Remove remaining old-html content

Replace the HTML table hack + static images that created the flow chart
with a graphviz graph.  The presentation could potentially be improved,
but the essential content from the old chart is there (in case it is
useful).

Remove all build system references to old-html, simplifying the system
and removing the need to document any of this.

Change-Id: Ic011c770676d4d6d1b560fcb521bfc523c142ad0

diff --git a/docs/CMakeLists.txt b/docs/CMakeLists.txt
index 8197b4fced9c0a29697bbb49b6de327d4231f7e1..9f4810910720ca46adac1f4008505c3fc66070a6 100644 (file)
--- a/docs/CMakeLists.txt
+++ b/docs/CMakeLists.txt
@@ -299,13 +299,6 @@ if(GMX_BUILD_WEBPAGE)
     endif()
 endif()
 
-# TODO Get rid of the remaining content in old-html
-add_custom_target(webpage-old-images
-    ${CMAKE_COMMAND} -E copy_directory ${CMAKE_CURRENT_SOURCE_DIR}/old-html ${HTML_OUTPUT_DIR}
-    COMMENT "Copying flowchart images"
-    VERBATIM
-    )
-
 if(HTML_BUILD_IS_POSSIBLE)
     # Make the PDF reference guide
     # TODO Try to make the PDF arrive directly in ${HTML_OUTPUT_DIR}
@@ -327,12 +320,8 @@ if(HTML_BUILD_IS_POSSIBLE)
 
     # Add a top-level target for the others to hook onto
     add_custom_target(webpage
-        DEPENDS
-           ${HTML_OUTPUT_DIR}/manual-${GMX_VERSION_STRING}.pdf
-           ${extra_webpage_dependencies}
-        VERBATIM
-        )
-    add_dependencies(webpage webpage-sphinx webpage-old-images doxygen-all)
+        DEPENDS ${HTML_OUTPUT_DIR}/manual-${GMX_VERSION_STRING}.pdf)
+    add_dependencies(webpage webpage-sphinx doxygen-all)
 else()
     add_custom_target(webpage
         COMMAND ${CMAKE_COMMAND} -E echo "Cannot build webpage because of missing requirements. Check cmake status output for reasons"

diff --git a/docs/conf.py b/docs/conf.py
index a7b172b5d6fe3d3796fa9ec9eb5b9c70bb98db9a..8a63cd7c43ddd0008e65152cafe9d90733e6f3d7 100644 (file)
--- a/docs/conf.py
+++ b/docs/conf.py
@@ -66,6 +66,7 @@ sys.path.append(gmx_sphinx_extension_path)
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
 extensions = [
+    'sphinx.ext.graphviz',
     'sphinx.ext.pngmath',
     'sphinx.ext.ifconfig',
     'gmxsphinx'

diff --git a/docs/old-html/images/flow_down.gif b/docs/old-html/images/flow_down.gif
deleted file mode 100644 (file)
index 5944f8a..0000000
Binary files a/docs/old-html/images/flow_down.gif and /dev/null differ

diff --git a/docs/old-html/images/flow_downleft.gif b/docs/old-html/images/flow_downleft.gif
deleted file mode 100644 (file)
index 9881eda..0000000
Binary files a/docs/old-html/images/flow_downleft.gif and /dev/null differ

diff --git a/docs/old-html/images/flow_hline.gif b/docs/old-html/images/flow_hline.gif
deleted file mode 100644 (file)
index ab236cc..0000000
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diff --git a/docs/old-html/images/flow_left.gif b/docs/old-html/images/flow_left.gif
deleted file mode 100644 (file)
index 6cf841a..0000000
Binary files a/docs/old-html/images/flow_left.gif and /dev/null differ

diff --git a/docs/old-html/images/flow_leftright.gif b/docs/old-html/images/flow_leftright.gif
deleted file mode 100644 (file)
index 38c3acb..0000000
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diff --git a/docs/old-html/images/flow_leftrightdown.gif b/docs/old-html/images/flow_leftrightdown.gif
deleted file mode 100644 (file)
index 851d516..0000000
Binary files a/docs/old-html/images/flow_leftrightdown.gif and /dev/null differ

diff --git a/docs/old-html/images/flow_leftrightup.gif b/docs/old-html/images/flow_leftrightup.gif
deleted file mode 100644 (file)
index fb90440..0000000
Binary files a/docs/old-html/images/flow_leftrightup.gif and /dev/null differ

