Merge pull request #483 from rdkit/fix/debug-build

Fix/debug build

Dockerfile

@@ -1,4 +1,39 @@
-FROM debian:buster as build-stage
+# 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)
+# docker build -t rdkit-minimallib --network=host \
+#  --build-arg "RDKIT_GIT_URL=https://github.com/myfork/rdkit.git" \
+#  --build-arg "RDKIT_BRANCH=mybranch" .
+#
+# 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 RDKIT_GIT_URL="https://github.com/rdkit/rdkit.git"
+ARG RDKIT_BRANCH="master"
+ARG EMSDK_VERSION="latest"
+ARG BOOST_MAJOR_VERSION="1"
+ARG BOOST_MINOR_VERSION="84"
+ARG BOOST_PATCH_VERSION="0"
+
+FROM debian:bookworm as build-stage
+ARG RDKIT_GIT_URL
+ARG RDKIT_BRANCH
+ARG EMSDK_VERSION
+ARG BOOST_MAJOR_VERSION
+ARG BOOST_MINOR_VERSION
+ARG BOOST_PATCH_VERSION
+
 LABEL maintainer="Greg Landrum <[email protected]>"
 
 RUN apt-get update && apt-get upgrade -y && apt install -y \
@@ -9,15 +44,17 @@ RUN apt-get update && apt-get upgrade -y && apt install -y \
   g++ \
   libeigen3-dev \
   git \
-  nodejs \
-  libfreetype6-dev
+  xz-utils \
+  nodejs
 
 ENV LANG C
 
 WORKDIR /opt
-RUN wget -q https://boostorg.jfrog.io/artifactory/main/release/1.67.0/source/boost_1_67_0.tar.gz && \
-  tar xzf boost_1_67_0.tar.gz 
-WORKDIR /opt/boost_1_67_0
+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://boostorg.jfrog.io/artifactory/main/release/${BOOST_DOT_VERSION}/source/boost_${BOOST_UNDERSCORE_VERSION}.tar.gz && \
+  tar xzf boost_${BOOST_UNDERSCORE_VERSION}.tar.gz
+WORKDIR /opt/boost_${BOOST_UNDERSCORE_VERSION}
 RUN ./bootstrap.sh --prefix=/opt/boost --with-libraries=system && \
   ./b2 install
 
@@ -26,21 +63,21 @@ WORKDIR /opt
 RUN git clone https://github.com/emscripten-core/emsdk.git
 
 WORKDIR /opt/emsdk
-RUN ./emsdk update-tags && \
-  ./emsdk install latest && \
-  ./emsdk activate latest
+RUN ./emsdk install ${EMSDK_VERSION} && \
+  ./emsdk activate ${EMSDK_VERSION}
+
+#RUN source ./emsdk_env.sh
 
 RUN mkdir /src
 WORKDIR /src
 ENV RDBASE=/src/rdkit
-ARG RDKIT_BRANCH=${RDKIT_BRANCH:-master}
-RUN git clone https://github.com/rdkit/rdkit.git
+RUN git clone ${RDKIT_GIT_URL}
 WORKDIR $RDBASE
 RUN git fetch --all --tags && \
-  git checkout $RDKIT_BRANCH
+  git checkout ${RDKIT_BRANCH}
 
 RUN mkdir build
-WORKDIR build
+WORKDIR $RDBASE/build
 
 RUN echo "source /opt/emsdk/emsdk_env.sh > /dev/null 2>&1" >> ~/.bashrc
 SHELL ["/bin/bash", "-c", "-l"]
@@ -60,6 +97,12 @@ RUN emcmake cmake -DBoost_INCLUDE_DIR=/opt/boost/include -DRDK_BUILD_FREETYPE_SU
 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/

package.json

@@ -1,7 +1,7 @@
 {
   "name": "@rdkit/rdkit",
-  "version": "2023.9.2-1.0.0",
-  "private": true,
+  "version": "2024.3.5-1.0.0",
+  "private": false,
   "description": "JavaScript distribution of cheminformatics functionality from the RDKit - a C++ library for cheminformatics.",
   "main": "dist/RDKit_minimal.js",
   "types": "dist/index.d.ts",

scripts/build_rdkitjs.sh

@@ -25,10 +25,27 @@ mkdir -p $MINIMALLIB_OUTPUT_PATH
 # legacy minimallib output path
 LEGACY_MINIMALLIB_OUTPUT_PATH="Code/MinimalLib/dist"
 rm -rf $LEGACY_MINIMALLIB_OUTPUT_PATH
-mkdir -p $LEGACY_MINIMALLIB_OUTPUT_PATH 
+mkdir -p $LEGACY_MINIMALLIB_OUTPUT_PATH
 
 # Build distribution files
-DOCKER_BUILDKIT=1 docker build --no-cache -f Dockerfile --build-arg RDKIT_BRANCH=$RDKIT_BRANCH -o $MINIMALLIB_OUTPUT_PATH .
+DOCKER_BUILDKIT=1 docker build --no-cache --platform=linux/amd64 -f Dockerfile --build-arg RDKIT_BRANCH=$RDKIT_BRANCH -o $MINIMALLIB_OUTPUT_PATH .
+
+# Make dist files executable
+chmod a+rwx $MINIMALLIB_OUTPUT_PATH/RDKit_minimal.js
+chmod a+rwx $MINIMALLIB_OUTPUT_PATH/RDKit_minimal.wasm
+
+# Add a copy of the distribution files at the original rdkit location
+# for backwards compatibility
+cp $MINIMALLIB_OUTPUT_PATH/RDKit_minimal.js $LEGACY_MINIMALLIB_OUTPUT_PATH/RDKit_minimal.js
+cp $MINIMALLIB_OUTPUT_PATH/RDKit_minimal.wasm $LEGACY_MINIMALLIB_OUTPUT_PATH/RDKit_minimal.wasm
+
+# Move docs file in dist folder for demos to work properly
+cp docs/demo.html $MINIMALLIB_OUTPUT_PATH/demo.html
+cp docs/GettingStartedInJS.html $MINIMALLIB_OUTPUT_PATH/GettingStartedInJS.html
+
+# Log build completed
+echo "Build completed"
+echo "MinimalLib distribution files are at $MINIMALLIB_OUTPUT_PATH"
 
 # Make dist files executable
 chmod a+rwx $MINIMALLIB_OUTPUT_PATH/RDKit_minimal.js

scripts/ci.sh

@@ -0,0 +1,8 @@
+set -e
+
+# Set branch to release
+RDKIT_BRANCH="$RDKIT_BRANCH"
+MINIMALLIB_OUTPUT_PATH="dist"
+
+# Build distribution files
+DOCKER_BUILDKIT=1 docker build --no-cache --platform=linux/amd64 -f Dockerfile --build-arg RDKIT_BRANCH=$RDKIT_BRANCH -o $MINIMALLIB_OUTPUT_PATH .