12.1. v0.13.0 (2021-07-08)¶
12.1.1. 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
Change the GraphCanon submodule from a relative path to the Github repository.
Rename the C++ graph loading functions
Rename the C++ rule loading functions
rcCommonto consistently enumerate common subgraphs that are not necessarily vertex-induced. Use
config.rc.useBoostCommonSubgraph = Falseto switch to the old behaviour.
BUILD_DOCoption for building from source now defaults to
Graph.fromSMILES()has changed order of parameters,
addis now the last one.
12.1.2. New Features¶
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.
Add the static methods
Allow dot (
.) bonds in SMILES strings.
Add the following functions for loading a possibly disconnected graph:
12.1.3. Bugs Fixed¶
Fixed typos in a few error messages.
Actually fail loading when errors in constraints are encountered.
Fix v0.12 problem with RPATH handling of
Doc, fix infinite search.
Fix exception visibility on macOS so they can be caught outside the library.
Tests, set C++ standard in CMake tests.
Fix error handling to throw the right exception with better message when the file can not be opened for the functions
Fixes to support Boost 1.76.
Fixes to support GCC 11.
Build system, use
add_custom_commandto avoid recompilation of docs and Latex format file on install. Fixes problem with failing to import
sudo make install.
Test, set C++ standard in CMake tests.
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
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 (mod).
Doc, clarify use of
--userfor home folder installation.
Doc, properly document that a
CWDPathis a valid argument for
12.2. v0.12.0 (2021-01-18)¶
12.2.1. Incompatible Changes¶
Require Boost 1.73 to avoid CMake issue in 1.72.
Require GraphCanon 0.5.
Require Sphinx 3.4.
mod::makeUniqueFilePrefix()has been renamed to
12.2.2. New Features¶
Added new higher-level installation instructions at Installation, with documentation for how to install via Conda and using the Docker image.
bindep.txtand Quick Start guide for Arch.
Brewfileto to make installation of dependencies much easier on macOS.
graphattributes to vertices and edges of the four graph interfaces of
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
Teach the post-processor to dynamically compile the format file if it is not installed.
mod_post --install-format-sudofor installing/updating the pre-compiled format file after MØD was installed. This can be used on an installation configured with
-DBUILD_POST_MOD_FMT=offor for resolving a known issue.
Make build work on macOS and add installation instructions.
Rule composition: when using
rcCommon, skip duplicate overlaps yielded by the underlying enumeration algorithm.
12.2.3. Bugs Fixed¶
Fix printing/stringification of a null vertices for
Fix conversion of
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..
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.
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:
Doc, improve documentation of the graph interfaces of
12.3. v0.11.0 (2020-08-31)¶
12.3.1. Incompatible Changes¶
Bump version requirement of Boost to 1.72.
DGPrinter.pushVertexColour()now requies a callback taking a
DGVertex, instead of a
DG. The previous style is removed in libMØD and deprecated in PyMØD.
dg::DG::dumpImport()has been renamed to
dgDump()has been renamed to
Do not install a pkg-config file. It was broken and there doesn’t seem to be an easy way to fix it.
12.3.2. New Features¶
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.
Support using either Open Babel 2 or 3 as dependency.
DGPrinter.graphPrinterwriteable as well.
12.3.3. Bugs Fixed¶
Fix handling of null pointers:
Fix handling of empty functions given as callbacks:
Improve parsing error messages.
Fix missing external ID for bracketed wildcard atoms with class label, e.g.,
Fix handling of an atom which contains a ring-closure and ring-opening using the same ID, e.g.,
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 Python export of
PostMØD: remove extranous escape of a quote in AWK script in
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.
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
Doc, various typo fixes.
Doc, clarify that
DGPrinter.setMirrorOverwrite()accepts a constant as well as a callback.
Doc, add return type to
requirements.txtto 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.
12.4. v0.10.0 (2020-02-05)¶
12.4.1. Incompatible Changes¶
dg::DG::derivationshas been removed. Use the repeated calls to
dg::DG::calc()has been removed. Use the new
The implementation of
dgDerivationshas changed and the function is now deprecated. Use repeated calls to
Information from strategies has been updated.
12.4.2. New Features¶
Rulenow has an overloaded operator
MOD_NO_DEPRECATEDto make it easier to find usage of deprecated behaviour.
