Consolidate MinimalLib Dockerfiles to avoid code duplication (#8412)

* Consolidate MinimalLib Dockerfiles to avoid code duplication Remove Dockerfile_legacy_browsers since IE11 is not used anymore * add project name to docker-compose YAML files * add projectName to azure pipelines DockerCompose section * updated scripts/build_rdkit.js and Dockerfiles to enable end-to-end builds * changes in response to review * - remove unused docker-compose file - update azure-pipelines.yml * fix service dependency * CI build should copy_from_local * docs update, make it work for local builds, minimize git clone * - changes in response to review - added an option to build from the local source tree to scripts/build_rdkitjs.sh --------- Co-authored-by: ptosco <paolo.tosco@novartis.com> Co-authored-by: greg landrum <greg.landrum@gmail.com>
2026-06-03 21:44:30 +08:00 · 2025-04-28 08:57:30 +02:00
parent 1215922df1
commit e87dc6ee0f
12 changed files with 296 additions and 278 deletions
--- a/Code/MinimalLib/README.md
+++ b/Code/MinimalLib/README.md
@@ -105,13 +105,27 @@ If you are using the MinimalLib for the first time, see the getting started exam

 ## Building the MinimalLib

-Make sure you are at the root of the [MinimalLib](https://github.com/rdkit/rdkit/tree/master/Code/MinimalLib), and run the following script.
+### Building from Github
+
+Make sure you are at the root of the [MinimalLib](https://github.com/rdkit/rdkit/tree/master/Code/MinimalLib), and run the following script:

 ```bash
-bash scripts/build_rdkitjs.sh <RDKit git release tag name>
-# Example: bash scripts/build_rdkitjs.sh Release_2021_03_1
+scripts/build_rdkitjs.sh <RDKit git release tag name>
+# Example: scripts/build_rdkitjs.sh Release_2025_03_2
 ```

-This command will take several minutes to complete, and will default to using the `master` branch if no version is provided. Also, checkout the `build_rdkitjs.sh` file and the minimallib `Dockerfile` to see how things are tied together.
+This command will take several minutes to complete, and will default to using the `master` branch if no version is provided. Also, checkout the `build_rdkitjs.sh` file to see how things are tied together.
+
+### Building from the local source tree
+
+Make sure you are at the root of the [MinimalLib](https://github.com/rdkit/rdkit/tree/master/Code/MinimalLib), and run the following script:
+
+```bash
+GET_SRC=copy_from_local scripts/build_rdkitjs.sh
+```
+
+This command will take several minutes to complete, and will use the local source tree
+
+### Using the RDKit package assets

 Once you have verified that the distribution files have been properly added in `Code/MinimalLib/dist`, refer to the [Using the RDKit package assets](#using-the-rdkit-package-assets) section for the next steps.
--- a/Code/MinimalLib/docker/Dockerfile_1_deps
+++ b/Code/MinimalLib/docker/Dockerfile_1_deps
@@ -0,0 +1,94 @@
+# Example usage of this Dockerfile:
+# (the --build-arg arguments are all optional)
+#
+# 1. cd to Code/MinimalLib/docker
+# cd Code/MinimalLib/docker
+#
+# 2. build the MinimalLib rdkit-minimallib-deps image:
+# docker build --target deps-stage -t rdkit-minimallib-deps \
+#   --build-arg http_proxy=$HTTP_PROXY \
+#   --build-arg https_proxy=$HTTP_PROXY \
+#   --network=host --build-arg "EXCEPTION_HANDLING=-fwasm-exceptions" \
+#   -f Dockerfile_1_deps .
