Merge pull request #495 from ICB-DCM/develop

Release 0.11.3

Author: yannikschaelte

CHANGELOG.rst

@@ -8,6 +8,15 @@ Release Notes
 ...........
 
 
+0.11.3 (2021-10-16)
+-------------------
+
+* Update to amici 0.11.19 for scaled residual support (#491)
+* Add links for online execution of notebooks on Google Colab and nbviewer
+  (#492)
+* Tests: Fix early stopping test for first generation (#494)
+
+
 0.11.2 (2021-10-07)
 -------------------
 

doc/_static/colab-badge.svg

@@ -140,6 +140,19 @@
 # If true, `todo` and `todoList` produce output, else they produce nothing.
 todo_include_todos = True
 
+# Add notebooks prolog to Google Colab and nbviewer
+nbsphinx_prolog = r"""
+{% set docname = 'github/icb-dcm/pyabc/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 ----------------------------------------------
 
@@ -175,7 +188,7 @@
 # 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']
 
 # Add any extra paths that contain custom files (such as robots.txt or
 # .htaccess) here, relative to this directory. These files are copied

doc/_static/nbviewer-badge.svg

@@ -3,7 +3,21 @@
 Examples
 ========
 
-The following examples should help to get a better idea of how to use pyABC.
+We provide a collection of example notebooks to get a better idea of how to
+use pyABC, 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.
+To run the notebooks online, at least an installation of pyABC is required,
+which can be performed by
+
+.. code:: sh
+
+   # install if not done yet
+   !pip install pyabc --quiet
+
+Potentially, further dependencies may be required.
 
 .. toctree::
    :maxdepth: 1

doc/conf.py

@@ -75,16 +75,33 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 1,
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# install if not done yet\n",
+    "!pip install pyabc --quiet"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
    "metadata": {},
    "outputs": [],
    "source": [
     "import numpy as np\n",
     "import matplotlib.pyplot as pyplot\n",
     "import pyabc\n",
     "import logging\n",
-    "import tempfile\n",
-    "\n",
+    "import tempfile"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 1,
+   "metadata": {},
+   "outputs": [],
+   "source": [
     "pyabc.settings.set_figure_params(\"pyabc\")  # for beautified plots\n",
     "\n",
     "\n",

doc/examples.rst

@@ -28,6 +28,16 @@
     "We want to combine different distance metrics operating on subsets of the data to one distance value. As a toy model, assume we want to combine a Laplace and a Normal distance."
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# install if not done yet\n",
+    "!pip install pyabc --quiet"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": 1,

doc/examples/adaptive_distances.ipynb

@@ -46,6 +46,16 @@
     "To simulate these models, we define a simple Gillespie simulator:"
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# install if not done yet\n",
+    "!pip install pyabc --quiet"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": 1,

doc/examples/aggregated_distances.ipynb

@@ -54,6 +54,16 @@
     "We will show how to estimate $\\Theta_1$ and $\\Theta_2$ using pyABC."
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# install if not done yet\n",
+    "!pip install pyabc --quiet"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": 1,

doc/examples/chemical_reaction.ipynb

@@ -16,6 +16,16 @@
     "Let’s start to import the necessary classes. We also set up matplotlib and we’re going to use numpy and pandas as well."
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# install if not done yet\n",
+    "!pip install pyabc --quiet"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": 1,

doc/examples/conversion_reaction.ipynb

@@ -29,6 +29,16 @@
     "To efficiently and correctly deal with discrete parameters, pyABC also implements discrete transitions as classes derived from `pyabc.transition.DiscreteTransition`. Let us show an example:"
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# install if not done yet\n",
+    "!pip install pyabc --quiet"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": 1,

doc/examples/data_plots.ipynb

@@ -47,6 +47,16 @@
     "Let's start with the necessary imports:"
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# install if not done yet\n",
+    "!pip install pyabc --quiet"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": 1,