-publish.yml'
+  pull_request:
+    branches: ["main","devel"]
+    types: [closed]
+    paths:
+      - '.github/workflows/reuse-build-and-publish.yml'
+      - '.devcontainer/devcontainer.json'
+      - 'Dockerfile'
+      - 'reinstall-cmake.sh'
+      - 'VERSION'
+
+permissions:
+  contents: read
+  packages: write
+
+jobs:
+  reuse-build-and-push:
+    if:  |
+      ${{ inputs.event_name }} == 'workflow_dispatch' ||
+      ${{ inputs.event_name }} == 'push' ||
+      (${{ inputs.event_name }} == 'pull_request' &&
+       ${{ inputs.pull_request }} == true)
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+
+      #- name: Extract version number
+      #  run: |
+      #    VER=$(cat VERSION)
+      #    echo "VERSION=$VER" >> $GITHUB_ENV
+
+      - name: Log in to the Container registry
+        uses: docker/login-action@v3
+        with:
+          registry: $REGISTRY
+          username: ${{ inputs.actor }}
+          password: ${{ secrets.github_token }}
+
+      - name: Extract metadata (tags, labels) for Docker
+        id: meta
+        uses: docker/metadata-action@v5
+        with:
+          images: $REGISTRY/${{ inputs.repository }}
+          tags: |
+            type=ref,event=branch
+            type=ref,event=pr
+            type=semver,pattern=${{ inputs.version }}
+            type=sha
+
+      - name: Build and push Docker image
+        uses: docker/build-push-action@v5
+        with:
+          context: .
+          push: true
+          tags: $REGISTRY/${{ inputs.image_name }}:${{ inputs.ref_name }}
+          build-args: |
+            CONTAINER_VERSION=${{ inputs.version }}
+          labels: ${{ steps.meta.outputs.labels }}

From 6a912a29f2a49e0bd8b03d3d24270369afdc6773 Mon Sep 17 00:00:00 2001
From: Iain Emsley <iain.emsley@warwick.ac.uk>
Date: Fri, 25 Jul 2025 09:38:21 +0100
Subject: [PATCH 011/109] Update call_jobs.yml and fix syntax

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

diff --git a/.github/workflows/call_jobs.yml b/.github/workflows/call_jobs.yml
index b5e00d312..746ff1907 100644
--- a/.github/workflows/call_jobs.yml
+++ b/.github/workflows/call_jobs.yml
@@ -1,9 +1,9 @@
 name: Call reusable workflows
 
 on:
-  pull_request:
+  push:
     branches:
-      - ["main","devel"]
+      - master
 
 jobs:
   call-workflow-amd64:

From 4178cc32e580f1fe955e45ab16063815cdc774d9 Mon Sep 17 00:00:00 2001
From: Iain Emsley <iain.emsley@warwick.ac.uk>
Date: Fri, 25 Jul 2025 09:39:17 +0100
Subject: [PATCH 012/109] Update call_jobs.yml and addd branch

---
 .github/workflows/call_jobs.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/call_jobs.yml b/.github/workflows/call_jobs.yml
index 746ff1907..97e84bd91 100644
--- a/.github/workflows/call_jobs.yml
+++ b/.github/workflows/call_jobs.yml
@@ -4,6 +4,7 @@ on:
   push:
     branches:
       - master
+      - devel
 
 jobs:
   call-workflow-amd64:

From d04a92acce40a4018e53ca5e47b0640b45c045b5 Mon Sep 17 00:00:00 2001
From: Iain Emsley <iain.emsley@warwick.ac.uk>
Date: Fri, 25 Jul 2025 09:40:30 +0100
Subject: [PATCH 013/109] Removed version

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

diff --git a/.github/workflows/call_jobs.yml b/.github/workflows/call_jobs.yml
index 97e84bd91..bf5d2d3bb 100644
--- a/.github/workflows/call_jobs.yml
+++ b/.github/workflows/call_jobs.yml
@@ -11,7 +11,7 @@ jobs:
     permissions:
       contents: read
       pull-requests: write
-    uses: r-devel/r-devel/.github/workflows/reuse-build-and-publish.yml@v1
+    uses: r-devel/r-devel/.github/workflows/reuse-build-and-publish.yml
     with:
       config-path: .github/labeler.yml
       event_name: ${{ github.event_name }}

From a231106e4c8c28504e7199940b5c8dba3043d848 Mon Sep 17 00:00:00 2001
From: Iain Emsley <iain.emsley@warwick.ac.uk>
Date: Fri, 25 Jul 2025 09:43:40 +0100
Subject: [PATCH 014/109] Change to gh token

---
 .github/workflows/reuse-build-and-publish.yml | 15 ++++++++++-----
 1 file changed, 10 insertions(+), 5 deletions(-)

diff --git a/.github/workflows/reuse-build-and-publish.yml b/.github/workflows/reuse-build-and-publish.yml
index 966260f6c..afbbfa756 100644
--- a/.github/workflows/reuse-build-and-publish.yml
+++ b/.github/workflows/reuse-build-and-publish.yml
@@ -42,15 +42,20 @@ on:
         required: true
         type: string
     secrets:
-      github_token:
+      gh_token:
         required: true
   push:
-    branches: ["main","devel"]
+    branches:
+      - main
+      - devel
     paths:
       - '.github/workflows/reuse-build-and-publish.yml'
   pull_request:
-    branches: ["main","devel"]
-    types: [closed]
+    branches:
+      - main
+      - devel
+    types:
+      - closed
     paths:
       - '.github/workflows/reuse-build-and-publish.yml'
       - '.devcontainer/devcontainer.json'
@@ -85,7 +90,7 @@ jobs:
         with:
           registry: $REGISTRY
           username: ${{ inputs.actor }}
-          password: ${{ secrets.github_token }}
+          password: ${{ secrets.gh_token }}
 
       - name: Extract metadata (tags, labels) for Docker
         id: meta

From b1360ae4d885adc4c6cf7941993c40c5ab5b38ac Mon Sep 17 00:00:00 2001
From: Iain Emsley <iain.emsley@warwick.ac.uk>
Date: Fri, 25 Jul 2025 09:48:34 +0100
Subject: [PATCH 015/109] Update reuse-build-and-publish.yml

---
 .github/workflows/reuse-build-and-publish.yml | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/.github/workflows/reuse-build-and-publish.yml b/.github/workflows/reuse-build-and-publish.yml
index afbbfa756..967bf7fb4 100644
--- a/.github/workflows/reuse-build-and-publish.yml
+++ b/.github/workflows/reuse-build-and-publish.yml
@@ -44,6 +44,10 @@ on:
     secrets:
       gh_token:
         required: true
+      username:
+        required: true
+      password:
+        required: true
   push:
     branches:
       - main

From 190dcf8b1e3fe6fa61bbb42ec5ab50b5213428ce Mon Sep 17 00:00:00 2001
From: Iain Emsley <iain.emsley@warwick.ac.uk>
Date: Fri, 25 Jul 2025 09:48:55 +0100
Subject: [PATCH 016/109] Update call_jobs.yml

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

diff --git a/.github/workflows/call_jobs.yml b/.github/workflows/call_jobs.yml
index bf5d2d3bb..d0da75510 100644
--- a/.github/workflows/call_jobs.yml
+++ b/.github/workflows/call_jobs.yml
@@ -23,3 +23,5 @@ jobs:
       actor: ${{ github.actor }}
     secrets:
       personal_access_token: ${{ secrets.GITHUB_TOKEN }}
+      username: ${{ secrets.username }}
+      password: ${{ secrets.password}}

From dc57ccc33a3f454838337198a20bdb55311ae7b4 Mon Sep 17 00:00:00 2001
From: Iain Emsley <iain.emsley@warwick.ac.uk>
Date: Fri, 25 Jul 2025 09:50:40 +0100
Subject: [PATCH 017/109] Update call_jobs.yml

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

diff --git a/.github/workflows/call_jobs.yml b/.github/workflows/call_jobs.yml
index d0da75510..c9de7bbf3 100644
--- a/.github/workflows/call_jobs.yml
+++ b/.github/workflows/call_jobs.yml
@@ -11,7 +11,7 @@ jobs:
     permissions:
       contents: read
       pull-requests: write
-    uses: r-devel/r-devel/.github/workflows/reuse-build-and-publish.yml
+    uses: r-devel/r-devel/.github/workflows/reuse-build-and-publish.yml@devel
     with:
       config-path: .github/labeler.yml
       event_name: ${{ github.event_name }}

From 0b1ad6453c7d5ba9349d75e70475f54ab47515c3 Mon Sep 17 00:00:00 2001
From: Iain Emsley <iain.emsley@warwick.ac.uk>
Date: Fri, 25 Jul 2025 09:52:45 +0100
Subject: [PATCH 018/109] Update call_jobs.yml

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

diff --git a/.github/workflows/call_jobs.yml b/.github/workflows/call_jobs.yml
index c9de7bbf3..d0da75510 100644
--- a/.github/workflows/call_jobs.yml
+++ b/.github/workflows/call_jobs.yml
@@ -11,7 +11,7 @@ jobs:
     permissions:
       contents: read
       pull-requests: write
-    uses: r-devel/r-devel/.github/workflows/reuse-build-and-publish.yml@devel
+    uses: r-devel/r-devel/.github/workflows/reuse-build-and-publish.yml
     with:
       config-path: .github/labeler.yml
       event_name: ${{ github.event_name }}

From 56ce47c6748b54ac86c12155896cf02655e34648 Mon Sep 17 00:00:00 2001
From: Iain Emsley <iain.emsley@warwick.ac.uk>
Date: Fri, 25 Jul 2025 09:53:58 +0100
Subject: [PATCH 019/109] Added branch

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

diff --git a/.github/workflows/call_jobs.yml b/.github/workflows/call_jobs.yml
index d0da75510..c9de7bbf3 100644
--- a/.github/workflows/call_jobs.yml
+++ b/.github/workflows/call_jobs.yml
@@ -11,7 +11,7 @@ jobs:
     permissions:
       contents: read
       pull-requests: write
-    uses: r-devel/r-devel/.github/workflows/reuse-build-and-publish.yml
+    uses: r-devel/r-devel/.github/workflows/reuse-build-and-publish.yml@devel
     with:
       config-path: .github/labeler.yml
       event_name: ${{ github.event_name }}

From e2a20d752d680020f609447b68d5ddf3a4762269 Mon Sep 17 00:00:00 2001
From: Iain Emsley <iain.emsley@warwick.ac.uk>
Date: Fri, 25 Jul 2025 10:04:18 +0100
Subject: [PATCH 020/109] Update call_jobs.yml

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

diff --git a/.github/workflows/call_jobs.yml b/.github/workflows/call_jobs.yml
index c9de7bbf3..b5591cda8 100644
--- a/.github/workflows/call_jobs.yml
+++ b/.github/workflows/call_jobs.yml
@@ -11,7 +11,7 @@ jobs:
     permissions:
       contents: read
       pull-requests: write
-    uses: r-devel/r-devel/.github/workflows/reuse-build-and-publish.yml@devel
+    uses: r-devel/.github/workflows/reuse-build-and-publish.yml@devel
     with:
       config-path: .github/labeler.yml
       event_name: ${{ github.event_name }}

From 38099d570578ce1964ff8464f4b6e11d2fe63338 Mon Sep 17 00:00:00 2001
From: Iain Emsley <iain.emsley@warwick.ac.uk>
Date: Fri, 25 Jul 2025 10:04:59 +0100
Subject: [PATCH 021/109] Update call_jobs.yml

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

diff --git a/.github/workflows/call_jobs.yml b/.github/workflows/call_jobs.yml
index b5591cda8..890a6399f 100644
--- a/.github/workflows/call_jobs.yml
+++ b/.github/workflows/call_jobs.yml
@@ -11,7 +11,7 @@ jobs:
     permissions:
       contents: read
       pull-requests: write
-    uses: r-devel/.github/workflows/reuse-build-and-publish.yml@devel
+    uses: iaine/r-devel/.github/workflows/reuse-build-and-publish.yml@devel
     with:
       config-path: .github/labeler.yml
       event_name: ${{ github.event_name }}

From ebcfe0e7ba27d47017afcbb16a3dd0a6e375545c Mon Sep 17 00:00:00 2001
From: Iain Emsley <iain.emsley@warwick.ac.uk>
Date: Fri, 25 Jul 2025 10:06:50 +0100
Subject: [PATCH 022/109] Fix path

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

diff --git a/.github/workflows/call_jobs.yml b/.github/workflows/call_jobs.yml
index 890a6399f..6317f5aa3 100644
--- a/.github/workflows/call_jobs.yml
+++ b/.github/workflows/call_jobs.yml
@@ -11,7 +11,7 @@ jobs:
     permissions:
       contents: read
       pull-requests: write
-    uses: iaine/r-devel/.github/workflows/reuse-build-and-publish.yml@devel
+    uses: iaine/r-dev-env/.github/workflows/reuse-build-and-publish.yml@devel
     with:
       config-path: .github/labeler.yml
       event_name: ${{ github.event_name }}

From ae74c0661cb12ec629058d654c44b500b8a5b459 Mon Sep 17 00:00:00 2001
From: Iain Emsley <iain.emsley@warwick.ac.uk>
Date: Fri, 25 Jul 2025 10:12:59 +0100
Subject: [PATCH 023/109] Update call_jobs.yml

---
 .github/workflows/call_jobs.yml | 5 +----
 1 file changed, 1 insertion(+), 4 deletions(-)

diff --git a/.github/workflows/call_jobs.yml b/.github/workflows/call_jobs.yml
index 6317f5aa3..d53573e50 100644
--- a/.github/workflows/call_jobs.yml
+++ b/.github/workflows/call_jobs.yml
@@ -21,7 +21,4 @@ jobs:
       image_name: ${{ github.repository }}
       ref_name: ${{ github.branch }}
       actor: ${{ github.actor }}
-    secrets:
-      personal_access_token: ${{ secrets.GITHUB_TOKEN }}
-      username: ${{ secrets.username }}
-      password: ${{ secrets.password}}
+    secrets: inherit

From bfb32dd6d359de769d0a65c5928b673d38397185 Mon Sep 17 00:00:00 2001
From: Iain Emsley <iain.emsley@warwick.ac.uk>
Date: Fri, 25 Jul 2025 10:14:44 +0100
Subject: [PATCH 024/109] Update reuse-build-and-publish.yml

---
 .github/workflows/reuse-build-and-publish.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/reuse-build-and-publish.yml b/.github/workflows/reuse-build-and-publish.yml
index 967bf7fb4..82f935e36 100644
--- a/.github/workflows/reuse-build-and-publish.yml
+++ b/.github/workflows/reuse-build-and-publish.yml
@@ -69,7 +69,7 @@ on:
 
 permissions:
   contents: read
-  packages: write
+  packages: none
 
 jobs:
   reuse-build-and-push:

