Fix documentation warnings and errors.

+ Apply the filter only to specific file patterns. Replacing all `$`
  characters by `\f$` creates a big issue in bash and other languages
  where `$` has another signification. This convenience feature is needed
  only for the hpp/cpp/cu* files.
+ Remove the `FILE_VERSION_FILTER` from the Doxyfile configuration: this
  command is used to extract the version of every file and is always ran.
  We already publish the version of Ginkgo so it's unneeded. In addition,
  when building out of source, the example files are not part of a git
  repository and that creates issues.
+ Remove the `doxygen_image_path` as it's unused and throws a warning
+ Use `Ginkgo_SOURCE_DIR` to locate the md files instead of `../..`.

BENCHMARKING.md

@@ -46,7 +46,7 @@ order to ensure best performance.
    benchmarking accuracy.
 
 In addition, the following specific options can be considered:
-1. When specifically using the adaptive block jacobi preconditioner,, enable
+1. When specifically using the adaptive block jacobi preconditioner, enable
    the `GINKGO_JACOBI_FULL_OPTIMIZATIONS` CMake flag. Be careful that this will
    use much more memory and time for the compilation due to compiler performance
    issues with register optimizations, in particular.
@@ -55,7 +55,7 @@ In addition, the following specific options can be considered:
    `overhead` LinOp. If your purpose is to check Ginkgo's overhead, make sure to
    try this mode.
 
-### 2: Using `ssget` to fetch the matrices
+### 2: Using ssget to fetch the matrices
 
 The benchmark suite tests Ginkgo's performance using the [SuiteSparse matrix
 collection](https://sparse.tamu.edu/) and artificially generated matrices. The
@@ -84,7 +84,9 @@ where `i` is the ID of the matrix to be downloaded. The following loop allows
 to download the full SuiteSparse matrix collection:
 
 ```bash
-for i in $(seq 0 $(ssget -n)); do ssget -f -i $i; done
+for i in $(seq 0 $(ssget -n)); do
+    ssget -f -i ${i}
+done
 ```
 
 Note that `ssget` can also be used to query properties of the matrix and filter
@@ -93,13 +95,14 @@ positive definite matrices with less than 500M non zero elements and 10M
 columns. Please refer to the [`ssget`
 documentation](https://github.com/ginkgo-project/ssget/blob/master/README.md)
 for more information.
+
 ```bash
 for i in $(seq 0 $(ssget -n)); do
-    posdef=$(ssget -p posdef -i $i)
-    cols=$(ssget -p cols -i $i)
-    nnz=$(ssget -p nonzeros -i $i)
+    posdef=$(ssget -p posdef -i ${i})
+    cols=$(ssget -p cols -i ${i})
+    nnz=$(ssget -p nonzeros -i ${i})
     if [ "$posdef" -eq 1 -a "$cols" -lt 10000000 -a "$nnz" -lt 500000000 ]; then
-        ssget -f -i $i
+        ssget -f -i ${i}
     fi
 done
 ```
@@ -113,22 +116,22 @@ script as well. The behavior of the suite can be modified using environment
 variables. Assuming the `bash` shell is used, these can either be specified via
 the `export` command to persist between multiple runs:
 
-```sh
+```bash
 export VARIABLE="value"
 ...
 make benchmark
 ```
 
 or specified on the fly, on the same line as the `make benchmark` command:
 
-```sh
+```bash
 VARIABLE="value" ... make benchmark
 ```
 
 Since `make` sets any variables passed to it as temporary environment variables,
 the following shorthand can also be used:
 
-```sh
+```bash
 make benchmark VARIABLE="value" ...
 ```
 
@@ -157,6 +160,7 @@ benchmark options). Here are the most important options:
     matrix id or name to benchmark. As an example, a matrix list file containing
     the following will ensure that benchmarks are ran for only those three
     matrices:
+
     ```
     1903
     Freescale/circuit5M
@@ -180,12 +184,13 @@ https://github.com/ginkgo-project/ginkgo-data/
 Once it's done, we want to clone the repository locally, put all
 results online and access the GPE for plotting the results. Here are the
 detailed steps:
+
 ```bash
 git clone https://github.com/<username>/ginkgo-data.git $HOME/ginkgo_benchmark/ginkgo-data
 # send the benchmarked data to the ginkgo-data repository
 # If needed, remove the old data so that no previous data is left.
 # rm -r ${HOME}/ginkgo_benchmark/ginkgo-data/data/${SYSTEM_NAME}
-rsync -rtv ${ginkgo_build}/benchmark/results/ $HOME/ginkgo_benchmark/ginkgo-data/data/
+rsync -rtv ${ginkgo_build_dir}/benchmark/results/ $HOME/ginkgo_benchmark/ginkgo-data/data/
 cd ${HOME}/ginkgo_benchmark/ginkgo-data/data/
 # The following updates the main `.json` files with the list of data.
 # Ensure a python 3 installation is available.

doc/conf/Doxyfile.in

@@ -24,7 +24,7 @@ STRIP_FROM_INC_PATH    = @DIR_BASE@/include
 EXCLUDE_PATTERNS       = */test/*
 PROJECT_LOGO           = @DIR_BASE@/assets/logo_doc.png
 USE_MDFILE_AS_MAINPAGE = @MAINPAGE@
-INPUT_FILTER           = @DIR_SCRIPT@/filter
+FILTER_PATTERNS        = *.cpp=@DIR_SCRIPT@/filter *.hpp=@DIR_SCRIPT@/filter *.cu*=@DIR_SCRIPT@/filter
 FILTER_SOURCE_FILES    = YES
 
 # Parsing options
@@ -55,9 +55,9 @@ MAX_INITIALIZER_LINES  = 30
 SHOW_USED_FILES        = YES
 SHOW_FILES             = YES
 SHOW_NAMESPACES        = YES
-FILE_VERSION_FILTER    = "@DIR_SCRIPT@/doxygen_version_extract.sh @PROJECT_SOURCE_DIR@"
 CITE_BIB_FILES         =
 INHERIT_DOCS           = YES
+USE_MATHJAX            = NO
 
 BUILTIN_STL_SUPPORT    = YES
 

doc/helpers.cmake

@@ -71,7 +71,7 @@ function(ginkgo_doc_gen name in pdf mainpage-in)
         ${DIR_BASE}/hip
         ${DIR_BASE}/reference
         )
-    set(doxygen_image_path "${CMAKE_SOURCE_DIR}/doc/images/")
+    set(doxygen_image_path "")
     file(GLOB doxygen_depend
         ${DOC_BASE}/headers/*.hpp
         ${DIR_BASE}/include/ginkgo/**/*.hpp
@@ -101,7 +101,7 @@ function(ginkgo_doc_gen name in pdf mainpage-in)
         ${doxygen_base_input}
         )
     # pick some markdown files we want as pages
-    set(doxygen_markdown_files "../../INSTALL.md ../../TESTING.md ../../BENCHMARKING.md ../../CONTRIBUTING.md ../../CITING.md")
+    set(doxygen_markdown_files "${Ginkgo_SOURCE_DIR}/INSTALL.md ${Ginkgo_SOURCE_DIR}/TESTING.md ${Ginkgo_SOURCE_DIR}/BENCHMARKING.md ${Ginkgo_SOURCE_DIR}/CONTRIBUTING.md ${Ginkgo_SOURCE_DIR}/CITING.md")
     ginkgo_to_string(doxygen_base_input_str ${doxygen_base_input} )
     ginkgo_to_string(doxygen_dev_input_str ${doxygen_dev_input} )
     ginkgo_to_string(doxygen_image_path_str ${doxygen_image_path} )