rename unit-test

CMakeLists.txt

@@ -159,29 +159,27 @@ endif()
 
 # test
 
-add_executable(unit-test ${PROJECT_SOURCE_DIR}/test/unit-test.cpp ${PROJECT_SOURCE_DIR}/src/dssp_wrapper.cpp)
+add_executable(dssp-unit-test ${PROJECT_SOURCE_DIR}/test/dssp-unit-test.cpp ${PROJECT_SOURCE_DIR}/src/dssp_wrapper.cpp)
 
 if(USE_RSRC)
-	mrc_target_resources(unit-test ${CIFPP_SHARE_DIR}/mmcif_pdbx.dic)
+	mrc_target_resources(dssp-unit-test ${CIFPP_SHARE_DIR}/mmcif_pdbx.dic)
 endif()
 
-target_include_directories(unit-test PRIVATE
+target_include_directories(dssp-unit-test PRIVATE
 	${CMAKE_CURRENT_SOURCE_DIR}/src
 	${CMAKE_CURRENT_SOURCE_DIR}/include
 )
 
-target_link_libraries(unit-test dssp_library cifpp::cifpp Boost::date_time)
+target_link_libraries(dssp-unit-test dssp_library cifpp::cifpp Boost::date_time)
 
 if(MSVC)
 	# Specify unwind semantics so that MSVC knowns how to handle exceptions
-	target_compile_options(unit-test PRIVATE /EHsc)
+	target_compile_options(dssp-unit-test PRIVATE /EHsc)
 endif()
 
 enable_testing()
 
-add_test(NAME unit-test
-	COMMAND $<TARGET_FILE:unit-test>
-	WORKING_DIRECTORY ${CMAKE_SOURCE_DIR}/test)
+add_test(NAME dssp-unit-test COMMAND $<TARGET_FILE:dssp-unit-test> -- ${PROJECT_SOURCE_DIR}/test)
 
 option(DSSP_BUILD_INSTALLER "Build an installer" OFF)
 if(DSSP_BUILD_INSTALLER)

test/dssp-test.cpp

-/*-
- * SPDX-License-Identifier: BSD-2-Clause
- *
- * Copyright (c) 2022 NKI/AVL, Netherlands Cancer Institute
- *
- * Redistribution and use in source and binary forms, with or without
- * modification, are permitted provided that the following conditions are met:
- *
- * 1. Redistributions of source code must retain the above copyright notice, this
- *    list of conditions and the following disclaimer
- * 2. Redistributions in binary form must reproduce the above copyright notice,
- *    this list of conditions and the following disclaimer in the documentation
- *    and/or other materials provided with the distribution.
- *
- * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
- * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
- * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
- * DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR
- * ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
- * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
- * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
- * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
- * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
- * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
- */
-
-#define BOOST_TEST_ALTERNATIVE_INIT_API
-#include <boost/test/included/unit_test.hpp>
-
-#include <charconv>
-#include <stdexcept>
-
-#include <cif++/cif.hpp>
-#include <cif++/dssp/DSSP.hpp>
-
-namespace tt = boost::test_tools;
-
-std::filesystem::path gTestDir = std::filesystem::current_path(); // filled in first test
-
-// --------------------------------------------------------------------
-
-cif::file operator""_cf(const char *text, size_t length)
-{
-	struct membuf : public std::streambuf
-	{
-		membuf(char *text, size_t length)
-		{
-			this->setg(text, text, text + length);
-		}
-	} buffer(const_cast<char *>(text), length);
-
-	std::istream is(&buffer);
-	return cif::file(is);
-}
-
-// --------------------------------------------------------------------
-
-bool init_unit_test()
-{
-	cif::VERBOSE = 1;
-
-	// not a test, just initialize test dir
-	if (boost::unit_test::framework::master_test_suite().argc == 2)
-		gTestDir = boost::unit_test::framework::master_test_suite().argv[1];
-
-	// do this now, avoids the need for installing
-	cif::add_file_resource("mmcif_pdbx.dic", gTestDir / ".." / "rsrc" / "mmcif_pdbx.dic");
-
-	// initialize CCD location
-	cif::add_file_resource("components.cif", gTestDir / ".." / "data" / "ccd-subset.cif");
-
-	return true;
-}
-
-// --------------------------------------------------------------------
-
-BOOST_AUTO_TEST_CASE(dssp_1)
-{
-	cif::file f(gTestDir / "1cbs.cif");
-
-	BOOST_ASSERT(f.is_valid());
-
-	std::ifstream t(gTestDir / "1cbs-dssp-test.tsv");
-
-	dssp::DSSP dssp(f.front(), 1, 3, true);
-
-	for (auto residue : dssp)
-	{
-		std::string line;
-		getline(t, line);
-
-		std::cout << line << std::endl;
-
-		auto f = cif::split(line, "\t");
-
-		BOOST_CHECK_EQUAL(f.size(), 3);
-		if (f.size() != 3)
-			continue;
-
-		int seqID;
-		std::from_chars(f[0].begin(), f[0].end(), seqID);
-		std::string asymID{ f[1] };
-		std::string secstr{ f[2] };
-		if (secstr == "_")
-			secstr = " ";
-
-		BOOST_CHECK_EQUAL(residue.asym_id(), asymID);
-		BOOST_CHECK_EQUAL(residue.seq_id(), seqID);
-		BOOST_CHECK_EQUAL((char)residue.type(), secstr.front());
-	}
-}
\ No newline at end of file

test/unit-test.cpp → test/dssp-unit-test.cpp

@@ -24,17 +24,58 @@
  * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
  */
 
