Create only one self sufficient docker image

* This image is multi-stage. Each stage tailored for one stage on the pipeline
* Final image has a much less weight due to copying binaries to a new image and downloading essential dependencies.

.ci/build.sh

+#!/usr/bin/env bash
+
 # build script for all CIs
+# requisites
+#   * DUNE_OPTIONS_FILE is defined
+#   * DUNECONTROL is defined or dunecontrol is in the PATH
+
+set -e
+
+if [[ -z "$DUNECONTROL" ]]
+then
+  DUNECONTROL="dunecontrol"
+fi
 
 # make sure we get the right mingw64 version of g++ on appveyor
 PATH=/mingw64/bin:$PATH
@@ -17,5 +29,5 @@ gcc --version
 cmake --version
 
 ${DUNECONTROL} --opts=${DUNE_OPTIONS_FILE} --only=dune-copasi all
-${DUNECONTROL} --opts=${DUNE_OPTIONS_FILE} --module=$repo bexec cmake --build . --target install
-rm -rf dune-copasi
+cmake --build dune-copasi/build-cmake --target install
+rm -rf dune-copasi/build-cmake

.ci/dune-logging.patch

@@ -10,3 +10,25 @@ index 693bab6..dd4ffae 100644
      PUBLIC DUNE_LOGGING_VENDORED_FMT=1
      )
  
+diff --git a/CMakeLists.txt b/CMakeLists.txt
+index 693bab6..ee2f2ff 100644
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -77,7 +77,7 @@ the command \"git submodule update --init --recursive\" in the dune-logging sour
+   # Install vendored headers
+   install(
+     FILES ${FMT_HEADERS}
+-    DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}/dune/vendor/fmt/fmt
++    DESTINATION include/dune/vendor/fmt/fmt
+     )
+ 
+   if(${CMAKE_SYSTEM_NAME} STREQUAL "Windows")
+@@ -145,7 +145,7 @@ the command \"git submodule update --init --recursive\" in the dune-logging sour
+     dune-logging-fmt
+     PUBLIC
+       $<BUILD_INTERFACE:${CMAKE_CURRENT_BINARY_DIR}/dune/vendor/fmt>
+-      $<INSTALL_INTERFACE:dune/vendor/fmt>
++      $<INSTALL_INTERFACE:include/dune/vendor/fmt>
+     )
+ 
+ endif()

.ci/setup.sh

+#!/usr/bin/env bash
+
 # dependencies setup script for Travis and AppVeyor CI
+# requisites
+#   * DUNE_OPTIONS_FILE is defined
+#   * DUNCONTROL defined or CMAKE_INSTALL_PREFIX should install in a folder reachable by PATH
+
+set -e
 
 DUNE_VERSION="2.7"
 
@@ -6,7 +13,6 @@ DUNE_VERSION="2.7"
 PATH=/mingw64/bin:$PATH
 echo "PATH=$PATH"
 echo "MSYSTEM: $MSYSTEM"
-echo "DUNECONTROL: ${DUNECONTROL}"
 echo "DUNE_OPTIONS_FILE: ${DUNE_OPTIONS_FILE}"
 cat ${DUNE_OPTIONS_FILE}
 echo "PWD: $PWD"
@@ -32,7 +38,6 @@ pip3 --version
 which cmake
 cmake --version
 
-
 # download Dune dependencies
 for repo in core/dune-common core/dune-geometry core/dune-grid core/dune-istl core/dune-localfunctions staging/dune-functions staging/dune-uggrid
 do
@@ -73,29 +78,39 @@ if [[ $MSYSTEM ]]; then
 fi
 
 # patch cmake macro to avoid build failure when fortran compiler not found, e.g. on osx
+cd dune-common
 if [[ "$OSTYPE" == "darwin"* ]]; then
-	cd dune-common
 	wget https://gist.githubusercontent.com/lkeegan/059984b71f8aeb0bbc062e85ad7ee377/raw/e9c7af42c47fe765547e60833a72b5ff1e78123c/cmake-patch.txt
 	echo '' >> cmake-patch.txt
 	git apply cmake-patch.txt
-	# another patch for missing header in cmake install list
-	git apply ../dune-copasi/.ci/dune-common.patch
-	cd ../
 fi
 
+# another patch for missing header in cmake install list
+git apply ../dune-copasi/.ci/dune-common.patch
+cd ../
+
+
 cd dune-logging
 git apply ../dune-copasi/.ci/dune-logging.patch
 cd ../
 
