Releases | Open Source Science

pybel - v0.15.5

What's Changed

Update citation enrichment functions by @cthoyt in https://github.com/pybel/pybel/pull/495
Rearrange extra dependencies for grounding
Use more modern project layout
Add py310 by @cthoyt in https://github.com/pybel/pybel/pull/497

Full Changelog: https://github.com/pybel/pybel/compare/v0.15.4...v0.15.5

- Python
Published by cthoyt about 4 years ago

pybel -

Update dependencies on PyOBO and the Bioregistry
Update README for Harvard funding!

- Python
Published by cthoyt over 4 years ago

pybel -

Added

Exposed transitivities parsed via nested statements through pybel.BELGraph.transitivities (https://github.com/pybel/pybel/issues/490).

Fixed

Some dependencies updated their interfaces (https://github.com/pybel/pybel/pull/491)

- Python
Published by cthoyt almost 5 years ago

pybel -

Added

Add support for directly regulates relationships

- Python
Published by cthoyt almost 5 years ago

pybel -

Added

Add support for named reactions (https://github.com/pybel/pybel/pull/485)

Changed

Switch to GitHub Actions
Use PyStow for file management
Use Bioregistry for prefix normalization

- Python
Published by cthoyt about 5 years ago

pybel -

Added

Support for homomultimers in ML triples export
Graph dispatches allow quick access to PyBEL functionality (https://github.com/pybel/pybel/pull/449)
Add "Streamable" BEL I/O (https://github.com/pybel/pybel/pull/451)
pybel.to_triples allows direct export of ML-ready triples to a numpy ndarray.
pybel.parse function allows for quick parsing of BEL strings
Add JSON Schema for validating nodes and edges (https://github.com/pybel/pybel/pull/450) thanks @aman527
Add BEL Repository functionality, previously located in https://github.com/pybel/bel-repository
Pickling can be done with gzip to greatly reduce size both on files (https://github.com/pybel/pybel/commit/d90578cb) and on bytes (https://github.com/pybel/pybel/commit/fcc99952)

Changed

PyBEL now supports Python 3.6+ only.
pybel.to_tsv renamed to pybel.to_triples_file
The citation entry in PyBEL JSON datastructure now uses namespace/identifier/name instead of db/db_id. The corresponding constants pybel.constants.CITATION_DB/pybel.constants.CITATION_DB_ID/ pybel.constants.CITATION_DB_NAME have been removed (https://github.com/pybel/pybel/pull/453).
The citation entry now relies on a subclass of pybel.language.Entity, which means empty strings are no longer allowed.
The inconsistent usage of subject/source as well as object/target has been normalized everywhere. This means the constants pybel.constants.SUBJECT/pybel.constants.OBJECT were removed and new constants pybel.constants.SOURCE_MODIFIER/pybel.constants.TARGET_MODIFIER were added (https://github.com/pybel/pybel/pull/453).
Remove the BEL default namespace. All usages get normalized to controlled vocabularies (mostly GO) automatically (https://github.com/pybel/pybel/pull/455).
Improve namespace/annotation database insertion with Pandas (https://github.com/pybel/pybel/pull/454)
Pickling now uses protocol 5 by default assisted by the pickle5 backport on Python 3.6 (https://github.com/pybel/pybel/commit/679dcab7)
Database now stores graphs in gzipped pickles (https://github.com/pybel/pybel/commit/9ee9bf21)
Unspecified molecular activities now use the top-level GO term (https://github.com/pybel/pybel/commit/d56993e6)
New annotation storage format using lists of annotations instead of dictionaries (https://github.com/pybel/pybel/pull/461)
Citations now wrapped in dedicated data structure (https://github.com/pybel/pybel/pull/468)

Fixed

Parser now correctly supports dashes and dots in namespaces as well as in names without quoting (https://github.com/pybel/pybel/pull/460)
Bug in creating list abundances with name and list definition (https://github.com/pybel/pybel/pull/465)

- Python
Published by cthoyt about 5 years ago

pybel -

Added

Importer from EMMAA (https://github.com/pybel/pybel/pull/432)
I/O for Amazon S3 (https://github.com/pybel/pybel/pull/431)
Improve TSV exporter (d7d12878, 74d51c1c, e1082523, 6ffc1df6)
Add identifier-based entity remapper (ba8aa933)
Add annotation grounding (https://github.com/pybel/pybel/pull/435, https://github.com/pybel/pybel/pull/443)
Add HiPathia export examples (https://github.com/pybel/pybel/pull/422)

