From 0208cf2e0ece42e6445aa27917f446aa1935bd60 Mon Sep 17 00:00:00 2001
From: Goran Jelic-Cizmek <goran.jelic-cizmek@epfl.ch>
Date: Wed, 4 Dec 2024 11:05:22 +0100
Subject: [PATCH 01/13] Add CI action for uploading Docker image for wheels

---
 .github/workflows/wheel_image.yml | 46 +++++++++++++++++++++++++++++++
 1 file changed, 46 insertions(+)
 create mode 100644 .github/workflows/wheel_image.yml

diff --git a/.github/workflows/wheel_image.yml b/.github/workflows/wheel_image.yml
new file mode 100644
index 0000000000..a5403918cb
--- /dev/null
+++ b/.github/workflows/wheel_image.yml
@@ -0,0 +1,46 @@
+name: Build custom Docker image for manylinux wheels
+
+on:
+  workflow_dispatch:
+    inputs:
+      base_image:
+        description: 'The base Docker image to use'
+        default: 'manylinux2014'
+        type: choice
+        options:
+          - 'manylinux2014'
+          - 'manylinux_2_28'
+          - 'manylinux_2_34'
+
+jobs:
+  docker:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        include:
+          - platform: 'linux/amd64'
+            tag: 'x86_64'
+          - platform: 'linux/arm64'
+            tag: 'aarch64'
+
+    steps:
+      - name: Login to Docker Hub
+        uses: docker/login-action@v3
+        with:
+          username: ${{ vars.DOCKERHUB_USERNAME }}
+          password: ${{ secrets.DOCKERHUB_TOKEN }}
+
+      - name: Set up QEMU
+        uses: docker/setup-qemu-action@v3
+
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v3
+
+      - name: Build and push
+        uses: docker/build-push-action@v6
+        with:
+          platforms: ${{ matrix.platform }}
+          push: true
+          tags: neuronsimulator/neuron_wheel:latest
+          build-args: |
+            MANYLINUX_IMAGE: ${{ github.event.inputs.base_image }}_${{ matrix.tag }}

From 0b6ceb535f6830998389f86e6738bf6c0aebe14e Mon Sep 17 00:00:00 2001
From: Goran Jelic-Cizmek <goran.jelic-cizmek@epfl.ch>
Date: Wed, 4 Dec 2024 11:14:26 +0100
Subject: [PATCH 02/13] Minor safety improvements

---
 .github/workflows/wheel_image.yml | 14 ++++++++++----
 1 file changed, 10 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/wheel_image.yml b/.github/workflows/wheel_image.yml
index a5403918cb..3ca5fa89c4 100644
--- a/.github/workflows/wheel_image.yml
+++ b/.github/workflows/wheel_image.yml
@@ -12,6 +12,12 @@ on:
           - 'manylinux_2_28'
           - 'manylinux_2_34'
 
+      upload:
+        description: 'Whether to upload (push) the image to DockerHub'
+        default: 'false'
+        required: true
+        type: 'boolean'
+
 jobs:
   docker:
     runs-on: ubuntu-latest
@@ -19,9 +25,9 @@ jobs:
       matrix:
         include:
           - platform: 'linux/amd64'
-            tag: 'x86_64'
+            arch: 'x86_64'
           - platform: 'linux/arm64'
-            tag: 'aarch64'
+            arch: 'aarch64'
 
     steps:
       - name: Login to Docker Hub
@@ -40,7 +46,7 @@ jobs:
         uses: docker/build-push-action@v6
         with:
           platforms: ${{ matrix.platform }}
-          push: true
+          push: ${{ github.event.inputs.upload }}
           tags: neuronsimulator/neuron_wheel:latest
           build-args: |
-            MANYLINUX_IMAGE: ${{ github.event.inputs.base_image }}_${{ matrix.tag }}
+            MANYLINUX_IMAGE: ${{ github.event.inputs.base_image }}_${{ matrix.arch }}

