Pybel

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Added
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- JGIF interchange (https://github.com/pybel/pybel/issues/193) and (https://github.com/pybel/pybel/issues/194)
- Configuration file parsing (https://github.com/pybel/pybel/issues/197)

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Changed
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- CX is now unstreamified on load, making compatibility with other CX sources (like NDEx) possible
- Testing now enables ``PYBEL_TEST_CONNECTION`` environment variable to set a persistient database
- Testing data cut down to reduce memory consumption

Added
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- NDEx upload and download

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Changed
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- Public IO changed for to/from_json and to/from_cx (https://github.com/pybel/pybel/issues/192)
- Better error output for metadata failure (https://github.com/pybel/pybel/issues/191)

Added
~~~~~
- Add BEL script line to edges (https://github.com/pybel/pybel/issues/155)
- Export to GSEA gene list (https://github.com/pybel/pybel/issues/189)
- Non-caching of namespaces support (https://github.com/pybel/pybel/issues/190)

Note: I made a mistake with the release on 0.5.6, so I just bumped the patch one more.

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Changed
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- Updated CX output to have full provenance and list definitions (https://github.com/pybel/pybel/issues/180)

Added
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- DOI and URL are now acceptable citation types (https://github.com/pybel/pybel/issues/188)
- Citation can now be given as a double of type and reference (https://github.com/pybel/pybel/issues/187)

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Fixed
~~~~~
- MySQL truncations of large BLOBs
- Session management problems

Changed
~~~~~~~
- If a namespace/annotation was redefined, will now thrown an exception instead of just a logging a warning
- Update minimum pickle parsing from 0.5.3 to 0.5.4 to reflect changes in parse exceptions

Added
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- Ability to drop graph that isn't in graph store from CLI

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Added
~~~~~
- Lenient parsing mode for unqualified translocations (https://github.com/pybel/pybel/issues/178)

Changed
~~~~~~~
- Check for dead URLs at BEL framework (https://github.com/pybel/pybel/issues/177)
- Don't throw warnings for versions that are in YYYYMMDD format (https://github.com/pybel/pybel/issues/175)
- Include character positions in some exceptions (https://github.com/pybel/pybel/issues/176)
- Update minimum pickle parsing from 0.4.2 to 0.5.3 to reflect the new parse exceptions's names and arguments