Pybel

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Added
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- Option for setting scopefunc in Manager
- Include extra citation information on inserting graph to database that might have come from citation enrichment
- Node model to tuple and json functions are now complete

Changed
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- Added members lists to the node data dictionaries for complex and composite nodes
- Added reactants and products lists to the node data dictionaries for reaction nodes

Fixed
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- GOCC and other location caching problem
- Node tuples for reactions are now using standard node tuples for reactants and products. This was a huge issue
but it had never come up before. DANGER - this means all old code will still work, but any node-tuple reliant
code will have unexpected results. This also means that the node hashes in the database for all reactions will
now be outdated, so the minimum version is being bumped.

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Changed
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- Change CacheManager class name to Manager
- Change references from build_manager to Manager.ensure
- Automatically update default database to minimum import version
- Constants for extra citation fields and update to_json for Citation model

Fixed
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- Bug in author insertion for non-unique authors

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Changed
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- Made new minimum unpickle version 0.8.0. From now on, all unpickle changes (before a 1.0.0 release) will be
accompanied by a minor version bump.
- Overall better handling of citation insertion
- Updated data models. Added to Citation model and renamed namespaceEntry in Node model.
- Better init function for BELGraph
- Force name and version to not be null in the database
- Update pickle references to use six module
- Update base cache manager - better connection handling and more exposed arguments

Added
~~~~~
- Get graph functions to cache manager
- Added more useful functions to cache manager
- Kwargs for setting name, version, and description in BELGraph init
- Getters and setters for version and description in BELGraph
- Node data to tuple functions (https://github.com/pybel/pybel/issues/145)

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Changed
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- Update logging for parsing of bad version strings
- Change where kwargs go in parse_lines function
- Make non-standard parsing modes part of kwargs

Fixed
~~~~~
- On-purpose singletons now properly identified (https://github.com/pybel/pybel/issues/218)

Added
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- CLI command for set connection (https://github.com/pybel/pybel/issues/220)
- GEF and GAP activities added for INDRA

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Changed
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- Externalized more parsing constants
- Updated version management
- Keep track of all singleton lines in parsing
- Update CLI
- Update JGIF export from CBN

Fixed
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- Change node hashing ot only use type and reference

Added
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- Node intersection merge
- Get most recent network by name in manager

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Changed
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- Externalized some PyParsing elements

Fixed
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- Version string tokenization