Ecosyste.ms: Issues

An open API service for providing issue and pull request metadata for open source projects.

GitHub / ndexbio/ndex2-client issues and pull requests

#99 - Adding Copy Icon and Functionality to Code Block Template

Issue - State: closed - Opened by devarsh10 9 months ago - 3 comments

#98 - Fix typo in generate_metadata()

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

#97 - Syntax fix

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

#96 - ndex2.create_nice_cx_from_networkx fails with numpy 1.24.X

Issue - State: closed - Opened by coleslaw481 over 1 year ago - 1 comment

#95 - Update README.rst

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

#94 - ndex2 on conda

Issue - State: closed - Opened by MOohTus over 1 year ago - 4 comments
Labels: enhancement

#92 - import ndex2 outputs warnings in python3.9

Issue - State: closed - Opened by coleslaw481 over 2 years ago - 2 comments
Labels: bug

#91 - Improve networkx conversion

Issue - State: closed - Opened by coleslaw481 over 2 years ago - 1 comment
Labels: enhancement

#90 - Empty list attributes are treated as strings when converting networkx to NiceCXNetwork

Issue - State: closed - Opened by coleslaw481 over 2 years ago - 1 comment
Labels: bug

#89 - apply_template method under NiceCXNetwork does NOT clear previous styles

Issue - State: closed - Opened by coleslaw481 over 2 years ago - 1 comment
Labels: bug

#88 - @context is lost either in loading of CX into NiceCXNetwork or during save to NDEx server

Issue - State: closed - Opened by coleslaw481 over 2 years ago - 1 comment
Labels: bug

#87 - Add CX2 endpoints to ndex2.client.Ndex2()`

Issue - State: closed - Opened by coleslaw481 over 2 years ago - 1 comment

#86 - Question: is uuid unique to each version?

Issue - State: closed - Opened by RemyLau almost 3 years ago - 2 comments

#85 - import of ndex2 takes too long to run

Issue - State: closed - Opened by coleslaw481 about 3 years ago - 1 comment
Labels: enhancement

#84 - Converting NiceCXNetwork to networkx and back does not handle node name consistently

Issue - State: closed - Opened by coleslaw481 over 3 years ago - 1 comment
Labels: bug

#83 - Boolean attributes are treated as integers when converting networkx to NiceCXNetwork

Issue - State: closed - Opened by coleslaw481 over 3 years ago - 1 comment
Labels: bug

#82 - NiceCXNetwork.update_to() documentation says returning empty string instead of network URL

Issue - State: closed - Opened by coleslaw481 over 3 years ago - 3 comments
Labels: bug

#81 - Switch NiceCXNetwork.update_to() to named parameters and add client parameter

Issue - State: closed - Opened by coleslaw481 over 3 years ago - 1 comment
Labels: enhancement

#80 - Switch NiceCXNetwork.upload_to() to named parameters and add client parameter

Issue - State: closed - Opened by coleslaw481 over 3 years ago - 1 comment
Labels: enhancement

#79 - NiceCXNetwork.to_networkx() fails with ValueError on networkx version 2.5.1

Issue - State: closed - Opened by coleslaw481 over 3 years ago - 1 comment
Labels: bug

#78 - get_network_ids_for_user not returning expected network_ids

Issue - State: closed - Opened by ariutta almost 4 years ago - 4 comments
Labels: bug

#77 - set_network_properties -> 500 Server Error

Issue - State: closed - Opened by ariutta about 4 years ago - 4 comments

#76 - Enum34 causing problems in Python 3.4+

Issue - State: closed - Opened by bgyori over 4 years ago - 4 comments

#75 - Remove ndex2.client.Ndex2.search_networks_by_property_filter() since it always raises an exception

Issue - State: open - Opened by coleslaw481 almost 5 years ago - 3 comments
Labels: enhancement

#74 - Drop support for v1 of NDEx

Issue - State: closed - Opened by coleslaw481 almost 5 years ago - 1 comment

#73 - Move ndex2cx.nice_cx_builder.py to ndex2 and remove ndex2cx

Issue - State: closed - Opened by coleslaw481 almost 5 years ago - 1 comment
Labels: bug

#72 - Remove ndex2.niceCXInterface.py

Issue - State: closed - Opened by coleslaw481 almost 5 years ago - 1 comment
Labels: enhancement

#71 - Ndex2 changes host if 'localhost' in host name

Issue - State: closed - Opened by coleslaw481 almost 5 years ago - 1 comment
Labels: bug, duplicate

