Add Doxygen support to configure, update documentation

.gitignore

@@ -28,3 +28,5 @@ stamp-h1
 ftimings-*-*.pc
 ftimings_*_test
 ftimings.mod
+docs/
+Doxyfile

Makefile.am

@@ -30,3 +30,5 @@ ftimings_@FC@_test_LDADD = libftimings-@FTIMINGS_API_VERSION@-@FC@.la
 # other files to distribute
 filesdir = $(datadir)/@PACKAGE@-@FC@/examples
 files_DATA = test/test_timings.F90
+
+include doxygen.am

configure.ac

@@ -22,13 +22,21 @@ LT_INIT
 
 PKG_PROG_PKG_CONFIG
 
+DX_PDF_FEATURE(OFF)
+DX_PS_FEATURE(OFF)
+DX_MAN_FEATURE(ON)
+DX_HTML_FEATURE(ON)
+DX_INIT_DOXYGEN([ftimings], [Doxyfile], [docs])
+
 AC_SUBST([FTIMINGS_SO_VERSION], [0:1:0])
 AC_SUBST([FTIMINGS_API_VERSION], [0.1])
 AC_SUBST([AM_CFLAGS])
 AC_SUBST([AM_FCFLAGS])
 AC_SUBST([AM_LDFLAGS])
+AC_SUBST([DOXYGEN_OUTPUT_DIR], [docs])
 
 AC_CONFIG_FILES([Makefile
+		 Doxyfile
 		 ftimings-${FTIMINGS_API_VERSION}-${FC}.pc:ftimings.pc.in
 		 ])
 AC_OUTPUT