-# python virtual environment does not work in windows yet
+MODULES="logging uggrid geometry grid localfunctions istl typetree functions pdelab multidomaingrid "
 if [[ ! $MSYSTEM ]]; then
-	${DUNECONTROL} --opts=${DUNE_OPTIONS_FILE} --module=dune-testtools all
+	MODULES+="testtools"
 fi
 
-for repo in dune-testtools dune-logging dune-pdelab dune-multidomaingrid
+./dune-common/bin/dunecontrol --opts=${DUNE_OPTIONS_FILE} --only=dune-common all
+cmake --build dune-common/build-cmake/ --target install
+rm -rf dune-common
+
+if [[ -z "$DUNECONTROL" ]]
+then
+  DUNECONTROL=dunecontrol
+fi
+
+for module in $MODULES
 do
-  ${DUNECONTROL} --opts=${DUNE_OPTIONS_FILE} --module=$repo all
+	${DUNECONTROL} --opts=${DUNE_OPTIONS_FILE} --only=dune-$module all
+	cmake --build dune-$module/build-cmake/ --target install
+	rm -rf dune-$module
 done
-
-${DUNECONTROL} --opts=${DUNE_OPTIONS_FILE} --module=$repo bexec cmake --build . --target install
-rm -rf dune-*

.ci/system_tests.sh

+#!/usr/bin/env bash
+
 # system tests script for all CIs
 
+set -e
+
 # make sure we get the right mingw64 version of g++ on appveyor
 PATH=/mingw64/bin:$PATH
 echo "PATH=$PATH"
@@ -13,7 +17,7 @@ g++ --version
 gcc --version
 cmake --version
 
-mkdir dune-copasi/test/cmake-build && cd dune-copasi/test/cmake-build
+mkdir dune-copasi/test/build-cmake && cd dune-copasi/test/build-cmake
 cmake --build ..
 cmake --target build_system_tests
 ctest -j4 -L "DUNE_SYSTEMTEST" --output-on-failure

.ci/unit_tests.sh

+#!/usr/bin/env bash
+
 # unit tests script for all CIs
 
+set -e
+
 # make sure we get the right mingw64 version of g++ on appveyor
 PATH=/mingw64/bin:$PATH
 echo "PATH=$PATH"
@@ -13,7 +17,7 @@ g++ --version
 gcc --version
 cmake --version
 
-mkdir dune-copasi/test/cmake-build && cd dune-copasi/test/cmake-build
+mkdir dune-copasi/test/build-cmake && cd dune-copasi/test/build-cmake
 cmake --build ..
 cmake --target build_unit_tests
 ctest -j4 -L "unit" --output-on-failure

.gitlab-ci.yml

@@ -31,45 +31,42 @@ stages:
   <<: *global_variables
   TOOLCHAIN: gcc-8-17
   DUNECI_OS: debian
-  DUNECI_BASE_IMAGE: ${CI_REGISTRY}/docker/ci/debian:10
-  DUNE_COPASI_BUILD_IMAGE: ${CI_REGISTRY}/copasi/dune-copasi/dependencies:${DUNECI_OS}-${TOOLCHAIN}-${BASE_IMAGE_VERSION}
-  DUNE_COPASI_DEPLOY_IMAGE: debian:buster
+  BASE_IMAGE: debian:10
+  DEPENDENCIES_IMAGE: ${CI_REGISTRY}/copasi/dune-copasi/dependencies:${DUNECI_OS}-${TOOLCHAIN}-${BASE_IMAGE_VERSION}
   DEPLOY_LATEST: "true"
 
 .debian_clang: &debian_clang
   <<: *global_variables
   TOOLCHAIN: clang-6-17
   DUNECI_OS: debian
-  DUNECI_BASE_IMAGE: ${CI_REGISTRY}/docker/ci/debian:10
-  DUNE_COPASI_BUILD_IMAGE: ${CI_REGISTRY}/copasi/dune-copasi/dependencies:${DUNECI_OS}-${TOOLCHAIN}-${BASE_IMAGE_VERSION}
-  DUNE_COPASI_DEPLOY_IMAGE: debian:buster
+  BASE_IMAGE: debian:10
+  DEPENDENCIES_IMAGE: ${CI_REGISTRY}/copasi/dune-copasi/dependencies:${DUNECI_OS}-${TOOLCHAIN}-${BASE_IMAGE_VERSION}
 
