Start to use Catch2 for new tests (#1732)

* backup

* build works

* works

* builds on linux

* rename the test

* add another test to make sure that works

CMakeLists.txt

@@ -14,6 +14,7 @@ set(CMAKE_MODULE_PATH
     ${CMAKE_MODULE_PATH} "${CMAKE_CURRENT_SOURCE_DIR}/Code/cmake/Modules/")
 
 add_library(rdkit_base INTERFACE)
+add_dependencies(rdkit_base catch)
 
 option(RDK_BUILD_SWIG_WRAPPERS "build the SWIG wrappers" OFF )
 option(RDK_BUILD_PYTHON_WRAPPERS "build the standard python wrappers" ON )
@@ -100,6 +101,12 @@ string(REGEX REPLACE "^0" "" RDKit_intMonth ${RDKit_Month} )
 set(RDKit_CodeDir "${CMAKE_CURRENT_SOURCE_DIR}/Code")
 set(RDKit_ExternalDir "${CMAKE_CURRENT_SOURCE_DIR}/External")
 
+#include catch
+add_subdirectory(${RDKit_ExternalDir}/catch)
+
+
+include_directories(${CATCH_INCLUDE_DIR} ${COMMON_INCLUDES})
+
 if(RDK_INSTALL_INTREE)
   set(RDKit_BinDir "${CMAKE_SOURCE_DIR}/bin")
   set(RDKit_LibDir "${CMAKE_SOURCE_DIR}/lib")

Code/GraphMol/CMakeLists.txt

@@ -136,3 +136,6 @@ rdkit_test(molBundleTest testMolBundle.cpp
           LINK_LIBRARIES SmilesParse GraphMol RDGeometryLib RDGeneral SubstructMatch FileParsers)
 
 rdkit_test(test-valgrind test-valgrind.cpp LINK_LIBRARIES SmilesParse GraphMol RDGeneral)
+
+rdkit_catch_test(testsCatch catch_tests.cpp
+           LINK_LIBRARIES SubstructMatch FileParsers SmilesParse GraphMol RDGeometryLib RDGeneral)

Code/GraphMol/SmilesParse/CMakeLists.txt

@@ -71,3 +71,4 @@ rdkit_test(smiTest2 test2.cpp LINK_LIBRARIES SmilesParse GraphMol RDGeneral RDGe
 rdkit_test(cxsmilesTest cxsmiles_test.cpp LINK_LIBRARIES FileParsers SmilesParse GraphMol RDGeneral RDGeometryLib )
 
 rdkit_test(smaTest1 smatest.cpp LINK_LIBRARIES SmilesParse SubstructMatch GraphMol RDGeneral RDGeometryLib )
+rdkit_catch_test(smiTestCatch catch_tests.cpp LINK_LIBRARIES FileParsers SmilesParse GraphMol RDGeneral RDGeometryLib )

Code/GraphMol/SmilesParse/catch_tests.cpp

@@ -0,0 +1,48 @@
+#define CATCH_CONFIG_MAIN  // This tells Catch to provide a main() - only do
+                           // this in one cpp file
+#include "catch.hpp"
+
+#include <GraphMol/RDKitBase.h>
+#include <GraphMol/SmilesParse/SmilesParse.h>
+#include <GraphMol/SmilesParse/SmilesWrite.h>
+
+using namespace RDKit;
+
+TEST_CASE("Github #1972", "[SMILES,bug]") {
+  SECTION("basics") {
+    std::vector<std::vector<std::string>> smiles = {
+        {"[C@@]1(Cl)(F)(I).Br1", "[C@@](Br)(Cl)(F)(I)"},
+        {"[C@@](Cl)(F)(I)1.Br1", "[C@@](Cl)(F)(I)Br"},
+        {"[C@@](Cl)1(F)(I).Br1", "[C@@](Cl)(Br)(F)(I)"},
+        {"[C@@](Cl)(F)1(I).Br1", "[C@@](Cl)(F)(Br)(I)"}};
+    for (const auto &pr : smiles) {
+      std::unique_ptr<ROMol> m1(SmilesToMol(pr[0]));
+      std::unique_ptr<ROMol> m2(SmilesToMol(pr[1]));
+      REQUIRE(m1);
+      REQUIRE(m2);
+      auto csmi1 = MolToSmiles(*m1);
+      auto csmi2 = MolToSmiles(*m2);
+      CHECK(csmi1 == csmi2);
+    }
+  }
+  SECTION("further examples") {
+    std::vector<std::vector<std::string>> smiles = {
+        {"[C@@]1(Cl)2(I).Br1.F2", "[C@@](Br)(Cl)(F)(I)"},
+        {"[C@@](Cl)2(I)1.Br1.F2", "[C@@](Cl)(F)(I)Br"},
+        {"[C@@]12(Cl)(I).Br1.F2", "[C@@](Br)(F)(Cl)(I)"},
+        {"[C@@]21(Cl)(I).Br1.F2", "[C@@](F)(Br)(Cl)(I)"},
+        {"[C@@](Cl)12(I).Br1.F2", "[C@@](Cl)(Br)(F)(I)"},
+        {"[C@@](Cl)21(I).Br1.F2", "[C@@](Cl)(F)(Br)(I)"},
+        {"[C@@](Cl)(I)21.Br1.F2", "[C@@](Cl)(I)(F)(Br)"},
+        {"[C@@](Cl)(I)12.Br1.F2", "[C@@](Cl)(I)(Br)(F)"}};
+    for (const auto &pr : smiles) {
+      std::unique_ptr<ROMol> m1(SmilesToMol(pr[0]));
+      std::unique_ptr<ROMol> m2(SmilesToMol(pr[1]));
+      REQUIRE(m1);
+      REQUIRE(m2);
+      auto csmi1 = MolToSmiles(*m1);
+      auto csmi2 = MolToSmiles(*m2);
+      CHECK(csmi1 == csmi2);
+    }
+  }
+}

