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seqan · Jun 2, 2022 · 2f31139 · 2f31139
1 parent f7893b5
commit 2f31139
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diff --git a/test/documentation/CMakeLists.txt b/test/documentation/CMakeLists.txt
@@ -29,21 +29,16 @@ include (seqan3-doxygen-layout.cmake)
 
 enable_testing ()
 
-### Copy over snippets from sharg
-### -----------------------------
-### This is needed to replace sharg with seqan3 in all snippets for correct documentation.
-set (SHARG_SNIPPET_OUTPUT_DIR "${CMAKE_BINARY_DIR}/sharg_snippets")
-file(MAKE_DIRECTORY ${SHARG_SNIPPET_OUTPUT_DIR})
-message(STATUS "Created sharg snippet directory: ${SHARG_SNIPPET_OUTPUT_DIR}")
-
-include (${CMAKE_SOURCE_DIR}/../cmake/seqan3_test_files.cmake)
-seqan3_test_files (sharg_snippet_files "${SEQAN3_INCLUDE_DIR}/../submodules/sharg-parser/test/snippet/" "*.cpp")
-
-foreach (sharg_snippet_filename ${sharg_snippet_files})
-    file(READ "${SEQAN3_INCLUDE_DIR}/../submodules/sharg-parser/test/snippet/${sharg_snippet_filename}" SNIPPET_INPUT_CONTENT)
-    string(REGEX REPLACE "sharg" "seqan3" SNIPPET_OUTPUT_CONTENT ${SNIPPET_INPUT_CONTENT})
-    file(WRITE "${SHARG_SNIPPET_OUTPUT_DIR}/${sharg_snippet_filename}" ${SNIPPET_OUTPUT_CONTENT})
-endforeach ()
+include ("${CMAKE_SOURCE_DIR}/seqan3-doxygen-copy-and-replace.cmake")
+
+file (MAKE_DIRECTORY ${CMAKE_BINARY_DIR}/additional_doc)
+
+# Copy over snippets from sharg into ${CMAKE_SOURCE_DIR}/sharg_snippets
+# This is needed to replace sharg with seqan3 in all snippets for correct documentation.
+copy_files_and_replace_seqan3 ("${SEQAN3_INCLUDE_DIR}/../submodules/sharg-parser/test/snippet/"
+                               "*.cpp"
+                               "sharg_snippets"
+                               "sharg")
 
 ### Add subdirectories
 if (SEQAN3_USER_DOC)

diff --git a/test/documentation/seqan3-doxygen-copy-and-replace.cmake b/test/documentation/seqan3-doxygen-copy-and-replace.cmake
@@ -0,0 +1,65 @@
+# -----------------------------------------------------------------------------------------------------
+# Copyright (c) 2006-2021, Knut Reinert & Freie Universität Berlin
+# Copyright (c) 2016-2021, Knut Reinert & MPI für molekulare Genetik
+# This file may be used, modified and/or redistributed under the terms of the 3-clause BSD-License
+# shipped with this file and also available at: https://github.com/seqan/seqan3/blob/master/LICENSE.md
+# -----------------------------------------------------------------------------------------------------
+
+cmake_minimum_required (VERSION 3.10)
+
+include (${CMAKE_SOURCE_DIR}/../cmake/seqan3_test_files.cmake)
+
+function (copy_files_and_replace_seqan3 INPUT_PATH WILDCARDS OUTPUT_DIR_NAME NAME_TO_REPLACE_WITH_SEQAN3)
+
+    # collect files to copy
+    seqan3_test_files (input_files "${INPUT_PATH}" "${WILDCARDS}")
+
+    # create output directory
+    file (MAKE_DIRECTORY ${CMAKE_BINARY_DIR}/additional_doc/${OUTPUT_DIR_NAME})
+
+    # for each file: (1) read the file, (2) replace ${NAME_TO_REPLACE_WITH_SEQAN3} with "seqan3", (3) write the file
+    foreach (input_filename ${input_files})
+        file (READ "${INPUT_PATH}/${input_filename}" INPUT_CONTENT)
+        string (REGEX REPLACE "${NAME_TO_REPLACE_WITH_SEQAN3}" "seqan3" OUTPUT_CONTENT ${INPUT_CONTENT})
+        file (WRITE "${CMAKE_BINARY_DIR}/additional_doc/${OUTPUT_DIR_NAME}/${input_filename}" ${OUTPUT_CONTENT})
+    endforeach ()
+
+endfunction()
+
+function (copy_tutorial_and_replace_seqan3 INPUT_PATH OUTPUT_DIR_NAME NAME_TO_REPLACE_WITH_SEQAN3)
+
+    # collect files to copy
+    seqan3_test_files (doc_index_md_files "${INPUT_PATH}" "index.md")
+
+    # create output directory
+    file (MAKE_DIRECTORY ${CMAKE_BINARY_DIR}/additional_doc/${OUTPUT_DIR_NAME})
+
+    # for each file: (1) read the file, (2) replace ${NAME_TO_REPLACE_WITH_SEQAN3} with "seqan3", (3) write the file
+    foreach (index_md_filename ${doc_index_md_files})
+
+        file (READ "${INPUT_PATH}/${index_md_filename}" INPUT_CONTENT)
+
+        string (REGEX REPLACE "${NAME_TO_REPLACE_WITH_SEQAN3}" "seqan3" OUTPUT_CONTENT ${INPUT_CONTENT})
+
+        # in case this is a documentation page, also change inlcudes and references.
+        # since the regex should not match any content in snippets, it's fine like this.
+        string(REGEX MATCHALL "[^ ]+\\.cpp" INCLUDED_CPP_FILES ${INPUT_CONTENT})
+
+        foreach (cpp_file_path ${INCLUDED_CPP_FILES})
+            get_filename_component(cpp_filename ${cpp_file_path} NAME)
+            file (READ "${INPUT_PATH}../../${cpp_file_path}" CPP_CONTENT)
+            string (REGEX REPLACE "${NAME_TO_REPLACE_WITH_SEQAN3}" "seqan3" CPP_OUTPUT_CONTENT ${CPP_CONTENT})
+            file (WRITE "${CMAKE_BINARY_DIR}/additional_doc/${OUTPUT_DIR_NAME}/${cpp_filename}" ${CPP_OUTPUT_CONTENT})
+        endforeach()
+
+        string (REGEX REPLACE
+                " [^ ]*/\([^/]*\)\.cpp"
+                " ${CMAKE_BINARY_DIR}/additional_doc/${OUTPUT_DIR_NAME}/\\1.cpp"
+                OUTPUT_CONTENT2
+                ${OUTPUT_CONTENT})
+        string (REGEX REPLACE "{#\(.*\)}" "{#seqan3_\\1}" OUTPUT_CONTENT3 ${OUTPUT_CONTENT2})
+
+        file (WRITE "${CMAKE_BINARY_DIR}/additional_doc/index_files/${index_md_filename}" ${OUTPUT_CONTENT3})
+    endforeach ()
+
+endfunction()
diff --git a/test/documentation/seqan3-doxygen-layout.cmake b/test/documentation/seqan3-doxygen-layout.cmake
@@ -8,6 +8,7 @@
 cmake_minimum_required (VERSION 3.10)
 
