Ecosyste.ms: Issues

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

GitHub / PEtab-dev/libpetab-python issues and pull requests

#253 - Doc: Exclude private members

Pull Request - State: closed - Opened by dweindl 10 months ago - 1 comment

#252 - maint: fix code style, check on gha

Pull Request - State: closed - Opened by dweindl 10 months ago - 1 comment

#251 - maint: black -> ruff

Pull Request - State: closed - Opened by dweindl 10 months ago - 1 comment

#250 - Typehint states it is optional, but no default value is provided.

Pull Request - State: closed - Opened by PaulJonasJost 11 months ago - 1 comment

#249 - Release 0.2.9

Pull Request - State: closed - Opened by dweindl 11 months ago

#248 - Fix `SbmlModel.get_free_parameter_ids_with_values` to handle InitialA…

Pull Request - State: closed - Opened by dweindl 11 months ago - 5 comments

#247 - Wrong plot_goodness_of_fit if different order of rows in measurement_df and simulation_df

Issue - State: open - Opened by plakrisenko 11 months ago - 1 comment
Labels: bug, visualization

#246 - Fix pytest.PytestRemovedIn9Warning / Marks applied to fixtures

Pull Request - State: closed - Opened by dweindl about 1 year ago

#245 - Release 0.2.8

Pull Request - State: closed - Opened by dweindl about 1 year ago - 1 comment

#244 - Require pyarrow

Pull Request - State: closed - Opened by dweindl about 1 year ago - 1 comment

#243 - Add petab.Problem.n_{estimated,measurements,priors}

Pull Request - State: closed - Opened by dweindl about 1 year ago - 1 comment

#242 - Fix pandas FutureWarning in petab/visualize/lint.py

Pull Request - State: closed - Opened by dweindl about 1 year ago - 1 comment

#241 - petab/visualize/lint.py pandas FutureWarning

Issue - State: closed - Opened by dweindl about 1 year ago

#240 - Release 0.2.7

Pull Request - State: closed - Opened by dweindl about 1 year ago

#239 - Fix flatten_timepoint_specific_output_overrides

Pull Request - State: closed - Opened by dweindl about 1 year ago - 1 comment

#238 - Release 0.2.6

Pull Request - State: closed - Opened by dweindl about 1 year ago - 1 comment

#237 - Update CODEOWNERS

Pull Request - State: closed - Opened by dweindl about 1 year ago - 1 comment

#236 - Doc: Clean up visualization examples

Pull Request - State: closed - Opened by dweindl about 1 year ago - 1 comment

#235 - Fix `flatten_timepoint_specific_output_overrides` not supporting obse…

Pull Request - State: closed - Opened by dweindl about 1 year ago - 1 comment

#233 - Release v0.2.5

Pull Request - State: closed - Opened by dilpath about 1 year ago - 1 comment

#232 - Vis: fix replicates sorting

Pull Request - State: closed - Opened by plakrisenko about 1 year ago - 1 comment

#231 - Treat observableParameter overrides as placeholders in noise formulae

Pull Request - State: closed - Opened by dilpath about 1 year ago - 2 comments

#230 - Startpoint sampling for a subset of parameters

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

#229 - Validator: check `datasetId` in visualizations table exists in measurements table

Issue - State: closed - Opened by dilpath over 1 year ago
Labels: validation

#228 - Fix accessing preequilibrationConditionId without checking for presence

Pull Request - State: closed - Opened by dweindl over 1 year ago - 2 comments

#227 - Release 0.2.4

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

#226 - Fix pandas 2.1.0 FutureWarnings

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

#225 - Add pre-commit-config, run black, isort, ...

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

#224 - pandas FutureWarning: Setting an item of incompatible dtype is deprecated

Issue - State: closed - Opened by dweindl over 1 year ago
Labels: good first issue

#223 - Handle missing nominalValue in Problem.get_x_nominal

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

#222 - Customizable figure size

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

#221 - Handle DataFrame/None as input to `get_visualization_df`

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

#220 - API for creating petab problems from scratch

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

#219 - Validator does not check for required column `noiseFormula` in observables table

Issue - State: open - Opened by dweindl over 1 year ago
Labels: validation

#217 - Improve error handling in Problem.from_yaml - format_version

Issue - State: open - Opened by dweindl over 1 year ago
Labels: validation

#216 - Release 0.2.3

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

#215 - Make validate_visualization_df work without matplotlib installation

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

#214 - Fix missing inplace=True in validation of visualization tables

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

#213 - Handle default for `plotTypeData` in validation of visualization tables

Issue - State: closed - Opened by dweindl over 1 year ago
Labels: bug, validation

#212 - PEtab validation should not require matplotlib

Issue - State: closed - Opened by dweindl over 1 year ago

#211 - Release 0.2.2

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

#210 - Filter/expect/prevent warnings in test suite

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

#209 - Fix IndexError during test_visualization_with__t_inf

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

#208 - GHA/pypi: trusted publishing

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

#207 - Make `SbmlModel.from_file(..., model_id)` optional

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

#206 - test_visualization_with__t_inf fails

Issue - State: closed - Opened by dweindl over 1 year ago
Labels: bug

#205 - Release 0.2.1

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

#204 - Fix Problem.to_files(model_file=...)

