yaml2sbml-dev/yaml2sbml issues and pull requests

#145 - Initial assignment feature

Issue - State: open - Opened by aidinbii 5 months ago - 1 comment

#144 - PEtab 2

Pull Request - State: open - Opened by dilpath over 1 year ago

#143 - Remove ODE requirement

Pull Request - State: open - Opened by dilpath over 1 year ago

#142 - Make ODE specification optional

Issue - State: open - Opened by shoepfl over 1 year ago - 2 comments

#141 - Update of outdated links in "Input Format for yaml2sbml"

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

#140 - initial fix of linter

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

#139 - Add CI as cron job on GitHub Actions

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

#138 - Error in creation of PEtab tables for the model

Issue - State: open - Opened by aidinbii almost 2 years ago - 10 comments

#137 - Prepare v025

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

#136 - Fix remove unit assignments

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

#135 - Avoid unit consistency checks

Pull Request - State: closed - Opened by dilpath about 3 years ago - 5 comments

#134 - Prepare v024 (#133)

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

#133 - Prepare v024

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

#132 - Zenodo badge

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

#131 - Version 0.2.3

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

#130 - Prepare v023

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

#129 - Adress reviewer comments to the text

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

#128 - Adress comments regarding the software in the JOSS reviewing process

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

#127 - Reviewer 2 comments for JOSS submission

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

#126 - JOSS review

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

#125 - Reviewer comments for JOSS submisson

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

#124 - Events in yaml2sbml

Issue - State: open - Opened by jvanhoefer over 3 years ago
Labels: enhancement

#123 - Fix tests

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

#122 - Version 0.2.2

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

#121 - Prepare v022

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

#120 - Fix pydocstyle was not called; update swig

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

#119 - [WIP]

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

#118 - Feature check sbml success

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

#117 - fix notebooks fixes #114

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

#116 - Add logo license; fixes #108

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

#115 - Add MacOS+Windows tests; clean up .gitignore

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

#114 - Format validation broken in Lotka Volterra jupyter notebook

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

#113 - Unfix AMICI version

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

#112 - add missing release notes (#111)

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

#111 - add missing release notes

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

#110 - New release

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

#109 - fix #99 fix #107

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

#108 - Add logo license

Issue - State: closed - Opened by yannikschaelte over 3 years ago
Labels: fixed but not released

#107 - Issues when state variable begins with a number

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

#106 - Use petablinter in example notebooks to demonstrate that the output is valid PEtab

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

#105 - fixes 98, fixes 101

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

#104 - Add documentation badge to README and readthedocs

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

#103 - Fix readme link to format specification

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

#102 - Logo not rendering on README

Issue - State: closed - Opened by martamatos over 3 years ago - 4 comments
Labels: bug

#101 - Definition of Model ID for use with pyPESTO and AMICI

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

#100 - Ensure data types in Model Editor

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

#99 - validation error for formulas starting with minus

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

#98 - option to have observables as assignments in yaml2sbml call

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

#97 - Feature v 021

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

#96 - Update issue templates

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

#95 - Fix codacy and coverage

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

#94 - add sphinx plugins; test docs build

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

#93 - Sphinx plugins

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

#92 - Add issue template

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

#91 - Fix Sorensen and Lotka-Volterra model editor notebooks

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

#90 - Notebooks fail

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

#89 - Tidy up outputs of notebooks

Issue - State: closed - Opened by yannikschaelte over 3 years ago - 5 comments
Labels: fixed but not released

#88 - Tox

Pull Request - State: closed - Opened by yannikschaelte over 3 years ago - 6 comments

#87 - Use setup.cfg file instead of setup.py

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

#86 - Rename master -> main?

Issue - State: closed - Opened by yannikschaelte over 3 years ago - 3 comments
Labels: question

#85 - typos in readme

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

#84 - Logo background

Issue - State: closed - Opened by jvanhoefer over 3 years ago - 5 comments
Labels: question

#83 - Enforce linear history in develop?

Issue - State: closed - Opened by yannikschaelte over 3 years ago - 6 comments
Labels: question

#82 - Add logo

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

#81 - Extend and simplify docs; remove requirement files

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

#80 - add gha deploy script

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

#79 - add long descrition

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

#78 - set long_description in setup.py

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

#77 - Tidy up Docs/Deploy

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

#76 - minor fixes for pypi deployment

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

#75 - Version 0.2.0

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

#74 - delete requirements, change to setup.py

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

#73 - Fix requirements, fixes #72

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

#72 - unify requirements.txt and setup.py

Issue - State: closed - Opened by jvanhoefer over 3 years ago - 2 comments
Labels: fixed but not released

#71 - Add sphinx docs

Pull Request - State: closed - Opened by martamatos over 3 years ago - 8 comments

#70 - Add Python versions to CI

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

#69 - Logo

Issue - State: closed - Opened by yannikschaelte over 3 years ago - 19 comments
Labels: fixed but not released

#68 - Finish up examples

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

#67 - Call nbmake on doc directory

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

#66 - rename over_write to overwrite

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

#65 - Remove Codacy again?

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

#64 - Feature model editor example closes #58

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

#63 - Sorensen example

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

#62 - Get master/develop branch hierarchy for development

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

#61 - YamlModel.load_from_yaml loads model, leads to inconsistent YamlModel

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

#60 - Documentation on readthedocs

Issue - State: closed - Opened by yannikschaelte over 3 years ago - 5 comments
Labels: fixed but not released

#59 - deploy to pypi

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

#58 - Example Notebook(s) for the model editor

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

#57 - add version closes #56

Pull Request - State: closed - Opened by jvanhoefer over 3 years ago - 5 comments

#56 - version

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

#55 - Rewrite README

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

#54 - Move tests to github actions; add optional amici dependency

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

#53 - Move tests to github actions

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

#52 - Feature validation in examples closes #51

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

#51 - Add yaml validation to examples

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

#50 - ignore warning closes #49

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

#48 - Improve tests (closes #18, #34)

Pull Request - State: closed - Opened by jvanhoefer over 3 years ago - 8 comments

#47 - add CLI for yaml_validation closes #42

Pull Request - State: closed - Opened by jvanhoefer over 3 years ago - 8 comments

#43 - update readme

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

#42 - add CLI for validate_yaml

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

GitHub / yaml2sbml-dev/yaml2sbml issues and pull requests