Changed

Updated default BEL Commons instance from https://bel-commons.scai.fraunhofer.de to https://bel-commons-dev.scai.fraunhofer.de
Add more namespaces for JGIF parsing to support CBN and BioDati import (9f74122d and https://github.com/pybel/pybel/pull/435; thanks @djinnome)
Make Jupyter notebook export accessible from top level at pybel.to_jupyter (4d76faad)

Fixed

Fix bug in display of nice labels in Jupyter notebook (775bdc30)

Removed

Remove default service URL for BEL Commons exporter. The Fraunhofer instance was taken down (a9a540fb).

- Python
Published by cthoyt over 5 years ago

pybel -

Changed

Updated GraphDati and BioDati exports (https://github.com/pybel/pybel/commit/c9f95344b72ff86239c8987d6b534000ba509a1f)
Refactoring of pybel.struct.filters and pybel.struct.mutation - some imports might have to be updated

Added

Importer from Fraunhofer OrientDB (https://github.com/pybel/pybel/pull/429)
Exporter for SPIA analytical tool (https://github.com/pybel/pybel/pull/430)

- Python
Published by cthoyt almost 6 years ago

pybel -

Changed

pybel.post_graphdati() has been renamed to pybel.to_biodati()
pybel.to_web() has been renamed to pybel.to_bel_commons()
pybel.from_web() has been renamed to pybel.from_bel_commons()

Added

Content importers from GraphDati format with pybel.from_graphdati() and pybel.from_graphdati() and enable usage of respective extensions *.bel.graphdati.json and *.bel.graphdati.json.gz with pybel.load() (https://github.com/pybel/pybel/pull/425)
Content importer from BioDati with pybel.from_biodati() (https://github.com/pybel/pybel/pull/425)
Add direct function for loading CBN files (so you don't have to load the JSON first) with pybel.from_cbn_jgif_file()
Added pybel.grounding.ground() function that uses the unlisted Python 3.7+ dependency, pyobo` to ground/normalize entities in a given BEL graph. This also takes care of upgrading legacy namespace names and mapping SCOMP/SFAM via FamPlex. (https://github.com/pybel/pybel/pull/426)

- Python
Published by cthoyt almost 6 years ago

pybel -

Added

Support for transcription factor relationships in TSV (machine learning) output

Fixed

Fixed incorrect parsing of OBO-style identifiers (https://github.com/pybel/pybel/pull/421)
Make sure pop() works in translocations (https://github.com/pybel/pybel/pull/421)
None and non-empty string checks in DSL (3156d519)
Fixed Jupyter export (the interface changed in Jinja2; d6e7e619)

- Python
Published by cthoyt almost 6 years ago

pybel -

Added

Add PyKEEN import hooks, so you can automatically load up a BEL file for machine learning with PyKEEN
Update TSV exporter for better ML-ready triples for PyKEEN
Added INDRA I/O options and pybel.from_bel_script_gz option
Add HiPathia Exporter (https://github.com/pybel/pybel/pull/414)
Add PyNPA Exporter (https://github.com/pybel/pybel/pull/413)
Add universal I/O functions pybel.load and pybel.dump (https://github.com/pybel/pybel/pull/417)

- Python
Published by cthoyt almost 6 years ago

pybel -

Added

Gzip variant of umbrella nodelink exporter
More entry points for exporting

Fixed

OBO-style export was broken if name and identifier weren't available. This works with whatever is available now
If CURIE is requested and both identifier and name are available, defaults to identifier.

- Python
Published by cthoyt about 6 years ago

pybel -

Added

Added BEP-0001 support (population abundance; https://github.com/pybel/pybel/issues/402)
Added BEP-0003 support (noCorrelation relation; https://github.com/pybel/pybel/issues/403)
Added BEP-0012 support (correlation relation; https://github.com/pybel/pybel/issues/403)
Added BEP-0011 support (binds relation; https://github.com/pybel/pybel/issues/403)
Add GraphDati exporter and BioDati uploader (https://github.com/pybel/pybel/issues/407)
Add Hetionet importer (https://github.com/pybel/pybel/issues/406)
Add several more I/O functions (pybel.to_bel_script_gz, etc.)

