add getting started notebook (#1023)

* initial commit nb * fix minor issues * update pre-commit deps * Updated changelog * Updated changelog --------- Co-authored-by: Yannik Schaelte <[email protected]> Co-authored-by: Paul Jonas Jost <[email protected]> Co-authored-by: PaulJonasJost <[email protected]>
ICB-DCM · Feb 23, 2023 · af414de · af414de
1 parent 591ff47
commit af414de
Show file tree

Hide file tree

Showing 13 changed files with 9,761 additions and 4 deletions.
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -11,12 +11,12 @@
 
 repos:
 - repo: https://github.com/psf/black
-  rev: 22.12.0
+  rev: 23.1.0
   hooks:
   - id: black
     description: The uncompromising code formatter
 - repo: https://github.com/pycqa/isort
-  rev: 5.11.1
+  rev: 5.12.0
   hooks:
   - id: isort
     name: isort (python)
@@ -27,7 +27,7 @@ repos:
     name: isort (pyi)
     types: [pyi]
 - repo: https://github.com/nbQA-dev/nbQA
-  rev: 1.5.3
+  rev: 1.6.3
   hooks:
   - id: nbqa-black
   - id: nbqa-pyupgrade

diff --git a/CHANGELOG.rst b/CHANGELOG.rst
@@ -6,14 +6,16 @@ Release notes
 ..........
 
 
-0.2.16 (2023-02-14)
+0.2.16 (2023-02-23)
 -------------------
 
 * Optimize:
     * sacess optimizer (#988, #997)
     * Warn only once if using ineffiecient objective settings (#996)
     * Hierarchical Optimization (#1006)
     * Fix cma documentation (#987)
+* Petab
+    * Improvement to create_startpoint_method() (#1018)
 * Sampling:
     * Dynesty sampler (#1002)
     * Fix test/sample/test_sample.py::test_samples_cis failures (#1004)
@@ -32,6 +34,8 @@ Release notes
     * black update (#1010)
     * Doc typo fixes (#995)
     * Doc: Install amici on RTD (#1016)
+    * Add getting_started notebook (#1023)
+    * remove alernative formats build (#1022)
 
 
 0.2.15 (2022-12-21)

diff --git a/doc/example.rst b/doc/example.rst
@@ -23,6 +23,7 @@ Getting started
 .. toctree::
    :maxdepth: 2
 
