12. Changes

12.1. v0.16.0 (2024-06-18)

12.1.1. Incompatible Changes

• Several classes have in Python become nested classes and changed name:

  • DGVertex to DG.Vertex

  • DGHyperEdge to DG.HyperEdge

  • DGVertexRange to DG.VertexRange

  • DGEdgeRange to DG.EdgeRange

  • DGInEdgeRange to DG.InEdgeRange

  • DGOutEdgeRange to DG.OutEdgeRange

  • DGSourceRange to DG.SourceRange

  • DGTargetRange to DG.TargetRange

  • DGRuleRange to DG.RuleRange

  • DGBuilder to DG.Builder

  • DGExecuteResult to DG.Builder.ExecuteResult

• The version requirement for Sphinx has been raised to 7.3.

12.1.2. New Features

• Added a new documentation section describing rule application constraints: Application Constraints.

• Added a new rule application constraint, Label Unification Constraint.

• Instead of VF2, use canonicalization when checking for isomorhpism of graph::Graph/Graph, when in term mode, when there are no variables in the attached terms, thereby speeding up the check.

• Make dg::Printer/DGPrinter copyable.

• Add optinal callbacks to dg::DG::build()/DG.build(), to enable real-time status of what is being added.

12.1.3. Bugs Fixed

• Summary generation: fix page numbers to use “of” instead of “af”.

• Fix adjacency constraint when in term mode and multiple labels in the constraint matches the same label in the candidate graph.

• Fix rule::Rule::makeInverse()/Rule.makeInverse() to not crash when the rule has no external IDs recorded.

• Document the value of the default nested graph::Printer/GraphPrinter in dg::Printer/DGPrinter.

• Clarify what mod -q does.

• Actually throw an exception when using dg::DG::Vertex::getGraph()/DG.Vertex.graph on a null vertex, instead of having undefined behaviour.

• Doc, show default arguments for rcEvaluator().

12.2. v0.15.0 (2024-01-26)

12.2.1. Incompatible Changes

• The graphs created by dg::Builder::addAbstract()/DG.Builder.addAbstract() will no longer be empty, but have a single vertex with the label set to the identifier given in the description.

• Repeated calls to dg::Builder::addAbstract()/DG.Builder.addAbstract() will no longer create subnetworks independently, but will act as if a single call was made with a concatenation of the inputs.

• CMake, change the option BUILD_TESTING_SANITIZERS to BUILD_WITH_SANITIZERS and default it to OFF. It did not cause libraries to be build with sanitizers as promised. Now it does, and is therefore not enabled by default.

• rule::Composer::eval()/RCEvaluator.eval() now by default prunes duplicate rules. The old behaviour can be obtained by setting the new parameter onlyUnique to false.

12.2.2. New Features

• Added support for LLDB in mod --debug. It will be used if GDB is not available.

• Added MOD_DEBUGGER to overwrite which debugger is invoked.

• Added graph::Graph::enumerateIsomorphisms()/Graph.enumerateIsomorphisms().

• Added graph::Union::printTermState()/UnionGraph.printTermState().

• Added verbosity argument for dg::DG::HyperEdge::print()/DG.HyperEdge.print() for printing debug information.

• Added printStereoWarnings flag to several loading functions:

  • graph::Graph::fromGMLString()/Graph.fromGMLString()/graphGMLString()

  • graph::Graph::fromGMLStringMulti()/Graph.fromGMLStringMulti()

  • graph::Graph::fromGMLFile()/Graph.fromGMLFile()/graphGML()

  • graph::Graph::fromGMLFileMulti()/Graph.fromGMLFileMulti()

  • graph::Graph::fromSMILES()/Graph.fromSMILES()/smiles()

  • rule::Rule::fromGMLString()/Rule.fromGMLString()/ruleGMLString()

  • rule::Rule::fromGMLFile()/Rule.fromGMLFile()/ruleGML()

  If the input contains stereo-information, then the full stereo-information is inferred. This flag suppresses printing of warnings from this inferrence. Warnings from inferrence requested at a later time are not affected.

• Changed default graph isomorphism algorithm selection strategy. Before it always ran VF2, now it will use one of several algorithms, depending on the graphs and the label settings: 1) canonical SMILES string comparison, 2) comparison of canonical forms of the graphs, and 3) VF2.

• Added callback parameters for dg::DG::build()/DG.build() to get notification when a new vertex or hyperedge is added to the derivation graph.

• Updated the “Quick Start” documentation for compiling from source, to account for the need for virtual environments in newer versions of operating systems.

• Added instructions for compiling in a Conda environment.

• Added dg::VertexMapper/DGVertexMapper for enumerating vertex maps of derivations (atom maps for reeactions in a chemical setting).

12.2.3. Bugs Fixed

• Fix CMake finding proper Python version on macOS when multiple are installed.

• Fix :ref:mod-wrapper: such that it uses the Python executable that was found during CMake configuration. The environment variable MOD_PYTHON can still be used to overwrite the Python executable.

• Fix post::enableCompileSummary()/post.enableCompileSummary(), to emit the correct command, instead of acting like post::enableInvokeMake()/post.enableInvokeMake().

• Elaborate Quick Start instructions for compiling to make it a bit easier to follow.

