Merge pull request #740 from ICB-DCM/develop

Release 0.2.8

.github/workflows/ci.yml

@@ -4,8 +4,11 @@ name: CI
 on:
   push:
     branches:
-    - master
+    - main
   pull_request:
+  schedule:
+    # run Monday and Thursday at 03:42 UTC
+    - cron: '42 3 * * MON,THU'
 
 # jobs
 jobs:

CHANGELOG.rst

@@ -6,6 +6,40 @@ Release notes
 ..........
 
 
+0.2.8 (2021-10-28)
+------------------
+
+* PEtab:
+    * Use correct measurement column name in `rdatas_to_simulation_df` (#721)
+    * Visualize optimized model fit via PEtab problem (#725)
+    * Un-ignore observable scaling tests (#742)
+    * New function to plot model trajectory with custom time points (#739)
+
+* Optimization:
+    * OOD Refactor startpoint generation (#732)
+    * Update to fides 0.6.0 (#733)
+    * Correctly report FVAL vs CHI2 values in fides (#741)
+
+* Ensemble:
+    * Option for using weighted ensemble means (#702)
+    * Default names and bounds for `Ensemble.from_sample` (#730)
+
+* Storage:
+    * Load optimization result from HDF5 history (#726)
+
+* General:
+    * Enable use of priors with least squares optimizers (#745)
+    * Add temporary CITATION.cff file (#734)
+    * Regular scheduled CI runs (#754)
+    * Allow to not copy objective in problem (#756)
+
+* Fixes:
+    * Fix non-exported visualization in notebook (#729)
+    * Mark some more tests as flaky (#704)
+    * Fix minor data type and OOD issues in parameter and waterfall plots
+      (#731)
+
+
 0.2.7 (2021-07-30)
 ------------------
 

CITATION.cff

@@ -0,0 +1,75 @@
+authors:
+   -
+      family-names: "Schälte"
+      given-names: "Yannik"
+      orcid: "https://orcid.org/0000-0003-1293-820X"
+   -
+      family-names: "Fröhlich"
+      given-names: "Fabian"
+      orcid: "https://orcid.org/0000-0002-5360-4292"
+   -
+      family-names: "Stapor"
+      given-names: "Paul"
+      orcid: "https://orcid.org/0000-0002-7567-3985"
+   -
+      family-names: "Vanhoefer"
+      given-names: "Jakob"
+      orcid: "https://orcid.org/0000-0002-3451-1701"
+   -
+      family-names: "Weindl"
+      given-names: "Daniel"
+      orcid: "https://orcid.org/0000-0001-9963-6057"
+   -
+      family-names: "Jost"
+      given-names: "Paul Jonas"
+      orcid: "https://orcid.org/0000-0001-7613-6244"
+   -
+      family-names: "Wang"
+      given-names: "Dantong"
+      orcid: "https://orcid.org/0000-0002-3277-5033"
+   -
+      family-names: "Lakrisenko"
+      given-names: "Polina"
+      orcid: "https://orcid.org/0000-0002-7626-8420"
+   -
+      family-names: "Raimúndez"
+      given-names: "Elba"
+      orcid: "https://orcid.org/0000-0002-2790-6668"
+   -
+      family-names: "Pathirana"
+      given-names: "Dilan"
+      orcid: "https://orcid.org/0000-0001-7000-2659"
+   -
+      family-names: "Schmiester"
+      given-names: "Leonard"
+      orcid: "https://orcid.org/0000-0001-7946-3232"
+   -
+      family-names: "Städter"
+      given-names: "Philipp"
+      orcid: "https://orcid.org/0000-0002-4586-6604"
+   -
+      family-names: "Contento"
+      given-names: "Lorenzo"
+      orcid: "https://orcid.org/0000-0002-7901-2172"
+   -
+      family-names: "Merkt"
+      given-names: "Simon"
+      orcid: "https://orcid.org/0000-0002-8017-4494"
+   -
+      family-names: "Dudkin"
+      given-names: "Erika"
+      orcid: "https://orcid.org/0000-0002-9649-0029"
+   -
+      family-names: "Grein"
+      given-names: "Stephan"
+      orcid: "https://orcid.org/0000-0001-9524-6633"
+   -
+      family-names = "Hasenauer"
+      given-names: "Jan"
+      orcid: "https://orcid.org/0000-0002-4935-3312"
+title: "pyPESTO - Parameter EStimation TOolbox for python"
+url: "https://github.com/ICB-DCM/pyPESTO"
+doi: 10.5281/zenodo.2553546
+version: 0.2.7
+date-released: 2021-03-08
+cff-version: 1.2.0

pypesto/ensemble/constants.py

@@ -32,6 +32,7 @@
 STANDARD_DEVIATION = 'std'
 PERCENTILE = 'percentile'
 SUMMARY = 'summary'
+WEIGHTED_SIGMA = 'weighted_sigma'
 
 X_NAMES = 'x_names'
 NX = 'n_x'