Fixes #3648 (#3654)

* Fixes #3648

Code now builds without either MAEParser or coordgen integration enabled.

* add CI build with minimal dependencies

* remove doctests from the new CI build

they need the cairo support

.azure-pipelines/linux_build_limitexternal.yml

@@ -0,0 +1,70 @@
+steps:
+- bash: |
+    sudo apt-get install g++ wget make libgl1-mesa-dev mesa-common-dev
+    source ${CONDA}/etc/profile.d/conda.sh
+    sudo chown -R ${USER} ${CONDA}
+    conda config --set always_yes yes --set changeps1 no
+    conda update -q conda
+    conda info -a
+    conda create --name rdkit_build $(python) cmake \
+        boost-cpp=$(boost_version) \
+        py-boost=$(boost_version) \
+        numpy pillow eigen pandas \
+        qt
+    conda activate rdkit_build
+    conda install -c rdkit nox cairo=1.14.6
+  displayName: Setup build environment
+- bash: |
+    source ${CONDA}/etc/profile.d/conda.sh
+    conda activate rdkit_build
+    mkdir build && cd build && \
+    cmake .. \
+    -DCMAKE_BUILD_TYPE=Release \
+    -DRDK_INSTALL_INTREE=ON \
+    -DRDK_INSTALL_STATIC_LIBS=OFF \
+    -DRDK_BUILD_CPP_TESTS=ON \
+    -DRDK_BUILD_PYTHON_WRAPPERS=ON \
+    -DRDK_USE_BOOST_REGEX=OFF \
+    -DRDK_BUILD_COORDGEN_SUPPORT=OFF \
+    -DRDK_BUILD_MAEPARSER_SUPPORT=OFF \
+    -DRDK_OPTIMIZE_POPCNT=ON \
+    -DRDK_BUILD_TEST_GZIP=OFF \
+    -DRDK_BUILD_FREESASA_SUPPORT=OFF \
+    -DRDK_BUILD_AVALON_SUPPORT=OFF \
+    -DRDK_BUILD_INCHI_SUPPORT=OFF \
+    -DRDK_BUILD_CAIRO_SUPPORT=OFF \
+    -DRDK_BUILD_QT_SUPPORT=OFF \
+    -DQt5_DIR=/usr/lib/x86_64-linux-gnu/cmake/Qt5 \
+    -DRDK_BUILD_SWIG_WRAPPERS=OFF \
+    -DRDK_SWIG_STATIC=OFF \
+    -DRDK_BUILD_THREADSAFE_SSS=ON \
+    -DRDK_TEST_MULTITHREADED=ON \
+    -DBoost_NO_SYSTEM_PATHS=ON \
+    -DBoost_NO_BOOST_CMAKE=TRUE \
+    -DRDK_BOOST_PYTHON3_NAME=$(python_name) \
+    -DPYTHON_EXECUTABLE=${CONDA_PREFIX}/bin/python3 \
+    -DCMAKE_INCLUDE_PATH="${CONDA_PREFIX}/include" \
+    -DCMAKE_LIBRARY_PATH="${CONDA_PREFIX}/lib"
+  displayName: Configure build (Run CMake)
+- bash: |
+    source ${CONDA}/etc/profile.d/conda.sh
+    conda activate rdkit_build
+    cd build
+    make -j $( $(number_of_cores) ) install
+  displayName: Build
+- bash: |
+    source ${CONDA}/etc/profile.d/conda.sh
+    conda activate rdkit_build
+    export RDBASE=`pwd`
+    export PYTHONPATH=${RDBASE}:${PYTHONPATH}
+    export LD_LIBRARY_PATH=${RDBASE}/lib:${CONDA_PREFIX}/lib:${LD_LIBRARY_PATH}
+    echo "LD_LIBRARY_PATH: " $LD_LIBRARY_PATH
+    export QT_QPA_PLATFORM='offscreen'
+    cd build
+    ctest -j $( $(number_of_cores) ) --output-on-failure -T Test
+  displayName: Run tests
+- task: PublishTestResults@2
+  inputs:
+    testResultsFormat: 'CTest'
+    testResultsFiles: 'build/Testing/*/Test.xml'
+    testRunTitle: $(system.phasedisplayname) CTest Test Run

Code/GraphMol/Depictor/RDDepictor.cpp

@@ -33,9 +33,9 @@
 #include <algorithm>
 
 namespace RDDepict {
-#ifdef RDK_BUILD_COORDGEN_SUPPORT
+
 bool preferCoordGen = false;
-#endif
+
 namespace DepictorLocal {
 // arings: indices of atoms in rings
 void embedFusedSystems(const RDKit::ROMol &mol,

Code/GraphMol/Depictor/RDDepictor.h

@@ -22,9 +22,8 @@ class ROMol;
 
 namespace RDDepict {
 
-#ifdef RDK_BUILD_COORDGEN_SUPPORT
-RDKIT_DEPICTOR_EXPORT extern bool preferCoordGen;
-#endif
+RDKIT_DEPICTOR_EXPORT extern bool
+    preferCoordGen;  // Ignored if coordgen support isn't active
 
 typedef boost::shared_array<double> DOUBLE_SMART_PTR;
 

Code/GraphMol/FileParsers/GeneralFileReader.h

@@ -144,14 +144,14 @@ std::unique_ptr<MolSupplier> getSupplier(const std::string& path,
     std::unique_ptr<MolSupplier> p(smsup);
     return p;
   }
-
+#ifdef RDK_BUILD_MAEPARSER_SUPPORT
   else if (fileFormat == "mae") {
     MaeMolSupplier* maesup =
         new MaeMolSupplier(strm, true, opt.sanitize, opt.removeHs);
     std::unique_ptr<MolSupplier> p(maesup);
     return p;
   }
-
+#endif
   else if (fileFormat == "tdt") {
     TDTMolSupplier* tdtsup = new TDTMolSupplier(
         strm, true, opt.nameRecord, opt.confId2D, opt.confId3D, opt.sanitize);

Code/GraphMol/FileParsers/testGeneralFileReader.cpp

@@ -163,6 +163,7 @@ void testSmi() {
 }
 
 void testMae() {
+#ifdef RDK_BUILD_MAEPARSER_SUPPORT
   //! Open uncompressed MAE file format
   std::string rdbase = getenv("RDBASE");
   std::string fname =
@@ -227,6 +228,7 @@ void testMae() {
   TEST_ASSERT(info->getResidueName() == "ARG ");
   TEST_ASSERT(info->getChainId() == "A");
   TEST_ASSERT(info->getResidueNumber() == 5);
+#endif
 }
 
 void testTdt() {

azure-pipelines.yml

@@ -102,3 +102,15 @@ jobs:
     number_of_cores: nproc
   steps:
   - template: .azure-pipelines/linux_build_fuzzer.yml
+- job: Ubuntu_18_04_x64_limitexternaldependencies
+  timeoutInMinutes: 90
+  pool:
+    vmImage: ubuntu-18.04
+  variables:
+    python: python=3.8
+    boost_version: 1.71.0
+    compiler: gxx_linux-64
+    number_of_cores: nproc
+    python_name: python38
+  steps:
+  - template: .azure-pipelines/linux_build_limitexternal.yml