Ecosyste.ms: Issues

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

GitHub / sys-bio/libOmexMeta issues and pull requests

#148 - need python 3.12 release

Issue - State: open - Opened by fbergmann about 1 month ago - 1 comment

#146 - Support notes from SBML models

Issue - State: open - Opened by nickerso over 1 year ago

#145 - Extend supported model formats to include CellML 2.0

Issue - State: open - Opened by nickerso over 1 year ago

#144 - Merge back to develop

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

#143 - Merge old changes from develop

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

#142 - Add support for python 3.11

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

#141 - Update to build for Python 3.10

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

#140 - Add support for python 3.10

Issue - State: closed - Opened by bilalshaikh42 about 2 years ago - 4 comments

#139 - Segmentation fault/Exception error

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

#137 - No support for MacOS 10.14

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

#136 - pxOmexMeta hangs on SBML-fbc models

Issue - State: open - Opened by jonrkarr about 3 years ago

#135 - Align XML version between `RDF.to_file` and `RDF.from_file`

Issue - State: open - Opened by jonrkarr about 3 years ago - 2 comments

#132 - Provide ability to temporarily configure the logger

Issue - State: open - Opened by jonrkarr about 3 years ago

#131 - Develop

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

#130 - Turn Logger into a container for storing issues that can be returned to user

Issue - State: closed - Opened by CiaranWelsh about 3 years ago - 2 comments

#128 - File Logger not working as expected

Issue - State: open - Opened by CiaranWelsh about 3 years ago - 9 comments

#126 - add option to unzip in windows ci doxygen install to enable overwrite

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

#125 - Develop

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

#124 - increment version

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

#123 - Develop

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

#121 - Merge logging changes

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

#120 - Merge logging changes

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

#119 - Develop merge master

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

#118 - Fixed releases link

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

#117 - Merge logging branch into develop

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

#116 - Spec update

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

#115 - Spec update

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

#113 - pyomexmeta fails on 1% of SBML files from BioModels

Issue - State: open - Opened by jonrkarr about 3 years ago - 5 comments
Labels: resolved-but-awaiting-confirmation

#112 - Changes in spec: 4 of four

Issue - State: closed - Opened by jhgennari about 3 years ago - 2 comments

#111 - Changes in spec: 3 of four

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

#110 - Changes in spec: 2 of four

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

#109 - Changes in spec: 1 of four

Issue - State: closed - Opened by jhgennari about 3 years ago - 1 comment
Labels: resolved-but-awaiting-confirmation

#108 - Automate testing of examples to avoid accumulating broken examples

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

#107 - Semantic extraction from SBML fails with segmentation faults for example models

Issue - State: open - Opened by jonrkarr about 3 years ago - 4 comments
Labels: resolved-but-awaiting-confirmation

#106 - Some SBML examples have invalid metaids (according to libSBML)

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

#105 - Update example of `to_editor` to current arguments

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

#103 - Provide ability to copy examples in documentation without line numbers

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

#102 - Provide ability to get error messages for failures with `RDF.to_file`

Issue - State: open - Opened by jonrkarr about 3 years ago - 7 comments
Labels: started

#101 - Validate that namespace URIs have trailing `#` or `/`

Issue - State: open - Opened by jonrkarr over 3 years ago - 2 comments
Labels: started

#100 - Use version suffix with `omexManifest/content@format`

Issue - State: open - Opened by jonrkarr over 3 years ago - 2 comments
Labels: need-assistance

#99 - What values are intended to be used for `omexManifest/content@format`?

Issue - State: open - Opened by jonrkarr over 3 years ago - 3 comments
Labels: need-assistance

#98 - Suggestion: recommend identifiers.org URIs where possible

Issue - State: open - Opened by jonrkarr over 3 years ago - 5 comments
Labels: started

#96 - What is the convention for defining namespaces for OMEX library and identifiers?

Issue - State: open - Opened by jonrkarr over 3 years ago - 4 comments
Labels: started, need-assistance

#95 - Provide error messages for invalid XML content

Issue - State: closed - Opened by jonrkarr over 3 years ago - 3 comments
Labels: started