#70 - Need safe wrapper for set_network_properties

Issue - State: closed - Opened by coleslaw481 almost 5 years ago - 1 comment
Labels: enhancement

#69 - Remove forced setting of localhost url if localhost in host name in Ndex2 client constructor

Issue - State: closed - Opened by coleslaw481 almost 5 years ago - 1 comment
Labels: bug

#68 - Remove deprecated methods from NiceCXNetwork

Issue - State: closed - Opened by coleslaw481 about 5 years ago - 1 comment
Labels: bug

#66 - Update client to use SSL to connect to REST service by default

Issue - State: closed - Opened by coleslaw481 about 5 years ago - 1 comment
Labels: enhancement

#65 - Avoid using `type` as variable name

Issue - State: closed - Opened by coleslaw481 about 5 years ago - 1 comment
Labels: bug

#64 - NiceCXNetwork.set_context should add data to @context NetworkAttribute

Issue - State: closed - Opened by coleslaw481 about 5 years ago - 1 comment
Labels: enhancement

#63 - Convert all print calls to use logging framework

Issue - State: closed - Opened by coleslaw481 about 5 years ago - 1 comment
Labels: enhancement

#62 - Add manifest and include required files

Pull Request - State: closed - Opened by bgyori about 5 years ago - 2 comments

#61 - Add get_networksets() method

Issue - State: closed - Opened by coleslaw481 about 5 years ago - 3 comments
Labels: enhancement

#60 - NiceCXNetwork.create_node() and create_edge overwrites existing nodes/edges

Issue - State: closed - Opened by coleslaw481 about 5 years ago - 1 comment
Labels: bug

#59 - add method to Ndex2 client to allow deletion of networksets

Issue - State: closed - Opened by coleslaw481 about 5 years ago - 1 comment
Labels: enhancement

#58 - Update conf.py

Pull Request - State: closed - Opened by jeff15610 over 5 years ago - 1 comment

#57 - Citation and supports in NiceCXNetwork

Issue - State: closed - Opened by bgyori over 5 years ago - 3 comments

#56 - Update client.py

Pull Request - State: closed - Opened by jeff15610 over 5 years ago

#55 - Avoid using `id` as variable name

Issue - State: closed - Opened by zachary822 over 5 years ago - 4 comments
Labels: bug

#53 - Error in translation of data type for node and edge attributes when going to and from networkx

Issue - State: closed - Opened by coleslaw481 over 5 years ago - 1 comment
Labels: bug

#52 - Add unit tests for all of the Ndex2 client class

Issue - State: open - Opened by coleslaw481 over 5 years ago

#51 - ndex2.create_nice_cx_from_networkx load network attributes from graph

Issue - State: closed - Opened by coleslaw481 over 5 years ago - 1 comment
Labels: bug

#49 - NiceCXNetwork.get_node_attribute_objects() incorrectly raises Warning

Issue - State: closed - Opened by coleslaw481 over 5 years ago - 2 comments
Labels: bug

#48 - Remove NiceCXNetwork.get_edge_attribute_object() since it always raises Warning

Issue - State: closed - Opened by coleslaw481 over 5 years ago - 1 comment
Labels: bug

#47 - Remove add_edge() and add_node() since they always raise Warning

Issue - State: closed - Opened by coleslaw481 over 5 years ago - 1 comment
Labels: bug

#46 - NiceCXNetwork.create_edge fails to correctly create edge when node dict passed in

Issue - State: closed - Opened by coleslaw481 over 5 years ago - 1 comment
Labels: bug

#45 - Add NiceCXNetwork.get_network_attribute_names() function

Issue - State: closed - Opened by coleslaw481 over 5 years ago - 1 comment
Labels: enhancement

#42 - NiceCXNetwork.set_node_attribute() fails if node object passed to it

Issue - State: closed - Opened by coleslaw481 almost 6 years ago - 1 comment
Labels: bug

#41 - NiceCXNetwork.set_node_attribute() incorrectly handles duplicate attributes

Issue - State: closed - Opened by coleslaw481 almost 6 years ago - 1 comment

#38 - This library should only raise NDEx exceptions/errors

Issue - State: open - Opened by coleslaw481 almost 6 years ago

#37 - Ndex2.save_new_network() needs to perform better checks to verify valid cx

Issue - State: closed - Opened by coleslaw481 almost 6 years ago - 1 comment

#36 - In NiceCXNetwork class ability to add to User-Agent for calls to NDEx service