• Fix rule::CompositionMatch::composeAll()/RCMatch.composeAll() when using terms and/or stereo information, to actually switch to those label settings.

• Allow term and stereo in graph::Graph::enumerateMonomorphisms()/Graph.enumerateMonomorphisms().

• Fix Graphviz instructions for Ubuntu in Quick Start, to point at newer source archives instead an old one.

• #16, added pkg-config to Brewfile.

• In the post-processor, fall back to compiling commonPreamble.fmt each time, if creating a symbolic link fails. This may happen, e.g., in certain scenarios inside a Docker container.

• When using dg::Printer::pushVertexLabel()/DGPrinter.pushVertexLabel() and dg::Printer::pushEdgeLabel()/DGPrinter.pushEdgeLabel(), returning an empty string from the callback is now treated as if nothing should be shown from this callback, instead of showing an empty string and a seperator.

• mod.sty, fix how options are passed to xcolor.

12.3. v0.14.0 (2022-11-29)

12.3.1. Incompatible Changes

Doc, several pages have changed URL:

• libmod/libmod.html to libmod/index.html

• pymod/pymod.html to pymod/index.html

• postmod/postmod.html to postmod/index.html

• modWrapper/modWrapper.html to exe/index.html

• epim/epim.html to epim/index.html

• dataDesc/dataDesc.html to formats/index.html

• dgStrat/dgStrat.html to dgStrat/index.html

• As default, a Python package is now installed with pip which enables import of mod without extra PYTHONPATH manipulation. This may potentially clash with other packages of the same name. Use -DBUILD_PY_MOD_PIP=off for CMake to disable this (see Compiling from Source).

• Due to a change in escaping of # characters in DG vertex/hyperedge labels when printing, some custom labels with additional escaping may need adjustment. See also the bug fix entry regarding this.

• Bump Boost version required to 1.76 or higher to avoid an incompatibility with Python 3.10 (https://github.com/boostorg/python/pull/344).

12.3.2. New Features

• Doc, a new section, Graph, Rule, and Molecule Model, and restructuring of Data Formats.

• The GraphDFS format now supports disconnected graphs through .-edges, similar to SMILES. The graph loading functions graph::Graph::fromDFSMulti() and Graph.fromDFSMulti() has been added to load disconnected graphs.

• Added rule::Rule::fromDFS()/Rule.fromDFS() for loading rules from a RuleDFS string, a new line-notation for rules based on GraphDFS.

• Added support for MOL and SD formats for loading graphs. The loading can be done through the functions

  • graph::Graph::fromMOLString()/Graph.fromMOLString(),

  • graph::Graph::fromMOLFile()/Graph.fromMOLFile(),

  • graph::Graph::fromMOLStringMulti()/Graph.fromMOLStringMulti(),

  • graph::Graph::fromMOLFileMulti()/Graph.fromMOLFileMulti(),

  • graph::Graph::fromSDString()/Graph.fromSDString(),

  • graph::Graph::fromSDFile()/Graph.fromSDFile(),

  • graph::Graph::fromSDStringMulti()/Graph.fromSDStringMulti(), and

  • graph::Graph::fromSDFileMulti()/Graph.fromSDFileMulti(),

• PyMØD: add installation of the bindings via pip. See the setting -DBUILD_PY_MOD_PIP=on in Compiling from Source.

• Added dg::Builder::addHyperEdge()/DG.Builder.addHyperEdge().

• Added graph::Printer::setRaiseIsotopes()/graph::Printer::getRaiseIsotopes()/GraphPrinter.raiseIsotopes. It was previously only available in the internal interface.

• Added graph::Printer::setWithGraphvizCoords()/graph::Printer::getWithGraphvizCoords()/GraphPrinter.withGraphvizCoords.

• Added graph::Printer::setGraphvizPrefix()/graph::Printer::getGraphvizPrefix()/GraphPrinter.graphvizPrefix.

• Whitespace is now allowed inside DFS Line Notation strings.

• Make mod --memcheck cause Valgrind to return non-zero on problems. Additionally add an atexit handler in Python to delete remaining global objects as this is not guaranteed otherwise.

• Several undocumented post-processing functions are now documented, and several internal functions are now exposed. See Post.hpp/Post.

• Added graph::Graph::enumerateMonomorphisms()/Graph.enumerateMonomorphisms().

• Added dg::Printer::setImageOverwrite()/DGPrinter.setImageOverwrite().

• Added dg::Builder::getDG()/DG.Builder.dg and DG.Builder.isActive.

12.3.3. Bugs Fixed

• Rule GML loading, check for edges dangling due to wrong vertex membership.

• dg::Builder::execute()/DG.Builder.execute() and dg::Builder::apply()/DG.Builder.apply(), properly ignore direct derivations with empty right-hand sides, instead of crashing.

• dg::DG::load()/DG.load() and dg::Builder::load()/DG.Builder.load(), reenable loading of very old dump formats.

• Fix critical bugs in rule::CompositionMatch/RCMatch.

• Doc, added missing cd mod step in Compiling from Source.

• Doc, add missing " in usage description for the Docker image.

• Doc, fix typo (\(C_3\) to \(C_4\)) in GraphDFS, and improve description of ring-closure semantics.