From e024c9a14eb2308772baa4e1c1f74a4428edb01c Mon Sep 17 00:00:00 2001
From: Iain Emsley <iain.emsley@warwick.ac.uk>
Date: Fri, 25 Jul 2025 10:16:39 +0100
Subject: [PATCH 025/109] Update reuse-build-and-publish.yml

---
 .github/workflows/reuse-build-and-publish.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/reuse-build-and-publish.yml b/.github/workflows/reuse-build-and-publish.yml
index 82f935e36..0b894f381 100644
--- a/.github/workflows/reuse-build-and-publish.yml
+++ b/.github/workflows/reuse-build-and-publish.yml
@@ -93,7 +93,7 @@ jobs:
         uses: docker/login-action@v3
         with:
           registry: $REGISTRY
-          username: ${{ inputs.actor }}
+          username: ${{ secrets.actor }}
           password: ${{ secrets.gh_token }}
 
       - name: Extract metadata (tags, labels) for Docker

From 5bb1553a38a88b0d70d6b05794879a083fae0c50 Mon Sep 17 00:00:00 2001
From: Iain Emsley <iain.emsley@warwick.ac.uk>
Date: Fri, 25 Jul 2025 10:25:23 +0100
Subject: [PATCH 026/109] Update reuse-build-and-publish.yml

---
 .github/workflows/reuse-build-and-publish.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/reuse-build-and-publish.yml b/.github/workflows/reuse-build-and-publish.yml
index 0b894f381..a12a2def1 100644
--- a/.github/workflows/reuse-build-and-publish.yml
+++ b/.github/workflows/reuse-build-and-publish.yml
@@ -93,8 +93,8 @@ jobs:
         uses: docker/login-action@v3
         with:
           registry: $REGISTRY
-          username: ${{ secrets.actor }}
-          password: ${{ secrets.gh_token }}
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
 
       - name: Extract metadata (tags, labels) for Docker
         id: meta

From bc360267c9ccb2c52daf863923ff5bab860fa6a4 Mon Sep 17 00:00:00 2001
From: Iain Emsley <iain.emsley@warwick.ac.uk>
Date: Fri, 25 Jul 2025 10:26:55 +0100
Subject: [PATCH 027/109] Update reuse-build-and-publish.yml

---
 .github/workflows/reuse-build-and-publish.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/reuse-build-and-publish.yml b/.github/workflows/reuse-build-and-publish.yml
index a12a2def1..3d9fddc51 100644
--- a/.github/workflows/reuse-build-and-publish.yml
+++ b/.github/workflows/reuse-build-and-publish.yml
@@ -92,7 +92,7 @@ jobs:
       - name: Log in to the Container registry
         uses: docker/login-action@v3
         with:
-          registry: $REGISTRY
+          registry: $env.REGISTRY
           username: ${{ github.actor }}
           password: ${{ secrets.GITHUB_TOKEN }}
 

From bb3373219acd3ce8b7617fc8c232724c610d3eed Mon Sep 17 00:00:00 2001
From: Iain Emsley <iain.emsley@warwick.ac.uk>
Date: Fri, 25 Jul 2025 10:27:48 +0100
Subject: [PATCH 028/109] Update reuse-build-and-publish.yml

---
 .github/workflows/reuse-build-and-publish.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/reuse-build-and-publish.yml b/.github/workflows/reuse-build-and-publish.yml
index 3d9fddc51..3ea21f9ed 100644
--- a/.github/workflows/reuse-build-and-publish.yml
+++ b/.github/workflows/reuse-build-and-publish.yml
@@ -92,7 +92,7 @@ jobs:
       - name: Log in to the Container registry
         uses: docker/login-action@v3
         with:
-          registry: $env.REGISTRY
+          registry: ${{ env.REGISTRY }}
           username: ${{ github.actor }}
           password: ${{ secrets.GITHUB_TOKEN }}
 

From 9a0c245820aa382383bacf0e731f4e9d89ea4e87 Mon Sep 17 00:00:00 2001
From: Iain Emsley <iain.emsley@warwick.ac.uk>
Date: Fri, 25 Jul 2025 10:28:52 +0100
Subject: [PATCH 029/109] Update reuse-build-and-publish.yml

---
 .github/workflows/reuse-build-and-publish.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/reuse-build-and-publish.yml b/.github/workflows/reuse-build-and-publish.yml
index 3ea21f9ed..b73826c0c 100644
--- a/.github/workflows/reuse-build-and-publish.yml
+++ b/.github/workflows/reuse-build-and-publish.yml
@@ -112,7 +112,7 @@ jobs:
         with:
           context: .
           push: true
-          tags: $REGISTRY/${{ inputs.image_name }}:${{ inputs.ref_name }}
+          tags: ${{ env.REGISTRY }}/${{ inputs.image_name }}:${{ inputs.ref_name }}
           build-args: |
             CONTAINER_VERSION=${{ inputs.version }}
           labels: ${{ steps.meta.outputs.labels }}

From 296869c5e024a064475dc378a0c92bd22c93c513 Mon Sep 17 00:00:00 2001
From: Iain Emsley <iain.emsley@warwick.ac.uk>
Date: Fri, 25 Jul 2025 10:31:46 +0100
Subject: [PATCH 030/109] Update reuse-build-and-publish.yml

---
 .github/workflows/reuse-build-and-publish.yml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/reuse-build-and-publish.yml b/.github/workflows/reuse-build-and-publish.yml
index b73826c0c..3a2d61597 100644
--- a/.github/workflows/reuse-build-and-publish.yml
+++ b/.github/workflows/reuse-build-and-publish.yml
@@ -9,6 +9,7 @@ name: Build and publish Docker image
 
 env:
   REGISTRY: ghcr.io
+  IMAGE_NAME: ${{ github.repository }}
 
 on:
   workflow_call:
@@ -112,7 +113,7 @@ jobs:
         with:
           context: .
           push: true
-          tags: ${{ env.REGISTRY }}/${{ inputs.image_name }}:${{ inputs.ref_name }}
+          tags: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}:${{ github.ref_name }}
           build-args: |
             CONTAINER_VERSION=${{ inputs.version }}
           labels: ${{ steps.meta.outputs.labels }}

From dd76ce8deccd546f01edc4af18ba66e4f69b4deb Mon Sep 17 00:00:00 2001
From: Iain Emsley <iain.emsley@warwick.ac.uk>
Date: Fri, 25 Jul 2025 10:40:13 +0100
Subject: [PATCH 031/109] Update reuse-build-and-publish.yml

---
 .github/workflows/reuse-build-and-publish.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/reuse-build-and-publish.yml b/.github/workflows/reuse-build-and-publish.yml
index 3a2d61597..a03e12554 100644
--- a/.github/workflows/reuse-build-and-publish.yml
+++ b/.github/workflows/reuse-build-and-publish.yml
@@ -70,7 +70,7 @@ on:
 
 permissions:
   contents: read
-  packages: none
+  packages:write
 
 jobs:
   reuse-build-and-push:

From 88d43b41970bce6409a2a42e7eb385547e85c5aa Mon Sep 17 00:00:00 2001
From: Iain Emsley <iain.emsley@warwick.ac.uk>
Date: Fri, 25 Jul 2025 10:41:10 +0100
Subject: [PATCH 032/109] Update reuse-build-and-publish.yml

---
 .github/workflows/reuse-build-and-publish.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/reuse-build-and-publish.yml b/.github/workflows/reuse-build-and-publish.yml
index a03e12554..3b79272c1 100644
--- a/.github/workflows/reuse-build-and-publish.yml
+++ b/.github/workflows/reuse-build-and-publish.yml
@@ -70,7 +70,7 @@ on:
 
 permissions:
   contents: read
-  packages:write
+  packages: write
 
 jobs:
   reuse-build-and-push:

From 904140bcc4eda86c426d3152c6e25d7bcda7f704 Mon Sep 17 00:00:00 2001
From: Iain Emsley <iain.emsley@warwick.ac.uk>
Date: Fri, 25 Jul 2025 10:50:36 +0100
Subject: [PATCH 033/109] version number

---
 .github/workflows/reuse-build-and-publish.yml | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/reuse-build-and-publish.yml b/.github/workflows/reuse-build-and-publish.yml
index 3b79272c1..386f45031 100644
--- a/.github/workflows/reuse-build-and-publish.yml
+++ b/.github/workflows/reuse-build-and-publish.yml
@@ -85,10 +85,10 @@ jobs:
       - name: Checkout repository
         uses: actions/checkout@v4
 
-      #- name: Extract version number
-      #  run: |
-      #    VER=$(cat VERSION)
-      #    echo "VERSION=$VER" >> $GITHUB_ENV
+      - name: Extract version number
+        run: |
+          VER=$(cat VERSION)
+          echo "VERSION=$VER" >> $GITHUB_ENV
 
       - name: Log in to the Container registry
         uses: docker/login-action@v3

From 9dd190ad25d8868fb0f89c66ccc108fda047560c Mon Sep 17 00:00:00 2001
From: Iain Emsley <iain.emsley@warwick.ac.uk>
Date: Fri, 25 Jul 2025 11:01:27 +0100
Subject: [PATCH 034/109] Update call_jobs.yml

---
 .github/workflows/call_jobs.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/call_jobs.yml b/.github/workflows/call_jobs.yml
index d53573e50..6dfacaf3e 100644
--- a/.github/workflows/call_jobs.yml
+++ b/.github/workflows/call_jobs.yml
@@ -10,6 +10,7 @@ jobs:
   call-workflow-amd64:
     permissions:
       contents: read
+      packages: write
       pull-requests: write
     uses: iaine/r-dev-env/.github/workflows/reuse-build-and-publish.yml@devel
     with:

From 9527f69ce4bad0b1fe88841c03aacc7868f1f9d4 Mon Sep 17 00:00:00 2001
From: Iain Emsley <iain.emsley@warwick.ac.uk>
Date: Fri, 25 Jul 2025 11:02:11 +0100
Subject: [PATCH 035/109] Update call_jobs.yml

---
 .github/workflows/call_jobs.yml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/.github/workflows/call_jobs.yml b/.github/workflows/call_jobs.yml
index 6dfacaf3e..716bb5910 100644
--- a/.github/workflows/call_jobs.yml
+++ b/.github/workflows/call_jobs.yml
@@ -14,7 +14,6 @@ jobs:
       pull-requests: write
     uses: iaine/r-dev-env/.github/workflows/reuse-build-and-publish.yml@devel
     with:
-      config-path: .github/labeler.yml
       event_name: ${{ github.event_name }}
       pull_request: ${{ github.pull_request.merged }}
       repository: ${{ github.event_name }}

From be45553c9149c527a7d82a554eb5e9d42092e4c7 Mon Sep 17 00:00:00 2001
From: Iain Emsley <iain.emsley@warwick.ac.uk>
Date: Fri, 25 Jul 2025 11:05:50 +0100
Subject: [PATCH 036/109] Update call_jobs.yml

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

diff --git a/.github/workflows/call_jobs.yml b/.github/workflows/call_jobs.yml
index 716bb5910..f10d1ed03 100644
--- a/.github/workflows/call_jobs.yml
+++ b/.github/workflows/call_jobs.yml
@@ -17,7 +17,7 @@ jobs:
       event_name: ${{ github.event_name }}
       pull_request: ${{ github.pull_request.merged }}
       repository: ${{ github.event_name }}
-      version: ${{ github.event_name }}
+      #version: ${{ github.event_name }}
       image_name: ${{ github.repository }}
       ref_name: ${{ github.branch }}
       actor: ${{ github.actor }}

From 3bbf9cbb757fcc740fdc02223ffe727446d69806 Mon Sep 17 00:00:00 2001
From: Iain Emsley <iain.emsley@warwick.ac.uk>
Date: Fri, 25 Jul 2025 11:07:14 +0100
Subject: [PATCH 037/109] Update call_jobs.yml

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

diff --git a/.github/workflows/call_jobs.yml b/.github/workflows/call_jobs.yml
index f10d1ed03..7fa1d6edb 100644
--- a/.github/workflows/call_jobs.yml
+++ b/.github/workflows/call_jobs.yml
@@ -17,7 +17,7 @@ jobs:
       event_name: ${{ github.event_name }}
       pull_request: ${{ github.pull_request.merged }}
       repository: ${{ github.event_name }}
-      #version: ${{ github.event_name }}
+      version: $(cat VERSION)
       image_name: ${{ github.repository }}
       ref_name: ${{ github.branch }}
       actor: ${{ github.actor }}

From cae71589f42144f3ff84adb6d337e464e11a0c60 Mon Sep 17 00:00:00 2001
From: Iain Emsley <iain.emsley@warwick.ac.uk>
Date: Fri, 25 Jul 2025 11:07:52 +0100
Subject: [PATCH 038/109] Update call_jobs.yml

---
 .github/workflows/call_jobs.yml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/.github/workflows/call_jobs.yml b/.github/workflows/call_jobs.yml
index 7fa1d6edb..daea65c0d 100644
--- a/.github/workflows/call_jobs.yml
+++ b/.github/workflows/call_jobs.yml
@@ -17,7 +17,6 @@ jobs:
       event_name: ${{ github.event_name }}
       pull_request: ${{ github.pull_request.merged }}
       repository: ${{ github.event_name }}
-      version: $(cat VERSION)
       image_name: ${{ github.repository }}
       ref_name: ${{ github.branch }}
       actor: ${{ github.actor }}

From aed9f657bedf64263a18565d0f4f49e5517372af Mon Sep 17 00:00:00 2001
From: Iain Emsley <iain.emsley@warwick.ac.uk>
Date: Fri, 25 Jul 2025 11:08:22 +0100
Subject: [PATCH 039/109] Update reuse-build-and-publish.yml

---
 .github/workflows/reuse-build-and-publish.yml | 4 ----
 1 file changed, 4 deletions(-)

diff --git a/.github/workflows/reuse-build-and-publish.yml b/.github/workflows/reuse-build-and-publish.yml
index 386f45031..84f229605 100644
--- a/.github/workflows/reuse-build-and-publish.yml
+++ b/.github/workflows/reuse-build-and-publish.yml
@@ -26,10 +26,6 @@ on:
         description: repository name
         required: true
         type: string
-      version: 
-        description: container version
-        required: true
-        type: number
       image_name:
         description: image name
         required: true

From 956907287efdc3e0cecb9eafac54a968600df1f2 Mon Sep 17 00:00:00 2001
From: Iain Emsley <iain.emsley@warwick.ac.uk>
Date: Fri, 25 Jul 2025 11:23:58 +0100
Subject: [PATCH 040/109] Update call_jobs.yml

---
 .github/workflows/call_jobs.yml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/.github/workflows/call_jobs.yml b/.github/workflows/call_jobs.yml
index daea65c0d..589a2d9b9 100644
--- a/.github/workflows/call_jobs.yml
+++ b/.github/workflows/call_jobs.yml
@@ -11,7 +11,6 @@ jobs:
     permissions:
       contents: read
       packages: write
-      pull-requests: write
     uses: iaine/r-dev-env/.github/workflows/reuse-build-and-publish.yml@devel
     with:
       event_name: ${{ github.event_name }}