diff --git a/docs/old-html/images/flow_leftup.gif b/docs/old-html/images/flow_leftup.gif
deleted file mode 100644 (file)
index 49bdefb..0000000
Binary files a/docs/old-html/images/flow_leftup.gif and /dev/null differ

diff --git a/docs/old-html/images/flow_right+left.gif b/docs/old-html/images/flow_right+left.gif
deleted file mode 100644 (file)
index 2a64990..0000000
Binary files a/docs/old-html/images/flow_right+left.gif and /dev/null differ

diff --git a/docs/old-html/images/flow_right.gif b/docs/old-html/images/flow_right.gif
deleted file mode 100644 (file)
index 3540eff..0000000
Binary files a/docs/old-html/images/flow_right.gif and /dev/null differ

diff --git a/docs/old-html/images/flow_rightleftdown.gif b/docs/old-html/images/flow_rightleftdown.gif
deleted file mode 100644 (file)
index 304edd2..0000000
Binary files a/docs/old-html/images/flow_rightleftdown.gif and /dev/null differ

diff --git a/docs/old-html/images/flow_uprightleft.gif b/docs/old-html/images/flow_uprightleft.gif
deleted file mode 100644 (file)
index f4cbd1e..0000000
Binary files a/docs/old-html/images/flow_uprightleft.gif and /dev/null differ

diff --git a/docs/old-html/images/flow_vline.gif b/docs/old-html/images/flow_vline.gif
deleted file mode 100644 (file)
index 684697a..0000000
Binary files a/docs/old-html/images/flow_vline.gif and /dev/null differ

diff --git a/docs/old-html/images/flow_vrule.gif b/docs/old-html/images/flow_vrule.gif
deleted file mode 100644 (file)
index 2fa7f17..0000000
Binary files a/docs/old-html/images/flow_vrule.gif and /dev/null differ

diff --git a/docs/user-guide/flow.rst b/docs/user-guide/flow.rst
index 6579c7c00834f4fd85431a6fafb5e629a1c0bbeb..52d1f817d3719c143f162da5fe2025e742affa80 100644 (file)
--- a/docs/user-guide/flow.rst
+++ b/docs/user-guide/flow.rst
@@ -7,204 +7,129 @@ A more detailed example is available in :doc:`getting-started`.
 Several steps of energy minimization may be necessary,
 these consist of cycles: :ref:`gmx grompp` -> :ref:`gmx mdrun`.
 