#94 - Editing invalid XML generates segmentation faults

Issue - State: open - Opened by jonrkarr over 3 years ago - 1 comment

#93 - Validate identifier and date objects

Issue - State: open - Opened by jonrkarr over 3 years ago - 1 comment

#92 - Queries on invalid imported files generate segmentation faults

Issue - State: closed - Opened by jonrkarr over 3 years ago - 1 comment

#91 - Provide option to get `pyomexmeta.RDF.query` as a Python object

Issue - State: closed - Opened by jonrkarr over 3 years ago - 2 comments

#90 - Format is missing from `pyomexmeta.RDF.query` example

Issue - State: closed - Opened by jonrkarr over 3 years ago - 1 comment

#89 - Provide more obvious way to get the underlying RDF graph than `RDF.query`

Issue - State: open - Opened by jonrkarr over 3 years ago - 4 comments

#87 - IMPORTANT: Provide way to get errors and warnings from parsing RDF files

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

#86 - Date examples need to be in opposite order

Issue - State: open - Opened by jonrkarr over 3 years ago

#85 - Encode creator/curator into XML

Issue - State: open - Opened by jonrkarr over 3 years ago - 4 comments

#84 - Examples indicate extra namespaces

Issue - State: closed - Opened by jonrkarr over 3 years ago - 1 comment

#83 - Documentation link is broken

Issue - State: closed - Opened by jonrkarr over 3 years ago - 1 comment

#82 - merge v1.2.10

Pull Request - State: closed - Opened by CiaranWelsh over 3 years ago

#81 - Fix for #78 (part 2, changes now exist in Python as well)

Pull Request - State: closed - Opened by CiaranWelsh over 3 years ago

#80 - publish v1.2.9

Pull Request - State: closed - Opened by CiaranWelsh over 3 years ago

#79 - Issue 78 model level annotations metaid

Pull Request - State: closed - Opened by CiaranWelsh over 3 years ago

#78 - Model level annotations should annotate model element rather than model file

Issue - State: closed - Opened by nickerso over 3 years ago - 2 comments
Labels: bug, Priority

#77 - Develop

Pull Request - State: closed - Opened by CiaranWelsh over 3 years ago

#76 - RDF:Bag problems

Pull Request - State: closed - Opened by CiaranWelsh over 3 years ago

#75 - Python docs

Pull Request - State: closed - Opened by CiaranWelsh over 3 years ago

#74 - An an option to the library to allow a user to strip out all annotations from an SBML file.

Issue - State: closed - Opened by hsauro over 3 years ago - 2 comments
Labels: enhancement

#73 - rebuld docs

Pull Request - State: closed - Opened by CiaranWelsh over 3 years ago

#72 - removing supplemental content from source documentation

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

#71 - RDF.from.file -- SBML annotation extraction doesn't always work

Issue - State: closed - Opened by jhgennari over 3 years ago - 1 comment
Labels: bug, Priority

#70 - Removing older copies of the application note supplementary notebook

Pull Request - State: closed - Opened by nickerso over 3 years ago

#69 - Merge version 1.2.7 from develop into master

Pull Request - State: closed - Opened by CiaranWelsh over 3 years ago

#68 - Add Python version information to install instructions

Issue - State: closed - Opened by CiaranWelsh over 3 years ago
Labels: documentation

#67 - rdf-bag issue

Pull Request - State: closed - Opened by CiaranWelsh over 3 years ago

#66 - VCARD for multiple creators not handled correctly

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

#65 - pip is unable to find pyomexmeta for Python 3.7

Issue - State: closed - Opened by jonrkarr over 3 years ago - 8 comments

#64 - Merge release 1.2.6 into master

Pull Request - State: closed - Opened by CiaranWelsh over 3 years ago

#63 - add different method for draw. The old one used pygraphviz which was …

Pull Request - State: closed - Opened by CiaranWelsh over 3 years ago - 1 comment

#62 - Issue 49 rdf bag

Pull Request - State: closed - Opened by CiaranWelsh over 3 years ago

#61 - Issue 43: taxon prefix not being used.

Pull Request - State: closed - Opened by CiaranWelsh over 3 years ago - 1 comment

#59 - Issue 49 rdf bag

Pull Request - State: closed - Opened by CiaranWelsh over 3 years ago

#58 - Expose rdf query return results as map (not string) to the user

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

#56 - Most methods are missing docstrings

Issue - State: closed - Opened by hsauro over 3 years ago - 3 comments
Labels: documentation

#53 - Discussion on local and model uri user interface

Issue - State: closed - Opened by jhgennari over 3 years ago - 3 comments
Labels: enhancement, design decision

#52 - Drop support for functions that require openssl and curl

Issue - State: open - Opened by CiaranWelsh over 3 years ago - 2 comments

#50 - How to deal with VCard?

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

#49 - Dealing with RDF Bag

Issue - State: closed - Opened by CiaranWelsh over 3 years ago - 4 comments

#43 - Use prefix for `hasTaxon` in turtle syntax

Issue - State: open - Opened by aram148 over 3 years ago - 7 comments

#42 - Create OMEX files from Biomodels rdf files and check them

Issue - State: open - Opened by hsauro over 3 years ago - 5 comments
Labels: enhancement

#41 - Add helper method to generate png or pdf of rdf graph

Issue - State: open - Opened by hsauro over 3 years ago - 2 comments

#40 - Add helper method to display rdf graph to screen

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

#37 - Update README.md

Pull Request - State: closed - Opened by aram148 over 3 years ago