Update rdkit and qt, and build zlib (#10)

.github/actions/build-external/action.yml

@@ -5,8 +5,8 @@ inputs:
   version:
     description: "Version of the dependency to build"
     required: true
-  os:
-    description: "Platform on which we are building"
+  build-output:
+    description: "Build output target"
     required: true
 
 outputs:
@@ -22,7 +22,7 @@ runs:
       id: cache-check
       with:
         path: build/external/${{ inputs.library }}-${{ inputs.version }}
-        key: ${{ inputs.library }}-${{ inputs.version }}-${{ inputs.os }}
+        key: ${{ inputs.library }}-${{ inputs.version }}-${{ runner.os }}-${{ matrix.build-output }}
 
     - name: Build
       if: ${{ steps.cache-check.outputs.cache-hit != 'true' }}

.github/workflows/sketcher-builder.yml

@@ -4,30 +4,33 @@ on:
   workflow_dispatch: ~
   push: ~
   pull_request: ~
+  schedule:
+    - cron: "0 4 * * *"
 
 env:
   BUILD_TYPE: Release
 
 jobs:
-  # TODO: clang-format hook
-  build_test_sketcher:
-    name: ${{ matrix.config.name }}
-    runs-on: ${{ matrix.config.os }}
+  build:
+    runs-on: ${{ matrix.os }}
     defaults:
       run:
         shell: bash
     strategy:
       fail-fast: false
       matrix:
-        config:
-        - {
-            name: "macOS",
-            os: macos-latest,
-            app: "build/sketcher_app",
-          }
+        os: [macos-latest]
+        build-output: [app]
+
     steps:
       - uses: actions/checkout@v4
 
+      - name: Create and activate virtualenv
+        run: |
+          python3 -m venv .venv
+          source .venv/bin/activate
+          echo PATH=$PATH >> $GITHUB_ENV
+
       - name: Install Python packages
         run: python3 -m pip install ninja clang-format==14.0.6
 
@@ -53,43 +56,52 @@ jobs:
         with:
           library: fmt
           version: ${{ fromJson(env.VERSIONS_JSON).fmt }}
-          os: ${{ matrix.config.os }}
+          build-output: ${{ matrix.build-output }}
+
+      - name: Fetch zlib
+        id: fetch-zlib
+        uses: ./.github/actions/build-external
+        with:
+          library: zlib
+          version: ${{ fromJson(env.VERSIONS_JSON).zlib }}
+          build-output: ${{ matrix.build-output }}
 
       - name: Fetch zstd
         id: fetch-zstd
         uses: ./.github/actions/build-external
         with:
           library: zstd
           version: ${{ fromJson(env.VERSIONS_JSON).zstd }}
-          os: ${{ matrix.config.os }}
+          build-output: ${{ matrix.build-output }}
 
       - name: Fetch Boost
         id: fetch-boost
         uses: ./.github/actions/build-external
         with:
           library: boost
           version: ${{ fromJson(env.VERSIONS_JSON).boost }}
-          os: ${{ matrix.config.os }}
+          build-output: ${{ matrix.build-output }}
 
       - name: Fetch RDKit
         id: fetch-rdkit
         uses: ./.github/actions/build-external
         with:
           library: rdkit
           version: ${{ fromJson(env.VERSIONS_JSON).rdkit }}
-          os: ${{ matrix.config.os }}
+          build-output: ${{ matrix.build-output }}
 
       - name: Fetch Qt
         id: fetch-qt
         uses: ./.github/actions/build-external
         with:
           library: qt
           version: ${{ fromJson(env.VERSIONS_JSON).qt }}
-          os: ${{ matrix.config.os }}
+          build-output: ${{ matrix.build-output }}
 
       - name: Configure CMake
         env:
             CMAKE_PREFIX_PATH: "${{ steps.fetch-fmt.outputs.path }};\
+                                ${{ steps.fetch-zlib.outputs.path }};\
                                 ${{ steps.fetch-zstd.outputs.path }};\
                                 ${{ steps.fetch-boost.outputs.path }};\
                                 ${{ steps.fetch-rdkit.outputs.path }};\
@@ -109,5 +121,5 @@ jobs:
       - name: Download sketcher executable
         uses: actions/upload-artifact@v4
         with:
-          name: sketcher_${{ matrix.config.name }}
-          path: ${{ matrix.config.app }}
+          name: sketcher_${{ matrix.build-output }}
+          path: build/sketcher_app

