Merge branch 'master' into i1276-pull-request-method-template

.github/workflows/copyright-test.yml

@@ -5,6 +5,8 @@ on:
     branches:
       - master
   pull_request:
+    # Run workflow when PR is changed, or when changed from draft to ready
+    types: [opened, synchronize, reopened, ready_for_review]
     branches:
       - '**'
 
@@ -14,13 +16,16 @@ jobs:
     name: Copyright
     runs-on: ubuntu-latest
 
+    # Skip job if it's a draft PR
+    if: github.event.pull_request.draft == false
+
     steps:
       - uses: actions/checkout@v1
 
-      - name: Set up Python 3.8
+      - name: Set up Python 3.9
         uses: actions/setup-python@v1
         with:
-          python-version: 3.8
+          python-version: 3.9
           architecture: x64
 
       - name: install pints

.github/workflows/coverage-test.yml

@@ -5,6 +5,8 @@ on:
     branches:
       - master
   pull_request:
+    # Run workflow when PR is changed, or when changed from draft to ready
+    types: [opened, synchronize, reopened, ready_for_review]
     branches:
       - '**'
 
@@ -14,20 +16,23 @@ jobs:
     name: Coverage
     runs-on: ubuntu-latest
 
+    # Skip job if it's a draft PR
+    if: github.event.pull_request.draft == false
+
     steps:
       - uses: actions/checkout@v1
 
-      - name: Set up Python 3.8
+      - name: Set up Python 3.9
         uses: actions/setup-python@v1
         with:
-          python-version: 3.8
+          python-version: 3.9
           architecture: x64
 
       - name: install pints
         run: |
           python --version
           python -m pip install --upgrade pip setuptools wheel
-          python -m pip install .
+          python -m pip install .[stan]
           python -m pip install coverage codecov
 
       - name: run coverage

.github/workflows/docs-test.yml

@@ -5,6 +5,8 @@ on:
     branches:
       - master
   pull_request:
+    # Run workflow when PR is changed, or when changed from draft to ready
+    types: [opened, synchronize, reopened, ready_for_review]
     branches:
       - '**'
 
@@ -14,13 +16,16 @@ jobs:
     name: Docs
     runs-on: ubuntu-latest
 
+    # Skip job if it's a draft PR
+    if: github.event.pull_request.draft == false
+
     steps:
       - uses: actions/checkout@v1
 
-      - name: Set up Python 3.8
+      - name: Set up Python 3.9
         uses: actions/setup-python@v1
         with:
-          python-version: 3.8
+          python-version: 3.9
           architecture: x64
 
       - name: install pints

.github/workflows/notebook-interfaces-test.yml

@@ -2,8 +2,8 @@ name: Notebooks (interfaces)
 
 on:
   schedule:
-    # 4am daily
-    - cron:  '0 4 * * *'
+    # 4am on monday (minute, hour, day, month, day-of-the-week)
+    - cron:  '0 4 * * 1'
 
 jobs:
 
@@ -14,20 +14,24 @@ jobs:
     steps:
       - uses: actions/checkout@v1
 
-      - name: Set up Python 3.8
+      - name: Set up Python 3.9
         uses: actions/setup-python@v1
         with:
-          python-version: 3.8
+          python-version: 3.9
           architecture: x64
 
-      - name: install pints
+      # We use e.g. install pints[stan] to install dependencies for interfaces
+      # that have some code in pints/interfaces. Dependencies that are not used
+      # by any code in the `pints` module are installed with pip (e.g.
+      # `pip install autograd`).
+      - name: install pints, interfaces, extra dependencies
         run: |
           python --version
           python -m pip install --upgrade pip setuptools wheel
-          python -m pip install .
-          python -m pip install .[dev]
+          python -m pip install .[dev,stan]
+          python -m pip install autograd
+          python -m pip install statsmodels
 
       - name: run jupyter notebooks
         run: |
-          python -m pip install statsmodels
           python run-tests.py --interfaces

.github/workflows/notebook-test.yml

@@ -2,8 +2,8 @@ name: Notebooks
 
 on:
   schedule:
-    # 4am daily
-    - cron:  '0 4 * * *'
+    # 4am on monday (minute, hour, day, month, day-of-the-week)
+    - cron:  '0 4 * * 1'
 
 jobs:
 
