Fix issues with continuous integration setup

.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

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()
 

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)

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.