CMakeLists.txt

@@ -14,15 +14,18 @@ string(JSON BOOST_VERSION GET ${VERSIONS} boost)
 string(JSON FMT_VERSION GET ${VERSIONS} fmt)
 string(JSON QT_VERSION GET ${VERSIONS} qt)
 string(JSON RDKIT_VERSION GET ${VERSIONS} rdkit)
+string(JSON ZLIB_VERSION GET ${VERSIONS} zlib)
 string(JSON ZSTD_VERSION GET ${VERSIONS} zstd)
 
 set(Boost_USE_STATIC_LIBS ON) # Ensure static libs are found
 
-find_package(Boost ${BOOST_VERSION} REQUIRED
-             COMPONENTS filesystem json serialization unit_test_framework)
+find_package(
+  Boost ${BOOST_VERSION} REQUIRED COMPONENTS filesystem iostreams json
+                                             serialization unit_test_framework)
 find_package(Qt6 ${QT_VERSION} REQUIRED COMPONENTS Widgets Svg)
 find_package(RDKit ${RDKIT_VERSION} REQUIRED)
 find_package(fmt ${FMT_VERSION} REQUIRED)
+find_package(ZLIB ${ZLIB_VERSION} REQUIRED)
 find_package(zstd ${ZSTD_VERSION} REQUIRED)
 
 # Common library/executable configuration
@@ -66,6 +69,7 @@ target_link_libraries(
           RDKit::DistGeomHelpers
           RDKit::RDInchiLib
           fmt::fmt
+          ZLIB::ZLIB
           zstd::libzstd_static)
 
 set(SKETCHER_LIB sketcher)

external/CMakeLists.txt

@@ -6,19 +6,24 @@ project(schrodinger_sketcher_external)
 set(CMAKE_CXX_STANDARD 17)
 set(CMAKE_CXX_STANDARD_REQUIRED ON)
 
-if(MSVC)
-  # Workaround until boost 1.83 which fixes the issue with std::unary_function
-  add_definitions(-D_HAS_AUTO_PTR_ETC=0)
-endif()
-
 # Collect dependency versions
 file(READ ${CMAKE_CURRENT_SOURCE_DIR}/versions.json VERSIONS)
 string(JSON BOOST_VERSION GET ${VERSIONS} boost)
 string(JSON FMT_VERSION GET ${VERSIONS} fmt)
 string(JSON QT_VERSION GET ${VERSIONS} qt)
 string(JSON RDKIT_VERSION GET ${VERSIONS} rdkit)
+string(JSON ZLIB_VERSION GET ${VERSIONS} zlib)
 string(JSON ZSTD_VERSION GET ${VERSIONS} zstd)
 
+# Ensure args passed to ExternalProject_Add's CMAKE_ARGS support semicolons
+function(set_cmake_arg VAR_NAME)
+  set(CMAKE_ARG ${ARGN})
+  string(REPLACE ";" "$<SEMICOLON>" CMAKE_ARG "${CMAKE_ARG}")
+  set(${VAR_NAME}
+      "${CMAKE_ARG}"
+      PARENT_SCOPE)
+endfunction()
+
 ExternalProject_Add(
   fmt
   GIT_REPOSITORY https://github.com/fmtlib/fmt.git
@@ -28,6 +33,17 @@ ExternalProject_Add(
     -DCMAKE_INSTALL_PREFIX=${CMAKE_CURRENT_BINARY_DIR}/fmt-${FMT_VERSION}
     -DCMAKE_BUILD_TYPE=Release -DFMT_DOC=OFF -DFMT_TEST=OFF -DFMT_INSTALL=ON)
 