doxygen.am

+## --------------------------------- ##
+## Format-independent Doxygen rules. ##
+## --------------------------------- ##
+
+if DX_COND_doc
+
+## ------------------------------- ##
+## Rules specific for HTML output. ##
+## ------------------------------- ##
+
+if DX_COND_html
+
+DX_CLEAN_HTML = @DX_DOCDIR@/html
+
+endif DX_COND_html
+
+## ------------------------------ ##
+## Rules specific for CHM output. ##
+## ------------------------------ ##
+
+if DX_COND_chm
+
+DX_CLEAN_CHM = @DX_DOCDIR@/chm
+
+if DX_COND_chi
+
+DX_CLEAN_CHI = @DX_DOCDIR@/@PACKAGE@.chi
+
+endif DX_COND_chi
+
+endif DX_COND_chm
+
+## ------------------------------ ##
+## Rules specific for MAN output. ##
+## ------------------------------ ##
+
+if DX_COND_man
+
+DX_CLEAN_MAN = @DX_DOCDIR@/man
+
+endif DX_COND_man
+
+## ------------------------------ ##
+## Rules specific for RTF output. ##
+## ------------------------------ ##
+
+if DX_COND_rtf
+
+DX_CLEAN_RTF = @DX_DOCDIR@/rtf
+
+endif DX_COND_rtf
+
+## ------------------------------ ##
+## Rules specific for XML output. ##
+## ------------------------------ ##
+
+if DX_COND_xml
+
+DX_CLEAN_XML = @DX_DOCDIR@/xml
+
+endif DX_COND_xml
+
+## ----------------------------- ##
+## Rules specific for PS output. ##
+## ----------------------------- ##
+
+if DX_COND_ps
+
+DX_CLEAN_PS = @DX_DOCDIR@/@PACKAGE@.ps
+
+DX_PS_GOAL = doxygen-ps
+
+doxygen-ps: @DX_DOCDIR@/@PACKAGE@.ps
+
+@DX_DOCDIR@/@PACKAGE@.ps: @DX_DOCDIR@/@PACKAGE@.tag
+	cd @DX_DOCDIR@/latex; \
+	rm -f *.aux *.toc *.idx *.ind *.ilg *.log *.out; \
+	$(DX_LATEX) refman.tex; \
+	$(MAKEINDEX_PATH) refman.idx; \
+	$(DX_LATEX) refman.tex; \
+	countdown=5; \
+	while $(DX_EGREP) 'Rerun (LaTeX|to get cross-references right)' \
+	                  refman.log > /dev/null 2>&1 \
+	   && test $$countdown -gt 0; do \
+	    $(DX_LATEX) refman.tex; \
+	    countdown=`expr $$countdown - 1`; \
+	done; \
+	$(DX_DVIPS) -o ../@PACKAGE@.ps refman.dvi
+
+endif DX_COND_ps
+
+## ------------------------------ ##
+## Rules specific for PDF output. ##
+## ------------------------------ ##
+
+if DX_COND_pdf
+
+DX_CLEAN_PDF = @DX_DOCDIR@/@PACKAGE@.pdf
+
+DX_PDF_GOAL = doxygen-pdf
+
+doxygen-pdf: @DX_DOCDIR@/@PACKAGE@.pdf
+
+@DX_DOCDIR@/@PACKAGE@.pdf: @DX_DOCDIR@/@PACKAGE@.tag
+	cd @DX_DOCDIR@/latex; \
+	rm -f *.aux *.toc *.idx *.ind *.ilg *.log *.out; \
+	$(DX_PDFLATEX) refman.tex; \
+	$(DX_MAKEINDEX) refman.idx; \
+	$(DX_PDFLATEX) refman.tex; \
+	countdown=5; \
+	while $(DX_EGREP) 'Rerun (LaTeX|to get cross-references right)' \
+	                  refman.log > /dev/null 2>&1 \
+	   && test $$countdown -gt 0; do \
+	    $(DX_PDFLATEX) refman.tex; \
+	    countdown=`expr $$countdown - 1`; \
+	done; \
+	mv refman.pdf ../@PACKAGE@.pdf
+
+endif DX_COND_pdf
+
+## ------------------------------------------------- ##
+## Rules specific for LaTeX (shared for PS and PDF). ##
+## ------------------------------------------------- ##
+
+if DX_COND_latex
+
+DX_CLEAN_LATEX = @DX_DOCDIR@/latex
+
+endif DX_COND_latex
+
+.PHONY: doxygen-run doxygen-doc $(DX_PS_GOAL) $(DX_PDF_GOAL)
+
+.INTERMEDIATE: doxygen-run $(DX_PS_GOAL) $(DX_PDF_GOAL)
+
+doxygen-run: @DX_DOCDIR@/@PACKAGE@.tag
+
+doxygen-doc: doxygen-run $(DX_PS_GOAL) $(DX_PDF_GOAL)
+
+@DX_DOCDIR@/@PACKAGE@.tag: $(DX_CONFIG) $(pkginclude_HEADERS)
+	rm -rf @DX_DOCDIR@
+	$(DX_ENV) $(DX_DOXYGEN) $(srcdir)/$(DX_CONFIG)
+
+DX_CLEANFILES = \
+	@DX_DOCDIR@/@PACKAGE@.tag \
+	-r \
+	$(DX_CLEAN_HTML) \
+	$(DX_CLEAN_CHM) \
+	$(DX_CLEAN_CHI) \
+	$(DX_CLEAN_MAN) \
+	$(DX_CLEAN_RTF) \
+	$(DX_CLEAN_XML) \
+	$(DX_CLEAN_PS) \
+	$(DX_CLEAN_PDF) \
+	$(DX_CLEAN_LATEX)
+
+endif DX_COND_doc

ftimings/ftimings.f90

+!> Ftimings
+!>
+!> An almost pure-fortran attempt to play with graph structures :)
 module ftimings
   use, intrinsic :: iso_c_binding, only : C_INT64_T, C_DOUBLE
   implicit none
   save
 
-  public timer_t
   private
 
+  ! this is mainly needed for Doxygen...
+  public timer_start, timer_stop, timer_free, timer_print, &
+         timer_enable, timer_disable, timer_is_enabled, &
+         timer_in_entries, timer_get, timer_since, timer_sort
+
   integer, parameter, private :: name_length = 32
   integer, parameter, private :: rk = C_DOUBLE
 