+
+
+ARG EMSDK_VERSION="latest"
+ARG EXCEPTION_HANDLING="-fexceptions -sNO_DISABLE_EXCEPTION_CATCHING"
+ARG BOOST_MAJOR_VERSION="1"
+ARG BOOST_MINOR_VERSION="87"
+ARG BOOST_PATCH_VERSION="0"
+ARG BOOST_DOT_VERSION
+ARG BOOST_UNDERSCORE_VERSION
+ARG FREETYPE_VERSION="2.13.3"
+ARG http_proxy
+ARG https_proxy
+
+FROM debian:bookworm AS deps-stage
+ARG EMSDK_VERSION
+ARG EXCEPTION_HANDLING
+ARG RDKIT_GIT_URL
+ARG RDKIT_BRANCH
+ARG BOOST_MAJOR_VERSION
+ARG BOOST_MINOR_VERSION
+ARG BOOST_PATCH_VERSION
+ARG FREETYPE_VERSION
+ARG http_proxy
+ARG https_proxy
+
+LABEL maintainer="Greg Landrum <greg.landrum@t5informatics.com>"
+
+RUN [ -n "${http_proxy}" ] && echo "export http_proxy=${http_proxy}" >> ~/.bashrc || true
+RUN [ -n "${https_proxy}" ] && echo "export https_proxy=${https_proxy}" >> ~/.bashrc || true
+SHELL ["/bin/bash", "-c", "-l"]
+ENV DEBIAN_FRONTEND=noninteractive
+
+RUN apt-get update && apt-get upgrade -y && apt install -y \
+  curl \
+  wget \
+  cmake \
+  python3 \
+  g++ \
+  libeigen3-dev \
+  git \
+  xz-utils \
+  nodejs
+
+# If you are in an organization, put your organization certs inside
+# the certs directory otherwise HTTPS might not work
+COPY certs /usr/local/share/ca-certificates/
+RUN update-ca-certificates
+
+ENV LANG C
+
+WORKDIR /opt
+RUN git clone https://github.com/emscripten-core/emsdk.git
+
+WORKDIR /src
+ARG BOOST_DOT_VERSION="${BOOST_MAJOR_VERSION}.${BOOST_MINOR_VERSION}.${BOOST_PATCH_VERSION}"
+ARG BOOST_UNDERSCORE_VERSION="${BOOST_MAJOR_VERSION}_${BOOST_MINOR_VERSION}_${BOOST_PATCH_VERSION}"
+RUN wget -q https://archives.boost.io/release/${BOOST_DOT_VERSION}/source/boost_${BOOST_UNDERSCORE_VERSION}.tar.gz && \
+  tar xzf boost_${BOOST_UNDERSCORE_VERSION}.tar.gz
+WORKDIR /src/boost_${BOOST_UNDERSCORE_VERSION}
+RUN ./bootstrap.sh --prefix=/opt/boost --with-libraries=system && \
+  ./b2 install
+
+WORKDIR /opt/emsdk
+RUN ./emsdk install ${EMSDK_VERSION} && \
+  ./emsdk activate ${EMSDK_VERSION}
+
+#RUN source ./emsdk_env.sh
+
+RUN echo "source /opt/emsdk/emsdk_env.sh > /dev/null 2>&1" >> ~/.bashrc
+
+WORKDIR /src
+RUN wget -q https://download.savannah.gnu.org/releases/freetype/freetype-${FREETYPE_VERSION}.tar.gz && \
+  tar xzf freetype-${FREETYPE_VERSION}.tar.gz
+WORKDIR /src/freetype-${FREETYPE_VERSION}
+RUN mkdir build
+WORKDIR /src/freetype-${FREETYPE_VERSION}/build
+RUN emcmake cmake -DCMAKE_BUILD_TYPE=Release -DWITH_ZLIB=OFF -DWITH_BZip2=OFF -DWITH_PNG=OFF \
+  -DCMAKE_C_FLAGS="${EXCEPTION_HANDLING}" -DCMAKE_EXE_LINKER_FLAGS="${EXCEPTION_HANDLING}" \
+  -DCMAKE_INSTALL_PREFIX=/opt/freetype ..
+RUN make -j2 && make -j2 install
+RUN echo "export BOOST_DOT_VERSION=${BOOST_DOT_VERSION}" >> ~/.bashrc
+RUN echo "export BOOST_UNDERSCORE_VERSION=${BOOST_UNDERSCORE_VERSION}" >> ~/.bashrc
--- a/Code/MinimalLib/docker/Dockerfile_2_rdkit_clone_from_github
+++ b/Code/MinimalLib/docker/Dockerfile_2_rdkit_clone_from_github
@@ -0,0 +1,28 @@
+# Example usage of this Dockerfile:
+# (the --build-arg arguments are all optional)
+#
+# 1. cd to Code/MinimalLib/docker
+# cd Code/MinimalLib/docker
+#
+# 2. build the MinimalLib rdkit-minimallib-rdkit-src image:
+# docker build --target clone-stage -t rdkit-minimallib-rdkit-src \
+#   --build-arg http_proxy=$HTTP_PROXY \
+#   --build-arg https_proxy=$HTTP_PROXY \
+#   --build-arg "RDKIT_GIT_URL=https://github.com/myfork/rdkit.git" \
+#   --build-arg "RDKIT_BRANCH=mybranch" \
+#   --network=host -f Dockerfile_rdkit_clone_from_github .
+
+
+ARG RDKIT_GIT_URL="https://github.com/rdkit/rdkit.git"
+ARG RDKIT_BRANCH="master"
+
+FROM rdkit-minimallib-deps AS clone-stage
+ARG RDKIT_GIT_URL
+ARG RDKIT_BRANCH
+
+LABEL maintainer="Greg Landrum <greg.landrum@t5informatics.com>"
+
+WORKDIR /src
+ENV RDBASE=/src/rdkit
+RUN git clone -b ${RDKIT_BRANCH} --depth 1 --single-branch ${RDKIT_GIT_URL} 
+WORKDIR $RDBASE
--- a/Code/MinimalLib/docker/Dockerfile_2_rdkit_copy_from_local
+++ b/Code/MinimalLib/docker/Dockerfile_2_rdkit_copy_from_local
@@ -0,0 +1,21 @@
+# Example usage of this Dockerfile:
+# (the --build-arg arguments are all optional)
+#
+# 1. cd to Code/MinimalLib/docker
+# cd Code/MinimalLib/docker
+#
+# 2. build the MinimalLib rdkit-minimallib-rdkit-src image:
+# docker build --target local-src-stage -t rdkit-minimallib-rdkit-src \
+#   --build-arg http_proxy=$HTTP_PROXY \
+#   --build-arg https_proxy=$HTTP_PROXY \
+#   --network=host -f Dockerfile_2_rdkit_copy_from_local ../../..
