buildah updates

Author: tdudgeon

buildah/Dockerfile-buildah

@@ -3,32 +3,39 @@
 # docker build -f Dockerfile-buildah .
 # docker tag b8bc8c47ce3f informaticsmatters/rdkit-buildah:latest
 
-FROM fedora:29
+FROM centos:8
 LABEL maintainer="Tim Dudgeon<[email protected]>"
 
 
-RUN dnf -y update && dnf -y upgrade && dnf -y install\
- gcc-c++\
- python3-devel\
- boost-devel\
- boost-python3-devel\
- eigen3-devel\
- cmake\
- tk-devel\
- readline-devel\
- zlib-devel\
- bzip2-devel\
- sqlite-devel\
- @development-tools\
- swig\
- git\
- zip\
- wget\
- java-1.8.0-openjdk-devel\
- cairo-devel\
- buildah &&\
- dnf clean all &&\
- rm -rf /var/cache/dnf
+RUN yum -y update &&\
+  sed -i 's/enabled=0/enabled=1/' /etc/yum.repos.d/CentOS-Linux-PowerTools.repo &&\
+  yum install -y\
+  --setopt=tsflags=nodocs\
+  --setopt=override_install_langs=en_US.utf8\
+  tk-devel\
+  readline-devel\
+  zlib-devel\
+  bzip2-devel\
+  sqlite-devel\
+  @development\
+  cmake3\
+  python3-devel\
+  python3-numpy\
+  boost-devel\
+  boost-python3-devel\
+  eigen3-devel\
+  java-11-openjdk-devel\
+  swig\
+  git\
+  wget\
+  zip\
+  unzip\
+  freetype-devel\
+  cairo-devel\
+  buildah &&\
+  yum clean all &&\
+  rm -rf /var/cache/yum
 
-ENV JAVA_HOME=/usr/lib/jvm/java-8-openjdk-amd64
+
+ENV JAVA_HOME=/usr/lib/jvm/java-11-openjdk
 

buildah/buildah-python3-image.sh

@@ -1,23 +1,25 @@
 #!/bin/bash
+#
 # Buildah build script for RDKit image with Python3.
 # Also inlcudes numpy and pandas.
 #
-# The RDKIT_BRANCH environment variable must be defined. This defines the RDKit branch to pull
+# The GIT_BRANCH environment variable must be defined. This defines the RDKit branch to pull
 # and is used to define the tag for the image that is built.
 #
 # The result is a buildah image that can be pushed to the local docker registry like this:
 # buildah push informaticsmatters/rdkit-python3-mini:latest docker-daemon:informaticsmatters/rdkit-python3-mini:$IMAGE_TAG
 
 set -e
 
+source ../params.sh
 
-if [ ! -v RDKIT_BRANCH ]; then
-  echo "RDKIT_BRANCH not defined"
+if [ ! -v GIT_BRANCH ]; then
+  echo "GIT_BRANCH not defined"
   exit 1
-elif [ "$RDKIT_BRANCH" = "master" ]; then
+elif [ "$GIT_BRANCH" = "master" ]; then
   export IMAGE_TAG="latest"
 else
-  export IMAGE_TAG=$RDKIT_BRANCH
+  export IMAGE_TAG=$GIT_BRANCH
 fi
 echo "Using image tag $IMAGE_TAG"
 
@@ -29,35 +31,37 @@ export scratchmnt=$(buildah mount $newcontainer)
 echo "Creating python3 container $newcontainer using $scratchmnt"
 
 # install the required packages
-dnf -y install\
+yum -y install\
+  --setopt override_install_langs=en_US.utf8\
+  --setopt install_weak_deps=false\
+  --setopt tsflags=nodocs\
+  --installroot $scratchmnt --releasever 8\
   bash\
   coreutils\
   cairo\
   python3\
   python3-devel\
   python3-numpy\
-  python3-pandas\
   boost\
   boost-python3\
   curl\
   zip\
   unzip\
-  procps-ng\
-  --installroot $scratchmnt --releasever 29\
-  --setopt override_install_langs=en_US.utf8\
-  --setopt install_weak_deps=false\
-  --setopt tsflags=nodocs
-dnf -y clean all --installroot $scratchmnt --releasever 29
+  procps-ng
+  
+yum -y clean all --installroot $scratchmnt --releasever 8
 rm -rf $scratchmnt/var/cache/dnf
 
 # create a symlink that allows to run python3 as python
-cd $scratchmnt/usr/bin && ln -s python3 python
+#cd $scratchmnt/usr/bin && ln -s python3 python
 
+# install RDKit
 cd /root/rdkit/build
-
-# install RDKit into the python container
 make DESTDIR=$scratchmnt install
 
+# create a symlink that allows to run python3 as python
+cd $scratchmnt/usr/bin && ln -s python3 python
+
 # set some config info
 buildah config\
   --label name=rdkit-python-mini\

buildah/buildah-python3-rdkit.sh

@@ -1,24 +1,25 @@
 #!/bin/bash
-# Build script for RDKit with Python3.
-# Also inlcudes numpy and pandas.
+# Buildah build script for RDKit with Python3.
+# Inlcudes InChi, Avalon, Cairo and Swig support.
 #
-# The RDKIT_BRANCH environment variable must be defined. This defines the RDKit branch to use.
 
 set -e
 
+source ../params.sh
 
-if [ ! -v RDKIT_BRANCH ]; then
-  echo "RDKIT_BRANCH not defined"
+
+if [ ! -v GIT_BRANCH ]; then
+  echo "GIT_BRANCH not defined"
   exit 1
 fi
-echo "Using RDKit branch $RDKIT_BRANCH"
+echo "Using RDKit branch $GIT_BRANCH"
 
 # checkout RDKit source code
 cd /root
 RDBASE=/root/rdkit
 rm -rf $RDBASE
 echo "Checking out RDKit source code"
-git clone -b $RDKIT_BRANCH --single-branch https://github.com/rdkit/rdkit.git
+git clone -b $GIT_BRANCH --single-branch https://github.com/rdkit/rdkit.git
 
 
 mkdir $RDBASE/build
@@ -27,18 +28,23 @@ cd $RDBASE/build
 # build RDKit for python
 echo "Running cmake"
 cmake -Wno-dev\
+  -DLIB_SUFFIX=64\
   -DRDK_INSTALL_INTREE=OFF\
   -DRDK_BUILD_INCHI_SUPPORT=ON\
   -DRDK_BUILD_AVALON_SUPPORT=ON\
   -DRDK_BUILD_CAIRO_SUPPORT=ON\
   -DRDK_BUILD_PYTHON_WRAPPERS=ON\
-  -DRDK_BUILD_SWIG_WRAPPERS=OFF\
+  -DRDK_BUILD_SWIG_WRAPPERS=ON\
   -DCMAKE_INSTALL_PREFIX=/usr\
+  -DCPACK_PACKAGE_RELOCATABLE=OFF\
   ..
 
 echo "Building RDKit"
 nproc=$(getconf _NPROCESSORS_ONLN)
 make -j $(( nproc > 2 ? nproc - 2 : 1 ))
 
+echo "Creating RPMs"
+cpack3 -G RPM
+
 echo "RDKit build complete"