Merge pull request #652 from ICB-DCM/develop

New Release v0.2.5

.github/ISSUE_TEMPLATE/blank.md

@@ -0,0 +1,8 @@
+---
+name: Blank issue
+about: A blank issue template
+title: ''
+labels: ''
+assignees: ''
+
+---

.github/ISSUE_TEMPLATE/bug-report.md

@@ -0,0 +1,22 @@
+---
+name: Bug report
+about: Create a report to help us improve
+title: ''
+labels: bug
+assignees: ''
+
+---
+
+**Bug description**
+[A clear and concise description of what the bug is.]
+
+**Expected behavior**
+[A clear and concise description of what you expected to happen.]
+
+**To reproduce**
+[A minimal example to reproduce this error, ideally a simple python script.]
+
+**Environment**
+- Operating system: [e.g. Ubuntu 20.04, macOS 11.2.1]
+- `pypesto` version: [via `pip show pypesto`]
+- Python version: [e.g. `python3 -V`]

.github/ISSUE_TEMPLATE/feature-request.md

@@ -0,0 +1,14 @@
+---
+name: Feature request
+about: Suggest an idea for this project
+title: ''
+labels: enhancement
+assignees: ''
+
+---
+
+**Feature description**
+[A clear and concise description of what you would like to have.]
+
+**Motivation/Application**
+[Why is this feature useful?]

.github/workflows/ci.yml

@@ -13,7 +13,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [3.8]
+        python-version: [3.9]
 
     steps:
     - name: Check out repository
@@ -47,7 +47,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [3.8]
+        python-version: [3.9]
 
     steps:
     - name: Check out repository
@@ -81,7 +81,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [3.8]
+        python-version: [3.9]
 
     steps:
     - name: Check out repository
@@ -177,7 +177,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [3.8]
+        python-version: [3.9]
 
     steps:
     - name: Check out repository
@@ -205,7 +205,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [3.8]
+        python-version: [3.9]
 
     steps:
     - name: Check out repository

.github/workflows/install_deps.sh

@@ -36,9 +36,9 @@ for par in "$@"; do
 
     pysb)
       # bionetgen
-      wget -q -O bionetgen.tar.gz \
-        https://bintray.com/jczech/bionetgen/download_file?file_path=BioNetGen-2.3.2-linux.tar.gz
-      tar -xzf bionetgen.tar.gz
+      wget -q -O bionetgen.tar \
+        https://github.com/RuleWorld/bionetgen/releases/download/BioNetGen-2.5.2/BioNetGen-2.5.2-linux.tgz
+      tar -xf bionetgen.tar
     ;;
 
     mpi)

.gitignore

@@ -109,5 +109,5 @@ test/doc/example/tmp/benchmark-models/
 test/amici_models/*
 *.hdf5
 *.dat
-/BioNetGen-2.3.2
-/bionetgen.tar.gz
+/BioNetGen-*.*.*
+/bionetgen.tar

CHANGELOG.rst

@@ -6,41 +6,79 @@ Release notes
 ..........
 
 
+0.2.5 (2021-05-04)
+------------------
+
+* Objectives:
+    * New Aesara objectve (#623, #629, #635)
+
+* Sampling:
+    * New Emcee sampler (#606)
+    * Fix compatibility to new Theano version (#650)
+
+* Storage:
+    * Improve hdf5 storage documentation (#612)
+    * Hdf5 history for MultiProcessEngine (#650)
+    * Minor fixes (#637, #638, #645, #649)
+
+* Visualization:
+    * Fix bounds of parameter plots (#601)
+    * Fix waterfall plots with multiple results (#611)
+
+* CI:
+    * Move CI tests on GitHub Actions to python 3.9 (#598)
+    * Add issue template (#604)
+    * Update BionetGen Link (#630)
+    * Introduce project.toml (#634)
+
+* General:
+    * Introduce progress bar for optimization, profiles and ensembles (#641)
+    * Extend gradient checking functionality (#644)
+
+* Minor fixes:
+    * Fix installation of ipopt (#599)
+    * Fix Zenodo link (#601)
+    * Fix duplicates in documentation (#603)
+    * Fix least squares optimizers (#617 #631 #632)
+    * Fix trust region options (#616)
+    * Fix slicing for new AMICI release (#621)
+    * Refactor and document latin hypercube sampling (#647)
+    * Fix missing SBML name in PEtab import (#648)
+
+
 0.2.4 (2021-03-12)
 ------------------
 
 * Ensembles/Sampling:
-
-  * General ensemble analysis, visualization, storage (#557, #565, #568)
-  * Calculate and plot MCMC parameter and prediction CIs via ensemble
-    definition, parallelize ensemble predictions (#490)
+    * General ensemble analysis, visualization, storage (#557, #565, #568)
+    * Calculate and plot MCMC parameter and prediction CIs via ensemble
+      definition, parallelize ensemble predictions (#490)
 
 * Optimization:
-  * New optimizer: SciPy Differential Evolution (#543)
-  * Set fides default to hybrid (#578)
+    * New optimizer: SciPy Differential Evolution (#543)
+    * Set fides default to hybrid (#578)
 
