Merge pull request #705 from mamba-org/apptainer-script

wholtz · web-flow · commit 5f62561ecb64 · 2026-03-21T21:44:51.000-07:00
Resume copying `_apptainer_shell.sh` into images
diff --git a/.github/workflows/push_latest.yml b/.github/workflows/push_latest.yml
@@ -19,7 +19,7 @@ env:
   LATEST_UBUNTU_BASE_IMAGE: 'ubuntu:25.10'
   LATEST_AMAZON_BASE_IMAGE: 'public.ecr.aws/amazonlinux/amazonlinux:2023'
   LATEST_ALPINE_BASE_IMAGE: 'frolvlad/alpine-glibc:alpine-3.22'
-  LATEST_CUDA_BASE_IMAGE: 'nvidia/cuda:13.1.0-base-ubuntu24.04'
+  LATEST_CUDA_BASE_IMAGE: 'nvidia/cuda:13.2.0-base-ubuntu24.04'
 
 jobs:
   build_docker_image_and_push:
@@ -40,8 +40,8 @@ jobs:
          - frolvlad/alpine-glibc:alpine-3.22
          - frolvlad/alpine-glibc:alpine-3.21
          - public.ecr.aws/amazonlinux/amazonlinux:2023
-         - nvidia/cuda:13.1.0-base-ubuntu24.04
-         - nvidia/cuda:13.1.0-base-ubuntu22.04
+         - nvidia/cuda:13.2.0-base-ubuntu24.04
+         - nvidia/cuda:13.2.0-base-ubuntu22.04
          - nvidia/cuda:12.9.1-base-ubuntu24.04
          - nvidia/cuda:12.9.1-base-ubuntu22.04
          - nvidia/cuda:12.8.1-base-ubuntu24.04
@@ -64,7 +64,7 @@ jobs:
     - name: Setup nox
       uses: wntrblm/nox@0eee2e45758dbd06d48ebb23476439f0f00e5cbd
     - name: Checkout source
-      uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8
+      uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd
       with:
         persist-credentials: false
         submodules: recursive
@@ -178,12 +178,12 @@ jobs:
     - name: Setup docker buildx
       uses: docker/setup-buildx-action@8d2750c68a42422c14e847fe6c8ac0403b4cbd6f
     - name: Login to DockerHub
-      uses: docker/login-action@5e57cd118135c172c3672efd75eb46360885c0ef
+      uses: docker/login-action@c94ce9fb468520275223c153574b00df6fe4bcc9
       with:
         username: ${{ secrets.DOCKERHUB_USERNAME }}
         password: ${{ secrets.DOCKERHUB_TOKEN }}
     - name: Login to GHCR
-      uses: docker/login-action@5e57cd118135c172c3672efd75eb46360885c0ef
+      uses: docker/login-action@c94ce9fb468520275223c153574b00df6fe4bcc9
       with:
         registry: ghcr.io
         username: ${{ github.repository_owner }}
@@ -251,7 +251,7 @@ jobs:
     runs-on: ubuntu-24.04
     steps:
     - name: Checkout source
-      uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8
+      uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd
       with:
         persist-credentials: false
     - name: Get artifacts
@@ -307,7 +307,7 @@ jobs:
       contents: write
     steps:
     - name: Checkout source
-      uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8
+      uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd
       with:
         persist-credentials: false
     - name: Get micromamba version number
diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
@@ -19,7 +19,7 @@ jobs:
     runs-on: ubuntu-24.04
     steps:
       - name: Checkout source
-        uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8
+        uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd
         with:
           submodules: recursive
           persist-credentials: false
@@ -35,7 +35,7 @@ jobs:
     runs-on: ubuntu-24.04
     steps:
       - name: Checkout source
-        uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8
+        uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd
         with:
           persist-credentials: false
       - name: Install curl and xz-utils
@@ -49,7 +49,7 @@ jobs:
     runs-on: ubuntu-24.04
     steps:
       - name: Checkout source
-        uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8
+        uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd
         with:
           persist-credentials: false
       - name: Setup nox
@@ -61,7 +61,7 @@ jobs:
     runs-on: ubuntu-24.04
     steps:
       - name: Checkout source
-        uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8
+        uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd
         with:
           persist-credentials: false
       - name: Setup nox
@@ -73,7 +73,7 @@ jobs:
     runs-on: ubuntu-24.04
     steps:
       - name: Checkout source
-        uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8
+        uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd
         with:
           persist-credentials: false
       - name: Setup nox
@@ -85,7 +85,7 @@ jobs:
     runs-on: ubuntu-24.04
     steps:
       - name: Checkout source
-        uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8
+        uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd
         with:
           persist-credentials: false
       - name: Setup nox
@@ -97,7 +97,7 @@ jobs:
     runs-on: ubuntu-24.04
     steps:
       - name: Checkout source
-        uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8
+        uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd
         with:
           persist-credentials: false
       - name: Setup nox
@@ -109,7 +109,7 @@ jobs:
     runs-on: ubuntu-24.04
     steps:
       - name: Checkout source
-        uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8
+        uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd
         with:
           persist-credentials: false
       - name: Setup nox
diff --git a/.github/workflows/update_version.yml b/.github/workflows/update_version.yml
@@ -18,11 +18,11 @@ jobs:
     runs-on: ubuntu-24.04
     steps:
     - name: Checkout source
-      uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8
+      uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd
       with:
         persist-credentials: false
     - name: Set up Python
-      uses: actions/setup-python@83679a892e2d95755f2dac6acb0bfd1e9ac5d548
+      uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405
       with:
         python-version: "3.10"
     - name: Check available versions
@@ -41,7 +41,7 @@ jobs:
       run: ./update.sh "${LATEST_VERSION}"
     - name: commit updated files
       if: steps.check_version.outputs.do_pr == 'True'
-      uses: peter-evans/create-pull-request@98357b18bf14b5342f975ff684046ec3b2a07725
+      uses: peter-evans/create-pull-request@c0f553fe549906ede9cf27b5156039d195d2ece0
       with:
         branch: "update-${{ steps.check_version.outputs.latest_version }}"
         commit-message: "Update to micromamba version ${{ steps.check_version.outputs.latest_version }}"
diff --git a/.github/workflows/zizmor.yml b/.github/workflows/zizmor.yml
@@ -18,11 +18,11 @@ jobs:
       security-events: write
     steps:
       - name: Checkout repository
-        uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8
+        uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd
         with:
           persist-credentials: false
 