• Fix graph::Graph::getGraphDFS()/Graph.graphDFS and graph::Graph::getGraphDFSWithIds()/Graph.graphDFSWithIds to not produce a defRingId directly followed by a ringClosure which is indistinguishable from just a defRingId when parsing the string again.

• Check for loop edges and parallel edges when loading graphs from DFS.

• PostMØD, avoid use of inline sed in compileTikz to make it work on macOS.

• For compiling from source on macOS, add cmake to Brewfile.

• Check for Boost.Python compiled against Python 3.10 through 3.20 as well.

• Py, use collections.abc.Iterable instead of the deprecated/removed collections.Iterable.

• Py, use inspect.getfullargspec() instead of the deprecated/removed inspect.getargspec().

• mod_post scrub more unreproducible meta-info from figure PDFs.

• Fix memory leaks in dg::Builder::apply()/DG.Builder.apply().

• Fix colour on changed stereo-information in the right-side graph when printing rules and direct derivations.

• Stop recreating vertex-orders for connected components of rule sides, thereby speeding up rule application (5-6% reduced run-time observed).

• Fix missing coordinates for rule depiction in rare non-chemical cases with vertices with label “H”.

• Fix rule composition with LabelType::Term/LabelType.Term, when two vertices are overlapping and there is an edge in the left side of the second rule, but not in the right side of the first rule.

• Fix Tikz coordinate node names in rule and stereo depictions to always include \modIdPrefix, to allow post-printing namespacing of node names.

• graph::Graph::fromSMILES()/Graph.fromSMILES(), properly parse abstract labels when multiple nests of balanced brackets are present.

• Fix handling of null pointers:

  • graph::Graph::isomorphism()/Graph.isomorphism().

  • graph::Graph::monomorphism()/Graph.monomorphism().

  • graph::Union::Union()/UnionGraph.__init__().

• Fix escaping of # characters in DG vertex/hyperedge labels when printing using a dg::Printer/DGPrinter with labelsAsLatexMath=True (the default).

12.4. v0.13.0 (2021-07-08)

12.4.1. Incompatible Changes

• The package name has been changed to simply “MØD”.

• Use more C++17 features, making some code not compile with GCC 7.

• Clang 9 seems to produce wrong code for PyMØD, resultining in segmentation faults during module import.

• Require Sphinx 3.5

• The return type of rule::Rule::getLabelType() has changed from using boost::optional to std::optional.

• Change the GraphCanon submodule from a relative path to the Github repository.

• Rename the C++ graph loading functions

  • graph::Graph::gmlString to graph::Graph::fromGMLString()

  • graph::Graph::gml to graph::Graph::fromGMLFile()

  • graph::Graph::graphDFS to graph::Graph::fromDFS()

  • graph::Graph::smiles to graph::Graph::fromSMILES()

  • graph::Graph::makeGraph to graph::Graph::create()

• Rename the C++ rule loading functions

  • rule::Rule::ruleGMLString to rule::Rule::fromGMLString()

  • rule::Rule::ruleGML to rule::Rule::fromGMLFile()

• Add warnings parameter to graph::Graph::create().

• Fix rcCommon to consistently enumerate common subgraphs that are not necessarily vertex-induced. Use config.rc.useBoostCommonSubgraph = False to switch to the old behaviour.

• The BUILD_DOC option for building from source now defaults to OFF.

• Add rule::CompositionMatch/RCMatch.

• The file parameter for DG.load() and DG.Builder.load() has been changed name from file to f.

• Graph.fromSMILES() has changed order of parameters, add is now the last one.

12.4.2. New Features

• Added printCombined parameter to rule::Rule::print()/Rule.print() to optionally print a figure where the rule is depicted as a single combined graph. This was previously always printed, but now it defaults to off.

• Added <-operator to graph::Union/UnionGraph, rule::Rule::LeftGraph/Rule.LeftGraph, rule::Rule::ContextGraph/Rule.ContextGraph, and rule::Rule::RightGraph/Rule.RightGraph.

• Added dg::Printer::getTikzpictureOption(), dg::Printer::setTikzpictureOption(), DGPrinter.tikzpictureOption.

• Added dg::DG::printNonHyper()/DG.printNonHyper().

• Allow limit=0 for repeat strategies, dg::Strategy::makeRepeat()/DGStrat.makeRepeat().

• Added overload for dg::DG::dump()/DG.dump() that takes a target filename as argument.

• Add the static methods

  • Graph.fromGMLString() (the same as graphGMLString())

  • Graph.fromGMLFile() (the same as graphGML())

  • Graph.fromDFS() (the same as graphDFS())

  • Graph.fromSMILES() (the same as smiles())

  • Rule.fromGMLString() (the same as ruleGMLString())

  • Rule.fromGMLFile() (the same as ruleGML())

• Allow dot (.) bonds in SMILES strings.

• Add the following functions for loading a possibly disconnected graph:

  • graph::Graph::fromSMILESMulti()/Graph.fromSMILESMulti()

  • graph::Graph::fromGMLStringMulti()/Graph.fromGMLStringMulti()

  • graph::Graph::fromGMLFileMulti()/Graph.fromGMLFileMulti()

• Add MOD_PYTHON and MOD_IPYTHON to overwrite the interpreter the wrapper script executes.

