Merge pull request #761 from ICB-DCM/develop

Release 0.2.9

.flake8

@@ -6,6 +6,14 @@
 
 per-file-ignores =
     # Imported but unused
-    */__init__.py:F401
+    */__init__.py:F401,D400,D205
     # Print and asserts
-    test/*:T001,S101
+    test/*:T001,S101,D
+    # Ignore errors in module docstring
+    pypesto/logging.py:D400,D205,D107
+    pypesto/problem.py:D400,D205,D107
+    pypesto/result.py:D400,D205,D107
+    pypesto/version.py:D
+    # ignore D100='Missing docstring in public module',
+    # D105='Missing docstring in magic method' and D107='Missing docstring in __init__'.
+    *:D100,D105,D107

.github/workflows/ci.yml

@@ -16,7 +16,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [3.9]
+        python-version: [3.7]
 
     steps:
     - name: Check out repository
@@ -50,7 +50,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [3.9]
+        python-version: [3.7]
 
     steps:
     - name: Check out repository
@@ -84,7 +84,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [3.9]
+        python-version: [3.7]
 
     steps:
     - name: Check out repository
@@ -180,7 +180,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [3.9]
+        python-version: [3.7]
 
     steps:
     - name: Check out repository
@@ -208,7 +208,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [3.9]
+        python-version: [3.7]
 
     steps:
     - name: Check out repository

CHANGELOG.rst

@@ -6,6 +6,21 @@ Release notes
 ..........
 
 
+0.2.9 (2021-11-03)
+------------------
+
+* General:
+    * Automatically save results (#749)
+    * Update all docstrings to numpy standard (#750)
+    * Add Google Colab and nbviewer links to all notebooks for online
+      execution (#758)
+    * Option to not save hess and sres in result (#760)
+    * Set minimum supported python version to 3.7 (#755)
+
+* Visualization:
+    * Parameterize start index in optimized model fit (#744)
+
+
 0.2.8 (2021-10-28)
 ------------------
 

CITATION.cff

@@ -64,7 +64,7 @@ authors:
       given-names: "Stephan"
       orcid: "https://orcid.org/0000-0001-9524-6633"
    -
-      family-names = "Hasenauer"
+      family-names: "Hasenauer"
       given-names: "Jan"
       orcid: "https://orcid.org/0000-0002-4935-3312"
 title: "pyPESTO - Parameter EStimation TOolbox for python"

README.md

@@ -8,7 +8,6 @@ parameter estimation.
 [![PyPI](https://badge.fury.io/py/pypesto.svg)](https://badge.fury.io/py/pypesto)
 [![CI](https://github.com/ICB-DCM/pyPESTO/workflows/CI/badge.svg)](https://github.com/ICB-DCM/pyPESTO/actions)
 [![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.2553546.svg)](https://doi.org/10.5281/zenodo.2553546)
 

doc/conf.py

@@ -110,6 +110,19 @@
 # If true, `todo` and `todoList` produce output, else they produce nothing.
 todo_include_todos = False
 
+# Add notebooks prolog to Google Colab and nbviewer
+nbsphinx_prolog = r"""
+{% set docname = 'github/icb-dcm/pypesto/blob/main/doc/' + env.doc2path(env.docname, base=None) %}
+.. raw:: html
+
+    <div class="note">
+      <a href="https://colab.research.google.com/{{ docname|e }}" target="_blank">
+      <img src="../_static/colab-badge.svg" alt="Open in Colab"/></a>
+      <a href="https://nbviewer.jupyter.org/{{ docname|e }}" target="_blank">
+      <img src="../_static/nbviewer-badge.svg" alt="Open in nbviewer"/></a>
+    </div>
+
+"""
 
 # -- Options for HTML output ----------------------------------------------
 
@@ -127,7 +140,9 @@
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,
 # so a file named "default.css" will overwrite the builtin "default.css".
-# html_static_path = ['_static']
+html_static_path = ['_static']
+
+# Favicon
 html_favicon = "logo/logo_favicon.png"
 
 # Custom sidebar templates, must be a dictionary that maps document names

doc/example.rst

@@ -1,7 +1,23 @@
 Examples
 ========
 
-The following examples cover typical use cases and should help get a better idea of how to use this package:
+We provide a collection of example notebooks to get a better idea of how to
+use pyPESTO, and illustrate core features.
+
+The notebooks can be run locally with an installation of jupyter
+(``pip install jupyter``), or online on Google Colab or nbviewer, following
+the links at the top of each notebook.
+At least an installation of pyPESTO is required, which can be performed by
+
+.. code:: sh
+
+   # install if not done yet
+   !pip install pypesto --quiet
+
+Potentially, further dependencies may be required.
+
+The following examples cover typical use cases and should help get a better
+idea of how to use this package:
 
 .. toctree::
    :maxdepth: 1

doc/example/amici_import.ipynb

@@ -9,6 +9,17 @@
     "This is an example using the \"boehm_ProteomeRes2014.xml\" model to demonstrate and test SBML import and AMICI Python interface."
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# install if not done yet\n",
+    "# !apt install libatlas-base-dev swig\n",
+    "# %pip install pypesto[amici] --quiet"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": 1,
@@ -566,7 +577,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -580,7 +591,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.8.8"
+   "version": "3.9.7"
   }
  },
  "nbformat": 4,