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Merged
dweindl merged 5 commits into from
Dec 18, 2023
Merged

Release 0.2.6 #238

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91ba4dc
Fix `flatten_timepoint_specific_output_overrides` not supporting obse…
dweindl Dec 14, 2023
1bebd15
Vis: fix replicates sorting (#232)
plakrisenko Dec 15, 2023
d2db5ba
Doc: Clean up visualization examples (#236)
dweindl Dec 18, 2023
f07c951
Update CODEOWNERS (#237)
dweindl Dec 18, 2023
097a15e
Bump version, release notes
dweindl Dec 18, 2023
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8 changes: 4 additions & 4 deletions .github/CODEOWNERS
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# default owners
* @PEtab-dev/libpetab-python-maintainers

/petab/visualize/ @plakrisenko
/tests/test_vis* @plakrisenko
/petab/visualize/ @m-philipps
/tests/test_vis* @m-philipps
/petab/simulate.py @dilpath
/tests/test_simulate.py @dilpath
/petab/calculate.py @yannikschaelte
/tests/test_calculate.py @yannikschaelte
/doc/ @dweindl
/doc/example @m-philipps
/doc/example/example_petablint.ipynb @dweindl
12 changes: 12 additions & 0 deletions CHANGELOG.md
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## 0.2 series

### 0.2.6

* Fixed `flatten_timepoint_specific_output_overrides` not supporting
observableParameter overrides as placeholders in noise formulae
by @dweindl in https://github.com/PEtab-dev/libpetab-python/pull/235
* Visualization: fixed replicate sorting
by @plakrisenko in https://github.com/PEtab-dev/libpetab-python/pull/232
* Doc: Revised visualization examples
by @dweindl in https://github.com/PEtab-dev/libpetab-python/pull/236

**Full Changelog**: https://github.com/PEtab-dev/libpetab-python/compare/v0.2.5...v0.2.6

### 0.2.5

* Fix accessing `preequilibrationConditionId` without checking for presence
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3 changes: 2 additions & 1 deletion doc/conf.py
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# myst_nb options
# https://myst-nb.readthedocs.io/en/latest/configuration.html
nb_execution_mode = "force"

nb_execution_raise_on_error = True
nb_execution_show_tb = True

source_suffix = {
".rst": "restructuredtext",
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2 changes: 0 additions & 2 deletions doc/example.rst
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Expand Up @@ -10,8 +10,6 @@ The following examples should help to get a better idea of how to use the PEtab

example/example_petablint.ipynb
example/example_visualization.ipynb
example/example_visualization_without_visspec.ipynb
example/example_visualization_with_visspec.ipynb