• Add graph::Graph::getLoadingWarnings()/Graph.loadingWarnings.

12.4.3. Bugs Fixed

• rule::Rule::fromGMLFile()/Rule.fromGMLFile() and rule::Rule::fromGMLString()/Rule.fromGMLString():

  • Fixed typos in a few error messages.

  • Actually fail loading when errors in constraints are encountered.

• Fix v0.12 problem with RPATH handling of libmod.

• Doc, fix infinite search.

• Fix exception visibility on macOS so they can be caught outside the library.

• Tests, set C++ standard in CMake tests.

• Added missing operator< to graph::Union::Vertex.

• Fix error handling to throw the right exception with better message when the file can not be opened for the functions graph::Graph::fromGMLFile()/Graph.fromGMLFile(), rule::Rule::fromGMLFile()/Rule.fromGMLFile(), dg::DG::load()/DG.load(), dg::Builder::load()/DG.Builder.load().

• Fixes to support Boost 1.76.

• Fixes to support GCC 11.

• Build system, use add_custom_command to avoid recompilation of docs and Latex format file on install. Fixes problem with failing to import sphinx when running sudo make install.

12.4.4. Other

• Test, set C++ standard in CMake tests.

• Doc, fix description of RCExpExp and RCExpComposeCommon.

• Doc, for libMØD classes, make a synopsis with links to declarations.

• Doc, fix documentation for post::makeUniqueFilePrefix() so it is documented to be in namespace post.

• Docker, for building the Ubuntu image, download Boost from the new URL.

• Conda, require a newer Graphviz version with rsvg from conda-forge instead of custom version.

• Refresh the messages from and the documentation on The Wrapper Script.

• Doc, clarify use of pip may need --user for home folder installation.

• Doc, properly document that a CWDPath is a valid argument for

  • DG.load(),

  • DG.Builder.load(),

  • Graph.fromGMLFile(), and

  • Rule.fromGMLFile().

• Doc, clarify conditions on methods in dg::DG/DG regarding “hasActiveBuilder” and “isLocked”.

12.5. v0.12.0 (2021-01-18)

12.5.1. Incompatible Changes

• Require C++17.

• Require Boost 1.73 to avoid CMake issue in 1.72.

• Require GraphCanon 0.5.

• Require Sphinx 3.4.

• Moved compilation instructions from Installation to Compiling from Source.

• Renamed DGStratGraphState to DGStrat.GraphState.

• Swap parameters for dg::DG::print() to be consistent with DG.print().

• The function mod::makeUniqueFilePrefix() has been renamed to mod::post::makeUniqueFilePrefix().

• Names for the left, context, and right graph of Rule has been moved and renamed to be nested types of Rule.

• Names for graph interface types for Graph, Rule, Rule.LeftGraph, Rule.ContextGraph, and Rule.RightGraph have been moved and renamed to be nested types of their graph class.

• Names for graph automorphism types for Graph have been moved and renamed to be nested types of Graph.

• rule::Composer::eval()/RCEvaluator.eval() now returns a list of results, possibly with duplicates, instead of only a collection of unique rules.

12.5.2. New Features

• A pre-compiled Conda installation is now available on Linux, see Installation and https://anaconda.org/jakobandersen/mod.

• Added new higher-level installation instructions at Installation, with documentation for how to install via Conda and using the Docker image.

• Update bindep.txt and Quick Start guide for Arch.

• Add Brewfile to to make installation of dependencies much easier on macOS.

• Improved verbose output from “add” strategies during dg::Builder::execute()/DG.Builder.execute().

• Improved rule application performance when evaluating rule strategies and executing dg::Builder::apply()/DG.Builder.apply().

• Added a relaxed mode to dg::Builder::apply()/DG.Builder.apply() via the onlyProper parameter.

• Add missing graph attributes to vertices and edges of the four graph interfaces of Rule.

• Add new class graph::Union/UnionGraph.

• Improve handling of pre-compiled Latex format files used in the post-processor (thanks also to Nikolai Nøjgaard):

  • Add build option to not install the file during normal installation. See -DBUILD_POST_MOD_FMT in Installation.

  • Teach the post-processor to dynamically compile the format file if it is not installed.

  • Add options mod_post --install-format and mod_post --install-format-sudo for installing/updating the pre-compiled format file after MØD was installed. This can be used on an installation configured with -DBUILD_POST_MOD_FMT=off or for resolving a known issue.

• Make AtomData/AtomData LessThanComparable.

• Make build work on macOS and add installation instructions.

• Rule composition: when using rcCommon, skip duplicate overlaps yielded by the underlying enumeration algorithm.

12.5.3. Bugs Fixed

• Flush stdout in the end of dg::ExecuteResult::list()/DG.Builder.ExecuteResult.list().

• Fix printing/stringification of a null vertices for graph::Graph/Graph, rule::Rule/Rule, rule::Rule::LeftGraph/Rule.LeftGraph, rule::Rule::ContextGraph/Rule.ContextGraph, rule::Rule::RightGraph/Rule.ContextGraph.

• Fix conversion of Graph.Edge to bool.

• Fix rule printing when hydrogens are collapsed to prevent occasional Latex errors on the form ! Package pgf Error: No shape named `v-coord-<num>' is known..

