Pybel

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Added
~~~~~
- Calculation of SHA512 hash to DSL abundances
- Documented the deployment extra for setup.py
- Added to and from JSON path IO functions
- PMI Contact for CBN import and more default namespaces
- Added common query builders to SQLAlchemy models

Fixed
~~~~~
- Fixed name/version lookup in the database
- Safer creation of directories (https://github.com/pybel/pybel/issues/#284)
- Make export to GraphML more boring and permissive
- Implement to_tuple for CentralDogma (https://github.com/pybel/pybel/issues/#281)
- Unicode compatibility error. Thanks bgyori! (https://github.com/pybel/pybel/pull/289)

Changed
~~~~~~~
- Made parsing of fragments permissive to quoting (https://github.com/pybel/pybel/issues/#282)
- Update citation handling
- Update namespace methods in CLI
- Added ``as_bel`` method to DSL
- Update authentication with BEL Commons (https://github.com/pybel/pybel/commit/4f6b8b0ecab411e1d2b110e00c8bac77ace88308)
- Unpin SQLAlchemy version. Most up-to-date should remain safe.

Removed
~~~~~~~
- Removed static function ``pybel.BELGraph.hash_node`` since it just wraps ``pybel.utils.node_to_tuple``
- Removed unnecessary configuration editing from CLI
- Removed OWL Parser (https://github.com/pybel/pybel/issues/290)
- Removed support for BELEQ files (https://github.com/pybel/pybel/issues/294)
- Remove artifactory code and migrated to https://github.com/pybel/pybel-artifactory. (https://github.com/pybel/pybel/issues/292)

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Added
~~~~~
- Added additional DSL shortcuts for building edges with the BELGraph
- Added example graphs (statins, BRAF, orthology examples)
- Added knowledge transfer function
- Added progress bar for parser

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Changed
~~~~~~~
- Updated SQL schema and made new minimum unpickle version 0.11.0.
- Parser now uses a compact representation of annotations instead of exploding to multiple edges (https://github.com/pybel/pybel/issues/261)
- Update annotation filtering functions to reflect new data format (https://github.com/pybel/pybel/issues/262)
- Update GraphML Output (https://github.com/pybel/pybel/issues/260)
- Better error message when missing namespace resource (https://github.com/pybel/pybel/issues/265)

Fixed
~~~~~
- Fixed more problems with edge store and testing (https://github.com/pybel/pybel/issues/225, https://github.com/pybel/pybel/issues/256, https://github.com/pybel/pybel/issues/257)
- Fixed windows testing (https://github.com/pybel/pybel/issues/243)
- Fixed broken network cascade, but is still slow (https://github.com/pybel/pybel/issues/256, https://github.com/pybel/pybel/issues/257, https://github.com/pybel/pybel/issues/259)
- Fixed JGIF import (https://github.com/pybel/pybel/issues/266) and added scripts directory (3dc6b1f)
- Fix extras in setup.py and requirements.txt

Added
~~~~~
- Additional regex format for date parsing from PubMed (https://github.com/pybel/pybel/issues/259)
- Add labels to nodes in GraphML output (https://github.com/pybel/pybel/issues/260)
- Add edge predicate builders (https://github.com/pybel/pybel/issues/262)
- Testing on multiple databases (SQLite, MySQL, PostgreSQL) (https://github.com/pybel/pybel/issues/238)
- Added ``pybel.struct.mutations`` module
- Added graph-based equivalency checking
- Add more documentation to BELGraph (https://github.com/pybel/pybel/issues/271)

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Fixed
~~~~~
- Fixed truncation description parsing to handle double quotes

Changed
~~~~~~~
- Made DSL functions into classes to allow inheritance and isinstance checking as well as
preliminary to_tuple functionality

Added
~~~~~
- Added more edge predicates (has_activity, has_degree, has_translocation, has_annotation)

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Changed
~~~~~~~
- Updated SQL schema and made new minimum unpickle version 0.10.0.
- Moved `pybel.parser.language` to `pybel.language`
- Moved `pybel.parser.canoncalize` to `pybel.tokens`
- Overhaul of `pybel.struct.filters` - included many more functions, tests, and updated nomenclature
- Update canoncalize functions to be generally reusable (take node data dictionaries)
- Make NDEx2, Neo4j, OWL parsing, and INDRA setup.py install extras

Fixed
~~~~~
- Names defined by regular expressions can now be included in the database cache (https://github.com/pybel/pybel/issues/250, https://github.com/pybel/pybel/issues/251)
- Fixed ``Manager.has_name_version`` (https://github.com/pybel/pybel/issues/246)
- Fixed CX output and upgraded to NDEx2 client
- When joining graphs, keep their metadata (https://github.com/pybel/pybel/commit/affaecc73d2b4affa8aeecb3834ed7c6f5697cac)

Added
~~~~~
- Included partOf relationship in BEL language (https://github.com/pybel/pybel/issues/244)
- Added additional date formats to parse from PubMed (https://github.com/pybel/pybel/issues/239)
- Filled out many more DSL functions and added testing
- Added ability to set relationship parsing policy in BEL Parser (https://github.com/pybel/pybel/commit/09614465d80d2931e901fd54d067a5151e327283)
- Implemented from PyBEL Web Function
- Implemented to INDRA function

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Changed
~~~~~~~
- Use ``HASH`` as dictionary key instead of ``ID``
- Allow DSL to create nodes without names but with identifiers
- Rename instance variables in parsers for consistency
- Greater usage of DSL in parser