Code/GraphMol/catch_tests.cpp

@@ -0,0 +1,45 @@
+#define CATCH_CONFIG_MAIN  // This tells Catch to provide a main() - only do
+                           // this in one cpp file
+#include "catch.hpp"
+
+#include <GraphMol/RDKitBase.h>
+#include <GraphMol/RDKitQueries.h>
+#include <GraphMol/Chirality.h>
+#include <GraphMol/SmilesParse/SmilesParse.h>
+#include <GraphMol/SmilesParse/SmilesWrite.h>
+#include <GraphMol/SmilesParse/SmartsWrite.h>
+
+using namespace RDKit;
+
+TEST_CASE("SMILES Parsing works", "[molops]") {
+  std::unique_ptr<RWMol> mol(SmilesToMol("C1CC1"));
+  REQUIRE(mol);
+  REQUIRE(mol->getNumAtoms() == 3);
+}
+
+TEST_CASE("Sanitization tests", "[molops]") {
+  std::unique_ptr<RWMol> mol(SmilesToMol("C1=CC=CC=C1Cc2ccccc2", false, false));
+  REQUIRE(mol);
+  REQUIRE(mol->getNumAtoms() == 13);
+
+  SECTION("properties") {
+    mol->updatePropertyCache();
+    CHECK(mol->getAtomWithIdx(0)->getTotalNumHs() == 1);
+    CHECK(!mol->getAtomWithIdx(0)->getIsAromatic());
+    CHECK(mol->getAtomWithIdx(7)->getIsAromatic());
+    SECTION("aromaticity") {
+      unsigned int opThatFailed;
+      MolOps::sanitizeMol(*mol, opThatFailed, MolOps::SANITIZE_SETAROMATICITY);
+      // mol->debugMol(std::cerr);
+      CHECK(mol->getAtomWithIdx(7)->getIsAromatic());
+      // blocked by #1730
+      // CHECK(mol->getAtomWithIdx(0)->getIsAromatic());
+    }
+    SECTION("kekulize") {
+      unsigned int opThatFailed;
+      MolOps::sanitizeMol(*mol, opThatFailed, MolOps::SANITIZE_KEKULIZE);
+      CHECK(!mol->getAtomWithIdx(0)->getIsAromatic());
+      CHECK(!mol->getAtomWithIdx(7)->getIsAromatic());
+    }
+  }
+}

Code/cmake/Modules/RDKitUtils.cmake

@@ -154,6 +154,21 @@ macro(rdkit_test)
   endif(RDK_BUILD_CPP_TESTS)
 endmacro(rdkit_test)
 
+macro(rdkit_catch_test)
+  PARSE_ARGUMENTS(RDKTEST
+    "LINK_LIBRARIES;DEPENDS;DEST"
+    ""
+    ${ARGN})
+  CAR(RDKTEST_NAME ${RDKTEST_DEFAULT_ARGS})
+  CDR(RDKTEST_SOURCES ${RDKTEST_DEFAULT_ARGS})
+  if(RDK_BUILD_CPP_TESTS)
+    add_executable(${RDKTEST_NAME} ${RDKTEST_SOURCES})
+    target_link_libraries(${RDKTEST_NAME} ${RDKTEST_LINK_LIBRARIES})
+    add_test(${RDKTEST_NAME} ${EXECUTABLE_OUTPUT_PATH}/${RDKTEST_NAME})
+    #ParseAndAddCatchTests(${RDKTEST_NAME})
+  endif(RDK_BUILD_CPP_TESTS)
+endmacro(rdkit_catch_test)
+
 macro(add_pytest)
   PARSE_ARGUMENTS(PYTEST
     "LINK_LIBRARIES;DEPENDS;DEST"

External/catch/CMakeLists.txt

@@ -0,0 +1,22 @@
+project(catch_builder CXX)
+
+# Includes Catch in the project:
+include(ExternalProject)
+
+ExternalProject_Add(
+    catch
+    SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/catch
+    GIT_REPOSITORY https://github.com/philsquared/Catch.git
+    GIT_TAG "v2.1.1"
+    TIMEOUT 10
+    UPDATE_COMMAND ""
+    CONFIGURE_COMMAND ""
+    BUILD_COMMAND ""
+    INSTALL_COMMAND ""
+    LOG_DOWNLOAD ON
+   )
+
+# Expose required variable (CATCH_INCLUDE_DIR) to parent scope
+ExternalProject_Get_Property(catch source_dir)
+set(CATCH_MODULE_PATH ${source_dir} CACHE INTERNAL "location of Catch")
+set(CATCH_INCLUDE_DIR ${CATCH_MODULE_PATH}/single_include CACHE INTERNAL "Path to include folder for Catch")