@@ -14,10 +14,10 @@ jobs:
     steps:
       - uses: actions/checkout@v1
 
-      - name: Set up Python 3.8
+      - name: Set up Python 3.9
         uses: actions/setup-python@v1
         with:
-          python-version: 3.8
+          python-version: 3.9
           architecture: x64
 
       - name: install pints

.github/workflows/style-test.yml

@@ -5,6 +5,8 @@ on:
     branches:
       - master
   pull_request:
+    # Run workflow when PR is changed, or when changed from draft to ready
+    types: [opened, synchronize, reopened, ready_for_review]
     branches:
       - '**'
 
@@ -14,13 +16,16 @@ jobs:
     name: Style
     runs-on: ubuntu-latest
 
+    # Skip job if it's a draft PR
+    if: github.event.pull_request.draft == false
+
     steps:
       - uses: actions/checkout@v1
 
-      - name: Set up Python 3.8
+      - name: Set up Python 3.9
         uses: actions/setup-python@v1
         with:
-          python-version: 3.8
+          python-version: 3.9
           architecture: x64
 
       - name: install pints

.github/workflows/unit-test-os-coverage.yml

@@ -5,6 +5,8 @@ on:
     branches:
       - master
   pull_request:
+    # Run workflow when PR is changed, or when changed from draft to ready
+    types: [opened, synchronize, reopened, ready_for_review]
     branches:
       - '**'
 
@@ -14,17 +16,20 @@ jobs:
     name: OS unit tests
     runs-on: ${{ matrix.os }}
 
+    # Skip job if it's a draft PR
+    if: github.event.pull_request.draft == false
+
     strategy:
       matrix:
-        os: [ubuntu-16.04, macos-latest, windows-latest]
+        os: [ubuntu-18.04, macos-latest, windows-latest]
 
     steps:
       - uses: actions/checkout@v1
 
-      - name: Set up Python 3.8
+      - name: Set up Python 3.9
         uses: actions/setup-python@v1
         with:
-          python-version: 3.8
+          python-version: 3.9
           architecture: x64
 
       - name: install pints

.github/workflows/unit-test-python-coverage.yml

@@ -5,6 +5,8 @@ on:
     branches:
       - master
   pull_request:
+    # Run workflow when PR is changed, or when changed from draft to ready
+    types: [opened, synchronize, reopened, ready_for_review]
     branches:
       - '**'
 
@@ -14,6 +16,9 @@ jobs:
     name: Python unit tests
     runs-on: ubuntu-latest
 
+    # Skip job if it's a draft PR
+    if: github.event.pull_request.draft == false
+
     strategy:
       matrix:
         python-version: [2.7, 3.5, 3.6, 3.7, 3.8, 3.9]
@@ -31,7 +36,7 @@ jobs:
         run: |
           python --version
           python -m pip install --upgrade pip setuptools wheel
-          python -m pip install .
+          python -m pip install .[stan]
 
       - name: run unit tests
         run: |

.github/workflows/upload-to-pypi.yml

@@ -14,10 +14,10 @@ jobs:
     steps:
       - uses: actions/checkout@v1
 
-      - name: Set up Python 3.8
+      - name: Set up Python 3.9
         uses: actions/setup-python@v1
         with:
-          python-version: 3.8
+          python-version: 3.9
           architecture: x64
 