• Add missing operator!= for AtomData.

• macOS build fixes:

  • Infinite recursion in doc building, due to missing toctrees.

  • Disable leak sanitizer when using AppleClang as compiler.

  • Disable more compiler/link options not in AppleClang.

12.5.4. Other

• Doc, rearrange and deduplicate documentation for graph interfaces in PyMØD. Introduce the Protocols section which documents common protocols that several classes implement. The documentation of the following classes has been simplified by mostly referring to these protocols:

  • Graph

  • Rule

• Doc, improve documentation of the graph interfaces of Rule.

12.6. v0.11.0 (2020-08-31)

12.6.1. Incompatible Changes

• Bump version requirement of Boost to 1.72.

• dg::Printer::pushVertexVisible()/DGPrinter.pushVertexVisible(), dg::Printer::pushVertexLabel()/DGPrinter.pushVertexLabel(), and dg::Printer::pushVertexColour()/DGPrinter.pushVertexColour() now requies a callback taking a dg::DG::Vertex/DG.Vertex, instead of a graph::Graph/Graph and dg::DG/DG. The previous style is removed in libMØD and deprecated in PyMØD.

• dg::DG::HyperEdge::print()/DG.HyperEdge.print() now throws exceptions if either no rules are associated with the hyperedge or if at least one of the associated rules does not lead to a derivation.

• dg::PrintData/DGPrintData, many interface changes, including proper argument checking.

• dg::DG::dumpImport() has been renamed to dg::DG::load().

• dgDump() has been renamed to DG.load().

• dg::DG::load()/DG.load() has additional arguments and pre-conditions.

• Do not install a pkg-config file. It was broken and there doesn’t seem to be an easy way to fix it.

12.6.2. New Features

• Added dg::Builder::apply()/DG.Builder.apply() as a lower-level function for computing proper direct derivations.

• graph::Graph::fromSMILES()/smiles():

  • Generalize the parser to accept almost arbitrary strings as symbols inside brackets. See SMILES. This is only allowed when passing allowPartial=True to smiles().

  • Generalize the parser to accept ring-bonds and branches in mixed order.

  • Generalize the parser to accept non-standard charges: +++, ++, ---, --, and magnitudes larger than +/-9.

• Added the PyMØD submodule EpiM.

• Added SmilesClassPolicy/SmilesClassPolicy argument to graph::Graph::fromSMILES()/smiles().

• Support using either Open Babel 2 or 3 as dependency.

• Make DGPrinter.graphPrinter writeable as well.

• Make graph::Printer/GraphPrinter equality comparable.

• Added dg::Printer::setGraphvizPrefix()/dg::Printer::getGraphvizPrefix()/DGPrinter.graphvizPrefix.

• Added makeUniqueFilePrefix/makeUniqueFilePrefix().

• Improve verbosity level 8 information from dg::Builder::execute()/DG.Builder.execute() to the universe size.

• Make LabelSettings/LabelSettings equality comparable.

• Added dg::Builder::load()/DG.Builder.load().

• Added rngUniformReal()/rngUniformReal().

12.6.3. Bugs Fixed

• Fix handling of null pointers:

  • Derivation/Derivation printing.

  • Derivations/Derivations printing.

  • dg::Builder::addDerivation()/DG.Builder.apply().

  • dg::Builder::execute()

  • dg::DG::make()/DG.__init__()

  • dg::DG::findVertex()/DG.findVertex()

  • (dg::DG::findEdge()/DG.findEdge())

  • Static and dynamic “add” strategies, dg::Strategy::makeAdd()/DGStrat.makeAddStatic() and DGStrat.makeAddDynamic().

  • Sequence strategies, dg::Strategy::makeSequence()/DGStrat.makeSequence()

  • Rule strategies, dg::Strategy::makeRule()/DGStrat.makeRule()

  • Parallel strategies, dg::Strategy::makeParallel()/DGStrat.makeParallel()

  • Filter strategies, dg::Strategy::makeFilter()

  • Execute strategies, dg::Strategy::makeExecute()

  • Left/right predicate strategies, dg::Strategy::makeLeftPredicate()/DGStrat.makeLeftPredicate(), dg::Strategy::makeRightPredicate()/DGStrat.makeRightPredicate()

  • Revive strategies, dg::Strategy::makeRevive()/DGStrat.makeRevive()

  • Repeat strategies, dg::Strategy::makeRepeat()/DGStrat.makeRepeat()

• Fix handling of empty functions given as callbacks:

  • dg::Printer::pushVertexVisible(),

  • dg::Printer::pushEdgeVisible(),

  • dg::Printer::pushVertexLabel(),

  • dg::Printer::pushEdgeLabel(),

  • dg::Printer::pushVertexColour(),

  • dg::Printer::pushEdgeColour(),

  • dg::Printer::setRotationOverwrite(), and

  • dg::Printer::setMirrorOverwrite().

• graph::Graph::fromSMILES()/smiles():

  • Improve parsing error messages.

  • Fix missing external ID for bracketed wildcard atoms with class label, e.g., [*:42].

  • Fix handling of an atom which contains a ring-closure and ring-opening using the same ID, e.g., C1CCCP11NNNN1.

