Merge branch 'develop'

.gitignore

@@ -1,5 +1,6 @@
 *.swp
 *~
+__pycache__/
 
 /aclocal.m4
 /ar-lib
@@ -19,7 +20,6 @@
 /m4/lt~obsolete.m4
 /Makefile.in
 /missing
-/pnapi/
 /preBuild/
 /VERSION
 /src/Makefile.am
@@ -50,6 +50,5 @@
 /doc/source/toc.rst
 /doc/source/libmod/[A-Z]*.rst
 /doc/source/pymod/[A-Z]*.rst
-
-/server/node_modules/
-/server/src/static/examples/list.json
+/doc/source/libmod/[^/]*/
+/doc/source/pymod/[^/]*/

ChangeLog.rst

@@ -1,3 +1,103 @@
+.. cpp:namespace:: mod
+.. py:module:: mod
+
+Changes
+#######
+
+Release 0.7.0 (2018-03-08)
+==========================
+
+Incompatible Changes
+--------------------
+
+- Boost >= 1.64 is now required.
+- Two new libraries,
+  `GraphCanon <https://github.com/jakobandersen/graph_canon>`__ and
+  `PermGroup <https://github.com/jakobandersen/perm_group>`__, are now required dependencies.
+- Sphinx 1.7.1 is now required for building the documentation.
+- :cpp:any:`dg::DG::HyperEdge::print`/:py:obj:`DGHyperEdge.print`
+  now also takes an argument for colouring vertices/edges
+  that are not matched by the rule. The default is now that matched vertices/edges
+  are the default colour, while those that are not matched are grey.
+- Most of the outer interface headers have now been moved to subfolders,
+  and their content has been moved to corresponding namespaces.
+  Several classes has been slightly renamed during the move,
+  and some headers has been split into multiple header files.
+- The previously deprecated class ``DerivationRef`` has now been removed along with
+  ``DG.derivations`` in the Python interface.
+- The previously deprecated method ``DG.vertexGraphs`` in the Python interface
+  has been removed.
+
+
+New Features
+------------
+
+- Added functions to map external ids of graphs and rules to internal vertices.
+- Added functions to get vertex coordinates for rules.
+- :cpp:any:`dg::DG::print`/:py:obj:`DG.print`
+  now returns the name of the PDF-file that will be created in post-processing.
+- Add :cpp:any:`dg::Printer::setWithInlineGraphs`/:py:obj:`DGPrinter.withInlineGraphs`
+  to input raw tex files for graphs in nodes instead of compiled PDFs.
+  The generated tex code for the graphs is different to ensure unique Tikz node names.
+- Add ``inline`` as a special argument for the graph Latex macros to input the raw tex file,
+  instead of including a compiled PDF.
+- Add :cpp:any:`graph::Graph::getSmilesWithIds`/:py:obj:`Graph.smilesWithIds`
+  for getting a string annotated with the internal vertex ids in form of the class labels.
+- The automorphism group of each graph is now available.
+
+
+Experimental New Features
+-------------------------
+
+- Vertex/edge labels in graphs/rules can now be interpreted as first-order terms.
+  Syntactic unification is then performed during morphism finding.
+  See where :cpp:any:`LabelSettings`/:py:obj:`LabelSettings` is being used.
+  Each rule has an optional :cpp:any:`LabelType`/:py:obj:`LabelType`
+  to signify whether it was designed for use with
+  :cpp:any:`LabelType::String`/:py:obj:`LabelType.String` or
+  :cpp:any:`LabelType::Term`/:py:obj:`LabelType.Term`.
+  Some algorithms will check this property for safety reasons, but the check can be disbled.
+- There is now a prototype-implementation of http://doi.org/10.1007/978-3-319-61470-0_4,
+  for adding stereo-information to graphs/rules.
+  Use :cpp:any:`LabelSettings`/:py:obj:`LabelSettings` objects to enable it.
+  See the paper for examples on how to use it. The full framework will be implemented and
+  documented in a future version.
+
+
+Bugs Fixed
+----------
+
+- Multiple rules for the same derivation is now properly recorded.
+- Fix documentation of :cpp:any:`rule::Rule::makeInverse`/:py:obj:`Rule.makeInverse`,
+  it throws :cpp:any:`LogicError`/:py:obj:`LogicError`
+  not :cpp:any:`InputError`/:py:obj:`InputError`.
+- Set the name of a rule from :cpp:any:`rule::Rule::makeInverse`/:py:obj:`Rule.makeInverse`
+  to something more descriptive.
+- Fix graph/rule depiction bug with non-zero rotation.
+- Fix DG dump loading to also load derivations with no rules.
+- Don't crash when trying :cpp:any:`dg::DG::findVertex`/:py:obj:`DG.findVertex`
+  with a graph not in the derivation graph.
+- Don't crash when trying to print derivations with multiple rules.
+- Fix documentation formatting errors.
+- #2, throw exceptions from :cpp:any:`dg::DG::ruleComp`/:py:obj:`dgRuleComp`
+  and :cpp:any:`dg::DG::calc`/:py:obj:`DG.calc` when isomorphic graphs are given.
+- Throw more appropriate exception if :cpp:any:`dg::DG::print`/:py:obj:`DG.print`
+  is called before :cpp:any:`dg::DG::calc`/:py:obj:`DG.calc`.
+- Various issues in graph/rule depiction related to positioning of hydrogens, charges, etc.
+- Build system: give better error messages if a file is given where a path is expected.
+- The produced SMILES strings are now truely canonical, as the new
+  `GraphCanon <https://github.com/jakobandersen/graph_canon>`__ library is used.
+- Fix :cpp:any:`AtomData`/:py:obj:`AtomData` to properly print radicals on uncharged atoms.
+- Throw more friendly exceptions when loading graphs/rules that have loop/parallel edges.
+
+
+Other
+-----
+
+- The documentation now has a "Known Issues" section, describing an issue where
+  post-processing may fail if ``pdflatex`` has been upgraded after installation
+
+
 Release 0.6.0 (2016-12-22)
 ==========================
 