+
+
+FROM rdkit-minimallib-deps AS local-src-stage
+
+LABEL maintainer="Greg Landrum <greg.landrum@t5informatics.com>"
+
+WORKDIR /
+COPY Code /src/rdkit/Code
+COPY External /src/rdkit/External
+COPY CMakeLists.txt license.txt *.in *.md *.cmake /src/rdkit/
--- a/Code/MinimalLib/docker/Dockerfile_3_rdkit_build
+++ b/Code/MinimalLib/docker/Dockerfile_3_rdkit_build
@@ -1,19 +1,49 @@
+# Note: there are docker-compose .yml files that handle the 3
+# build steps automatically for you; see the comments in the
+# respective docker-compose files for details.
+# However, if you prefer to run individual docker commands rather
+# than using docker-compose, you can do so by following the
+# instructions below.
+#
 # Example usage of this Dockerfile:
-# (the build-arg arguments are all optional)
+# (the --build-arg arguments are all optional)
 #
 # 1. cd to Code/MinimalLib/docker
 # cd Code/MinimalLib/docker
 #
-# 2. build the JS and WASM libraries
+# 2. build the MinimalLib rdkit-minimallib-deps image:
+# docker build --target deps-stage -t rdkit-minimallib-deps \
+#   --build-arg http_proxy=$HTTP_PROXY \
+#   --build-arg https_proxy=$HTTP_PROXY \
+#   --network=host --build-arg "EXCEPTION_HANDLING=-fwasm-exceptions" \
+#   -f Dockerfile_1_deps .
+#
+# 3. build the MinimalLib rdkit-minimallib-rdkit-src image:
+#   3a. from a git clone:
+#   docker build --target clone-stage -t rdkit-minimallib-rdkit-src \
+#     --build-arg http_proxy=$HTTP_PROXY \
+#     --build-arg https_proxy=$HTTP_PROXY \
+#     --build-arg "RDKIT_GIT_URL=https://github.com/myfork/rdkit.git" \
+#     --build-arg "RDKIT_BRANCH=mybranch" \
+#     --network=host -f Dockerfile_rdkit_clone_from_github .
+#   or
+#   3b. from an existing local source tree:
+#   docker build --target local-src-stage -t rdkit-minimallib-rdkit-src \
+#     --build-arg http_proxy=$HTTP_PROXY \
+#     --build-arg https_proxy=$HTTP_PROXY \
+#     --network=host -f Dockerfile_2_rdkit_copy_from_local ../../..
+#
+# 4. build the MinimalLib rdkit-minimallib image:
 #    (the build-arg arguments are all optional; in the following
 #     example we select the more performant, though still experimental,
 #     native WASM exception handling):
 # docker build -t rdkit-minimallib --network=host \
-#  --build-arg "RDKIT_GIT_URL=https://github.com/myfork/rdkit.git" \
-#  --build-arg "RDKIT_BRANCH=mybranch" \
-#  --build-arg "EXCEPTION_HANDLING=-fwasm-exceptions".
+#   --build-arg http_proxy=$HTTP_PROXY \
+#   --build-arg https_proxy=$HTTP_PROXY \
+#   --build-arg "EXCEPTION_HANDLING=-fwasm-exceptions" \
+#   -f Dockerfile_3_rdkit_build .
