From c8809f2a712eb3642cdf86ad36779c4fce0e09fc Mon Sep 17 00:00:00 2001 From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com> Date: Mon, 10 Nov 2025 09:37:10 +0000 Subject: [PATCH 01/10] Initial plan From aea748b79bb738d270d6293009a0c27d1533062b Mon Sep 17 00:00:00 2001 From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com> Date: Mon, 10 Nov 2025 09:39:23 +0000 Subject: [PATCH 02/10] Add C++ hello world with Snakemake workflow and conda environment Co-authored-by: imallona <8280371+imallona@users.noreply.github.com> --- .gitignore | 3 +++ env/build.yaml | 6 ++++++ src/CMakeLists.txt | 8 ++++++++ src/hello.cpp | 6 ++++++ workflow/Snakefile | 31 +++++++++++++++++++++++++++++++ 5 files changed, 54 insertions(+) create mode 100644 .gitignore create mode 100644 env/build.yaml create mode 100644 src/CMakeLists.txt create mode 100644 src/hello.cpp create mode 100644 workflow/Snakefile diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000..8d26926 --- /dev/null +++ b/.gitignore @@ -0,0 +1,3 @@ +build/ +output/ +.snakemake/ diff --git a/env/build.yaml b/env/build.yaml new file mode 100644 index 0000000..ccf7379 --- /dev/null +++ b/env/build.yaml @@ -0,0 +1,6 @@ +channels: + - conda-forge + - bioconda +dependencies: + - cmake>=3.10 + - cxx-compiler diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt new file mode 100644 index 0000000..9e27484 --- /dev/null +++ b/src/CMakeLists.txt @@ -0,0 +1,8 @@ +cmake_minimum_required(VERSION 3.10) + +project(HelloWorld) + +set(CMAKE_CXX_STANDARD 11) +set(CMAKE_CXX_STANDARD_REQUIRED True) + +add_executable(hello hello.cpp) diff --git a/src/hello.cpp b/src/hello.cpp new file mode 100644 index 0000000..ff68290 --- /dev/null +++ b/src/hello.cpp @@ -0,0 +1,6 @@ +#include + +int main() { + std::cout << "Hello World!" << std::endl; + return 0; +} diff --git a/workflow/Snakefile b/workflow/Snakefile new file mode 100644 index 0000000..25a60cf --- /dev/null +++ b/workflow/Snakefile @@ -0,0 +1,31 @@ +rule all: + input: + "output/hello_output.txt" + +rule compile: + input: + cpp="src/hello.cpp", + cmake="src/CMakeLists.txt" + output: + "build/hello" + conda: + "../env/build.yaml" + shell: + """ + mkdir -p build + cd build + cmake ../src + cmake --build . + cp hello ../build/hello + """ + +rule run: + input: + "build/hello" + output: + "output/hello_output.txt" + shell: + """ + mkdir -p output + {input} > {output} + """ From 0cca1d9787ebb0593f7df0135d1033d0b6091e17 Mon Sep 17 00:00:00 2001 From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com> Date: Mon, 10 Nov 2025 09:41:01 +0000 Subject: [PATCH 03/10] Fix Snakefile build logic and update README with usage documentation Co-authored-by: imallona <8280371+imallona@users.noreply.github.com> --- README.md | 39 +++++++++++++++++++++++++++++++++++++++ workflow/Snakefile | 1 - 2 files changed, 39 insertions(+), 1 deletion(-) diff --git a/README.md b/README.md index 69082c7..66c6fa7 100644 --- a/README.md +++ b/README.md @@ -1,2 +1,41 @@ # drab RNA-seq count tables, revisited + +## C++ Hello World Example + +This repository includes a simple C++ "Hello World" example that demonstrates: +- Building C++ code with CMake +- Managing dependencies with Conda +- Orchestrating workflows with Snakemake + +### Structure + +- `src/`: Contains C++ source code and CMakeLists.txt +- `env/`: Contains Conda environment specifications +- `workflow/`: Contains Snakefile for build automation + +### Usage + +To build and run the example using Snakemake: + +```bash +cd workflow +snakemake --use-conda --cores 1 +``` + +This will: +1. Create a conda environment with cmake and g++ +2. Compile the C++ code +3. Run the executable and save output to `output/hello_output.txt` + +### Manual Build + +To build manually without Snakemake: + +```bash +mkdir -p build +cd build +cmake ../src +cmake --build . +./hello +``` diff --git a/workflow/Snakefile b/workflow/Snakefile index 25a60cf..0c3bef1 100644 --- a/workflow/Snakefile +++ b/workflow/Snakefile @@ -16,7 +16,6 @@ rule compile: cd build cmake ../src cmake --build . - cp hello ../build/hello """ rule run: From d36b394c01e86da54a759d6987fd129dced48f0f Mon Sep 17 00:00:00 2001 From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com> Date: Mon, 10 Nov 2025 09:42:27 +0000 Subject: [PATCH 04/10] Add GitHub Actions workflow for Snakemake execution Co-authored-by: imallona <8280371+imallona@users.noreply.github.com> --- .github/workflows/snakemake.yml | 52 +++++++++++++++++++++++++++++++++ README.md | 9 ++++++ 2 files changed, 61 insertions(+) create mode 100644 .github/workflows/snakemake.yml diff --git a/.github/workflows/snakemake.yml b/.github/workflows/snakemake.yml new file mode 100644 index 0000000..5370415 --- /dev/null +++ b/.github/workflows/snakemake.yml @@ -0,0 +1,52 @@ +name: Run Snakemake Workflow + +on: + pull_request: + branches: + - main + workflow_dispatch: + +jobs: + snakemake: + runs-on: ubuntu-latest + + steps: + - name: Checkout repository + uses: actions/checkout@v4 + + - name: Setup Mambaforge + uses: conda-incubator/setup-miniconda@v3 + with: + miniforge-variant: Mambaforge + miniforge-version: latest + activate-environment: snakemake + use-mamba: true + + - name: Install Snakemake + shell: bash -el {0} + run: | + mamba install -c conda-forge -c bioconda snakemake + + - name: Run Snakemake workflow + shell: bash -el {0} + run: | + cd workflow + snakemake --use-conda --cores 1 + + - name: Verify output + shell: bash -el {0} + run: | + cat workflow/output/hello_output.txt + if [ "$(cat workflow/output/hello_output.txt)" = "Hello World!" ]; then + echo "✓ Output verified successfully!" + else + echo "✗ Output verification failed!" + exit 1 + fi + + - name: Upload output artifact + uses: actions/upload-artifact@v4 + if: always() + with: + name: workflow-output + path: workflow/output/ diff --git a/README.md b/README.md index 66c6fa7..7f1edce 100644 --- a/README.md +++ b/README.md @@ -39,3 +39,12 @@ cmake ../src cmake --build . ./hello ``` + +### CI/CD + +This repository includes a GitHub Actions workflow that: +- Runs automatically on pull requests to main +- Can be manually triggered via workflow_dispatch +- Uses conda-incubator/setup-miniconda to set up Mambaforge +- Installs Snakemake and runs the workflow +- Verifies the output and uploads artifacts From 6656d093619202275ac5f2e3e35566d8ba79835b Mon Sep 17 00:00:00 2001 From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com> Date: Mon, 10 Nov 2025 09:44:29 +0000 Subject: [PATCH 05/10] Add explicit permissions to GitHub workflow for security Co-authored-by: imallona <8280371+imallona@users.noreply.github.com> --- .github/workflows/snakemake.yml | 2 + _codeql_detected_source_root | 1 + src/_codeql_build_dir/CMakeCache.txt | 394 ++++++++ .../CMakeFiles/3.31.6/CMakeCCompiler.cmake | 81 ++ .../CMakeFiles/3.31.6/CMakeCXXCompiler.cmake | 101 ++ .../3.31.6/CMakeDetermineCompilerABI_C.bin | Bin 0 -> 15968 bytes .../3.31.6/CMakeDetermineCompilerABI_CXX.bin | Bin 0 -> 15992 bytes .../CMakeFiles/3.31.6/CMakeSystem.cmake | 15 + .../3.31.6/CompilerIdC/CMakeCCompilerId.c | 904 +++++++++++++++++ .../CMakeFiles/3.31.6/CompilerIdC/a.out | Bin 0 -> 16088 bytes .../CompilerIdCXX/CMakeCXXCompilerId.cpp | 919 ++++++++++++++++++ .../CMakeFiles/3.31.6/CompilerIdCXX/a.out | Bin 0 -> 16096 bytes .../CMakeFiles/CMakeConfigureLog.yaml | 566 +++++++++++ .../CMakeDirectoryInformation.cmake | 16 + .../CMakeFiles/Makefile.cmake | 141 +++ src/_codeql_build_dir/CMakeFiles/Makefile2 | 125 +++ .../CMakeFiles/TargetDirectories.txt | 3 + .../CMakeFiles/cmake.check_cache | 1 + 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DEC(__FCC_patchlevel__) +# endif +# if defined(__fcc_version) +# define