Merge pull request #376 from DEploid-dev/375_updaet

resolve #375

.github/workflows/ccpp.yml

@@ -88,13 +88,18 @@ jobs:
         echo "::set-output name=timestamp::${stamp}"
 
     - name: ccache cache files
-      uses: actions/cache@v2
+      uses: actions/cache@v4
       with:
          path: ~/.ccache
          key: ${{ matrix.name }}-ccache-${{ steps.ccache_cache_timestamp.outputs.timestamp }}
          restore-keys: |
            ${{ matrix.name }}-ccache-
 
+    - name: Use Node.js 16.x
+      uses: actions/setup-node@v3
+      with:
+        node-version: 16.x
+
     - name: configure
       run: ./bootstrap
 
@@ -123,15 +128,17 @@ jobs:
     - name: docs
       run:  if [ $TRAVIS_OS_NAME == linux ]; then cd docs/doxygen; doxygen Doxyfile;  fi
 
-#    - name: run coverage
-#      if: matrix.name == 'ubuntu-gcc-10'
-#      run: |
-#         tests/test-coverage-coverall.sh
+    # - name: run coverage
+    #  if: matrix.name == 'ubuntu-gcc-10'
+    #  run: |
+    #     tests/test-coverage-coverall.sh
 
 #  See: https://github.com/marketplace/actions/coveralls-github-action
-    - name: Coveralls
-      if: matrix.name == 'ubuntu-gcc-10'
-      uses: coverallsapp/[email protected]
-      with:
-        github-token: ${{ secrets.GITHUB_TOKEN }}
-      #run: coveralls --exclude lib --exclude tests --exclude src/random --exclude src/codeCogs/ --exclude src/export/ --exclude src/gzstream/ --gcov-options '\-lp'
+    # - name: Coveralls
+    #  if: matrix.name == 'ubuntu-gcc-10'
+    #  uses: coverallsapp/[email protected]
+    #  with:
+    #    github-token: ${{ secrets.GITHUB_TOKEN }}
+      # run: coveralls --exclude lib --exclude tests --exclude src/random --exclude src/codeCogs/ --exclude src/export/ --exclude src/gzstream/ --gcov-options '\-lp'
+
+

Makefile.am

@@ -13,10 +13,10 @@ bin_PROGRAMS = dEploid dEploid_dbg
 man1_MANS = docs/_build/man/dEploid.1
 
 TESTS = unit_tests io_unit_tests
-check_PROGRAMS = unit_tests_1 unit_tests_2 unit_tests dEploid_dbg io_unit_tests current_unit_tests # dEploid_prof
+check_PROGRAMS = unit_tests dEploid_dbg io_unit_tests current_unit_tests # dEploid_prof
 PROG = DEPLOID
 
-common_flags = -std=c++17 -Isrc/ -Isrc/codeCogs/ -Isrc/vcf/src/ -DDEPLOIDVERSION=\"${DEPLOIDVERSION}\" -DLASSOVERSION=\"${LASSOVERSION}\" -DCOMPILEDATE=\"${COMPILEDATE}\" -Wall  -Wextra
+common_flags = -std=c++2a -Isrc/ -Isrc/codeCogs/ -Isrc/vcf/src/ -DDEPLOIDVERSION=\"${DEPLOIDVERSION}\" -DLASSOVERSION=\"${LASSOVERSION}\" -DCOMPILEDATE=\"${COMPILEDATE}\" -Wall  -Wextra
 
 common_LDADD = -lz
 
@@ -57,37 +57,19 @@ dEploid_LDADD = $(common_LDADD)
 dEploid_dbg_LDADD = $(common_LDADD)
 dEploid_prof_LDADD = $(common_LDADD)
 
-unit_tests_1_SOURCES_0 = tests/unittest/test_ibd.cpp \
-					 tests/unittest/test_panel.cpp \
-					 tests/unittest/test_utilities.cpp
-
-unit_tests_2_SOURCES_0 = tests/unittest/test_mcmc.cpp \
+unit_tests_SOURCES = $(common_src) \
+					 tests/unittest/test_runner.cpp \
+					 tests/unittest/test_ibd.cpp \
 					 tests/unittest/test_updateSingleHap.cpp \
+					 tests/unittest/test_utilities.cpp \
+					 tests/unittest/test_panel.cpp \
+					 tests/unittest/test_mcmc.cpp \
 					 tests/unittest/test_updatePairHap.cpp \
 					 tests/unittest/test_workflow.cpp
 
-unit_tests_1_SOURCES = $(common_src) \
-					 $(unit_tests_1_SOURCES_0) \
-					 tests/unittest/test_runner.cpp
-
-unit_tests_2_SOURCES = $(common_src) \
-					 $(unit_tests_2_SOURCES_0) \
-					 tests/unittest/test_runner.cpp
-
-unit_tests_SOURCES = $(common_src) \
-					 $(unit_tests_1_SOURCES_0) \
-                     $(unit_tests_2_SOURCES_0) \
-					 tests/unittest/test_runner.cpp
-
 unit_tests_CXXFLAGS = $(common_flags) -DNDEBUG -DUNITTEST -Wno-write-strings --coverage
 unit_tests_LDADD    = -lcppunit -ldl $(common_LDADD)
 
-unit_tests_1_CXXFLAGS = $(common_flags) -DNDEBUG -DUNITTEST -Wno-write-strings --coverage
-unit_tests_1_LDADD    = -lcppunit -ldl $(common_LDADD)
-
-unit_tests_2_CXXFLAGS = $(common_flags) -DNDEBUG -DUNITTEST -Wno-write-strings --coverage
-unit_tests_2_LDADD    = -lcppunit -ldl $(common_LDADD)
-
 io_unit_tests_SOURCES = $(common_src) \
 					 tests/unittest/test_runner.cpp \
 					 tests/unittest/test_dEploidIO.cpp
@@ -116,4 +98,3 @@ if ENABLE_BASH_COMPLETION
 bashcompletiondir = $(BASH_COMPLETION_DIR)
 dist_bashcompletion_DATA = src/dEploid_completion.sh
 endif
-

src/param.hpp

@@ -79,12 +79,12 @@ friend class DEploidIO;
     }
 
  public:
-    Parameter <T> () { }
-    Parameter <T> (T value) {
+    Parameter() { }
+    Parameter(T value) {
         this->init(value);
     }
     T getValue() const;
-    Parameter <T> (const Parameter <T> &currentParam) {
+    Parameter(const Parameter<T> &currentParam) {
         this->makeCopy(currentParam);
     }
     ~Parameter() { }