-.. raw:: html
-
-   <CENTER>
-   <TABLE BORDER=0 CELLMARGIN=0 CELLPADDING=0 CELLSPACING=0>
-
-   <TR>
-   <TD COLSPAN="2" STYLE="text-align:right"> <A HREF="file-formats.html#pdb" onMouseOver="window.status='Protein Databank file'; return true">eiwit.pdb</A></TD>
-   <TD STYLE="text-align:right"><IMG SRC=../images/flow_leftrightdown.gif></TD>
-   <TD></TD>
-   <TD></TD>
-   <TD></TD>
-   </TR>
-
-   <TR>
-   <TD COLSPAN=2>Generate a GROMACS topology </TD>
-   <TD></TD>
-   <TD BGCOLOR=#777777 COLSPAN=3 STYLE="text-align:center"><A HREF=../programs/gmx-pdb2gmx.html onMouseOver="window.status='Convert PDB file to GROMAX coordinate file and topology'; return true"><B>gmx pdb2gmx</B></A></TD>
-   <TD><IMG SRC=../images/flow_vrule.gif></TD>
-   </TR>
-
-
-   <TR>
-   <TD></TD>
-   <TD></TD>
-   <TD></TD>
-   <TD STYLE="text-align:center"><IMG SRC=../images/flow_vline.gif BORDER=0></TD>
-   <TD WIDTH=20></TD>
-   <TD STYLE="text-align:center"><IMG SRC=../images/flow_vline.gif></TD>
-   </TR>
-
-   <TR>
-   <TD></TD>
-   <TD></TD>
-   <TD></TD>
-   <TD STYLE="text-align:center"><A HREF="file-formats.html#gro" onMouseOver="window.status='GROMACS coordinate file containing molecules from PDB file'; return true">conf.gro</A></TD>
-   <TD></TD>
-   <TD STYLE="text-align:center"> <A HREF="file-formats.html#top" onMouseOver="window.status='GROMACS ascii topology file'; return true">topol.top</A> </TD>
-   </TR>
-
-   <TR>
-   <TD></TD>
-   <TD></TD>
-   <TD></TD>
-   <TD STYLE="text-align:center"><IMG SRC=../images/flow_down.gif BORDER=0></TD>
-   <TD></TD>
-   <TD ROWSPAN=5 COLSPAN=1 STYLE="text-align:center"><IMG SRC=../images/flow_vline.gif><BR><IMG SRC=../images/flow_vline.gif><BR><IMG SRC=../images/flow_vline.gif><BR><IMG SRC=../images/flow_vline.gif><BR><IMG SRC=../images/flow_down.gif></TD>
-   </TR>
-
-   <TR>
-   <TD COLSPAN=2>Enlarge the box</TD>
-   <TD></TD>
-   <TD STYLE="text-align:center" BGCOLOR=#777777><A HREF=../programs/gmx-editconf.html onMouseOver="window.status='Adjust boxsize and placement of molecule'; return true"><B>gmx editconf</B></A></TD>
-   <TD></TD>
-   <TD><IMG SRC=../images/flow_vrule.gif></TD>
-   </TR>
-
-   <TR>
-   <TD></TD>
-   <TD></TD>
-   <TD></TD>
-   <TD STYLE="text-align:center"><IMG SRC=../images/flow_vline.gif></TD>
-   <TD></TD>
-   </TR>
-
-   <TR>
-   <TD></TD>
-   <TD></TD>
-   <TD></TD>
-   <TD STYLE="text-align:center"> <A HREF="file-formats.html#gro" onMouseOver="window.status='GROMACS coordinate file with adjusted box etc.'; return true">conf.gro</A> </TD>
-   <TD></TD>
-   </TR>
-
-
-   <TR>
-   <TD></TD>
-   <TD></TD>
-   <TD></TD>
-   <TD STYLE="text-align:center"><IMG SRC=../images/flow_down.gif></TD>
-   <TD></TD>
-   </TR>
-
-   <TR>
-   <TD COLSPAN=2>Solvate protein</TD>
-   <TD></TD>
-   <TD COLSPAN=3 STYLE="text-align:center" BGCOLOR=#777777>&nbsp;<A HREF=../programs/gmx-solvate.html onMouseOver="window.status='Fill box with water (solvate molecule)'; return true"><B>gmx solvate</B></A>&nbsp;</TD>
-   <TD><IMG SRC=../images/flow_vrule.gif></TD>
-   </TR>
-
-   <TR>
-   <TD></TD>
-   <TD></TD>
-   <TD></TD>
-   <TD STYLE="text-align:center"><IMG SRC=../images/flow_vline.gif></TD>
-   <TD></TD>
-   <TD STYLE="text-align:center"><IMG SRC=../images/flow_vline.gif></TD>
-   </TR>
-
-   <TR>
-   <TD></TD>
-   <TD></TD>
-   <TD></TD>
-   <TD STYLE="text-align:center"><A HREF="file-formats.html#gro" onMouseOver="window.status='GROMACS coordinate file with water molecules added'; return true">conf.gro</A></TD>
-   <TD></TD>
-   <TD STYLE="text-align:center"> <A HREF="file-formats.html#top" onMouseOver="window.status='GROMACS ascii topology file with water molecules added'; return true">topol.top</A> </TD>
