Release 0.0.0a17 #172
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Release 0.0.0a17 #172
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Add PEtab problem illustration to format description
…des and update doc
here just making the example work now, deletion of experimentId then in #111
* try new travis login * re-fix and update version * tmp do on test branch * undo tmp changes. new password seems to work. updated to 0.0.0a15 meanwhile, so next version must be 0.0.0a16
* adding main file for visualization * adding file for grouping the data which should be plotted * adding file with plotting routine for distinct cases * added file comments, tidy up the code * fix pep8 * update version * some beauty corrections * now: function which should be used, to plot data * style corrections * new example file * minor edits * add test example for visualization with specification file routine * add typehints * minor corrections * flake8 corrections * update folder structure * minor changes & __init__ * move visualization folder to petab subdir * create viz notebook; tidy up code; fix imports and flake8 * add seaborn as requirement * fix flake8, correct link to benchmarking repo
* adding local files for testing visualization * adding the possibility to plot without visualization file or simulation file * update documentation and tests * add the possibility to group plots via simple lists, if no visualization specification file is around * extend and tidy up the examples accordingly * regroup code into new files, try to have each function smaller and better understandable * update gitignore for macOS * updated tests to capture warnings and exceptions * Delete the check for identical noise before plotting points of a dataset - I can think of many applications, in which I want to plot one dataset in which points with different noise values appear. We should allow this to the user * add the check for NANs in a dataset to avoid plotting empty datasets and cluttering the legend
* added an initial parameter sampling functionality * add tests for startpoint sampling * added documentation for the additional columns intialization and objectivePriorType and Parameters
* render svg text * render svg and keep old version as raw inkscape file * have PEtab.svg as inkscape svg since this seems to have little overhead and simplifies editing
…des and update doc
…thub.com:ICB-DCM/PEtab into feature_125_flatten_timepoint_specific_overrides
…ameters flatten_timepoint_specific_output_overrides (#128) (Closes #125) Co-authored-by: elba.raimundez <[email protected]>
… wrong grouping (#147)
* Fix create_parameter_df: Exclude rule targets * Update test
(In future, please update on merge to `develop`)
Codecov Report
@@ Coverage Diff @@
## master #172 +/- ##
==========================================
+ Coverage 68.44% 70.75% +2.31%
==========================================
Files 11 11
Lines 1090 1149 +59
Branches 256 267 +11
==========================================
+ Hits 746 813 +67
+ Misses 307 288 -19
- Partials 37 48 +11
Continue to review full report at Codecov.
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Closing in order to cleanup git history mess |
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Library:
flatten_timepoint_specific_output_overrides ([WIP] Helper function to deal with timepoint-specific parameters #128) (Closes Add support for time-point specific overrides to petab.parameter_mapping #125)
wrong grouping (Fix get_noise_distributions: so far we got 'normal' everywhere due to… #147)
(Closes Validator: verify condition table column names occur as model parameters #150) (Verify condition table column names occur as model parameters (Closes… #151)
noise parameters (Closes Specific error messages if sbml not well-defined #118) (More informative error messages in case of wrongly set observable and… #155)
parameter table (Closes Extend validator to check if all required parameters are present in parameter table #43) (Extend validator to check if all required parameters are present in p… #159)