From cbb235e06b908b03f93197d4d43161201a3836d5 Mon Sep 17 00:00:00 2001
From: Iain Emsley <iain.emsley@warwick.ac.uk>
Date: Fri, 25 Jul 2025 11:31:49 +0100
Subject: [PATCH 041/109] Update reuse-build-and-publish.yml

---
 .github/workflows/reuse-build-and-publish.yml | 7 -------
 1 file changed, 7 deletions(-)

diff --git a/.github/workflows/reuse-build-and-publish.yml b/.github/workflows/reuse-build-and-publish.yml
index 84f229605..c61c31228 100644
--- a/.github/workflows/reuse-build-and-publish.yml
+++ b/.github/workflows/reuse-build-and-publish.yml
@@ -38,13 +38,6 @@ on:
         description: github actor 
         required: true
         type: string
-    secrets:
-      gh_token:
-        required: true
-      username:
-        required: true
-      password:
-        required: true
   push:
     branches:
       - main

From 5c8400f1521cee343aabb3c2b0ade3d593cd2134 Mon Sep 17 00:00:00 2001
From: Iain Emsley <iain.emsley@warwick.ac.uk>
Date: Fri, 25 Jul 2025 11:37:10 +0100
Subject: [PATCH 042/109] Update workflow name

---
 .github/workflows/reuse-build-and-publish.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/reuse-build-and-publish.yml b/.github/workflows/reuse-build-and-publish.yml
index c61c31228..fd4ddc0ce 100644
--- a/.github/workflows/reuse-build-and-publish.yml
+++ b/.github/workflows/reuse-build-and-publish.yml
@@ -5,7 +5,7 @@
 
 #https://github.com/r-devel/r-dev-env/issues/252
 
-name: Build and publish Docker image
+name: Build and publish amd 64 Docker image
 
 env:
   REGISTRY: ghcr.io

From bd527554282d34acf8319f7c5f41c03415fead78 Mon Sep 17 00:00:00 2001
From: Iain Emsley <iain.emsley@warwick.ac.uk>
Date: Fri, 25 Jul 2025 11:37:55 +0100
Subject: [PATCH 043/109] Update reuse-build-and-publish.yml

---
 .github/workflows/reuse-build-and-publish.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/reuse-build-and-publish.yml b/.github/workflows/reuse-build-and-publish.yml
index fd4ddc0ce..a169a8481 100644
--- a/.github/workflows/reuse-build-and-publish.yml
+++ b/.github/workflows/reuse-build-and-publish.yml
@@ -83,7 +83,7 @@ jobs:
         uses: docker/login-action@v3
         with:
           registry: ${{ env.REGISTRY }}
-          username: ${{ github.actor }}
+          username: ${{ inputs.actor }}
           password: ${{ secrets.GITHUB_TOKEN }}
 
       - name: Extract metadata (tags, labels) for Docker

From f4f5b123f0415b674ec605a242da63067bbc74e5 Mon Sep 17 00:00:00 2001
From: Iain Emsley <iain.emsley@warwick.ac.uk>
Date: Fri, 25 Jul 2025 11:39:33 +0100
Subject: [PATCH 044/109] Remove actor

---
 .github/workflows/reuse-build-and-publish.yml | 6 +-----
 1 file changed, 1 insertion(+), 5 deletions(-)

diff --git a/.github/workflows/reuse-build-and-publish.yml b/.github/workflows/reuse-build-and-publish.yml
index a169a8481..3d1a686a7 100644
--- a/.github/workflows/reuse-build-and-publish.yml
+++ b/.github/workflows/reuse-build-and-publish.yml
@@ -34,10 +34,6 @@ on:
         description: ref name
         required: true
         type: string
-      actor: 
-        description: github actor 
-        required: true
-        type: string
   push:
     branches:
       - main
@@ -83,7 +79,7 @@ jobs:
         uses: docker/login-action@v3
         with:
           registry: ${{ env.REGISTRY }}
-          username: ${{ inputs.actor }}
+          username: ${{ github.actor }}
           password: ${{ secrets.GITHUB_TOKEN }}
 
       - name: Extract metadata (tags, labels) for Docker

From a1e77a436adcd153de144abddea2dda0309e0142 Mon Sep 17 00:00:00 2001
From: Iain Emsley <iain.emsley@warwick.ac.uk>
Date: Fri, 25 Jul 2025 11:40:13 +0100
Subject: [PATCH 045/109] Align call inputs with file inputs

---
 .github/workflows/call_jobs.yml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/.github/workflows/call_jobs.yml b/.github/workflows/call_jobs.yml
index 589a2d9b9..5666b20fb 100644
--- a/.github/workflows/call_jobs.yml
+++ b/.github/workflows/call_jobs.yml
@@ -18,5 +18,4 @@ jobs:
       repository: ${{ github.event_name }}
       image_name: ${{ github.repository }}
       ref_name: ${{ github.branch }}
-      actor: ${{ github.actor }}
     secrets: inherit

From 9b584745c6089cdb66a420ff948d630e0bd734a2 Mon Sep 17 00:00:00 2001
From: Iain Emsley <iain.emsley@warwick.ac.uk>
Date: Fri, 25 Jul 2025 11:47:16 +0100
Subject: [PATCH 046/109] Update call_jobs.yml

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

diff --git a/.github/workflows/call_jobs.yml b/.github/workflows/call_jobs.yml
index 5666b20fb..11f2f39b0 100644
--- a/.github/workflows/call_jobs.yml
+++ b/.github/workflows/call_jobs.yml
@@ -15,7 +15,7 @@ jobs:
     with:
       event_name: ${{ github.event_name }}
       pull_request: ${{ github.pull_request.merged }}
-      repository: ${{ github.event_name }}
+      repository: ${{ github.repository }}
       image_name: ${{ github.repository }}
       ref_name: ${{ github.branch }}
     secrets: inherit

From 0ad67e74c9757bac73a4b36b8724c5d31c62676a Mon Sep 17 00:00:00 2001
From: Iain Emsley <Iain.Emsley@warwick.ac.uk>
Date: Mon, 28 Jul 2025 11:16:18 +0100
Subject: [PATCH 047/109] Cleaning up workflows

---
 .github/workflows/call_jobs.yml               |  2 +-
 .github/workflows/reuse-build-and-publish.yml | 18 +++++++++---------
 2 files changed, 10 insertions(+), 10 deletions(-)

diff --git a/.github/workflows/call_jobs.yml b/.github/workflows/call_jobs.yml
index 11f2f39b0..a9fb8306f 100644
--- a/.github/workflows/call_jobs.yml
+++ b/.github/workflows/call_jobs.yml
@@ -16,6 +16,6 @@ jobs:
       event_name: ${{ github.event_name }}
       pull_request: ${{ github.pull_request.merged }}
       repository: ${{ github.repository }}
-      image_name: ${{ github.repository }}
       ref_name: ${{ github.branch }}
+      actor: ${{ github.actor }}
     secrets: inherit
diff --git a/.github/workflows/reuse-build-and-publish.yml b/.github/workflows/reuse-build-and-publish.yml
index 3d1a686a7..cd38b6e57 100644
--- a/.github/workflows/reuse-build-and-publish.yml
+++ b/.github/workflows/reuse-build-and-publish.yml
@@ -26,14 +26,14 @@ on:
         description: repository name
         required: true
         type: string
-      image_name:
-        description: image name
-        required: true
-        type: string
       ref_name: 
         description: ref name
         required: true
         type: string
+      actor: 
+        description: actor
+        required: true
+        type: string
   push:
     branches:
       - main
@@ -79,18 +79,18 @@ jobs:
         uses: docker/login-action@v3
         with:
           registry: ${{ env.REGISTRY }}
-          username: ${{ github.actor }}
+          username: ${{ inputs.actor }}
           password: ${{ secrets.GITHUB_TOKEN }}
 
       - name: Extract metadata (tags, labels) for Docker
         id: meta
         uses: docker/metadata-action@v5
         with:
-          images: $REGISTRY/${{ inputs.repository }}
+          images: ${{ env.REGISTRY }}/${{ inputs.repository }}
           tags: |
             type=ref,event=branch
             type=ref,event=pr
-            type=semver,pattern=${{ inputs.version }}
+            type=semver,pattern=${{ $VER }}
             type=sha
 
       - name: Build and push Docker image
@@ -98,7 +98,7 @@ jobs:
         with:
           context: .
           push: true
-          tags: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}:${{ github.ref_name }}
+          tags: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}:${{ inputs.ref_name }}
           build-args: |
-            CONTAINER_VERSION=${{ inputs.version }}
+            CONTAINER_VERSION=${{ $VER }}
           labels: ${{ steps.meta.outputs.labels }}

From 354128167eb87356274d0d2743c160d82f65bd00 Mon Sep 17 00:00:00 2001
From: Iain Emsley <Iain.Emsley@warwick.ac.uk>
Date: Mon, 28 Jul 2025 11:17:13 +0100
Subject: [PATCH 048/109] Cleaning up workflows

---
 .github/workflows/reuse-build-and-publish.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/reuse-build-and-publish.yml b/.github/workflows/reuse-build-and-publish.yml
index cd38b6e57..ef051d4e9 100644
--- a/.github/workflows/reuse-build-and-publish.yml
+++ b/.github/workflows/reuse-build-and-publish.yml
@@ -90,7 +90,7 @@ jobs:
           tags: |
             type=ref,event=branch
             type=ref,event=pr
-            type=semver,pattern=${{ $VER }}
+            type=semver,pattern=${{ VER }}
             type=sha
 
       - name: Build and push Docker image
@@ -100,5 +100,5 @@ jobs:
           push: true
           tags: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}:${{ inputs.ref_name }}
           build-args: |
-            CONTAINER_VERSION=${{ $VER }}
+            CONTAINER_VERSION=${{ VER }}
           labels: ${{ steps.meta.outputs.labels }}

From 89135e9c86b75ad09be9e7e9c7fbe06b124f392b Mon Sep 17 00:00:00 2001
From: Iain Emsley <Iain.Emsley@warwick.ac.uk>
Date: Mon, 28 Jul 2025 11:19:11 +0100
Subject: [PATCH 049/109] Cleaning up workflows

---
 .github/workflows/reuse-build-and-publish.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/reuse-build-and-publish.yml b/.github/workflows/reuse-build-and-publish.yml
index ef051d4e9..5b1a93a8c 100644
--- a/.github/workflows/reuse-build-and-publish.yml
+++ b/.github/workflows/reuse-build-and-publish.yml
@@ -100,5 +100,5 @@ jobs:
           push: true
           tags: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}:${{ inputs.ref_name }}
           build-args: |
-            CONTAINER_VERSION=${{ VER }}
+            CONTAINER_VERSION=${{ env.VERSION }}
           labels: ${{ steps.meta.outputs.labels }}

From 8cf5866a18e085bc097f1d6ea826f3398177a543 Mon Sep 17 00:00:00 2001
From: Iain Emsley <Iain.Emsley@warwick.ac.uk>
Date: Mon, 28 Jul 2025 11:20:00 +0100
Subject: [PATCH 050/109] Cleaning up workflows

---
 .github/workflows/reuse-build-and-publish.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/reuse-build-and-publish.yml b/.github/workflows/reuse-build-and-publish.yml
index 5b1a93a8c..f139806c5 100644
--- a/.github/workflows/reuse-build-and-publish.yml
+++ b/.github/workflows/reuse-build-and-publish.yml
@@ -90,7 +90,7 @@ jobs:
           tags: |
             type=ref,event=branch
             type=ref,event=pr
-            type=semver,pattern=${{ VER }}
+            type=semver,pattern=${{ env.VERSION }}
             type=sha
 
       - name: Build and push Docker image

From ec32dee43b6d2e62e0ba6321bdd6daa1ae16c3e2 Mon Sep 17 00:00:00 2001
From: Iain Emsley <Iain.Emsley@warwick.ac.uk>
Date: Mon, 28 Jul 2025 11:25:09 +0100
Subject: [PATCH 051/109] Cleaning up workflows

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

diff --git a/.github/workflows/call_jobs.yml b/.github/workflows/call_jobs.yml
index a9fb8306f..374423c91 100644
--- a/.github/workflows/call_jobs.yml
+++ b/.github/workflows/call_jobs.yml
@@ -16,6 +16,6 @@ jobs:
       event_name: ${{ github.event_name }}
       pull_request: ${{ github.pull_request.merged }}
       repository: ${{ github.repository }}
-      ref_name: ${{ github.branch }}
+      ref_name: ${{ github.ref_name }}
       actor: ${{ github.actor }}
     secrets: inherit

From dd156dcdce0d0ba974110ddfd1a1cd3cb4a67854 Mon Sep 17 00:00:00 2001
From: Iain Emsley <Iain.Emsley@warwick.ac.uk>
Date: Mon, 28 Jul 2025 11:42:22 +0100
Subject: [PATCH 052/109] Cleaning up workflows

---
 .github/workflows/call_jobs.yml               |  3 ++-
 .github/workflows/reuse-build-and-publish.yml | 18 +++++++++---------
 2 files changed, 11 insertions(+), 10 deletions(-)

diff --git a/.github/workflows/call_jobs.yml b/.github/workflows/call_jobs.yml
index 374423c91..c1e9245f9 100644
--- a/.github/workflows/call_jobs.yml
+++ b/.github/workflows/call_jobs.yml
@@ -15,7 +15,8 @@ jobs:
     with:
       event_name: ${{ github.event_name }}
       pull_request: ${{ github.pull_request.merged }}
-      repository: ${{ github.repository }}
+      image_name: ${{ github.repository }}
       ref_name: ${{ github.ref_name }}
       actor: ${{ github.actor }}
+      registry: ghcr.io
     secrets: inherit
diff --git a/.github/workflows/reuse-build-and-publish.yml b/.github/workflows/reuse-build-and-publish.yml
index f139806c5..7b5101bf8 100644
--- a/.github/workflows/reuse-build-and-publish.yml
+++ b/.github/workflows/reuse-build-and-publish.yml
@@ -7,10 +7,6 @@
 
 name: Build and publish amd 64 Docker image
 
-env:
-  REGISTRY: ghcr.io
-  IMAGE_NAME: ${{ github.repository }}
-
 on:
   workflow_call:
     inputs:
@@ -22,8 +18,8 @@ on:
         description: pull request
         required: false
         type: string
-      repository: 
-        description: repository name
+      image_name: 
+        description: image name
         required: true
         type: string
       ref_name: 
@@ -34,6 +30,10 @@ on:
         description: actor
         required: true
         type: string
+      registry: 
+        description: registry
+        required: true
+        type: string
   push:
     branches:
       - main
@@ -78,7 +78,7 @@ jobs:
       - name: Log in to the Container registry
         uses: docker/login-action@v3
         with:
-          registry: ${{ env.REGISTRY }}
+          registry: ${{ inputs.repository }}
           username: ${{ inputs.actor }}
           password: ${{ secrets.GITHUB_TOKEN }}
 