 #
-# 3. create a temporary container and copy built libraries
+# 5. create a temporary container and copy built libraries
 #    from the container to your local filesystem, then destroy
 #    the temporary container
 # docker create --name=rdkit-minimallib-container rdkit-minimallib:latest --entrypoint /
@@ -22,78 +52,15 @@
 # docker rm rdkit-minimallib-container


-ARG RDKIT_GIT_URL="https://github.com/rdkit/rdkit.git"
-ARG RDKIT_BRANCH="master"
-ARG EMSDK_VERSION="latest"
 ARG EXCEPTION_HANDLING="-fexceptions -sNO_DISABLE_EXCEPTION_CATCHING"
-ARG BOOST_MAJOR_VERSION="1"
-ARG BOOST_MINOR_VERSION="87"
-ARG BOOST_PATCH_VERSION="0"
-ARG FREETYPE_VERSION="2.13.3"

-FROM debian:bookworm as build-stage
-ARG RDKIT_GIT_URL
-ARG RDKIT_BRANCH
-ARG EMSDK_VERSION
+FROM rdkit-minimallib-rdkit-src AS build-stage
 ARG EXCEPTION_HANDLING
-ARG BOOST_MAJOR_VERSION
-ARG BOOST_MINOR_VERSION
-ARG BOOST_PATCH_VERSION
-ARG FREETYPE_VERSION

 LABEL maintainer="Greg Landrum <greg.landrum@t5informatics.com>"

-RUN apt-get update && apt-get upgrade -y && apt install -y \
-  curl \
-  wget \
-  cmake \
-  python3 \
-  g++ \
-  libeigen3-dev \
-  git \
-  xz-utils \
-  nodejs
-
-ENV LANG C
-
-WORKDIR /src
-ARG BOOST_DOT_VERSION="${BOOST_MAJOR_VERSION}.${BOOST_MINOR_VERSION}.${BOOST_PATCH_VERSION}"
-ARG BOOST_UNDERSCORE_VERSION="${BOOST_MAJOR_VERSION}_${BOOST_MINOR_VERSION}_${BOOST_PATCH_VERSION}"
-RUN wget -q https://archives.boost.io/release/${BOOST_DOT_VERSION}/source/boost_${BOOST_UNDERSCORE_VERSION}.tar.gz && \
-  tar xzf boost_${BOOST_UNDERSCORE_VERSION}.tar.gz
-WORKDIR /src/boost_${BOOST_UNDERSCORE_VERSION}
-RUN ./bootstrap.sh --prefix=/opt/boost --with-libraries=system && \
-  ./b2 install
-
-WORKDIR /opt
-RUN git clone https://github.com/emscripten-core/emsdk.git
-
-WORKDIR /opt/emsdk
-RUN ./emsdk install ${EMSDK_VERSION} && \
-  ./emsdk activate ${EMSDK_VERSION}
-
-#RUN source ./emsdk_env.sh
-
-RUN echo "source /opt/emsdk/emsdk_env.sh > /dev/null 2>&1" >> ~/.bashrc
-SHELL ["/bin/bash", "-c", "-l"]
-
-WORKDIR /src
-RUN wget -q https://download.savannah.gnu.org/releases/freetype/freetype-${FREETYPE_VERSION}.tar.gz && \
-  tar xzf freetype-${FREETYPE_VERSION}.tar.gz
-WORKDIR /src/freetype-${FREETYPE_VERSION}
-RUN mkdir build
-WORKDIR /src/freetype-${FREETYPE_VERSION}/build
-RUN emcmake cmake -DCMAKE_BUILD_TYPE=Release -DWITH_ZLIB=OFF -DWITH_BZip2=OFF -DWITH_PNG=OFF \
-  -DCMAKE_C_FLAGS="${EXCEPTION_HANDLING}" -DCMAKE_EXE_LINKER_FLAGS="${EXCEPTION_HANDLING}" \
-  -DCMAKE_INSTALL_PREFIX=/opt/freetype ..
-RUN make -j2 && make -j2 install
-
 WORKDIR /src
 ENV RDBASE=/src/rdkit
-RUN git clone ${RDKIT_GIT_URL}
-WORKDIR $RDBASE
-RUN git fetch --all --tags && \
-  git checkout ${RDKIT_BRANCH}
 RUN mkdir build
 WORKDIR $RDBASE/build
 RUN emcmake cmake -DRDK_BUILD_FREETYPE_SUPPORT=ON -DRDK_BUILD_MINIMAL_LIB=ON \
--- a/Code/MinimalLib/docker/Dockerfile_4_rdkit_export
+++ b/Code/MinimalLib/docker/Dockerfile_4_rdkit_export
@@ -0,0 +1,3 @@
+FROM rdkit-minimallib AS export-stage
+
+LABEL maintainer="Greg Landrum <greg.landrum@t5informatics.com>"
--- a/Code/MinimalLib/docker/Dockerfile_CI
+++ b/Code/MinimalLib/docker/Dockerfile_CI
@@ -1,133 +0,0 @@
-# Example usage of this Dockerfile:
-# (the build-arg arguments are all optional)
-#
-# 1. cd to Code/MinimalLib/docker
-# cd Code/MinimalLib/docker
-#
-# 2. build the JS and WASM libraries
-#    (the build-arg arguments are all optional; in the following
-#     example we select the more performant, though still experimental,
-#     native WASM exception handling):
-# docker build -t rdkit-minimallib --network=host \
-#  --build-arg "RDKIT_GIT_URL=https://github.com/myfork/rdkit.git" \
-#  --build-arg "RDKIT_BRANCH=mybranch" \
-#  --build-arg "EXCEPTION_HANDLING=-fwasm-exceptions".