-#define BOOST_TEST_MODULE DSSP_Test
-#include <boost/test/included/unit_test.hpp>
-#include <boost/algorithm/string.hpp>
-
 #include <stdexcept>
 
-#include "DSSP.hpp"
+#define BOOST_TEST_ALTERNATIVE_INIT_API
+#include <boost/algorithm/string.hpp>
+#include <boost/test/included/unit_test.hpp>
 
+#include "DSSP.hpp"
 #include "dssp_wrapper.hpp"
 
 namespace ba = boost::algorithm;
+namespace fs = std::filesystem;
+
+// --------------------------------------------------------------------
+
+cif::file operator""_cf(const char *text, size_t length)
+{
+	struct membuf : public std::streambuf
+	{
+		membuf(char *text, size_t length)
+		{
+			this->setg(text, text, text + length);
+		}
+	} buffer(const_cast<char *>(text), length);
+
+	std::istream is(&buffer);
+	return cif::file(is);
+}
+
+// --------------------------------------------------------------------
+
+fs::path gTestDir = fs::current_path();
+
+bool init_unit_test()
+{
+	cif::VERBOSE = 1;
+
+	// not a test, just initialize test dir
+	if (boost::unit_test::framework::master_test_suite().argc == 2)
+	{
+		gTestDir = boost::unit_test::framework::master_test_suite().argv[1];
+
+		cif::add_data_directory(gTestDir / ".." / "rsrc");
+	}
+
+	// // do this now, avoids the need for installing
+	// cif::add_file_resource("mmcif_pdbx.dic", gTestDir / ".." / "rsrc" / "mmcif_pdbx.dic");
+
+	// // initialize CCD location
+	// cif::add_file_resource("components.cif", gTestDir / ".." / "data" / "ccd-subset.cif");
+
+	return true;
+}
 
 // --------------------------------------------------------------------
 
@@ -42,7 +83,7 @@ BOOST_AUTO_TEST_CASE(ut_dssp)
 {
 	using namespace std::literals;
 
-	cif::file f("1cbs.cif.gz");
+	cif::file f(gTestDir / "1cbs.cif.gz");
 	BOOST_ASSERT(f.is_valid());
 
 	dssp::DSSP dssp(f.front(), 1, 3, true);
@@ -51,18 +92,18 @@ BOOST_AUTO_TEST_CASE(ut_dssp)
 
 	writeDSSP(dssp, test);
 
-	std::ifstream reference("1cbs.dssp");
+	std::ifstream reference(gTestDir / "1cbs.dssp");
 
 	BOOST_CHECK(reference.is_open());
 
 	std::string line_t, line_r;
 	BOOST_CHECK(std::getline(test, line_t) and std::getline(reference, line_r));
 
-	const char* kHeaderLineStart = "==== Secondary Structure Definition by the program DSSP, NKI version 4.0                           ====";
+	const char *kHeaderLineStart = "==== Secondary Structure Definition by the program DSSP, NKI version 4.0                           ====";
 	BOOST_CHECK(line_t.compare(0, std::strlen(kHeaderLineStart), kHeaderLineStart) == 0);
 	BOOST_CHECK(line_r.compare(0, std::strlen(kHeaderLineStart), kHeaderLineStart) == 0);
 
-	for (int line_nr = 2; ; ++line_nr)
+	for (int line_nr = 2;; ++line_nr)
 	{
 		bool done_t = not std::getline(test, line_t);
 		bool done_r = not std::getline(reference, line_r);
@@ -88,7 +129,7 @@ BOOST_AUTO_TEST_CASE(ut_mmcif_2)
 	using namespace std::literals;
 	using namespace cif::literals;
 
-	cif::file f("1cbs.cif.gz");
+	cif::file f(gTestDir / "1cbs.cif.gz");
 	BOOST_ASSERT(f.is_valid());
 
 	dssp::DSSP dssp(f.front(), 1, 3, true);
@@ -97,7 +138,7 @@ BOOST_AUTO_TEST_CASE(ut_mmcif_2)
 
 	annotateDSSP(f.front(), dssp, true, test);
 
-	cif::file rf("1cbs-dssp.cif");
+	cif::file rf(gTestDir / "1cbs-dssp.cif");
 
 	// structure.datablock()["software"].erase("name"_key == "dssp");
 	// rs.datablock()["software"].erase("name"_key == "dssp");
@@ -107,3 +148,41 @@ BOOST_AUTO_TEST_CASE(ut_mmcif_2)
 
 	// BOOST_CHECK(f.front() == rf.front());
 }
+
+// --------------------------------------------------------------------
+
+BOOST_AUTO_TEST_CASE(dssp_1)
+{
+	cif::file f(gTestDir / "1cbs.cif");
+
+	BOOST_ASSERT(f.is_valid());
+
+	std::ifstream t(gTestDir / "1cbs-dssp-test.tsv");
+
+	dssp::DSSP dssp(f.front(), 1, 3, true);
+
+	for (auto residue : dssp)
+	{
+		std::string line;
+		getline(t, line);
+
+		std::cout << line << std::endl;
+
+		auto f = cif::split(line, "\t");
+
+		BOOST_CHECK_EQUAL(f.size(), 3);
+		if (f.size() != 3)
+			continue;
+
+		int seqID;
+		std::from_chars(f[0].begin(), f[0].end(), seqID);
+		std::string asymID{ f[1] };
+		std::string secstr{ f[2] };
+		if (secstr == "_")
+			secstr = " ";
+
+		BOOST_CHECK_EQUAL(residue.asym_id(), asymID);
+		BOOST_CHECK_EQUAL(residue.seq_id(), seqID);
+		BOOST_CHECK_EQUAL((char)residue.type(), secstr.front());
+	}
+}
\ No newline at end of file