diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml index 51aac77..aeef94d 100644 --- a/.github/workflows/test.yml +++ b/.github/workflows/test.yml @@ -62,7 +62,7 @@ jobs: - name: Build C extension run: pip install -e . --no-build-isolation - name: Install test requirements - run: python -m pip install -r pyhmmer/tests/requirements.txt + run: python -m pip install -r src/pyhmmer/tests/requirements.txt - name: Test with coverage run: python -m coverage run -m unittest pyhmmer.tests -vv - name: Upload to Codecov @@ -166,7 +166,7 @@ jobs: - name: Build C extension run: arch -x86_64 pip install -e . --no-build-isolation - name: Install test requirements - run: python -m pip install -r pyhmmer/tests/requirements.txt + run: python -m pip install -r src/pyhmmer/tests/requirements.txt if: matrix.python-impl == 'CPython' - name: Test with coverage run: python -m coverage run -m unittest pyhmmer.tests -vv diff --git a/CMakeLists.txt b/CMakeLists.txt index d5eaa01..33af1fc 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -17,8 +17,9 @@ include("src/scripts/cmake/CythonExtension.cmake") if(HAVE_SSE4) set(eslENABLE_SSE4 true) - if(SSE4_C_FLAGS) - add_compile_options(${SSE4_C_FLAGS}) + string(STRIP "${SSE4_C_FLAGS}" IMPL_FLAGS) + if(IMPL_FLAGS) + add_compile_options(${IMPL_FLAGS}) endif() endif() diff --git a/src/easel/CMakeLists.txt b/src/easel/CMakeLists.txt index 748760e..fd1d68c 100644 --- a/src/easel/CMakeLists.txt +++ b/src/easel/CMakeLists.txt @@ -12,7 +12,7 @@ CHECK_INCLUDE_FILE("sys/types.h" HAVE_SYS_TYPES_H) CHECK_INCLUDE_FILE("unistd.h" HAVE_UNISTD_H) CHECK_INCLUDE_FILE("endian.h" HAVE_ENDIAN_H) CHECK_INCLUDE_FILE("netinet/in.h" HAVE_NETINET_IN_H) -CHECK_INCLUDE_FILE("sys/[aram.h" HAVE_SYS_PARAM_H) +CHECK_INCLUDE_FILE("sys/param.h" HAVE_SYS_PARAM_H) CHECK_INCLUDE_FILE("sys/sysctl.h" HAVE_SYS_SYSCTL_H) CHECK_FUNCTION_EXISTS(aligned_alloc HAVE_ALIGNED_ALLOC) diff --git a/src/easel/esl_config.h.in b/src/easel/esl_config.h.in index 4e05d21..acf2228 100644 --- a/src/easel/esl_config.h.in +++ b/src/easel/esl_config.h.in @@ -79,15 +79,15 @@ /* Types */ #cmakedefine WORDS_BIGENDIAN -#cmakedefine int8_t -#cmakedefine int16_t -#cmakedefine int32_t -#cmakedefine int64_t -#cmakedefine uint8_t -#cmakedefine uint16_t -#cmakedefine uint32_t -#cmakedefine uint64_t -#cmakedefine off_t +// #cmakedefine int8_t +// #cmakedefine int16_t +// #cmakedefine int32_t +// #cmakedefine int64_t +// #cmakedefine uint8_t +// #cmakedefine uint16_t +// #cmakedefine uint32_t +// #cmakedefine uint64_t +// #cmakedefine off_t /* Compiler characteristics */ #cmakedefine HAVE_FUNC_ATTRIBUTE_NORETURN // Compiler supports __attribute__((__noreturn__)), helps w/ clang static analysis.