-#
-# 3. create a temporary container and copy built libraries
-#    from the container to your local filesystem, then destroy
-#    the temporary container
-# docker create --name=rdkit-minimallib-container rdkit-minimallib:latest --entrypoint /
-# docker cp rdkit-minimallib-container:/RDKit_minimal.js ../demo
-# docker cp rdkit-minimallib-container:/RDKit_minimal.wasm ../demo
-# docker rm rdkit-minimallib-container
-
-
-ARG EMSDK_VERSION="latest"
-ARG EXCEPTION_HANDLING="-fexceptions -sNO_DISABLE_EXCEPTION_CATCHING"
-ARG BOOST_MAJOR_VERSION="1"
-ARG BOOST_MINOR_VERSION="87"
-ARG BOOST_PATCH_VERSION="0"
-ARG FREETYPE_VERSION="2.13.3"
-
-FROM debian:bookworm AS build-stage
-ARG EMSDK_VERSION
-ARG EXCEPTION_HANDLING
-ARG BOOST_MAJOR_VERSION
-ARG BOOST_MINOR_VERSION
-ARG BOOST_PATCH_VERSION
-ARG FREETYPE_VERSION
-
-LABEL maintainer="Greg Landrum <greg.landrum@t5informatics.com>"
-
-RUN apt-get update && apt-get upgrade -y && apt install -y \
-  curl \
-  wget \
-  cmake \
-  python3 \
-  g++ \
-  libeigen3-dev \
-  git \
-  xz-utils \
-  nodejs
-
-ENV LANG C
-
-WORKDIR /opt
-RUN git clone https://github.com/emscripten-core/emsdk.git
-
-WORKDIR /src
-ARG BOOST_DOT_VERSION="${BOOST_MAJOR_VERSION}.${BOOST_MINOR_VERSION}.${BOOST_PATCH_VERSION}"
-ARG BOOST_UNDERSCORE_VERSION="${BOOST_MAJOR_VERSION}_${BOOST_MINOR_VERSION}_${BOOST_PATCH_VERSION}"
-RUN wget -q https://archives.boost.io/release/${BOOST_DOT_VERSION}/source/boost_${BOOST_UNDERSCORE_VERSION}.tar.gz && \
-  tar xzf boost_${BOOST_UNDERSCORE_VERSION}.tar.gz
-WORKDIR /src/boost_${BOOST_UNDERSCORE_VERSION}
-RUN ./bootstrap.sh --prefix=/opt/boost --with-libraries=system && \
-  ./b2 install
-
-WORKDIR /opt/emsdk
-RUN ./emsdk install ${EMSDK_VERSION} && \
-  ./emsdk activate ${EMSDK_VERSION}
-
-#RUN source ./emsdk_env.sh
-
-RUN echo "source /opt/emsdk/emsdk_env.sh > /dev/null 2>&1" >> ~/.bashrc
-SHELL ["/bin/bash", "-c", "-l"]
-
-WORKDIR /src
-RUN wget -q https://download.savannah.gnu.org/releases/freetype/freetype-${FREETYPE_VERSION}.tar.gz && \
-  tar xzf freetype-${FREETYPE_VERSION}.tar.gz
-WORKDIR /src/freetype-${FREETYPE_VERSION}
-RUN mkdir build
-WORKDIR /src/freetype-${FREETYPE_VERSION}/build
-RUN emcmake cmake -DCMAKE_BUILD_TYPE=Release -DWITH_ZLIB=OFF -DWITH_BZip2=OFF -DWITH_PNG=OFF \
-  -DCMAKE_C_FLAGS="${EXCEPTION_HANDLING}" -DCMAKE_EXE_LINKER_FLAGS="${EXCEPTION_HANDLING}" \
-  -DCMAKE_INSTALL_PREFIX=/opt/freetype ..
-RUN make -j2 && make -j2 install
-
-WORKDIR /
-COPY Code /src/rdkit/Code
-COPY External /src/rdkit/External
-COPY CMakeLists.txt license.txt *.in *.md *.cmake /src/rdkit
-ENV RDBASE=/src/rdkit
-
-WORKDIR $RDBASE
-RUN mkdir build
-WORKDIR $RDBASE/build
-RUN emcmake cmake -DRDK_BUILD_FREETYPE_SUPPORT=ON -DRDK_BUILD_MINIMAL_LIB=ON \
-  -DRDK_BUILD_PYTHON_WRAPPERS=OFF -DRDK_BUILD_CPP_TESTS=OFF -DRDK_BUILD_INCHI_SUPPORT=ON \
-  -DRDK_USE_BOOST_SERIALIZATION=OFF -DRDK_OPTIMIZE_POPCNT=OFF -DRDK_BUILD_THREADSAFE_SSS=OFF \
-  -DRDK_BUILD_DESCRIPTORS3D=OFF -DRDK_TEST_MULTITHREADED=OFF \
-  -DRDK_BUILD_MAEPARSER_SUPPORT=OFF -DRDK_BUILD_COORDGEN_SUPPORT=ON \
-  -DBoost_DIR=/opt/boost/lib/cmake/Boost-${BOOST_DOT_VERSION} \
-  -Dboost_headers_DIR=/opt/boost/lib/cmake/boost_headers-${BOOST_DOT_VERSION} \
-  -DRDK_BUILD_SLN_SUPPORT=OFF -DRDK_USE_BOOST_IOSTREAMS=OFF \
-  -DFREETYPE_INCLUDE_DIRS=/opt/freetype/include/freetype2 \
-  -DFREETYPE_LIBRARY=/opt/freetype/lib/libfreetype.a \
-  -DCMAKE_CXX_FLAGS="${EXCEPTION_HANDLING} -O3 -DNDEBUG" \
-  -DCMAKE_C_FLAGS="${EXCEPTION_HANDLING} -O3 -DNDEBUG -DCOMPILE_ANSI_ONLY" \
-  -DCMAKE_EXE_LINKER_FLAGS="${EXCEPTION_HANDLING} -s STACK_OVERFLOW_CHECK=1 -s USE_PTHREADS=0 -s ALLOW_MEMORY_GROWTH=1 -s MAXIMUM_MEMORY=4GB -s MODULARIZE=1 -s EXPORT_NAME=\"'initRDKitModule'\"" ..