+ExternalProject_Add(
+  zlib
+  GIT_REPOSITORY https://github.com/madler/zlib.git
+  GIT_TAG v${ZLIB_VERSION}
+  GIT_SHALLOW TRUE
+  PATCH_COMMAND git apply ${CMAKE_CURRENT_SOURCE_DIR}/zlib.patch
+  UPDATE_DISCONNECTED 1 # required to not apply patch again once populated
+  CMAKE_ARGS
+    -DCMAKE_INSTALL_PREFIX=${CMAKE_CURRENT_BINARY_DIR}/zlib-${ZLIB_VERSION}
+    -DCMAKE_BUILD_TYPE=Release -DBUILD_SHARED_LIBS=OFF)
+
 ExternalProject_Add(
   zstd
   GIT_REPOSITORY https://github.com/facebook/zstd.git
@@ -39,37 +55,46 @@ ExternalProject_Add(
     -DCMAKE_BUILD_TYPE=Release -DZSTD_BUILD_SHARED=OFF
     -DZSTD_BUILD_PROGRAMS=OFF)
 
-set(BOOST_INCLUDE_LIBS
-    # RDKit required libraries
-    assign
-    crc
-    format
-    flyweight
-    graph
-    iostreams
-    json
-    multi_array
-    multiprecision
-    program_options
-    serialization
-    # rdkit_extensions required libraries
-    beast
-    bimap
-    filesystem
-    test)
-# Use generator expression to sidestep CMAKE_ARGS removing semicolons
-string(REPLACE ";" "$<SEMICOLON>" BOOST_INCLUDE_LIBS "${BOOST_INCLUDE_LIBS}")
+set_cmake_arg(
+  BOOST_INCLUDE_LIBS
+  # RDKit required libraries
+  assign
+  crc
+  format
+  flyweight
+  graph
+  iostreams
+  json
+  multi_array
+  multiprecision
+  program_options
+  serialization
+  # rdkit_extensions required libraries
+  beast
+  bimap
+  filesystem
+  test)
+set_cmake_arg(
+  BOOST_CMAKE_PREFIX ${CMAKE_CURRENT_BINARY_DIR}/zlib-${ZLIB_VERSION}
+  ${CMAKE_CURRENT_BINARY_DIR}/zstd-${ZSTD_VERSION})
 ExternalProject_Add(
   boost
   GIT_REPOSITORY https://github.com/boostorg/boost.git
   GIT_TAG boost-${BOOST_VERSION}
   GIT_SHALLOW TRUE
   CMAKE_ARGS
     -DCMAKE_INSTALL_PREFIX=${CMAKE_CURRENT_BINARY_DIR}/boost-${BOOST_VERSION}
-    -DCMAKE_BUILD_TYPE=Release -DBUILD_SHARED_LIBS=OFF
-    -DBOOST_INCLUDE_LIBRARIES=${BOOST_INCLUDE_LIBS})
+    -DCMAKE_BUILD_TYPE=Release
+    -DCMAKE_PREFIX_PATH=${BOOST_CMAKE_PREFIX}
+    -DBUILD_SHARED_LIBS=OFF
+    -DBOOST_INCLUDE_LIBRARIES=${BOOST_INCLUDE_LIBS}
+    -DBOOST_RUNTIME_LINK=static
+    -DBOOST_IOSTREAMS_ENABLE_BZIP2=OFF)
 
 string(REPLACE "." "_" RDKIT_GIT_TAG ${RDKIT_VERSION})
+set_cmake_arg(
+  RDKIT_CMAKE_PREFIX ${CMAKE_CURRENT_BINARY_DIR}/boost-${BOOST_VERSION}
+  ${CMAKE_CURRENT_BINARY_DIR}/zlib-${ZLIB_VERSION})
 ExternalProject_Add(
   rdkit
   GIT_REPOSITORY https://github.com/rdkit/rdkit.git
@@ -80,7 +105,7 @@ ExternalProject_Add(
   CMAKE_ARGS
     -DCMAKE_INSTALL_PREFIX=${CMAKE_CURRENT_BINARY_DIR}/rdkit-${RDKIT_VERSION}
     -DCMAKE_BUILD_TYPE=Release
-    -DCMAKE_PREFIX_PATH=${CMAKE_CURRENT_BINARY_DIR}/boost-${BOOST_VERSION}
+    -DCMAKE_PREFIX_PATH=${RDKIT_CMAKE_PREFIX}
     -DBUILD_SHARED_LIBS=OFF
     -DBoost_USE_STATIC_LIBS=ON
     -DRDK_BUILD_CPP_TESTS=OFF
@@ -97,19 +122,18 @@ ExternalProject_Add(
     -DRDK_OPTIMIZE_POPCNT=OFF
     -DRDK_USE_BOOST_STACKTRACE=OFF)
 