@@ -17,10 +24,12 @@ module ftimings
     end function
   end interface
 
+  ! Private type node_t, representing a graph node
+  !
   type node_t
-    character(len=name_length) :: name
-    integer(kind=C_INT64_T) :: micros
-    integer :: count
+    character(len=name_length) :: name             ! Descriptive name, used when printing the timings
+    integer(kind=C_INT64_T) :: micros              ! Cumulative microseconds spent in this node
+    integer :: count                               ! Number of calls
     type(node_t), pointer :: firstChild => NULL()
     type(node_t), pointer :: lastChild => NULL()
     type(node_t), pointer :: parent => NULL()
@@ -37,11 +46,37 @@ module ftimings
       procedure, pass :: sort_children => node_sort_children
   end type
 
-  type timer_t
+  !> Type for a timer instance.
+  !>
+  !> Typical usage:
+  !> \code{.f90}
+  !>   type(timer_t) :: timer
+  !>
+  !>   call timer%enable()
+  !>
+  !>   call timer%start("section")
+  !>     ...
+  !>   call timer%start("subsection")
+  !>     ...
+  !>   call timer%stop("subsection")
+  !>     ...
+  !>   call timer%stop("section")
+  !>
+  !>   call timer%print()
+  !> \endcode
+  !>
+  !> Every first call to timer%start() at a certain point in the graph
+  !> allocates a small amount of memory. If the timer is no longer needed,
+  !> all that memory can be freed again with
+  !>
+  !> \code{.f90}
+  !>   call timer%free()
+  !> \endcode
+  type, public :: timer_t
     private
-    logical :: active = .false.
-    type(node_t), pointer :: root => NULL()
-    type(node_t), pointer :: current_node => NULL()
+    logical :: active = .false.                         !< If set to .false., most operations return immediately without any action
+    type(node_t), pointer :: root => NULL()             !< Start of graph
+    type(node_t), pointer :: current_node => NULL()     !< Current position in the graph
     contains
       procedure, pass :: start => timer_start
       procedure, pass :: stop => timer_stop
@@ -56,8 +91,8 @@ module ftimings
       procedure, pass :: sort => timer_sort
   end type
 
-  character(len=name_length), parameter :: own = "(own)"
-  character(len=name_length), parameter :: below = "(below threshold)"
+  character(len=name_length), private, parameter :: own = "(own)"
+  character(len=name_length), private, parameter :: below = "(below threshold)"
 
   contains
 
@@ -199,22 +234,25 @@ module ftimings
     enddo
   end function
 
-  subroutine node_print_line(indent_level, label, number, total)
+  subroutine node_print_line(indent_level, label, number, total, unit)
     integer, intent(in) :: indent_level
     character(len=name_length), intent(in) :: label
     integer(kind=C_INT64_T), intent(in) :: number, total
     character(len=64) :: format_spec
+    integer :: unit
 
     write(format_spec,'("(",i0,"x,""|_ "",a",i0,",2x,f10.6,10x,f5.3)")') (indent_level + 1) * 2 + 2, name_length
-    write(*,format_spec) label, real(number, kind=rk) * 1e-6_rk, real(number, kind=rk) / real(total, kind=rk)
+    write(unit,format_spec) label, real(number, kind=rk) * 1e-6_rk, real(number, kind=rk) / real(total, kind=rk)
   end subroutine
 
-  recursive subroutine node_print_graph(self, indent_level, threshold, is_sorted, total)
+  recursive subroutine node_print_graph(self, indent_level, threshold, is_sorted, total, unit)
+    use, intrinsic :: iso_fortran_env, only : output_unit
     class(node_t), intent(in) :: self
     integer, intent(in) :: indent_level
     real(kind=rk), intent(in), optional :: threshold
     logical, intent(in), optional :: is_sorted
     integer(kind=C_INT64_T), intent(in), optional :: total
+    integer, optional :: unit
 
     type(node_t), pointer :: node
     character(len=64) :: format_spec
@@ -223,6 +261,8 @@ module ftimings
     integer(kind=C_INT64_T) :: current_us, own_us, below_threshold_us, total_act
     real(kind=rk) :: threshold_act
     logical :: is_sorted_act, print_own, print_threshold
+    integer :: unit_act
+
 
     if (present(threshold)) then
       threshold_act = threshold
@@ -244,6 +284,12 @@ module ftimings
       total_act = current_us
     endif
 