-   </TR>
-
-   <TR>
-   <TD COLSPAN=2 STYLE="text-align:right"><A HREF="file-formats.html#mdp" onMouseOver="window.status='Parameter file for grompp (controls all MD parameters)'; return true">grompp.mdp</A></TD>
-   <TD STYLE="text-align:right">&nbsp;<IMG SRC=../images/flow_leftrightdown.gif></TD>
-   <TD STYLE="text-align:center"><IMG SRC=../images/flow_down.gif></TD>
-   <TD></TD>
-   <TD STYLE="text-align:center"><IMG SRC=../images/flow_down.gif></TD>
-   <TD></TD>
-   </TR>
-
-
-   <TR>
-   <TD COLSPAN=2>Generate mdrun input file</TD>
-   <TD></TD>
-   <TD COLSPAN=3 STYLE="text-align:center" BGCOLOR=#777777><A HREF=../programs/gmx-grompp.html onMouseOver="window.status='Process parameters, coordinates and topology and write binary topology'; return true"><B>gmx grompp</B></A></TD>
-   <TD><IMG SRC=../images/flow_vrule.gif></TD>
-   <TD></TD>
-   <TD></TD>
-   </TR>
-
-   <TR>
-   <TD></TD>
-   <TD></TD>
-   <TD></TD>
-   <TD></TD>
-   <TD STYLE="text-align:center"><IMG SRC=../images/flow_vline.gif></TD>
-   <TD ROWSPAN=3 STYLE="text-align:right"><IMG SRC=../images/flow_rightleftdown.gif></TD>
-   <TD STYLE="text-align:center;vertical-align:bottom">Continuation</TD>
-   </TR>
-
-   <TR>
-   <TD COLSPAN=2></TD>
-   <TD></TD>
-   <TD COLSPAN=3 STYLE="text-align:center"> <A HREF="file-formats.html#tpr" onMouseOver="window.status='Portable GROMACS binary run input file (contains all information to start MD run)'; return true">topol.tpr</A></TD>
-   <TD STYLE="text-align:center"><A HREF="file-formats.html#cpt" onMouseOver="window.status='Checkpoint file'; return true">state.cpt</A></TD>
-   </TR>
-
-   <TR>
-   <TD></TD>
-   <TD></TD>
-   <TD></TD>
-   <TD></TD>
-   <TD STYLE="text-align:center"><IMG SRC=../images/flow_down.gif></TD>
-   <TD ROWSPAN=2 STYLE="text-align:center">
-   <IMG SRC=../images/flow_vline.gif><BR>
-   <IMG SRC=../images/flow_leftup.gif></TD>
-   </TR>
-
-   <TR>
-   <TD COLSPAN=2>Run the simulation (EM or MD)</TD>
-   <TD></TD>
-   <TD  COLSPAN=3 STYLE="text-align:center" BGCOLOR=#777777>&nbsp;<A HREF=../programs/gmx-mdrun.html onMouseOver="window.status='The moment you have all been waiting for! START YOUR MD RUN'; return true"><B>gmx mdrun</B></A>&nbsp;</TD>
-   <TD></TD>
-   </TR>
-
-   <TR>
-   <TD></TD>
-   <TD></TD>
-   <TD></TD>
-   <TD STYLE="text-align:center"><IMG SRC=../images/flow_vline.gif></TD>
-   <TD></TD>
-   <TD STYLE="text-align:center"><IMG SRC=../images/flow_vline.gif></TD>
-   </TR>
-
-   <TR>
-   <TD></TD>
-   <TD></TD>
-   <TD></TD>
-   <TD STYLE="text-align:center"> <A HREF="file-formats.html#xtc" onMouseOver="window.status='Portable compressed trajectory'; return true">traj.xtc</A> /
-   <A HREF="file-formats.html#trr" onMouseOver="window.status='Full precision portable trajectory'; return true">traj.trr</A> </TD>
-   <TD></TD>
-   <TD STYLE="text-align:center"> <A HREF="file-formats.html#edr" onMouseOver="window.status='Portable energy file'; return true">ener.edr</A> </TD>
-   </TR>
-
-   <TR>
-   <TD></TD>
-   <TD></TD>
-   <TD></TD>
-   <TD STYLE="text-align:center"><IMG SRC=../images/flow_down.gif></TD>
-   <TD></TD>
-   <TD STYLE="text-align:center"><IMG SRC=../images/flow_down.gif></TD>
-   </TR>
-
-   <TR>
-   <TD COLSPAN=2>Analysis</TD>
-   <TD></TD>
-   <TD STYLE="text-align:center" BGCOLOR=#777777><A HREF="../programs/bytopic.html" onMouseOver="window.status='Your favourite GROMACS analysis tool'; return true"><B>g_...</B></A><BR><A HREF=../programs/gmx-view.html onMouseOver="window.status='gmx view, the GROMACS trajectory viewer'; return true"><B>gmx view</B></A></TD>
-   <TD></TD>