12.4.3. Bugs Fixed¶
Changed assert to a proper error message at code related to Open Babel. If MØD, or an extension library, is loaded with
RTLD_GLOBALflag, there can be multiple copies of Open Babel symbols at the same time, which prevent MØD from accessing Open Babel operations..
Build: disallow use of experimental Boost CMake support due to a linking problem.
Various fixes for documentation formatting including new themeing.
Installation, highlight the more relevant
Bump recommended lower bound on GCC version to 6.1 in the documentation.
Documentation, added explicit example section.
12.5. v0.9.0 (2019-08-02)¶
12.5.1. 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.
dg::DG::getGraphDatabase()now returns a
std::vectorinstead of a
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.
12.5.2. New Features¶
12.5.3. Bugs Fixed¶
Fixed off-by-one error in DG dump loading,
Fixed issues with
autoin function signatures which is not yet in the C++ standard.
12.6. v0.8.0 (2019-04-04)¶
12.6.1. Incompatible Changes¶
Graph.molarMasshas 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.
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.
12.6.2. New Features¶
Added support for isotopes (see Molecule Encoding).
DG.calc. to allow disabling of messages to stdout during calculation.
Added include of the PGFPlots package in the summary preamble.
Graph.graphDFSWithIdsfor getting a string annotated with the internal vertex ids in form of the class labels. This mirrors the previously added
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.
The vertices and edges of all graph interfaces now have a conversion to bool:
The vertices of all graph interfaces now have a proper hash support.
12.6.3. Bugs Fixed¶
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.
Fixed documentation of the constructor for
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.
Now compiles with
-fno-stack-protector(some OS distributions messes with default flags).
The Makefile from
mod --get-latexnow cleans
.navfiles as well.
12.7. v0.7.0 (2018-03-08)¶
12.7.1. Incompatible Changes¶
Boost >= 1.64 is now required.
Sphinx 1.7.1 is now required for building the documentation.
DGHyperEdge.printnow 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
DerivationRefhas now been removed along with
DG.derivationsin the Python interface.
The previously deprecated method
DG.vertexGraphsin the Python interface has been removed.
12.7.2. New Features¶
Added functions to map external ids of graphs and rules to internal vertices.
Added functions to get vertex coordinates for rules.
DGPrinter.withInlineGraphsto 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.
inlineas a special argument for the graph Latex macros to input the raw tex file, instead of including a compiled PDF.
The automorphism group of each graph is now available.
12.7.3. 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
LabelSettingsis being used. Each rule has an optional
LabelTypeto signify whether it was designed for use with
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
LabelSettingsobjects 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.
12.7.4. Bugs Fixed¶
Multiple rules for the same derivation is now properly recorded.
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 to print derivations with multiple rules.
Fix documentation formatting errors.
#2, throw exceptions from
DG.calcwhen isomorphic graphs are given.
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.
Throw more friendly exceptions when loading graphs/rules that have loop/parallel edges.
The documentation now has a “Known Issues” section, describing an issue where post-processing may fail if
pdflatexhas been upgraded after installation
12.8. v0.6.0 (2016-12-22)¶
12.8.1. 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
constrainAdjmust now enclose the operator in double quotes.
DG: remove most of the interface related to
DerivationRef. Use the graph interface instead. E.g.,
DG.derivationsreturn the edges instead in the Python interface. It is removed in the C++ interface. It will be removed from Python in the future.
DG::vertexGraphsin Python, remove in C++.
Move the graph interface for DG and Graph into separate headers:
GraphPrinterinto a separate header.
DGPrintDatainto a separate header.
All SBML features have been removed from the library.
DG::printMatrixfunction has been removed.
DG.calcwill no longer print a message when it is done.
DGHyperEdge.print, change the default match colour.
Add < operator to vertices and edges of Graph, Rule, and DG.
12.8.2. New Features¶
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.
-vas alias for
--versionin the wrapper script.
Add quite mode,
-q, to the wrapper script.
12.8.3. 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
constrainAdjduring certain types of rule composition.
Properly handle empty vertex/hyperedge ranges for DGs. Thanks to Robert Haas for reporting.
12.9. v0.5.0 (2016-03-07)¶
Initial public version.