Ecosyste.ms: Issues

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

GitHub / SynBioDex/pySBOL issues and pull requests

#138 - pull malfunctions on Debian and CentOS

Issue - State: closed - Opened by breakthewall almost 3 years ago - 33 comments

#137 - Bump junit from 4.12 to 4.13.1 in /Win_64_3/sbol/test

Pull Request - State: closed - Opened by dependabot[bot] about 3 years ago
Labels: dependencies

#136 - Bump junit from 4.12 to 4.13.1 in /Mac_64_3/sbol/test

Pull Request - State: closed - Opened by dependabot[bot] about 3 years ago
Labels: dependencies

#135 - Bump junit from 4.12 to 4.13.1 in /Win_64_2/sbol/test

Pull Request - State: closed - Opened by dependabot[bot] about 3 years ago
Labels: dependencies

#134 - Retrieving the names of SBOL roles

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

#133 - write/export functions crash Colab Notebook

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

#132 - Failed testSBOL

Issue - State: open - Opened by eyesmo about 4 years ago - 3 comments

#131 - Bump junit from 4.12 to 4.13.1 in /Linux_64_3/sbol/test

Pull Request - State: closed - Opened by dependabot[bot] about 4 years ago - 1 comment
Labels: dependencies

#130 - Add deprecation notice to README

Pull Request - State: closed - Opened by tcmitchell about 4 years ago - 1 comment

#129 - Bump junit from 4.12 to 4.13.1 in /Win_32_2/sbol/test

Pull Request - State: closed - Opened by dependabot[bot] about 4 years ago - 1 comment
Labels: dependencies

#128 - Bump junit from 4.12 to 4.13.1 in /Win_32_3/sbol/test

Pull Request - State: closed - Opened by dependabot[bot] about 4 years ago - 1 comment
Labels: dependencies

#127 - Bump junit from 4.12 to 4.13.1 in /Mac_64_2/sbol/test

Pull Request - State: closed - Opened by dependabot[bot] about 4 years ago - 1 comment
Labels: dependencies

#126 - Bump junit from 3.8.1 to 4.13.1 in /tutorial

Pull Request - State: closed - Opened by dependabot[bot] about 4 years ago - 1 comment
Labels: dependencies

#125 - Post deprecation and pointer

Issue - State: closed - Opened by jakebeal about 4 years ago

#124 - pysbol 2.3.2.post5 error: Cannot Validate Online

Issue - State: open - Opened by ms03831 over 4 years ago

#123 - python 3.8.3 Windows 10 Can't find pysbol

Issue - State: open - Opened by ms03831 over 4 years ago - 1 comment

#122 - SSL CA cert error

Issue - State: open - Opened by dsanleo over 4 years ago - 4 comments

#121 - pySBOL Interaction does not support advertised argument

Issue - State: open - Opened by rpgoldman over 4 years ago - 13 comments

#120 - Typo in FunctionalComponent docstring

Issue - State: closed - Opened by rpgoldman over 4 years ago - 1 comment

#119 - Editing a Primary Structure error

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

#118 - JVM OOM when trying to parse GenBank file

Issue - State: closed - Opened by ifiddes over 4 years ago - 2 comments

#117 - Need a PartShop integration test for nonrecursive download

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

#116 - Travis CI needs to run integration tests with SynBioHub

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

#115 - Wrap GenBank, FASTA, GFF3 SynBioHub download options

Issue - State: open - Opened by cjmyers almost 5 years ago - 2 comments

#114 - Create .travis.yml

Pull Request - State: closed - Opened by jakebeal about 5 years ago - 1 comment

#113 - Travis-CI testing

Issue - State: closed - Opened by jakebeal about 5 years ago - 1 comment

#112 - pySBOL validation missing spaces and duplicate URIs

Issue - State: open - Opened by breecummins about 5 years ago

#111 - Handle sourceLocation values to support deletions.

