CHANGELOG

r20250728
- !feat: enable new standardization mode: aromatized with implicit Hs. This provides support for future reaction rule datasets. `aromatized with implicit Hs` is now the standardization mode used by default, to be used with up-to-date version of reaction rules (i.e. RetroRules rr03). To use RetroPath2.0 with previous collections of reaction rules (e.g. : RetroRules releases rr01 and rr02).
- feat: speed up by 5-10x execution time
- feat: speed up by 10x loading time of reaction rules

r20220224
- fix: solve issue due to coeff column missing when no results are found

r20220104
- Compatibility improvement: workflow exported using KNIME 4.3.0

r20211221
- Bug fix: output the right number of compounds in reaction SMILES according stoichiometric coefficients
- Replace some deprecated Joiner nodes

r20210127
- Update scope-viewer to release 20190926 (compatible with RetroPath RL)
- Feat: SVG generation is now based of RDKit renderer, Marvin extension is now longer needed
- Feat: add FAQ about RetroPath2.0 and rp2paths

r20191007
- Scope viewer update. For details see https://github.com/brsynth/scope-viewer
- License update, we're now under GPL v3

r20181009
- Bug fix: multiple EC number annotation correctly displayed in Scope Viewer
- Updated installation procedure

r20180919
- Bug fix: reset input/output settings not reseted by default

r20180730
- Bug fix: SVG generation is now based of Marvin node, due to bug in RDKit node in KNIME v3.6.0

r20180216
- Feature update: Scope Viewer generates crosslinks to Selenzyme

r20171218
- Citation update: "How to cite" section that points out to the Metabolic Engineering paper.

r20171026
- Bug fix: Cannot generate InChIKey in some case. Now using SMILES as starting point for generating the InChIKey.

r20170927
- Bug fix: Open Babel nodes lead to errors (only on Mac OS) since the last KNIME update (v3.4.1). Replacing the Open Babel nodes by RDKit nodes.

v2.12
- Global result: pre-existing global result file is removed if needed.
- Parse bug (when using the python snippet): fixing the way invalid compounds are filtered out in the Parse metanode.

v2.11
- Scope Viewer: adding interactive links to the MetaNetX database for MNX reactions and known MNX compounds.
- Scope Viewer: adding links for querying google using compound InChIKey
- Scope: improving scope generation using reaction filters. See advanced features for more details.
- Scope: adding a check step after all filtering tasks.
- Output configuration: user now just need to provide the desired names for output files (the full path for each file is not any more required).

v2.10
- Result: adding a "Source in Sink" output file that reports source compounds already in Sink.
- Scope bug: SQL handler does not complain any more about validation of queries.
- Dev feature: adding a global workflow variable in order to set the size of the source chunk (dev.source-chunk-size)
- Dev feature: adding a python Snippet allowing an alternative way for firing rules (drastically reduce the memory consumption). See advanced user features for more details.

v2.9
- Result file: the global result file is now written at the end of each iteartion (instead of at the end of the whole workflow).
- Workflow variable: the scope of some worfklow variables (input.* output.* WFVAR.*) is constrained
- Dev feature: Adding a python wrapper that can be used for firing rules (instead of the OneComponentReaction Knime node)
- Rule prefiltering: rule prefiltering (before firing rule) is always made for mono-substrate rule.
- Source handling: the chunk size of the "Source" outter loop is now set to 1 (instead of 100).

v2.8
- Configuration nodes: updating documentation
- Front workflow page simplification
- Scope: more information in JSON output.
- Scope bug: better handling of In Sink information.
- Scope bug: Marvin SVG renderer does not exist for column SMILES (if ChemAxon not installed). Switching to rdkit SVG renderer.
- Scope viewer: legend & how-to.
- Scope viewer: adding a side panel for node visualisation.
- Scope viewer BUG: fixing compatilibility with CORS security policy in some web browsers (cannot load .svg depictions)

v2.7
- Scope, reverse : transformation producing source are removed. Eventual resulting unfireable transformations and unreachable transformation compounds are removed.
- Scope : fixing bug (exit code 4) when all scopes are empty.
- Scope : source compounds are now tagged as such in .json files.
- Bug fix: source, sink and cofactors name can be provided as integer values
- Bug fix: workflow able to run even when not any sink is provided
- Bug fix: better handling sink info
- svg renderer: switching to rdkit

v2.6
- Defaults values for input and output are now handled with workflow (global) variables, which allow us to set them through command-line
- Workflow compatible with Knime v3.3

v2.5
- Output scope for each source (in progress)
- Fixing generation of Transformation IDs (nested loops)
- Improving accessibility to standardization options (Input config Metanode)
- Workflow comptaible with Knime v3.2.1 and upper

v2.4.1
- Fixing joiner allowing to retrieve original source name (Joiner in PARSE)

v2.4
- Filter out transformations involving products that cannot be sanitized (PARSE metanode)
- Convert score as double (Rules metanode)
- Add  substrate information in results (BUILD metanode)
- Fixing path to cofactor file (Source.. metanode)

v2.3
- Insertion of the standardization nodes (both input and in PARSE)
- Corrected a few typo
- Use node "File input" instead of "string input" for files (except output file path)