+    if (present(unit)) then
+      unit_act = unit
+    else
+      unit_act = output_unit
+    endif
+
     own_us = current_us - self%sum_of_children()
     below_threshold_us = self%sum_of_children_below(threshold)
 
@@ -266,18 +312,29 @@ module ftimings
       do i = len(trim(name)) + 2, name_length
         name(i:i) = "."
       end do
-      write(*,format_spec) name, real(current_us, kind=rk) * 1e-6_rk, real(current_us, kind=rk) / real(total_act, kind=rk)
+      write(unit_act,format_spec) &
+        name, real(current_us, kind=rk) * 1e-6_rk, real(current_us, kind=rk) / real(total_act, kind=rk)
     else
       return
     endif
 
+    ! \todo this is very clumsy:
+    !
+    ! we have to insert the (own) and (below threshold) entries
+    ! i) at the start, if printing unsorted or
+    ! ii) at the place they would appear, if sorted
+    !
+    ! at the moment a lot of copied lines are necessary for this,
+    ! and there is no correct sorting between (own) and (below threshold)
+    ! in all cases
+    !
     if ((.not. is_sorted_act) .and. print_own) then
-      call node_print_line(indent_level, own, own_us, current_us)
+      call node_print_line(indent_level, own, own_us, current_us, unit_act)
       print_own = .false.
     endif
 
     if ((.not. is_sorted_act) .and. print_threshold) then
-      call node_print_line(indent_level, below, below_threshold_us, current_us)
+      call node_print_line(indent_level, below, below_threshold_us, current_us, unit_act)
       print_threshold = .false.
     endif
 
@@ -286,49 +343,81 @@ module ftimings
 
       if (print_own) then
         if (node%get_micros() <= own_us) then
-          call node_print_line(indent_level, own, own_us, current_us)
+          call node_print_line(indent_level, own, own_us, current_us, unit_act)
           print_own = .false.
         endif
       endif
 
       if (print_threshold) then
         if (node%get_micros() <= below_threshold_us) then
-          call node_print_line(indent_level, below, below_threshold_us, current_us)
+          call node_print_line(indent_level, below, below_threshold_us, current_us, unit_act)
           print_threshold = .false.
         endif
       endif
 
-      call node%print_graph(indent_level + 1, threshold, is_sorted, current_us)
+      call node%print_graph(indent_level + 1, threshold, is_sorted, current_us, unit_act)
       node => node%nextSibling
     end do
 
     if (print_own) then
-      call node_print_line(indent_level, own, own_us, current_us)
+      call node_print_line(indent_level, own, own_us, current_us, unit_act)
     endif
     if (print_threshold) then
-      call node_print_line(indent_level, below, below_threshold_us, current_us)
+      call node_print_line(indent_level, below, below_threshold_us, current_us, unit_act)
     endif
 
   end subroutine
 
-  ! Public module interface:
-
+  !> Active the timer, without this, most methods are no-ops.
+  !>
+  !> \implements timer_t::enable
   subroutine timer_enable(self)
     class(timer_t), intent(inout), target :: self
     self%active = .true.
   end subroutine
 
+  !> Deactive the timer
+  !>
+  !> \implements timer_t::disable
   subroutine timer_disable(self)
     class(timer_t), intent(inout), target :: self
     self%active = .false.
   end subroutine
 
+  !> \implements timer_t::is_enabled
   function timer_is_enabled(self) result(is)
     class(timer_t), intent(inout), target :: self
     logical :: is
     is = self%active
   end function
 
