Recent Releases of biocypher
biocypher - v0.10.1
What's Changed
- correct description of
label_as_edgeby @slobentanzer in https://github.com/biocypher/biocypher/pull/454 - perform type checking to prevent import failure by @slobentanzer in https://github.com/biocypher/biocypher/pull/458
Full Changelog: https://github.com/biocypher/biocypher/compare/v0.10.0...v0.10.1
- Python
Published by github-actions[bot] 10 months ago
biocypher - v0.9.7
What's Changed
- Bump version: 0.9.5 → 0.9.6 by @ecarrenolozano in https://github.com/biocypher/biocypher/pull/446
- Remove unused docstring parameter for translate init class by @lvvittor in https://github.com/biocypher/biocypher/pull/448
- update cff file to not override title on zenodo by @slobentanzer in https://github.com/biocypher/biocypher/pull/450
New Contributors
- @lvvittor made their first contribution in https://github.com/biocypher/biocypher/pull/448
Full Changelog: https://github.com/biocypher/biocypher/compare/v0.9.6...v0.9.7
- Python
Published by github-actions[bot] 11 months ago
biocypher - v0.9.4
What's Changed
- Fix neo4j import script not correctly generated due to problematic writer instance management by @kpto in https://github.com/biocypher/biocypher/pull/440
Full Changelog: https://github.com/biocypher/biocypher/compare/v0.9.3...v0.9.4
- Python
Published by github-actions[bot] about 1 year ago
biocypher - v0.9.3
What's Changed
- Added a method to trim long filenames for the download functions by @vd-dragan21 in https://github.com/biocypher/biocypher/pull/434
New Contributors
- @vd-dragan21 made their first contribution in https://github.com/biocypher/biocypher/pull/434
Full Changelog: https://github.com/biocypher/biocypher/compare/v0.9.2...v0.9.3
- Python
Published by github-actions[bot] about 1 year ago
biocypher - v0.9.2
What's Changed
- Add/modify GitHub issues templates by @ecarrenolozano in https://github.com/biocypher/biocypher/pull/429
- remove reliance on
stringcaselibrary by @slobentanzer in https://github.com/biocypher/biocypher/pull/431
Full Changelog: https://github.com/biocypher/biocypher/compare/v0.9.1...v0.9.2
- Python
Published by github-actions[bot] about 1 year ago
biocypher - v0.9.1
What's Changed
- add dedicated pandas configs by @slobentanzer in https://github.com/biocypher/biocypher/pull/427
- Fix-in-memory-and-tutorial by @slobentanzer in https://github.com/biocypher/biocypher/pull/428
Full Changelog: https://github.com/biocypher/biocypher/compare/v0.9.0...v0.9.1
- Python
Published by github-actions[bot] about 1 year ago
biocypher - v0.7.0
What's Changed
- update github action config: by @slobentanzer in https://github.com/biocypher/biocypher/pull/409
- Dev-networkx-ruff by @slobentanzer in https://github.com/biocypher/biocypher/pull/403
Full Changelog: https://github.com/biocypher/biocypher/compare/v0.6.2...v0.7.0
- Python
Published by github-actions[bot] over 1 year ago
biocypher - v0.6.2
What's Changed
- Fix neo4j CSV output not escaping quote character and cause import error by @kpto in https://github.com/biocypher/biocypher/pull/405
New Contributors
- @kpto made their first contribution in https://github.com/biocypher/biocypher/pull/405
Full Changelog: https://github.com/biocypher/biocypher/compare/v0.6.1...v0.6.2
- Python
Published by github-actions[bot] over 1 year ago
biocypher - v0.6.1
What's Changed
- Create config.yml by @slobentanzer in https://github.com/biocypher/biocypher/pull/375
- use GPT alternative to try and find the error with validations by @slobentanzer in https://github.com/biocypher/biocypher/pull/376
- Folder for drawio diagrams by @ecarrenolozano in https://github.com/biocypher/biocypher/pull/379
- add specific resource classes to init in order to allow import by @slobentanzer in https://github.com/biocypher/biocypher/pull/388
