Merge pull request #389 from elfi-dev/dev

Release v0.8.1

.github/workflows/pytest.yml

@@ -0,0 +1,42 @@
+# This workflow will install Python dependencies, run tests and lint with a variety of Python versions
+# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
+
+name: pytest
+
+on:
+  pull_request:
+  push:
+    branches: [main]
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: [3.6, 3.7, 3.8]
+
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v2
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        python -m pip install flake8 pytest
+        python -m pip install numpy
+        if [ -f requirements-dev.txt ]; then pip install -r requirements-dev.txt; fi        
+        python -m pip install -e .
+
+    - name: Lint with flake8
+      run: |
+        # stop the build if there are Python syntax errors or undefined names
+        flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
+        # exit-zero treats all errors as warnings
+        flake8 . --count --exit-zero --max-complexity=10 --max-line-length=99 --statistics
+    - name: Test with pytest
+      run: |
+        make test

.gitignore

@@ -30,6 +30,7 @@ var/
 
 # Images
 *.png
+!elfi_logo_text_nobg.png
 *.svg
 *.jpg
 *.jpeg

.readthedocs.yml

@@ -19,6 +19,6 @@ formats:
 
 # Optionally set the version of Python and requirements required to build your docs
 python:
-  version: 3.5
+  version: 3.6
   install:
     - requirements: requirements.txt

CHANGELOG.rst

@@ -1,5 +1,20 @@
 Changelog
 =========
+
+0.8.1 (2021-10-12)
+------------------
+- Relax tightly pinned dependency on a version of dask[distributed]
+- Change lotka-volterra priors to follow the given reference
+- Fix README.md badges
+- Fix a few small issues with CONTRIBUTING.rst
+- Add Github Actions based CI workflow
+- Add the skeleton of TestBench-functionality for comparing methods
+- Fix a bug of plot_traces() not working if there is only 1 chain 
+- Fix histograms in pair_plot diagonals and improve visual outlook
+- Improve axes creation and visual outlook
+- Fix a bug where precomputed evidence size was not taken into account when reporting BOLFI-results
+- Fix a bug where observable nodes were not colored gray when using `elfi.draw`
+- Add `plot_predicted_node_pairs` in visualization.py.
 
 0.8.0 (2021-03-29)
 ------------------

CONTRIBUTING.rst

@@ -63,13 +63,16 @@ Get Started!
 Ready to contribute? Here's how to set up `ELFI` for local development.
 
 1. Fork the `elfi` repo on GitHub.
-2. Clone your fork locally::
+2. Clone your fork locally and add the base repository as a remote::
 
-    $ git clone [email protected]:your_name_here/elfi.git
+    $ git clone [email protected]:your_github_handle_here/elfi.git
+    $ cd elfi
+    $ git remote add upstream [email protected]:elfi-dev/elfi.git
 
 3. Make sure you have `Python 3 <https://www.python.org/>`_ and
    `Anaconda Distribution <https://www.anaconda.com/>`_ installed on your
-   machine. Check your conda and Python versions::
+   machine. Check your conda and Python versions. Currently supported Python versions
+   are 3.6, 3.7, 3.8::
 
    $ conda -V
    $ python -V
@@ -106,9 +109,15 @@ Ready to contribute? Here's how to set up `ELFI` for local development.
 
     $ git add .
     $ git commit -m "Your detailed description of your changes."
+
+9. After committing your changes, you may sync with the base repository if there has been changes::
+    $ git fetch upstream
+    $ git rebase upstream/dev
+
+10. Push the changes::
     $ git push origin name-of-your-bugfix-or-feature
 
-9. Submit a pull request through the GitHub website.
+11. Submit a pull request through the GitHub website.
 
 Style Guidelines
 ----------------
@@ -123,12 +132,12 @@ Pull Request Guidelines
 Before you submit a pull request, check that it meets these guidelines:
 
 1. The pull request should include tests that will be run automatically using
-   Travis-CI.
+   Github Actions.
 2. If the pull request adds functionality, the docs should be updated. Put
    your new functionality into a function with a docstring, and add the
-   feature to the list in README.rst.
-3. The pull request should work for Python 3.6 and later. Check
-   https://travis-ci.org/elfi-dev/elfi/pull_requests
+   feature to the list in README.md.
+3. The pull request should work for Python 3.6, or later. Check
+   https://github.com/elfi-dev/elfi/actions/workflows/pytest.yml
    and make sure that the tests pass for all supported Python versions.
 
