Ecosyste.ms: Issues

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

GitHub / SynBioDex/SBOL-utilities issues and pull requests

#209 - Prepare 1.0a17 release

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

#208 - Move sbol_factory and pySBOL3 dependencies to more recent versions

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

#206 - Fill in missing GenBank information from SBOL fields

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

#205 - Ensure all GenBank features are in term translation list

Issue - State: open - Opened by jakebeal almost 2 years ago - 4 comments
Labels: enhancement, good first issue

#204 - Switch all usages of SBOL_INLINE and SBOL_REVERSE_COMPLEMENT to SO

Issue - State: open - Opened by jakebeal almost 2 years ago - 2 comments
Labels: enhancement, good first issue

#203 - Identified genbank customs

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

#202 - iGEM Quality Checker System

Pull Request - State: open - Opened by rkrishnasanka almost 2 years ago - 1 comment

#201 - Kludge defuzz fuzzy features

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

#200 - Fuzzy locations break document validity

Issue - State: open - Opened by jakebeal almost 2 years ago - 6 comments
Labels: bug

#199 - Fix SeqFeature not hashable error

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

#198 - TypeError: unhashable type: 'SeqFeature'

Issue - State: closed - Opened by tcmitchell almost 2 years ago - 1 comment

#197 - Add testing for Python 3.11

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

#196 - fixing-utilities-names

Pull Request - State: closed - Opened by ahmedtarek26 about 2 years ago

#195 - find feature function

Pull Request - State: closed - Opened by ahmedtarek26 about 2 years ago - 3 comments

#194 - tyto bug is fixed: roll forward to new version

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

#193 - Short package names

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

#192 - SEP055 implementation

Pull Request - State: closed - Opened by Gonza10V about 2 years ago

#191 - Command-line excel-to-sbol sheet configurations

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

#190 - Excel to package

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

#189 - Handle Strain Information

Issue - State: open - Opened by hgscott about 2 years ago

#188 - fix: 0-indexed parsing of start locations by BioPython bug

Pull Request - State: closed - Opened by mohitdmak over 2 years ago
Labels: bug, sbol3-genbank

#187 - todo: remove temporary workaround implemented for pySBOL3 bug once its fix is incorporated

Issue - State: open - Opened by mohitdmak over 2 years ago
Labels: bug, sbol3-genbank

#186 - final merge: Offline SBOL3 <-> GenBank Converter; Integration with previous online Converter

Pull Request - State: closed - Opened by mohitdmak over 2 years ago - 6 comments
Labels: enhancement, sbol3-genbank

#185 - find_feature

Issue - State: open - Opened by jakebeal over 2 years ago
Labels: enhancement, good first issue

#183 - add: support to set and reset genbank location types in a round trip

Pull Request - State: closed - Opened by mohitdmak over 2 years ago - 3 comments

#182 - add: support to set and reset genbank location types in a round trip

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

#181 - add: support for remaining iGEM testsuite files

Pull Request - State: closed - Opened by mohitdmak over 2 years ago - 5 comments

#180 - converter to write only setted GenBank fields?

Issue - State: open - Opened by mohitdmak over 2 years ago - 2 comments
Labels: question, sbol3-genbank

#179 - Excel to package, fat and dissociated packages

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

#178 - sbol2 to sbol3 with Combinatorial Design

Issue - State: open - Opened by guillaume-gricourt over 2 years ago - 1 comment
Labels: bug, duplicate

#177 - Parse taxonomy in a better way by creating new top level object property

Issue - State: open - Opened by mohitdmak over 2 years ago
Labels: enhancement, sbol3-genbank

#176 - add: ability to store and retrieve feature qualifiers

Pull Request - State: closed - Opened by mohitdmak over 2 years ago - 5 comments
Labels: enhancement, sbol3-genbank

#175 - Package validation

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

#174 - add: attempt to store reference info

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

#173 - Ignore sbol objects that can't be parsed to GenBank objects

Pull Request - State: closed - Opened by mohitdmak over 2 years ago - 3 comments
Labels: enhancement, sbol3-genbank

