From 1509b4bdcf843aee8000e57cc1d89f48c9bd348e Mon Sep 17 00:00:00 2001 From: bertrandboudaud Date: Wed, 10 Nov 2021 16:56:37 +0100 Subject: [PATCH 01/12] Enabled OpenMP for MacOS --- .circleci/config.yml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/.circleci/config.yml b/.circleci/config.yml index 66f563137..3e29af77a 100644 --- a/.circleci/config.yml +++ b/.circleci/config.yml @@ -109,6 +109,7 @@ jobs: brew remove yarn node brew install cmake qt5 sdl2 brew install cppcheck gnuplot + brew install libomp pip3 install -r tools/smartpeak/requirements.txt - run: name: "Pull latest (only release)" @@ -131,7 +132,7 @@ jobs: tar -xzf contrib_build.tar.gz sed -i '' 's/std::auto_ptr/std::unique_ptr/g' include/seqan/basic/test_system.h cd ~/OpenMS && mkdir openms_debug_build && cd openms_debug_build && - cmake -DCMAKE_CXX_COMPILER=clang++ -DCMAKE_C_COMPILER=clang -DCMAKE_CXX_STANDARD=14 -DCMAKE_CXX_EXTENSIONS=OFF -DCMAKE_PREFIX_PATH="$(brew --prefix qt5)" -DOPENMS_CONTRIB_LIBS=~/OpenMS/contrib_build/ -DHAS_XSERVER=OFF -DWITH_GUI=OFF -DENABLE_TUTORIALS=OFF -DENABLE_DOCS=OFF -DGIT_TRACKING=OFF -DENABLE_UPDATE_CHECK=OFF -DCMAKE_BUILD_TYPE=Release -DPYOPENMS=OFF -DOPENMS_COVERAGE=OFF .. + cmake -DCMAKE_CXX_COMPILER=clang++ -DCMAKE_C_COMPILER=clang -DCMAKE_CXX_STANDARD=14 -DCMAKE_CXX_EXTENSIONS=OFF -DCMAKE_PREFIX_PATH="$(brew --prefix qt5)" -DOPENMS_CONTRIB_LIBS=~/OpenMS/contrib_build/ -DHAS_XSERVER=OFF -DWITH_GUI=OFF -DENABLE_TUTORIALS=OFF -DENABLE_DOCS=OFF -DGIT_TRACKING=OFF -DENABLE_UPDATE_CHECK=OFF -DCMAKE_BUILD_TYPE=Release -DPYOPENMS=OFF -DOPENMS_COVERAGE=OFF -DOpenMP_CXX_FLAGS="-Xpreprocessor -fopenmp -I/usr/local/opt/libomp/include" -DOpenMP_CXX_LIB_NAMES="omp" -DOpenMP_omp_LIBRARY=/usr/local/opt/libomp/lib/libomp.dylib .. make -j4 OpenMS - run: name: Building SmartPeak (Including SuperBuild) From 2deaefb6e25f342a91728cd9081d6b47333e85f9 Mon Sep 17 00:00:00 2001 From: bertrandboudaud Date: Wed, 10 Nov 2021 17:58:21 +0100 Subject: [PATCH 02/12] Added test --- .circleci/config.yml | 3 +- .../class_tests/smartpeak/CMakeLists.txt | 1 + .../include/SmartPeak/test_config.h.in | 2 ++ .../smartpeak/source/Task_test.cpp | 29 +++++++++++++++++++ 4 files changed, 34 insertions(+), 1 deletion(-) diff --git a/.circleci/config.yml b/.circleci/config.yml index 3e29af77a..b0cd7f939 100644 --- a/.circleci/config.yml +++ b/.circleci/config.yml @@ -132,7 +132,8 @@ jobs: tar -xzf contrib_build.tar.gz sed -i '' 's/std::auto_ptr/std::unique_ptr/g' include/seqan/basic/test_system.h cd ~/OpenMS && mkdir openms_debug_build && cd openms_debug_build && - cmake -DCMAKE_CXX_COMPILER=clang++ -DCMAKE_C_COMPILER=clang -DCMAKE_CXX_STANDARD=14 -DCMAKE_CXX_EXTENSIONS=OFF -DCMAKE_PREFIX_PATH="$(brew --prefix qt5)" -DOPENMS_CONTRIB_LIBS=~/OpenMS/contrib_build/ -DHAS_XSERVER=OFF -DWITH_GUI=OFF -DENABLE_TUTORIALS=OFF -DENABLE_DOCS=OFF -DGIT_TRACKING=OFF -DENABLE_UPDATE_CHECK=OFF -DCMAKE_BUILD_TYPE=Release -DPYOPENMS=OFF -DOPENMS_COVERAGE=OFF -DOpenMP_CXX_FLAGS="-Xpreprocessor -fopenmp -I/usr/local/opt/libomp/include" -DOpenMP_CXX_LIB_NAMES="omp" -DOpenMP_omp_LIBRARY=/usr/local/opt/libomp/lib/libomp.dylib .. +# cmake -DCMAKE_CXX_COMPILER=clang++ -DCMAKE_C_COMPILER=clang -DCMAKE_CXX_STANDARD=14 -DCMAKE_CXX_EXTENSIONS=OFF -DCMAKE_PREFIX_PATH="$(brew --prefix qt5)" -DOPENMS_CONTRIB_LIBS=~/OpenMS/contrib_build/ -DHAS_XSERVER=OFF -DWITH_GUI=OFF -DENABLE_TUTORIALS=OFF -DENABLE_DOCS=OFF -DGIT_TRACKING=OFF -DENABLE_UPDATE_CHECK=OFF -DCMAKE_BUILD_TYPE=Release -DPYOPENMS=OFF -DOPENMS_COVERAGE=OFF -DOpenMP_CXX_FLAGS="-Xpreprocessor -fopenmp -I/usr/local/opt/libomp/include" -DOpenMP_CXX_LIB_NAMES="omp" -DOpenMP_omp_LIBRARY=/usr/local/opt/libomp/lib/libomp.dylib .. + cmake -DCMAKE_CXX_COMPILER=clang++ -DCMAKE_C_COMPILER=clang -DCMAKE_CXX_STANDARD=14 -DCMAKE_CXX_EXTENSIONS=OFF -DCMAKE_PREFIX_PATH="$(brew --prefix qt5)" -DOPENMS_CONTRIB_LIBS=~/OpenMS/contrib_build/ -DHAS_XSERVER=OFF -DWITH_GUI=OFF -DENABLE_TUTORIALS=OFF -DENABLE_DOCS=OFF -DGIT_TRACKING=OFF -DENABLE_UPDATE_CHECK=OFF -DCMAKE_BUILD_TYPE=Release -DPYOPENMS=OFF -DOPENMS_COVERAGE=OFF .. make -j4 OpenMS - run: name: Building SmartPeak (Including SuperBuild) diff --git a/src/tests/class_tests/smartpeak/CMakeLists.txt b/src/tests/class_tests/smartpeak/CMakeLists.txt index aa2452225..b62cd8f9c 100644 --- a/src/tests/class_tests/smartpeak/CMakeLists.txt +++ b/src/tests/class_tests/smartpeak/CMakeLists.txt @@ -6,6 +6,7 @@ project("SmartPeak_class_tests_smartpeak") #------------------------------------------------------------------------------ # Configure test file to get the TEST_DATA_PATH into the tests set(CF_SMARTPEAK_TEST_DATA_PATH "${PROJECT_SOURCE_DIR}/data/") +set(CF_SMARTPEAK_EXAMPLES_DATA_PATH "${PROJECT_SOURCE_DIR}/../../../examples/data/") set (CONFIGURED_TEST_CONFIG_H "${PROJECT_BINARY_DIR}/include/SmartPeak/test_config.h") configure_file(${PROJECT_SOURCE_DIR}/include/SmartPeak/test_config.h.in ${CONFIGURED_TEST_CONFIG_H}) diff --git a/src/tests/class_tests/smartpeak/include/SmartPeak/test_config.h.in b/src/tests/class_tests/smartpeak/include/SmartPeak/test_config.h.in index 33dd627b2..3cedacb1b 100644 --- a/src/tests/class_tests/smartpeak/include/SmartPeak/test_config.h.in +++ b/src/tests/class_tests/smartpeak/include/SmartPeak/test_config.h.in @@ -5,5 +5,7 @@ // Macro to construct a c string containing the complete path to the test data #define SMARTPEAK_GET_TEST_DATA_PATH(filename) (std::string("@CF_SMARTPEAK_TEST_DATA_PATH@") + filename).c_str() #define SMARTPEAK_GET_TEST_DATA_PATH_MESSAGE(prefix,filename,suffix) (prefix + std::string("@CF_SMARTPEAK_TEST_DATA_PATH@") + filename + suffix).c_str() +#define SMARTPEAK_GET_EXAMPLES_DATA_PATH(filename) (std::string("@CF_SMARTPEAK_EXAMPLES_DATA_PATH@") + filename).c_str() +#define SMARTPEAK_GET_EXAMPLES_DATA_PATH_MESSAGE(prefix,filename,suffix) (prefix + std::string("@CF_SMARTPEAK_EXAMPLES_DATA_PATH@") + filename + suffix).c_str() #endif // SMARTPEAK_TEST_CONFIG_H diff --git a/src/tests/class_tests/smartpeak/source/Task_test.cpp b/src/tests/class_tests/smartpeak/source/Task_test.cpp index b68240f7f..c3bac0548 100644 --- a/src/tests/class_tests/smartpeak/source/Task_test.cpp +++ b/src/tests/class_tests/smartpeak/source/Task_test.cpp @@ -246,4 +246,33 @@ TEST(Task, Task_options_change_output_dirs) auto er = cli::ExportReport{}; EXPECT_TRUE(er(am)); EXPECT_TRUE(std::filesystem::exists(report_output_dir / "FeatureDB.csv")); +} + +TEST(Task, Task_run_LCMS_MRM_QCs_example_10_threads) +{ + namespace cli = SmartPeak::cli; + std::filesystem::path seq_path = SMARTPEAK_GET_EXAMPLES_DATA_PATH("LCMS_MRM_QCs"); + std::string seq = std::string{ seq_path.lexically_normal().generic_string() }; + std::vector args = std::vector{ + "Task_test", + "--load-session", seq, + "--verbose", + "--allow-inconsistent", + "--log-dir", ".", + "--disable-colors", + "-no-pg", + "--parameter", "SequenceProcessor:n_thread=10" + }; + auto pa = cli::Parser{ args }; + auto as = cli::ApplicationSettings{ pa }; + auto am = cli::ApplicationManager{ as }; + am + .add(std::make_shared()) + .add(std::make_shared()) + .add(std::make_shared()) + .add(std::make_shared()) + .add(std::make_shared()) + .add(std::make_shared()) + .add(std::make_shared()); + am.run(); } \ No newline at end of file From 2ff436f21f9b9b5a268579d30d31b490fa3c97c8 Mon Sep 17 00:00:00 2001 From: bertrandboudaud Date: Wed, 10 Nov 2021 18:00:21 +0100 Subject: [PATCH 03/12] Fixed yaml --- .circleci/config.yml | 1 - 1 file changed, 1 deletion(-) diff --git a/.circleci/config.yml b/.circleci/config.yml index b0cd7f939..4f071b0d5 100644 --- a/.circleci/config.yml +++ b/.circleci/config.yml @@ -132,7 +132,6 @@ jobs: tar -xzf contrib_build.tar.gz sed -i '' 's/std::auto_ptr/std::unique_ptr/g' include/seqan/basic/test_system.h cd ~/OpenMS && mkdir openms_debug_build && cd openms_debug_build && -# cmake -DCMAKE_CXX_COMPILER=clang++ -DCMAKE_C_COMPILER=clang -DCMAKE_CXX_STANDARD=14 -DCMAKE_CXX_EXTENSIONS=OFF -DCMAKE_PREFIX_PATH="$(brew --prefix qt5)" -DOPENMS_CONTRIB_LIBS=~/OpenMS/contrib_build/ -DHAS_XSERVER=OFF -DWITH_GUI=OFF -DENABLE_TUTORIALS=OFF -DENABLE_DOCS=OFF -DGIT_TRACKING=OFF -DENABLE_UPDATE_CHECK=OFF -DCMAKE_BUILD_TYPE=Release -DPYOPENMS=OFF -DOPENMS_COVERAGE=OFF -DOpenMP_CXX_FLAGS="-Xpreprocessor -fopenmp -I/usr/local/opt/libomp/include" -DOpenMP_CXX_LIB_NAMES="omp" -DOpenMP_omp_LIBRARY=/usr/local/opt/libomp/lib/libomp.dylib .. cmake -DCMAKE_CXX_COMPILER=clang++ -DCMAKE_C_COMPILER=clang -DCMAKE_CXX_STANDARD=14 -DCMAKE_CXX_EXTENSIONS=OFF -DCMAKE_PREFIX_PATH="$(brew --prefix qt5)" -DOPENMS_CONTRIB_LIBS=~/OpenMS/contrib_build/ -DHAS_XSERVER=OFF -DWITH_GUI=OFF -DENABLE_TUTORIALS=OFF -DENABLE_DOCS=OFF -DGIT_TRACKING=OFF -DENABLE_UPDATE_CHECK=OFF -DCMAKE_BUILD_TYPE=Release -DPYOPENMS=OFF -DOPENMS_COVERAGE=OFF .. make -j4 OpenMS - run: From 74ebcdcbb9fbbda28d2fd3dad37f93fc16fce510 Mon Sep 17 00:00:00 2001 From: bertrandboudaud Date: Thu, 11 Nov 2021 12:16:33 +0100 Subject: [PATCH 04/12] Increased to 20 threads --- src/tests/class_tests/smartpeak/source/Task_test.cpp | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/tests/class_tests/smartpeak/source/Task_test.cpp b/src/tests/class_tests/smartpeak/source/Task_test.cpp index c3bac0548..4f7c42cae 100644 --- a/src/tests/class_tests/smartpeak/source/Task_test.cpp +++ b/src/tests/class_tests/smartpeak/source/Task_test.cpp @@ -248,7 +248,7 @@ TEST(Task, Task_options_change_output_dirs) EXPECT_TRUE(std::filesystem::exists(report_output_dir / "FeatureDB.csv")); } -TEST(Task, Task_run_LCMS_MRM_QCs_example_10_threads) +TEST(Task, Task_run_LCMS_MRM_QCs_example_20_threads) { namespace cli = SmartPeak::cli; std::filesystem::path seq_path = SMARTPEAK_GET_EXAMPLES_DATA_PATH("LCMS_MRM_QCs"); @@ -261,7 +261,7 @@ TEST(Task, Task_run_LCMS_MRM_QCs_example_10_threads) "--log-dir", ".", "--disable-colors", "-no-pg", - "--parameter", "SequenceProcessor:n_thread=10" + "--parameter", "SequenceProcessor:n_thread=20" }; auto pa = cli::Parser{ args }; auto as = cli::ApplicationSettings{ pa }; From 6a82bc9df4d6e05ab073321eb3140824cdd508f2 Mon Sep 17 00:00:00 2001 From: bertrandboudaud Date: Thu, 11 Nov 2021 14:36:22 +0100 Subject: [PATCH 05/12] disabling openmp --- .circleci/config.yml | 1 - 1 file changed, 1 deletion(-) diff --git a/.circleci/config.yml b/.circleci/config.yml index 4f071b0d5..66f563137 100644 --- a/.circleci/config.yml +++ b/.circleci/config.yml @@ -109,7 +109,6 @@ jobs: brew remove yarn node brew install cmake qt5 sdl2 brew install cppcheck gnuplot - brew install libomp pip3 install -r tools/smartpeak/requirements.txt - run: name: "Pull latest (only release)" From fbdfcabe6cb8311aed10d67958bfcd2d13c927c2 Mon Sep 17 00:00:00 2001 From: berbou Date: Fri, 12 Nov 2021 09:04:25 +0100 Subject: [PATCH 06/12] Enable OpenMP forOopenMS build --- .circleci/config.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.circleci/config.yml b/.circleci/config.yml index 66f563137..4f071b0d5 100644 --- a/.circleci/config.yml +++ b/.circleci/config.yml @@ -109,6 +109,7 @@ jobs: brew remove yarn node brew install cmake qt5 sdl2 brew install cppcheck gnuplot + brew install libomp pip3 install -r tools/smartpeak/requirements.txt - run: name: "Pull latest (only release)" From 247ddf530b65351f19e89d75af595af955158236 Mon Sep 17 00:00:00 2001 From: berbou Date: Mon, 15 Nov 2021 08:00:48 +0100 Subject: [PATCH 07/12] run examples for mac os --- .circleci/config.yml | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/.circleci/config.yml b/.circleci/config.yml index 4f071b0d5..f3cfc795e 100644 --- a/.circleci/config.yml +++ b/.circleci/config.yml @@ -155,6 +155,10 @@ jobs: cd ~/SmartPeak export PYTHONPATH="${PWD}/tools" python3 -m unittest discover -s ./tools/smartpeak + - run: + name: Running SmartPeak Examples + command: | + ~/SmartPeak/.circleci/run_examples.sh ~/smartpeak_release_build/bin - run: name: Packing SmartPeak command: | From 8157323eba71a1ae509bb28db21777ab87458845 Mon Sep 17 00:00:00 2001 From: berbou Date: Mon, 15 Nov 2021 09:12:00 +0100 Subject: [PATCH 08/12] fixed path to run examples on MacOS --- .circleci/config.