@@ -86,7 +86,7 @@ jobs:
         id: meta
         uses: docker/metadata-action@v5
         with:
-          images: ${{ env.REGISTRY }}/${{ inputs.repository }}
+          images: ${{ inputs.registry }}/${{ inputs.image_name }}
           tags: |
             type=ref,event=branch
             type=ref,event=pr
@@ -98,7 +98,7 @@ jobs:
         with:
           context: .
           push: true
-          tags: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}:${{ inputs.ref_name }}
+          tags: ${{ inputs.registry }}/${{ inputs.image_name }}:${{ inputs.ref_name }}
           build-args: |
             CONTAINER_VERSION=${{ env.VERSION }}
           labels: ${{ steps.meta.outputs.labels }}

From 9983aebc0173161a9d26e383a4a7e69c1381f4a0 Mon Sep 17 00:00:00 2001
From: Iain Emsley <Iain.Emsley@warwick.ac.uk>
Date: Mon, 28 Jul 2025 11:48:20 +0100
Subject: [PATCH 053/109] Cleaning up workflows

---
 .github/workflows/reuse-build-and-publish.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/reuse-build-and-publish.yml b/.github/workflows/reuse-build-and-publish.yml
index 7b5101bf8..4dca96823 100644
--- a/.github/workflows/reuse-build-and-publish.yml
+++ b/.github/workflows/reuse-build-and-publish.yml
@@ -79,7 +79,7 @@ jobs:
         uses: docker/login-action@v3
         with:
           registry: ${{ inputs.repository }}
-          username: ${{ inputs.actor }}
+          username: ${{ github.actor }}
           password: ${{ secrets.GITHUB_TOKEN }}
 
       - name: Extract metadata (tags, labels) for Docker

From a863bec59eae7b69218d2c3e6d86c8020ca3e89d Mon Sep 17 00:00:00 2001
From: Iain Emsley <Iain.Emsley@warwick.ac.uk>
Date: Mon, 28 Jul 2025 11:51:56 +0100
Subject: [PATCH 054/109] Cleaning up workflows

---
 .github/workflows/reuse-build-and-publish.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/reuse-build-and-publish.yml b/.github/workflows/reuse-build-and-publish.yml
index 4dca96823..8d3ab4c24 100644
--- a/.github/workflows/reuse-build-and-publish.yml
+++ b/.github/workflows/reuse-build-and-publish.yml
@@ -78,7 +78,7 @@ jobs:
       - name: Log in to the Container registry
         uses: docker/login-action@v3
         with:
-          registry: ${{ inputs.repository }}
+          registry: ${{ inputs.registry }}
           username: ${{ github.actor }}
           password: ${{ secrets.GITHUB_TOKEN }}
 

From 7bd0a7f3f98385292b32d5634fb68a051e11304f Mon Sep 17 00:00:00 2001
From: Iain Emsley <iain.emsley@warwick.ac.uk>
Date: Tue, 29 Jul 2025 12:30:26 +0100
Subject: [PATCH 055/109] Update reuse-build-and-publish.yml

---
 .github/workflows/reuse-build-and-publish.yml | 35 +------------------
 1 file changed, 1 insertion(+), 34 deletions(-)

diff --git a/.github/workflows/reuse-build-and-publish.yml b/.github/workflows/reuse-build-and-publish.yml
index 8d3ab4c24..b67b86924 100644
--- a/.github/workflows/reuse-build-and-publish.yml
+++ b/.github/workflows/reuse-build-and-publish.yml
@@ -3,21 +3,11 @@
 # separate terms of service, privacy policy, and support
 # documentation.
 
-#https://github.com/r-devel/r-dev-env/issues/252
-
 name: Build and publish amd 64 Docker image
 
 on:
   workflow_call:
     inputs:
-      event_name: 
-        description: event name
-        required: true
-        type: string
-      pull_request: 
-        description: pull request
-        required: false
-        type: string
       image_name: 
         description: image name
         required: true
@@ -34,36 +24,13 @@ on:
         description: registry
         required: true
         type: string
-  push:
-    branches:
-      - main
-      - devel
-    paths:
-      - '.github/workflows/reuse-build-and-publish.yml'
-  pull_request:
-    branches:
-      - main
-      - devel
-    types:
-      - closed
-    paths:
-      - '.github/workflows/reuse-build-and-publish.yml'
-      - '.devcontainer/devcontainer.json'
-      - 'Dockerfile'
-      - 'reinstall-cmake.sh'
-      - 'VERSION'
-
 permissions:
   contents: read
   packages: write
 
 jobs:
   reuse-build-and-push:
-    if:  |
-      ${{ inputs.event_name }} == 'workflow_dispatch' ||
-      ${{ inputs.event_name }} == 'push' ||
-      (${{ inputs.event_name }} == 'pull_request' &&
-       ${{ inputs.pull_request }} == true)
+
     runs-on: ubuntu-latest
 
     steps:

From 9bdd69713dfbf876ee58dc9d31cb3751dba2c7b0 Mon Sep 17 00:00:00 2001
From: Iain Emsley <iain.emsley@warwick.ac.uk>
Date: Tue, 29 Jul 2025 12:31:24 +0100
Subject: [PATCH 056/109] Update call_jobs.yml

---
 .github/workflows/call_jobs.yml | 16 +++++++++++++++-
 1 file changed, 15 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/call_jobs.yml b/.github/workflows/call_jobs.yml
index c1e9245f9..1eb028d67 100644
--- a/.github/workflows/call_jobs.yml
+++ b/.github/workflows/call_jobs.yml
@@ -3,8 +3,22 @@ name: Call reusable workflows
 on:
   push:
     branches:
-      - master
+      - main
       - devel
+    paths:
+      - '.github/workflows/reuse-build-and-publish-amd.yml'
+  pull_request:
+    branches:
+      - main
+      - devel
+    types:
+      - closed
+    paths:
+      - '.github/workflows/reuse-build-and-publish-amd.yml'
+      - '.devcontainer/devcontainer.json'
+      - 'Dockerfile'
+      - 'reinstall-cmake.sh'
+      - 'VERSION'
 
 jobs:
   call-workflow-amd64:

From f97403c10d3d2a8cc48420efa56f611743267ef7 Mon Sep 17 00:00:00 2001
From: Iain Emsley <iain.emsley@warwick.ac.uk>
Date: Tue, 29 Jul 2025 12:31:43 +0100
Subject: [PATCH 057/109] Update call_jobs.yml

---
 .github/workflows/call_jobs.yml | 2 --
 1 file changed, 2 deletions(-)

diff --git a/.github/workflows/call_jobs.yml b/.github/workflows/call_jobs.yml
index 1eb028d67..ef3cd3c0b 100644
--- a/.github/workflows/call_jobs.yml
+++ b/.github/workflows/call_jobs.yml
@@ -27,8 +27,6 @@ jobs:
       packages: write
     uses: iaine/r-dev-env/.github/workflows/reuse-build-and-publish.yml@devel
     with:
-      event_name: ${{ github.event_name }}
-      pull_request: ${{ github.pull_request.merged }}
       image_name: ${{ github.repository }}
       ref_name: ${{ github.ref_name }}
       actor: ${{ github.actor }}

From 838c64640879d831b91a2813cb8bfd00ddf43ad5 Mon Sep 17 00:00:00 2001
From: Iain Emsley <iain.emsley@warwick.ac.uk>
Date: Tue, 29 Jul 2025 12:34:52 +0100
Subject: [PATCH 058/109] Update reuse-build-and-publish.yml

---
 .github/workflows/reuse-build-and-publish.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/reuse-build-and-publish.yml b/.github/workflows/reuse-build-and-publish.yml
index b67b86924..8c004531c 100644
--- a/.github/workflows/reuse-build-and-publish.yml
+++ b/.github/workflows/reuse-build-and-publish.yml
@@ -65,6 +65,7 @@ jobs:
         with:
           context: .
           push: true
+          pull_request: true
           tags: ${{ inputs.registry }}/${{ inputs.image_name }}:${{ inputs.ref_name }}
           build-args: |
             CONTAINER_VERSION=${{ env.VERSION }}

From 47d4920c1bae1c67167739b564279e2cdcdc7eb1 Mon Sep 17 00:00:00 2001
From: Iain Emsley <iain.emsley@warwick.ac.uk>
Date: Tue, 29 Jul 2025 12:38:38 +0100
Subject: [PATCH 059/109] Update call_jobs.yml

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

diff --git a/.github/workflows/call_jobs.yml b/.github/workflows/call_jobs.yml
index ef3cd3c0b..7b1b34da8 100644
--- a/.github/workflows/call_jobs.yml
+++ b/.github/workflows/call_jobs.yml
@@ -25,7 +25,7 @@ jobs:
     permissions:
       contents: read
       packages: write
-    uses: iaine/r-dev-env/.github/workflows/reuse-build-and-publish.yml@devel
+    uses: iaine/r-dev-env/.github/workflows/reuse-build-and-publish.yml@${{ github.ref_name }}
     with:
       image_name: ${{ github.repository }}
       ref_name: ${{ github.ref_name }}

From 3098c5378d1445364ed96e912454b5554293580e Mon Sep 17 00:00:00 2001
From: Iain Emsley <iain.emsley@warwick.ac.uk>
Date: Tue, 29 Jul 2025 12:41:44 +0100
Subject: [PATCH 060/109] Update call_jobs.yml

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

diff --git a/.github/workflows/call_jobs.yml b/.github/workflows/call_jobs.yml
index 7b1b34da8..7a751a852 100644
--- a/.github/workflows/call_jobs.yml
+++ b/.github/workflows/call_jobs.yml
@@ -1,12 +1,6 @@
 name: Call reusable workflows
 
 on:
-  push:
-    branches:
-      - main
-      - devel
-    paths:
-      - '.github/workflows/reuse-build-and-publish-amd.yml'
   pull_request:
     branches:
       - main
@@ -25,7 +19,7 @@ jobs:
     permissions:
       contents: read
       packages: write
-    uses: iaine/r-dev-env/.github/workflows/reuse-build-and-publish.yml@${{ github.ref_name }}
+    uses: r-devel/r-dev-env/.github/workflows/reuse-build-and-publish.yml@${{ github.ref_name }}
     with:
       image_name: ${{ github.repository }}
       ref_name: ${{ github.ref_name }}

From fe6319cec280fd5a78d5644a348dcbe8f5544404 Mon Sep 17 00:00:00 2001
From: Iain Emsley <iain.emsley@warwick.ac.uk>
Date: Tue, 29 Jul 2025 12:49:14 +0100
Subject: [PATCH 061/109] Ref name fix to call

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

diff --git a/.github/workflows/call_jobs.yml b/.github/workflows/call_jobs.yml
index 7a751a852..7457b3274 100644
--- a/.github/workflows/call_jobs.yml
+++ b/.github/workflows/call_jobs.yml
@@ -19,7 +19,7 @@ jobs:
     permissions:
       contents: read
       packages: write
-    uses: r-devel/r-dev-env/.github/workflows/reuse-build-and-publish.yml@${{ github.ref_name }}
+    uses: r-devel/r-dev-env/.github/workflows/reuse-build-and-publish.yml@${{github.ref_name}}
     with:
       image_name: ${{ github.repository }}
       ref_name: ${{ github.ref_name }}

From 26921c865d0ce6ffa8567e62995d9f2cc48e20fe Mon Sep 17 00:00:00 2001
From: Iain Emsley <iain.emsley@warwick.ac.uk>
Date: Tue, 29 Jul 2025 12:54:34 +0100
Subject: [PATCH 062/109] Update call_jobs.yml

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

diff --git a/.github/workflows/call_jobs.yml b/.github/workflows/call_jobs.yml
index 7457b3274..a42da7000 100644
--- a/.github/workflows/call_jobs.yml
+++ b/.github/workflows/call_jobs.yml
@@ -1,6 +1,9 @@
 name: Call reusable workflows
 
 on:
+  push:
+    branches:
+      - devel
   pull_request:
     branches:
       - main

From c67b970910a34869cc5ae07ad42aa35e7e3d0e46 Mon Sep 17 00:00:00 2001
From: Iain Emsley <iain.emsley@warwick.ac.uk>
Date: Tue, 29 Jul 2025 12:55:19 +0100
Subject: [PATCH 063/109] Update call_jobs.yml

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

diff --git a/.github/workflows/call_jobs.yml b/.github/workflows/call_jobs.yml
index a42da7000..f712ee0b4 100644
--- a/.github/workflows/call_jobs.yml
+++ b/.github/workflows/call_jobs.yml
@@ -22,7 +22,7 @@ jobs:
     permissions:
       contents: read
       packages: write
-    uses: r-devel/r-dev-env/.github/workflows/reuse-build-and-publish.yml@${{github.ref_name}}
+    uses: iaine/r-dev-env/.github/workflows/reuse-build-and-publish.yml@${{github.ref_name}}
     with:
       image_name: ${{ github.repository }}
       ref_name: ${{ github.ref_name }}

From b7a7f32e7bacab43b7295a5cb12d4a2b536fea62 Mon Sep 17 00:00:00 2001
From: Iain Emsley <iain.emsley@warwick.ac.uk>
Date: Tue, 29 Jul 2025 12:57:48 +0100
Subject: [PATCH 064/109] Update call_jobs.yml

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

diff --git a/.github/workflows/call_jobs.yml b/.github/workflows/call_jobs.yml
index f712ee0b4..084aa8d47 100644
--- a/.github/workflows/call_jobs.yml
+++ b/.github/workflows/call_jobs.yml
@@ -22,7 +22,7 @@ jobs:
     permissions:
       contents: read
       packages: write
-    uses: iaine/r-dev-env/.github/workflows/reuse-build-and-publish.yml@${{github.ref_name}}
+    uses: iaine/r-dev-env/.github/workflows/reuse-build-and-publish.yml@$GITHUB_REF
     with:
       image_name: ${{ github.repository }}
       ref_name: ${{ github.ref_name }}

From 2fa7f0572f1c6e9b59cdfa789163d6edf71fbe8d Mon Sep 17 00:00:00 2001
From: Iain Emsley <iain.emsley@warwick.ac.uk>
Date: Tue, 29 Jul 2025 12:58:44 +0100
Subject: [PATCH 065/109] Adding ref

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

diff --git a/.github/workflows/call_jobs.yml b/.github/workflows/call_jobs.yml
index 084aa8d47..e37d6474a 100644
--- a/.github/workflows/call_jobs.yml
+++ b/.github/workflows/call_jobs.yml
@@ -22,7 +22,7 @@ jobs:
     permissions:
       contents: read
       packages: write
-    uses: iaine/r-dev-env/.github/workflows/reuse-build-and-publish.yml@$GITHUB_REF
+    uses: iaine/r-dev-env/.github/workflows/reuse-build-and-publish.yml@${{ github.ref_name }}
     with:
       image_name: ${{ github.repository }}
       ref_name: ${{ github.ref_name }}

From 180861e057e04a018650dbac8b1434189056b85d Mon Sep 17 00:00:00 2001
From: Iain Emsley <iain.emsley@warwick.ac.uk>
Date: Tue, 29 Jul 2025 12:59:32 +0100
Subject: [PATCH 066/109] remove whitespace