+set_cmake_arg(QT_SUBMODULES qtbase qtsvg)
 ExternalProject_Add(
   qt
   GIT_REPOSITORY https://github.com/qt/qt5.git
-  GIT_TAG v${QT_VERSION}-lts-lgpl
+  GIT_TAG v${QT_VERSION}
   GIT_SUBMODULES qtbase qtsvg
   GIT_SHALLOW TRUE
-  PATCH_COMMAND cd qtsvg && git apply ${CMAKE_CURRENT_SOURCE_DIR}/qtsvg.patch
-  UPDATE_DISCONNECTED 1 # required to not apply patch again once populated
   CMAKE_ARGS -DCMAKE_INSTALL_PREFIX=${CMAKE_CURRENT_BINARY_DIR}/qt-${QT_VERSION}
              -DCMAKE_BUILD_TYPE=Release
              -DBUILD_SHARED_LIBS=OFF
              -DQT_BUILD_EXAMPLES=OFF
-             -DQT_BUILD_SUBMODULES=qtbase$<SEMICOLON>qtsvg
+             -DQT_BUILD_SUBMODULES=${QT_SUBMODULES}
              -DQT_BUILD_TESTS=OFF
              -DQT_FEATURE_brotli=OFF
              -DQT_FEATURE_sql=OFF

external/rdkit.patch

@@ -1,25 +1,3 @@
-diff --git a/CMakeLists.txt b/CMakeLists.txt
-index 37d618000..37c82d6fa 100644
---- a/CMakeLists.txt
-+++ b/CMakeLists.txt
-@@ -448,7 +448,7 @@ else()
- endif()
-
- if(RDK_USE_BOOST_SERIALIZATION)
--    find_package(Boost ${RDK_BOOST_VERSION} COMPONENTS system serialization iostreams REQUIRED)
-+    find_package(Boost ${RDK_BOOST_VERSION} COMPONENTS serialization iostreams REQUIRED)
-     target_link_libraries(rdkit_base INTERFACE ${Boost_LIBRARIES})
-     target_compile_definitions(rdkit_base INTERFACE -DRDK_USE_BOOST_SERIALIZATION)
-     if(NOT Boost_USE_STATIC_LIBS)
-@@ -458,7 +458,7 @@ endif()
-
- if(RDK_USE_BOOST_IOSTREAMS)
-     target_compile_definitions(rdkit_base INTERFACE -DRDK_USE_BOOST_IOSTREAMS)
--    find_package(Boost ${RDK_BOOST_VERSION} COMPONENTS system iostreams REQUIRED)
-+    find_package(Boost ${RDK_BOOST_VERSION} COMPONENTS iostreams REQUIRED)
-     target_link_libraries(rdkit_base INTERFACE ${Boost_LIBRARIES})
-
-     if (NOT Boost_USE_STATIC_LIBS)
 diff --git a/Code/cmake/Modules/RDKitUtils.cmake b/Code/cmake/Modules/RDKitUtils.cmake
 index 7c4f5add5..1e79aa1c0 100644
 --- a/Code/cmake/Modules/RDKitUtils.cmake

external/versions.json

@@ -1,7 +1,9 @@
 {
-    "boost": "1.81.0",
+    "boost": "1.83.0",
     "fmt": "10.1.0",
-    "qt": "6.2.7",
-    "rdkit": "2023.09.4",
+    "qt": "6.5.3",
+    "rdkit": "2024.03.2",
+    "sqlite": "3.42.0",
+    "zlib": "1.2.11",
     "zstd": "1.5.5"
 }

external/zlib.patch

@@ -0,0 +1,13 @@
+diff --git a/CMakeLists.txt b/CMakeLists.txt
+index 3d9b58d..f0e8e2b 100644
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -184,7 +184,7 @@ elseif(BUILD_SHARED_LIBS AND WIN32)
+ endif()
+
+ if(NOT SKIP_INSTALL_LIBRARIES AND NOT SKIP_INSTALL_ALL )
+-    install(TARGETS zlib zlibstatic
++    install(TARGETS zlibstatic
+         RUNTIME DESTINATION "${INSTALL_BIN_DIR}"
+         ARCHIVE DESTINATION "${INSTALL_LIB_DIR}"
+         LIBRARY DESTINATION "${INSTALL_LIB_DIR}" )