ToRNAdoFold and Infernal-as-library

.gitmodules

@@ -1,6 +1,3 @@
-[submodule "lib/ViennaRNA"]
-	path = lib/viennarna/ViennaRNA
-	url = https://github.com/ViennaRNA/ViennaRNA.git
 [submodule "util/regression"]
     path = lib/mmseqs/util/regression
     url = https://github.com/soedinglab/MMseqs2-Regression.git

CMakeLists.txt

@@ -31,18 +31,14 @@ if (RIBOSEEK_FRAMEWORK_ONLY)
     set(FRAMEWORK_ONLY 1 CACHE INTERNAL "" FORCE)
 endif()
 
-# Infernal bridge for cmbuild
-set(ENABLE_INFERNAL_BRIDGE 1 CACHE BOOL "Enable embedded Infernal-backed CM build bridge")
 set(INFERNAL_ROOT "${CMAKE_CURRENT_SOURCE_DIR}/lib/infernal/vendor" CACHE PATH "Path to vendored Infernal source/build tree")
-if (ENABLE_INFERNAL_BRIDGE)
-    if (NOT EXISTS ${INFERNAL_ROOT}/src/cmbuild.c)
-        message(FATAL_ERROR "ENABLE_INFERNAL_BRIDGE=ON requires INFERNAL_ROOT with src/cmbuild.c")
-    endif ()
-    add_subdirectory(lib/infernal)
+set(INFERNAL_CONFIG_DIR "${CMAKE_CURRENT_SOURCE_DIR}/lib/infernal/config")
+if (NOT EXISTS ${INFERNAL_ROOT}/src/infernal.h)
+    message(FATAL_ERROR "riboseek requires vendored infernal at INFERNAL_ROOT")
 endif ()
+add_subdirectory(lib/infernal)
 
-# ViennaRNA minimal library (hand-rolled CMake wrapper, autotools-free)
-add_subdirectory(lib/viennarna)
+add_subdirectory(lib/tornadofold EXCLUDE_FROM_ALL)
 
 add_subdirectory(data)
 add_subdirectory(src)