 .ubuntu_gcc: &ubuntu_gcc
   <<: *global_variables
   TOOLCHAIN: gcc-7-17
   DUNECI_OS: ubuntu
-  DUNECI_BASE_IMAGE: ${CI_REGISTRY}/docker/ci/ubuntu:18.04
-  DUNE_COPASI_BUILD_IMAGE: ${CI_REGISTRY}/copasi/dune-copasi/dependencies:${DUNECI_OS}-${TOOLCHAIN}-${BASE_IMAGE_VERSION}
-  DUNE_COPASI_DEPLOY_IMAGE: ubuntu:18.04
+  BASE_IMAGE: ubuntu:18.04
+  DEPENDENCIES_IMAGE: ${CI_REGISTRY}/copasi/dune-copasi/dependencies:${DUNECI_OS}-${TOOLCHAIN}-${BASE_IMAGE_VERSION}
 
 .ubuntu_clang: &ubuntu_clang
   <<: *global_variables
   TOOLCHAIN: clang-6-17
   DUNECI_OS: ubuntu
-  DUNECI_BASE_IMAGE: ${CI_REGISTRY}/docker/ci/ubuntu:18.04
-  DUNE_COPASI_BUILD_IMAGE: ${CI_REGISTRY}/copasi/dune-copasi/dependencies:${DUNECI_OS}-${TOOLCHAIN}-${BASE_IMAGE_VERSION}
-  DUNE_COPASI_DEPLOY_IMAGE: ubuntu:18.04
+  BASE_IMAGE: ubuntu:18.04
+  DEPENDENCIES_IMAGE: ${CI_REGISTRY}/copasi/dune-copasi/dependencies:${DUNECI_OS}-${TOOLCHAIN}-${BASE_IMAGE_VERSION}
 
 .setup: &setup
   image: ${DOCKER_IMAGE}
   stage: setup
   script:
     - echo "$CI_REGISTRY_PASSWORD" | docker login -u $CI_REGISTRY_USER --password-stdin $CI_REGISTRY/copasi/dune-copasi
-    - docker build -f docker/dependencies.dockerfile
-        --build-arg BASE_IMAGE=${DUNECI_BASE_IMAGE}
+    - docker build
+        --build-arg BASE_IMAGE=${BASE_IMAGE}
         --build-arg TOOLCHAIN=${TOOLCHAIN}
-        -t ${DUNE_COPASI_BUILD_IMAGE} .
-    - docker push ${DUNE_COPASI_BUILD_IMAGE}
+        --target setup-env
+        -t ${DEPENDENCIES_IMAGE} .
+    - docker push ${DEPENDENCIES_IMAGE}
     - docker logout $CI_REGISTRY/copasi/dune-copasi
   rules:
     - if: '$REBUILD_BASE_IMAGE'
@@ -79,7 +76,7 @@ stages:
   <<: *dind_docker_tags
 
 .build: &build
-  image: ${DUNE_COPASI_BUILD_IMAGE}
+  image: ${DEPENDENCIES_IMAGE}
   stage: build
   script:
     - cd ..
@@ -91,7 +88,7 @@ stages:
   <<: *default_tags
 
 .unit_tests: &unit_tests
-  image: ${DUNE_COPASI_BUILD_IMAGE}
+  image: ${DEPENDENCIES_IMAGE}
   stage: unit_tests
   script:
     - echo 'CMAKE_FLAGS+=" -DCMAKE_BUILD_TYPE=Debug"' >> /duneci/cmake-flags/dune_copasi.opts
@@ -105,7 +102,7 @@ stages:
   <<: *default_tags
 
 .system_tests: &system_tests
-  image: ${DUNE_COPASI_BUILD_IMAGE}
+  image: ${DEPENDENCIES_IMAGE}
   stage: system_tests
   script:
     - cd ..
@@ -124,14 +121,13 @@ stages:
   script:
     - echo "$CI_REGISTRY_PASSWORD" | docker login -u $CI_REGISTRY_USER --password-stdin $CI_REGISTRY/copasi/dune-copasi
     - DOCKER_TAG="${DUNECI_OS}-${TOOLCHAIN}-${CI_COMMIT_REF_NAME}"
-    - docker build -f docker/dune-copasi.dockerfile
-      --build-arg BUILD_IMAGE=${DUNE_COPASI_BUILD_IMAGE}
-      --build-arg PRODUCTION_IMAGE=${DUNE_COPASI_DEPLOY_IMAGE}
-      --build-arg BRANCH=${CI_COMMIT_REF_NAME}
+    - docker build
+      --build-arg BASE_IMAGE=${BASE_IMAGE}
+      --build-arg TOOLCHAIN=${TOOLCHAIN}
+      --cache-from ${DEPENDENCIES_IMAGE}
       -t $CI_REGISTRY/copasi/dune-copasi/dune-copasi:${DOCKER_TAG} .
     - docker push $CI_REGISTRY/copasi/dune-copasi/dune-copasi:${DOCKER_TAG}
-    - |
-      if [ "$CI_COMMIT_BRANCH" == "latest" && $DEPLOY_LATEST ]; then
+    - if [ "$CI_COMMIT_BRANCH" == "latest" && $DEPLOY_LATEST ]; then
         docker tag $CI_REGISTRY/copasi/dune-copasi/dune-copasi:${DOCKER_TAG} $CI_REGISTRY/copasi/dune-copasi/dune-copasi:latest
         docker push $CI_REGISTRY/copasi/dune-copasi/dune-copasi:latest
       fi
@@ -149,8 +145,7 @@ stages:
   script:
     - mkdir -m 777 dunecopasi && cd dunecopasi
     - cp test/test_cell.mini dunecopasi
-    - docker run -v $PWD $CI_REGISTRY/copasi/dune-copasi/dune-copasi:${DOCKER_TAG} dune_copasi_md test_cell.mini
-
+    - docker run -v $PWD $CI_REGISTRY/copasi/dune-copasi/dune-copasi:${DOCKER_TAG} dune-copasi-md test_cell.mini
 