#172 - Supporting all GenBank files in test/test_files for round tripping

Pull Request - State: closed - Opened by mohitdmak over 2 years ago
Labels: enhancement, sbol3-genbank

#170 - Modification needed for the new extended Component class to store extraneous GenBank properties

Issue - State: open - Opened by mohitdmak over 2 years ago
Labels: enhancement, sbol3-genbank

#169 - Store GenBank References's location information as SBOL3 properties

Issue - State: closed - Opened by mohitdmak over 2 years ago - 1 comment
Labels: enhancement, sbol3-genbank

#168 - Refactor SBOL/Genbank converter to be more modular

Issue - State: open - Opened by tcmitchell over 2 years ago
Labels: sbol3-genbank

#167 - Work on the GenBank files in SBOLTestSuite

Issue - State: open - Opened by tcmitchell over 2 years ago
Labels: sbol3-genbank

#166 - Support all of the sample files in the iGEM distribution

Issue - State: open - Opened by tcmitchell over 2 years ago
Labels: sbol3-genbank

#165 - Support all of the GenBank examples in test/test-files

Issue - State: closed - Opened by tcmitchell over 2 years ago
Labels: sbol3-genbank

#164 - Ignore SBOL objects that cannot be converted to Genbank

Issue - State: closed - Opened by tcmitchell over 2 years ago - 1 comment
Labels: sbol3-genbank

#163 - update RDF validation

Pull Request - State: closed - Opened by Gonza10V over 2 years ago

#162 - Synchronise with develop

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

#161 - new rdflib 6.2 no longer puts spurious whitespace in .nt files

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

#160 - add: support to parse and store features with multiple locations; modify final feature sort

Pull Request - State: closed - Opened by mohitdmak over 2 years ago - 2 comments
Labels: enhancement, sbol3-genbank

#158 - feat: storing and retrieving extraneous genbank properties in sbol3 components

Pull Request - State: closed - Opened by mohitdmak over 2 years ago - 8 comments
Labels: enhancement, sbol3-genbank

#157 - digestion

Pull Request - State: open - Opened by Gonza10V over 2 years ago
Labels: enhancement

#156 - Namespace defaults should use pySBOL3 defaulting rules

Issue - State: open - Opened by jakebeal over 2 years ago - 6 comments
Labels: good first issue

#155 - Hardcoded values for various properties while converting from SBOL3 -> GenBank

Issue - State: open - Opened by mohitdmak over 2 years ago
Labels: question, sbol3-genbank

#154 - Hardcoded values for various properties while converting from GenBank -> SBOL3

Issue - State: open - Opened by mohitdmak over 2 years ago
Labels: question, sbol3-genbank

#153 - Store multiple feature locations in genbank converter

Issue - State: open - Opened by tcmitchell over 2 years ago
Labels: sbol3-genbank

#152 - Include `SubComponents` in genbank converter

Issue - State: open - Opened by tcmitchell over 2 years ago
Labels: sbol3-genbank

#151 - Remove the `write` argument to the sbol3 genbank converter

Issue - State: open - Opened by tcmitchell over 2 years ago
Labels: sbol3-genbank

#150 - Handle GenBank header lines in genbank converter

Issue - State: closed - Opened by tcmitchell over 2 years ago
Labels: sbol3-genbank

#149 - Handle multiple feature types in genbank converter

Issue - State: open - Opened by tcmitchell over 2 years ago
Labels: sbol3-genbank

#148 - Handle Features with multiple locations in genbank converter

Issue - State: open - Opened by tcmitchell over 2 years ago
Labels: sbol3-genbank

#147 - Handle components with no sequence in genbank converter

Issue - State: closed - Opened by tcmitchell over 2 years ago - 1 comment
Labels: sbol3-genbank

#146 - translating from GenBank ontology terms to SO and vice versa

Issue - State: closed - Opened by mohitdmak over 2 years ago - 1 comment
Labels: enhancement, question