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

diff --git a/.github/workflows/call_jobs.yml b/.github/workflows/call_jobs.yml
index e37d6474a..f712ee0b4 100644
--- a/.github/workflows/call_jobs.yml
+++ b/.github/workflows/call_jobs.yml
@@ -22,7 +22,7 @@ jobs:
     permissions:
       contents: read
       packages: write
-    uses: iaine/r-dev-env/.github/workflows/reuse-build-and-publish.yml@${{ github.ref_name }}
+    uses: iaine/r-dev-env/.github/workflows/reuse-build-and-publish.yml@${{github.ref_name}}
     with:
       image_name: ${{ github.repository }}
       ref_name: ${{ github.ref_name }}

From baae071f19d4fc9f94a8577c18e983986f8430b5 Mon Sep 17 00:00:00 2001
From: Iain Emsley <iain.emsley@warwick.ac.uk>
Date: Tue, 29 Jul 2025 13:10:06 +0100
Subject: [PATCH 067/109] call locally

https://github.blog/changelog/2022-01-25-github-actions-reusable-workflows-can-be-referenced-locally/
---
 .github/workflows/call_jobs.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/call_jobs.yml b/.github/workflows/call_jobs.yml
index f712ee0b4..aa81edc45 100644
--- a/.github/workflows/call_jobs.yml
+++ b/.github/workflows/call_jobs.yml
@@ -22,7 +22,7 @@ jobs:
     permissions:
       contents: read
       packages: write
-    uses: iaine/r-dev-env/.github/workflows/reuse-build-and-publish.yml@${{github.ref_name}}
+    uses: ./.github/workflows/reuse-build-and-publish.yml@${{github.ref_name}}
     with:
       image_name: ${{ github.repository }}
       ref_name: ${{ github.ref_name }}

From 3a11ab9a09814f7e7b5f800efe428ff21cd7f588 Mon Sep 17 00:00:00 2001
From: Iain Emsley <iain.emsley@warwick.ac.uk>
Date: Tue, 29 Jul 2025 13:10:47 +0100
Subject: [PATCH 068/109] Update call_jobs.yml

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

diff --git a/.github/workflows/call_jobs.yml b/.github/workflows/call_jobs.yml
index aa81edc45..380db5015 100644
--- a/.github/workflows/call_jobs.yml
+++ b/.github/workflows/call_jobs.yml
@@ -22,7 +22,7 @@ jobs:
     permissions:
       contents: read
       packages: write
-    uses: ./.github/workflows/reuse-build-and-publish.yml@${{github.ref_name}}
+    uses: ./.github/workflows/reuse-build-and-publish.yml
     with:
       image_name: ${{ github.repository }}
       ref_name: ${{ github.ref_name }}

From cd4ec5fdd209471b5e8ef284a588636528de8ebf Mon Sep 17 00:00:00 2001
From: Iain Emsley <iain.emsley@warwick.ac.uk>
Date: Tue, 29 Jul 2025 13:52:41 +0100
Subject: [PATCH 069/109] Update pull-request

---
 .github/workflows/reuse-build-and-publish.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/reuse-build-and-publish.yml b/.github/workflows/reuse-build-and-publish.yml
index 8c004531c..968290fe7 100644
--- a/.github/workflows/reuse-build-and-publish.yml
+++ b/.github/workflows/reuse-build-and-publish.yml
@@ -65,7 +65,7 @@ jobs:
         with:
           context: .
           push: true
-          pull_request: true
+          pull: true
           tags: ${{ inputs.registry }}/${{ inputs.image_name }}:${{ inputs.ref_name }}
           build-args: |
             CONTAINER_VERSION=${{ env.VERSION }}

From a03fa0614fafa72b6b875b01bbbe83f29a153137 Mon Sep 17 00:00:00 2001
From: Iain Emsley <iain.emsley@warwick.ac.uk>
Date: Tue, 29 Jul 2025 14:18:24 +0100
Subject: [PATCH 070/109] Testing if statement

---
 .github/workflows/call_jobs.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/call_jobs.yml b/.github/workflows/call_jobs.yml
index 380db5015..df4de252a 100644
--- a/.github/workflows/call_jobs.yml
+++ b/.github/workflows/call_jobs.yml
@@ -22,6 +22,7 @@ jobs:
     permissions:
       contents: read
       packages: write
+    if: ${{ github.ref_name == 'main' }} || ${{ github.ref_name == 'devel' }}
     uses: ./.github/workflows/reuse-build-and-publish.yml
     with:
       image_name: ${{ github.repository }}

From ab06202be54a96b3a36cb58e675a1a5603f9d507 Mon Sep 17 00:00:00 2001
From: Iain Emsley <iain.emsley@warwick.ac.uk>
Date: Tue, 29 Jul 2025 14:23:08 +0100
Subject: [PATCH 071/109] Update call_jobs.yml with workflows

---
 .github/workflows/call_jobs.yml | 15 ++++++++++++---
 1 file changed, 12 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/call_jobs.yml b/.github/workflows/call_jobs.yml
index df4de252a..96e6cebd6 100644
--- a/.github/workflows/call_jobs.yml
+++ b/.github/workflows/call_jobs.yml
@@ -18,12 +18,21 @@ on:
       - 'VERSION'
 
 jobs:
-  call-workflow-amd64:
+  call-workflow-amd64-main:
+    if: ${{ github.ref_name == 'main' }}
     permissions:
       contents: read
       packages: write
-    if: ${{ github.ref_name == 'main' }} || ${{ github.ref_name == 'devel' }}
-    uses: ./.github/workflows/reuse-build-and-publish.yml
+    uses: iaine/r-dev-env/.github/workflows/reuse-build-and-publish.yml@main
+    with:
+      image_name: ${{ github.repository }}
+      ref_name: ${{ github.ref_name }}
+      actor: ${{ github.actor }}
+      registry: ghcr.io
+    secrets: inherit
+  call-workflow-amd64-devel:
+    if: ${{ github.ref_name == 'devel' }}
+    uses: iaine/r-dev-env/.github/workflows/reuse-build-and-publish.yml@devel
     with:
       image_name: ${{ github.repository }}
       ref_name: ${{ github.ref_name }}

From bdb0f08a9444c414a1208d76a6cdd66b61970bd4 Mon Sep 17 00:00:00 2001
From: Iain Emsley <iain.emsley@warwick.ac.uk>
Date: Tue, 29 Jul 2025 14:24:14 +0100
Subject: [PATCH 072/109] Update call_jobs.yml

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

diff --git a/.github/workflows/call_jobs.yml b/.github/workflows/call_jobs.yml
index 96e6cebd6..da24892ed 100644
--- a/.github/workflows/call_jobs.yml
+++ b/.github/workflows/call_jobs.yml
@@ -23,7 +23,7 @@ jobs:
     permissions:
       contents: read
       packages: write
-    uses: iaine/r-dev-env/.github/workflows/reuse-build-and-publish.yml@main
+    uses: ./.github/workflows/reuse-build-and-publish.yml
     with:
       image_name: ${{ github.repository }}
       ref_name: ${{ github.ref_name }}

From f99c69f0efc35559903dabdc5571ce3c204e7f3d Mon Sep 17 00:00:00 2001
From: Iain Emsley <Iain.Emsley@warwick.ac.uk>
Date: Mon, 11 Aug 2025 10:43:27 +0100
Subject: [PATCH 073/109] Initial manifest script

---
 scripts/manifestR.R | 229 ++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 229 insertions(+)
 create mode 100644 scripts/manifestR.R

diff --git a/scripts/manifestR.R b/scripts/manifestR.R
new file mode 100644
index 000000000..78ad78b45
--- /dev/null
+++ b/scripts/manifestR.R
@@ -0,0 +1,229 @@
+# manifestR.R
+#
+# Files takes the container arguments and creates two files inside the
+# given container. These are the build history and manifest files.
+#
+# The build history file has the locations of the manifest and git history
+# files. This is stored in the location given in histlines argument.
+#
+# The manifest file has the installed apt and R packages written into it
+# along with the build time and commit hash for this build. This is is stored
+# in the manifestdir location.
+#
+# Both are stored as markdown files on the container itself.
+
+library(optparse)
+
+option_list <- list(
+  make_option(c("-r", "--registry"), type = "character", default = "ghcr.io",
+              help = "Registry name"),
+  make_option(c("-o", "--owner"), type = "character", default = "r-devel",
+              help = "Current owner of the Repository"),
+  make_option(c("-i", "--image"), type = "character", default = "devel",
+              help = "Provide the image name [default %default]"),
+  make_option(c("-v", "--version"), type = "double", default = 0.3,
+              help = "version of the image  [default %default]"),
+  make_option(c("-t", "--historydir"), type = "character",
+              default = "/tmp/hist_lines/", help = "location of history lines"),
+  make_option(c("-m", "--manifestdir"), type = "character",
+              default = "/tmp/manifests/",
+              help = "Manifest file location  [default %default]"),
+  make_option(c("-p", "--repository"), type = "character",
+              default = "r-dev-env", help = "Repository name [ %default]")
+)
+
+parser <- OptionParser(usage = "%prog [options] file",
+                       option_list = option_list)
+
+args <- parse_args(parser, positional_arguments = 0)
+opt <- args$options
+
+#set up constants
+build_time <- as.numeric(Sys.time())
+tm <- as.POSIXlt(build_time, "UTC")
+utc_time <- strftime(tm, "%Y-%m-%dT%H:%M:%S%z")
+
+manifest_filename <- paste("manifest-", build_time, ".md", collapse = NULL,
+                           sep = "")
+
+history_filename <- paste("history-", build_time, ".md", collapse = NULL,
+                          sep = "")
+
+#set up docker
+docker_id <- paste(opt$registry, "/", opt$owner, "/", opt$repository, ":",
+                   opt$image, collapse = NULL, sep = "")
+
+#container_id = system2("docker", args = c("run", "-it -d",  docker_id, "bash"),
+#                       stdout = TRUE)
+
+write_all <- function() {
+  write_manifest_details()
+  write_history_details()
+}
+
+write_manifest_details <- function() {
+  details <- get_manifest_details()
+  write_manifest(details, opt$manifestdir, manifest_filename)
+}
+
+write_history_details <- function() {
+  details <- get_build_history()
+  write_manifest(details, opt$historydir, history_filename)
+}
+
+write_manifest <- function(manifestdata, filepth, filename) {
+
+  my_directory <- file.path(filepth)
+  if (!dir.exists(my_directory)) {
+    dir.create(my_directory)
+  }
+
+  file_conn <- file(manifest_filename)
+  writeLines(manifestdata, paste(my_directory, filename,
+                                 sep = "/", collapse = NULL))
+  close(file_conn)
+}
+
+get_manifest_details <- function() {
+
+  buildregistry <- paste("registry", opt$registry, sep = ":")
+  buildowner <- paste("owner", opt$owner, sep = ":")
+  buildimage <- paste("image", opt$image, sep = ":")
+  buildrepository <- paste("repository", opt$repository, sep = ":")
+  buildtime <- paste("timestamp", build_time, sep = ":")
+
+  r_ver <- r_version()
+  rbuildversion <- paste("### R Version: ", r_ver, sep = "\n")
+
+  r_package <- r_packages()
+  rbuildpackages <- paste("### R Packages: ", r_package, sep = "\n")
+
+  apt_package <- apt_packages()
+  aptbuildpackages <- paste("### APT Packages: ", apt_package, sep = "\n")
+
+  manifest_d <- manifest_string()
+
+  title <- paste(opt$owner, opt$repository, sep = "/")
+  build_title <- paste("# Build manifest for image ", title, ":", opt$image,
+                       sep = "")
+
+  builds <- paste(build_title, buildregistry, buildrepository, buildowner,
+                  buildimage, buildtime, manifest_d,
+                  rbuildversion, rbuildpackages, aptbuildpackages, " ",
+                  sep = "\n\n")
+
+  builds
+}
+
+get_build_history <- function() {
+
+  platform <- "amd64"
+
+  tags <- "default"
+
+  commit <- get_commit_hash()
+
+  diff_url <- paste("https://github.com/", opt$repository, collapse = NULL,
+                    sep = "")
+
+  diff <- paste("[Git diff](", diff_url, "/commit/", commit, ")",
+                collapse = NULL, sep = "")
+  dockerfile <- paste("[Dockerfile](", diff_url, "/blob/", commit, ")",
+                      collapse = NULL, sep = "")
+  manif <- paste("[Build manifest] (./", manifest_filename, ")",
+                 collapse = NULL, sep = "")
+
+  build_history <- paste(diff, dockerfile, manif, sep = "<br />")
+
+  image_manifest <- paste("{", tags, ":", platform, "}", collapse = NULL,
+                          sep = "")
+
+  build_conf <- paste(utc_time, image_manifest, build_history, sep = " | ")
+
+  build_conf
+}
+
+
+## Git helpers
+get_commit_hash <- function() {
+  arguments <- c("rev-parse", "HEAD")
+  hash <- system2("git", args = arguments, stdout = TRUE)
+  hash
+}
+
+get_commit_hash_tag <- function() {
+  x <- get_commit_hash()
+  tag <- substr(x, nchar(x) - 12 + 1, nchar(x))
+  tag
+}
+
+##Linux Helper
+get_linux_release <- function() {
+  os <- docker_command(c("lsb_release", "-a"))
+  release <- paste(os, sep = " ", collapse = "\n")
+  release
+}
+
+#packages
+r_version <- function() {
+
+  r_version <- docker_command(c("R", "--version"))
+  details <- strsplit(r_version, "\r", fixed = TRUE)
+  version <- paste(details[[1]], details[[3]], sep = " ", collapse = "\n\n")
+  version
+}
+
+r_packages <- function() {
+
+  # from dockerstack
+  r <- docker_command(c("R", "--silent", "-e",
+                        "'installed.packages(.Library)[, c(1,3)]'"))
+  #tidy the response by removing final > and the initial commands
+  package <- paste(unlist(strsplit(r, "\r", fixed = TRUE)[3:length(r) - 1]),
+                   sep = " ", collapse = "\n")
+  package
+}
+
+apt_packages <- function() {
+  e <- docker_command(c("apt", "list", "--installed"))
+  #remove listing line and then clean up response
+  install <- paste(strsplit(e, "\r", fixed = TRUE)[2:length(e)], sep = " ",
+                   collapse = " \n")
+  remove_local <- gsub("\\[installed,local\\]", "", install)
+  install1 <- gsub("\\[32m", "", remove_local)
+  installed <- unlist(paste(gsub("\\[0m/now", "", install1), sep = " ",
+                            collapse = " \n"))
+  installed
+}
+
+# manifest
+manifest_string <- function() {
+  m <- paste("default", get_commit_hash_tag(), utc_time, get_linux_release(),
+             collapse = NULL, sep = " ")
+  m
+}
+
+# Docker functions
+docker_start <- function() {
+  args <- system2("docker", args = c("run", "-it -d",  docker_id,
+                                     "bash"), stdout = TRUE)
+  args
+}
+
+docker_stop <- function() {
+  system2("docker", args = c("stop",  container_id))
+}
+
+docker_command <- function(arguments) {
+  docker <- paste("exec", "-it",  container_id, "bash", "-c",
+                  sep = " ", collapse = "")
+
+  a <- paste('"', paste(arguments, sep = " ", collapse = " "), '"',
+             collapse = NULL)
+
+  cmd <- system2("docker", args = c(docker, a), stdout = TRUE)
+  cmd
+}
+
+container_id <- docker_start()
+write_all()

