Setup compilation of HMMER impl for NEON and VMX platforms

pyproject.toml

@@ -73,8 +73,8 @@ cmake.define.CMAKE_CXX_COMPILER_LAUNCHER = "sccache"
 if.env.MOLD = true
 cmake.define.CMAKE_LINKER_TYPE = "mold"
 
-#[tool.coverage.run]
-#plugins = ["Cython.Coverage"]
+[tool.coverage.run]
+plugins = ["Cython.Coverage"]
 
 [tool.cibuildwheel]
 before-build = "pip install scikit-build-core cython"
@@ -99,12 +99,6 @@ exclude_lines = [
     "raise AllocationError",
 ]
 
-[tool.coverage.paths]
-source = [
-    "src/pyhmmer/",
-    "build/Debug/src/pyhmmer/",
-]
-
 [tool.mypy]
 disallow_any_decorated = true
 disallow_any_generics = true

src/hmmer/src/CMakeLists.txt

@@ -93,6 +93,39 @@ if(HMMER_IMPL STREQUAL "SSE")
         impl_sse/stotrace.c
         impl_sse/vitfilter.c
     )
+elseif(HMMER_IMPL STREQUAL "NEON")
+    set(HMMER_SOURCES
+        ${HMMER_SOURCES}
+        impl_neon/decoding.c
+        impl_neon/fwdback.c
+        impl_neon/io.c
+        impl_neon/mpi.c
+        impl_neon/msvfilter.c
+        impl_neon/null2.c
+        impl_neon/optacc.c
+        impl_neon/p7_omx.c
+        impl_neon/p7_oprofile.c
+        impl_neon/ssvfilter.c
+        impl_neon/stotrace.c
+        impl_neon/vitfilter.c
+    )
+elseif(HMMER_IMPL STREQUAL "VMX")
+    set(HMMER_SOURCES
+        ${HMMER_SOURCES}
+        impl_vmx/decoding.c
+        impl_vmx/fwdback.c
+        impl_vmx/io.c
+        impl_vmx/mpi.c
+        impl_vmx/msvfilter.c
+        impl_vmx/null2.c
+        impl_vmx/optacc.c
+        impl_vmx/p7_omx.c
+        impl_vmx/p7_oprofile.c
+        impl_vmx/stotrace.c
+        impl_vmx/vitfilter.c
+    )
+else()
+    message(FATAL_ERROR "No HMMER implementation defined")
 endif()
 
 add_library(libhmmer ${HMMER_SOURCES})