New Contributors
- @ecarrenolozano made their first contribution in https://github.com/biocypher/biocypher/pull/379
Full Changelog: https://github.com/biocypher/biocypher/compare/v0.6.0...v0.6.1
- Python
Published by github-actions[bot] over 1 year ago
biocypher - v0.6.0
What's Changed
- add function for caching API requests and refine the args description by @ryxx0811 in https://github.com/biocypher/biocypher/pull/369
New Contributors
- @ryxx0811 made their first contribution in https://github.com/biocypher/biocypher/pull/369
Full Changelog: https://github.com/biocypher/biocypher/compare/v0.5.44...v0.6.0
- Python
Published by github-actions[bot] over 1 year ago
biocypher - v0.5.42
What's Changed
- first version of RDF conversion by @LoesvdBiggelaar in https://github.com/biocypher/biocypher/pull/337
- #273: add unit test for duplicated tail ontologies by @nilskre in https://github.com/biocypher/biocypher/pull/325
- Ontology reverse id label yaml config by @nilskre in https://github.com/biocypher/biocypher/pull/327
- #339: adapt pr cicd config to limit number of runs for neo4j v4 and v5 by @nilskre in https://github.com/biocypher/biocypher/pull/340
- Rdf output adapter by @slobentanzer in https://github.com/biocypher/biocypher/pull/338
New Contributors
- @LoesvdBiggelaar made their first contribution in https://github.com/biocypher/biocypher/pull/337
Full Changelog: https://github.com/biocypher/biocypher/compare/v0.5.41...v0.5.42
- Python
Published by github-actions[bot] about 2 years ago
biocypher - v0.5.41
What's Changed
- Neo4j version 5 patch by @mbaric758 in https://github.com/biocypher/biocypher/pull/321
- #321: fix cicd pipeline by @nilskre in https://github.com/biocypher/biocypher/pull/336
New Contributors
- @mbaric758 made their first contribution in https://github.com/biocypher/biocypher/pull/321
Full Changelog: https://github.com/biocypher/biocypher/compare/v0.5.40...v0.5.41
- Python
Published by github-actions[bot] about 2 years ago
biocypher - v0.5.39
What's Changed
- doc(error messages): more detailled errors by @jdreo in https://github.com/biocypher/biocypher/pull/328
- refactor(write): return the path of the import call file by @jdreo in https://github.com/biocypher/biocypher/pull/329
Full Changelog: https://github.com/biocypher/biocypher/compare/v0.5.38...v0.5.39
- Python
Published by github-actions[bot] about 2 years ago
biocypher - v0.5.38
What's Changed
- Add a document for building Pole standalone Docker image by @fengsh27 in https://github.com/biocypher/biocypher/pull/317
- #310: improve runtime of rdflib to networkx transformation by @nilskre in https://github.com/biocypher/biocypher/pull/311
New Contributors
- @fengsh27 made their first contribution in https://github.com/biocypher/biocypher/pull/317
Full Changelog: https://github.com/biocypher/biocypher/compare/v0.5.37...v0.5.38
- Python
Published by github-actions[bot] over 2 years ago
biocypher - v0.5.29
What's Changed
- issue #278: fix ontology root label check by @nilskre in https://github.com/biocypher/biocypher/pull/282
- Pyopensci really last fixes by @nilskre in https://github.com/biocypher/biocypher/pull/283
Full Changelog: https://github.com/biocypher/biocypher/compare/v0.5.28...v0.5.29
- Python
Published by slobentanzer over 2 years ago
biocypher - v0.5.27
What's Changed
- test commit by @slobentanzer in https://github.com/biocypher/biocypher/pull/271
- Py open sci review by @nilskre in https://github.com/biocypher/biocypher/pull/270
- Py open sci review part 2 by @nilskre in https://github.com/biocypher/biocypher/pull/274
- Ontology by @slobentanzer in https://github.com/biocypher/biocypher/pull/276
- More support for schema_info generation by @slobentanzer in https://github.com/biocypher/biocypher/pull/277