+   example/getting_started.ipynb
    example/rosenbrock.ipynb
 
 PEtab and AMICI

diff --git a/doc/example/boehm_JProteomeRes2014/Boehm_JProteomeRes2014.yaml b/doc/example/boehm_JProteomeRes2014/Boehm_JProteomeRes2014.yaml
@@ -0,0 +1,13 @@
+format_version: 1
+parameter_file: parameters_Boehm_JProteomeRes2014.tsv
+problems:
+- condition_files:
+  - experimentalCondition_Boehm_JProteomeRes2014.tsv
+  measurement_files:
+  - measurementData_Boehm_JProteomeRes2014.tsv
+  observable_files:
+  - observables_Boehm_JProteomeRes2014.tsv
+  sbml_files:
+  - boehm_JProteomeRes2014.xml
+  visualization_files:
+  - visualizationSpecification_Boehm_JProteomeRes2014.tsv
diff --git a/doc/example/boehm_JProteomeRes2014/experimentalCondition_Boehm_JProteomeRes2014.tsv b/doc/example/boehm_JProteomeRes2014/experimentalCondition_Boehm_JProteomeRes2014.tsv
@@ -0,0 +1,2 @@
+conditionId	conditionName
+model1_data1	condition1
diff --git a/doc/example/boehm_JProteomeRes2014/measurementData_Boehm_JProteomeRes2014.tsv b/doc/example/boehm_JProteomeRes2014/measurementData_Boehm_JProteomeRes2014.tsv
@@ -0,0 +1,49 @@
+observableId	preequilibrationConditionId	simulationConditionId	measurement	time	observableParameters	noiseParameters	datasetId
+pSTAT5A_rel		model1_data1	7.901072999	0.0		sd_pSTAT5A_rel	model1_data1_pSTAT5A_rel
+pSTAT5A_rel		model1_data1	66.36349397	2.5		sd_pSTAT5A_rel	model1_data1_pSTAT5A_rel
+pSTAT5A_rel		model1_data1	81.17132392	5.0		sd_pSTAT5A_rel	model1_data1_pSTAT5A_rel
+pSTAT5A_rel		model1_data1	94.73030806	10.0		sd_pSTAT5A_rel	model1_data1_pSTAT5A_rel
+pSTAT5A_rel		model1_data1	95.11648305	15.0		sd_pSTAT5A_rel	model1_data1_pSTAT5A_rel
+pSTAT5A_rel		model1_data1	91.44171655	20.0		sd_pSTAT5A_rel	model1_data1_pSTAT5A_rel
+pSTAT5A_rel		model1_data1	91.25709923	30.0		sd_pSTAT5A_rel	model1_data1_pSTAT5A_rel
+pSTAT5A_rel		model1_data1	93.67229784	40.0		sd_pSTAT5A_rel	model1_data1_pSTAT5A_rel
+pSTAT5A_rel		model1_data1	88.75423282	50.0		sd_pSTAT5A_rel	model1_data1_pSTAT5A_rel
+pSTAT5A_rel		model1_data1	85.26970322	60.0		sd_pSTAT5A_rel	model1_data1_pSTAT5A_rel
+pSTAT5A_rel		model1_data1	81.13239534	80.0		sd_pSTAT5A_rel	model1_data1_pSTAT5A_rel
+pSTAT5A_rel		model1_data1	76.13592848	100.0		sd_pSTAT5A_rel	model1_data1_pSTAT5A_rel
+pSTAT5A_rel		model1_data1	65.24805913	120.0		sd_pSTAT5A_rel	model1_data1_pSTAT5A_rel
+pSTAT5A_rel		model1_data1	42.59965871	160.0		sd_pSTAT5A_rel	model1_data1_pSTAT5A_rel
+pSTAT5A_rel		model1_data1	25.15779754	200.0		sd_pSTAT5A_rel	model1_data1_pSTAT5A_rel
+pSTAT5A_rel		model1_data1	15.4301824	240.0		sd_pSTAT5A_rel	model1_data1_pSTAT5A_rel
+pSTAT5B_rel		model1_data1	4.596533343	0.0		sd_pSTAT5B_rel	model1_data1_pSTAT5B_rel
+pSTAT5B_rel		model1_data1	29.63454599	2.5		sd_pSTAT5B_rel	model1_data1_pSTAT5B_rel
+pSTAT5B_rel		model1_data1	46.04380647	5.0		sd_pSTAT5B_rel	model1_data1_pSTAT5B_rel
+pSTAT5B_rel		model1_data1	81.97473362	10.0		sd_pSTAT5B_rel	model1_data1_pSTAT5B_rel
+pSTAT5B_rel		model1_data1	80.5716093	15.0		sd_pSTAT5B_rel	model1_data1_pSTAT5B_rel
+pSTAT5B_rel		model1_data1	79.03571964	20.0		sd_pSTAT5B_rel	model1_data1_pSTAT5B_rel
+pSTAT5B_rel		model1_data1	75.67238037	30.0		sd_pSTAT5B_rel	model1_data1_pSTAT5B_rel
+pSTAT5B_rel		model1_data1	71.62471986	40.0		sd_pSTAT5B_rel	model1_data1_pSTAT5B_rel
+pSTAT5B_rel		model1_data1	69.06286328	50.0		sd_pSTAT5B_rel	model1_data1_pSTAT5B_rel
+pSTAT5B_rel		model1_data1	67.14738432	60.0		sd_pSTAT5B_rel	model1_data1_pSTAT5B_rel
+pSTAT5B_rel		model1_data1	60.89947629	80.0		sd_pSTAT5B_rel	model1_data1_pSTAT5B_rel
+pSTAT5B_rel		model1_data1	54.80925777	100.0		sd_pSTAT5B_rel	model1_data1_pSTAT5B_rel
+pSTAT5B_rel		model1_data1	43.98128998	120.0		sd_pSTAT5B_rel	model1_data1_pSTAT5B_rel
+pSTAT5B_rel		model1_data1	29.77145816	160.0		sd_pSTAT5B_rel	model1_data1_pSTAT5B_rel
+pSTAT5B_rel		model1_data1	20.08901656	200.0		sd_pSTAT5B_rel	model1_data1_pSTAT5B_rel
+pSTAT5B_rel		model1_data1	10.96184517	240.0		sd_pSTAT5B_rel	model1_data1_pSTAT5B_rel
+rSTAT5A_rel		model1_data1	14.72316822	0.0		sd_rSTAT5A_rel	model1_data1_rSTAT5A_rel
+rSTAT5A_rel		model1_data1	33.76234229	2.5		sd_rSTAT5A_rel	model1_data1_rSTAT5A_rel
+rSTAT5A_rel		model1_data1	36.79985129	5.0		sd_rSTAT5A_rel	model1_data1_rSTAT5A_rel
+rSTAT5A_rel		model1_data1	49.71760229	10.0		sd_rSTAT5A_rel	model1_data1_rSTAT5A_rel
+rSTAT5A_rel		model1_data1	46.9281201	15.0		sd_rSTAT5A_rel	model1_data1_rSTAT5A_rel
+rSTAT5A_rel		model1_data1	47.83657456	20.0		sd_rSTAT5A_rel	model1_data1_rSTAT5A_rel
+rSTAT5A_rel		model1_data1	46.92872725	30.0		sd_rSTAT5A_rel	model1_data1_rSTAT5A_rel
+rSTAT5A_rel		model1_data1	40.59775294	40.0		sd_rSTAT5A_rel	model1_data1_rSTAT5A_rel
+rSTAT5A_rel		model1_data1	43.78366389	50.0		sd_rSTAT5A_rel	model1_data1_rSTAT5A_rel
+rSTAT5A_rel		model1_data1	44.45738765	60.0		sd_rSTAT5A_rel	model1_data1_rSTAT5A_rel
+rSTAT5A_rel		model1_data1	41.32715926	80.0		sd_rSTAT5A_rel	model1_data1_rSTAT5A_rel
+rSTAT5A_rel		model1_data1	41.06273321	100.0		sd_rSTAT5A_rel	model1_data1_rSTAT5A_rel
+rSTAT5A_rel		model1_data1	39.23583003	120.0		sd_rSTAT5A_rel	model1_data1_rSTAT5A_rel
+rSTAT5A_rel		model1_data1	36.61946054	160.0		sd_rSTAT5A_rel	model1_data1_rSTAT5A_rel
+rSTAT5A_rel		model1_data1	34.8937144	200.0		sd_rSTAT5A_rel	model1_data1_rSTAT5A_rel
+rSTAT5A_rel		model1_data1	32.21107716	240.0		sd_rSTAT5A_rel	model1_data1_rSTAT5A_rel
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1,2 @@
		conditionId conditionName
		model1_data1 condition1