 # debian gcc
 setup:debian_gcc:

Dockerfile

+ARG BASE_IMAGE=debian:10
+ARG DUNECI_PARALLEL=2
+
+# setup of dune dependencies
+FROM registry.dune-project.org/docker/ci/${BASE_IMAGE} AS setup-env
+
+ARG TOOLCHAIN=clang-6-17
+
+ENV DUNE_OPTIONS_FILE=/duneci/dune.opts
+ENV PATH=/duneci/install/bin:$PATH
+
+RUN    ln -s /duneci/toolchains/${TOOLCHAIN} /duneci/toolchain \
+    && export PATH=/duneci/install/bin:$PATH
+RUN    echo 'CMAKE_FLAGS+=" -DDUNE_PYTHON_VIRTUALENV_SETUP=1"' >> /duneci/cmake-flags/enable_virtualenv \
+    && echo 'CMAKE_FLAGS+=" -DDUNE_PYTHON_VIRTUALENV_PATH=/duneci/install/dune-python-venv"' >> /duneci/cmake-flags/enable_virtualenv \
+    && echo 'CMAKE_FLAGS+=" -DCMAKE_PREFIX_PATH:PATH=/duneci/install"' >> /duneci/cmake-flags/install_path \
+    && echo 'CMAKE_FLAGS+=" -DCMAKE_INSTALL_PREFIX:PATH=/duneci/install"' >> /duneci/cmake-flags/install_path \
+    && echo 'CMAKE_FLAGS+=" -DCMAKE_GENERATOR="Ninja' >> /duneci/cmake-flags/cmake_generator
+WORKDIR /duneci/modules
+RUN mkdir -p /duneci/modules/dune-copasi/.ci
+COPY --chown=duneci ./.ci /duneci/modules/dune-copasi/.ci
+RUN bash dune-copasi/.ci/setup.sh
+
+# build and install dune-copasi from the setup-env
+FROM setup-env AS build-env
+
+ENV DUNE_OPTIONS_FILE=/duneci/dune.opts
+ENV PATH=/duneci/install/bin:$PATH
+
+RUN    echo 'CMAKE_FLAGS+=" -DDUNE_COPASI_SD_EXECUTABLE=ON"' >> /duneci/cmake-flags/production \
+    && echo 'CMAKE_FLAGS+=" -DDUNE_COPASI_MD_EXECUTABLE=ON"' >> /duneci/cmake-flags/production \
+    && echo 'CMAKE_FLAGS+=" -DCMAKE_CXX_FLAGS_RELEASE='"'"'-O3 -fvisibility=hidden -fpic -static-libstdc++'"'"' "' >> /duneci/cmake-flags/production \
+    && echo 'CMAKE_FLAGS+=" -DCMAKE_BUILD_TYPE=Release"' >> /duneci/cmake-flags/production
+
+WORKDIR /duneci/modules
+COPY --chown=duneci ./ /duneci/modules/dune-copasi
+RUN bash dune-copasi/.ci/build.sh
+
+# move results to a -lighter- production  image
+FROM ${BASE_IMAGE} AS production-env
+LABEL maintainer="santiago.ospina@iwr.uni-heidelberg.de"
+
+COPY --from=build-env /duneci/install /usr/local
+
+RUN rm -f /etc/apt/apt.conf.d/docker-gzip-indexes \
+  && rm -rf /var/lib/apt/lists/*
+RUN export DEBIAN_FRONTEND=noninteractive; \
+  apt-get update && apt-get dist-upgrade --no-install-recommends --yes \
+  && apt-get install --no-install-recommends --yes \
+  libscotchparmetis-dev \
+  libldl2 \
+  libspqr2 \
+  libumfpack5 \
+  libarpack++2c2a \
+  libsuperlu5 \
+  libgmpxx4ldbl \
+  libopenblas-base \
+  libtiff5 \
+  libmuparser2v5 \
+  && apt-get clean && rm -rf /var/lib/apt/lists/*
+
+RUN adduser --disabled-password --home /dunecopasi --uid 50000 dunecopasi
+
+WORKDIR /dunecopasi
+VOLUME ["/dunecopasi"]
+USER dunecopasi