Issue - State: closed - Opened by coleslaw481 almost 6 years ago - 1 comment

#35 - Update User-Agent to reflect actual version of software

Issue - State: closed - Opened by coleslaw481 almost 6 years ago

#34 - Passing None to user_agent parameterin Ndex2() constructor raises TypeError

Issue - State: closed - Opened by coleslaw481 almost 6 years ago - 1 comment

#33 - Add timeout flag to all web request calls

Issue - State: closed - Opened by coleslaw481 almost 6 years ago - 1 comment

#32 - Replace print statements with logging calls in `ndex2/client.py`

Issue - State: closed - Opened by coleslaw481 almost 6 years ago - 1 comment

#31 - Eliminate circular import between ndex2 and ndex2cx/nice_cx_builder.py

Issue - State: closed - Opened by coleslaw481 almost 6 years ago - 1 comment

#30 - Verify consistent conversion of cx for networkx 1.11 and 2.0+

Issue - State: closed - Opened by coleslaw481 almost 6 years ago - 1 comment
Labels: bug

#28 - Ndex2 constructor does not properly handle invalid json from server

Issue - State: closed - Opened by coleslaw481 almost 6 years ago - 1 comment

#27 - Enable logic to obtain credentials from configuration file and environment variable

Issue - State: open - Opened by coleslaw481 almost 6 years ago - 2 comments
Labels: enhancement

#26 - Log folder created in installation folder

Issue - State: closed - Opened by bgyori almost 6 years ago - 4 comments

#25 - Update home link and migration of directory creation into get_logger

Pull Request - State: closed - Opened by coleslaw481 about 6 years ago

#24 - `neo4jrestclient` should be included in setup.py

Issue - State: closed - Opened by shfong about 6 years ago - 3 comments

#23 - NetworkX Version

Issue - State: closed - Opened by stevencox about 6 years ago - 8 comments

#22 - Migrating networkx from 1.11 to 2.X

Issue - State: closed - Opened by shfong about 6 years ago - 2 comments

#21 - Update uploader functions

Pull Request - State: closed - Opened by cthoyt over 6 years ago

#20 - NiceCXNetwork.to_cx doesn't create valid CX for NDEx

Issue - State: closed - Opened by cthoyt over 6 years ago - 3 comments

#19 - Rename non-pythonic module names

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

#18 - Use different strategy for enum install

Pull Request - State: closed - Opened by bgyori over 6 years ago

#17 - Enum issue during Python 3 setup

Issue - State: closed - Opened by bgyori over 6 years ago

#16 - Set sphinx theme to sphinx_rtd_theme

Pull Request - State: closed - Opened by cthoyt almost 7 years ago

#15 - Request - use ReadTheDocs theme in documentation

Issue - State: closed - Opened by cthoyt almost 7 years ago

#14 - Documented version doesn't reflect software version

Issue - State: closed - Opened by cthoyt almost 7 years ago - 1 comment

#13 - pandas to nicecx does not allow control of represents vs. name

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

#12 - apply_template should always set cyVisualProperties

Issue - State: closed - Opened by dexterpratt almost 7 years ago - 1 comment

#11 - add opaque aspect needs to update metadata

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

#10 - add_opaque_aspect should add an entire aspect, not an aspect element

Issue - State: closed - Opened by dexterpratt almost 7 years ago - 1 comment

#9 - Network that causes error making nice CX

Issue - State: closed - Opened by dexterpratt almost 7 years ago - 1 comment

#8 - Python2 Incompatability - Enum

Issue - State: closed - Opened by cthoyt almost 7 years ago - 1 comment

#7 - Extensibility of type assertions

Issue - State: closed - Opened by cthoyt almost 7 years ago - 1 comment

#6 - Tests fail because pysolr not listed as requirement

Issue - State: closed - Opened by cthoyt almost 7 years ago - 1 comment

#5 - ReadTheDocs and Sphinx Documentation

Issue - State: closed - Opened by cthoyt almost 7 years ago - 1 comment

#4 - Documentation doesn't match reality

Issue - State: closed - Opened by cthoyt almost 7 years ago - 1 comment

#3 - Adding Travis tests

Pull Request - State: closed - Opened by bgyori about 7 years ago

#2 - CircleCI fails during the first step of build

Issue - State: closed - Opened by bgyori about 7 years ago - 1 comment

#1 - Fix requirements

Pull Request - State: closed - Opened by bgyori about 7 years ago