Next PEtab version #126
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Next PEtab version #126
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paulstapor
commented
Aug 20, 2019
•
paulstapor
commented
- Adding a new visualization framework (using a visualization specification file)
- added new columns to the measurement table: datasetId
- adding use of the prior column
- Closes Why is there a version 0.0.0a15 on PyPI while master is at 0.0.0a14? #124
- Fix, test and deprecate petab.sbml.constant_species_to_parameters
- fix deploy
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
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Wait for tonight? Otherwise good. |
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Maybe after the prior stuff merge (useful for parPE)? Or before? |
* added an initial parameter sampling functionality * add tests for startpoint sampling * added documentation for the additional columns intialization and objectivePriorType and Parameters
dweindl
approved these changes
Aug 27, 2019
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Okay, I can't merge that one, I'm not authorized, as I see... Please, somebody else o that... ;) |
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I'm also not authorized (any more?) |
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I set @MerktSimon @elbaraim @erikadudki as maintainers as recently discussed. Please merge and create new release. |
jvanhoefer
approved these changes
Aug 27, 2019
Codecov Report
@@ Coverage Diff @@
## master #126 +/- ##
==========================================
+ Coverage 60.14% 68.44% +8.29%
==========================================
Files 7 11 +4
Lines 803 1090 +287
Branches 173 256 +83
==========================================
+ Hits 483 746 +263
- Misses 292 307 +15
- Partials 28 37 +9
Continue to review full report at Codecov.
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* 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
jvanhoefer
approved these changes
Sep 10, 2019
This was referenced Sep 11, 2019
Closed
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