#145 - SEP 054: package installation and lookup

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

#144 - Create calculate_complexity_score.py

Pull Request - State: closed - Opened by jguillen15 over 2 years ago - 5 comments

#143 - add: new support for SBOL3 to GenBank conversion

Pull Request - State: closed - Opened by mohitdmak over 2 years ago - 1 comment
Labels: enhancement

#142 - add: new support for GenBank to SBOL3 conversion

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

#141 - adding part insert, part in backbone, and digestion

Pull Request - State: closed - Opened by Gonza10V over 2 years ago
Labels: enhancement

#140 - Import Excel to CSV exporting from iGEM-distribution

Issue - State: open - Opened by jakebeal over 2 years ago
Labels: enhancement

#139 - Fix 134: cross-platform testing of graph-sbol

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

#138 - Backbone generalization

Issue - State: open - Opened by Gonza10V over 2 years ago
Labels: enhancement

#137 - Add "how to contribute" information.

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

#136 - add: new converter to existing console script with fallback option to legacy converter

Pull Request - State: closed - Opened by mohitdmak over 2 years ago - 1 comment
Labels: enhancement

#135 - add: genbank conversion support for multiple records and features

Pull Request - State: closed - Opened by mohitdmak over 2 years ago - 7 comments

#134 - test_dotfile_generation failed

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

#133 - fix(chore): bioconda runner env cmdline

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

#132 - conda package - javascript

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

#131 - add: initial simple conversion gb/sbol3 with sample files

Pull Request - State: closed - Opened by mohitdmak over 2 years ago - 7 comments

#130 - Display Node.js version in build logs

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

#127 - Add CONTRIBUTING file

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

#125 - Gonzalo internship

Pull Request - State: closed - Opened by Gonza10V over 2 years ago
Labels: enhancement

#122 - convert2to3 fails on windows

Issue - State: closed - Opened by JMante1 almost 3 years ago - 16 comments
Labels: bug

#121 - conda package

Issue - State: closed - Opened by breakthewall almost 3 years ago - 19 comments

#111 - Add filter by roles functionality

Pull Request - State: closed - Opened by mohitdmak about 3 years ago - 6 comments

#105 - Setup.py changes in scripts

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

#98 - added helper function to check composite

Pull Request - State: closed - Opened by Akshat-Kumar-0610 about 3 years ago - 1 comment

#93 - Duplication of graph_sbol utility in the root directory

Issue - State: closed - Opened by karin-sionov about 3 years ago - 1 comment

#91 - Fix inconsistency of utilities names in the documentation

Issue - State: open - Opened by karin-sionov about 3 years ago - 4 comments
Labels: bug, documentation, good first issue

#86 - Add tests for docstring coverage

Issue - State: closed - Opened by noahsprent about 3 years ago
Labels: documentation, good first issue

#83 - SBOL3/2 conversion of orientations

Issue - State: closed - Opened by jakebeal about 3 years ago
Labels: bug, good first issue

#79 - Switch readthedocs to main

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

#71 - Filter to collect TopLevel objects

Issue - State: closed - Opened by jakebeal about 3 years ago
Labels: good first issue

#70 - Function to check if a Component is a DNA part

Issue - State: closed - Opened by jakebeal about 3 years ago
Labels: good first issue

#63 - Validation function for Packages

Issue - State: closed - Opened by jakebeal about 3 years ago
Labels: duplicate, good first issue

#60 - Create Module from SBOL document

Issue - State: closed - Opened by jakebeal about 3 years ago - 1 comment
Labels: good first issue

#58 - Problems with contained_components

Issue - State: closed - Opened by Gonza10V over 3 years ago - 5 comments
Labels: enhancement

#53 - Error using convert3to2

Issue - State: closed - Opened by Gonza10V over 3 years ago - 8 comments
Labels: bug

#37 - Excel-to-sbol should also strip names

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

#31 - Return to pySBOL3 head

Issue - State: closed - Opened by jakebeal over 3 years ago

#11 - Add license

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