- Py open sci review part 3 by @nilskre in https://github.com/biocypher/biocypher/pull/275
- Pyopensci review by @slobentanzer in https://github.com/biocypher/biocypher/pull/280
New Contributors
- @nilskre made their first contribution in https://github.com/biocypher/biocypher/pull/270
Full Changelog: https://github.com/biocypher/biocypher/compare/v0.5.23...v0.5.27
- Python
Published by github-actions[bot] over 2 years ago
biocypher - v0.5.24
What's Changed
- test commit by @slobentanzer in https://github.com/biocypher/biocypher/pull/271
- Ontology by @slobentanzer in https://github.com/biocypher/biocypher/pull/276
Full Changelog: https://github.com/biocypher/biocypher/compare/v0.5.23...v0.5.24
- Python
Published by slobentanzer over 2 years ago
biocypher - v0.5.21
What's Changed
- Extend-schema by @slobentanzer in https://github.com/biocypher/biocypher/pull/265
- Get-module by @slobentanzer in https://github.com/biocypher/biocypher/pull/268
Full Changelog: https://github.com/biocypher/biocypher/compare/v0.5.20...v0.5.21
- Python
Published by slobentanzer almost 3 years ago
biocypher - v0.5.20
Write extended schema for communication with LLMs using biochatter, refactor dependencies of ontology and translator modules, implement relationships as nodes in Pandas module, refactor deduplication of edges in write module, refactor tests and fixture scopes.
Full Changelog: https://github.com/biocypher/biocypher/compare/v0.5.19...v0.5.20
- Python
Published by slobentanzer almost 3 years ago
biocypher - v0.5.16
What's Changed
- Optional-id by @slobentanzer in https://github.com/biocypher/biocypher/pull/212
- draft pandas-tutorial in jupyter by @dbdimitrov in https://github.com/biocypher/biocypher/pull/209
Full Changelog: https://github.com/biocypher/biocypher/compare/v0.5.14...v0.5.16
- Python
Published by slobentanzer almost 3 years ago
biocypher - Fix debug level logging
Fixed configuration mistake that prevented log level of the file handler to be "debug".
- Python
Published by slobentanzer about 3 years ago
biocypher - Added Pandas dataframe support
Functions:
- bc.add() to add nodes and edges to the in-memory store
- bc.to_df() to return a dictionary of individual Pandas dataframes, one per type of node/edge
Also added deduplicator module and class to share this functionality between writer and Pandas modules.
- Python
Published by slobentanzer about 3 years ago
biocypher - Output module refactor
This refactor introduces batch writing capabilities for PostgreSQL and ArangoDB. This support is experimental and will be refined in coming releases.
- Python
Published by slobentanzer about 3 years ago
biocypher - Core refactor: modularisation
This release introduces a breaking change in the configuration part of BioCypher. The organisation of the YAML configuration file has changed, compartmentalising settings into biocypher core settings and other, DBMS-specific settings. Please refer to https://biocypher.org/installation.html#configuration for more info.
The refactoring modularises the architecture of BioCypher. The interface function that was previously entangled with Neo4j Driver functionality has been moved to the new core class BioCypher. This class organises the interplay between input sources, ontologies, and output formats, guided by the user configuration. It can request offline file writers as well as online DBMS connectors, which it then uses to write the input data stream based on the ontology mapping defined by the user.
The previous Driver module is still usable, but simply redirects to the new BioCypher interface class and gives a deprecation warning. Some parameters are not available any more and need to be configured in the biocypher_config.yaml.
In addition, small utility and usability changes have been introduced.
- Python
Published by slobentanzer about 3 years ago