Removed

Removed support for label relation
Removed support for node attributes and description

Updated

Updated programmatic citation handling. Now a tuple of strings (database, identifier) can be passed anywhere a citation is needed.

Fixed

Fixed output of BEP-0008 (OBO-style identifiers)
Fixed convenience functions for BELGraph.add_inhibits and BELGraph.add_activates (there was a typo and it was adding the opposite relation in both)
Fixed that graph edge adder functions don't add two-way edges (https://github.com/pybel/pybel/issues/409)

- Python
Published by cthoyt about 6 years ago

pybel -

Added

Umbrella node-link JSON exporter(https://github.com/pybel/pybel/pull/400)
GraphML exporter with umbrella nodes (https://github.com/pybel/pybel/pull/400)

- Python
Published by cthoyt about 6 years ago

pybel -

Adds more IO functions

- Python
Published by cthoyt over 6 years ago

pybel -

Fixes autoflushing in the manager

- Python
Published by cthoyt over 6 years ago

pybel -

- Python
Published by cthoyt over 6 years ago

pybel -

Added

BELGraph class now has built-in summaries for authors and citations
Added first Jupyter notebook into documentation. More to come!

Changed

Authors are always stored as lists inside edges
Nodes in node-link JSON always have the BEL string included
Updated documentation for data model and DSL
Enforce keyword argument usage in BELGraph.addqualifiededge
Use iterator in pybel.union so graphs can be lazily loaded and combine

Removed

Remove remaining traces of namespace hierarchy table

Fixed

Union function also takes union of locally defined annotations now
Handling of special translocations (sec, surf; https://github.com/pybel/pybel/issues/377)
Fixed public header in pybel.to_web
Fixed public interface to pipeline and queries
Fixed parsing of gene methylations/modifications

- Python
Published by cthoyt almost 7 years ago

pybel -

Fixed

Fix handling of node JSON with identifier but not name (https://github.com/pybel/pybel/issues/375)
Fix handling of isolated nodes in pybel.union (https://github.com/pybel/pybel/issues/373)

- Python
Published by cthoyt about 7 years ago

pybel -

Added

Add JSON to node and edge SQL models (https://github.com/pybel/pybel/pull/358)
Add more properties to the Fragment class
Node pruning command to CLI
Type hints (https://github.com/pybel/pybel/issues/369)

Changed

Use a declarative setup (https://github.com/pybel/pybel/issues/360)
Pass flake8 (https://github.com/pybel/pybel/issues/363)
Change handling of locally defined namespaces in parser
Excise pybel.resources module to new package bel_resources

Fixed

Add sha512 to JSON of edges' nodes when retrieving from the database
Add nested sha512 identifiers when outputting node-link (https://github.com/pybel/pybel/issues/370)
Fixed handling of invalid entities in the BEL parser (https://github.com/pybel/pybel/issues/368)
Fixed merging of locally defined annotations when using pybel.union (https://github.com/pybel/pybel/issues/372)

Removed

Dropped Python 2.7 support (https://github.com/pybel/pybel/issues/285)
Dropped Python 3.4 support (https://github.com/pybel/pybel/issues/286)

- Python
Published by cthoyt about 7 years ago

pybel -

Added

Serialization functions can be accessed directly from the BELGraph class (https://github.com/pybel/pybel/pull/344)
Added several useful node filter functions (Thanks @ddomingof; https://github.com/pybel/pybel/pull/347)
Add a function for removing extraneous citation metadata

Changed

pybel.struct.graph.BELgraph.summarize() now prints the number of warnings, even if it is zero

Fixed

Platform specificity for requirements in setup.py (Thanks @scolby33; https://github.com/pybel/pybel/pull/346)
Print statement problem (Thanks @smoe; https://github.com/pybel/pybel/pull/351)
Import paths for INDRA (Thanks @bgyori; https://github.com/pybel/pybel/pull/339
Improvements on flake8 status (Thanks @tehw0lf; https://github.com/pybel/pybel/pull/353)
Ensure complexes have at least one member (Thanks @10mubeen for pointing this out)
Make "Other" as the default namespace domain for generating BEL namespace files