Examples of systems biology parameter estimation problems specified in PEtab
can be found in the `systems biology benchmark model collection <https://github.com/Benchmarking-Initiative/Benchmark-Models-PEtab>`_.
38 changes: 19 additions & 19 deletions doc/example/example_Fujita/visuSpecs/Fujita_visuSpec_datasetIds.tsv
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plotId plotTypeSimulation plotTypeData datasetId xValues legendEntry
plot1 LinePlot provided model1_data1_pEGFR_tot time Data 1, pEGFR total
plot1 LinePlot provided model1_data2_pEGFR_tot time Data 2, pEGFR total
plot1 LinePlot provided model1_data3_pEGFR_tot time Data 3, pEGFR total
plot1 LinePlot provided model1_data4_pEGFR_tot time Data 4, pEGFR total
plot1 LinePlot provided model1_data5_pEGFR_tot time Data 5, pEGFR total
plot1 LinePlot provided model1_data6_pEGFR_tot time Data 6, pEGFR total
plot2 LinePlot provided model1_data1_pAkt_tot time Data 1, pAkt total
plot2 LinePlot provided model1_data2_pAkt_tot time Data 2, pAkt total
plot2 LinePlot provided model1_data3_pAkt_tot time Data 3, pAkt total
plot2 LinePlot provided model1_data4_pAkt_tot time Data 4, pAkt total
plot2 LinePlot provided model1_data5_pAkt_tot time Data 5, pAkt total
plot2 LinePlot provided model1_data6_pAkt_tot time Data 6, pAkt total
plot3 LinePlot provided model1_data1_pS6_tot time Data 1, pS6 total
plot3 LinePlot provided model1_data2_pS6_tot time Data 2, pS6 total
plot3 LinePlot provided model1_data3_pS6_tot time Data 3, pS6 total
plot3 LinePlot provided model1_data4_pS6_tot time Data 4, pS6 total
plot3 LinePlot provided model1_data5_pS6_tot time Data 5, pS6 total
plot3 LinePlot provided model1_data6_pS6_tot time Data 6, pS6 total
plotId plotTypeData datasetId xValues legendEntry
plot1 provided model1_data1_pEGFR_tot time Data 1, pEGFR total
plot1 provided model1_data2_pEGFR_tot time Data 2, pEGFR total
plot1 provided model1_data3_pEGFR_tot time Data 3, pEGFR total
plot1 provided model1_data4_pEGFR_tot time Data 4, pEGFR total
plot1 provided model1_data5_pEGFR_tot time Data 5, pEGFR total
plot1 provided model1_data6_pEGFR_tot time Data 6, pEGFR total
plot2 provided model1_data1_pAkt_tot time Data 1, pAkt total
plot2 provided model1_data2_pAkt_tot time Data 2, pAkt total
plot2 provided model1_data3_pAkt_tot time Data 3, pAkt total
plot2 provided model1_data4_pAkt_tot time Data 4, pAkt total
plot2 provided model1_data5_pAkt_tot time Data 5, pAkt total
plot2 provided model1_data6_pAkt_tot time Data 6, pAkt total
plot3 provided model1_data1_pS6_tot time Data 1, pS6 total
plot3 provided model1_data2_pS6_tot time Data 2, pS6 total
plot3 provided model1_data3_pS6_tot time Data 3, pS6 total
plot3 provided model1_data4_pS6_tot time Data 4, pS6 total
plot3 provided model1_data5_pS6_tot time Data 5, pS6 total
plot3 provided model1_data6_pS6_tot time Data 6, pS6 total
14 changes: 7 additions & 7 deletions doc/example/example_Fujita/visuSpecs/Fujita_visuSpec_individual_datasets.tsv
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plotId plotTypeSimulation plotTypeData datasetId xValues
plot1 LinePlot provided model1_data1_pEGFR_tot time
plot2 LinePlot provided model1_data2_pEGFR_tot time
plot2 LinePlot provided model1_data3_pEGFR_tot time
plot3 LinePlot provided model1_data4_pEGFR_tot time
plot3 LinePlot provided model1_data5_pEGFR_tot time
plot3 LinePlot provided model1_data6_pEGFR_tot time
plotId plotTypeData datasetId xValues
plot1 provided model1_data1_pEGFR_tot time
plot2 provided model1_data2_pEGFR_tot time
plot2 provided model1_data3_pEGFR_tot time
plot3 provided model1_data4_pEGFR_tot time
plot3 provided model1_data5_pEGFR_tot time
plot3 provided model1_data6_pEGFR_tot time
11 changes: 11 additions & 0 deletions doc/example/example_Isensee/Isensee.yaml
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format_version: 1
parameter_file:
problems:
- condition_files:
- Isensee_experimentalCondition.tsv
measurement_files:
- Isensee_measurementData.tsv
observable_files: []
sbml_files: []
visualization_files:
- Isensee_visualizationSpecification.tsv
9 changes: 9 additions & 0 deletions doc/example/example_Isensee/Isensee_no_vis.yaml
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format_version: 1
parameter_file:
problems:
- condition_files:
- Isensee_experimentalCondition.tsv
measurement_files:
- Isensee_measurementData.tsv
observable_files: []
sbml_files: []
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