@@ -9,34 +109,39 @@ Incompatible Changes
   Version 1.60 do not work due to https://github.com/boostorg/python/issues/56.
 - Make filenames in post-processing more Latex friendly.
 - Rules specified in GML using ``constrainAdj`` must now enclose the operator in double quotes.  
-- DG: remove most of the interface related to ``DerivationRef``. Use the graph interface instead. E.g.,
+- DG: remove most of the interface related to ``DerivationRef``.
+  Use the graph interface instead. E.g.,
 
-  - Deprecate ``DerivationRef``. They now interconvert with ``DG::HyperEdge``.
-  - Change ``DG::getDerivationRef`` into ``DG::findEdge``.
-  - Make ``DG::derivations`` return the edges instead in the Python interface.
+  - Deprecate ``DerivationRef``. They now interconvert with
+    :cpp:any:`dg::DG::HyperEdge`/:py:obj:`DGHyperEdge`.
+  - Change ``DG::getDerivationRef`` into :cpp:any:`dg::DG::findEdge`/:py:obj:`DG.findEdge`.
+  - Make ``DG.derivations`` return the edges instead in the Python interface.
     It is removed in the C++ interface. It will be removed from Python in the future.
   - Remove ``DG::inDerivations`` and ``DG::outDerivations``.
   - Deprecate ``DG::vertexGraphs`` in Python, remove in C++.
 
 - Move the graph interface for DG and Graph into separate headers:
   ``DGGraphInterface.h`` and ``GraphGraphInterface.h``.
-- Move GraphPrinter into a separate header.
-- Move DGPrinter and DGPrintData into a separate header.
+- Move ``GraphPrinter`` into a separate header.
+- Move ``DGPrinter`` and ``DGPrintData`` into a separate header.
 - All SBML features have been removed from the library.
-- The deprecated DG::printMatrix function has been removed.
-- DG::calc will no longer print a message when it is done.
-- DG::print by default now only prints the hypergraph rendering.
-  (For now, set Config::DG::printNonHyper to enable printing of the non-hypergraph rendering)
-- Graph::print and Rule::print will now emit only one depiction when the two printers are equal.
-- Rule::print, change the default colours used to indicate changes. Now different colours are used in L, K, R.
-- DGHyperEdge::print, change the default match colour.
+- The deprecated ``DG::printMatrix`` function has been removed.
+- :cpp:any:`dg::DG::calc`/:py:obj:`DG.calc` will no longer print a message when it is done.
+- :cpp:any:`dg::DG::print`/:py:obj:`DG.print` by default now only prints the hypergraph rendering.
+  (For now, set ``Config::DG::printNonHyper`` to enable printing of the non-hypergraph rendering)
+- :cpp:any:`graph::Graph::print`/:py:obj:`Graph.print` and
+  :cpp:any:`rule::Rule::print`/:py:obj:`Rule.print` will now emit only one depiction when
+  the two printers are equal.
+- :cpp:any:`rule::Rule::print`/:py:obj:`Rule.print`, change the default colours used to indicate
+  changes. Now different colours are used in L, K, R.
+- :py:obj:`DGHyperEdge.print`, change the default match colour.
 - Add < operator to vertices and edges of Graph, Rule, and DG.
 
 
 New Features
 ------------
 
-- ``Rule::makeInverse``.
+- :cpp:any:`rule::Rule::makeInverse`/:py:obj:`Rule.makeInverse`.
 - Reimplementation of GML parsing. It is now less strict with respect to ordering.
 - Rule application constraint that checks the shortest path between two given vertices.
 - Interactive mode for the wrapper script (option ``-i``).
@@ -51,7 +156,8 @@ New Features
   unique, then none of them are available for querying.
 - Add ``-v`` as alias for ``--version`` in the wrapper script.
 - Add quite mode, ``-q``, to the wrapper script.
-- Add ``rotation`` to GraphPrinter. Internally computed coordinates will be rotated by ``rotation`` degrees.
+- Add :cpp:any:`graph::Printer::setRotation`/:py:obj:`GraphPrinter.rotation`.
+  Internally computed coordinates will be rotated by the set amount of degrees.
 
 
 Bugs Fixed

Makefile.am

@@ -1,4 +1,6 @@
 SUBDIRS = src doc
+EXTRA_DIST =			\
+	ChangeLog.rst
 
 dist_pkgdata_DATA = \
 	VERSION