update installer scripts, add build action

.github/workflows/container_build_push.yml

@@ -0,0 +1,89 @@
+name: container-build-push
+
+on:
+  push:
+    branches:
+      - 'main'
+      - 'espenhgn/issue20'
+    tags:
+      - "v*.*.*"
+
+jobs:
+  docker:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Docker meta
+        id: meta
+        uses: docker/metadata-action@v5
+        with:
+          # list of Docker images to use as base name for tags
+          images: |
+            ghcr.io/${{ github.repository_owner }}/mixer            
+          # generate Docker tags based on the following events/attributes
+          tags: |
+            type=schedule
+            type=ref,event=branch
+            type=ref,event=pr
+            type=semver,pattern={{version}}
+            type=semver,pattern={{major}}.{{minor}}
+            type=semver,pattern={{major}}
+            type=sha
+            type=raw,value=latest,enable={{is_default_branch}} 
+      - name: Set up QEMU
+        uses: docker/setup-qemu-action@v3
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v3
+      - name: Login to GitHub Container Registry
+        if: github.event_name != 'pull_request'
+        uses: docker/login-action@v3
+        with:
+          registry: ghcr.io
+          username: ${{ github.repository_owner }}
+          password: ${{ secrets.GITHUB_TOKEN }}      
+      - name: Build and push
+        uses: docker/build-push-action@v5
+        with:
+          context: "{{defaultContext}}:"
+          push: ${{ github.event_name != 'pull_request' }}
+          tags: ${{ steps.meta.outputs.tags }}
+          labels: ${{ steps.meta.outputs.labels }}
+          file:
+            ./Dockerfile
+          platforms: linux/amd64
+
+  build-apptainer-container:
+    needs: docker
+    runs-on: ubuntu-latest
+    permissions:
+      contents: read
+      packages: write
+    name: Build Apptainer Container
+    steps:
+      - name: Check out code for the container builds
+        uses: actions/checkout@v4
+      - name: Docker meta 
+        id: meta
+        uses: docker/metadata-action@v5
+        with:
+          images: |
+            ghcr.io/${{ github.repository_owner }}/mixer            
+          tags: |
+            type=semver,pattern={{version}}
+            type=ref,event=branch
+            type=sha
+            type=raw,value=latest,enable={{is_default_branch}}
+      - name: Build and push Apptainer container
+        run: |
+          tags="${{ steps.meta.outputs.tags }}"
+          csv_tags=$(printf "%s\n" "$tags" | awk -F: 'NR==1{printf "%s,", $0; next} {printf "%s,", $NF}' | sed 's/,$//')
+          IFS= read -r first_tag <<EOF
+          $tags
+          EOF
+          echo "The first tag is: $first_tag"
+          echo "CSV-tags are: $csv_tags"
+          echo ${{ secrets.GITHUB_TOKEN }} | oras login --username ${{ github.repository_owner }} --password-stdin ghcr.io
+          docker pull kaczmarj/apptainer:latest
+          docker run --rm --privileged -v $(pwd):/work kaczmarj/apptainer build mixer.sif docker://"$first_tag"
+          oras push "$csv_tags" --artifact-type application/vnd.acme.rocket.config mixer.sif
+          rm mixer.sif
+        shell: sh

src/dockerfiles/mixer/Dockerfile

@@ -9,26 +9,22 @@ RUN chmod +x apt_get_essential.sh && \
     bash apt_get_essential.sh
 
 WORKDIR /tmp
-COPY /scripts/install_miniconda3.sh .
-RUN chmod +x install_miniconda3.sh && \
-    bash install_miniconda3.sh
-
-RUN conda install conda=23.9.0 && \
-    conda config --add channels conda-forge && \
-    conda config --set channel_priority strict && \
-    conda install \
+COPY /scripts/install_mambaforge.sh .
+RUN chmod +x install_mambaforge.sh && \
+    bash install_mambaforge.sh
+
+RUN mamba install python=3.8.18 \
     jupyterlab=4.0.7 \
     matplotlib=3.7.3 \
     matplotlib-venn=0.11.9 \
     numpy=1.24.4 \
     numdifftools=0.9.41 \
     pandas=2.0.3 \
-    python=3.8 \
     scipy=1.10.1 \
     seaborn=0.13.0 \
     statsmodels=0.14.0 \
     --yes && \
-    conda clean -a -y
+    mamba clean -a -y
 
 WORKDIR /tools/plink
 COPY /scripts/install_plink.sh /tmp

src/scripts/apt_get_essential.sh

@@ -13,18 +13,18 @@ apt-get install -y --no-install-recommends \
    build-essential=12.8ubuntu1.1 \
    bzip2=1.0.8-2 \
    cmake=3.16.3-1ubuntu1.20.04.1 \
-   curl=7.68.0-1ubuntu2.21 \
+   curl=7.68.0-1ubuntu2.22 \
    dos2unix=7.4.0-2 \
    gdb=9.2-0ubuntu1~20.04.1 \
    gfortran=4:9.3.0-1ubuntu2 \
    git=1:2.25.1-1ubuntu3.11 \
-   less=551-1ubuntu0.1 \
+   less=551-1ubuntu0.3 \
    libatlas-base-dev=3.10.3-8ubuntu7 \
-   libcurl4=7.68.0-1ubuntu2.21 \
-   libcurl4-openssl-dev=7.68.0-1ubuntu2.21 \
+   libcurl4=7.68.0-1ubuntu2.22 \
+   libcurl4-openssl-dev=7.68.0-1ubuntu2.22 \
    libgomp1=10.5.0-1ubuntu1~20.04 \
    libgsl-dev=2.5+dfsg-6+deb10u1build0.20.04.1 \
-   libnss3=2:3.49.1-1ubuntu1.9 \
+   libnss3=2:3.98-0ubuntu0.20.04.2 \
    libpcre2-dev=10.34-7ubuntu0.1 \
    libquadmath0=10.5.0-1ubuntu1~20.04 \
    libxt-dev=1:1.1.5-1 \
@@ -36,7 +36,7 @@ apt-get install -y --no-install-recommends \
    tar=1.30+dfsg-7ubuntu0.20.04.3 \
    tofrodos=1.7.13+ds-4 \
    unzip=6.0-25ubuntu1.1 \
-   vim=2:8.1.2269-1ubuntu5.20 \
+   vim=2:8.1.2269-1ubuntu5.22 \
    wget=1.20.3-1ubuntu2 \
    zlib1g-dev=1:1.2.11.dfsg-2ubuntu1.5
 

src/scripts/install_mambaforge.sh

@@ -0,0 +1,9 @@
+#!/bin/sh
+set -euo pipefail
+
+curl -sSL https://github.com/conda-forge/miniforge/releases/download/24.3.0-0/Mambaforge-24.3.0-0-$(uname)-$(uname -m).sh -o /tmp/mambaforge.sh \
+  && mkdir /root/.conda \
+  && bash /tmp/mambaforge.sh -bfp /usr/local \
+  && rm -rf /tmp/mambaforge.sh
+
+export PATH=$PATH:/opt/conda/bin