From 0e6433da6c30ebb68cc3c2bff2459b1c733b6c8a Mon Sep 17 00:00:00 2001
From: Goran Jelic-Cizmek <goran.jelic-cizmek@epfl.ch>
Date: Wed, 4 Dec 2024 11:47:46 +0100
Subject: [PATCH 03/13] Make image tag customizable

---
 .github/workflows/wheel_image.yml | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/wheel_image.yml b/.github/workflows/wheel_image.yml
index 3ca5fa89c4..8a12726145 100644
--- a/.github/workflows/wheel_image.yml
+++ b/.github/workflows/wheel_image.yml
@@ -18,6 +18,11 @@ on:
         required: true
         type: 'boolean'
 
+      tag:
+        description: 'The tag for the final Docker image'
+        default: 'latest'
+        required: true
+
 jobs:
   docker:
     runs-on: ubuntu-latest
@@ -47,6 +52,6 @@ jobs:
         with:
           platforms: ${{ matrix.platform }}
           push: ${{ github.event.inputs.upload }}
-          tags: neuronsimulator/neuron_wheel:latest
+          tags: neuronsimulator/neuron_wheel:${{ github.event.inputs.tag }}
           build-args: |
             MANYLINUX_IMAGE: ${{ github.event.inputs.base_image }}_${{ matrix.arch }}

From 1904ec2636d6f2acc21029a46887ec6d1ffbebdc Mon Sep 17 00:00:00 2001
From: Goran Jelic-Cizmek <goran.jelic-cizmek@epfl.ch>
Date: Wed, 4 Dec 2024 13:48:06 +0100
Subject: [PATCH 04/13] Use arch in tag because BuildKit is complicated

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

diff --git a/.github/workflows/wheel_image.yml b/.github/workflows/wheel_image.yml
index 8a12726145..d826830c71 100644
--- a/.github/workflows/wheel_image.yml
+++ b/.github/workflows/wheel_image.yml
@@ -52,6 +52,6 @@ jobs:
         with:
           platforms: ${{ matrix.platform }}
           push: ${{ github.event.inputs.upload }}
-          tags: neuronsimulator/neuron_wheel:${{ github.event.inputs.tag }}
+          tags: neuronsimulator/neuron_wheel:${{ github.event.inputs.tag }}-${{ matrix.arch }}
           build-args: |
             MANYLINUX_IMAGE: ${{ github.event.inputs.base_image }}_${{ matrix.arch }}

From dcc62f8245b885eda9100da4dee0fd37d390046a Mon Sep 17 00:00:00 2001
From: Goran Jelic-Cizmek <goran.jelic-cizmek@epfl.ch>
Date: Mon, 9 Dec 2024 14:20:35 +0100
Subject: [PATCH 05/13] Allow uploading to GHCR

---
 .github/workflows/wheel_image.yml | 21 +++++++++++++++++++--
 1 file changed, 19 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/wheel_image.yml b/.github/workflows/wheel_image.yml
index d826830c71..0644392164 100644
--- a/.github/workflows/wheel_image.yml
+++ b/.github/workflows/wheel_image.yml
@@ -13,11 +13,19 @@ on:
           - 'manylinux_2_34'
 
       upload:
-        description: 'Whether to upload (push) the image to DockerHub'
+        description: 'Whether to upload (push) the image to the container registry'
         default: 'false'
         required: true
         type: 'boolean'
 
+      container_registry:
+        description: 'The name of the container registry to upload the image to (only useful if used with upload=true)'
+        default: 'ghcr.io'
+        required: true
+        options:
+          - 'ghcr.io'
+          - 'docker.io'
+
       tag:
         description: 'The tag for the final Docker image'
         default: 'latest'
@@ -36,11 +44,20 @@ jobs:
 
     steps:
       - name: Login to Docker Hub
+        if: ${{ github.event.inputs.upload }} == 'true' && ${{ github.event.inputs.container_registry }} == 'docker.io'
         uses: docker/login-action@v3
         with:
           username: ${{ vars.DOCKERHUB_USERNAME }}
           password: ${{ secrets.DOCKERHUB_TOKEN }}
 