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.circleci/config.yml b/.circleci/config.yml index f3cfc795e..30b20652d 100644 --- a/.circleci/config.yml +++ b/.circleci/config.yml @@ -158,7 +158,7 @@ jobs: - run: name: Running SmartPeak Examples command: | - ~/SmartPeak/.circleci/run_examples.sh ~/smartpeak_release_build/bin + ~/SmartPeak/.circleci/run_examples.sh ~/SmartPeak/smartpeak_release_build/bin - run: name: Packing SmartPeak command: | From fbcead5a0d060d7d3e2cf43be56f96015a02b485 Mon Sep 17 00:00:00 2001 From: berbou Date: Mon, 15 Nov 2021 09:57:24 +0100 Subject: [PATCH 09/12] disabled openmp --- .circleci/config.yml | 1 - 1 file changed, 1 deletion(-) diff --git a/.circleci/config.yml b/.circleci/config.yml index 30b20652d..b09ea6c10 100644 --- a/.circleci/config.yml +++ b/.circleci/config.yml @@ -109,7 +109,6 @@ jobs: brew remove yarn node brew install cmake qt5 sdl2 brew install cppcheck gnuplot - brew install libomp pip3 install -r tools/smartpeak/requirements.txt - run: name: "Pull latest (only release)" From 6bab478792dbebaa2cf3f4b165dd19ea9ece5752 Mon Sep 17 00:00:00 2001 From: bertrandboudaud Date: Mon, 15 Nov 2021 11:12:49 +0100 Subject: [PATCH 10/12] Enabled OpenMP, CI launches examples on MacOS builds --- .circleci/config.yml | 2 +- .../class_tests/smartpeak/CMakeLists.txt | 1 - .../include/SmartPeak/test_config.h.in | 2 -- .../smartpeak/source/Task_test.cpp | 29 ------------------- 4 files changed, 1 insertion(+), 33 deletions(-) diff --git a/.circleci/config.yml b/.circleci/config.yml index b09ea6c10..6cd36773d 100644 --- a/.circleci/config.yml +++ b/.circleci/config.yml @@ -109,7 +109,7 @@ jobs: brew remove yarn node brew install cmake qt5 sdl2 brew install cppcheck gnuplot - pip3 install -r tools/smartpeak/requirements.txt + brew install libomp pip3 install -r tools/smartpeak/requirements.txt - run: name: "Pull latest (only release)" command: | diff --git a/src/tests/class_tests/smartpeak/CMakeLists.txt b/src/tests/class_tests/smartpeak/CMakeLists.txt index b62cd8f9c..aa2452225 100644 --- a/src/tests/class_tests/smartpeak/CMakeLists.txt +++ b/src/tests/class_tests/smartpeak/CMakeLists.txt @@ -6,7 +6,6 @@ project("SmartPeak_class_tests_smartpeak") #------------------------------------------------------------------------------ # Configure test file to get the TEST_DATA_PATH into the tests set(CF_SMARTPEAK_TEST_DATA_PATH "${PROJECT_SOURCE_DIR}/data/") -set(CF_SMARTPEAK_EXAMPLES_DATA_PATH "${PROJECT_SOURCE_DIR}/../../../examples/data/") set (CONFIGURED_TEST_CONFIG_H "${PROJECT_BINARY_DIR}/include/SmartPeak/test_config.h") configure_file(${PROJECT_SOURCE_DIR}/include/SmartPeak/test_config.h.in ${CONFIGURED_TEST_CONFIG_H}) diff --git a/src/tests/class_tests/smartpeak/include/SmartPeak/test_config.h.in b/src/tests/class_tests/smartpeak/include/SmartPeak/test_config.h.in index 3cedacb1b..33dd627b2 100644 --- a/src/tests/class_tests/smartpeak/include/SmartPeak/test_config.h.in +++ b/src/tests/class_tests/smartpeak/include/SmartPeak/test_config.h.in @@ -5,7 +5,5 @@ // Macro to construct a c string containing the complete path to the test data #define SMARTPEAK_GET_TEST_DATA_PATH(filename) (std::string("@CF_SMARTPEAK_TEST_DATA_PATH@") + filename).c_str() #define SMARTPEAK_GET_TEST_DATA_PATH_MESSAGE(prefix,filename,suffix) (prefix + std::string("@CF_SMARTPEAK_TEST_DATA_PATH@") + filename + suffix).c_str() -#define