[doc] switch to core's doc infrastructure

Author: h-2

build_system/biocpp_io-config-version.cmake

@@ -20,6 +20,7 @@ find_path (BIOCPP_IO_INCLUDE_DIR NAMES bio/io.hpp HINTS "${BIOCPP_IO_CLONE_DIR}/
 file(STRINGS "${BIOCPP_IO_INCLUDE_DIR}/bio/io.hpp" BIOCPP_IO_LIBRARY_HEADER REGEX "#define BIOCPP_IO_VERSION_(MAJOR|MINOR|PATCH)")
 string(REGEX REPLACE "#define BIOCPP_IO_VERSION_(MAJOR|MINOR|PATCH) " "" PACKAGE_VERSION "${BIOCPP_IO_LIBRARY_HEADER}")
 string(REGEX REPLACE ";" "." PACKAGE_VERSION "${PACKAGE_VERSION}")
+set(BIOCPP_IO_VERSION ${PACKAGE_VERSION} CACHE STRING "Version of the I/O library")
 
 if(PACKAGE_VERSION VERSION_LESS PACKAGE_FIND_VERSION)
     set(PACKAGE_VERSION_COMPATIBLE FALSE)

doc/main_page.md

@@ -1,4 +1,4 @@
-# Welcome {#mainpage}
+# Welcome {#io_mainpage}
 
 Welcome to the documentation of the BioC++ I/O library.
 This web-site contains the API reference (documentation of our interfaces) and some small Tutorials and HowTos.

test/documentation/CMakeLists.txt

@@ -1,33 +1,35 @@
 # Minimum cmake version
 cmake_minimum_required(VERSION 3.7)
 
-### Get our version and directories
+## Setup I/O library
 include (../../build_system/biocpp_io-config-version.cmake)
-set (BIOCPP_IO_VERSION "${PACKAGE_VERSION}")
 
 project (biocpp_io_doc LANGUAGES NONE VERSION "${BIOCPP_IO_VERSION}")
 
-if (NOT EXISTS "${BIOCPP_IO_INCLUDE_DIR}/bio/io.hpp")
-    message (FATAL_ERROR "Could not find the BioC++ I/O library. Not building documentation.")
+if (NOT IS_DIRECTORY "${BIOCPP_IO_CLONE_DIR}/doc")
+    message (FATAL_ERROR "Could not find BioC++ I/O library. Not building documentation.")
 endif ()
-message (STATUS "Found BioC++ I/O library: ${BIOCPP_IO_INCLUDE_DIR} (${BIOCPP_IO_VERSION})")
+message (STATUS "BioC++ I/O library: ${BIOCPP_IO_CLONE_DIR} (${BIOCPP_IO_VERSION})")
 
-### Get core's version and directories
+### Find core infrastructure which is needed and core content which is optional
 include(../biocpp_require_core_infrastructure.cmake)
-biocpp_require_core_infrastructure(FALSE)
+biocpp_require_core_infrastructure(FALSE) # false means that find_package is not called
 
-set (BIOCPP_IO_DOXYGEN_INPUT_DIR "${CMAKE_SOURCE_DIR}")
+if (NOT IS_DIRECTORY "${BIOCPP_CORE_CLONE_DIR}/doc")
+    message (FATAL_ERROR "Could not find BioC++ Core. Not building documentation.")
+endif ()
+message (STATUS "BioC++ Core library: ${BIOCPP_CORE_CLONE_DIR} (${BIOCPP_CORE_VERSION})")
 
-#TODO: use the .cmake file from the core repo and remove this one
-#TODO: also just use the doxygen_cfg.in if possible
-include (bio-doxygen.cmake)
+## Configure documentation build
+option(BIOCPP_DOXY_CORE "Build documentation for core module." ON)
+option(BIOCPP_DOXY_IO "Build documentation for core module." ON)
 
-enable_testing ()
+if (BIOCPP_DOXY_CORE)
+    include (${BIOCPP_CORE_CLONE_DIR}/test/documentation/biocpp-doxygen-module.cmake)
+endif()
 
-if (BIOCPP_IO_USER_DOC)
-    add_subdirectory(doc_usr)
-endif ()
+if (BIOCPP_DOXY_IO)
+    include (bio-doxygen-module.cmake)
+endif()
 
-if (BIOCPP_IO_DEV_DOC)
-    add_subdirectory(doc_dev)
-endif ()
+include (${BIOCPP_CORE_CLONE_DIR}/test/documentation/biocpp-doxygen.cmake)

test/documentation/DoxygenLayout.xml

@@ -0,0 +1,4 @@
+    <tab type="usergroup" visible="yes" title="Record-based I/O" intro="">
+      <tab type="user" visible="yes" title="Introduction" url="\ref record_based_intro" intro=""/>
+      <tab type="user" visible="yes" title="Record FAQ" url="\ref record_faq" intro=""/>
+    </tab>

test/documentation/DoxygenLayout.xml.module

@@ -0,0 +1,14 @@
+cmake_minimum_required (VERSION 3.7)
+
+LIST(APPEND BIOCPP_DOXYGEN_MODULE_LAYOUT ${BIOCPP_IO_CLONE_DIR}/test/documentation/DoxygenLayout.xml.module)
+
+set (BIOCPP_DOXYGEN_INCLUDE_PATH "${BIOCPP_DOXYGEN_INCLUDE_PATH} ${BIOCPP_IO_INCLUDE_DIR}")
+
+set (BIOCPP_DOXYGEN_INPUT "${BIOCPP_DOXYGEN_INPUT}                      \
+                           ${BIOCPP_IO_CLONE_DIR}/include               \
+                           ${BIOCPP_IO_CLONE_DIR}/doc                   \
+                           ${BIOCPP_IO_CLONE_DIR}/CHANGELOG.md")
+
+set (BIOCPP_DOXYGEN_EXAMPLE_PATH "${BIOCPP_DOXYGEN_EXAMPLE_PATH} ${BIOCPP_IO_CLONE_DIR}")
+
+set(BIOCPP_VERSION "${BIOCPP_VERSION} io-${BIOCPP_IO_VERSION}")