+      - name: Login to GitHub container registry
+        if: ${{ github.event.inputs.upload }} == 'true' && ${{ github.event.inputs.container_registry }} == 'ghcr.io'
+        uses: docker/login-action@v3
+        with:
+          registry: 'ghcr.io'
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+
       - name: Set up QEMU
         uses: docker/setup-qemu-action@v3
 
@@ -52,6 +69,6 @@ jobs:
         with:
           platforms: ${{ matrix.platform }}
           push: ${{ github.event.inputs.upload }}
-          tags: neuronsimulator/neuron_wheel:${{ github.event.inputs.tag }}-${{ matrix.arch }}
+          tags: ${{ github.event.inputs.container_registry }}/neuronsimulator/neuron_wheel:${{ github.event.inputs.tag }}-${{ matrix.arch }}
           build-args: |
             MANYLINUX_IMAGE: ${{ github.event.inputs.base_image }}_${{ matrix.arch }}

From 20fa088a4246a5ce9a2fed7d3fe0b792c554c977 Mon Sep 17 00:00:00 2001
From: Goran Jelic-Cizmek <goran.jelic-cizmek@epfl.ch>
Date: Mon, 9 Dec 2024 15:21:14 +0100
Subject: [PATCH 06/13] Trigger CI for first time

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

diff --git a/.github/workflows/wheel_image.yml b/.github/workflows/wheel_image.yml
index 0644392164..c024477f00 100644
--- a/.github/workflows/wheel_image.yml
+++ b/.github/workflows/wheel_image.yml
@@ -1,6 +1,7 @@
 name: Build custom Docker image for manylinux wheels
 
 on:
+  push:
   workflow_dispatch:
     inputs:
       base_image:

From 005313d84f644b52e0de98f48849802d85508988 Mon Sep 17 00:00:00 2001
From: Goran Jelic-Cizmek <goran.jelic-cizmek@epfl.ch>
Date: Mon, 9 Dec 2024 15:21:53 +0100
Subject: [PATCH 07/13] Revert "Trigger CI for first time"

This reverts commit 20fa088a4246a5ce9a2fed7d3fe0b792c554c977.
---
 .github/workflows/wheel_image.yml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/.github/workflows/wheel_image.yml b/.github/workflows/wheel_image.yml
index c024477f00..0644392164 100644
--- a/.github/workflows/wheel_image.yml
+++ b/.github/workflows/wheel_image.yml
@@ -1,7 +1,6 @@
 name: Build custom Docker image for manylinux wheels
 
 on:
-  push:
   workflow_dispatch:
     inputs:
       base_image:

From cc5328653e8eb87c2c6ea14c37f4fcbfc537c070 Mon Sep 17 00:00:00 2001
From: Goran Jelic-Cizmek <goran.jelic-cizmek@epfl.ch>
Date: Mon, 9 Dec 2024 15:24:42 +0100
Subject: [PATCH 08/13] Fixes

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

diff --git a/.github/workflows/wheel_image.yml b/.github/workflows/wheel_image.yml
index 0644392164..063d028e91 100644
--- a/.github/workflows/wheel_image.yml
+++ b/.github/workflows/wheel_image.yml
@@ -44,14 +44,14 @@ jobs:
 
     steps:
       - name: Login to Docker Hub
-        if: ${{ github.event.inputs.upload }} == 'true' && ${{ github.event.inputs.container_registry }} == 'docker.io'
+        if: github.event.inputs.upload == 'true' && github.event.inputs.container_registry == 'docker.io'
         uses: docker/login-action@v3
         with:
           username: ${{ vars.DOCKERHUB_USERNAME }}
           password: ${{ secrets.DOCKERHUB_TOKEN }}
 
       - name: Login to GitHub container registry
-        if: ${{ github.event.inputs.upload }} == 'true' && ${{ github.event.inputs.container_registry }} == 'ghcr.io'
+        if: github.event.inputs.upload == 'true' && github.event.inputs.container_registry == 'ghcr.io'
         uses: docker/login-action@v3
         with:
           registry: 'ghcr.io'