From ee8573db3d83b28c05f56de3478b74adac6d8a98 Mon Sep 17 00:00:00 2001
From: Iain Emsley <Iain.Emsley@warwick.ac.uk>
Date: Mon, 11 Aug 2025 10:44:45 +0100
Subject: [PATCH 074/109] Updated with manifest

---
 .github/workflows/reuse-build-and-publish.yml | 23 +++++++++++++++++++
 1 file changed, 23 insertions(+)

diff --git a/.github/workflows/reuse-build-and-publish.yml b/.github/workflows/reuse-build-and-publish.yml
index 8d3ab4c24..b584e2fcc 100644
--- a/.github/workflows/reuse-build-and-publish.yml
+++ b/.github/workflows/reuse-build-and-publish.yml
@@ -102,3 +102,26 @@ jobs:
           build-args: |
             CONTAINER_VERSION=${{ env.VERSION }}
           labels: ${{ steps.meta.outputs.labels }}
+      - name: Write manifest and build history file 🏷
+        run: |
+          Rscript manifestR.R \
+            --registry ${{ env.REGISTRY }} \
+            --owner ${{ env.OWNER }} \
+            --image ${{ inputs.image }} \
+            --variant ${{ inputs.variant }} \
+            --hist-lines-dir /tmp/r-dev/hist_lines/ \
+            --manifests-dir /tmp/r-dev/manifests/ \
+            --repository ${{ github.repository }}
+        shell: bash
+      - name: Upload manifest file 💾
+        uses: actions/upload-artifact@v4
+        with:
+          name: ${{ inputs.image }}-${{ inputs.platform }}-${{ inputs.variant }}-manifest
+          path: /tmp/jupyter/manifests/${{ inputs.platform }}-${{ inputs.variant }}-${{ inputs.image }}-*.md
+          retention-days: 3
+      - name: Upload build history line 💾
+        uses: actions/upload-artifact@v4
+        with:
+          name: ${{ inputs.image }}-${{ inputs.platform }}-${{ inputs.variant }}-history_line
+          path: /tmp/jupyter/hist_lines/${{ inputs.platform }}-${{ inputs.variant }}-${{ inputs.image }}-*.txt
+          retention-days: 3

From 3bab5acb5c3a211f972ec0ff4c5f1b58c5619338 Mon Sep 17 00:00:00 2001
From: Iain Emsley <Iain.Emsley@warwick.ac.uk>
Date: Mon, 11 Aug 2025 10:57:15 +0100
Subject: [PATCH 075/109] Updated with manifest and added r-base to run

---
 .github/workflows/reuse-build-and-publish.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/reuse-build-and-publish.yml b/.github/workflows/reuse-build-and-publish.yml
index 3b5763731..dbf3e819b 100644
--- a/.github/workflows/reuse-build-and-publish.yml
+++ b/.github/workflows/reuse-build-and-publish.yml
@@ -72,7 +72,7 @@ jobs:
           labels: ${{ steps.meta.outputs.labels }}
       - name: Write manifest and build history file 🏷
         run: |
-          Rscript manifestR.R \
+          apt install r-base -y && Rscript manifestR.R \
             --registry ${{ env.REGISTRY }} \
             --owner ${{ env.OWNER }} \
             --image ${{ inputs.image }} \

From b87815528ccf04faba408a2e7d60e7ff77a43d2d Mon Sep 17 00:00:00 2001
From: Iain Emsley <Iain.Emsley@warwick.ac.uk>
Date: Mon, 11 Aug 2025 10:58:40 +0100
Subject: [PATCH 076/109] Updated paths

---
 .github/workflows/reuse-build-and-publish.yml | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/reuse-build-and-publish.yml b/.github/workflows/reuse-build-and-publish.yml
index dbf3e819b..8cec7168c 100644
--- a/.github/workflows/reuse-build-and-publish.yml
+++ b/.github/workflows/reuse-build-and-publish.yml
@@ -77,19 +77,19 @@ jobs:
             --owner ${{ env.OWNER }} \
             --image ${{ inputs.image }} \
             --variant ${{ inputs.variant }} \
-            --hist-lines-dir /tmp/r-dev/hist_lines/ \
-            --manifests-dir /tmp/r-dev/manifests/ \
+            --hist-lines-dir /tmp/r-devel/hist_lines/ \
+            --manifests-dir /tmp/r-devel/manifests/ \
             --repository ${{ github.repository }}
         shell: bash
       - name: Upload manifest file 💾
         uses: actions/upload-artifact@v4
         with:
           name: ${{ inputs.image }}-${{ inputs.platform }}-${{ inputs.variant }}-manifest
-          path: /tmp/jupyter/manifests/${{ inputs.platform }}-${{ inputs.variant }}-${{ inputs.image }}-*.md
+          path: /tmp/r-devel/manifests/${{ inputs.platform }}-${{ inputs.variant }}-${{ inputs.image }}-*.md
           retention-days: 3
       - name: Upload build history line 💾
         uses: actions/upload-artifact@v4
         with:
           name: ${{ inputs.image }}-${{ inputs.platform }}-${{ inputs.variant }}-history_line
-          path: /tmp/jupyter/hist_lines/${{ inputs.platform }}-${{ inputs.variant }}-${{ inputs.image }}-*.txt
+          path: /tmp/r-devel/hist_lines/${{ inputs.platform }}-${{ inputs.variant }}-${{ inputs.image }}-*.txt
           retention-days: 3

From 8db1e0c9a94ae7c338edbdabdc530058651b7bbc Mon Sep 17 00:00:00 2001
From: Iain Emsley <Iain.Emsley@warwick.ac.uk>
Date: Mon, 11 Aug 2025 11:08:48 +0100
Subject: [PATCH 077/109] Updated apt-get

---
 .github/workflows/reuse-build-and-publish.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/reuse-build-and-publish.yml b/.github/workflows/reuse-build-and-publish.yml
index 8cec7168c..75cd464da 100644
--- a/.github/workflows/reuse-build-and-publish.yml
+++ b/.github/workflows/reuse-build-and-publish.yml
@@ -72,7 +72,7 @@ jobs:
           labels: ${{ steps.meta.outputs.labels }}
       - name: Write manifest and build history file 🏷
         run: |
-          apt install r-base -y && Rscript manifestR.R \
+          sudo apt-get install r-base -y && Rscript manifestR.R \
             --registry ${{ env.REGISTRY }} \
             --owner ${{ env.OWNER }} \
             --image ${{ inputs.image }} \

From 006d100392e8f7bb78bfafbe303886655feb54ba Mon Sep 17 00:00:00 2001
From: Iain Emsley <Iain.Emsley@warwick.ac.uk>
Date: Mon, 11 Aug 2025 11:21:32 +0100
Subject: [PATCH 078/109] Updated apt-get

---
 .github/workflows/reuse-build-and-publish.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/reuse-build-and-publish.yml b/.github/workflows/reuse-build-and-publish.yml
index 75cd464da..05d72b952 100644
--- a/.github/workflows/reuse-build-and-publish.yml
+++ b/.github/workflows/reuse-build-and-publish.yml
@@ -72,7 +72,7 @@ jobs:
           labels: ${{ steps.meta.outputs.labels }}
       - name: Write manifest and build history file 🏷
         run: |
-          sudo apt-get install r-base -y && Rscript manifestR.R \
+          sudo apt-get install r-base -y && Rscript scripts/manifestR.R \
             --registry ${{ env.REGISTRY }} \
             --owner ${{ env.OWNER }} \
             --image ${{ inputs.image }} \

From 982c2ea55366b1c3349d409fa128fdcf06c0857c Mon Sep 17 00:00:00 2001
From: Iain Emsley <Iain.Emsley@warwick.ac.uk>
Date: Mon, 11 Aug 2025 11:34:16 +0100
Subject: [PATCH 079/109] Fixing R libraries

---
 .github/workflows/reuse-build-and-publish.yml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/reuse-build-and-publish.yml b/.github/workflows/reuse-build-and-publish.yml
index 05d72b952..6e4be4db6 100644
--- a/.github/workflows/reuse-build-and-publish.yml
+++ b/.github/workflows/reuse-build-and-publish.yml
@@ -72,7 +72,8 @@ jobs:
           labels: ${{ steps.meta.outputs.labels }}
       - name: Write manifest and build history file 🏷
         run: |
-          sudo apt-get install r-base -y && Rscript scripts/manifestR.R \
+          sudo apt-get install r-base -y && Rscript -e "install.packages('optparse') \
+            && Rscript scripts/manifestR.R \
             --registry ${{ env.REGISTRY }} \
             --owner ${{ env.OWNER }} \
             --image ${{ inputs.image }} \

From c19fd2956eb9de9fb0a47bc7662aee9acf62cd26 Mon Sep 17 00:00:00 2001
From: Iain Emsley <Iain.Emsley@warwick.ac.uk>
Date: Mon, 11 Aug 2025 11:50:09 +0100
Subject: [PATCH 080/109] Fixing R libraries

---
 .github/workflows/reuse-build-and-publish.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/reuse-build-and-publish.yml b/.github/workflows/reuse-build-and-publish.yml
index 6e4be4db6..3331641b1 100644
--- a/.github/workflows/reuse-build-and-publish.yml
+++ b/.github/workflows/reuse-build-and-publish.yml
@@ -72,7 +72,7 @@ jobs:
           labels: ${{ steps.meta.outputs.labels }}
       - name: Write manifest and build history file 🏷
         run: |
-          sudo apt-get install r-base -y && Rscript -e "install.packages('optparse') \
+          sudo apt-get install r-base -y && Rscript -e "install.packages('optparse')" \
             && Rscript scripts/manifestR.R \
             --registry ${{ env.REGISTRY }} \
             --owner ${{ env.OWNER }} \

From 454edb9cc5e097c47e576f61889480518dc018a1 Mon Sep 17 00:00:00 2001
From: Iain Emsley <Iain.Emsley@warwick.ac.uk>
Date: Mon, 11 Aug 2025 12:32:24 +0100
Subject: [PATCH 081/109] Fixing R libraries

---
 .github/workflows/reuse-build-and-publish.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/reuse-build-and-publish.yml b/.github/workflows/reuse-build-and-publish.yml
index 3331641b1..f30e2c0aa 100644
--- a/.github/workflows/reuse-build-and-publish.yml
+++ b/.github/workflows/reuse-build-and-publish.yml
@@ -72,7 +72,7 @@ jobs:
           labels: ${{ steps.meta.outputs.labels }}
       - name: Write manifest and build history file 🏷
         run: |
-          sudo apt-get install r-base -y && Rscript -e "install.packages('optparse')" \
+          sudo apt-get install r-base -y && sudo Rscript -e "install.packages('optparse')" \
             && Rscript scripts/manifestR.R \
             --registry ${{ env.REGISTRY }} \
             --owner ${{ env.OWNER }} \

From 2d278dd2e867c144fae836358ab9638deb110f74 Mon Sep 17 00:00:00 2001
From: Iain Emsley <Iain.Emsley@warwick.ac.uk>
Date: Mon, 11 Aug 2025 14:09:21 +0100
Subject: [PATCH 082/109] Fixing input variables

---
 .github/workflows/reuse-build-and-publish.yml | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/.github/workflows/reuse-build-and-publish.yml b/.github/workflows/reuse-build-and-publish.yml
index f30e2c0aa..a8b9b72aa 100644
--- a/.github/workflows/reuse-build-and-publish.yml
+++ b/.github/workflows/reuse-build-and-publish.yml
@@ -74,13 +74,13 @@ jobs:
         run: |
           sudo apt-get install r-base -y && sudo Rscript -e "install.packages('optparse')" \
             && Rscript scripts/manifestR.R \
-            --registry ${{ env.REGISTRY }} \
-            --owner ${{ env.OWNER }} \
-            --image ${{ inputs.image }} \
-            --variant ${{ inputs.variant }} \
+            --registry ${{ inputs.registry }} \
+            --owner ${{ inputs.actor}} \
+            --image ${{ inputs.image_name }} \
+            --version ${{ inputs.ref_name }} \
             --hist-lines-dir /tmp/r-devel/hist_lines/ \
             --manifests-dir /tmp/r-devel/manifests/ \
-            --repository ${{ github.repository }}
+            --repository ${{ inputs.ref_name }}
         shell: bash
       - name: Upload manifest file 💾
         uses: actions/upload-artifact@v4

From 1b5e4708be20e9473db1bfe0ba157cc2c45d51c0 Mon Sep 17 00:00:00 2001
From: Iain Emsley <Iain.Emsley@warwick.ac.uk>
Date: Mon, 11 Aug 2025 14:23:26 +0100
Subject: [PATCH 083/109] Removed version

---
 .github/workflows/reuse-build-and-publish.yml | 1 -
 scripts/manifestR.R                           | 2 --
 2 files changed, 3 deletions(-)

diff --git a/.github/workflows/reuse-build-and-publish.yml b/.github/workflows/reuse-build-and-publish.yml
index a8b9b72aa..25f98ba29 100644
--- a/.github/workflows/reuse-build-and-publish.yml
+++ b/.github/workflows/reuse-build-and-publish.yml
@@ -77,7 +77,6 @@ jobs:
             --registry ${{ inputs.registry }} \
             --owner ${{ inputs.actor}} \
             --image ${{ inputs.image_name }} \
-            --version ${{ inputs.ref_name }} \
             --hist-lines-dir /tmp/r-devel/hist_lines/ \
             --manifests-dir /tmp/r-devel/manifests/ \
             --repository ${{ inputs.ref_name }}
diff --git a/scripts/manifestR.R b/scripts/manifestR.R
index 78ad78b45..a578a4d4e 100644
--- a/scripts/manifestR.R
+++ b/scripts/manifestR.R
@@ -21,8 +21,6 @@ option_list <- list(
               help = "Current owner of the Repository"),
   make_option(c("-i", "--image"), type = "character", default = "devel",
               help = "Provide the image name [default %default]"),
-  make_option(c("-v", "--version"), type = "double", default = 0.3,
-              help = "version of the image  [default %default]"),
   make_option(c("-t", "--historydir"), type = "character",
               default = "/tmp/hist_lines/", help = "location of history lines"),
   make_option(c("-m", "--manifestdir"), type = "character",

From 871ef23c75ba661aa29f59724b4776fc90e97f7c Mon Sep 17 00:00:00 2001
From: Iain Emsley <Iain.Emsley@warwick.ac.uk>
Date: Mon, 11 Aug 2025 14:36:31 +0100
Subject: [PATCH 084/109] Updated histrory long line