 * AMICI:
-
-  * Make `guess_steadystate` less restrictive (#561) and have a more
-    intuitive default behavior (#562, #582)
-  * Customize time points (#490)
+    * Make `guess_steadystate` less restrictive (#561) and have a more
+      intuitive default behavior (#562, #582)
+    * Customize time points (#490)
 
 * Storage:
-  * Save HDF5 history with SingleCoreEngine (#564)
-  * Add read/write function for whole results (#589)
+    * Save HDF5 history with SingleCoreEngine (#564)
+    * Add read/write function for whole results (#589)
 
 * Engines:
-  * MPI based distributed parallelization (#542)
+    * MPI based distributed parallelization (#542)
 
 * Visualization:
-  * Speed up waterfall plots by resizing scales only once (#577)
-  * Change waterfall default offset to 1 - minimum (#593)
+    * Speed up waterfall plots by resizing scales only once (#577)
+    * Change waterfall default offset to 1 - minimum (#593)
 
 * CI:
-  * Move GHA CI tests to pull request level for better cooperability (#574)
-  * Streamline test environments using tox and pre-commit hooks (#579)
-  * Test profile and sampling storage (#585)
-  * Update for Ubuntu 20.04, add rerun on failure (#587)
+    * Move GHA CI tests to pull request level for better cooperability (#574)
+    * Streamline test environments using tox and pre-commit hooks (#579)
+    * Test profile and sampling storage (#585)
+    * Update for Ubuntu 20.04, add rerun on failure (#587)
 
 * Minor fixes (release notes #558, nlop tests #559, close files #495,
   visualization #554, deployment #560, flakiness #570,

README.md

@@ -10,7 +10,7 @@ parameter estimation.
 [![Coverage](https://codecov.io/gh/ICB-DCM/pyPESTO/branch/master/graph/badge.svg)](https://codecov.io/gh/ICB-DCM/pyPESTO)
 [![Quality](https://api.codacy.com/project/badge/Grade/134432ddad0e464b8494587ff370f661)](https://www.codacy.com/app/dweindl/pyPESTO?utm_source=github.com&utm_medium=referral&utm_content=ICB-DCM/pyPESTO&utm_campaign=Badge_Grade)
 [![Documentation](https://readthedocs.org/projects/pypesto/badge/?version=latest)](https://pypesto.readthedocs.io)
-[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.2600850.svg)](https://zenodo.org/record/2600850#.XVuwkHduJfF)
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.4614930.svg)](https://doi.org/10.5281/zenodo.4614930)
 
 ## Feature overview
 

doc/README.md

@@ -1,42 +1,3 @@
 # Documentation
 
-The `doc/` folder contains the files for building the pyPESTO documentation.
-
-
-## Requirements
-
-The documentation is based on sphinx. Install via
-
-```
-pip3 install sphinx
-```
-
-Furthermore, the files specified in `../.rtd_pip_reqs.txt` and `../.rtd_apt_reqs.txt` are required. Install via
-
-```
-pip3 install --upgrade -r ../.rtd_pip_reqs.txt
-```
-
-and
-
-```
-cat ../.rtd_apt_reqs.txt | xargs sudo apt install -y
-```
-
-respectively.
-
-
-## Build the documentation
-
-The documentation can be built in different formats, e.g. in html via
-
-```
-make html
-```
-
-The built documentation can then be found locally in the `_build`
-sub-directory.
-
-The documentation is built and published automatically on readthedocs.io
-every time the master branch on github.com is changed. It is recommended
-to compile and check the documentation manually beforehand.
+Find instructions on how to edit and build documentation in [contribute.rst](contribute.rst).

doc/api.rst

@@ -0,0 +1,23 @@
+API reference
+=============
+
+.. automodule:: pypesto
+
+.. toctree::
+   :maxdepth: 2
+   :caption: API reference
+
+   api_objective
+   api_problem
+   api_predict
+   api_petab
+   api_optimize
+   api_profile
+   api_sample
+   api_result
+   api_visualize
+   api_engine
+   api_startpoint
+   api_store
+   api_logging
+   api_ensemble

doc/authors.rst

@@ -14,7 +14,7 @@ with major contributions by:
 - Dantong Wang
 - Daniel Weindl
 - Polina Lakrisenko
-- Elba Raimundez
+- Elba Raimúndez
 - Leonard Schmiester
 - Dilan Pathirana
 - Paul Jonas Jost

doc/conf.py

@@ -51,6 +51,7 @@
     'special-members': '__init__, __call__',
     'imported-members': True,
     'show-inheritance': True,
+    'autodoc_inherit_docstrings': True,
 }
 
 # links for intersphinx
@@ -101,7 +102,7 @@
 # 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', 'example/tmp']
+                    '**.ipynb_checkpoints', 'example/tmp', 'README.md']
 
 # The name of the Pygments (syntax highlighting) style to use.
 pygments_style = 'sphinx'