chore(astera): add actl overlay + Harbor build-images CI

.actlignore

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+# Large trajectory outputs should live on /mnt/diffuse-shared (or the pod home
+# PVC), not in the synced source checkout. Keep source-controlled templates such
+# as artifacts/*.mdp synced.
+*.cpt
+*.dcd
+*.edr
+*.trr
+*.xtc

.github/workflows/build-images.yml

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+name: Build & push md-workflows images
+
+# Builds the three-stage image chain on the self-hosted Astera builder and pushes to Harbor.
+#
+# Security: this workflow has NO pull_request trigger, so fork PRs can never reach the
+# self-hosted runner or the Harbor credentials. Heavy builds run only on push to `astera`
+# (path-filtered) and manual dispatch. Credentials live in the `harbor` GitHub Environment,
+# which must be restricted to the `astera` deployment branch; the `astera-sh-builder` runner
+# should sit in a runner group scoped to this repo. See the runbook in the PR description.
+on:
+  push:
+    branches: [astera]
+    paths:
+      - Dockerfile.base
+      - Dockerfile.gromacs
+      - Dockerfile.actl
+      - pyproject.toml
+      - md_workflows/**
+      - .github/workflows/build-images.yml
+  workflow_dispatch:
+
+permissions:
+  contents: read
+
+concurrency:
+  group: build-images-${{ github.ref }}
+  cancel-in-progress: true
+
+env:
+  REGISTRY: harbor.astera.sh
+  # base + gromacs (bake the non-redistributable ChimeraX) live in the proprietary project,
+  # distinguished by a stage tag prefix. The final consumable actl image lands in library.
+  PROPRIETARY_IMAGE: harbor.astera.sh/diffuse-proprietary/md-workflows
+  LIBRARY_IMAGE: harbor.astera.sh/library/md-workflows
+
+jobs:
+  version:
+    name: Compute version
+    runs-on: ubuntu-latest
+    outputs:
+      semver: ${{ steps.v.outputs.semver }}
+      build: ${{ steps.v.outputs.build }}
+      sha: ${{ steps.v.outputs.sha }}
+    steps:
+      - uses: actions/checkout@v4
+      - id: v
+        name: Derive version from pyproject.toml
+        run: |
+          set -euo pipefail
+          SEMVER=$(grep -m1 -E '^version[[:space:]]*=' pyproject.toml | sed -E 's/.*"([^"]+)".*/\1/')
+          if [ -z "${SEMVER}" ]; then echo "could not parse version from pyproject.toml" >&2; exit 1; fi
+          SHORT="${GITHUB_SHA::7}"
+          echo "semver=${SEMVER}"                       >> "$GITHUB_OUTPUT"
+          echo "build=${SEMVER}-b${{ github.run_number }}" >> "$GITHUB_OUTPUT"
+          echo "sha=sha-${SHORT}"                       >> "$GITHUB_OUTPUT"
+          echo "Resolved: ${SEMVER} / ${SEMVER}-b${{ github.run_number }} / sha-${SHORT}"
+
+  base:
+    name: Build base
+    needs: version
+    runs-on: [self-hosted, diffuse-sh-builder]
+    environment: harbor
+    outputs:
+      digest: ${{ steps.build.outputs.digest }}
+    steps:
+      - uses: actions/checkout@v4
+      - uses: docker/setup-buildx-action@v3
+      - name: Login to Harbor
+        uses: docker/login-action@v3
+        with:
+          registry: ${{ env.REGISTRY }}
+          username: ${{ secrets.HARBOR_USERNAME }}
+          password: ${{ secrets.HARBOR_PASSWORD }}
+      - id: build
+        uses: docker/build-push-action@v6
+        with:
+          context: .
+          file: Dockerfile.base
+          platforms: linux/amd64
+          push: true
+          provenance: false
+          tags: |
+            ${{ env.PROPRIETARY_IMAGE }}:base-${{ needs.version.outputs.semver }}
