Merge pull request #238 from PEtab-dev/release_0.2.6

Release 0.2.6

.github/CODEOWNERS

@@ -3,10 +3,10 @@
 # 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

CHANGELOG.md

@@ -2,6 +2,18 @@
 
 ## 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

doc/conf.py

@@ -84,7 +84,8 @@
 # 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",

doc/example.rst

@@ -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>`_.

doc/example/example_Fujita/visuSpecs/Fujita_visuSpec_datasetIds.tsv

@@ -1,19 +1,19 @@
-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

doc/example/example_Fujita/visuSpecs/Fujita_visuSpec_individual_datasets.tsv

@@ -1,7 +1,7 @@
-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

doc/example/example_Isensee/Isensee.yaml

@@ -0,0 +1,11 @@
+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

doc/example/example_Isensee/Isensee_no_vis.yaml

@@ -0,0 +1,9 @@
+format_version: 1
+parameter_file:
+problems:
+- condition_files:
+  - Isensee_experimentalCondition.tsv
+  measurement_files:
+  - Isensee_measurementData.tsv
+  observable_files: []
+  sbml_files: []