SMARTPEAK_GET_EXAMPLES_DATA_PATH(filename) (std::string("@CF_SMARTPEAK_EXAMPLES_DATA_PATH@") + filename).c_str() -#define SMARTPEAK_GET_EXAMPLES_DATA_PATH_MESSAGE(prefix,filename,suffix) (prefix + std::string("@CF_SMARTPEAK_EXAMPLES_DATA_PATH@") + filename + suffix).c_str() #endif // SMARTPEAK_TEST_CONFIG_H diff --git a/src/tests/class_tests/smartpeak/source/Task_test.cpp b/src/tests/class_tests/smartpeak/source/Task_test.cpp index 4f7c42cae..b68240f7f 100644 --- a/src/tests/class_tests/smartpeak/source/Task_test.cpp +++ b/src/tests/class_tests/smartpeak/source/Task_test.cpp @@ -246,33 +246,4 @@ TEST(Task, Task_options_change_output_dirs) auto er = cli::ExportReport{}; EXPECT_TRUE(er(am)); EXPECT_TRUE(std::filesystem::exists(report_output_dir / "FeatureDB.csv")); -} - -TEST(Task, Task_run_LCMS_MRM_QCs_example_20_threads) -{ - namespace cli = SmartPeak::cli; - std::filesystem::path seq_path = SMARTPEAK_GET_EXAMPLES_DATA_PATH("LCMS_MRM_QCs"); - std::string seq = std::string{ seq_path.lexically_normal().generic_string() }; - std::vector args = std::vector{ - "Task_test", - "--load-session", seq, - "--verbose", - "--allow-inconsistent", - "--log-dir", ".", - "--disable-colors", - "-no-pg", - "--parameter", "SequenceProcessor:n_thread=20" - }; - auto pa = cli::Parser{ args }; - auto as = cli::ApplicationSettings{ pa }; - auto am = cli::ApplicationManager{ as }; - am - .add(std::make_shared()) - .add(std::make_shared()) - .add(std::make_shared()) - .add(std::make_shared()) - .add(std::make_shared()) - .add(std::make_shared()) - .add(std::make_shared()); - am.run(); } \ No newline at end of file From a689d478b5ec3d39f8547282b76aa51a402025d8 Mon Sep 17 00:00:00 2001 From: bertrandboudaud Date: Mon, 15 Nov 2021 11:17:37 +0100 Subject: [PATCH 11/12] Removed patch for OpenMP --- .circleci/config.yml | 1 - 1 file changed, 1 deletion(-) diff --git a/.circleci/config.yml b/.circleci/config.yml index 6cd36773d..32525edc3 100644 --- a/.circleci/config.yml +++ b/.circleci/config.yml @@ -125,7 +125,6 @@ jobs: cd ~ && git clone --branch develop --depth 1 https://github.com/OpenMS/OpenMS.git && cd OpenMS - sed -i '' 's/#pragma omp parallel for//g' src/openms/source/FORMAT/HANDLERS/MzMLHandler.cpp mkdir contrib_build && cd contrib_build curl -C - -O https://abibuilder.informatik.uni-tuebingen.de/archive/openms/contrib/macOS/10.15.4/x64/appleclang-11.0.0/contrib_build.tar.gz tar -xzf contrib_build.tar.gz From 082dd18007b9c49ea16082d5c718fde0e1dfadf1 Mon Sep 17 00:00:00 2001 From: bertrandboudaud Date: Mon, 15 Nov 2021 12:22:22 +0100 Subject: [PATCH 12/12] Fixed pip install command --- .circleci/config.yml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/.circleci/config.yml b/.circleci/config.yml index 32525edc3..88b163e8b 100644 --- a/.circleci/config.yml +++ b/.circleci/config.yml @@ -109,7 +109,8 @@ jobs: brew remove yarn node brew install cmake qt5 sdl2 brew install cppcheck gnuplot - brew install libomp pip3 install -r tools/smartpeak/requirements.txt + brew install libomp + pip3 install -r tools/smartpeak/requirements.txt - run: name: "Pull latest (only release)" command: |