Merge pull request #229 from ICB-DCM/develop

Release 0.0.11
ICB-DCM · Mar 18, 2020 · 07fd9da · 07fd9da
2 parents dca6253 + c2b9838
commit 07fd9da
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Showing 34 changed files with 1,622 additions and 1,222 deletions.
diff --git a/.gitignore b/.gitignore
@@ -101,3 +101,4 @@ tmp/*
 amici_models/*
 *.txt
 test/doc/example/tmp/benchmark-models/
+test/amici_models/*
diff --git a/.travis.yml b/.travis.yml
@@ -1,7 +1,7 @@
 language: python
 python:
   - "3.6"
- 
+
 os:
   - linux
 dist:
@@ -26,6 +26,10 @@ install:
   - mkdir -p ~/bin/ && ln -s /usr/bin/swig3.0 ~/bin/swig && export PATH=~/bin/:$PATH
   - pip3 install --upgrade -r ./.travis_pip_reqs.txt
   - pip3 install .
+  - pip3 install https://github.com/petab-dev/petab/archive/develop.zip # REMOVE ME
+  - pip3 install -e git+https://github.com/icb-dcm/amici.git@develop#egg=amici\&subdirectory=python/sdist # REMOVE ME
+  - git clone --depth 1 https://github.com/petab-dev/petab_test_suite tmp/petab_test_suite
+  - pip3 install -e tmp/petab_test_suite
 
 # run tests
 script:

diff --git a/.travis_pip_reqs.txt b/.travis_pip_reqs.txt
@@ -9,8 +9,6 @@ flake8
 dlib
 pyswarm
 gitpython
-petab>=0.0.0a16
-amici>=0.10.13
 sphinx
 nbsphinx
 sphinx_rtd_theme
diff --git a/README.md b/README.md
@@ -19,7 +19,7 @@ pyPESTO features include:
 * Profile computation
 * Result visualization
 * Interface to [AMICI](https://github.com/ICB-DCM/AMICI/) for efficient simulation and sensitivity analysis of ordinary differential equation (ODE) models
-* Parameter estimation pipeline for systems biology problems specified in [SBML](http://sbml.org/) and [PEtab](https://github.com/ICB-DCM/PEtab)
+* Parameter estimation pipeline for systems biology problems specified in [SBML](http://sbml.org/) and [PEtab](https://github.com/PEtab-dev/PEtab)
 * Parameter estimation with qualitative data as described in [Schmiester et al. (2019)](https://www.biorxiv.org/content/10.1101/848648v1). This is currently implemented in the `feature_ordinal` branch.
 
 ## Quick install

diff --git a/doc/conf.py b/doc/conf.py
@@ -79,7 +79,7 @@
 # directories to ignore when looking for source files.
 # This patterns also effect to html_static_path and html_extra_path
 exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store',
-                    '**.ipynb_checkpoints']
+                    '**.ipynb_checkpoints', 'example/tmp']
 
 # The name of the Pygments (syntax highlighting) style to use.
 pygments_style = 'sphinx'

diff --git a/doc/example/boehm_JProteomeRes2014.ipynb b/doc/example/boehm_JProteomeRes2014.ipynb
diff --git a/doc/example/petab_import.ipynb b/doc/example/petab_import.ipynb
diff --git a/doc/example/rosenbrock.ipynb b/doc/example/rosenbrock.ipynb
diff --git a/doc/releasenotes.rst b/doc/releasenotes.rst
@@ -6,6 +6,18 @@ Release notes
 ..........
 
 
+0.0.11 (2020-03-17)
+-------------------
+
+* Rewrite AmiciObjective and PetabAmiciObjective simulation routine to directly use
+  amici.petab_objective routines (#209, #219, #225).
+* Implement petab test suite checks (#228).
+* Various error fixes, in particular regarding PEtab and visualization.
+* Improve trace structure.
+* Fix conversion between fval and chi2, fix FIM (all #223).
+
+
+
 0.0.10 (2019-12-04)
 -------------------
 

diff --git a/pypesto/objective/__init__.py b/pypesto/objective/__init__.py
@@ -7,10 +7,15 @@
 from .objective import Objective
 from .amici_objective import AmiciObjective
 from .aggregated import AggregatedObjective
-from .petab_import import PetabImporter
 from .options import ObjectiveOptions
 from .util import res_to_chi2, sres_to_schi2
 
+# PEtab is an optional dependency
+try:
+    from .petab_import import PetabImporter
+except ModuleNotFoundError:
+    PetabImporter = None
+
 __all__ = ["Objective",
            "ObjectiveOptions",
            "res_to_chi2",