---
 .github/workflows/reuse-build-and-publish.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/reuse-build-and-publish.yml b/.github/workflows/reuse-build-and-publish.yml
index 25f98ba29..5c55068cb 100644
--- a/.github/workflows/reuse-build-and-publish.yml
+++ b/.github/workflows/reuse-build-and-publish.yml
@@ -77,8 +77,8 @@ jobs:
             --registry ${{ inputs.registry }} \
             --owner ${{ inputs.actor}} \
             --image ${{ inputs.image_name }} \
-            --hist-lines-dir /tmp/r-devel/hist_lines/ \
-            --manifests-dir /tmp/r-devel/manifests/ \
+            --historydir /tmp/r-devel/hist_lines/ \
+            --manifestdir /tmp/r-devel/manifests/ \
             --repository ${{ inputs.ref_name }}
         shell: bash
       - name: Upload manifest file 💾

From dced3fe29f23a4c9913cb0c2487e0830c4231379 Mon Sep 17 00:00:00 2001
From: Iain Emsley <Iain.Emsley@warwick.ac.uk>
Date: Mon, 11 Aug 2025 14:58:05 +0100
Subject: [PATCH 085/109] Updated bash run

---
 scripts/manifestR.R | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/scripts/manifestR.R b/scripts/manifestR.R
index a578a4d4e..ff10d7575 100644
--- a/scripts/manifestR.R
+++ b/scripts/manifestR.R
@@ -203,8 +203,8 @@ manifest_string <- function() {
 
 # Docker functions
 docker_start <- function() {
-  args <- system2("docker", args = c("run", "-it -d",  docker_id,
-                                     "bash"), stdout = TRUE)
+  args <- system2("docker", args = c("run", "-it -d",  docker_id),
+                                     stdout = TRUE)
   args
 }
 

From 40450f087f7e947c21a0442e43a523744b5d12b1 Mon Sep 17 00:00:00 2001
From: Iain Emsley <Iain.Emsley@warwick.ac.uk>
Date: Mon, 11 Aug 2025 15:41:12 +0100
Subject: [PATCH 086/109] Updated bash run

---
 scripts/manifestR.R | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/scripts/manifestR.R b/scripts/manifestR.R
index ff10d7575..6d6a752b2 100644
--- a/scripts/manifestR.R
+++ b/scripts/manifestR.R
@@ -51,8 +51,8 @@ history_filename <- paste("history-", build_time, ".md", collapse = NULL,
 docker_id <- paste(opt$registry, "/", opt$owner, "/", opt$repository, ":",
                    opt$image, collapse = NULL, sep = "")
 
-#container_id = system2("docker", args = c("run", "-it -d",  docker_id, "bash"),
-#                       stdout = TRUE)
+container_id = system2("docker", args = c("run", "-it -d",  docker_id, "bash"),
+                       stdout = TRUE)
 
 write_all <- function() {
   write_manifest_details()
@@ -223,5 +223,5 @@ docker_command <- function(arguments) {
   cmd
 }
 
-container_id <- docker_start()
+#container_id <- docker_start()
 write_all()

From 7f02e95cf450cfb44415a2f20f9f511b866b35dc Mon Sep 17 00:00:00 2001
From: Iain Emsley <Iain.Emsley@warwick.ac.uk>
Date: Mon, 11 Aug 2025 16:07:26 +0100
Subject: [PATCH 087/109] Updated bash run

---
 .github/workflows/reuse-build-and-publish.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/reuse-build-and-publish.yml b/.github/workflows/reuse-build-and-publish.yml
index 5c55068cb..1407835fa 100644
--- a/.github/workflows/reuse-build-and-publish.yml
+++ b/.github/workflows/reuse-build-and-publish.yml
@@ -76,10 +76,10 @@ jobs:
             && Rscript scripts/manifestR.R \
             --registry ${{ inputs.registry }} \
             --owner ${{ inputs.actor}} \
-            --image ${{ inputs.image_name }} \
+            --image ${{ inputs.ref_name }} \
             --historydir /tmp/r-devel/hist_lines/ \
             --manifestdir /tmp/r-devel/manifests/ \
-            --repository ${{ inputs.ref_name }}
+            --repository ${{ inputs.image_name }}
         shell: bash
       - name: Upload manifest file 💾
         uses: actions/upload-artifact@v4

From 28bb525653a6c4790c041356dcd076556099cda4 Mon Sep 17 00:00:00 2001
From: Iain Emsley <Iain.Emsley@warwick.ac.uk>
Date: Mon, 11 Aug 2025 16:19:15 +0100
Subject: [PATCH 088/109] Updated bash run

---
 scripts/manifestR.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/scripts/manifestR.R b/scripts/manifestR.R
index 6d6a752b2..d2e5c9bd3 100644
--- a/scripts/manifestR.R
+++ b/scripts/manifestR.R
@@ -48,7 +48,7 @@ history_filename <- paste("history-", build_time, ".md", collapse = NULL,
                           sep = "")
 
 #set up docker
-docker_id <- paste(opt$registry, "/", opt$owner, "/", opt$repository, ":",
+docker_id <- paste(opt$registry, "/", opt$repository, ":",
                    opt$image, collapse = NULL, sep = "")
 
 container_id = system2("docker", args = c("run", "-it -d",  docker_id, "bash"),

From 8655adc1a8d6b7e60f0a182acf9966cc6671bf50 Mon Sep 17 00:00:00 2001
From: Iain Emsley <Iain.Emsley@warwick.ac.uk>
Date: Mon, 11 Aug 2025 16:30:38 +0100
Subject: [PATCH 089/109] Updated bash run

---
 scripts/manifestR.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/scripts/manifestR.R b/scripts/manifestR.R
index d2e5c9bd3..3890e0499 100644
--- a/scripts/manifestR.R
+++ b/scripts/manifestR.R
@@ -213,7 +213,7 @@ docker_stop <- function() {
 }
 
 docker_command <- function(arguments) {
-  docker <- paste("exec", "-it",  container_id, "bash", "-c",
+  docker <- paste("run", "-it -d",  docker_id, "bash", "-c",
                   sep = " ", collapse = "")
 
   a <- paste('"', paste(arguments, sep = " ", collapse = " "), '"',

From 908b7c24d766fef28bd7a5c67f6f007de02e1435 Mon Sep 17 00:00:00 2001
From: Iain Emsley <Iain.Emsley@warwick.ac.uk>
Date: Mon, 11 Aug 2025 16:45:34 +0100
Subject: [PATCH 090/109] Lookign at details

---
 scripts/manifestR.R | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/scripts/manifestR.R b/scripts/manifestR.R
index 3890e0499..dd23d76aa 100644
--- a/scripts/manifestR.R
+++ b/scripts/manifestR.R
@@ -167,7 +167,8 @@ r_version <- function() {
 
   r_version <- docker_command(c("R", "--version"))
   details <- strsplit(r_version, "\r", fixed = TRUE)
-  version <- paste(details[[1]], details[[3]], sep = " ", collapse = "\n\n")
+  #version <- paste(details[[1]], details[[3]], sep = " ", collapse = "\n\n")
+  version <- paste(details, sep = " ", collapse = "\n\n")
   version
 }
 

From 206070748cd32e13e0d4a4c06bf66575de826159 Mon Sep 17 00:00:00 2001
From: Iain Emsley <Iain.Emsley@warwick.ac.uk>
Date: Mon, 11 Aug 2025 17:06:38 +0100
Subject: [PATCH 091/109] Updated file details

---
 .github/workflows/reuse-build-and-publish.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/reuse-build-and-publish.yml b/.github/workflows/reuse-build-and-publish.yml
index 1407835fa..23fac4a61 100644
--- a/.github/workflows/reuse-build-and-publish.yml
+++ b/.github/workflows/reuse-build-and-publish.yml
@@ -77,8 +77,8 @@ jobs:
             --registry ${{ inputs.registry }} \
             --owner ${{ inputs.actor}} \
             --image ${{ inputs.ref_name }} \
-            --historydir /tmp/r-devel/hist_lines/ \
-            --manifestdir /tmp/r-devel/manifests/ \
+            --historydir /tmp/hist_lines \
+            --manifestdir /tmp/manifests \
             --repository ${{ inputs.image_name }}
         shell: bash
       - name: Upload manifest file 💾

From 381681394fc6c0aa35dee4394919561f9e716b6e Mon Sep 17 00:00:00 2001
From: Iain Emsley <Iain.Emsley@warwick.ac.uk>
Date: Mon, 11 Aug 2025 17:12:29 +0100
Subject: [PATCH 092/109] Added recursive in and altered file paths

---
 .github/workflows/reuse-build-and-publish.yml | 12 ++++++------
 scripts/manifestR.R                           |  2 +-
 2 files changed, 7 insertions(+), 7 deletions(-)

diff --git a/.github/workflows/reuse-build-and-publish.yml b/.github/workflows/reuse-build-and-publish.yml
index 23fac4a61..e751e1d75 100644
--- a/.github/workflows/reuse-build-and-publish.yml
+++ b/.github/workflows/reuse-build-and-publish.yml
@@ -77,19 +77,19 @@ jobs:
             --registry ${{ inputs.registry }} \
             --owner ${{ inputs.actor}} \
             --image ${{ inputs.ref_name }} \
-            --historydir /tmp/hist_lines \
-            --manifestdir /tmp/manifests \
+            --historydir /tmp/r-devel/hist_lines \
+            --manifestdir /tmp/r-devel/manifests \
             --repository ${{ inputs.image_name }}
         shell: bash
       - name: Upload manifest file 💾
         uses: actions/upload-artifact@v4
         with:
-          name: ${{ inputs.image }}-${{ inputs.platform }}-${{ inputs.variant }}-manifest
-          path: /tmp/r-devel/manifests/${{ inputs.platform }}-${{ inputs.variant }}-${{ inputs.image }}-*.md
+          name: ${{ inputs.image }}-manifest
+          path: /tmp/r-devel/manifests/${{ inputs.image }}-*.md
           retention-days: 3
       - name: Upload build history line 💾
         uses: actions/upload-artifact@v4
         with:
-          name: ${{ inputs.image }}-${{ inputs.platform }}-${{ inputs.variant }}-history_line
-          path: /tmp/r-devel/hist_lines/${{ inputs.platform }}-${{ inputs.variant }}-${{ inputs.image }}-*.txt
+          name: ${{ inputs.image }}-history_line
+          path: /tmp/r-devel/hist_lines/${{ inputs.image }}-*.txt
           retention-days: 3
diff --git a/scripts/manifestR.R b/scripts/manifestR.R
index dd23d76aa..e88697056 100644
--- a/scripts/manifestR.R
+++ b/scripts/manifestR.R
@@ -73,7 +73,7 @@ write_manifest <- function(manifestdata, filepth, filename) {
 
   my_directory <- file.path(filepth)
   if (!dir.exists(my_directory)) {
-    dir.create(my_directory)
+    dir.create(my_directory, recursive = TRUE)
   }
 
   file_conn <- file(manifest_filename)

From be9724dc2886b06336b425ec21ba737612a49e40 Mon Sep 17 00:00:00 2001
From: Iain Emsley <Iain.Emsley@warwick.ac.uk>
Date: Mon, 11 Aug 2025 17:35:52 +0100
Subject: [PATCH 093/109] Altered file paths

---
 .github/workflows/reuse-build-and-publish.yml | 4 ++--
 scripts/manifestR.R                           | 2 +-
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/reuse-build-and-publish.yml b/.github/workflows/reuse-build-and-publish.yml
index e751e1d75..a643e3aba 100644
--- a/.github/workflows/reuse-build-and-publish.yml
+++ b/.github/workflows/reuse-build-and-publish.yml
@@ -85,11 +85,11 @@ jobs:
         uses: actions/upload-artifact@v4
         with:
           name: ${{ inputs.image }}-manifest
-          path: /tmp/r-devel/manifests/${{ inputs.image }}-*.md
+          path: /tmp/r-devel/manifests/manifest-*.md
           retention-days: 3
       - name: Upload build history line 💾
         uses: actions/upload-artifact@v4
         with:
           name: ${{ inputs.image }}-history_line
-          path: /tmp/r-devel/hist_lines/${{ inputs.image }}-*.txt
+          path: /tmp/r-devel/hist_lines/history-*.txt
           retention-days: 3
diff --git a/scripts/manifestR.R b/scripts/manifestR.R
index e88697056..6795f53a7 100644
--- a/scripts/manifestR.R
+++ b/scripts/manifestR.R
@@ -44,7 +44,7 @@ utc_time <- strftime(tm, "%Y-%m-%dT%H:%M:%S%z")
 manifest_filename <- paste("manifest-", build_time, ".md", collapse = NULL,
                            sep = "")
 
-history_filename <- paste("history-", build_time, ".md", collapse = NULL,
+history_filename <- paste("history-", build_time, ".txt", collapse = NULL,
                           sep = "")
 
 #set up docker

From 8c4b8b156cca484f62396ebe1ad685f366957ccf Mon Sep 17 00:00:00 2001
From: Iain Emsley <Iain.Emsley@warwick.ac.uk>
Date: Mon, 11 Aug 2025 17:54:11 +0100
Subject: [PATCH 094/109] Docker commands

---
 scripts/manifestR.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/scripts/manifestR.R b/scripts/manifestR.R
index 6795f53a7..228903b7a 100644
--- a/scripts/manifestR.R
+++ b/scripts/manifestR.R
@@ -214,7 +214,7 @@ docker_stop <- function() {
 }
 
 docker_command <- function(arguments) {
-  docker <- paste("run", "-it -d",  docker_id, "bash", "-c",
+  docker <- paste("run", "-it",  docker_id, "bash", "-c",
                   sep = " ", collapse = "")
 
   a <- paste('"', paste(arguments, sep = " ", collapse = " "), '"',

From 47fedb03eaa3de2482a8a3884c3bf00090133a08 Mon Sep 17 00:00:00 2001
From: Iain Emsley <Iain.Emsley@warwick.ac.uk>
Date: Mon, 11 Aug 2025 19:18:19 +0100
Subject: [PATCH 095/109] Update command

---
 scripts/manifestR.R | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/scripts/manifestR.R b/scripts/manifestR.R
index 228903b7a..32277ef6e 100644
--- a/scripts/manifestR.R
+++ b/scripts/manifestR.R
@@ -204,7 +204,7 @@ manifest_string <- function() {
 
 # Docker functions
 docker_start <- function() {
-  args <- system2("docker", args = c("run", "-it -d",  docker_id),
+  args <- system2("docker", args = c("run", "-i -d",  docker_id),
                                      stdout = TRUE)
   args
 }
@@ -214,7 +214,7 @@ docker_stop <- function() {
 }
 
 docker_command <- function(arguments) {
-  docker <- paste("run", "-it",  docker_id, "bash", "-c",
+  docker <- paste("exec", "-i",  docker_id, "bash", "-c",
                   sep = " ", collapse = "")
 
   a <- paste('"', paste(arguments, sep = " ", collapse = " "), '"',

From ab84fe8051699a0ef6314adff1716febe921b416 Mon Sep 17 00:00:00 2001
From: Iain Emsley <Iain.Emsley@warwick.ac.uk>
Date: Mon, 11 Aug 2025 19:18:22 +0100
Subject: [PATCH 096/109] Update command