COMPILER_VERSION_INTERNAL DEC(__fcc_version) +# elif defined(__FCC_VERSION) +# define COMPILER_VERSION_INTERNAL DEC(__FCC_VERSION) +# endif + + +#elif defined(__ghs__) +# define COMPILER_ID "GHS" +/* __GHS_VERSION_NUMBER = VVVVRP */ +# ifdef __GHS_VERSION_NUMBER +# define COMPILER_VERSION_MAJOR DEC(__GHS_VERSION_NUMBER / 100) +# define COMPILER_VERSION_MINOR DEC(__GHS_VERSION_NUMBER / 10 % 10) +# define COMPILER_VERSION_PATCH DEC(__GHS_VERSION_NUMBER % 10) +# endif + +#elif defined(__TASKING__) +# define COMPILER_ID "Tasking" + # define COMPILER_VERSION_MAJOR DEC(__VERSION__/1000) + # define COMPILER_VERSION_MINOR DEC(__VERSION__ % 100) +# define COMPILER_VERSION_INTERNAL DEC(__VERSION__) + +#elif defined(__ORANGEC__) +# define COMPILER_ID "OrangeC" +# define COMPILER_VERSION_MAJOR DEC(__ORANGEC_MAJOR__) +# define COMPILER_VERSION_MINOR DEC(__ORANGEC_MINOR__) +# define COMPILER_VERSION_PATCH DEC(__ORANGEC_PATCHLEVEL__) + +#elif defined(__TINYC__) +# define COMPILER_ID "TinyCC" + +#elif defined(__BCC__) +# define COMPILER_ID "Bruce" + +#elif defined(__SCO_VERSION__) +# define COMPILER_ID "SCO" + +#elif defined(__ARMCC_VERSION) && !defined(__clang__) +# define COMPILER_ID "ARMCC" +#if __ARMCC_VERSION >= 1000000 + /* __ARMCC_VERSION = VRRPPPP */ + # define COMPILER_VERSION_MAJOR DEC(__ARMCC_VERSION/1000000) + # define COMPILER_VERSION_MINOR DEC(__ARMCC_VERSION/10000 % 100) + # define COMPILER_VERSION_PATCH DEC(__ARMCC_VERSION % 10000) +#else + /* __ARMCC_VERSION = VRPPPP */ + # define COMPILER_VERSION_MAJOR DEC(__ARMCC_VERSION/100000) + # define COMPILER_VERSION_MINOR DEC(__ARMCC_VERSION/10000 % 10) + # define COMPILER_VERSION_PATCH DEC(__ARMCC_VERSION % 10000) +#endif + + +#elif defined(__clang__) && defined(__apple_build_version__) +# define COMPILER_ID "AppleClang" +# if defined(_MSC_VER) +# define SIMULATE_ID "MSVC" +# endif +# define COMPILER_VERSION_MAJOR DEC(__clang_major__) +# define COMPILER_VERSION_MINOR DEC(__clang_minor__) +# define COMPILER_VERSION_PATCH DEC(__clang_patchlevel__) +# if defined(_MSC_VER) + /* _MSC_VER = VVRR */ +# define SIMULATE_VERSION_MAJOR DEC(_MSC_VER / 100) +# define SIMULATE_VERSION_MINOR DEC(_MSC_VER % 100) +# endif +# define COMPILER_VERSION_TWEAK DEC(__apple_build_version__) + +#elif defined(__clang__) && defined(__ARMCOMPILER_VERSION) +# define COMPILER_ID "ARMClang" + # define COMPILER_VERSION_MAJOR DEC(__ARMCOMPILER_VERSION/1000000) + # define COMPILER_VERSION_MINOR DEC(__ARMCOMPILER_VERSION/10000 % 100) + # define COMPILER_VERSION_PATCH DEC(__ARMCOMPILER_VERSION/100 % 100) +# define COMPILER_VERSION_INTERNAL DEC(__ARMCOMPILER_VERSION) + +#elif defined(__clang__) && defined(__ti__) +# define COMPILER_ID "TIClang" + # define COMPILER_VERSION_MAJOR DEC(__ti_major__) + # define COMPILER_VERSION_MINOR DEC(__ti_minor__) + # define COMPILER_VERSION_PATCH DEC(__ti_patchlevel__) +# define COMPILER_VERSION_INTERNAL DEC(__ti_version__) + +#elif defined(__clang__) +# define COMPILER_ID "Clang" +# if defined(_MSC_VER) +# define SIMULATE_ID "MSVC" +# endif +# define COMPILER_VERSION_MAJOR DEC(__clang_major__) +# define COMPILER_VERSION_MINOR DEC(__clang_minor__) +# define COMPILER_VERSION_PATCH DEC(__clang_patchlevel__) +# if defined(_MSC_VER) + /* _MSC_VER = VVRR */ +# define SIMULATE_VERSION_MAJOR DEC(_MSC_VER / 100) +# define SIMULATE_VERSION_MINOR DEC(_MSC_VER % 100) +# endif + +#elif defined(__LCC__) && (defined(__GNUC__) || defined(__GNUG__) || defined(__MCST__)) +# define COMPILER_ID "LCC" +# define COMPILER_VERSION_MAJOR DEC(__LCC__ / 100) +# define COMPILER_VERSION_MINOR DEC(__LCC__ % 100) +# if defined(__LCC_MINOR__) +# define COMPILER_VERSION_PATCH DEC(__LCC_MINOR__) +# endif +# if defined(__GNUC__) && defined(__GNUC_MINOR__) +# define SIMULATE_ID "GNU" +# define SIMULATE_VERSION_MAJOR DEC(__GNUC__) +# define SIMULATE_VERSION_MINOR DEC(__GNUC_MINOR__) +# if defined(__GNUC_PATCHLEVEL__) +# define SIMULATE_VERSION_PATCH DEC(__GNUC_PATCHLEVEL__) +# endif +# endif + +#elif defined(__GNUC__) +# define COMPILER_ID "GNU" +# define COMPILER_VERSION_MAJOR DEC(__GNUC__) +# if defined(__GNUC_MINOR__) +# define COMPILER_VERSION_MINOR DEC(__GNUC_MINOR__) +# endif +# if defined(__GNUC_PATCHLEVEL__) +# define COMPILER_VERSION_PATCH DEC(__GNUC_PATCHLEVEL__) +# endif + +#elif defined(_MSC_VER) +# define COMPILER_ID "MSVC" + /* _MSC_VER = VVRR */ +# define COMPILER_VERSION_MAJOR DEC(_MSC_VER / 100) +# define COMPILER_VERSION_MINOR DEC(_MSC_VER % 100) +# if defined(_MSC_FULL_VER) +# if _MSC_VER >= 1400 + /* _MSC_FULL_VER = VVRRPPPPP */ +# define COMPILER_VERSION_PATCH DEC(_MSC_FULL_VER % 100000) +# else + /* _MSC_FULL_VER = VVRRPPPP */ +# define COMPILER_VERSION_PATCH DEC(_MSC_FULL_VER % 10000) +# endif +# endif +# if defined(_MSC_BUILD) +# define COMPILER_VERSION_TWEAK DEC(_MSC_BUILD) +# endif + +#elif defined(_ADI_COMPILER) +# define COMPILER_ID "ADSP" +#if defined(__VERSIONNUM__) + /* __VERSIONNUM__ = 0xVVRRPPTT */ +# define COMPILER_VERSION_MAJOR DEC(__VERSIONNUM__ >> 24 & 0xFF) +# define COMPILER_VERSION_MINOR DEC(__VERSIONNUM__ >> 16 & 0xFF) +# define COMPILER_VERSION_PATCH DEC(__VERSIONNUM__ >> 8 & 0xFF) +# define COMPILER_VERSION_TWEAK DEC(__VERSIONNUM__ & 0xFF) +#endif + +#elif defined(__IAR_SYSTEMS_ICC__) || defined(__IAR_SYSTEMS_ICC) +# define COMPILER_ID "IAR" +# if defined(__VER__) && defined(__ICCARM__) +# define COMPILER_VERSION_MAJOR DEC((__VER__) / 1000000) +# define COMPILER_VERSION_MINOR DEC(((__VER__) / 1000) % 1000) +# define COMPILER_VERSION_PATCH DEC((__VER__) % 1000) +# define COMPILER_VERSION_INTERNAL DEC(__IAR_SYSTEMS_ICC__) +# elif defined(__VER__) && (defined(__ICCAVR__) || defined(__ICCRX__) || defined(__ICCRH850__) || defined(__ICCRL78__) || defined(__ICC430__) || defined(__ICCRISCV__) || defined(__ICCV850__) || defined(__ICC8051__) || defined(__ICCSTM8__)) +# define COMPILER_VERSION_MAJOR DEC((__VER__) / 100) +# define COMPILER_VERSION_MINOR DEC((__VER__) - (((__VER__) / 100)*100)) +# define COMPILER_VERSION_PATCH DEC(__SUBVERSION__) +# define COMPILER_VERSION_INTERNAL DEC(__IAR_SYSTEMS_ICC__) +# endif + +#elif defined(__SDCC_VERSION_MAJOR) || defined(SDCC) +# define COMPILER_ID "SDCC" +# if defined(__SDCC_VERSION_MAJOR) +# define COMPILER_VERSION_MAJOR DEC(__SDCC_VERSION_MAJOR) +# define COMPILER_VERSION_MINOR DEC(__SDCC_VERSION_MINOR) +# define COMPILER_VERSION_PATCH DEC(__SDCC_VERSION_PATCH) +# else + /* SDCC = VRP */ +# define COMPILER_VERSION_MAJOR DEC(SDCC/100) +# define COMPILER_VERSION_MINOR DEC(SDCC/10 % 10) +# define COMPILER_VERSION_PATCH DEC(SDCC % 10) +# endif + + +/* These compilers are either not known or too old to define an + identification macro. Try to identify the platform and guess that + it is the native compiler. */ +#elif defined(__hpux) || defined(__hpua) +# define COMPILER_ID "HP" + +#else /* unknown compiler */ +# define COMPILER_ID "" +#endif + +/* Construct the string literal in pieces to prevent the source from + getting matched. Store it in a pointer rather than an array + because some compilers will just produce instructions to fill the + array rather than assigning a pointer to a static array. */ +char const* info_compiler = "INFO" ":" "compiler[" COMPILER_ID "]"; +#ifdef SIMULATE_ID +char const* info_simulate = "INFO" ":" "simulate[" SIMULATE_ID "]"; +#endif + +#ifdef __QNXNTO__ +char const* qnxnto = "INFO" ":" "qnxnto[]"; +#endif + +#if defined(__CRAYXT_COMPUTE_LINUX_TARGET) +char const *info_cray = "INFO" ":" "compiler_wrapper[CrayPrgEnv]"; +#endif + +#define STRINGIFY_HELPER(X) #X +#define STRINGIFY(X) STRINGIFY_HELPER(X) + +/* Identify known platforms by name. */ +#if defined(__linux) || defined(__linux__) || defined(linux) +# define PLATFORM_ID "Linux" + +#elif defined(__MSYS__) +# define PLATFORM_ID "MSYS" + +#elif defined(__CYGWIN__) +# define PLATFORM_ID "Cygwin" + +#elif defined(__MINGW32__) +# define PLATFORM_ID "MinGW" + +#elif defined(__APPLE__) +# define PLATFORM_ID "Darwin" + +#elif defined(_WIN32) || defined(__WIN32__) || defined(WIN32) +# define PLATFORM_ID "Windows" + +#elif defined(__FreeBSD__) || defined(__FreeBSD) +# define PLATFORM_ID "FreeBSD" + +#elif defined(__NetBSD__) || defined(__NetBSD) +# define PLATFORM_ID "NetBSD" + +#elif defined(__OpenBSD__) || defined(__OPENBSD) +# define PLATFORM_ID "OpenBSD" + +#elif defined(__sun) || defined(sun) +# define PLATFORM_ID "SunOS" + +#elif defined(_AIX) || defined(__AIX) || defined(__AIX__) || defined(__aix) || defined(__aix__) +# define PLATFORM_ID "AIX" + +#elif defined(__hpux) || defined(__hpux__) +# define PLATFORM_ID "HP-UX" + +#elif defined(__HAIKU__) +# define PLATFORM_ID "Haiku" + +#elif defined(__BeOS) || defined(__BEOS__) || defined(_BEOS) +# define PLATFORM_ID "BeOS" + +#elif defined(__QNX__) || defined(__QNXNTO__) +# define PLATFORM_ID "QNX" + +#elif defined(__tru64) || defined(_tru64) || defined(__TRU64__) +# define PLATFORM_ID "Tru64" + +#elif defined(__riscos) || defined(__riscos__) +# define PLATFORM_ID "RISCos" + +#elif defined(__sinix) || defined(__sinix__) || defined(__SINIX__) +# define PLATFORM_ID "SINIX" + +#elif defined(__UNIX_SV__) +# define PLATFORM_ID "UNIX_SV" + +#elif defined(__bsdos__) +# define PLATFORM_ID "BSDOS" + +#elif defined(_MPRAS) || defined(MPRAS) +# define PLATFORM_ID "MP-RAS" + +#elif defined(__osf) || defined(__osf__) +# define PLATFORM_ID "OSF1" + +#elif defined(_SCO_SV) || defined(SCO_SV) || defined(sco_sv) +# define PLATFORM_ID "SCO_SV" + +#elif defined(__ultrix) || defined(__ultrix__) || defined(_ULTRIX) +# define PLATFORM_ID "ULTRIX" + +#elif defined(__XENIX__) || defined(_XENIX) || defined(XENIX) +# define PLATFORM_ID "Xenix" + +#elif defined(__WATCOMC__) +# if defined(__LINUX__) +# define PLATFORM_ID "Linux" + +# elif defined(__DOS__) +# define PLATFORM_ID "DOS" + +# elif defined(__OS2__) +# define PLATFORM_ID "OS2" + +# elif defined(__WINDOWS__) +# define PLATFORM_ID "Windows3x" + +# elif defined(__VXWORKS__) +# define PLATFORM_ID "VxWorks" + +# else /* unknown platform */ +# define PLATFORM_ID +# endif + +#elif defined(__INTEGRITY) +# if defined(INT_178B) +# define PLATFORM_ID "Integrity178" + +# else /* regular Integrity */ +# define PLATFORM_ID "Integrity" +# endif + +# elif defined(_ADI_COMPILER) +# define PLATFORM_ID "ADSP" + +#else /* unknown platform */ +# define PLATFORM_ID + +#endif + +/* For windows compilers MSVC and Intel we can determine + the architecture of the compiler being used. This is because + the compilers do not have flags that can change the architecture, + but rather depend on which compiler is being used +*/ +#if defined(_WIN32) && defined(_MSC_VER) +# if defined(_M_IA64) +# define ARCHITECTURE_ID "IA64" + +# elif defined(_M_ARM64EC) +# define ARCHITECTURE_ID "ARM64EC" + +# elif defined(_M_X64) || defined(_M_AMD64) +# define ARCHITECTURE_ID "x64" + +# elif defined(_M_IX86) +# define ARCHITECTURE_ID "X86" + +# elif defined(_M_ARM64) +# define ARCHITECTURE_ID "ARM64" + +# elif defined(_M_ARM) +# if _M_ARM == 4 +# define ARCHITECTURE_ID "ARMV4I" +# elif _M_ARM == 5 +# define ARCHITECTURE_ID "ARMV5I" +# else +# define ARCHITECTURE_ID "ARMV" STRINGIFY(_M_ARM) +# endif + +# elif defined(_M_MIPS) +# define ARCHITECTURE_ID "MIPS" + +# elif defined(_M_SH) +# define ARCHITECTURE_ID "SHx" + +# else /* unknown architecture */ +# define ARCHITECTURE_ID "" +# endif + +#elif defined(__WATCOMC__) +# if defined(_M_I86) +# define ARCHITECTURE_ID "I86" + +# elif defined(_M_IX86) +# define ARCHITECTURE_ID "X86" + +# else /* unknown architecture */ +# define ARCHITECTURE_ID "" +# endif + +#elif defined(__IAR_SYSTEMS_ICC__) || defined(__IAR_SYSTEMS_ICC) +# if defined(__ICCARM__) +# define ARCHITECTURE_ID "ARM" + +# elif defined(__ICCRX__) +# define ARCHITECTURE_ID "RX" + +# elif defined(__ICCRH850__) +# define ARCHITECTURE_ID "RH850" + +# elif defined(__ICCRL78__) +# define ARCHITECTURE_ID "RL78" + +# elif defined(__ICCRISCV__) +# define ARCHITECTURE_ID "RISCV" + +# elif defined(__ICCAVR__) +# define ARCHITECTURE_ID "AVR" + +# elif defined(__ICC430__) +# define ARCHITECTURE_ID "MSP430" + +# elif defined(__ICCV850__) +# define ARCHITECTURE_ID "V850" + +# elif defined(__ICC8051__) +# define ARCHITECTURE_ID "8051" + +# elif defined(__ICCSTM8__) +# define ARCHITECTURE_ID "STM8" + +# else /* unknown architecture */ +# define ARCHITECTURE_ID "" +# endif + +#elif defined(__ghs__) +# if defined(__PPC64__) +# define ARCHITECTURE_ID "PPC64" + +# elif defined(__ppc__) +# define ARCHITECTURE_ID "PPC" + +# elif defined(__ARM__) +# define ARCHITECTURE_ID "ARM" + +# elif defined(__x86_64__) +# define ARCHITECTURE_ID "x64" + +# elif defined(__i386__) +# define ARCHITECTURE_ID "X86" + +# else /* unknown architecture */ +# define ARCHITECTURE_ID "" +# endif + +#elif defined(__clang__) && defined(__ti__) +# if defined(__ARM_ARCH) +# define ARCHITECTURE_ID "ARM" + +# else /* unknown architecture */ +# define ARCHITECTURE_ID "" +# endif + +#elif defined(__TI_COMPILER_VERSION__) +# if defined(__TI_ARM__) +# define ARCHITECTURE_ID "ARM" + +# elif defined(__MSP430__) +# define ARCHITECTURE_ID "MSP430" + +# elif defined(__TMS320C28XX__) +# define ARCHITECTURE_ID "TMS320C28x" + +# elif defined(__TMS320C6X__) || defined(_TMS320C6X) +# define ARCHITECTURE_ID "TMS320C6x" + +# else /* unknown architecture */ +# define ARCHITECTURE_ID "" +# endif + +# elif defined(__ADSPSHARC__) +# define ARCHITECTURE_ID "SHARC" + +# elif defined(__ADSPBLACKFIN__) +# define ARCHITECTURE_ID "Blackfin" + +#elif defined(__TASKING__) + +# if defined(__CTC__) || defined(__CPTC__) +# define ARCHITECTURE_ID "TriCore" + +# elif defined(__CMCS__) +# define ARCHITECTURE_ID "MCS" + +# elif defined(__CARM__) +# define ARCHITECTURE_ID "ARM" + +# elif defined(__CARC__) +# define ARCHITECTURE_ID "ARC" + +# elif defined(__C51__) +# define ARCHITECTURE_ID "8051" + +# elif defined(__CPCP__) +# define ARCHITECTURE_ID "PCP" + +# else +# define ARCHITECTURE_ID "" +# endif + +#else +# define ARCHITECTURE_ID +#endif + +/* Convert integer to decimal digit literals. */ +#define DEC(n) \ + ('0' + (((n) / 10000000)%10)), \ + ('0' + (((n) / 1000000)%10)), \ + ('0' + (((n) / 100000)%10)), \ + ('0' + (((n) / 10000)%10)), \ + ('0' + (((n) / 1000)%10)), \ + ('0' + (((n) / 100)%10)), \ + ('0' + (((n) / 10)%10)), \ + ('0' + ((n) % 10)) + +/* Convert integer to hex digit literals. */ +#define HEX(n) \ + ('0' + ((n)>>28 & 0xF)), \ + ('0' + ((n)>>24 & 0xF)), \ + ('0' + ((n)>>20 & 0xF)), \ + ('0' + ((n)>>16 & 0xF)), \ + ('0' + ((n)>>12 & 0xF)), \ + ('0' + ((n)>>8 & 0xF)), \ + ('0' + ((n)>>4 & 0xF)), \ + ('0' + ((n) & 0xF)) + +/* Construct a string literal encoding the version number. */ +#ifdef COMPILER_VERSION +char const* info_version = "INFO" ":" "compiler_version[" COMPILER_VERSION "]"; + +/* Construct a string literal encoding the version number components. */ +#elif defined(COMPILER_VERSION_MAJOR) +char const info_version[] = { + 'I', 'N', 'F', 'O', ':', + 'c','o','m','p','i','l','e','r','_','v','e','r','s','i','o','n','[', + COMPILER_VERSION_MAJOR, +# ifdef COMPILER_VERSION_MINOR + '.', COMPILER_VERSION_MINOR, +# ifdef COMPILER_VERSION_PATCH + '.', COMPILER_VERSION_PATCH, +# ifdef COMPILER_VERSION_TWEAK + '.', COMPILER_VERSION_TWEAK, +# endif +# endif +# endif + ']','\0'}; +#endif + +/* Construct a string literal encoding the internal version number. */ +#ifdef COMPILER_VERSION_INTERNAL +char const info_version_internal[] = { + 'I', 'N', 'F', 