indralab/pybiopax issues and pull requests

#49 - Added pathway_order and next_step to a list

Pull Request - State: closed - Opened by tmushayahama over 1 year ago - 4 comments

#48 - Add attributes to NucleicAcid reference BioPAX classes

Pull Request - State: closed - Opened by bgyori over 1 year ago

#47 - regionType for SequenceLocation but not NucleicAcidRegionReference

Issue - State: closed - Opened by quirinmanz over 1 year ago - 2 comments

#46 - Add global tqdm config

Pull Request - State: closed - Opened by bgyori almost 2 years ago - 1 comment

#45 - Add py.typed

Pull Request - State: closed - Opened by bgyori almost 2 years ago

#44 - Pass tqdm kwargs

Issue - State: closed - Opened by eggplants almost 2 years ago - 7 comments

#43 - Provide type information

Issue - State: closed - Opened by eggplants almost 2 years ago

#42 - Make new pypi release

Issue - State: closed - Opened by matthiaskoenig about 2 years ago - 1 comment

#41 - Notebook demonstrating model construction

Pull Request - State: closed - Opened by bgyori about 2 years ago

#40 - Adding second protein to BioPax model gives TypeError

Issue - State: closed - Opened by aditya-ml about 2 years ago - 2 comments

#39 - Improve BioPAX class attribute documentation

Pull Request - State: closed - Opened by bgyori about 2 years ago

#38 - Enable passing a list of BioPaxObject to BioPaxModel

Pull Request - State: closed - Opened by cthoyt over 2 years ago

#37 - Use empty list by default if list-type is None

Pull Request - State: closed - Opened by bgyori over 2 years ago

#36 - Example/documentation for creating BioPax from scratch

Issue - State: closed - Opened by matthiaskoenig over 2 years ago - 5 comments

#35 - Add functions to get database references from a model

Pull Request - State: closed - Opened by bgyori over 2 years ago

#34 - Add utilities for analyzing ontology terms and identifiers in a biopax file

Issue - State: closed - Opened by cmungall over 2 years ago - 6 comments

#33 - Converting BioPAX to signed directed pairwise graph

Issue - State: closed - Opened by agitter over 2 years ago - 2 comments

#32 - Fix references

Pull Request - State: closed - Opened by bgyori over 2 years ago

#31 - Add dedicated state of the field section

Pull Request - State: closed - Opened by bgyori over 2 years ago

#30 - State of the field section in JOSS paper

Issue - State: closed - Opened by leonweber over 2 years ago - 1 comment

#29 - Paper links to specific notebook version

Pull Request - State: closed - Opened by bgyori over 2 years ago

#28 - Visualizing BioPaxModels in Python?

Issue - State: closed - Opened by dhimmel over 2 years ago - 1 comment

#27 - Add source files for JOSS submission

Pull Request - State: closed - Opened by bgyori almost 3 years ago

#26 - Improve testing, documentation and notebooks

Pull Request - State: closed - Opened by bgyori almost 3 years ago

#25 - Synchronize contributions and setup with testing

Pull Request - State: closed - Opened by bgyori almost 3 years ago

#24 - Improvements to API and docs

Pull Request - State: closed - Opened by bgyori almost 3 years ago

#23 - Add Pathway Commons traversal demo notebook

Pull Request - State: closed - Opened by cthoyt almost 3 years ago

#22 - API Cleanup

Pull Request - State: closed - Opened by cthoyt almost 3 years ago

#21 - Add CREEDS analysis

Pull Request - State: closed - Opened by cthoyt almost 3 years ago - 1 comment

#20 - Add ability to pass tqdm kwargs in API functions

Pull Request - State: closed - Opened by cthoyt about 3 years ago - 2 comments

#19 - Update types in I/O functions

Pull Request - State: closed - Opened by cthoyt about 3 years ago

#18 - Implement path search based on path string specification

Pull Request - State: closed - Opened by bgyori about 3 years ago

#17 - Fix tqdm

Pull Request - State: closed - Opened by bgyori about 3 years ago

#16 - Implement reverse links as properties

Pull Request - State: closed - Opened by bgyori about 3 years ago

#15 - Implement mixin properties and aggregate names

Pull Request - State: closed - Opened by bgyori about 3 years ago

#14 - Add additional BioPAX remote resources

Pull Request - State: closed - Opened by cthoyt about 3 years ago - 4 comments

#13 - Add tutorial notebook and contrib guidelines

Pull Request - State: closed - Opened by bgyori about 3 years ago

#12 - Clean up project metadata

Pull Request - State: closed - Opened by cthoyt about 3 years ago

#11 - Type annotate code

Pull Request - State: closed - Opened by cthoyt about 3 years ago

#10 - Make participants of Interactions list-like

Pull Request - State: closed - Opened by bgyori almost 4 years ago

#9 - Interactions with multiple participants

Issue - State: closed - Opened by annaritz almost 4 years ago - 5 comments

#8 - Migrate from Travis to GitHub Actions

Pull Request - State: closed - Opened by bgyori almost 4 years ago