  • When there is a bond mismatch in a ring closure (e.g., C-1CCCC=1), throw a InputError/InputError instead of a FatalError/FatalError.

• Isotope and Charge are now comparable with integers.

• dg::DG::print()/DG.print(), fix missing labels on shortcut edges when using a dg::Printer/DGPrinter with “labels as Latex math” set to false.

• dg::Builder::addAbstract()/DG.Builder.addAbstract():

  • Improve parsing error messages.

  • Fix assertion on non-ASCII input.

• include(), read files in binary instead of ASCII.

• PostMØD: scale figures based on height as well to avoid them being clipped. Thanks to Christoph Flamm.

• Fix rule::Rule::getGMLString()/Rule.getGMLString() to not perform coordinate instantiation when not needed.

• Fix Python export of Rule.ContextGraph.Vertex.

• Properly throw exceptions from all pop functions in dg::Printer/DGPrinter when there is nothing to pop.

• PostMØD: remove extranous escape of a quote in AWK script in coordsFromGV.

• Graph printing, fix coordinate overwrite when printing the same graph multiple times, but with different rotation or mirror settings, the layout of the last printing would be used for all of them. Those with non-zero rotation and mirroring now have their own file name.

• DG printing: fix bending of head/tail arrows when a tail vertex is also a head vertex so arrows don’t overlap.

• #8: remove some linker flags when AppleClang is used.

12.6.4. Other

• Doc, update theming again to increase readability.

• Doc, add more formal API for the embedded strategy language for derivation graphs.

• Doc, fix typo resulting in missing documentation of

  • AtomData.atomId

  • AtomData.isotope

  • DG.Vertex.inDegree

  • DG.Vertex.outDegree

• Doc, various typo fixes.

• mod, don’t log output when invoked with --debug.

• Doc, clarify that DGPrinter.pushVertexVisible(), DGPrinter.pushEdgeVisible(), DGPrinter.pushVertexLabel(), DGPrinter.pushEdgeLabel(), DGPrinter.pushVertexColour(), DGPrinter.pushEdgeColour(), DGPrinter.setRotationOverwrite(), DGPrinter.setMirrorOverwrite() accepts a constant as well as a callback.

• Doc, fix callback type for DGPrinter.setRotationOverwrite() and DGPrinter.setMirrorOverwrite(). They must take a Graph, not a GraphPrinter.

• Doc, add return type to DG.findEdge().

• Added bindep.txt and requirements.txt to make installation of dependencies much easier. The installation instructions are updated with a Quick Start guide and notes on the use of the dependency files.

• CMake, default BUILD_EXAMPLES=on.

12.7. v0.10.0 (2020-02-05)

12.7.1. Incompatible Changes

• dg::DG::abstract/dgAbstract has been removed. Use dg::Builder::addAbstract()/DG.Builder.addAbstract() instead. Added slightly better documentation as well, Abstract Derivation Graphs.

• dg::DG::derivations has been removed. Use the repeated calls to dg::Builder::addDerivation() instead.

• dg::DG::ruleComp and dg::DG::calc() has been removed. Use the new dg::Builder::execute() instead.

• dgRuleComp and DG.calc has been deprecated, and their implementation is now based on DG.Builder.execute(). Use DG.Builder.execute() directly instead.

• The implementation of dgDerivations has changed and the function is now deprecated. Use repeated calls to DG.Builder.addDerivation() instead.

• dg::Strategy::makeAdd() overloads, DGStrat.makeAddStatic(), and DGStrat.makeAddDynamic() now requires another argument of type IsomorphismPolicy/IsomorphismPolicy.

• Add Subset and Add Universe now accepts a new optional keyword argument graphPolicy of type IsomorphismPolicy.

• dg::DG::list/DG.list has been removed, use dg::ExecuteResult::list()/DG.Builder.ExecuteResult.list() instead.

• Information from strategies has been updated.

12.7.2. New Features

• Added new incremental build interface for DG/dg::DG. It includes:

  • DG.__init__()/dg::DG::make() for constructing a derivation graph with this new interface.

  • DG.build()/dg::DG::build() for obtaining an RAII-style proxy object for controlling the construction (DG.Builder/dg::Builder).

  • DG.hasActiveBuilder/dg::DG::hasActiveBuilder()

  • DG.locked/dg::DG::isLocked()

• Added Derivations/Derivations as an alternative to Derivation/Derivation which contains a list of rules instead of at most a single rule. The latter is implicitly convertible to the former.

• Rule now has an overloaded operator <.

• IsomorphismPolicy/IsomorphismPolicy has been added to help configure various algorithms by users.

• Added DG.labelSettings/dg::DG::getLabelSettings().

• Added MOD_NO_DEPRECATED to make it easier to find usage of deprecated behaviour.

• Added Rule.isomorphicLeftRight()/rule::Rule::isomorphicLeftRight().

12.7.3. Bugs Fixed

• Changed assert to a proper error message at code related to Open Babel. If MØD, or an extension library, is loaded with dlopen without the RTLD_GLOBAL flag, there can be multiple copies of Open Babel symbols at the same time, which prevent MØD from accessing Open Babel operations..

• Document and check proper preconditions on dg::DG/DG.

• Document and check precondition on dg::DG::HyperEdge::getInverse()/DG.HyperEdge.inverse, that it is only avilable after the DG is locked.