- Python
Published by cthoyt over 7 years ago

pybel -

- Python
Published by cthoyt over 7 years ago

pybel -

Changed

Update edge hashing algorithm (this invalidates old hashes)
Edge hashes are now used as keys instead of being put inside edge data dictionaries
Improved graph operations with new location of edge hashes
Update Node/Link JSON schema
Improve contains and has_node functions to handle DSL objects
Require usage of DSL when creating BELGraph instances
Use DSL completely in ORM
Add SHA512 to authors to avoid issues with MySQL's collation

Removed

Remove pybel.tokens.node_to_tuple function and pybel.tokens.node_to_bel functions
All tuple-related functions in the DSL (AKA the tupleectomy)

- Python
Published by cthoyt over 7 years ago

pybel -

Added

Automatic generation of CLI documentation with sphinx-click
Several edge creation convenience functions to the BELGraph
Graph summary functions

Changed

Improve Drop networks (Thanks @scolby33) (https://github.com/pybel/pybel/pull/319)
Huge improvements to documentation and code style reccomended by flake8

Fixed

Fixed handling of tuples (64d0685)

Removed

Remove function BELGraph.iter_data

- Python
Published by cthoyt over 7 years ago

pybel -

Added

Several subgraph functions (https://github.com/pybel/pybel/pull/315)

Changed

Better SQL implementation of getrecentnetworks (https://github.com/pybel/pybel/pull/312)

- Python
Published by cthoyt over 7 years ago

pybel -

Removed

Removed CX and NDEx IO in favor of https://github.com/pybel/pybel-cx (#308)

Changed

Better (less annoying) logging for deprecated transformations
Turn off SQL echoing by default
Update getting annotation entries
Better options for using TQDM while parsing

Added

Flag to INDRA machine to run locally
Add require annotations option to parser (https://github.com/pybel/pybel/issues/255)
Data missing key node predicate builder

- Python
Published by cthoyt over 7 years ago

pybel -

Added

Deprecation system for pipeline functions (for when they're renamed)

Changed

Rely on edge predicates more heavily in selection/induction/expansion transformations
Rename several functions related to the "central dogma" for more clarity

- Python
Published by cthoyt over 7 years ago

pybel -

Fixed

Bug where data did not get copied to sub-graphs on induction (https://github.com/pybel/pybel/issues/#307)

- Python
Published by cthoyt over 7 years ago

pybel -

Added

Added getannotationvalues function to pybel.struct.summary ## Removed
Removed Manager.ensure function ## Fixed
Fixed a bug in Manager.from_connection (https://github.com/pybel/pybel/issues/#306)

- Python
Published by cthoyt over 7 years ago

pybel -

Changed

Changed arguments in pybel.struct.mutations.getsubgraphsby_annotation
Moved utility functions in pybel.struct.mutations

- Python
Published by cthoyt over 7 years ago

pybel -

Changed

Use BELGraph.fresh_copy instead of importing the class in mutator functions ## Added
Add pipeline (https://github.com/pybel/pybel/issues/301)
Testing of neighborhood functions
Added several transformation and grouping functions for BELGraph
INDRA Machine in CLI ## Fixed
Add missing field from BaseAbundance (https://github.com/pybel/pybel/issues/302)

- Python
Published by cthoyt over 7 years ago

pybel -

Accidentally put the v0.11.3 tag on develop. This one is the real one, I promise.

Added

Made testing code and date install as part of main package(https://github.com/pybel/pybel/pull/298)

Removed

Remove extension hook and extension loader (https://github.com/pybel/pybel/pull/300)

- Python
Published by cthoyt over 7 years ago

pybel -

- Python
Published by cthoyt over 7 years ago

pybel -

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)

- Python
Published by cthoyt almost 8 years ago

pybel -

- Python
Published by cthoyt about 8 years ago

pybel -

- Python
Published by cthoyt about 8 years ago

pybel -

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 (hasactivity, hasdegree, hastranslocation, hasannotation)

- Python
Published by cthoyt about 8 years ago

pybel -

- Python
Published by cthoyt about 8 years ago

pybel -

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

- Python
Published by cthoyt over 8 years ago

pybel -

Added

Additional keyword arguments for JSON output functions

Changed

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)