-   <TD STYLE="text-align:center" BGCOLOR=#777777><A HREF=../programs/gmx-energy.html onMouseOver="window.status='Energy plots, averages and  fluctuations'; return true"><B>gmx energy</B></A></TD>
-   <TD><IMG SRC=../images/flow_vrule.gif></TD>
-   </TR>
-
-
-   </TABLE>
-   </CENTER>
-
+.. URL="file-formats.html#pdb"
+.. ../programs/gmx-pdb2gmx.html
+
+.. digraph:: flowchart
+
+   node [ shape=box, width=1.5 ]
+
+   input_pdb [
+     label="eiwit.pdb"
+     tooltip="Protein Databank file"
+     URL="file-formats.html#pdb"
+     shape=none, width=0, height=0, margin=0
+     group=input
+   ]
+   pdb2gmx [
+     label="Generate a GROMACS topology\ngmx pdb2gmx"
+     tooltip="Convert PDB file to GROMACS coordinate file and topology"
+     URL="../programs/gmx-pdb2gmx.html"
+     width=3
+     group=main
+   ]
+
+   input_pdb -> pdb2gmx [ headport=e ]
+
+   editconf [
+     label="Enlarge the box\ngmx editconf"
+     tooltip="Adjust box size and placement of molecule"
+     URL="../programs/gmx-editconf.html"
+   ]
+
+   pdb2gmx -> editconf [
+     label="conf.gro"
+     labeltooltip="GROMACS coordinate file containing molecules from PDB file"
+     URL="file-formats.html#gro"
+   ]
+
+   solvate [
+     label="Solvate protein\ngmx solvate"
+     tooltip="Fill box with water (solvate molecule)"
+     URL="../programs/gmx-solvate.html"
+     width=3
+     group=main
+   ]
+
+   pdb2gmx -> solvate [
+     label="topol.top"
+     labeltooltip="GROMACS ascii topology file"
+     URL="file-formats.html#top"
+   ]
+   editconf -> solvate [
+     label="conf.gro"
+     labeltooltip="GROMACS coordinate file with adjusted box etc."
+     URL="file-formats.html#gro"
+   ]
+
+   input_mdp [
+     label="grompp.mdp"
+     tooltip="Parameter file from grompp (controls all MD parameters)"
+     URL="file-formats.html#mdp"
+     shape=none, width=0, height=0, margin=0
+     group=input
+   ]
+   grompp [
+     label="Generate mdrun input file\ngmx grompp"
+     tooltip="Process parameters, coordinates and topology and write binary topology"
+     URL="../programs/gmx-grompp.html"
+     width=3
+     group=main
+   ]
+
+   input_pdb -> input_mdp [ style=invis, minlen=3 ]
+
+   input_mdp -> grompp [ headport=e, weight=0 ]
+   solvate -> grompp [
+     label="conf.gro"
+     labeltooltip="GROMACS coordinate file with water molecules added"
+     URL="file-formats.html#gro"
+   ]
+   solvate -> grompp [
+     label="topol.top"
+     labeltooltip="GROMACS ascii topology file with water molecules added"
+     URL="file-formats.html#top"
+   ]
+
+   mdrun [
+     label="Run the simulation (EM or MD)\ngmx mdrun"
+     tooltip="The moment you have all been waiting for! START YOUR MD RUN"
+     URL="../programs/gmx-mdrun.html"
+     width=3
+     group=main
+   ]
+
+   grompp -> mdrun [
+     label="topol.tpr"
+     labeltooltip="Portable GROMACS binary run input file (contains all information to start MD run)"
+     URL="file-formats.html#tpr"
+   ]
+   mdrun -> mdrun [
+     label="Continuation\nstate.cpt"
+     labeltooltip="Checkpoint file"
+     URL="file-formats.html#cpt"
+   ]
+
+   analysis [
+     label="Analysis\ngmx ...\ngmx view"
+     tooltip="Your favourite GROMACS analysis tool"
+     URL="../programs/bytopic.html"
+   ]
+
+   mdrun -> analysis [
+     label="traj.xtc / traj.trr"
+     labeltooltip="Portable compressed trajectory / full precision portable trajectory"
+     URL="file-formats.html#xtc"
+   ]
+
+   energy [
+     label="Analysis\ngmx energy"
+     tooltip="Energy plots, averages and fluctuations"
+     URL="../programs/gmx-energy.html"
+   ]
+
+   mdrun -> energy [
+     label="ener.edr"
+     labeltooltip="Portable energy file"
+     URL="file-formats.html#edr"
+   ]