From 1b441dfeffbb1f4b1174188e95486dcb9eb438ba Mon Sep 17 00:00:00 2001
From: Goran Jelic-Cizmek <goran.jelic-cizmek@epfl.ch>
Date: Mon, 9 Dec 2024 15:33:12 +0100
Subject: [PATCH 09/13] Fix path

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

diff --git a/.github/workflows/wheel_image.yml b/.github/workflows/wheel_image.yml
index 063d028e91..e4f7faee10 100644
--- a/.github/workflows/wheel_image.yml
+++ b/.github/workflows/wheel_image.yml
@@ -33,6 +33,7 @@ on:
 
 jobs:
   docker:
+    name: 'Create Docker image for manylinux wheels'
     runs-on: ubuntu-latest
     strategy:
       matrix:
@@ -67,6 +68,7 @@ jobs:
       - name: Build and push
         uses: docker/build-push-action@v6
         with:
+          file: packaging/python/Dockerfile
           platforms: ${{ matrix.platform }}
           push: ${{ github.event.inputs.upload }}
           tags: ${{ github.event.inputs.container_registry }}/neuronsimulator/neuron_wheel:${{ github.event.inputs.tag }}-${{ matrix.arch }}

From 0e3c6a727f0b1a3ce7bf11e2fbdbbfc3768ef41e Mon Sep 17 00:00:00 2001
From: Goran Jelic-Cizmek <goran.jelic-cizmek@epfl.ch>
Date: Mon, 9 Dec 2024 15:49:17 +0100
Subject: [PATCH 10/13] Do not copy dockerfile

---
 packaging/python/Dockerfile | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/packaging/python/Dockerfile b/packaging/python/Dockerfile
index 36c7d0ad4f..07bb55d3fb 100644
--- a/packaging/python/Dockerfile
+++ b/packaging/python/Dockerfile
@@ -87,9 +87,6 @@ ENV PATH /nrnwheel/openmpi/bin:$PATH
 RUN yum -y install epel-release libX11-devel libXcomposite-devel vim-enhanced && yum -y clean all && rm -rf /var/cache
 RUN yum -y remove ncurses-devel
 
-# Copy Dockerfile for reference
-COPY Dockerfile .
-
 # build wheels from there
 WORKDIR /root
 

From de6cb905757fcf23f8779a57b84ebb07c9e665a1 Mon Sep 17 00:00:00 2001
From: Goran Jelic-Cizmek <goran.jelic-cizmek@epfl.ch>
Date: Mon, 9 Dec 2024 16:22:53 +0100
Subject: [PATCH 11/13] Add context dir

---
 .github/workflows/wheel_image.yml | 4 ++--
 packaging/python/Dockerfile       | 3 +++
 2 files changed, 5 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/wheel_image.yml b/.github/workflows/wheel_image.yml
index e4f7faee10..b53b884b63 100644
--- a/.github/workflows/wheel_image.yml
+++ b/.github/workflows/wheel_image.yml
@@ -68,9 +68,9 @@ jobs:
       - name: Build and push
         uses: docker/build-push-action@v6
         with:
-          file: packaging/python/Dockerfile
+          context: "{{defaultContext}}:packaging/python"
           platforms: ${{ matrix.platform }}
           push: ${{ github.event.inputs.upload }}
           tags: ${{ github.event.inputs.container_registry }}/neuronsimulator/neuron_wheel:${{ github.event.inputs.tag }}-${{ matrix.arch }}
           build-args: |
-            MANYLINUX_IMAGE: ${{ github.event.inputs.base_image }}_${{ matrix.arch }}
+            MANYLINUX_IMAGE=${{ github.event.inputs.base_image }}_${{ matrix.arch }}
diff --git a/packaging/python/Dockerfile b/packaging/python/Dockerfile
index 07bb55d3fb..36c7d0ad4f 100644
--- a/packaging/python/Dockerfile
+++ b/packaging/python/Dockerfile
@@ -87,6 +87,9 @@ ENV PATH /nrnwheel/openmpi/bin:$PATH
 RUN yum -y install epel-release libX11-devel libXcomposite-devel vim-enhanced && yum -y clean all && rm -rf /var/cache
 RUN yum -y remove ncurses-devel
 