 Tips

README.md

@@ -1,10 +1,11 @@
-**Version 0.8.0 released!** See the [CHANGELOG](CHANGELOG.rst) and [notebooks](https://github.com/elfi-dev/notebooks).
+**Version 0.8.1 released!** See the [CHANGELOG](CHANGELOG.rst) and [notebooks](https://github.com/elfi-dev/notebooks).
+
+<img src="https://raw.githubusercontent.com/elfi-dev/elfi/dev/docs/logos/elfi_logo_text_nobg.png" width="200" />
 
 ELFI - Engine for Likelihood-Free Inference
 ===========================================
 
-[![Build Status](https://travis-ci.org/elfi-dev/elfi.svg?branch=master)](https://travis-ci.org/elfi-dev/elfi)
-[![Code Health](https://landscape.io/github/elfi-dev/elfi/dev/landscape.svg?style=flat)](https://landscape.io/github/elfi-dev/elfi/dev)
+[![Build Status](https://github.com/elfi-dev/elfi/actions/workflows/pytest.yml/badge.svg)](https://github.com/elfi-devs/elfi/actions)
 [![Documentation Status](https://readthedocs.org/projects/elfi/badge/?version=latest)](http://elfi.readthedocs.io/en/latest/?badge=latest)
 [![Gitter](https://badges.gitter.im/elfi-dev/elfi.svg)](https://gitter.im/elfi-dev/elfi?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge)
 [![DOI](https://zenodo.org/badge/69855441.svg)](https://zenodo.org/badge/latestdoi/69855441)

elfi/__init__.py

@@ -20,12 +20,14 @@
 from elfi.model.elfi_model import *
 from elfi.model.extensions import ScipyLikeDistribution as Distribution
 from elfi.store import OutputPool, ArrayPool
+from elfi.testbench.testbench import Testbench, TestbenchMethod
 from elfi.visualization.visualization import nx_draw as draw
 from elfi.visualization.visualization import plot_params_vs_node
+from elfi.visualization.visualization import plot_predicted_summaries
 from elfi.methods.bo.gpy_regression import GPyRegression
 
 __author__ = 'ELFI authors'
 __email__ = '[email protected]'
 
 # make sure __version_ is on the last non-empty line (read by setup.py)
-__version__ = '0.8.0'
+__version__ = '0.8.1'

elfi/examples/lotka_volterra.py

@@ -170,9 +170,9 @@ def get_model(n_obs=50, true_params=None, seed_obs=None, **kwargs):
     priors = []
     sumstats = []
 
-    priors.append(elfi.Prior(ExpUniform, -2, 0, model=m, name='r1'))
-    priors.append(elfi.Prior(ExpUniform, -5, -2.5, model=m, name='r2'))  # easily kills populations
-    priors.append(elfi.Prior(ExpUniform, -2, 0, model=m, name='r3'))
+    priors.append(elfi.Prior(ExpUniform, -6., 2., model=m, name='r1'))
+    priors.append(elfi.Prior(ExpUniform, -6., 2., model=m, name='r2'))  # easily kills populations
+    priors.append(elfi.Prior(ExpUniform, -6., 2., model=m, name='r3'))
     priors.append(elfi.Prior('poisson', 50, model=m, name='prey0'))
     priors.append(elfi.Prior('poisson', 100, model=m, name='predator0'))
     priors.append(elfi.Prior(ExpUniform, np.log(0.5), np.log(50), model=m, name='sigma'))

elfi/methods/inference/bolfi.py

@@ -587,5 +587,5 @@ def sample(self,
             parameter_names=self.parameter_names,
             warmup=warmup,
             threshold=float(posterior.threshold),
-            n_sim=self.state['n_sim'],
+            n_sim=self.state['n_evidence'],
             seed=self.seed)

elfi/methods/mcmc.py

@@ -127,7 +127,7 @@ def nuts(n_iter,
     No-U-Turn Sampler, an improved version of the Hamiltonian (Markov Chain) Monte Carlo sampler.
 
     Based on Algorithm 6 in
-    Hoffman & Gelman, depthMLR 15, 1351-1381, 2014.
+    Hoffman & Gelman, JMLR 15, 1593-1623, 2014.
 
     Parameters
     ----------