+  !> Start a timing section
+  !>
+  !> \param name        A descriptive name
+  !> \param replace     If .true. (default .false.), replace any entries at the
+  !>                    current position with the same name. If .false., add the
+  !>                    time to a possibly existing entry
+  !>
+  !> Care must be taken to balance any invocations of %start() and %stop(), e.g.
+  !> the following is valid
+  !>
+  !> \code{.f90}
+  !>   call timer%start("A")
+  !>   call timer%start("B")
+  !>   call timer%stop("B")
+  !>   call timer%stop("A")
+  !> \endcode
+  !>
+  !> while the following is not
+  !>
+  !> \code{.f90}
+  !>   call timer%start("A")
+  !>   call timer%start("B")
+  !>   call timer%stop("A")
+  !>   call timer%stop("B")
+  !> \endcode
+  !>
+  !> \implements timer_t::start
   subroutine timer_start(self, name, replace)
     class(timer_t), intent(inout), target :: self
     character(len=*), intent(in)  :: name
@@ -400,6 +489,11 @@ module ftimings
 
   end subroutine
 
+  !> End a timing segment, \sa timer_start
+  !>
+  !> \param name        The exact same name as was used for %start()
+  !>
+  !> \implements timer_t::stop
   subroutine timer_stop(self, name)
     class(timer_t), intent(inout), target :: self
     character(len=*), intent(in) :: name
@@ -454,6 +548,9 @@ module ftimings
 
   end subroutine
 
+  !> Deallocate all objects associated with (but not including) self
+  !>
+  !> \implements timer_t::free
   subroutine timer_free(self)
     class(timer_t), intent(inout), target :: self
     if (associated(self%root)) then
@@ -463,6 +560,17 @@ module ftimings
     nullify(self%current_node)
   end subroutine
 
+  !> Print a timing graph
+  !>
+  !> \param name1       If given, first descend one level to the node with name name1
+  !> \param name2       If given, also descend another level to the node with name2 there
+  !> \param name3       etc.
+  !> \param name4       etc.
+  !> \param threshold   If given, subsume any entries with a value of threshold
+  !>                    seconds in a single node "(below threshold)"
+  !> \param is_sorted   Assume a sorted graph for inserting "(own)" and "(below threshold)"
+  !>
+  !> \implements timer_t::print
   subroutine timer_print(self, name1, name2, name3, name4, threshold, is_sorted)
     class(timer_t), intent(in), target :: self
     character(len=*), intent(in), optional :: name1, name2, name3, name4
@@ -512,10 +620,12 @@ module ftimings
   !>
   !> \param name1, .., namei-1  The path to the starting node
   !> \param namei               The name of all sub-entries below this
-  !>                            node to which are summed together
+  !>                            node which should be summed together
   !>
   !> For example timer%in_entries("foo", "bar", "parallel") returns
   !> the sum of all entries named "parallel" below the foo->bar node
+  !>
+  !> \implements timer_t::in_entries
   function timer_in_entries(self, name1, name2, name3, name4) result(s)
     class(timer_t), intent(in), target :: self
     character(len=*), intent(in) :: name1
@@ -561,10 +671,17 @@ module ftimings
     s = real(node%sum_of_children_with_name(name), kind=rk) * 1e-6_rk
   end function
 
-  function timer_get(self, name1, name2, name3, name4, name5) result(s)
+  !> Access a specific, already stopped entry of the graph by specifying the
+  !> names of the nodes along the graph from the root node
+  !>
+  !> The result is only meaningfull if the entry was never appended by
+  !> additional %start() calls.
+  !>
+  !> \implements timer_t::get
+  function timer_get(self, name1, name2, name3, name4, name5, name6) result(s)
     class(timer_t), intent(in), target :: self
     ! this is clunky, but what can you do..
-    character(len=*), intent(in), optional :: name1, name2, name3, name4, name5
+    character(len=*), intent(in), optional :: name1, name2, name3, name4, name5, name6
     real(kind=rk) :: s
     type(node_t), pointer :: node
 
@@ -610,6 +727,13 @@ module ftimings
         return
       endif
     end if
+    if (present(name6)) then
+      node => node%get_child(name6)
+      if (.not. associated(node)) then
+        write(0,'(a)') "Could not descend to """ // trim(name6)  // """"
+        return
+      endif
+    end if
     if (node%is_running()) then
       write(0,'(a)') "Timer """ // trim(node%name) // """ not yet stopped"
       return
@@ -617,6 +741,14 @@ module ftimings
     s = real(node%micros, kind=rk) * 1e-6_rk
   end function
 