Issue - State: closed - Opened by jakebeal about 5 years ago - 1 comment

#110 - Enhancement request: Support for known cardinality

Issue - State: closed - Opened by rpgoldman about 5 years ago - 1 comment

#109 - Enhancement request: Interned objects for python identity

Issue - State: open - Opened by rpgoldman about 5 years ago

#108 - Implement `insert` method

Issue - State: closed - Opened by bbartley about 5 years ago - 2 comments

#107 - Unable to submit large files to SynBioHub

Issue - State: closed - Opened by cjmyers about 5 years ago

#106 - Assemble sequences with multiple locations

Issue - State: open - Opened by bbartley about 5 years ago - 2 comments

#105 - Autoconfigure certificate authorty path

Issue - State: closed - Opened by jakebeal about 5 years ago - 3 comments
Labels: Enhancement

#104 - downloadAttachment Method of PartShop Downloads non-UTF-8 Encoded File

Issue - State: open - Opened by nroehner about 5 years ago
Labels: Bug

#103 - How do I delete specific objects from a Document?

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

#102 - Fix URL to constants.h

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

#101 - pySBOL adds trailing slash with no version

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

#100 - setAnnotation works only in some versions

Issue - State: open - Opened by dashaveraksa over 5 years ago - 7 comments

#99 - What is release 2.3.1?

Issue - State: closed - Opened by jakebeal over 5 years ago - 1 comment

#98 - Support for measures

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

#97 - Activity usages

Issue - State: open - Opened by eoberortner over 5 years ago - 2 comments

#96 - Python quit unexpectedly

Issue - State: closed - Opened by eoberortner over 5 years ago - 11 comments

#95 - GenBank to SBOL

Issue - State: closed - Opened by bchan over 5 years ago - 8 comments

#94 - Error when running SBOL unit tests

Issue - State: closed - Opened by bchan over 5 years ago - 4 comments

#93 - get an error when using partShop submit

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

#92 - URLs Partshop submission SBOL type added to the part ID

Issue - State: open - Opened by jurquiza over 5 years ago - 1 comment

#91 - error when printing obj in example documentation

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

#90 - Need Copy/Import Method that Does Not Require Namespace Parameter

Issue - State: closed - Opened by nroehner over 5 years ago - 2 comments
Labels: Enhancement

#88 - Incomplete RDF is produced when using Python3

Issue - State: closed - Opened by dissys over 5 years ago - 1 comment

#87 - Enable search on private graphs

Issue - State: closed - Opened by bbartley over 5 years ago - 1 comment
Labels: wontfix

#86 - SBOL 2.3 compatibility

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

#85 - python 3.7 support

Issue - State: closed - Opened by jakebeal about 6 years ago - 1 comment

#84 - Activity hadPlan field is dropped

Issue - State: closed - Opened by mehersam over 6 years ago - 1 comment
Labels: round-trip testing

#83 - Model source URI changed

Issue - State: open - Opened by mehersam over 6 years ago - 1 comment
Labels: round-trip testing

#82 - GTL annotations are dropped and version is added

Issue - State: open - Opened by mehersam over 6 years ago - 2 comments
Labels: round-trip testing

#81 - VariableComponent version was inserted

Issue - State: closed - Opened by mehersam over 6 years ago - 1 comment
Labels: round-trip testing

#80 - Attachment annotations dropped e.g time create

Issue - State: open - Opened by mehersam over 6 years ago - 1 comment
Labels: round-trip testing

#79 - Attachment Source URI changed to full URI

Issue - State: open - Opened by mehersam over 6 years ago - 1 comment
Labels: round-trip testing

#78 - CD ‘information’ nested annotations dropped

Issue - State: closed - Opened by mehersam over 6 years ago - 1 comment
Labels: round-trip testing

#77 - Activity displayId field is modified

Issue - State: closed - Opened by mehersam over 6 years ago - 1 comment
Labels: round-trip testing

#76 - Do not include types in the URIs

Issue - State: open - Opened by cjmyers over 6 years ago - 2 comments

#75 - Should not change namespaces of copied/imported objects

Issue - State: open - Opened by cjmyers over 6 years ago

#74 - Writing Large Files is Unusually Inefficient

Issue - State: open - Opened by nroehner over 6 years ago

#73 - Support import/conversion from GFF

Issue - State: open - Opened by jakebeal over 6 years ago
Labels: Enhancement

#72 - Ubuntu pySBOL

Issue - State: open - Opened by tcmitchell over 6 years ago - 1 comment

#71 - Test pySBOL Fail

Issue - State: closed - Opened by tramyn almost 7 years ago - 4 comments
Labels: Bug

#70 - Double check and update the document

Issue - State: open - Opened by kirichoi almost 7 years ago

#67 - Calling Document.getTopLevel() and Finding Nothing Causes Crash During Subsequent Write