-
-# "patch" to make the InChI code work with emscripten:
-RUN cp /src/rdkit/External/INCHI-API/src/INCHI_BASE/src/util.c /src/rdkit/External/INCHI-API/src/INCHI_BASE/src/util.c.bak && \
-  sed 's/&& defined(__APPLE__)//' /src/rdkit/External/INCHI-API/src/INCHI_BASE/src/util.c.bak > /src/rdkit/External/INCHI-API/src/INCHI_BASE/src/util.c
-
-# comment out a line which causes a compilation error on some platforms
-# (based on the change which has already been applied to the RapidJSON master branch, see
-# https://github.com/Tencent/rapidjson/blob/ab1842a2dae061284c0a62dca1cc6d5e7e37e346/include/rapidjson/document.h#L414)
-RUN sed -i 's|^\( *\)\(GenericStringRef\& operator=(const GenericStringRef\& rhs) { s = rhs.s; length = rhs.length; } *\)$|\1//\2|' \
-  /src/rdkit/External/rapidjson-1.1.0/include/rapidjson/document.h
-
-# build and "install"
-RUN make -j2 RDKit_minimal && \
-  cp Code/MinimalLib/RDKit_minimal.* ../Code/MinimalLib/demo/
-
-# run the tests
-WORKDIR /src/rdkit/Code/MinimalLib/tests
-RUN /opt/emsdk/node/*/bin/node tests.js
-
-# # Copy js and wasm rdkit files to use in browser
-# # This feature requires the BuildKit backend
-# # https://docs.docker.com/engine/reference/commandline/build/#custom-build-outputs
-# FROM scratch AS export-stage
-# COPY --from=build-stage /src/rdkit/Code/MinimalLib/demo /
-# COPY --from=build-stage /src/rdkit/Code/MinimalLib/docs /
--- a/Code/MinimalLib/docker/Dockerfile_legacy_browsers
+++ b/Code/MinimalLib/docker/Dockerfile_legacy_browsers
@@ -1,61 +0,0 @@
-# Example usage of this Dockerfile:
-# (the build-arg arguments are all optional)
-#
-# 1. cd to Code/MinimalLib/docker
-# cd Code/MinimalLib/docker
-#
-# 2. generate an image of the build-stage from the main Dockerfile.
-#    The build-arg arguments are all optional and have appropriate
-#    defaults. Regarding EMSDK_VERSION, 3.1.50 is the last
-#    emsdk version that supports the MIN_IE_VERSION=11 flag.
-# docker build --target build-stage -t rdkit-minimallib-build-stage --network=host \
-#  --build-arg "EMSDK_VERSION=3.1.50" \
-#  --build-arg "RDKIT_GIT_URL=https://github.com/myfork/rdkit.git" \
-#  --build-arg "RDKIT_BRANCH=mybranch" .
-#
-# 3. build the JS-only version of MinimalLib for legacy browsers
-#    (requires the rdkit-minimallib-build-stage image built in step 2).
-#    The build-arg arguments are all optional and have appropriate
-#    defaults.
-# docker build -t rdkit-minimallib-legacy --network=host \
-#   --build-arg "EXTRA_CMAKE_EXE_LINKER_FLAGS=-s MIN_IE_VERSION=11" \
-#   -f Dockerfile_legacy_browsers .