+# Copy Dockerfile for reference
+COPY Dockerfile .
+
 # build wheels from there
 WORKDIR /root
 

From c5429d6e5b01119e0bf0e63f3100dd50704785b4 Mon Sep 17 00:00:00 2001
From: Goran Jelic-Cizmek <goran.jelic-cizmek@epfl.ch>
Date: Tue, 10 Dec 2024 09:26:08 +0100
Subject: [PATCH 12/13] Update Dockerfile

Remove Python 3.13t (the free-threaded build) as we do not support it
yet.
---
 packaging/python/Dockerfile | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/packaging/python/Dockerfile b/packaging/python/Dockerfile
index 36c7d0ad4f..95931335cc 100644
--- a/packaging/python/Dockerfile
+++ b/packaging/python/Dockerfile
@@ -93,4 +93,7 @@ COPY Dockerfile .
 # build wheels from there
 WORKDIR /root
 
+# remove Python 3.13t since we do not support the free-threaded build yet
+RUN rm -fr /opt/python/cp313-cp313t
+
 ENV NMODL_PYLIB=/nrnwheel/python/lib/libpython3.10.so.1.0

From 7d5e83a75f709ddc16bb1b278e10bf61b85f892e Mon Sep 17 00:00:00 2001
From: Goran Jelic-Cizmek <goran.jelic-cizmek@epfl.ch>
Date: Mon, 20 Jan 2025 15:17:51 +0100
Subject: [PATCH 13/13] Try out ARM runners

See
https://github.blog/changelog/2025-01-16-linux-arm64-hosted-runners-now-available-for-free-in-public-repositories-public-preview/
---
 .github/workflows/wheel_image.yml | 14 +++++---------
 1 file changed, 5 insertions(+), 9 deletions(-)

diff --git a/.github/workflows/wheel_image.yml b/.github/workflows/wheel_image.yml
index b53b884b63..3d2a097dd2 100644
--- a/.github/workflows/wheel_image.yml
+++ b/.github/workflows/wheel_image.yml
@@ -28,20 +28,22 @@ on:
 
       tag:
         description: 'The tag for the final Docker image'
-        default: 'latest'
+        default: 'latest-'
         required: true
 
 jobs:
   docker:
     name: 'Create Docker image for manylinux wheels'
-    runs-on: ubuntu-latest
+    runs-on: ${{ matrix.base_image }}
     strategy:
       matrix:
         include:
           - platform: 'linux/amd64'
             arch: 'x86_64'
+            base_image: 'ubuntu-22.04'
           - platform: 'linux/arm64'
             arch: 'aarch64'
+            base_image: 'ubuntu-22.04-arm'
 
     steps:
       - name: Login to Docker Hub
@@ -59,18 +61,12 @@ jobs:
           username: ${{ github.actor }}
           password: ${{ secrets.GITHUB_TOKEN }}
 
-      - name: Set up QEMU
-        uses: docker/setup-qemu-action@v3
-
-      - name: Set up Docker Buildx
-        uses: docker/setup-buildx-action@v3
-
       - name: Build and push
         uses: docker/build-push-action@v6
         with:
           context: "{{defaultContext}}:packaging/python"
           platforms: ${{ matrix.platform }}
           push: ${{ github.event.inputs.upload }}
-          tags: ${{ github.event.inputs.container_registry }}/neuronsimulator/neuron_wheel:${{ github.event.inputs.tag }}-${{ matrix.arch }}
+          tags: ${{ github.event.inputs.container_registry }}/neuronsimulator/neuron_wheel:${{ github.event.inputs.tag }}${{ github.event.inputs.base_image }}_${{ matrix.arch }}
           build-args: |
             MANYLINUX_IMAGE=${{ github.event.inputs.base_image }}_${{ matrix.arch }}