- Python
Published by cthoyt over 8 years ago

pybel -

- Python
Published by cthoyt over 8 years ago

pybel -

- Python
Published by cthoyt over 8 years ago

pybel -

- Python
Published by cthoyt over 8 years ago

pybel -

- Python
Published by cthoyt over 8 years ago

pybel -

- Python
Published by cthoyt over 8 years ago

pybel -

- Python
Published by cthoyt over 8 years ago

pybel -

- Python
Published by cthoyt over 8 years ago

pybel -

- Python
Published by cthoyt over 8 years ago

pybel -

- Python
Published by cthoyt over 8 years ago

pybel -

- Python
Published by cthoyt over 8 years ago

pybel -

Changed

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

Fixed

Change node hashing to only use type and reference

Added

Node intersection merge
Get most recent network by name in manager

- Python
Published by cthoyt over 8 years ago

pybel -

Changed

Externalized some PyParsing elements

Fixed

Version string tokenization

- Python
Published by cthoyt over 8 years ago

pybel -

Added

Added Project key to document metadata parser (https://github.com/pybel/pybel/issues/215)
Reusable protocols for hashing nodes and edges

Fixed

Edge store working (https://github.com/pybel/pybel/issues/212)

Changed

Update resource urls (https://github.com/pybel/pybel/issues/211)
General improvements to exception handling
Made new minimum unpickle version 0.7.0

- Python
Published by cthoyt over 8 years ago

pybel -

Add environment variable for data locations

- Python
Published by cthoyt over 8 years ago

pybel -

Fixed

Bug with getting multiple networks by id (#208)

- Python
Published by cthoyt over 8 years ago

pybel -

Changed

Merge OWL and BEL namespaces (https://github.com/pybel/pybel/issues/118)
Remove lots of unused/redundant code
Lots of functions renamed and moved... Sorry people.

Added

Multiple options for graph joining
Filter functions (https://github.com/pybel/pybel/issues/206)

- Python
Published by cthoyt over 8 years ago

pybel -

Changed

Added line numbers to parsing exceptions
Update minimum pickle parsing from 0.5.10 to 0.5.11 to reflect changes in parsing exceptions

- Python
Published by cthoyt over 8 years ago

pybel -

Added

Network outer join (https://github.com/pybel/pybel/issues/205)
Network full join with hash (https://github.com/pybel/pybel/issues/204 and https://github.com/pybel/pybel/issues/204)
Option to suppress singleton warnings (https://github.com/pybel/pybel/issues/200)

Changed

Moved pybel.graph to :mod:pybel.struct.graph
Parse exceptions are renamed
Update minimum pickle parsing from 0.5.4 to 0.5.10 to reflect the new parse exceptions's names and arguments

Fixed

Rewrote the CSV Exporter (https://github.com/pybel/pybel/issues/201)

- Python
Published by cthoyt over 8 years ago

pybel -

Added

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)

- Python
Published by cthoyt almost 9 years ago

pybel -

Changed

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

NDEx upload and download

- Python
Published by cthoyt almost 9 years ago

pybel -

Changed

Public IO changed for to/fromjson and to/fromcx (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)

- Python
Published by cthoyt almost 9 years ago

pybel -

Changed

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

Added

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)

- Python
Published by cthoyt almost 9 years ago

pybel -

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

Added

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

- Python
Published by cthoyt almost 9 years ago

pybel -

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

- Python
Published by cthoyt almost 9 years ago

pybel -

Fixed

Ensure existence of namespaces/annotations during graph upload

- Python
Published by cthoyt almost 9 years ago

pybel -

Added

Parsing of labels (#173)

Fixed

Parsing of hasComponents lists (#172)

- Python
Published by cthoyt almost 9 years ago

pybel -

Added

Debugging on lines starting with #: comments
Added missing relations in pybel.constants

Changed

Merge definition and graph cache
Warn when not using semantic versioning

- Python
Published by cthoyt almost 9 years ago

pybel -

Added

File paths in definition parsing
Quotes around variant string

Changed

Reorganized package to split line parsing from core data structure

- Python
Published by cthoyt almost 9 years ago

pybel -

Added

Documentation for constants
Date validation on parse-time

Changed

Externalized strings from modifier parsers
Move pybel.cx.hash_tuple to pybel.utils.hash_tuple