-#
-# 4. create a temporary container and copy built libraries
-#    from the container to your local filesystem, then destroy
-#    the temporary container
-# docker create --name=rdkit-minimallib-legacy-container rdkit-minimallib-legacy:latest --entrypoint /
-# docker cp rdkit-minimallib-legacy-container:/RDKit_minimal_legacy.js ../demo
-# docker rm rdkit-minimallib-legacy-container
-#
-# To test in a legacy browser, do the following:
-# sed 's|RDKit_minimal\.js|RDKit_minimal_legacy.js|' < ../demo/demo.html > ../demo/demo_legacy.html
-# then point your browser to demo_legacy.html
-
-
-FROM rdkit-minimallib-build-stage as build-stage-legacy
-ARG EXTRA_CMAKE_EXE_LINKER_FLAGS=""
-
-WORKDIR $RDBASE/build
-RUN emcmake cmake -DRDK_MINIMAL_LIB_SUPPORT_LEGACY_BROWSERS=ON \
-  -DCMAKE_EXE_LINKER_FLAGS="-s SINGLE_FILE=1 -s LEGACY_VM_SUPPORT=1 ${EXTRA_CMAKE_EXE_LINKER_FLAGS} -s WASM=0 --memory-init-file 0 -s MODULARIZE=1 -s EXPORT_NAME=\"'initRDKitModule'\"" ..
-
-# build and "install"
-RUN make -j2 RDKit_minimal && echo -e '\
-var toObj=function(c){if(null===c||"undefined"===typeof c)throw new TypeError("this is null or undefined");return Object(c)};Uint8Array.prototype.fill||Object.defineProperty(Uint8Array.prototype,"fill",{value:function(c,b,d){var e=toObj(this),a=e.length>>>0;b>>=0;b=0>b?Math.max(a+b,0):Math.min(b,a);d="undefined"===typeof d?a:d>>0;for(a=0>d?Math.max(a+d,0):Math.min(d,a);b<a;)e[b]=c,++b;return e}});\n\
-Uint8Array.prototype.copyWithin||Object.defineProperty(Uint8Array.prototype,"copyWithin",{value:function(c,b,d){var e=toObj(this),a=e.length>>>0;c>>=0;c=0>c?Math.max(a+c,0):Math.min(c,a);b>>=0;b=0>b?Math.max(a+b,0):Math.min(b,a);d="undefined"===typeof d?a:d>>0;a=Math.min((0>d?Math.max(a+d,0):Math.min(d,a))-b,a-c);d=1;b<c&&c<b+a&&(d=-1,b+=a-1,c+=a-1);for(;0<a;)b in e?e[c]=e[b]:delete e[c],b+=d,c+=d,--a;return e}});\n\
-String.prototype.includes||Object.defineProperty(String.prototype,"includes",{value:function(c,b){var d=toObj(this);if(c instanceof RegExp)throw new TypeError("first argument must not be a RegExp");return-1!==d.indexOf(c,b||0)}});\n\
-Array.prototype.includes||Object.defineProperty(Array.prototype,"includes",{value:function(c,b){var d=toObj(this),e=d.length>>>0;if(0===e)return!1;var a=b||0;for(a=Math.max(0<=a?a:e-Math.abs(a),0);a<e;){var f=d[a],g=c;if(f===g||"number"===typeof f&&"number"===typeof g&&isNaN(f)&&isNaN(g))return!0;++a}return!1}});String.prototype.startsWith||Object.defineProperty(String.prototype,"startsWith",{value:function(c,b){var d=toObj(this),e=0<b?b|0:0;return d.substring(e,e+c.length)===c}});\n\
-' > ../Code/MinimalLib/demo/RDKit_minimal_legacy.js && \
-    sed 's|\(var *initRDKitModule *= *(\)\(() *=>\)\( *{\)|\1function()\3|' \
-      < Code/MinimalLib/RDKit_minimal.js >> ../Code/MinimalLib/demo/RDKit_minimal_legacy.js
-
-# run the tests
-WORKDIR /src/rdkit/Code/MinimalLib/tests
-RUN RDKIT_MINIMAL_JS="../demo/RDKit_minimal_legacy.js" /opt/emsdk/node/*/bin/node tests.js
-
-# Copy pure js RDKit MinimalLib file to use in legacy browsers
-# This feature requires the BuildKit backend
-# https://docs.docker.com/engine/reference/commandline/build/#custom-build-outputs
-FROM scratch as export-stage-legacy
-COPY --from=build-stage-legacy /src/rdkit/Code/MinimalLib/demo/RDKit_minimal_legacy.js /
--- a/Code/MinimalLib/docker/certs/.gitignore
+++ b/Code/MinimalLib/docker/certs/.gitignore
--- a/Code/MinimalLib/docker/docker_compose_build_minimallib.yml
+++ b/Code/MinimalLib/docker/docker_compose_build_minimallib.yml
@@ -0,0 +1,66 @@
+# This docker-compose file is used to build the RDKit MinimalLib
+# from either GitHub or a local source tree.
+# The build consists of three stages (services):
+# 1. `deps`: This service builds the dependencies required for RDKit.
+# 2. `rdkit_get_src`: This service gets the RDKit source code from
+#    either from GitHub (GET_SRC=clone_from_github, the default)
+#    or from a local source tree (GET_SRC=copy_from_local)
+#    into the Docker image.
