Update config.yml

.circleci/config.yml

@@ -1,8 +1,11 @@
-version: 2.0
+version: 2.1
+orbs:
+  coveralls: coveralls/coveralls@2.2.5
+
 jobs:
-  "14.04":
+  v1804:
     docker:
-      - image: circleci/buildpack-deps:14.04
+      - image: cimg/base:2022.08-18.04
     working_directory: /home/circleci/DEploid
     steps:
       - checkout
@@ -16,35 +19,35 @@ jobs:
       - run:
           name: Install dependencies and set path
           command: |
-           sudo apt-get update
-           curl -fsSL https://git.io/vHGMF | bash
-           sudo apt-get install libcppunit-dev
-           sudo apt-get install valgrind
+            sudo apt-get update
+            curl -fsSL https://git.io/vHGMF | bash
+            sudo apt-get install libcppunit-dev
+            sudo apt-get install valgrind
       - run:
-           name: Getting ready
-           command: |
+          name: Getting ready
+          command: |
             g++ --version
             ./bootstrap
       - run:
-           name: Compile
-           command: |
+          name: Compile
+          command: |
             make
             sudo make install
             make check
       - run:
-           name: Run tests
-           command: |
+          name: Run tests
+          command: |
             ./tests/test_binary.sh
             ./tests/testPOS.sh
             ./tests/test_binaryVcfVsTxt.sh
             ./tests/test-against-previous-version.sh
             ./tests/test_binaryReproducible.sh
         #- valgrind  --leak-check=full -v --show-leak-kinds=all ./unit_tests
-    #- coveralls --exclude lib --exclude tests --exclude src/random --exclude src/codeCogs/ --exclude src/export/ --gcov-options '\-lp'
+        #- coveralls --exclude lib --exclude tests --exclude src/random --exclude src/codeCogs/ --exclude src/export/ --gcov-options '\-lp'
 
-  "16.04":
+  v2004:
     docker:
-      - image: circleci/buildpack-deps:16.04
+      - image: cimg/base:2022.08 # stable-20.04
     working_directory: /home/circleci/DEploid
     steps:
       - checkout
@@ -58,33 +61,33 @@ jobs:
       - run:
           name: Install dependencies and set path
           command: |
-           sudo apt-get update
-           curl -fsSL https://git.io/vHGMF | bash
-           sudo apt-get install libcppunit-dev
-           sudo apt-get install valgrind
+            sudo apt-get update
+            curl -fsSL https://git.io/vHGMF | bash
+            sudo apt-get install libcppunit-dev
+            sudo apt-get install valgrind
       - run:
-           name: Getting ready
-           command: |
+          name: Getting ready
+          command: |
             g++ --version
             ./bootstrap
       - run:
-           name: Compile
-           command: |
+          name: Compile
+          command: |
             make
             sudo make install
             make check
       - run:
-           name: Run tests
-           command: |
+          name: Run tests
+          command: |
             ./tests/test_binary.sh
             ./tests/testPOS.sh
             ./tests/test_binaryVcfVsTxt.sh
             ./tests/test-against-previous-version.sh
             ./tests/test_binaryReproducible.sh
 
-  "20.04":
+  v2204:
     docker:
-      - image: circleci/buildpack-deps:20.04
+      - image: cimg/base:2024.12
     working_directory: /home/circleci/DEploid
     steps:
       - checkout
@@ -98,35 +101,38 @@ jobs:
       - run:
           name: Install dependencies and set path
           command: |
-           sudo apt-get update
-           curl -fsSL https://git.io/vHGMF | bash
-           sudo apt-get install libcppunit-dev
-           sudo apt-get install valgrind
+            sudo apt-get update
+            curl -fsSL https://git.io/vHGMF | bash
+            sudo apt-get install libcppunit-dev automake
+            sudo apt-get install valgrind lcov
       - run:
-           name: Getting ready
-           command: |
+          name: Getting ready
+          command: |
             g++ --version
             ./bootstrap
       - run:
-           name: Compile
-           command: |
+          name: Compile
+          command: |
             make
             sudo make install
             make check
       - run:
-           name: Run tests
-           command: |
-            ./tests/test_binary.sh
-            ./tests/testPOS.sh
-            ./tests/test_binaryVcfVsTxt.sh
-            ./tests/test-against-previous-version.sh
-            ./tests/test_binaryReproducible.sh
-
+          name: Run tests
+          command: |
+            # ./tests/test_binary.sh
+            # ./tests/testPOS.sh
+            # ./tests/test_binaryVcfVsTxt.sh
+            # ./tests/test-against-previous-version.sh
+            # ./tests/test_binaryReproducible.sh
+            # valgrind  --leak-check=full -v --show-leak-kinds=all ./unit_tests_1
+            # coveralls --exclude lib --exclude tests --exclude src/random --exclude src/codeCogs/ --exclude src/export/ --gcov-options '\-lp'
+            ./tests/test-coverage-coverall.sh
+      - coveralls/upload
 
 workflows:
-  version: 2
-  build:
+  myworkflow:
     jobs:
-      - "20.04"
-     # - "14.04"
-     # - "16.04"
+      - v2204
+      - v2004
+      # - v1804  # this is too old, bash_complete not available
+

Makefile.am

@@ -13,7 +13,7 @@ bin_PROGRAMS = dEploid dEploid_dbg
 man1_MANS = docs/_build/man/dEploid.1
 
 TESTS = unit_tests io_unit_tests
-check_PROGRAMS = unit_tests dEploid_dbg io_unit_tests current_unit_tests # dEploid_prof
+check_PROGRAMS = unit_tests_1 unit_tests_2 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
@@ -57,19 +57,37 @@ dEploid_LDADD = $(common_LDADD)
 dEploid_dbg_LDADD = $(common_LDADD)
 dEploid_prof_LDADD = $(common_LDADD)
 
-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 \
+unit_tests_1_SOURCES_0 = tests/unittest/test_ibd.cpp \
 					 tests/unittest/test_panel.cpp \
-					 tests/unittest/test_mcmc.cpp \
+					 tests/unittest/test_utilities.cpp
+
+unit_tests_2_SOURCES_0 = tests/unittest/test_mcmc.cpp \
+					 tests/unittest/test_updateSingleHap.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

bootstrap

@@ -23,5 +23,5 @@ echo " done."
 
 aclocal
 autoconf
-automake -a
+automake -a --force-missing --add-missing
 ./configure

tests/test-coverage-coverall.sh

@@ -4,8 +4,8 @@
 make -mj
 
 # Generate html report
-lcov --ignore-errors version --base-directory . --directory . --zerocounters -q
+lcov --base-directory . --directory . --zerocounters -q
 make check -mj
-lcov --ignore-errors version --base-directory . --directory . -c -o coverage/lcov.info
+lcov --base-directory . --directory . -c -o coverage/lcov.info
 # --rc lcov_branch_coverage=1 option will turn on branch check
-lcov --ignore-errors version --remove coverage/lcov.info "/usr*" "src/codeCogs/*" "src/vcf/*" "src/lasso/*" "src/export/*" "src/gzstream/*" "tests/unittest/*" -o coverage/lcov.info # remove output for external libraries
+lcov --remove coverage/lcov.info "/usr*" "src/codeCogs/*" "src/vcf/*" "src/lasso/*" "src/export/*" "src/gzstream/*" "tests/unittest/*" -o coverage/lcov.info # remove output for external libraries