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

#203 - Fix PySBModel.get_parameter_value

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

#202 - Fix sympy symbol name clashes

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

#201 - Release 0.2.0

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

#200 - Require Python 3.9

Pull Request - State: closed - Opened by dweindl over 1 year ago - 3 comments

#199 - Simulator: rename measurement column to simulation

Pull Request - State: closed - Opened by dilpath almost 2 years ago - 6 comments

#198 - Calculation of LLH in `calculate_llh` / `calculate_single_llh`

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

#197 - petab.get_model_for_condition may remove rateRules where it shouldn't

Issue - State: open - Opened by dweindl almost 2 years ago
Labels: bug

#196 - Add pyproject.toml

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

#195 - Fix test suite branch / path

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

#194 - Fix get_model_for_condition

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

#193 - prevent strings being parsed as nan in get_visualization_df

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

#192 - add goodness of fit plot

Pull Request - State: closed - Opened by plakrisenko about 2 years ago - 1 comment

#191 - add histogram to residuals plot and center zero

Pull Request - State: closed - Opened by plakrisenko about 2 years ago - 1 comment

#190 - CODEOWNERS

Pull Request - State: closed - Opened by dweindl about 2 years ago - 1 comment

#189 - Handle yValues default in vis validation

Pull Request - State: closed - Opened by dweindl about 2 years ago - 1 comment

#188 - Startpoints as dict

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

#187 - Residuals plot

Pull Request - State: closed - Opened by plakrisenko about 2 years ago - 1 comment

#186 - GHA: Replace deprecated `set-output`

Pull Request - State: closed - Opened by dweindl about 2 years ago - 1 comment

#185 - Vis: Don't fail on missing simulations

Pull Request - State: closed - Opened by dweindl about 2 years ago - 1 comment

#184 - Add validation for visualization files

Pull Request - State: closed - Opened by dweindl about 2 years ago - 1 comment

#183 - Release 0.1.30

Pull Request - State: closed - Opened by dweindl over 2 years ago - 1 comment

#182 - Move tests to tox

Pull Request - State: closed - Opened by yannikschaelte over 2 years ago - 1 comment

#181 - Update deprecated functions in tests

Pull Request - State: closed - Opened by yannikschaelte over 2 years ago - 1 comment

#180 - Fix deprecated tight layout matplotlib

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

#179 - Use petab identifier for combine archives

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

#178 - Add petab.Problem.__str__

Pull Request - State: closed - Opened by dweindl over 2 years ago - 1 comment

#177 - Fix test dependencies: scipy

Pull Request - State: closed - Opened by dweindl over 2 years ago - 1 comment

#176 - Incorrect check in linter on transformed parameter bounds

Issue - State: closed - Opened by matthiaskoenig over 2 years ago - 8 comments

#175 - Vis: Handle missing data more gracefully

Pull Request - State: closed - Opened by dweindl over 2 years ago - 1 comment

#174 - Release 0.1.29

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

#173 - Fix relative paths for model files

Pull Request - State: closed - Opened by dilpath over 2 years ago - 1 comment

#172 - Simplification of PEtab problems

Pull Request - State: closed - Opened by dweindl over 2 years ago - 1 comment

#171 - Method to unflatten simulation df produced by flattened PEtab problem

Pull Request - State: closed - Opened by dilpath over 2 years ago - 1 comment

#170 - Release 0.1.28

Pull Request - State: closed - Opened by dweindl over 2 years ago - 1 comment

#169 - Fix deprecation warning from `get_model_for_condition`

Pull Request - State: closed - Opened by dweindl over 2 years ago - 1 comment

#168 - Fix SBML validation

Pull Request - State: closed - Opened by dweindl over 2 years ago - 1 comment

#167 - `log_sbml_errors` ignores error severity

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

#166 - model.is_valid logs sbml errors twice

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

#165 - Fix typehints and deprecation warning

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

#164 - incorrect deprecation warning

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

#163 - Various cleanup

Pull Request - State: closed - Opened by dweindl over 2 years ago - 1 comment

#162 - Python support policy

Pull Request - State: closed - Opened by dweindl over 2 years ago - 1 comment

#161 - Fix validation for output parameters columns in the condition table

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

#160 - Release 0.1.27

Pull Request - State: closed - Opened by dweindl over 2 years ago - 1 comment

#159 - Argument forwarding for Problem.get_optimization_to_simulation_parameter_mapping

Pull Request - State: closed - Opened by dweindl over 2 years ago - 1 comment

#158 - Drop Python 3.7 support?

Issue - State: closed - Opened by dweindl over 2 years ago - 3 comments
Labels: question

#157 - Fix reading multiple parameter subset files from YAML

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

#156 - Fix use of multiple parameter files

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

#155 - Develop

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

#154 - Parameters dropped when using subset parameter files

Issue - State: closed - Opened by m-philipps over 2 years ago