Issue - State: closed - Opened by nroehner almost 7 years ago - 1 comment
Labels: Bug

#66 - Calling getModuleDefinition Finds ComponentDefinition with Target URI

Issue - State: open - Opened by nroehner almost 7 years ago
Labels: Bug

#65 - Write Crashes When Adding Custom Objects to Document via For Loop

Issue - State: closed - Opened by nroehner almost 7 years ago
Labels: Bug

#64 - Make API easier and more obvious to use, avoid get() and set() methods

Issue - State: closed - Opened by hsauro almost 7 years ago
Labels: Enhancement

#63 - Update documentation to add instruction on updating pySBOL through pip

Issue - State: closed - Opened by kirichoi almost 7 years ago
Labels: Documentation

#62 - iterating over the types list of ComponentDefinition

Issue - State: closed - Opened by eoberortner about 7 years ago - 3 comments

#61 - Need documentation for configuration options

Issue - State: closed - Opened by bbartley about 7 years ago - 1 comment
Labels: Documentation

#60 - Need online documentation for extension class

Issue - State: closed - Opened by bbartley about 7 years ago - 1 comment
Labels: Documentation

#59 - Add documentation for devs

Issue - State: closed - Opened by kirichoi about 7 years ago - 1 comment
Labels: Documentation

#58 - Support conda

Issue - State: closed - Opened by kirichoi about 7 years ago - 1 comment
Labels: Enhancement

#57 - Example gene_cassette from https://pysbol2.readthedocs.io/en/latest/sbol_examples.html

Issue - State: closed - Opened by JulesBobVerne over 7 years ago - 3 comments
Labels: Bug, Priority

#56 - Module version is inaccessible in Python 2.7 but seems to be OK in 3.6

Issue - State: closed - Opened by bbartley over 7 years ago - 3 comments

#55 - sequences.get() defaults to wrong URI

Issue - State: closed - Opened by kirichoi over 7 years ago - 3 comments
Labels: Bug, Priority

#54 - testSBOL() tries to write to protected directory

Issue - State: closed - Opened by bbartley over 7 years ago - 1 comment
Labels: Bug

#53 - assertItemsEqual() is Python 2.7 specific

Issue - State: closed - Opened by kirichoi over 7 years ago - 1 comment
Labels: Bug, Priority

#52 - Refactor getAll() and getObjects() into a single method

Issue - State: closed - Opened by kirichoi over 7 years ago - 3 comments
Labels: Enhancement

#51 - Range.end property is inaccessible

Issue - State: closed - Opened by bbartley over 7 years ago - 1 comment
Labels: Bug

#50 - SynBioHub URLs should be https not http

Issue - State: closed - Opened by bbartley over 7 years ago
Labels: Documentation

#49 - Need example for iterating through a primary sequence of components

Issue - State: closed - Opened by bbartley over 7 years ago - 1 comment
Labels: Documentation

#48 - Add tests for iterators and memory management

Issue - State: closed - Opened by bbartley over 7 years ago - 2 comments
Labels: Enhancement

#47 - Installing on BioLinux

Issue - State: closed - Opened by alihum over 7 years ago - 1 comment

#46 - Setup.py not installing test files on Windows

Issue - State: closed - Opened by kirichoi over 7 years ago - 3 comments
Labels: Bug, Urgent

#45 - Pip install directs to outdated wheel

Issue - State: closed - Opened by kirichoi almost 8 years ago - 2 comments
Labels: Bug, Urgent

#44 - Upload tutorial examples

Issue - State: closed - Opened by tramyn almost 8 years ago - 1 comment
Labels: Documentation

#43 - Upload videos of compiling examples on different IDE tool

Issue - State: closed - Opened by tramyn almost 8 years ago - 1 comment
Labels: Documentation

#42 - Move instructions on pip to pySBOL doc

Issue - State: closed - Opened by kirichoi almost 8 years ago

#39 - Need to discuss strategies for memory management

Issue - State: closed - Opened by bbartley almost 8 years ago - 17 comments
Labels: Bug, Urgent

#36 - Change wasDerivedFrom to a set

Issue - State: closed - Opened by cjmyers almost 8 years ago - 1 comment

#13 - Support pip

Issue - State: closed - Opened by kirichoi about 8 years ago - 14 comments
Labels: Enhancement, Priority