doc/docusaurus/docs/install_use.md

@@ -194,9 +194,11 @@ target_link_libraries(my_app PRIVATE dune::dune-copasi)
 # ...
 ```
 
-If the `CMAKE_INSTALL_PREFIX` options was used on installation, be sure to also
-include it on the app build settings:
+If the `CMAKE_INSTALL_PREFIX` options was used on CMake configuration
+dune-copasi, be sure to also include it as a CMake prefix
+`-CMAKE_PREFIX_PATH` on the app build settings. This way, CMake can find our
+targets:
 
 ```bash
-cmake -DCMAKE_INSTALL_PREFIX=/opt/dune /path/to/app/source/
+cmake --DCMAKE_PREFIX_PATH=/opt/dune /path/to/app/source/
 ```

docker/dependencies.dockerfile

-ARG BASE_IMAGE=registry.dune-project.org/docker/ci/ubuntu:18.04
-FROM ${BASE_IMAGE}
-ARG DUNECI_PARALLEL=2
-
-ARG TOOLCHAIN=clang-6-17
-ARG DUNE_OPTIONS_FILE=/duneci/dune.opts
-ARG DUNECONTROL=/duneci/modules/dune-common/bin/dunecontrol
-
-RUN ln -s /duneci/toolchains/${TOOLCHAIN} /duneci/toolchain
-
-ENV PATH=/duneci/install/bin:$PATH
-
-RUN echo 'CMAKE_FLAGS+=" -DDUNE_PYTHON_VIRTUALENV_SETUP=1 -DDUNE_PYTHON_VIRTUALENV_PATH=/duneci/install/dune-python-venv"' >> /duneci/cmake-flags/enable_virtualenv
-RUN echo 'CMAKE_FLAGS+=" -DCMAKE_PREFIX_PATH:PATH=/duneci/install"' >> /duneci/cmake-flags/install_path
-RUN echo 'CMAKE_FLAGS+=" -DCMAKE_INSTALL_PREFIX:PATH=/duneci/install"' >> /duneci/cmake-flags/install_path
-COPY .ci/setup.sh /duneci/modules/setup.sh
-RUN cd /duneci/modules/ && bash setup.sh

docker/dune-copasi.dockerfile

-ARG BUILD_IMAGE
-ARG PRODUCTION_IMAGE
-
-FROM ${BUILD_IMAGE} AS build-env
-
-ARG BRANCH=master
-ARG DUNECI_PARALLEL=2
-
-RUN    echo 'CMAKE_FLAGS=" -G '"'"'Unix Makefiles'"'"'"' >> /duneci/cmake-flags/production \
-    && echo 'CMAKE_FLAGS+=" -DDUNE_USE_ONLY_STATIC_LIBS=ON"' >> /duneci/cmake-flags/production \
-    && echo 'CMAKE_FLAGS+=" -DDUNE_COPASI_SD_EXECUTABLE=ON"' >> /duneci/cmake-flags/production \
-    && echo 'CMAKE_FLAGS+=" -DDUNE_COPASI_MD_EXECUTABLE=ON"' >> /duneci/cmake-flags/production \
-    && echo 'CMAKE_FLAGS+=" -DCMAKE_CXX_FLAGS='"'"'-fvisibility=hidden -fpic -static-libstdc++'"'"' "' /duneci/cmake-flags/production
-
-RUN duneci-install-module -b ${BRANCH} https://gitlab.dune-project.org/copasi/dune-copasi.git
-RUN dunecontrol --opts=/duneci/dune.opts --only=dune-copasi bexec cmake --build . -- install
-
-FROM ${PRODUCTION_IMAGE} AS production-env
-LABEL maintainer="santiago.ospina@iwr.uni-heidelberg.de"
-
-COPY --from=0 /duneci/install /usr/local
-RUN adduser --disabled-password --home /dunecopasi --uid 50000 dunecopasi
-
-WORKDIR /dunecopasi
-VOLUME ["/dunecopasi"]
-USER dunecopasi