• Properly throw an exception if DGStrat.makeSequence()/dg::Strategy::makeSequence() if given an empty list of strategies.

• Properly implementing stringification of LabelType/LabelType, LabelRelation/LabelRelation, LabelSettings/LabelSettings, and IsomorphismPolicy/IsomorphismPolicy.

• Build: disallow use of experimental Boost CMake support due to a linking problem.

12.7.4. Other

• Various fixes for documentation formatting including new themeing.

• Installation, highlight the more relevant CMAKE_PREFIX_PATH instead of CMAKE_PROGRAM_PATH.

• Bump recommended lower bound on GCC version to 6.1 in the documentation.

• Updated documentation for mod::Derivation/Derivation.

• Documentation, added explicit example section.

12.8. v0.9.0 (2019-08-02)

12.8.1. Incompatible Changes

• Change to CMake as build system. See Installation for how to build the package, or used it as a submodule in another CMake project.

• Now requires v0.4 of GraphCanon (and PermGroup).

• dg::DG::getGraphDatabase() now returns a std::vector instead of a std::unordered_set.

• Hide internal symbols in the library to increase optimization opportunities, and hide symbols in library dependencies. Libraries linking against libmod may stop linking, but configuration options has been added to disable symbol hiding.

12.8.2. New Features

• dgDump/dg::DG::dump should now be much, much faster in parsing the input file and loading the contained derivation graph.

• dgRuleComp/dg::DG::ruleComp should now be much faster during calculation.

• Added Graph.instantiateStereo()/graph::Graph::instantiateStereo().

• Added rngReseed()/rngReseed().

12.8.3. Bugs Fixed

• Fixed off-by-one error in DG dump loading, dgDump/dg::DG::dump.

• Fixed issues with auto in function signatures which is not yet in the C++ standard.

12.8.4. Other

• The functions prefixFilename(), pushFilePrefix(), and popFilePrefix() used by the include() function are now documented. A new class CWDPath has been added.

• Use interprocedural/link-time optimization as default. It can be disabled with a configuration option.

12.9. v0.8.0 (2019-04-04)

12.9.1. Incompatible Changes

• Now requires v0.3 of GraphCanon (and PermGroup).

• graph::Graph::getMolarMass/Graph.molarMass has been removed.

• Python interface: remove auto-generated hash-functions from all classes. Note, most code broken by this was already silemtly broken.

• Python interface: consistently disable all custom attributes on all classes.

• Removed dg::Strategy::GraphState::getHyperEdges/DGStratGraphState.hyperEdges. Use the graph interface of dg::DG/DG instead.

• All atoms, including hydrogens, are now present with ids in strings from graph::Graph::getSmilesWithIds()/Graph.smilesWithIds.

• dg::DG::print()/DG.print now returns a pair of strings, instead of just one string. The first entry is the old return value. The second entry is the tex-file to depend on for layout coordinates.

• SMILES parsing: disallow isotope 0 as it is equivalent to not specifying an isotope.

• All classes in the Python interface without a custom hash function has their hash function removed. This is to prevent inconsistencies between hash and equality.

12.9.2. New Features

• Added support for isotopes (see Molecule Encoding).

• Added graph::Graph::getExactMass()/Graph.exactMass.

• Added optional printInfo parameter to dg::DG::calc/DG.calc. to allow disabling of messages to stdout during calculation.

• The graph interface on dg::DG/DG can now be used before and during calculation.

• Added include of the PGFPlots package in the summary preamble.

• Added AtomId::symbol()/AtomId.symbol.

• Added an add parameter to graphGMLString, graphGML, graphDFS, smiles, ruleGMLString, and ruleGML. It controls whether the graph/rule is appended to inputGraphs/inputRules or not. It defaults to True.

• Add graph::Graph::getGraphDFSWithIds()/Graph.graphDFSWithIds for getting a string annotated with the internal vertex ids in form of the class labels. This mirrors the previously added graph::Graph::getSmilesWithIds()/Graph.smilesWithIds.

• Improve error messages from GML parsing of lists.

• Changed the return type of dg::DG::getGraphDatabase() from a std::set to a std::unordered_set.

• dg::DG::HyperEdge::print()/DG.HyperEdge.print() now returns a list of file data.

• The vertices and edges of all graph interfaces now have a conversion to bool:

  • graph::Graph::Vertex/Graph.Vertex, graph::Graph::Edge/Graph.Edge

  • rule::Rule::Vertex/Rule.Vertex, rule::Rule::Edge/Rule.Edge

  • rule::Rule::LeftGraph::Vertex/Rule.LeftGraph.Vertex, rule::Rule::LeftGraph::Edge/Rule.LeftGraph.Edge

  • rule::Rule::ContextGraph::Vertex/Rule.ContextGraph.Vertex, rule::Rule::ContextGraph::Edge/Rule.ContextGraph.Edge

  • rule::Rule::RightGraph::Vertex/Rule.RightGraph.Vertex, rule::Rule::RightGraph::Edge/Rule.RightGraph.Edge

  • dg::DG::Vertex/DG.Vertex, dg::DG::HyperEdge/DG.HyperEdge

• The vertices of all graph interfaces now have a proper hash support.

