Greg Landrum 1a3ce773cf Molecule metadata in PNGs (#3316) ...

* reader stub. Navigates the file successfullly

* works

* works

* read out all metadata, not just ours

* first pass at reading out molecules

* support mol blocks too

* add python wrapper for parser

* add direct writer

* get rid of multiple definitions in PNParser.h

* update from code review

* robustification

* handle reading compressed metadata

* support compressing metadata too

* reorder arguments to make this more consistent

* add writers to python wrappers

* forgotten file

* add pickle support

* explicit zlib dependency

* get windows builds working
at least with conda boost+zlib

* switch to using boost::iostreams to do the compression/decompression

* switch to using a vector of string pairs to store the metadata

need this so that we can contain "duplicate" keys

* add metadata output to MolDraw2DCairo
still need python test

* add a python test

* initial work at reading/writing reactions from PNGs

refactor the ReactionParser.h header a bit

* cleanup debug messages

* reaction PNG support -> python

* ReactionPickler no longer includes all ProductTemplate props

* handle metadata at the MolDraw2D level
Currently only supported by MolDraw2DCairo, it's worth extending this to SVG too

* support reading multiple molecules from a png

* support multiple molecules from files and in python

* stop duplicating tags with multiple molecules

* update to get windll builds working
this change should be propagated to more cmakelists.txt files

* make sure the metadata ends up in the notebook

* make sure PNGs in the notebook also have metadata

efficiency improvements for some notebook bits (i.e stop going PNG->Image->PNG)

* no need to pretend that we might be using PIL anymore

* documentation

* update docs to show new functionality

* not sure why the doctests failed on linux

* still trying to diagnose those failures

* protect doctests in case python interpreters are being re-used

* switch tags

* the wrapped functions to read png data from files weren't working

* <sigh>... windows dlls

2020-08-25 07:51:18 +02:00

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