 include (${SEQAN3_INCLUDE_DIR}/../test/cmake/seqan3_test_files.cmake)
+include ("${CMAKE_SOURCE_DIR}/seqan3-doxygen-copy-and-replace.cmake")
 
 # Replaces documentation entries in variable `DOXYGEN_LAYOUT`
 #
@@ -69,5 +70,11 @@ replace_in_doxygen_layout ("${SEQAN3_INCLUDE_DIR}/../doc/about/" "About")
 replace_in_doxygen_layout ("${SEQAN3_INCLUDE_DIR}/../doc/setup/" "Setup")
 replace_in_doxygen_layout ("${SEQAN3_INCLUDE_DIR}/../doc/tutorial/" "Tutorial")
 replace_in_doxygen_layout ("${SEQAN3_INCLUDE_DIR}/../doc/howto/" "How-To")
+# add sharg doc
+copy_tutorial_and_replace_seqan3 ("${SEQAN3_INCLUDE_DIR}/../submodules/sharg-parser/doc/tutorial/" "sharg_tut" "sharg")
+replace_in_doxygen_layout ("${CMAKE_BINARY_DIR}/additional_doc/index_files" "Tutorial")
+
+copy_tutorial_and_replace_seqan3 ("${SEQAN3_INCLUDE_DIR}/../submodules/sharg-parser/doc/howto/" "sharg_howto" "sharg")
+replace_in_doxygen_layout ("${CMAKE_BINARY_DIR}/additional_doc/index_files" "How-To")
 
 file (WRITE "${CMAKE_BINARY_DIR}/DoxygenLayout.xml" ${DOXYGEN_LAYOUT})
diff --git a/test/documentation/seqan3_doxygen_cfg.in b/test/documentation/seqan3_doxygen_cfg.in
@@ -15,6 +15,7 @@ INPUT                  = ${SEQAN3_DOXYGEN_SOURCE_DIR}/submodules/sharg-parser/in
                          ${SEQAN3_DOXYGEN_SOURCE_DIR}/LICENSE.md                        \
                          ${SEQAN3_DOXYGEN_SOURCE_DIR}/CHANGELOG.md                      \
                          ${SEQAN3_DOXYGEN_SOURCE_DIR}/CODE_OF_CONDUCT.md                \
+                         ${CMAKE_BINARY_DIR}/additional_doc/index_files                 \
                          ${SEQAN3_DOXYGEN_SOURCE_DIR}/CONTRIBUTING.md
 STRIP_FROM_PATH        = ${SEQAN3_DOXYGEN_SOURCE_DIR}/include \
                          ${SEQAN3_DOXYGEN_SOURCE_DIR}/submodules/sharg-parser/include
@@ -25,7 +26,7 @@ IMAGE_PATH             = ${SEQAN3_DOXYGEN_SOURCE_DIR}/doc \
                          ${SEQAN3_DOXYGEN_SOURCE_DIR}/test/documentation
 
 # Replace namespace sharg with seqan3 when including the API documentation of sharg
-FILTER_PATTERNS= *sharg*.hpp="sed -e 's/sharg/seqan3/g' -e 's/SHARG/SEQAN3/g' -e 's;\\include .*/;\\include ${CMAKE_BINARY_DIR}/sharg_snippets/;g'"
+FILTER_PATTERNS= *sharg*.hpp="sed -e 's/sharg/seqan3/g' -e 's/SHARG/SEQAN3/g' -e 's;\\include .*/;\\include ${CMAKE_BINARY_DIR}/additional_doc/sharg_snippets/;g'"
 
 ## DOT SUPPORT
 HAVE_DOT               = ${SEQAN3_DOXYGEN_HAVE_DOT}