Pybel

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Added
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- Additional keyword arguments for JSON output functions

Changed
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- Updated parser intermediate data structure. Should have no affect on end users.
- Smarter serialization of PyBEL data dictionaries to BEL

Fixed
~~~~~
- Better handling of citations that have authors pre-parsed into lists (https://github.com/pybel/pybel/issues/247)

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Added
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- Updates to DSL
- More node filters and predicates
- Added "partOf" relationship (https://github.com/pybel/pybel/issues/244)
- Added more regular expressions for date parsing (https://github.com/pybel/pybel/issues/239)

Fixed
~~~~~
- Fixed incorrect checking of network storage (https://github.com/pybel/pybel/issues/246)

Changed
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- Reorganized resources module to reduce dependencies on PyBEL Tools, which has lots of other big requirements
- Moved ``pybel.summary`` module to ``pybel.struct.summary``

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Fixed
~~~~~
- Problem with uploading products, reactants, and members to NDEx (230)
- Checking for adding uncachable nodes when populating edge store

Added
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- Database seeding functions
- Citation management
- Added PubMed Central as type in citation

Removed
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- Don't keep blobs in node or edge cache anymore

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Added
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- Convenience functions for adding qualified and unqualified edges to BELGraph class
- Sialic Acid Example BEL Graph
- EGF Example BEL Graph
- Added PyBEL Web export and stub for import
- BioPAX Import
- Dedicated BEL Syntax error

Changed
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- Update the BEL Script canonicalization rules to group citations then evidences better
- Removed requirement of annotation entry in edge data dictionaries
- Confident enough to make using the edge store True by default

Fixed
~~~~~
- Fixed unset list parsing so it doesn't need quotes (234)

Removed
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- In-memory caching of authors

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Fixed
~~~~~
- JSON Serialization bug for authors in Citation Model

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Added
~~~~~
- INDRA Import
- Usage of built-in operators on BEL Graphs

Changed
~~~~~~~
- Update list recent networks function to work better with SQL 99 compliant (basically everything except the
old version of MySQL and SQLite) RDBMS
- Better tests for queries to edge store
- Better testing when extensions not installed (c1ac850)
- Update documentation to new OpenBEL website links

Fixed
~~~~~
- Fix crash when uploading network to edge store that has annotation pattern definitions (still needs some work though)
- Added foreign keys for first and last authors in Citation model (requires database rebuild)
- Froze NetworkX version at 1.11 since 2.0 breaks everything

Removed
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- Don't cache SQLAlchemy models locally (3d7d238)