Add unit test case (#40)

* Add Catch2 unit test

* Fix unit test

* Add git support in Dockerfile

* Add git in CI basic packages

* Fix file path in parse_pdqt_test.cpp

* Update CMakeLists.txt to link unit_tests with lib and cuda

.github/workflows/ci_test_unidock.yml

@@ -20,7 +20,7 @@ jobs:
     - name: install basic packages
       run: |
         apt-get update
-        apt-get install -y build-essential cmake libboost-all-dev ninja-build
+        apt-get install -y build-essential cmake libboost-all-dev ninja-build git
 
     - if: ${{ env.ACT }}
       name: Hack container for local development

unidock/CMakeLists.txt

@@ -41,6 +41,15 @@ add_compile_definitions(VERSION="v${PROJECT_VERSION}")
 find_package(OpenMP REQUIRED) # OpenMP only required in main.cpp
 find_package(Boost 1.72 REQUIRED
 	COMPONENTS system thread serialization filesystem program_options timer)
+Include(FetchContent)
+
+	FetchContent_Declare(
+	  Catch2
+	  GIT_REPOSITORY https://github.com/catchorg/Catch2.git
+	  GIT_TAG        v3.4.0 # or a later release
+	)
+
+	FetchContent_MakeAvailable(Catch2)
 include_directories(${Boost_INCLUDE_DIRS})
 include_directories(src/lib src/cuda)
 add_executable(${VINA_BIN_NAME} src/main/main.cpp)
@@ -55,11 +64,19 @@ add_library(lib OBJECT
 	src/lib/ad4cache.cpp src/lib/cache.cpp src/lib/non_cache.cpp src/lib/conf_independent.cpp src/lib/coords.cpp src/lib/grid.cpp src/lib/szv_grid.cpp src/lib/model.cpp src/lib/mutate.cpp src/lib/parallel_mc.cpp src/lib/parse_pdbqt.cpp src/lib/quasi_newton.cpp src/lib/quaternion.cpp src/lib/random.cpp src/lib/utils.cpp src/lib/vina.cpp src/lib/precalculate.h)
 	# src/lib/monte_carlo
 # set(CMAKE_CURRENT_SOURCE_DIR ${CMAKE_SOURCE_DIR}/src/cuda)
+include_directories(${CMAKE_SOURCE_DIR}/unittest)
+file(GLOB_RECURSE TEST_SOURCES ${CMAKE_SOURCE_DIR}/unittest/*.cpp ${CMAKE_SOURCE_DIR}/unittest/*.hpp)
+add_executable(unit_tests ${TEST_SOURCES})
+
+
 add_library(cuda OBJECT src/lib/monte_carlo.h src/cuda/monte_carlo.cu src/cuda/precalculate.cu)
 target_link_libraries(${VINA_BIN_NAME} cuda lib)
 target_include_directories(${VINA_BIN_NAME} PUBLIC ${CMAKE_CUDA_TOOLKIT_INCLUDE_DIRECTORIES}) # For detecting CUDA memory size
 install(PROGRAMS ${CMAKE_CURRENT_BINARY_DIR}/${VINA_BIN_NAME} TYPE BIN)
-
+target_link_libraries(unit_tests Boost::system Boost::thread Boost::serialization Boost::filesystem Boost::program_options Boost::timer)
+target_link_libraries(unit_tests OpenMP::OpenMP_CXX)
+target_link_libraries(unit_tests lib cuda)
+target_link_libraries(unit_tests Catch2::Catch2WithMain)
 file(GLOB_RECURSE sources CONFIGURE_DEPENDS src/*.cpp src/*.h src/*.cu)
 set(CLANG_FORMAT clang-format)
 

unidock/Dockerfile

@@ -5,7 +5,7 @@ ARG CUDA_VERSION=12.0.0
 FROM nvidia/cuda:${CUDA_VERSION}-devel-ubuntu22.04
 
 RUN apt-get update && apt install -y cmake \
-    libboost-system-dev libboost-thread-dev libboost-serialization-dev libboost-filesystem-dev libboost-program-options-dev libboost-timer-dev
+    libboost-system-dev libboost-thread-dev libboost-serialization-dev libboost-filesystem-dev libboost-program-options-dev libboost-timer-dev git
 
 COPY . /opt/unidock
 

unidock/src/lib/parse_pdbqt.cpp

@@ -157,9 +157,7 @@ struct movable_atom : public atom {
     }
 };
 
-struct rigid {
-    atomv atoms;
-};
+
 
 typedef std::vector<movable_atom> mav;
 

unidock/src/lib/parse_pdbqt.h

@@ -26,7 +26,9 @@
 #include <string>
 #include "model.h"
 #include <set>
-
+struct rigid {
+    atomv atoms;
+};
 model parse_receptor_pdbqt(const std::string &rigid = std::string(),
                            const std::string &flex = std::string(),
                            atom_type::t atype = atom_type::XS);  // can throw struct_parse_error
@@ -47,4 +49,6 @@ model parse_ligand_pdbqt_from_string(const std::string &string_name,
                                      atom_type::t atype);  // can exit with code EXIT_FAILURE
 model parse_ligand_pdbqt_from_string_no_failure(
     const std::string &string_name, atom_type::t atype);  // can return empty model as failure
+void parse_pdbqt_rigid(const path& name, rigid& r);
+
 #endif

unidock/src/main/main.cpp

@@ -177,7 +177,7 @@ int predict_peak_memory(int batch_size, int exhaustiveness, int all_atom2_number
     // states
     gpu_memory
         += (int64_t)(1) * batch_size * exhaustiveness * 64;  // sizeof(curandStatePhilox4_32_10_t)
-
+        
     return gpu_memory / (1024 * 1024);
 }
 

unidock/unittest/ParseTests/parse_pdqt_test.cpp

@@ -0,0 +1,13 @@
+#include <catch2/catch_test_macros.hpp>
+#include "parse_pdbqt.h"
+#include "atom.h"
+
+
+TEST_CASE("parse pdbqt rigid", "[parse_pdbqt_rigid]") {
+    // Test pdbqt atom number
+    std::string valid_pdbqt_receptor_path = "../unittest/ParseTests/def.pdbqt";
+    rigid r;
+    REQUIRE_NOTHROW(parse_pdbqt_rigid(valid_pdbqt_receptor_path, r));
+    REQUIRE(r.atoms.size() == 1613);
+
+}