-      - uses: hynek/setup-cached-uv@ae460f75dcef535482cb6754a8ca5ad6aac63ce7
+      - uses: hynek/setup-cached-uv@547e6a40c3f94f7d2973b2abde9ccb9b5325ac06
 
       - name: Run zizmor 🌈
         run: uvx zizmor --format sarif . > results.sarif
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -3,12 +3,14 @@
 This change log covers changes to the docker image and does not include
 [changes to the micromamba program](https://github.com/mamba-org/mamba/blob/main/CHANGELOG.md).
 
-## 12 January 2026
+## 21 March 2026
 
-- Updated to micromamba version 2.5.0
+- Resume copying `_apptainer_shell.sh` into images
+- Update CUDA v13.1.0 images to CUDA v13.2.0
 
 ## 12 January 2026
 
+- Updated to micromamba version 2.5.0
 - No longer clobber `$HOME` values passed via
   `docker run -e HOME ...` (for `$HOME` values other than `/`).
 
diff --git a/alpine.Dockerfile b/alpine.Dockerfile
@@ -42,6 +42,9 @@ USER $MAMBA_USER
 
 WORKDIR /tmp
 
+# for use with 'apptainer shell --shell /usr/local/bin/_apptainer_shell.sh ...'
+COPY _apptainer_shell.sh /usr/local/bin/_apptainer_shell.sh
+
 # Script which launches commands passed to "docker run"
 COPY _entrypoint.sh /usr/local/bin/_entrypoint.sh
 COPY _activate_current_env.sh /usr/local/bin/_activate_current_env.sh
diff --git a/debian.Dockerfile b/debian.Dockerfile
@@ -40,6 +40,9 @@ USER $MAMBA_USER
 
 WORKDIR /tmp
 
+# for use with 'apptainer shell --shell /usr/local/bin/_apptainer_shell.sh ...'
+COPY _apptainer_shell.sh /usr/local/bin/_apptainer_shell.sh
+
 # Script which launches commands passed to "docker run"
 COPY _entrypoint.sh /usr/local/bin/_entrypoint.sh
 COPY _activate_current_env.sh /usr/local/bin/_activate_current_env.sh
diff --git a/fedora.Dockerfile b/fedora.Dockerfile
@@ -30,6 +30,7 @@ COPY --from=stage1 "${MAMBA_EXE}" "${MAMBA_EXE}"
 COPY _dockerfile_initialize_user_accounts.sh /usr/local/bin/_dockerfile_initialize_user_accounts.sh
 COPY _dockerfile_setup_root_prefix.sh /usr/local/bin/_dockerfile_setup_root_prefix.sh
 
+# hadolint ignore=DL3033
 RUN yum update -y && yum install -y \
       shadow-utils \
     && yum clean all \
@@ -40,6 +41,9 @@ USER $MAMBA_USER
 
 WORKDIR /tmp
 
+# for use with 'apptainer shell --shell /usr/local/bin/_apptainer_shell.sh ...'
+COPY _apptainer_shell.sh /usr/local/bin/_apptainer_shell.sh
+
 # Script which launches commands passed to "docker run"
 COPY _entrypoint.sh /usr/local/bin/_entrypoint.sh
 COPY _activate_current_env.sh /usr/local/bin/_activate_current_env.sh