• Added dg::Printer::setRotationOverwrite()/DGPrinter.setRotationOverwrite() and dg::Printer::setMirrorOverwrite()/DGPrinter.setMirrorOverwrite().

12.9.3. Bugs Fixed

• Throw InputError/InputError when loading a DG dump when a rule in the dump can not be linked to a rule from the user.

• Fix molecule decoding of atoms with negative charge and a radical.

• Fix dangling reference bug in first-order term handling.

• Fix inifiinite loop bug in first-order term handling.

• Remove extraneous template parameter lists to make it compile on GCC 8.

• Fix the documentation of Graph.minExternalId, Graph.maxExternalId, Rule.minExternalId, and Rule.maxExternalId. It was not being rendered.

• Fixed documentation of the constructor for AtomData.

• Fix dangling references in morphism callbacks.

• Make sure Open Babel is not called in some cases where it is not needed.

• Find the library file for Boost.Python for Boost >= 1.67.

• Fix ambiguity between variadic arguments and function parameter packs, making term morphisms and stereo morphisms slow.

• Removed sanity check from GraphDFS loading which dominated the run time.

• Document inputGraphs and inputRules.

12.9.4. Other

• Now compiles with -fno-stack-protector (some OS distributions messes with default flags).

• The Makefile from mod --get-latex now cleans .vrb, .snm, and .nav files as well.

12.10. v0.7.0 (2018-03-08)

12.10.1. Incompatible Changes

• Boost >= 1.64 is now required.

• Two new libraries, GraphCanon and PermGroup, are now required dependencies.

• Sphinx 1.7.1 is now required for building the documentation.

• dg::DG::HyperEdge::print()/DG.HyperEdge.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.

12.10.2. New Features

• Added functions to map external ids of graphs and rules to internal vertices.

• Added functions to get vertex coordinates for rules.

• dg::DG::print()/DG.print now returns the name of the PDF-file that will be created in post-processing.

• Add dg::Printer::setWithInlineGraphs()/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 graph::Graph::getSmilesWithIds()/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.

12.10.3. 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 LabelSettings/LabelSettings is being used. Each rule has an optional LabelType/LabelType to signify whether it was designed for use with LabelType::String/LabelType.String or LabelType::Term/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 LabelSettings/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.

12.10.4. Bugs Fixed

• Multiple rules for the same derivation is now properly recorded.

• Fix documentation of rule::Rule::makeInverse()/Rule.makeInverse, it throws LogicError/LogicError not InputError/InputError.

• Set the name of a rule from rule::Rule::makeInverse()/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 dg::DG::findVertex()/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 dg::DG::ruleComp/dgRuleComp and dg::DG::calc/DG.calc when isomorphic graphs are given.

• Throw more appropriate exception if dg::DG::print()/DG.print is called before dg::DG::calc/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 library is used.

• Fix AtomData/AtomData to properly print radicals on uncharged atoms.

• Throw more friendly exceptions when loading graphs/rules that have loop/parallel edges.

12.10.5. Other

• The documentation now has a “Known Issues” section, describing an issue where post-processing may fail if pdflatex has been upgraded after installation

12.11. v0.6.0 (2016-12-22)

12.11.1. Incompatible Changes

• A C++14 compiler is now required (e.g., GCC 5.1 or later).

• The required Boost version is now either 1.59 or at least 1.61. 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.,

  • Deprecate DerivationRef. They now interconvert with dg::DG::HyperEdge/DG.HyperEdge.

  • Change DG::getDerivationRef into dg::DG::findEdge()/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.

• All SBML features have been removed from the library.

• The deprecated DG::printMatrix function has been removed.

• dg::DG::calc/DG.calc will no longer print a message when it is done.

• dg::DG::print()/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::Graph::print()/Graph.print and rule::Rule::print()/Rule.print will now emit only one depiction when the two printers are equal.

• rule::Rule::print()/Rule.print, change the default colours used to indicate changes. Now different colours are used in L, K, R.

• DG.HyperEdge.print, change the default match colour.

• Add < operator to vertices and edges of Graph, Rule, and DG.

12.11.2. New Features

• rule::Rule::makeInverse()/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). It will use IPython as interpreter if it is available.

• The molecule model now includes radicals. The SMILES format has been extended to support radicals as well.

• Plugin infrastructure to load additional Python modules when using the wrapper script.

• Graph interface for rules: for a rule \(L \leftarrow K\rightarrow R`\), the three graphs can be accessed. The rule it self acts as the graph that is the pushout of the rule span.

• Graph loading: the ids used in GML and GraphDFS, as well as the class labels in SMILES can now be converted into vertices for the loaded graphs. If the class labels of a SMILES string are not 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 graph::Printer::setRotation()/GraphPrinter.rotation. Internally computed coordinates will be rotated by the set amount of degrees.

12.11.3. Bugs Fixed

• operator<< for Derivation: only try to print the rule if there is one.

• Properly throw an exception when graph GML parsing fails.

• Don’t throw an exception while throwing an exception when graphs are disconnected.

• Fix bug in checking of certain constrainAdj during certain types of rule composition.

• Properly handle empty vertex/hyperedge ranges for DGs. Thanks to Robert Haas for reporting.

12.12. v0.5.0 (2016-03-07)

Initial public version.