Doc: Instructions for AMICI with singularity (#1964)

* how to create a container
* make Dockerfile compatible with spython/singularity
* mv docker/ container/

.github/workflows/deploy_protected.yml

@@ -7,7 +7,7 @@ on:
       - release**
   pull_request:
     paths:
-      - docker/Dockerfile
+      - container/Dockerfile
   workflow_dispatch:
 
 jobs:
@@ -27,7 +27,7 @@ jobs:
       with:
         python-version: ${{ matrix.python-version }}
     - uses: actions/checkout@v3
-    - run: git archive -o docker/amici.tar.gz --format=tar.gz HEAD
+    - run: git archive -o container/amici.tar.gz --format=tar.gz HEAD
     - name: Set up QEMU
       uses: docker/setup-qemu-action@v2
     - name: Set up Docker Buildx
@@ -38,7 +38,7 @@ jobs:
         name: dweindl/amici
         username: ${{ secrets.DOCKER_USERNAME }}
         password: ${{ secrets.DOCKER_PASSWORD }}
-        workdir: docker/
+        workdir: container/
         dockerfile: Dockerfile
         tag_names: true
         platforms: linux/amd64,linux/arm64

container/Dockerfile

@@ -0,0 +1,25 @@
+FROM ubuntu:22.04
+
+# install dependencies
+
+RUN apt-get update && apt-get install -y \
+    g++ \
+    libatlas-base-dev \
+    python-is-python3 \
+    python3 \
+    python3-dev \
+    python3-pip \
+    python3-venv \
+    swig
+
+# prepare python install
+
+COPY amici.tar.gz /from_host/
+
+RUN pip3 install --upgrade pip build && \
+    mkdir -p /from_host/amici/ && \
+    cd /from_host/amici && \
+    tar -xzf ../amici.tar.gz && cd python/sdist && \
+    python3 -m build --sdist && \
+    pip3 install -v $(ls -t dist/amici-*.tar.gz | head -1)[petab] && \
+    rm -rf /from_host

container/README.md

@@ -0,0 +1,51 @@
+# Using AMICI inside containers
+
+AMICI docker images are regularly published to
+https://hub.docker.com/r/dweindl/amici.
+
+## Docker / Podman
+
+The commands below are for use with Docker. When using Podman, just replace
+`docker` by `podman`.
+
+### Create an image
+
+In the AMICI base directory run:
+
+```bash
+git archive -o container/amici.tar.gz --format=tar.gz HEAD
+cd container && docker build -t $USER/amici:latest .
+```
+Note that this will include files from the last commit, but no uncommitted
+changes.  
+
+### Pull published image
+
+```bash
+docker pull dweindl/amici:latest
+```
+
+## Singularity / Apptainer
+
+### Create an image
+
+In the AMICI base directory run:
+
+```bash
+# prepare amici files to be copied to the image
+# Note that this will include files from the last commit, but no uncommitted
+# changes.  
+git archive -o container/amici.tar.gz --format=tar.gz HEAD
+# install spython if necessary
+test -x "$(command -v spython)" || pip install spython
+# convert Dockerfile to singularity/apptainer definition using spython
+(cd container/ && spython recipe Dockerfile amici.def)
+# build image
+(cd container/ && singularity build amici.sif amici.def)
+```
+
+### Pull published image
+
+```bash
+singularity pull docker://dweindl/amici:latest
+```