---
 scripts/manifestR.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/scripts/manifestR.R b/scripts/manifestR.R
index 32277ef6e..ca7a4b6ac 100644
--- a/scripts/manifestR.R
+++ b/scripts/manifestR.R
@@ -51,7 +51,7 @@ history_filename <- paste("history-", build_time, ".txt", collapse = NULL,
 docker_id <- paste(opt$registry, "/", opt$repository, ":",
                    opt$image, collapse = NULL, sep = "")
 
-container_id = system2("docker", args = c("run", "-it -d",  docker_id, "bash"),
+container_id = system2("docker", args = c("run", "-i -d",  docker_id, "bash"),
                        stdout = TRUE)
 
 write_all <- function() {

From ead2182ef36556ca02c363e947c32ff3eed2953b Mon Sep 17 00:00:00 2001
From: Iain Emsley <Iain.Emsley@warwick.ac.uk>
Date: Mon, 11 Aug 2025 19:30:52 +0100
Subject: [PATCH 097/109] Update command

---
 scripts/manifestR.R | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/scripts/manifestR.R b/scripts/manifestR.R
index ca7a4b6ac..317c18c0f 100644
--- a/scripts/manifestR.R
+++ b/scripts/manifestR.R
@@ -51,8 +51,8 @@ history_filename <- paste("history-", build_time, ".txt", collapse = NULL,
 docker_id <- paste(opt$registry, "/", opt$repository, ":",
                    opt$image, collapse = NULL, sep = "")
 
-container_id = system2("docker", args = c("run", "-i -d",  docker_id, "bash"),
-                       stdout = TRUE)
+#container_id = system2("docker", args = c("run", "-i -d",  docker_id, "bash"),
+#                       stdout = TRUE)
 
 write_all <- function() {
   write_manifest_details()
@@ -224,5 +224,5 @@ docker_command <- function(arguments) {
   cmd
 }
 
-#container_id <- docker_start()
+container_id <- docker_start()
 write_all()

From 08908938cf1ecd9c37f3a76c54b2dace0930149b Mon Sep 17 00:00:00 2001
From: Iain Emsley <Iain.Emsley@warwick.ac.uk>
Date: Mon, 11 Aug 2025 19:42:06 +0100
Subject: [PATCH 098/109] Update command

---
 scripts/manifestR.R | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/scripts/manifestR.R b/scripts/manifestR.R
index 317c18c0f..0bcb3d499 100644
--- a/scripts/manifestR.R
+++ b/scripts/manifestR.R
@@ -204,8 +204,8 @@ manifest_string <- function() {
 
 # Docker functions
 docker_start <- function() {
-  args <- system2("docker", args = c("run", "-i -d",  docker_id),
-                                     stdout = TRUE)
+  args <- system2("docker", args = c("run", "-i -d", "-a stdout", "-a stderr",
+                                     docker_id), stdout = TRUE)
   args
 }
 
@@ -214,7 +214,7 @@ docker_stop <- function() {
 }
 
 docker_command <- function(arguments) {
-  docker <- paste("exec", "-i",  docker_id, "bash", "-c",
+  docker <- paste("exec", "-i",  container_id, "bash", "-c",
                   sep = " ", collapse = "")
 
   a <- paste('"', paste(arguments, sep = " ", collapse = " "), '"',

From 1c609cd0fb07db20ae2b512954269ddb0c62bc47 Mon Sep 17 00:00:00 2001
From: Iain Emsley <Iain.Emsley@warwick.ac.uk>
Date: Mon, 11 Aug 2025 19:53:21 +0100
Subject: [PATCH 099/109] Update command wth bash

---
 scripts/manifestR.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/scripts/manifestR.R b/scripts/manifestR.R
index 0bcb3d499..f22f8dc7e 100644
--- a/scripts/manifestR.R
+++ b/scripts/manifestR.R
@@ -205,7 +205,7 @@ manifest_string <- function() {
 # Docker functions
 docker_start <- function() {
   args <- system2("docker", args = c("run", "-i -d", "-a stdout", "-a stderr",
-                                     docker_id), stdout = TRUE)
+                                     docker_id, "bash"), stdout = TRUE)
   args
 }
 

From c1e5eb13777c4f018726c4097dd06f0093cfa3ff Mon Sep 17 00:00:00 2001
From: Iain Emsley <Iain.Emsley@warwick.ac.uk>
Date: Mon, 11 Aug 2025 20:11:11 +0100
Subject: [PATCH 100/109] Update command wth bash

---
 scripts/manifestR.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/scripts/manifestR.R b/scripts/manifestR.R
index f22f8dc7e..ea1e984d8 100644
--- a/scripts/manifestR.R
+++ b/scripts/manifestR.R
@@ -204,7 +204,7 @@ manifest_string <- function() {
 
 # Docker functions
 docker_start <- function() {
-  args <- system2("docker", args = c("run", "-i -d", "-a stdout", "-a stderr",
+  args <- system2("docker", args = c("run", "-i", "-a stdout", "-a stderr",
                                      docker_id, "bash"), stdout = TRUE)
   args
 }

From 24035982e6c8f0055fcc468fa13f049610c5af31 Mon Sep 17 00:00:00 2001
From: Iain Emsley <Iain.Emsley@warwick.ac.uk>
Date: Mon, 11 Aug 2025 20:20:04 +0100
Subject: [PATCH 101/109] Update command wth bash

---
 scripts/manifestR.R | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/scripts/manifestR.R b/scripts/manifestR.R
index ea1e984d8..a6cb64789 100644
--- a/scripts/manifestR.R
+++ b/scripts/manifestR.R
@@ -204,8 +204,8 @@ manifest_string <- function() {
 
 # Docker functions
 docker_start <- function() {
-  args <- system2("docker", args = c("run", "-i", "-a stdout", "-a stderr",
-                                     docker_id, "bash"), stdout = TRUE)
+  args <- system2("docker", args = c("run", "-i -d", docker_id, "bash"),
+                  stdout = TRUE)
   args
 }
 

From 259cc0e4c608c52c8c99409d84b47f7b3ec92b63 Mon Sep 17 00:00:00 2001
From: Iain Emsley <Iain.Emsley@warwick.ac.uk>
Date: Tue, 12 Aug 2025 09:44:49 +0100
Subject: [PATCH 102/109] Added platform variable

---
 .github/workflows/call_jobs.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/call_jobs.yml b/.github/workflows/call_jobs.yml
index da24892ed..94a63062f 100644
--- a/.github/workflows/call_jobs.yml
+++ b/.github/workflows/call_jobs.yml
@@ -38,4 +38,5 @@ jobs:
       ref_name: ${{ github.ref_name }}
       actor: ${{ github.actor }}
       registry: ghcr.io
+      platform: amd64
     secrets: inherit

From 2d854879803d1d423bf783a727dc7387ed62bd9a Mon Sep 17 00:00:00 2001
From: Iain Emsley <Iain.Emsley@warwick.ac.uk>
Date: Tue, 12 Aug 2025 09:45:12 +0100
Subject: [PATCH 103/109] Added platform variable and altered manifest line'

---
 .github/workflows/reuse-build-and-publish.yml | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/reuse-build-and-publish.yml b/.github/workflows/reuse-build-and-publish.yml
index a643e3aba..f515a539c 100644
--- a/.github/workflows/reuse-build-and-publish.yml
+++ b/.github/workflows/reuse-build-and-publish.yml
@@ -24,6 +24,10 @@ on:
         description: registry
         required: true
         type: string
+      platform: 
+        description: platform
+        required: true
+        type: string
 permissions:
   contents: read
   packages: write
@@ -84,12 +88,12 @@ jobs:
       - name: Upload manifest file 💾
         uses: actions/upload-artifact@v4
         with:
-          name: ${{ inputs.image }}-manifest
+          name: ${{ inputs.platform }}-manifest
           path: /tmp/r-devel/manifests/manifest-*.md
           retention-days: 3
       - name: Upload build history line 💾
         uses: actions/upload-artifact@v4
         with:
-          name: ${{ inputs.image }}-history_line
+          name: ${{ inputs.platform }}-history_line
           path: /tmp/r-devel/hist_lines/history-*.txt
           retention-days: 3

From f5f3653b4d720033cf57d51fa06fe620e2f77eb4 Mon Sep 17 00:00:00 2001
From: Iain Emsley <Iain.Emsley@warwick.ac.uk>
Date: Tue, 12 Aug 2025 09:47:19 +0100
Subject: [PATCH 104/109] Added platform variable

---
 .github/workflows/call_jobs.yml | 10 ----------
 1 file changed, 10 deletions(-)

diff --git a/.github/workflows/call_jobs.yml b/.github/workflows/call_jobs.yml
index 94a63062f..67b60671f 100644
--- a/.github/workflows/call_jobs.yml
+++ b/.github/workflows/call_jobs.yml
@@ -19,20 +19,10 @@ on:
 
 jobs:
   call-workflow-amd64-main:
-    if: ${{ github.ref_name == 'main' }}
     permissions:
       contents: read
       packages: write
     uses: ./.github/workflows/reuse-build-and-publish.yml
-    with:
-      image_name: ${{ github.repository }}
-      ref_name: ${{ github.ref_name }}
-      actor: ${{ github.actor }}
-      registry: ghcr.io
-    secrets: inherit
-  call-workflow-amd64-devel:
-    if: ${{ github.ref_name == 'devel' }}
-    uses: iaine/r-dev-env/.github/workflows/reuse-build-and-publish.yml@devel
     with:
       image_name: ${{ github.repository }}
       ref_name: ${{ github.ref_name }}

From c486c8e6aebc74a46c2d1786c1e358a26529973d Mon Sep 17 00:00:00 2001
From: Iain Emsley <Iain.Emsley@warwick.ac.uk>
Date: Tue, 12 Aug 2025 10:06:44 +0100
Subject: [PATCH 105/109] Added platform variable

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

diff --git a/.github/workflows/call_jobs.yml b/.github/workflows/call_jobs.yml
index 67b60671f..dad635459 100644
--- a/.github/workflows/call_jobs.yml
+++ b/.github/workflows/call_jobs.yml
@@ -18,7 +18,7 @@ on:
       - 'VERSION'
 
 jobs:
-  call-workflow-amd64-main:
+  call-workflow-amd64:
     permissions:
       contents: read
       packages: write

From 87e5fb289b856caf6986c3ea1da9d116b14c9a0d Mon Sep 17 00:00:00 2001
From: Iain Emsley <Iain.Emsley@warwick.ac.uk>
Date: Tue, 12 Aug 2025 10:08:11 +0100
Subject: [PATCH 106/109] Tidying test variable

---
 .github/workflows/call_jobs.yml | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/.github/workflows/call_jobs.yml b/.github/workflows/call_jobs.yml
index dad635459..86567b839 100644
--- a/.github/workflows/call_jobs.yml
+++ b/.github/workflows/call_jobs.yml
@@ -1,9 +1,6 @@
 name: Call reusable workflows
 
 on:
-  push:
-    branches:
-      - devel
   pull_request:
     branches:
       - main

From ad801a70948bb74036aea59e3b597a6e869134af Mon Sep 17 00:00:00 2001
From: Iain Emsley <Iain.Emsley@warwick.ac.uk>
Date: Tue, 12 Aug 2025 10:09:01 +0100
Subject: [PATCH 107/109] Tidy manifest name

---
 scripts/{manifestR.R => manifest.R} | 0
 1 file changed, 0 insertions(+), 0 deletions(-)
 rename scripts/{manifestR.R => manifest.R} (100%)

diff --git a/scripts/manifestR.R b/scripts/manifest.R
similarity index 100%
rename from scripts/manifestR.R
rename to scripts/manifest.R

From b1d20e4f458fb46c43a197649291e6a64d0f1f21 Mon Sep 17 00:00:00 2001
From: Iain Emsley <Iain.Emsley@warwick.ac.uk>
Date: Tue, 12 Aug 2025 10:11:11 +0100
Subject: [PATCH 108/109] Added platform to variable

---
 .github/workflows/reuse-build-and-publish.yml | 18 +++++++++---------
 1 file changed, 9 insertions(+), 9 deletions(-)

diff --git a/.github/workflows/reuse-build-and-publish.yml b/.github/workflows/reuse-build-and-publish.yml
index f515a539c..9ea4a6a22 100644
--- a/.github/workflows/reuse-build-and-publish.yml
+++ b/.github/workflows/reuse-build-and-publish.yml
@@ -8,23 +8,23 @@ name: Build and publish amd 64 Docker image
 on:
   workflow_call:
     inputs:
-      image_name: 
+      image_name:
         description: image name
         required: true
         type: string
-      ref_name: 
+      ref_name:
         description: ref name
         required: true
         type: string
-      actor: 
+      actor:
         description: actor
         required: true
         type: string
-      registry: 
+      registry:
         description: registry
         required: true
         type: string
-      platform: 
+      platform:
         description: platform
         required: true
         type: string
@@ -74,10 +74,10 @@ jobs:
           build-args: |
             CONTAINER_VERSION=${{ env.VERSION }}
           labels: ${{ steps.meta.outputs.labels }}
-      - name: Write manifest and build history file 🏷
+      - name: Write manifest and build history file
         run: |
           sudo apt-get install r-base -y && sudo Rscript -e "install.packages('optparse')" \
-            && Rscript scripts/manifestR.R \
+            && Rscript scripts/manifest.R \
             --registry ${{ inputs.registry }} \
             --owner ${{ inputs.actor}} \
             --image ${{ inputs.ref_name }} \
@@ -85,13 +85,13 @@ jobs:
             --manifestdir /tmp/r-devel/manifests \
             --repository ${{ inputs.image_name }}
         shell: bash
-      - name: Upload manifest file 💾
+      - name: Upload manifest file
         uses: actions/upload-artifact@v4
         with:
           name: ${{ inputs.platform }}-manifest
           path: /tmp/r-devel/manifests/manifest-*.md
           retention-days: 3
-      - name: Upload build history line 💾
+      - name: Upload build history line
         uses: actions/upload-artifact@v4
         with:
           name: ${{ inputs.platform }}-history_line

From 93558ffd1db9a2e135e288c13b8da07bbb3f569c Mon Sep 17 00:00:00 2001
From: Iain Emsley <Iain.Emsley@warwick.ac.uk>
Date: Tue, 12 Aug 2025 10:12:31 +0100
Subject: [PATCH 109/109] Tidied name

---
 scripts/manifest.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/scripts/manifest.R b/scripts/manifest.R
index a6cb64789..83fbc66cb 100644
--- a/scripts/manifest.R
+++ b/scripts/manifest.R
@@ -1,4 +1,4 @@
-# manifestR.R
+# manifest.R
 #
 # Files takes the container arguments and creates two files inside the
 # given container. These are the build history and manifest files.