+            ${{ env.PROPRIETARY_IMAGE }}:base-${{ needs.version.outputs.build }}
+            ${{ env.PROPRIETARY_IMAGE }}:base-${{ needs.version.outputs.sha }}
+            ${{ env.PROPRIETARY_IMAGE }}:base
+          cache-from: type=registry,ref=${{ env.PROPRIETARY_IMAGE }}:base-buildcache
+          cache-to: type=registry,ref=${{ env.PROPRIETARY_IMAGE }}:base-buildcache,mode=max
+
+  gromacs:
+    name: Build gromacs
+    needs: [version, base]
+    runs-on: [self-hosted, diffuse-sh-builder]
+    environment: harbor
+    outputs:
+      digest: ${{ steps.build.outputs.digest }}
+    steps:
+      - uses: actions/checkout@v4
+      - uses: docker/setup-buildx-action@v3
+      - name: Login to Harbor
+        uses: docker/login-action@v3
+        with:
+          registry: ${{ env.REGISTRY }}
+          username: ${{ secrets.HARBOR_USERNAME }}
+          password: ${{ secrets.HARBOR_PASSWORD }}
+      - id: build
+        uses: docker/build-push-action@v6
+        with:
+          context: .
+          file: Dockerfile.gromacs
+          platforms: linux/amd64
+          push: true
+          provenance: false
+          build-args: |
+            BASE_IMAGE=${{ env.PROPRIETARY_IMAGE }}@${{ needs.base.outputs.digest }}
+          tags: |
+            ${{ env.PROPRIETARY_IMAGE }}:gromacs-${{ needs.version.outputs.semver }}
+            ${{ env.PROPRIETARY_IMAGE }}:gromacs-${{ needs.version.outputs.build }}
+            ${{ env.PROPRIETARY_IMAGE }}:gromacs-${{ needs.version.outputs.sha }}
+            ${{ env.PROPRIETARY_IMAGE }}:gromacs
+          cache-from: type=registry,ref=${{ env.PROPRIETARY_IMAGE }}:gromacs-buildcache
+          cache-to: type=registry,ref=${{ env.PROPRIETARY_IMAGE }}:gromacs-buildcache,mode=max
+
+  actl:
+    name: Build actl (consumable)
+    needs: [version, gromacs]
+    runs-on: [self-hosted, diffuse-sh-builder]
+    environment: harbor
+    outputs:
+      digest: ${{ steps.build.outputs.digest }}
+    steps:
+      - uses: actions/checkout@v4
+      - uses: docker/setup-buildx-action@v3
+      - name: Login to Harbor
+        uses: docker/login-action@v3
+        with:
+          registry: ${{ env.REGISTRY }}
+          username: ${{ secrets.HARBOR_USERNAME }}
+          password: ${{ secrets.HARBOR_PASSWORD }}
+      - id: build
+        uses: docker/build-push-action@v6
+        with:
+          context: .
+          file: Dockerfile.actl
+          platforms: linux/amd64
+          push: true
+          provenance: false
+          build-args: |
+            GROMACS_IMAGE=${{ env.PROPRIETARY_IMAGE }}@${{ needs.gromacs.outputs.digest }}
+          tags: |
+            ${{ env.LIBRARY_IMAGE }}:${{ needs.version.outputs.semver }}
+            ${{ env.LIBRARY_IMAGE }}:${{ needs.version.outputs.build }}
+            ${{ env.LIBRARY_IMAGE }}:${{ needs.version.outputs.sha }}
+            ${{ env.LIBRARY_IMAGE }}:actl
+            ${{ env.LIBRARY_IMAGE }}:latest
+          cache-from: type=registry,ref=${{ env.LIBRARY_IMAGE }}:actl-buildcache
+          cache-to: type=registry,ref=${{ env.LIBRARY_IMAGE }}:actl-buildcache,mode=max
+      - name: Report digests
+        run: |
+          echo "base    digest: ${{ needs.base.outputs.digest }}"  || true
+          echo "gromacs digest: ${{ needs.gromacs.outputs.digest }}"
+          echo "actl    digest: ${{ steps.build.outputs.digest }}"
+          echo "Published ${{ env.LIBRARY_IMAGE }}:${{ needs.version.outputs.build }}"