       - name: install dependencies

CHANGELOG.md

@@ -17,12 +17,16 @@ All notable changes to this project will be documented in this file.
 - [#1112](https://github.com/pints-team/pints/pull/1112) A new `NoUTurnMCMC` sampler (NUTS) was added, along with a `DualAveragingAdaption` class to adaptively tune related Hamiltonian Monte Carlo methods.
 - [#1025](https://github.com/pints-team/pints/pull/1025) Added a stochastic logistic growth problem for use with ABC.
 ### Changed
+- [#1250](https://github.com/pints-team/pints/pull/1250) The returned values from `SingleChainMCMC.tell()` and `MultiChainMCMC.tell()` have been extended from current position `x` to `x, fx, accepted`, where `fx` is the current log likelihood and `accepted` is a bool indicating whether tell performed an acceptance step in this call.
 - [#1195](https://github.com/pints-team/pints/pull/1195) The installation instructions have been updated to reflect that PINTS in now pip-installable.
 - [#1191](https://github.com/pints-team/pints/pull/1191) Warnings are now emitted using `warnings.warn` rather than `logging.getLogger(..).warning`. This makes them show up like other warnings, and allows them to be suppressed with [filterwarnings](https://docs.python.org/3/library/warnings.html#warnings.filterwarnings).
 - [#1112](https://github.com/pints-team/pints/pull/1112) The new NUTS method is only supported on Python 3.3 and newer; a warning will be emitted when importing PINTS in older versions.
 - [#1112](https://github.com/pints-team/pints/pull/1112) The `pints.Logger` can now deal with `None` being logged in place of a proper value.
+- [#1355](https://github.com/pints-team/pints/pull/1112) When called with `parallel=True` the method `pints.evaluate()` will now limit the number of workers it uses to the number of tasks it needs to process.
 ### Deprecated
 - [#1201](https://github.com/pints-team/pints/pull/1201) The method `pints.rhat_all_params` was accidentally removed in 0.3.0, but is now back in deprecated form.
+### Removed
+- [#1250](https://github.com/pints-team/pints/pull/1250) The methods `SingleChainMCMC.current_log_pdf()` and `MultiChainMCMC.current_log_pdf()` have been removed.
 ### Fixed
 - [#1264](https://github.com/pints-team/pints/pull/1264) Fixed a bug relating to how NUTS handles nans when values outside the range of the priors are proposed.
 - [#1257](https://github.com/pints-team/pints/pull/1257) Fixed a bug in `GaussianLogPrior`, which meant the distribution could be instantiated with a non-positive standard deviation.

docs/source/conf.py

@@ -16,11 +16,7 @@
 # add these directories to sys.path here. If the directory is relative to the
 # documentation root, use os.path.abspath to make it absolute, like shown here.
 #
-# import os
-# import sys
-# sys.path.insert(0, os.path.abspath('.'))
 import pints
-import sphinx
 
 # -- General configuration ------------------------------------------------
 
@@ -40,17 +36,10 @@
 ]
 
 # Autodoc defaults
-if int(sphinx.__version__.split('.')[1]) < 8:
-    autodoc_default_flags = [
-        'members',
-        'inherited-members',
-        # 'show-inheritance',
-    ]
-else:
-    autodoc_default_options = {
-        'members': None,
-        'inherited-members': None,
-    }
+autodoc_default_options = {
+    'members': None,
+    'inherited-members': None,
+}
 
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ['_templates']
@@ -66,7 +55,7 @@
 
 # General information about the project.
 project = u'Pints'
-copyright = u'2019, Pints Authors'
+copyright = u'2021, Pints Authors'
 author = u'Pints Authors'
 
 # The version info for the project you're documenting, acts as replacement for

examples/README.md

@@ -94,7 +94,7 @@ relevant code.
 ## Statistical modelling
 - [Autoregressive moving average errors](./stats/autoregressive-moving-average-errors.ipynb)
 - [Cauchy sampling error](./stats/cauchy-sampling-error.ipynb)
-- [Constant and multiplicative Gaussian error](./stats/constant_and_multiplicative_gaussian_error.ipynb)
+- [Constant and multiplicative Gaussian error](./stats/constant-and-multiplicative-gaussian-error.ipynb)
 - [Integrated noise model](./stats/integrated-gaussian-log-likelihood.ipynb)
 - [Log priors](./stats/log-priors.ipynb)
 - [Multiplicative Gaussian noise](./stats/multiplicative-gaussian-errors.ipynb)
@@ -133,9 +133,10 @@ relevant code.
 - [Twisted Gaussian Banana](./toy/distribution-twisted-gaussian.ipynb)
 
 ## Interfaces
+- [Automatic differentiation using autograd](./interfaces/automatic-differentiation-using-autograd.ipynb)
+- [Stan](./interfaces/stan.ipynb)
 - [Statsmodels ARIMA](./interfaces/statsmodels-arima.ipynb)
 - [Statsmodels state space](.interfaces/statsmodels-state-space.ipynb)
 
 ## Miscellaneous
-- [Automatic differentiation using autograd](./toy/automatic-differentiation-using-autograd.ipynb)
 - [The example shown on the landing page](./sampling/readme-example.ipynb)