+  !> Access a specific, not yet stopped entry of the graph by specifying the
+  !> names of the nodes along the graph from the root node and return the
+  !> seconds that have passed since the entry was created.
+  !>
+  !> The result is only meaningfull if the entry was never appended by
+  !> additional %start() calls.
+  !>
+  !> \implements timer_t::since
   function timer_since(self, name1, name2, name3, name4) result(s)
     class(timer_t), intent(in), target :: self
     character(len=*), intent(in), optional :: name1, name2, name3, name4
@@ -661,7 +793,7 @@ module ftimings
     s = real(node%micros + microseconds_since_epoch(), kind=rk) * 1e-6_rk
   end function
 
-  ! sort a node_t linked list and return the first and last element
+  ! In-place sort a node_t linked list and return the first and last element,
   subroutine sort_nodes(head, tail)
     type(node_t), pointer, intent(inout) :: head, tail
 
@@ -742,6 +874,10 @@ module ftimings
     end do
   end subroutine
 
+  !> Sort the graph on each level.
+  !> Warning: This irrevocable destroys the old ordering.
+  !>
+  !> \implements timer_t::sort
   subroutine timer_sort(self)
     class(timer_t), intent(inout), target :: self
     type(node_t), pointer :: node

m4/ax_prog_doxygen.m4

+# ===========================================================================
+#      http://www.gnu.org/software/autoconf-archive/ax_prog_doxygen.html
+# ===========================================================================
+#
+# SYNOPSIS
+#
+#   DX_INIT_DOXYGEN(PROJECT-NAME, DOXYFILE-PATH, [OUTPUT-DIR])
+#   DX_DOXYGEN_FEATURE(ON|OFF)
+#   DX_DOT_FEATURE(ON|OFF)
+#   DX_HTML_FEATURE(ON|OFF)
+#   DX_CHM_FEATURE(ON|OFF)
+#   DX_CHI_FEATURE(ON|OFF)
+#   DX_MAN_FEATURE(ON|OFF)
+#   DX_RTF_FEATURE(ON|OFF)
+#   DX_XML_FEATURE(ON|OFF)
+#   DX_PDF_FEATURE(ON|OFF)
+#   DX_PS_FEATURE(ON|OFF)
+#
+# DESCRIPTION
+#
+#   The DX_*_FEATURE macros control the default setting for the given
+#   Doxygen feature. Supported features are 'DOXYGEN' itself, 'DOT' for
+#   generating graphics, 'HTML' for plain HTML, 'CHM' for compressed HTML
+#   help (for MS users), 'CHI' for generating a seperate .chi file by the
+#   .chm file, and 'MAN', 'RTF', 'XML', 'PDF' and 'PS' for the appropriate
+#   output formats. The environment variable DOXYGEN_PAPER_SIZE may be
+#   specified to override the default 'a4wide' paper size.
+#
+#   By default, HTML, PDF and PS documentation is generated as this seems to
+#   be the most popular and portable combination. MAN pages created by
+#   Doxygen are usually problematic, though by picking an appropriate subset
+#   and doing some massaging they might be better than nothing. CHM and RTF
+#   are specific for MS (note that you can't generate both HTML and CHM at
+#   the same time). The XML is rather useless unless you apply specialized
+#   post-processing to it.
+#
+#   The macros mainly control the default state of the feature. The use can
+#   override the default by specifying --enable or --disable. The macros
+#   ensure that contradictory flags are not given (e.g.,
+#   --enable-doxygen-html and --enable-doxygen-chm,
+#   --enable-doxygen-anything with --disable-doxygen, etc.) Finally, each
+#   feature will be automatically disabled (with a warning) if the required
+#   programs are missing.
+#
+#   Once all the feature defaults have been specified, call DX_INIT_DOXYGEN
+#   with the following parameters: a one-word name for the project for use
+#   as a filename base etc., an optional configuration file name (the
+#   default is 'Doxyfile', the same as Doxygen's default), and an optional
+#   output directory name (the default is 'doxygen-doc').
+#
+#   Automake Support
+#
+#   The following is a template aminclude.am file for use with Automake.
+#   Make targets and variables values are controlled by the various