v0.13.0

What's Changed

• Update .readthedocs.yaml to resolve build error by @himoto in #255
• Use default ddof(=0) by @himoto in #256
• Remove unused variable: __version__ by @himoto in #257
• Don't use Sphinx version 7 or more by @himoto in #259
• Fix pepy badge by @himoto in #263
• Remove Sphinx version constraints by @himoto in #262
• Specify minimal sphinx-rtd-theme version by @himoto in #264
• Update MANIFEST.in by @himoto in #266
• Update citation infomation by @himoto in #267
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #260

Full Changelog: v0.12.0...v0.13.0

v0.12.0 (May 2023)

What's Changed

• Update email address by @himoto in #249
• Remove Sphinx version constraint by @himoto in #251
• Add support for Python 3.11 and numpy 1.24 by @himoto in #252
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #246
• Release v0.12.0 by @himoto in #253

Full Changelog: v0.11.1...v0.12.0

v0.11.1

What's Changed

• Add file name by @himoto in #238
• Update arguments of run_analysis function by @himoto in #240
• Move package setup to toml file by @himoto in #243
• Release v0.11.1 by @himoto in #244

Full Changelog: v0.11.0...v0.11.1

v0.11.0 (January 2023)

What's Changed

• Set pyvis version <0.3 by @himoto in #201
• Update citation info by @himoto in #197
• Fix maxdepth to 2 by @himoto in #202
• Add CodeQL workflow for GitHub code scanning by @lgtm-com in #204
• Fix #205 by @himoto in #206
• Update template by @himoto in #207
• Update util in analysis/ by @himoto in #208
• Explicit return by @himoto in #210
• Explicitly return None by @himoto in #211
• Use Tee class instead of _Logger by @himoto in #213
• Update action/checkout@v2 -> v3 by @himoto in #215
• Fix docstring in Optimizer by @himoto in #217
• Remove LGTM.com code quality badges by @himoto in #219
• Update julia_template.py by @himoto in #222
• Update docs by @himoto in #224
• Fix a typo in state_transition rule by @himoto in #225
• Improve instructions for executing example models by @himoto in #227
• Suppress numba warning by @himoto in #229
• Update solver.py by @himoto in #230
• Update state_transition rule in Text2Model by @himoto in #232
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #164
• Release v0.11.0 by @himoto in #237

New Contributors

• @lgtm-com made their first contribution in #204

Full Changelog: v0.10.0...v0.11.0

v0.10.0 (September 2022)

What's Changed

• State transition by @himoto in #169
• Generalisation of mass action kinetics by @formersbach in #172
• Drop support for old template by @himoto in #176
• Fix typo in tutorial by @himoto in #178
• Fix module name: model_object by @himoto in #181
• Transfer graphing from BioMass to Text2Model by @formersbach in #177
• Update docs to be compatible with the newest features by @himoto in #182
• Fix f-string in is_phosphorylated rule by @himoto in #184
• Refactor code for sensitivity analysis by @himoto in #186
• Redirect rules by @himoto in #188
• Fix issue #189 by @formersbach in #190
• Fix docstring by @himoto in #191
• Fixes #192 by @formersbach in #193
• Update graphing tutorial to new graph function. by @formersbach in #195

Full Changelog: v0.9.1...v0.10.0

v0.9.1

What's Changed

• Enable running biomass without Graphviz by @himoto in #162

Full Changelog: v0.9.0...v0.9.1

v0.9.0 (July 2022)

What's Changed

• Adding interactive plotting option. by @formersbach in #144
• Changed how graph is passed to pygraphvis, fixing issue #147 by @formersbach in #148
• Add graph visualization tutorial, resolves #145 by @formersbach in #149
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #146
• Fixes documentation and changes default save directory of graph.py by @formersbach in #154
• Remove exec by @himoto in #157

Full Changelog: v0.8.0...v0.9.0

v0.8.0 (June 2022)

What's Changed

• Graph representation of biological model by @formersbach in #131
• Drop support of Python <= 3.7 by @himoto in #132
• Update graph.py by @himoto in #133
• From text to model by @himoto in #136
• Release v0.8.0 by @himoto in #138
• Fix error in multi_observables_options by @himoto in #140
• Fix dead link by @himoto in #142

New Contributors

• @formersbach made their first contribution in #131

Full Changelog: v0.7.2...v0.8.0

v0.7.2

What's Changed

• Make error messages more user friendly by @himoto in #123
• Fix #124 by @himoto in #125
• Release v0.7.2 by @himoto in #128

Full Changelog: v0.7.1...v0.7.2

v0.7.1

What's Changed

• Create tutorial by @himoto in #118
• Update logo by @himoto in #119
• Release v0.7.1 by @himoto in #121

Full Changelog: v0.7.0...v0.7.1