+# 3. `rdkit_build`: This service builds the RDKit MinimalLib using
+#    the dependencies built in the first service and the source code
+#    copied in the second service.
+#
+# Example usage:
+# (the --build-arg are all optional)
+#
+# GET_SRC=copy_from_local \
+# docker-compose -f docker_compose_build_minimallib.yml build \
+#   --build-arg http_proxy=$HTTP_PROXY \
+#   --build-arg http_proxy=$HTTP_PROXY \
+#   --build-arg https_proxy=$HTTP_PROXY \
+#   --build-arg "EXCEPTION_HANDLING=-fwasm-exceptions" \
+#   2>&1 | tee docker-compose.log
+#
+# Once the build is finished, you can run the following command to
+# export the buildartifacts to your local filesystem:
+#
+# DOCKER_BUILDKIT=1 docker build -f Dockerfile_4_rdkit_export -o ../demo .
+
+services:
+  rdkit_deps:
+    environment:
+      - NETWORK_MODE=${NETWORK_MODE:-bridge}
+      - NETWORK=${NETWORK:-rdkit_network}
+    network_mode: ${NETWORK_MODE}
+    build:
+      network: ${NETWORK}
+      context: .
+      dockerfile: Dockerfile_1_deps
+    image: rdkit-minimallib-deps:latest
+
+  rdkit_get_src:
+    environment:
+      - NETWORK_MODE=${NETWORK_MODE:-bridge}
+      - NETWORK=${NETWORK:-rdkit_network}
+      - GET_SRC=${GET_SRC:-clone_from_github}
+    network_mode: ${NETWORK_MODE}
+    build:
+      network: ${NETWORK}
+      context: ../../..
+      dockerfile: ./Code/MinimalLib/docker/Dockerfile_2_rdkit_${GET_SRC}
+    image: rdkit-minimallib-rdkit-src:latest
+    depends_on:
+      - rdkit_deps
+
+  rdkit_build:
+    environment:
+      - NETWORK_MODE=${NETWORK_MODE:-bridge}
+      - NETWORK=${NETWORK:-rdkit_network}
+    network_mode: ${NETWORK_MODE}
+    build:
+      network: ${NETWORK}
+      context: .
+      dockerfile: Dockerfile_3_rdkit_build
+    image: rdkit-minimallib:latest
+    depends_on:
+      - rdkit_get_src
--- a/Code/MinimalLib/scripts/build_rdkitjs.sh
+++ b/Code/MinimalLib/scripts/build_rdkitjs.sh
@@ -1,15 +1,33 @@
+#!/usr/bin/env bash
+
 set -e

 # Clean and create distribution folder
-MINIMALLIB_OUTPUT_PATH="Code/MinimalLib/dist"
+cwd=$(realpath $0)
+cwd=$(dirname $cwd)
+cwd=$(dirname $cwd)
+cd $cwd
+MINIMALLIB_OUTPUT_PATH=$(realpath dist)
 rm -rf $MINIMALLIB_OUTPUT_PATH
 mkdir -p $MINIMALLIB_OUTPUT_PATH

 # Build distribution files
-RDKIT_BRANCH=${1:-master}
-RDKIT_GIT_URL=${2:-"https://github.com/rdkit/rdkit.git"}
-echo "Building distribution files for release $RDKIT_BRANCH from repo $RDKIT_GIT_URL"
-DOCKER_BUILDKIT=1 docker build --no-cache -f docker/Dockerfile --build-arg RDKIT_BRANCH=$RDKIT_BRANCH --build-arg RDKIT_GIT_URL=$RDKIT_GIT_URL -o $MINIMALLIB_OUTPUT_PATH .
+if [ "$GET_SRC" = copy_from_local ]; then
+    echo "Building distribution files from local source tree"
+    docker-compose -f docker/docker_compose_build_minimallib.yml build \
+        --no-cache \
+        --build-arg "EXCEPTION_HANDLING=-fwasm-exceptions"
+else
+    RDKIT_BRANCH=${1:-master}
+    RDKIT_GIT_URL=${2:-"https://github.com/rdkit/rdkit.git"}
+    echo "Building distribution files for release $RDKIT_BRANCH from repo $RDKIT_GIT_URL"
+    GET_SRC=clone_from_github docker-compose -f docker/docker_compose_build_minimallib.yml build \
+        --no-cache \
+        --build-arg "EXCEPTION_HANDLING=-fwasm-exceptions" \
+        --build-arg "RDKIT_GIT_URL=$RDKIT_GIT_URL" \
+        --build-arg "RDKIT_GIT_BRANCH=$RDKIT_BRANCH"
+fi
+DOCKER_BUILDKIT=1 docker build -f docker/Dockerfile_4_rdkit_export  -o $MINIMALLIB_OUTPUT_PATH .

 # Make files executable
 chmod a+rwx $MINIMALLIB_OUTPUT_PATH/RDKit_minimal.js