Fixed

Output to CX on CLI crashing
Assignment of graph metadata on reload

- Python
Published by cthoyt almost 9 years ago

pybel -

Added

Node property data model and I/O
Edge property data model and I/O

Changed

Update version checking to be more lenient

Removed

Origin completion option on BEL parsing. See PyBEL Tools

- Python
Published by cthoyt almost 9 years ago

pybel -

Added

More output options for BEL
Explicit parsing of hasVariant, hasReactant, and hasProduct

Fixed

Allow parsing of non-standard ordering of annotations
Superfluous output of single nodes when writing BEL scripts

- Python
Published by cthoyt almost 9 years ago

pybel -

Added

Stable CX import and export
Edge Store data models and loading
Alternative control parsing technique without citation clearing
Node name calculator

- Python
Published by cthoyt almost 9 years ago

pybel -

Fixed

Fixed has_members not adding annotations tag
Reliance on node identifiers in canonicalization of complexes and composites
Fixed graph iterator filter

- Python
Published by cthoyt about 9 years ago

pybel -

- Python
Published by cthoyt about 9 years ago

pybel -

- Python
Published by cthoyt about 9 years ago

pybel -

Added

Experimental CX export for use with NDEx

Changed

Better testing with thorough BEL

Fixed

ParseResult objects no longer propagate through graph
Fixed outputting to JSON

Removed

Support for importing GraphML is no longer continued because there's too much information loss

- Python
Published by cthoyt about 9 years ago

pybel -

Added

Annotation pattern definitions
Alternative JSON output to in-memory dictionary

Changed

Removed url rewriting for OpenBEL Framework
Group all annotations in edge data (see Data Model in docs)

- Python
Published by cthoyt about 9 years ago

pybel -

Added

Added equivalentTo relation
Added OWL annotation support
Version integrity checking
Dump cache functionality

Changed

Merged GENE, GENEVARIANT, and GENEFUSION

- Python
Published by cthoyt about 9 years ago

pybel -

Replaced ontospy parsing with onto2nx for Windows compatibility

- Python
Published by cthoyt about 9 years ago

pybel -

Added

Add thorough testing of BEL document

Changed

Improved string externalization
Update to data model for fusions
Improved parser performance

- Python
Published by cthoyt about 9 years ago

pybel -

Added

Codec support for opening files by path

Changed

Protein modifications, gene modifications, and variants are now stored as dictionaries in the latent data structure
Many constants have been externalized
BEL default names, like kinaseActivity are automatically assigned a sentinel value as a namespace

- Python
Published by cthoyt about 9 years ago

pybel -

make HGVS parsing less complicated
add warning tracking

- Python
Published by cthoyt about 9 years ago

pybel -

Gene modification support
Namespace equivalence models and manager
Extension loading

- Python
Published by cthoyt about 9 years ago

pybel -

Rudimentary Graph cache implementation and management
Better CLI
Bug fixes

- Python
Published by cthoyt about 9 years ago

pybel -

This release includes three main features: - OWL Support - Refactored definitions database - Canonical BEL output

- Python
Published by cthoyt about 9 years ago

pybel -

- Python
Published by cthoyt over 9 years ago

pybel -

Fixes for node canonicalization, node data, and I/O

- Python
Published by cthoyt over 9 years ago

pybel -

Parser performance improvements, making logging lazy, added additional language features

- Python
Published by cthoyt over 9 years ago

pybel -

Super speed improvements

- Python
Published by cthoyt over 9 years ago

pybel -

- Python
Published by cthoyt over 9 years ago

pybel -

Hotfix for CLI encoding problems

- Python
Published by cthoyt over 9 years ago

pybel -

Finished annotation/full definitions cache manager
Fixed CLI bugs
Performance improvements

- Python
Published by cthoyt over 9 years ago

pybel -

Addition of Definition Cache Manager for extra fast downloads
Public release of PyBEL!

- Python
Published by cthoyt over 9 years ago

pybel -

This version is ready for use, but still needs minor tweaks and speed improvements before calling it 'production ready'

- Python
Published by cthoyt over 9 years ago

pybel -

- Python
Published by cthoyt over 9 years ago

pybel -

- Python
Published by cthoyt over 9 years ago

pybel -

This is the first release, that supports the most basic operations offered by PyBEL, including: - parsing of BEL language - importing BEL files by URL, file path, or iterable of lines

- Python
Published by cthoyt over 9 years ago

Recent Releases of pybel

pybel - v0.15.5

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