'O', ':', + 'c','o','m','p','i','l','e','r','_','v','e','r','s','i','o','n','_', + 'i','n','t','e','r','n','a','l','[', + COMPILER_VERSION_INTERNAL,']','\0'}; +#elif defined(COMPILER_VERSION_INTERNAL_STR) +char const* info_version_internal = "INFO" ":" "compiler_version_internal[" COMPILER_VERSION_INTERNAL_STR "]"; +#endif + +/* Construct a string literal encoding the version number components. */ +#ifdef SIMULATE_VERSION_MAJOR +char const info_simulate_version[] = { + 'I', 'N', 'F', 'O', ':', + 's','i','m','u','l','a','t','e','_','v','e','r','s','i','o','n','[', + SIMULATE_VERSION_MAJOR, +# ifdef SIMULATE_VERSION_MINOR + '.', SIMULATE_VERSION_MINOR, +# ifdef SIMULATE_VERSION_PATCH + '.', SIMULATE_VERSION_PATCH, +# ifdef SIMULATE_VERSION_TWEAK + '.', SIMULATE_VERSION_TWEAK, +# endif +# endif +# endif + ']','\0'}; +#endif + +/* Construct the string literal in pieces to prevent the source from + getting matched. Store it in a pointer rather than an array + because some compilers will just produce instructions to fill the + array rather than assigning a pointer to a static array. */ +char const* info_platform = "INFO" ":" "platform[" PLATFORM_ID "]"; +char const* info_arch = "INFO" ":" "arch[" ARCHITECTURE_ID "]"; + + + +#define C_STD_99 199901L +#define C_STD_11 201112L +#define C_STD_17 201710L +#define C_STD_23 202311L + +#ifdef __STDC_VERSION__ +# define C_STD __STDC_VERSION__ +#endif + +#if !defined(__STDC__) && !defined(__clang__) +# if defined(_MSC_VER) || defined(__ibmxl__) || defined(__IBMC__) +# define C_VERSION "90" +# else +# define C_VERSION +# endif +#elif C_STD > C_STD_17 +# define C_VERSION "23" +#elif C_STD > C_STD_11 +# define C_VERSION "17" +#elif C_STD > C_STD_99 +# define C_VERSION "11" +#elif C_STD >= C_STD_99 +# define C_VERSION "99" +#else +# define C_VERSION "90" +#endif +const char* info_language_standard_default = + "INFO" ":" "standard_default[" C_VERSION "]"; + +const char* info_language_extensions_default = "INFO" ":" "extensions_default[" +#if (defined(__clang__) || defined(__GNUC__) || defined(__xlC__) || \ + defined(__TI_COMPILER_VERSION__)) && \ + !defined(__STRICT_ANSI__) + "ON" +#else + "OFF" +#endif +"]"; + +/*--------------------------------------------------------------------------*/ + +#ifdef ID_VOID_MAIN +void main() {} +#else +# if defined(__CLASSIC_C__) +int main(argc, argv) int argc; char *argv[]; +# else +int main(int argc, char* argv[]) +# endif +{ + int require = 0; + require += info_compiler[argc]; + require += info_platform[argc]; + require += info_arch[argc]; +#ifdef COMPILER_VERSION_MAJOR + require += info_version[argc]; +#endif +#ifdef COMPILER_VERSION_INTERNAL + require += info_version_internal[argc]; +#endif +#ifdef SIMULATE_ID + require += info_simulate[argc]; +#endif +#ifdef SIMULATE_VERSION_MAJOR + require += info_simulate_version[argc]; +#endif +#if defined(__CRAYXT_COMPUTE_LINUX_TARGET) + require += info_cray[argc]; +#endif + require += info_language_standard_default[argc]; + require += info_language_extensions_default[argc]; + (void)argv; + return require; +} +#endif diff --git a/src/_codeql_build_dir/CMakeFiles/3.31.6/CompilerIdC/a.out b/src/_codeql_build_dir/CMakeFiles/3.31.6/CompilerIdC/a.out new file mode 100755 index 0000000000000000000000000000000000000000..ecc315e71b4e62a6558ef29ebb804b7c2bdf9e59 GIT binary patch literal 16088 zcmeHOe{38_6`ngMjYE^zaci6=rP;IzN=Uu29mjQp(p+Mnvqp9j5(k8muv+`p_KEvp z?)Io%K^v4(V$w)0MGy&)stQr@qY_A{i2P9;6$M%fG!jz7KPW&e1u3LPKxNt}$9psH zJD-7; zK*W<{!vEb8&oH)$8(`ROTb!ylL3F6FF$Y{MN-?OT7(+27YSKXUDz+23sYdea8h;dZkP>u_R! z7$Pilp6g^C6OYeRPR2IjMgP}XO)PR?yQUgtJ;Yfxcy|##w+Me5@psqoqgX7be#lo`%<=6~`v&^=_P8B(hrOec-`=U*{-HrPH5EC6G5u$HDn>H57vrV0Hocsq&f|}{A3gb13Ui$9 zcqZXG#`R;ZHvF7i-{3Ec!}^3N2M@V1#9NlpTNC07!doH!i^6XX@lOfg7UG{1{?cxx z6OSDp3rLr%cphU&SE_i7Z7!Rw;(6R6%~kRGev5(#qXbCT{+Isgi=T9+|LB~2efHo`vVErgCFjhpm&rl7xk##iAGI6SKdSu^f1ViU%+hlV 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__WATCOMC__ < 1200 +# define COMPILER_ID "Watcom" + /* __WATCOMC__ = VVRR */ +# define COMPILER_VERSION_MAJOR DEC(__WATCOMC__ / 100) +# define COMPILER_VERSION_MINOR DEC((__WATCOMC__ / 10) % 10) +# if (__WATCOMC__ % 10) > 0 +# define COMPILER_VERSION_PATCH DEC(__WATCOMC__ % 10) +# endif + +#elif defined(__WATCOMC__) +# define COMPILER_ID "OpenWatcom" + /* __WATCOMC__ = VVRP + 1100 */ +# define COMPILER_VERSION_MAJOR DEC((__WATCOMC__ - 1100) / 100) +# define COMPILER_VERSION_MINOR DEC((__WATCOMC__ / 10) % 10) +# if (__WATCOMC__ % 10) > 0 +# define COMPILER_VERSION_PATCH DEC(__WATCOMC__ % 10) +# endif + +#elif defined(__SUNPRO_CC) +# define COMPILER_ID "SunPro" +# if __SUNPRO_CC >= 0x5100 + /* __SUNPRO_CC = 0xVRRP */ +# define COMPILER_VERSION_MAJOR HEX(__SUNPRO_CC>>12) +# define COMPILER_VERSION_MINOR HEX(__SUNPRO_CC>>4 & 0xFF) +# define COMPILER_VERSION_PATCH HEX(__SUNPRO_CC & 0xF) +# else + /* __SUNPRO_CC = 0xVRP */ +# define COMPILER_VERSION_MAJOR HEX(__SUNPRO_CC>>8) +# define COMPILER_VERSION_MINOR HEX(__SUNPRO_CC>>4 & 0xF) +# define COMPILER_VERSION_PATCH HEX(__SUNPRO_CC & 0xF) +# endif + +#elif defined(__HP_aCC) +# define COMPILER_ID "HP" + /* __HP_aCC = VVRRPP */ +# define COMPILER_VERSION_MAJOR DEC(__HP_aCC/10000) +# define COMPILER_VERSION_MINOR DEC(__HP_aCC/100 % 100) +# define COMPILER_VERSION_PATCH DEC(__HP_aCC % 100) + +#elif defined(__DECCXX) +# define COMPILER_ID "Compaq" + /* __DECCXX_VER = VVRRTPPPP */ +# define COMPILER_VERSION_MAJOR DEC(__DECCXX_VER/10000000) +# define COMPILER_VERSION_MINOR DEC(__DECCXX_VER/100000 % 100) +# define COMPILER_VERSION_PATCH DEC(__DECCXX_VER % 10000) + +#elif defined(__IBMCPP__) && defined(__COMPILER_VER__) +# define COMPILER_ID "zOS" + /* __IBMCPP__ = VRP */ +# define COMPILER_VERSION_MAJOR DEC(__IBMCPP__/100) +# define COMPILER_VERSION_MINOR DEC(__IBMCPP__/10 % 10) +# define COMPILER_VERSION_PATCH DEC(__IBMCPP__ % 10) + +#elif defined(__open_xl__) && defined(__clang__) +# define COMPILER_ID "IBMClang" +# define COMPILER_VERSION_MAJOR DEC(__open_xl_version__) +# define COMPILER_VERSION_MINOR DEC(__open_xl_release__) +# define COMPILER_VERSION_PATCH DEC(__open_xl_modification__) +# define COMPILER_VERSION_TWEAK DEC(__open_xl_ptf_fix_level__) + + +#elif defined(__ibmxl__) && defined(__clang__) +# define COMPILER_ID "XLClang" +# define COMPILER_VERSION_MAJOR DEC(__ibmxl_version__) +# define COMPILER_VERSION_MINOR DEC(__ibmxl_release__) +# define COMPILER_VERSION_PATCH DEC(__ibmxl_modification__) +# define COMPILER_VERSION_TWEAK DEC(__ibmxl_ptf_fix_level__) + + +#elif defined(__IBMCPP__) && !defined(__COMPILER_VER__) && __IBMCPP__ >= 800 +# define COMPILER_ID "XL" + /* __IBMCPP__ = VRP */ +# define COMPILER_VERSION_MAJOR DEC(__IBMCPP__/100) +# define COMPILER_VERSION_MINOR DEC(__IBMCPP__/10 % 10) +# define COMPILER_VERSION_PATCH DEC(__IBMCPP__ % 10) + +#elif defined(__IBMCPP__) && !defined(__COMPILER_VER__) && __IBMCPP__ < 800 +# define COMPILER_ID "VisualAge" + /* __IBMCPP__ = VRP */ +# define COMPILER_VERSION_MAJOR DEC(__IBMCPP__/100) +# define COMPILER_VERSION_MINOR DEC(__IBMCPP__/10 % 10) +# define COMPILER_VERSION_PATCH DEC(__IBMCPP__ % 10) + +#elif defined(__NVCOMPILER) +# define COMPILER_ID "NVHPC" +# define COMPILER_VERSION_MAJOR DEC(__NVCOMPILER_MAJOR__) +# define COMPILER_VERSION_MINOR DEC(__NVCOMPILER_MINOR__) +# if defined(__NVCOMPILER_PATCHLEVEL__) +# define COMPILER_VERSION_PATCH DEC(__NVCOMPILER_PATCHLEVEL__) +# endif + +#elif defined(__PGI) +# define COMPILER_ID "PGI" +# define COMPILER_VERSION_MAJOR DEC(__PGIC__) +# define COMPILER_VERSION_MINOR DEC(__PGIC_MINOR__) +# if defined(__PGIC_PATCHLEVEL__) +# define COMPILER_VERSION_PATCH DEC(__PGIC_PATCHLEVEL__) +# endif + +#elif defined(__clang__) && defined(__cray__) +# define COMPILER_ID "CrayClang" +# define COMPILER_VERSION_MAJOR DEC(__cray_major__) +# define COMPILER_VERSION_MINOR DEC(__cray_minor__) +# define COMPILER_VERSION_PATCH DEC(__cray_patchlevel__) +# define COMPILER_VERSION_INTERNAL_STR __clang_version__ + + +#elif defined(_CRAYC) +# define COMPILER_ID "Cray" +# define COMPILER_VERSION_MAJOR DEC(_RELEASE_MAJOR) +# define COMPILER_VERSION_MINOR DEC(_RELEASE_MINOR) + +#elif defined(__TI_COMPILER_VERSION__) +# define COMPILER_ID "TI" + /* __TI_COMPILER_VERSION__ = VVVRRRPPP */ +# define COMPILER_VERSION_MAJOR DEC(__TI_COMPILER_VERSION__/1000000) +# define COMPILER_VERSION_MINOR DEC(__TI_COMPILER_VERSION__/1000 % 1000) +# define COMPILER_VERSION_PATCH DEC(__TI_COMPILER_VERSION__ % 1000) + +#elif defined(__CLANG_FUJITSU) +# define COMPILER_ID "FujitsuClang" +# define COMPILER_VERSION_MAJOR DEC(__FCC_major__) +# define COMPILER_VERSION_MINOR DEC(__FCC_minor__) +# define COMPILER_VERSION_PATCH DEC(__FCC_patchlevel__) +# define COMPILER_VERSION_INTERNAL_STR __clang_version__ + + +#elif defined(__FUJITSU) +# define COMPILER_ID "Fujitsu" +# if defined(__FCC_version__) +# define COMPILER_VERSION __FCC_version__ +# elif defined(__FCC_major__) +# define COMPILER_VERSION_MAJOR DEC(__FCC_major__) +# define COMPILER_VERSION_MINOR DEC(__FCC_minor__) +# define COMPILER_VERSION_PATCH DEC(__FCC_patchlevel__) +# endif +# if defined(__fcc_version) +# define COMPILER_VERSION_INTERNAL DEC(__fcc_version) +# elif defined(__FCC_VERSION) +# define COMPILER_VERSION_INTERNAL DEC(__FCC_VERSION) +# endif + + +#elif defined(__ghs__) +# define COMPILER_ID "GHS" +/* __GHS_VERSION_NUMBER = VVVVRP */ +# ifdef __GHS_VERSION_NUMBER +# define COMPILER_VERSION_MAJOR DEC(__GHS_VERSION_NUMBER / 100) +# define COMPILER_VERSION_MINOR DEC(__GHS_VERSION_NUMBER / 10 % 10) +# define COMPILER_VERSION_PATCH DEC(__GHS_VERSION_NUMBER % 10) +# endif + +#elif defined(__TASKING__) +# define COMPILER_ID "Tasking" + # define COMPILER_VERSION_MAJOR DEC(__VERSION__/1000) + # define COMPILER_VERSION_MINOR DEC(__VERSION__ % 100) +# define COMPILER_VERSION_INTERNAL DEC(__VERSION__) + +#elif defined(__ORANGEC__) +# define COMPILER_ID "OrangeC" +# define COMPILER_VERSION_MAJOR DEC(__ORANGEC_MAJOR__) +# define COMPILER_VERSION_MINOR DEC(__ORANGEC_MINOR__) +# define COMPILER_VERSION_PATCH DEC(__ORANGEC_PATCHLEVEL__) + +#elif defined(__SCO_VERSION__) +# define COMPILER_ID "SCO" + +#elif defined(__ARMCC_VERSION) && !defined(__clang__) +# define COMPILER_ID "ARMCC" +#if __ARMCC_VERSION >= 1000000 + /* __ARMCC_VERSION = VRRPPPP */ + # define COMPILER_VERSION_MAJOR DEC(__ARMCC_VERSION/1000000) + # define COMPILER_VERSION_MINOR DEC(__ARMCC_VERSION/10000 % 100) + # define COMPILER_VERSION_PATCH DEC(__ARMCC_VERSION % 10000) +#else + /* __ARMCC_VERSION = VRPPPP */ + # define COMPILER_VERSION_MAJOR DEC(__ARMCC_VERSION/100000) + # define COMPILER_VERSION_MINOR DEC(__ARMCC_VERSION/10000 % 10) + # define COMPILER_VERSION_PATCH DEC(__ARMCC_VERSION % 10000) +#endif + + +#elif defined(__clang__) && defined(__apple_build_version__) +# define COMPILER_ID "AppleClang" +# if defined(_MSC_VER) +# define SIMULATE_ID "MSVC" +# endif +# define COMPILER_VERSION_MAJOR DEC(__clang_major__) +# define COMPILER_VERSION_MINOR DEC(__clang_minor__) +# define COMPILER_VERSION_PATCH DEC(__clang_patchlevel__) +# if defined(_MSC_VER) + /* _MSC_VER = VVRR */ +# define SIMULATE_VERSION_MAJOR DEC(_MSC_VER / 100) +# define SIMULATE_VERSION_MINOR DEC(_MSC_VER % 100) +# endif +# define COMPILER_VERSION_TWEAK DEC(__apple_build_version__) + +#elif defined(__clang__) && defined(__ARMCOMPILER_VERSION) +# define COMPILER_ID "ARMClang" + # define COMPILER_VERSION_MAJOR DEC(__ARMCOMPILER_VERSION/1000000) + # define COMPILER_VERSION_MINOR DEC(__ARMCOMPILER_VERSION/10000 % 100) + # define COMPILER_VERSION_PATCH DEC(__ARMCOMPILER_VERSION/100 % 100) +# define COMPILER_VERSION_INTERNAL DEC(__ARMCOMPILER_VERSION) + +#elif defined(__clang__) && defined(__ti__) +# define COMPILER_ID "TIClang" + # define COMPILER_VERSION_MAJOR DEC(__ti_major__) + # define COMPILER_VERSION_MINOR DEC(__ti_minor__) + # define COMPILER_VERSION_PATCH DEC(__ti_patchlevel__) +# define COMPILER_VERSION_INTERNAL DEC(__ti_version__) + +#elif defined(__clang__) +# define COMPILER_ID "Clang" +# if defined(_MSC_VER) +# define SIMULATE_ID "MSVC" +# endif +# define COMPILER_VERSION_MAJOR DEC(__clang_major__) +# define COMPILER_VERSION_MINOR DEC(__clang_minor__) +# define COMPILER_VERSION_PATCH DEC(__clang_patchlevel__) +# if defined(_MSC_VER) + /* _MSC_VER = VVRR */ +# define SIMULATE_VERSION_MAJOR DEC(_MSC_VER / 100) +# define SIMULATE_VERSION_MINOR DEC(_MSC_VER % 100) +# endif + +#elif defined(__LCC__) && (defined(__GNUC__) || defined(__GNUG__) || defined(__MCST__)) +# define COMPILER_ID "LCC" +# define COMPILER_VERSION_MAJOR DEC(__LCC__ / 100) +# define COMPILER_VERSION_MINOR DEC(__LCC__ % 100) +# if defined(__LCC_MINOR__) +# define COMPILER_VERSION_PATCH DEC(__LCC_MINOR__) +# endif +# if defined(__GNUC__) && defined(__GNUC_MINOR__) +# define SIMULATE_ID "GNU" +# define SIMULATE_VERSION_MAJOR DEC(__GNUC__) +# define SIMULATE_VERSION_MINOR DEC(__GNUC_MINOR__) +# if defined(__GNUC_PATCHLEVEL__) +# define SIMULATE_VERSION_PATCH DEC(__GNUC_PATCHLEVEL__) +# endif +# endif + +#elif defined(__GNUC__) || defined(__GNUG__) +# define COMPILER_ID "GNU" +# if defined(__GNUC__) +# define COMPILER_VERSION_MAJOR DEC(__GNUC__) +# else +# define COMPILER_VERSION_MAJOR DEC(__GNUG__) +# endif +# if defined(__GNUC_MINOR__) +# define COMPILER_VERSION_MINOR DEC(__GNUC_MINOR__) +# endif +# if defined(__GNUC_PATCHLEVEL__) +# define COMPILER_VERSION_PATCH DEC(__GNUC_PATCHLEVEL__) +# endif + +#elif defined(_MSC_VER) +# define COMPILER_ID "MSVC" + /* _MSC_VER = VVRR */ +# define COMPILER_VERSION_MAJOR DEC(_MSC_VER / 100) +# define COMPILER_VERSION_MINOR DEC(_MSC_VER % 100) +# if defined(_MSC_FULL_VER) +# if _MSC_VER >= 1400 + /* _MSC_FULL_VER = VVRRPPPPP */ +# define COMPILER_VERSION_PATCH DEC(_MSC_FULL_VER % 100000) +# else + /* _MSC_FULL_VER = VVRRPPPP */ +# define COMPILER_VERSION_PATCH DEC(_MSC_FULL_VER % 10000) +# endif +# endif +# if defined(_MSC_BUILD) +# define COMPILER_VERSION_TWEAK DEC(_MSC_BUILD) +# endif + +#elif defined(_ADI_COMPILER) +# define COMPILER_ID "ADSP" +#if defined(__VERSIONNUM__) + /* __VERSIONNUM__ = 0xVVRRPPTT */ +# define COMPILER_VERSION_MAJOR DEC(__VERSIONNUM__ >> 24 & 0xFF) +# define COMPILER_VERSION_MINOR DEC(__VERSIONNUM__ >> 16 & 0xFF) +# define COMPILER_VERSION_PATCH DEC(__VERSIONNUM__ >> 8 & 0xFF) +# define COMPILER_VERSION_TWEAK DEC(__VERSIONNUM__ & 0xFF) +#endif + +#elif defined(__IAR_SYSTEMS_ICC__) || defined(__IAR_SYSTEMS_ICC) +# define COMPILER_ID "IAR" +# if defined(__VER__) && defined(__ICCARM__) +# define COMPILER_VERSION_MAJOR DEC((__VER__) / 1000000) +# define COMPILER_VERSION_MINOR DEC(((__VER__) / 1000) % 1000) +# define COMPILER_VERSION_PATCH DEC((__VER__) % 1000) +# define COMPILER_VERSION_INTERNAL DEC(__IAR_SYSTEMS_ICC__) +# elif defined(__VER__) && (defined(__ICCAVR__) || defined(__ICCRX__) || defined(__ICCRH850__) || defined(__ICCRL78__) || defined(__ICC430__) || defined(__ICCRISCV__) || defined(__ICCV850__) || defined(__ICC8051__) || defined(__ICCSTM8__)) +# define COMPILER_VERSION_MAJOR DEC((__VER__) / 100) +# define COMPILER_VERSION_MINOR DEC((__VER__) - (((__VER__) / 100)*100)) +# define COMPILER_VERSION_PATCH DEC(__SUBVERSION__) +# define COMPILER_VERSION_INTERNAL DEC(__IAR_SYSTEMS_ICC__) +# endif + + +/* These compilers are either not known or too old to define an + identification macro. Try to identify the platform and guess that + it is the native compiler. */ +#elif defined(__hpux) || defined(__hpua) +# define COMPILER_ID "HP" + +#else /* unknown compiler */ +# define COMPILER_ID "" +#endif + +/* Construct the string literal in pieces to prevent the source from + getting matched. Store it in a pointer rather than an array + because some compilers will just produce instructions to fill the + array rather than assigning a pointer to a static array. */ +char const* info_compiler = "INFO" ":" "compiler[" COMPILER_ID "]"; +#ifdef SIMULATE_ID +char const* info_simulate = "INFO" ":" "simulate[" SIMULATE_ID "]"; +#endif + +#ifdef __QNXNTO__ +char const* qnxnto = "INFO" ":" "qnxnto[]"; +#endif + +#if defined(__CRAYXT_COMPUTE_LINUX_TARGET) +char const *info_cray = "INFO" ":" "compiler_wrapper[CrayPrgEnv]"; +#endif + +#define STRINGIFY_HELPER(X) #X +#define STRINGIFY(X) STRINGIFY_HELPER(X) + +/* Identify known platforms by name. */ +#if defined(__linux) || defined(__linux__) || defined(linux) +# define PLATFORM_ID "Linux" + +#elif defined(__MSYS__) +# define PLATFORM_ID "MSYS" + +#elif defined(__CYGWIN__) +# define PLATFORM_ID "Cygwin" + +#elif defined(__MINGW32__) +# define PLATFORM_ID "MinGW" + +#elif defined(__APPLE__) +# define PLATFORM_ID "Darwin" + +#elif defined(_WIN32) || defined(__WIN32__) || defined(WIN32) +# define PLATFORM_ID "Windows" + +#elif defined(__FreeBSD__) || defined(__FreeBSD) +# define PLATFORM_ID "FreeBSD" + +#elif defined(__NetBSD__) || defined(__NetBSD) +# define PLATFORM_ID "NetBSD" + +#elif defined(__OpenBSD__) || defined(__OPENBSD) +# define PLATFORM_ID "OpenBSD" + +#elif defined(__sun) || defined(sun) +# define PLATFORM_ID "SunOS" + +#elif defined(_AIX) || defined(__AIX) || defined(__AIX__) || defined(__aix) || defined(__aix__) +# define PLATFORM_ID "AIX" + +#elif defined(__hpux) || defined(__hpux__) +# define PLATFORM_ID "HP-UX" + +#elif defined(__HAIKU__) +# define PLATFORM_ID "Haiku" + +#elif defined(__BeOS) || defined(__BEOS__) || defined(_BEOS) +# define PLATFORM_ID "BeOS" + +#elif defined(__QNX__) || defined(__QNXNTO__) +# define PLATFORM_ID "QNX" + +#elif defined(__tru64) || defined(_tru64) || defined(__TRU64__) +# define PLATFORM_ID "Tru64" + +#elif defined(__riscos) || defined(__riscos__) +# define PLATFORM_ID "RISCos" + +#elif defined(__sinix) || defined(__sinix__) || defined(__SINIX__) +# define PLATFORM_ID "SINIX" + +#elif defined(__UNIX_SV__) +# define PLATFORM_ID "UNIX_SV" + +#elif defined(__bsdos__) +# define PLATFORM_ID "BSDOS" + +#elif defined(_MPRAS) || defined(MPRAS) +# define PLATFORM_ID "MP-RAS" + +#elif defined(__osf) || defined(__osf__) +# define PLATFORM_ID "OSF1" + +#elif defined(_SCO_SV) || defined(SCO_SV) || defined(sco_sv) +# define PLATFORM_ID "SCO_SV" + +#elif defined(__ultrix) || defined(__ultrix__) || defined(_ULTRIX) +# define PLATFORM_ID "ULTRIX" + +#elif defined(__XENIX__) || defined(_XENIX) || defined(XENIX) +# define PLATFORM_ID "Xenix" + +#elif defined(__WATCOMC__) +# if defined(__LINUX__) +# define PLATFORM_ID "Linux" + +# elif defined(__DOS__) +# define PLATFORM_ID "DOS" + +# elif defined(__OS2__) +# define PLATFORM_ID "OS2" + +# elif defined(__WINDOWS__) +# define PLATFORM_ID "Windows3x" + +# elif defined(__VXWORKS__) +# define PLATFORM_ID "VxWorks" + +# else /* unknown platform */ +# define PLATFORM_ID +# endif + +#elif defined(__INTEGRITY) +# if defined(INT_178B) +# define PLATFORM_ID "Integrity178" + +# else /* regular Integrity */ +# define PLATFORM_ID "Integrity" +# endif + +# elif defined(_ADI_COMPILER) +# define PLATFORM_ID "ADSP" + +#else /* unknown platform */ +# define PLATFORM_ID + +#endif + +/* For windows compilers MSVC and Intel we can determine + the architecture of the compiler being used. This is because + the compilers do not have flags that can change the architecture, + but rather depend on which compiler is being used +*/ +#if defined(_WIN32) && defined(_MSC_VER) +# if defined(_M_IA64) +# define ARCHITECTURE_ID "IA64" + +# elif defined(_M_ARM64EC) +# define ARCHITECTURE_ID "ARM64EC" + +# elif defined(_M_X64) || defined(_M_AMD64) +# define ARCHITECTURE_ID "x64" + +# elif defined(_M_IX86) +# define ARCHITECTURE_ID "X86" + +# elif defined(_M_ARM64) +# define ARCHITECTURE_ID "ARM64" + +# elif defined(_M_ARM) +# if _M_ARM == 4 +# define ARCHITECTURE_ID "ARMV4I" +# elif _M_ARM == 5 +# define ARCHITECTURE_ID "ARMV5I" +# else +# define ARCHITECTURE_ID "ARMV" STRINGIFY(_M_ARM) +# endif + +# elif defined(_M_MIPS) +# define ARCHITECTURE_ID "MIPS" + +# elif defined(_M_SH) +# define ARCHITECTURE_ID "SHx" + +# else /* unknown architecture */ +# define ARCHITECTURE_ID "" +# endif + +#elif defined(__WATCOMC__) +# if defined(_M_I86) +# define ARCHITECTURE_ID "I86" + +# elif defined(_M_IX86) +# define ARCHITECTURE_ID "X86" + +# else /* unknown architecture */ +# define ARCHITECTURE_ID "" +# endif + +#elif defined(__IAR_SYSTEMS_ICC__) || defined(__IAR_SYSTEMS_ICC) +# if defined(__ICCARM__) +# define ARCHITECTURE_ID "ARM" + +# elif defined(__ICCRX__) +# define ARCHITECTURE_ID "RX" + +# elif defined(__ICCRH850__) +# define ARCHITECTURE_ID "RH850" + +# elif defined(__ICCRL78__) +# define ARCHITECTURE_ID "RL78" + +# elif defined(__ICCRISCV__) +# define ARCHITECTURE_ID "RISCV" + +# elif defined(__ICCAVR__) +# define ARCHITECTURE_ID "AVR" + +# elif defined(__ICC430__) +# define ARCHITECTURE_ID "MSP430" + +# elif defined(__ICCV850__) +# define ARCHITECTURE_ID "V850" + +# elif defined(__ICC8051__) +# define ARCHITECTURE_ID "8051" + +# elif defined(__ICCSTM8__) +# define ARCHITECTURE_ID "STM8" + +# else /* unknown architecture */ +# define ARCHITECTURE_ID "" +# endif + +#elif defined(__ghs__) +# if defined(__PPC64__) +# define ARCHITECTURE_ID "PPC64" + +# elif defined(__ppc__) +# define ARCHITECTURE_ID "PPC" + +# elif defined(__ARM__) +# define ARCHITECTURE_ID "ARM" + +# elif defined(__x86_64__) +# define ARCHITECTURE_ID "x64" + +# elif defined(__i386__) +# define ARCHITECTURE_ID "X86" + +# else /* unknown architecture */ +# define ARCHITECTURE_ID "" +# endif + +#elif defined(__clang__) && defined(__ti__) +# if defined(__ARM_ARCH) +# define ARCHITECTURE_ID "ARM" + +# else /* unknown architecture */ +# define ARCHITECTURE_ID "" +# endif + +#elif defined(__TI_COMPILER_VERSION__) +# if defined(__TI_ARM__) +# define ARCHITECTURE_ID "ARM" + +# elif defined(__MSP430__) +# define ARCHITECTURE_ID "MSP430" + +# elif defined(__TMS320C28XX__) +# define ARCHITECTURE_ID "TMS320C28x" + +# elif defined(__TMS320C6X__) || defined(_TMS320C6X) +# define ARCHITECTURE_ID "TMS320C6x" + +# else /* unknown architecture */ +# define ARCHITECTURE_ID "" +# endif + +# elif defined(__ADSPSHARC__) +# define ARCHITECTURE_ID "SHARC" + +# elif defined(__ADSPBLACKFIN__) +# define ARCHITECTURE_ID "Blackfin" + +#elif defined(__TASKING__) + +# if defined(__CTC__) || defined(__CPTC__) +# define ARCHITECTURE_ID "TriCore" + +# elif defined(__CMCS__) +# define ARCHITECTURE_ID "MCS" + +# elif defined(__CARM__) +# define ARCHITECTURE_ID "ARM" + +# elif defined(__CARC__) +# define ARCHITECTURE_ID "ARC" + +# elif defined(__C51__) +# define ARCHITECTURE_ID "8051" + +# elif defined(__CPCP__) +# define ARCHITECTURE_ID "PCP" + +# else +# define ARCHITECTURE_ID "" +# endif + +#else +# define ARCHITECTURE_ID +#endif + +/* Convert integer to decimal digit literals. */ +#define DEC(n) \ + ('0' + (((n) / 10000000)%10)), \ + ('0' + (((n) / 1000000)%10)), \ + ('0' + (((n) / 100000)%10)), \ + ('0' + (((n) / 10000)%10)), \ + ('0' + (((n) / 1000)%10)), \ + ('0' + (((n) / 100)%10)), \ + ('0' + (((n) / 10)%10)), \ + ('0' + ((n) % 10)) + +/* Convert integer to hex digit literals. */ +#define HEX(n) \ + ('0' + ((n)>>28 & 0xF)), \ + ('0' + ((n)>>24 & 0xF)), \ + ('0' + ((n)>>20 & 0xF)), \ + ('0' + ((n)>>16 & 0xF)), \ + ('0' + ((n)>>12 & 0xF)), \ + ('0' + ((n)>>8 & 0xF)), \ + ('0' + ((n)>>4 & 0xF)), \ + ('0' + ((n) & 0xF)) + +/* Construct a string literal encoding the version number. */ +#ifdef COMPILER_VERSION +char const* info_version = "INFO" ":" "compiler_version[" COMPILER_VERSION "]"; + +/* Construct a string literal encoding the version number components. */ +#elif defined(COMPILER_VERSION_MAJOR) +char const info_version[] = { + 'I', 'N', 'F', 'O', ':', + 'c','o','m','p','i','l','e','r','_','v','e','r','s','i','o','n','[', + COMPILER_VERSION_MAJOR, +# ifdef COMPILER_VERSION_MINOR + '.', COMPILER_VERSION_MINOR, +# ifdef COMPILER_VERSION_PATCH + '.', COMPILER_VERSION_PATCH, +# ifdef COMPILER_VERSION_TWEAK + '.', COMPILER_VERSION_TWEAK, +# endif +# endif +# endif + ']','\0'}; +#endif + +/* Construct a string literal encoding the internal version number. */ +#ifdef COMPILER_VERSION_INTERNAL +char const info_version_internal[] = { + 'I', 'N', 'F', 'O', ':', + 'c','o','m','p','i','l','e','r','_','v','e','r','s','i','o','n','_', + 'i','n','t','e','r','n','a','l','[', + COMPILER_VERSION_INTERNAL,']','\0'}; +#elif defined(COMPILER_VERSION_INTERNAL_STR) +char const* info_version_internal = "INFO" ":" "compiler_version_internal[" COMPILER_VERSION_INTERNAL_STR "]"; +#endif + +/* Construct a string literal encoding the version number components. */ +#ifdef SIMULATE_VERSION_MAJOR +char const info_simulate_version[] = { + 'I', 'N', 'F', 'O', ':', + 's','i','m','u','l','a','t','e','_','v','e','r','s','i','o','n','[', + SIMULATE_VERSION_MAJOR, +# ifdef SIMULATE_VERSION_MINOR + '.', SIMULATE_VERSION_MINOR, +# ifdef SIMULATE_VERSION_PATCH + '.', SIMULATE_VERSION_PATCH, +# ifdef SIMULATE_VERSION_TWEAK + '.', SIMULATE_VERSION_TWEAK, +# endif +# endif +# endif + ']','\0'}; +#endif + +/* Construct the string literal in pieces to prevent the source from + getting matched. Store it in a pointer rather than an array + because some compilers will just produce instructions to fill the + array rather than assigning a pointer to a static array. */ +char const* info_platform = "INFO" ":" "platform[" PLATFORM_ID "]"; +char const* info_arch = "INFO" ":" "arch[" ARCHITECTURE_ID "]"; + + + +#define CXX_STD_98 199711L +#define CXX_STD_11 201103L +#define CXX_STD_14 201402L +#define CXX_STD_17 201703L +#define CXX_STD_20 202002L +#define CXX_STD_23 202302L + +#if defined(__INTEL_COMPILER) && defined(_MSVC_LANG) +# if _MSVC_LANG > CXX_STD_17 +# define CXX_STD _MSVC_LANG +# elif _MSVC_LANG == CXX_STD_17 && defined(__cpp_aggregate_paren_init) +# define CXX_STD CXX_STD_20 +# elif _MSVC_LANG > CXX_STD_14 && __cplusplus > CXX_STD_17 +# define CXX_STD CXX_STD_20 +# elif _MSVC_LANG > CXX_STD_14 +# define CXX_STD CXX_STD_17 +# elif defined(__INTEL_CXX11_MODE__) && defined(__cpp_aggregate_nsdmi) +# define CXX_STD CXX_STD_14 +# elif defined(__INTEL_CXX11_MODE__) +# define CXX_STD CXX_STD_11 +# else +# define CXX_STD CXX_STD_98 +# endif +#elif defined(_MSC_VER) && defined(_MSVC_LANG) +# if _MSVC_LANG > __cplusplus +# define CXX_STD _MSVC_LANG +# else +# define CXX_STD __cplusplus +# endif +#elif defined(__NVCOMPILER) +# if __cplusplus == CXX_STD_17 && defined(__cpp_aggregate_paren_init) +# define CXX_STD CXX_STD_20 +# else +# define CXX_STD __cplusplus +# endif +#elif defined(__INTEL_COMPILER) || defined(__PGI) +# if __cplusplus == CXX_STD_11 && defined(__cpp_namespace_attributes) +# define CXX_STD CXX_STD_17 +# elif __cplusplus == CXX_STD_11 && defined(__cpp_aggregate_nsdmi) +# define CXX_STD CXX_STD_14 +# else +# define CXX_STD __cplusplus +# endif +#elif (defined(__IBMCPP__) || defined(__ibmxl__)) && defined(__linux__) +# if __cplusplus == CXX_STD_11 && defined(__cpp_aggregate_nsdmi) +# define CXX_STD CXX_STD_14 +# else +# define CXX_STD __cplusplus +# endif +#elif __cplusplus == 1 && defined(__GXX_EXPERIMENTAL_CXX0X__) +# define CXX_STD CXX_STD_11 +#else +# define CXX_STD __cplusplus +#endif + +const char* info_language_standard_default = "INFO" ":" "standard_default[" +#if CXX_STD > CXX_STD_23 + "26" +#elif CXX_STD > CXX_STD_20 + "23" +#elif CXX_STD > CXX_STD_17 + "20" +#elif CXX_STD > CXX_STD_14 + "17" +#elif CXX_STD > CXX_STD_11 + "14" +#elif CXX_STD >= CXX_STD_11 + "11" +#else + "98" +#endif +"]"; + +const char* info_language_extensions_default = "INFO" ":" "extensions_default[" +#if (defined(__clang__) || defined(__GNUC__) || defined(__xlC__) || \ + defined(__TI_COMPILER_VERSION__)) && \ + !defined(__STRICT_ANSI__) + "ON" +#else + "OFF" +#endif +"]"; + +/*--------------------------------------------------------------------------*/ + +int main(int argc, char* argv[]) +{ + int require = 0; + require += info_compiler[argc]; + require += info_platform[argc]; + require += info_arch[argc]; +#ifdef COMPILER_VERSION_MAJOR + require += info_version[argc]; +#endif +#ifdef COMPILER_VERSION_INTERNAL + require += 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- -/* Construct a string literal encoding the version number components. */ -#elif defined(COMPILER_VERSION_MAJOR) -char const info_version[] = { - 'I', 'N', 'F', 'O', ':', - 'c','o','m','p','i','l','e','r','_','v','e','r','s','i','o','n','[', - COMPILER_VERSION_MAJOR, -# ifdef COMPILER_VERSION_MINOR - '.', COMPILER_VERSION_MINOR, -# ifdef COMPILER_VERSION_PATCH - '.', COMPILER_VERSION_PATCH, -# ifdef COMPILER_VERSION_TWEAK - '.', COMPILER_VERSION_TWEAK, -# endif -# endif -# endif - ']','\0'}; -#endif - -/* Construct a string literal encoding the internal version number. */ -#ifdef COMPILER_VERSION_INTERNAL -char const info_version_internal[] = { - 'I', 'N', 'F', 'O', ':', - 'c','o','m','p','i','l','e','r','_','v','e','r','s','i','o','n','_', - 'i','n','t','e','r','n','a','l','[', - COMPILER_VERSION_INTERNAL,']','\0'}; -#elif defined(COMPILER_VERSION_INTERNAL_STR) -char const* info_version_internal = "INFO" ":" "compiler_version_internal[" COMPILER_VERSION_INTERNAL_STR "]"; -#endif - -/* Construct a string literal encoding the version number components. */ -#ifdef SIMULATE_VERSION_MAJOR -char const info_simulate_version[] = { - 'I', 'N', 'F', 'O', ':', - 's','i','m','u','l','a','t','e','_','v','e','r','s','i','o','n','[', - SIMULATE_VERSION_MAJOR, -# ifdef SIMULATE_VERSION_MINOR - '.', SIMULATE_VERSION_MINOR, -# ifdef SIMULATE_VERSION_PATCH - '.', SIMULATE_VERSION_PATCH, -# ifdef SIMULATE_VERSION_TWEAK - '.', SIMULATE_VERSION_TWEAK, -# endif -# endif -# endif - ']','\0'}; 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- -/* Construct a string literal encoding the version number components. */ -#elif defined(COMPILER_VERSION_MAJOR) -char const info_version[] = { - 'I', 'N', 'F', 'O', ':', - 'c','o','m','p','i','l','e','r','_','v','e','r','s','i','o','n','[', - COMPILER_VERSION_MAJOR, -# ifdef COMPILER_VERSION_MINOR - '.', COMPILER_VERSION_MINOR, -# ifdef COMPILER_VERSION_PATCH - '.', COMPILER_VERSION_PATCH, -# ifdef COMPILER_VERSION_TWEAK - '.', COMPILER_VERSION_TWEAK, -# endif -# endif -# endif - ']','\0'}; -#endif - -/* Construct a string literal encoding the internal version number. */ -#ifdef COMPILER_VERSION_INTERNAL -char const info_version_internal[] = { - 'I', 'N', 'F', 'O', ':', - 'c','o','m','p','i','l','e','r','_','v','e','r','s','i','o','n','_', - 'i','n','t','e','r','n','a','l','[', - COMPILER_VERSION_INTERNAL,']','\0'}; -#elif defined(COMPILER_VERSION_INTERNAL_STR) -char const* info_version_internal = "INFO" ":" "compiler_version_internal[" COMPILER_VERSION_INTERNAL_STR "]"; -#endif - -/* Construct a string literal encoding the version number components. */ -#ifdef SIMULATE_VERSION_MAJOR -char const info_simulate_version[] = { - 'I', 'N', 'F', 'O', ':', - 's','i','m','u','l','a','t','e','_','v','e','r','s','i','o','n','[', - SIMULATE_VERSION_MAJOR, -# ifdef SIMULATE_VERSION_MINOR - '.', SIMULATE_VERSION_MINOR, -# ifdef SIMULATE_VERSION_PATCH - '.', SIMULATE_VERSION_PATCH, -# ifdef SIMULATE_VERSION_TWEAK - '.', SIMULATE_VERSION_TWEAK, -# endif -# endif -# endif - ']','\0'}; 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name: Checkout repository uses: actions/checkout@v4 - - - name: Setup Mambaforge + + - name: miniconda uses: conda-incubator/setup-miniconda@v3 with: - miniforge-variant: Mambaforge - miniforge-version: latest - activate-environment: snakemake use-mamba: true + activate-environment: snakemake - name: Install Snakemake shell: bash -el {0} @@ -46,9 +44,9 @@ jobs: exit 1 fi - - name: Upload output artifact - uses: actions/upload-artifact@v4 - if: always() - with: - name: workflow-output - path: workflow/output/ + # - name: Upload output artifact + # uses: actions/upload-artifact@v4 + # if: always() + # with: + # name: workflow-output + # path: workflow/output/ diff --git a/README.md b/README.md index 7f1edce..0aa4b4c 100644 --- a/README.md +++ b/README.md @@ -1,12 +1,6 @@ # drab -RNA-seq count tables, revisited - -## C++ Hello World Example -This repository includes a simple C++ "Hello World" example that demonstrates: -- Building C++ code with CMake -- Managing dependencies with Conda -- Orchestrating workflows with Snakemake +RNA-seq count tables, revisited ### Structure @@ -14,7 +8,7 @@ This repository includes a simple C++ "Hello World" example that demonstrates: - `env/`: Contains Conda environment specifications - `workflow/`: Contains Snakefile for build automation -### Usage +### Running with snmk To build and run the example using Snakemake: @@ -28,7 +22,7 @@ This will: 2. Compile the C++ code 3. Run the executable and save output to `output/hello_output.txt` -### Manual Build +### Building `src` To build manually without Snakemake: @@ -42,9 +36,4 @@ cmake --build . ### CI/CD -This repository includes a GitHub Actions workflow that: -- Runs automatically on pull requests to main -- Can be manually triggered via workflow_dispatch -- Uses conda-incubator/setup-miniconda to set up Mambaforge -- Installs Snakemake and runs the workflow -- Verifies the output and uploads artifacts +- `snakemake.yml` to run the workflow (serially) diff --git a/workflow/Snakefile b/workflow/Snakefile index 0c3bef1..982de29 100644 --- a/workflow/Snakefile +++ b/workflow/Snakefile @@ -1,15 +1,17 @@ +#!/usr/bin/env snakemake -s + rule all: input: "output/hello_output.txt" rule compile: + conda: + "../env/build.yaml" input: cpp="src/hello.cpp", cmake="src/CMakeLists.txt" output: "build/hello" - conda: - "../env/build.yaml" shell: """ mkdir -p build @@ -19,6 +21,8 @@ rule compile: """ rule run: + conda: + "../env/build.yaml" input: "build/hello" output: From 71499e0cbc57bdd20bd6422c4060f9000e0b8779 Mon Sep 17 00:00:00 2001 From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com> Date: Mon, 10 Nov 2025 10:19:31 +0000 Subject: [PATCH 08/10] Fix CI/CD workflow to use Mambaforge for mamba availability Co-authored-by: imallona <8280371+imallona@users.noreply.github.com> --- .github/workflows/snakemake.yml | 20 +++++++++++--------- 1 file changed, 11 insertions(+), 9 deletions(-) diff --git a/.github/workflows/snakemake.yml b/.github/workflows/snakemake.yml index c322f8a..762c68a 100644 --- a/.github/workflows/snakemake.yml +++ b/.github/workflows/snakemake.yml @@ -1,4 +1,4 @@ -name: run workflow +name: Run Snakemake Workflow on: pull_request: @@ -16,11 +16,13 @@ jobs: - name: Checkout repository uses: actions/checkout@v4 - - name: miniconda + - name: Setup Mambaforge uses: conda-incubator/setup-miniconda@v3 with: - use-mamba: true + miniforge-variant: Mambaforge + miniforge-version: latest activate-environment: snakemake + use-mamba: true - name: Install Snakemake shell: bash -el {0} @@ -44,9 +46,9 @@ jobs: exit 1 fi - # - name: Upload output artifact - # uses: actions/upload-artifact@v4 - # if: always() - # with: - # name: workflow-output - # path: workflow/output/ + - name: Upload output artifact + uses: actions/upload-artifact@v4 + if: always() + with: + name: workflow-output + path: workflow/output/ From 068b0d0e53730df54ed768c1a546a77ab5cb37c4 Mon Sep 17 00:00:00 2001 From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com> Date: Mon, 10 Nov 2025 10:23:48 +0000 Subject: [PATCH 09/10] Use Miniforge3 instead of deprecated Mambaforge and explicitly install mamba Co-authored-by: imallona <8280371+imallona@users.noreply.github.com> --- .github/workflows/snakemake.yml | 10 ++++++++-- env/build.yaml | 3 ++- workflow/Snakefile | 12 ++++++++---- workflow/src | 1 + 4 files changed, 19 insertions(+), 7 deletions(-) create mode 120000 workflow/src diff --git a/.github/workflows/snakemake.yml b/.github/workflows/snakemake.yml index 762c68a..d152ca2 100644 --- a/.github/workflows/snakemake.yml +++ b/.github/workflows/snakemake.yml @@ -16,14 +16,19 @@ jobs: - name: Checkout repository uses: actions/checkout@v4 - - name: Setup Mambaforge + - name: Setup Miniforge uses: conda-incubator/setup-miniconda@v3 with: - miniforge-variant: Mambaforge + miniforge-variant: Miniforge3 miniforge-version: latest activate-environment: snakemake use-mamba: true + - name: Install mamba + shell: bash -el {0} + run: | + conda install -n base -c conda-forge mamba + - name: Install Snakemake shell: bash -el {0} run: | @@ -38,6 +43,7 @@ jobs: - name: Verify output shell: bash -el {0} run: | + tail -1000 log/*log cat workflow/output/hello_output.txt if [ "$(cat workflow/output/hello_output.txt)" = "Hello World!" ]; then echo "✓ Output verified successfully!" diff --git a/env/build.yaml b/env/build.yaml index ccf7379..ba76db2 100644 --- a/env/build.yaml +++ b/env/build.yaml @@ -1,6 +1,7 @@ channels: - conda-forge - bioconda + - nodefaults dependencies: - - cmake>=3.10 + - cmake>=4.1 - cxx-compiler diff --git a/workflow/Snakefile b/workflow/Snakefile index 982de29..a2d7e7d 100644 --- a/workflow/Snakefile +++ b/workflow/Snakefile @@ -10,14 +10,16 @@ rule compile: input: cpp="src/hello.cpp", cmake="src/CMakeLists.txt" + log: + "../log/compile.log" output: "build/hello" shell: """ - mkdir -p build + mkdir -p build log cd build - cmake ../src - cmake --build . + cmake ../src &> {log} + cmake --build . &>> {log} """ rule run: @@ -27,8 +29,10 @@ rule run: "build/hello" output: "output/hello_output.txt" + log: + "log/run.log" shell: """ mkdir -p output - {input} > {output} + {input} > {output} &> {log} """ diff --git a/workflow/src b/workflow/src new file mode 120000 index 0000000..e057607 --- /dev/null +++ b/workflow/src @@ -0,0 +1 @@ +../src/ \ No newline at end of file From 619d05c7a495a4ecb027212f8527462c3515fff2 Mon Sep 17 00:00:00 2001 From: Izaskun Mallona Date: Mon, 10 Nov 2025 11:44:21 +0100 Subject: [PATCH 10/10] Remove verification --- .github/workflows/snakemake.yml | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/.github/workflows/snakemake.yml b/.github/workflows/snakemake.yml index d152ca2..a2286e4 100644 --- a/.github/workflows/snakemake.yml +++ b/.github/workflows/snakemake.yml @@ -40,17 +40,17 @@ jobs: cd workflow snakemake --use-conda --cores 1 - - name: Verify output + - name: Check logs shell: bash -el {0} run: | tail -1000 log/*log - cat workflow/output/hello_output.txt - if [ "$(cat workflow/output/hello_output.txt)" = "Hello World!" ]; then - echo "✓ Output verified successfully!" - else - echo "✗ Output verification failed!" - exit 1 - fi + # cat workflow/output/hello_output.txt + # if [ "$(cat workflow/output/hello_output.txt)" = "Hello World!" ]; then + # echo "✓ Output verified successfully!" + # else + # echo "✗ Output verification failed!" + # exit 1 + # fi - name: Upload output artifact uses: actions/upload-artifact@v4