Dockerfile.actl

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+# syntax=docker/dockerfile:1
+# ==================== md-workflows Astera ACTL overlay (stage 3 of 3) ====================
+# Layers Astera workspace conventions on top of the GROMACS stage (Dockerfile.gromacs): the
+# /home/dev persisted home, editor/sync/debug tools, root-oriented interactive pods, and the
+# global shell init that keeps the baked lunus env active. The scientific stack (CUDA 12.6,
+# GROMACS sm_90 + AVX_512, md-workflows) is inherited unchanged from the gromacs image.
+#
+# Build locally (after building md-gromacs:local):
+#   docker buildx build --platform linux/amd64 \
+#     -f Dockerfile.actl --build-arg GROMACS_IMAGE=md-gromacs:local \
+#     -t harbor.astera.sh/library/md-workflows:local-actl .
+ARG GROMACS_IMAGE=md-gromacs:local
+FROM ${GROMACS_IMAGE} AS actl
+
+USER root
+
+ARG ACTL_PACKAGES="bash ca-certificates curl wget rsync tini vim nano emacs-nox git zsh htop tmux ncdu iputils-ping dnsutils"
+
+ENV DEBIAN_FRONTEND=noninteractive \
+    HOME=/home/dev \
+    XDG_CONFIG_HOME=/home/dev/.config \
+    XDG_CACHE_HOME=/home/dev/.cache \
+    XDG_DATA_HOME=/home/dev/.local/share \
+    SHELL=/bin/bash \
+    MAMBA_ROOT_PREFIX=/opt/micromamba \
+    MAMBA_EXE=/opt/micromamba/bin/micromamba \
+    CONDA_PREFIX=/opt/micromamba/envs/lunus \
+    PYTHONPATH=/home/dev/workspace:/opt/md-workflows \
+    PATH="/opt/micromamba/bin:/opt/micromamba/envs/lunus/bin:/usr/local/gromacs/bin:${PATH}"
+
+RUN apt-get update && apt-get install -y --no-install-recommends \
+        ${ACTL_PACKAGES} \
+        bc \
+        bzip2 \
+        coreutils \
+        libgomp1 \
+    && rm -rf /var/lib/apt/lists/* \
+    && apt-get clean \
+    && mkdir -p /home/dev/.config /home/dev/.cache /home/dev/.local/share /home/dev/workspace /etc/zsh \
+    && cat > /usr/local/share/actl-md-workflows-shell-init.sh <<'EOF'
+# Keep the baked md-workflows/lunus environment active while letting ACTL's
+# synced checkout at /home/dev/workspace override the baked package for edits.
+if [ -d /opt/micromamba/envs/lunus/bin ]; then
+  case ":${PATH}:" in
+    *:/opt/micromamba/envs/lunus/bin:*) ;;
+    *) PATH="/opt/micromamba/envs/lunus/bin:${PATH}" ;;
+  esac
+  export PATH
+  CONDA_PREFIX=/opt/micromamba/envs/lunus
+  export CONDA_PREFIX
+fi
+
+if [ -x /opt/micromamba/bin/micromamba ]; then
+  case "${ZSH_VERSION:+zsh}${BASH_VERSION:+bash}" in
+    zsh*) eval "$(/opt/micromamba/bin/micromamba shell hook --shell zsh 2>/dev/null)" || true ;;
+    *bash*) eval "$(/opt/micromamba/bin/micromamba shell hook --shell bash 2>/dev/null)" || true ;;
+  esac
+fi
+
+if [ -d /home/dev/workspace ]; then
+  case ":${PYTHONPATH:-}:" in
+    *:/home/dev/workspace:*) ;;
+    *) PYTHONPATH="/home/dev/workspace${PYTHONPATH:+:${PYTHONPATH}}" ;;
+  esac
+fi
+if [ -d /opt/md-workflows ]; then
+  case ":${PYTHONPATH:-}:" in
+    *:/opt/md-workflows:*) ;;
+    *) PYTHONPATH="${PYTHONPATH:+${PYTHONPATH}:}/opt/md-workflows" ;;
+  esac
+fi
+export PYTHONPATH
+
+case "$-" in
+  *i*)
+    if [ -d /home/dev/workspace ]; then
+      cd /home/dev/workspace || true
+    fi
+    ;;
+esac
+EOF
+RUN chmod 0644 /usr/local/share/actl-md-workflows-shell-init.sh \
+    && printf '\n# Astera md-workflows environment\n[ -r /usr/local/share/actl-md-workflows-shell-init.sh ] && . /usr/local/share/actl-md-workflows-shell-init.sh\n' >> /etc/bash.bashrc \
+    && printf '\n# Astera md-workflows environment\n[ -r /usr/local/share/actl-md-workflows-shell-init.sh ] && . /usr/local/share/actl-md-workflows-shell-init.sh\n' >> /etc/zsh/zshrc \
+    && for cmd in \
+        md_workflows.mdmx gmx micromamba curl wget rsync tini vim nano emacs git zsh htop tmux ncdu ping dig; do \
+          command -v "${cmd}" >/dev/null; \
+        done
+
+WORKDIR /home/dev
+SHELL ["/bin/bash", "-c"]
+CMD ["bash"]