Update build process for LillyMol 7.0 (#25)

Author: xuyan-ru

Dockerfile

@@ -1,56 +1,34 @@
-FROM gcc:10.2
+FROM gcc:13.2
 
-ENV LILLYMOL_HOME=/LillyMol \
-    BUILD_DIR=Linux
-
-# Install Eigen
-# (No need to install zlib since zlib1g and zlib1g-dev are alreday in the gcc base image)
 RUN apt-get update && \ 
-    apt-get upgrade -y && \
-    apt-get install -y libeigen3-dev && \
-    cd /usr/include && \
-        ln -sf eigen3/Eigen Eigen
+    apt-get upgrade -y
 
 RUN apt-get install npm -y && \
-    npm install -g @bazel/bazelisk && \
-    apt-get install cmake -y
-
-RUN apt-get install python3-pip -y && \
-    pip3 install pandas && \
-    apt-get install libblas-dev -y && \
-    apt-get install liblapack-dev -y && \
-    pip3 install scipy
-
-COPY . ./LillyMol
-
-WORKDIR /LillyMol
+    npm install -g @bazel/bazelisk
 
-RUN mkdir bin && \
-    mkdir bin/Linux && \
-    cd src && \
-    ./build_third_party.sh
-
-WORKDIR /LillyMol/src
+RUN apt-get install libblas-dev -y && \
+    apt-get install liblapack-dev -y 
 
-RUN cp /tmp/WORKSPACE .
+RUN apt-get install python3-minimal -y && \
+    apt-get install python3-pandas python3-scipy python3-absl python3-pybind11 python3-protobuf -y
 
-WORKDIR /LillyMol/src/build_deps
+RUN rm -f /usr/bin/python && ln -s /usr/bin/python3 /usr/bin/python
 
-RUN sed -i 's/\/workspaces\/LillyMolPrivate\/bin\/Linux\//\/LillyMol\/bin\/Linux\//g' install.bzl
+COPY . ./LillyMol
 
-WORKDIR /LillyMol
+ENV LILLYMOL_HOME=/LillyMol \
+    BUILD_DIR=Linux
 
+# This step probably not necessary since now, third party
+# dependencies are all linked static. Maybe that will change.
 ENV LD_LIBRARY_PATH=/LillyMol/third_party/lib
 
-RUN mkdir /node && \
-    mkdir /node/scratch
-
 WORKDIR /LillyMol/src
 
+ENV BUILD_BDB=1
+ENV BUILD_PYTHON=1
+
+RUN ./build_third_party.sh
 RUN ./build_from_src.sh
 
 WORKDIR /LillyMol
-
-RUN rm -f /usr/bin/python && ln -s /usr/bin/python3 /usr/bin/python
-
-# RUN apt-get install python3-pip -Y

Makefile

@@ -0,0 +1,48 @@
+# Copyright 2018 Eli Lilly and Company 
+# 
+# 
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License. 
+# You may obtain a copy of the License at  
+# 
+#     http://www.apache.org/licenses/LICENSE-2.0  
+# 
+# Unless required by applicable law or agreed to in writing, software 
+# distributed under the License is distributed on an "AS IS" BASIS, 
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 
+# See the License for the specific language governing permissions and 
+# limitations under the License. 
+########################################################################
+
+.PHONY: default
+.PHONY: all
+
+# A default target that will probably work in most cases.
+# Note it does not build BerkeleyDB dependent tools or Python bindings.
+default:
+	bash -c 'if [[ -z "$$(type -p bazelisk)" && -z "$$(type -p bazel)" ]] ; then echo "No bazel/bazelisk, see README.md" && exit 1 ; fi'
+	echo "Default build does not build targets 'berkeleydb' and 'python'"
+	cd src && ./build_third_party.sh
+	cd src && ./build_from_src.sh
+
+all:
+	bash -c 'if [[ -z "$$(type -p bazelisk)" && -z "$$(type -p bazel)" ]] ; then echo "No bazel/bazelisk, see README.md" && exit 1 ; fi'
+	cd src && BUILD_BDB=1 BUILD_PYTHON=1 ./build_third_party.sh
+	cd src && BUILD_BDB=1 BUILD_PYTHON=1 ./build_from_src.sh
+
+berkeleydb:
+	bash -c 'if [[ -z "$$(type -p bazelisk)" && -z "$$(type -p bazel)" ]] ; then echo "No bazel/bazelisk, see README.md" && exit 1 ; fi'
+	cd src && BUILD_BDB=1 ./build_third_party.sh
+	cd src && BUILD_BDB=1 ./build_from_src.sh
+
+python:
+	bash -c 'if [[ -z "$$(type -p bazelisk)" && -z "$$(type -p bazel)" ]] ; then echo "No bazel/bazelisk, see README.md" && exit 1 ; fi'
+	cd src && BUILD_PYTHON=1 ./build_third_party.sh
+	cd src && BUILD_PYTHON=1 ./build_from_src.sh
+
+build_docker:
+	docker build -f Dockerfile -t lillymol .
+     
+test_lillymol:
+	docker container exec lilly_mol bash -c "cd test/ && ./run_all_test.sh"
+	docker container exec lilly_mol bash -c "cd src/ && ./run_python_unit_tests.sh 2>&1"