Merge branch 'main' into first-examples

pints-team · Dec 18, 2024 · c6ce243 · c6ce243
2 parents 9ffbe94 + 5c646fd
commit c6ce243
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diff --git a/.github/workflows/copyright-test.yml b/.github/workflows/copyright-test.yml
@@ -20,12 +20,12 @@ jobs:
     if: github.event.pull_request.draft == false
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - name: Set up Python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
-            python-version: '3.11'
+            python-version: '3.13'
 
       - name: install pints
         run: |

diff --git a/.github/workflows/coverage-test.yml b/.github/workflows/coverage-test.yml
@@ -20,12 +20,13 @@ jobs:
     if: github.event.pull_request.draft == false
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - name: Set up Python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
-          python-version: '3.11'
+          # Testing on version that Stan currently supports
+          python-version: '3.12'
 
       - name: install pints
         run: |

diff --git a/.github/workflows/docs-test.yml b/.github/workflows/docs-test.yml
@@ -20,12 +20,12 @@ jobs:
     if: github.event.pull_request.draft == false
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - name: Set up Python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
-          python-version: '3.11'
+          python-version: '3.13'
 
       - name: install pints
         run: |

diff --git a/.github/workflows/notebook-interfaces-test.yml b/.github/workflows/notebook-interfaces-test.yml
@@ -12,12 +12,12 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - name: Set up Python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
-          python-version: '3.11'
+          python-version: '3.13'
 
       # We use e.g. install pints[stan] to install dependencies for interfaces
       # that have some code in pints/interfaces. Dependencies that are not used

diff --git a/.github/workflows/notebook-test.yml b/.github/workflows/notebook-test.yml
@@ -12,12 +12,12 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - name: Set up Python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
-          python-version: '3.11'
+          python-version: '3.13'
 
       - name: install pints
         run: |

diff --git a/.github/workflows/style-test.yml b/.github/workflows/style-test.yml
@@ -20,10 +20,13 @@ jobs:
     if: github.event.pull_request.draft == false
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - name: Set up Python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.13'
+
 
       - name: install pints
         run: |

diff --git a/.github/workflows/unit-test-os-coverage.yml b/.github/workflows/unit-test-os-coverage.yml
@@ -25,12 +25,12 @@ jobs:
         # Note: Ubuntu 22 is checked by other tests
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - name: Set up Python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
-          python-version: '3.11'
+          python-version: '3.13'
 
       - name: install pints
         run: |

diff --git a/.github/workflows/unit-test-python-coverage.yml b/.github/workflows/unit-test-python-coverage.yml
@@ -21,14 +21,14 @@ jobs:
 
     strategy:
       matrix:
-        python-version: ['3.7', '3.8', '3.9', '3.10']
+        python-version: ['3.8', '3.9', '3.10', '3.11', '3.12']
         # Note: Latest version is tested by coverage test and os tests
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
           architecture: x64
@@ -40,7 +40,7 @@ jobs:
           python -m pip install .
 
       - name: install stan
-        if: matrix.python-version != '3.6'
+        if: ${{ matrix.python-version >= '3.10' && matrix.python-version < '3.13' }}
         run : python -m pip install .[stan]
 
       - name: run unit tests

diff --git a/.github/workflows/upload-to-pypi.yml b/.github/workflows/upload-to-pypi.yml
@@ -12,10 +12,10 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - name: Set up Python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: '3.11'
 

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -5,10 +5,13 @@ All notable changes to this project will be documented in this file.
 ## Unreleased
 
 ### Added
+- [#1527](https://github.com/pints-team/pints/pull/1527) Added a `ComposedBoundaries` class that lets you compose multiple `Boundaries` classes into a higher dimensional one.
+- [#1500](https://github.com/pints-team/pints/pull/1500) Added a `CensoredGaussianLogLikelihood` class that calculates the censored Gaussian log-likelihood.
 - [#1505](https://github.com/pints-team/pints/pull/1505) Added notes to `ErrorMeasure` and `LogPDF` to say parameters must be real and continuous.
 - [#1499](https://github.com/pints-team/pints/pull/1499) Added a log-uniform prior class.
 ### Changed
 - [#1503](https://github.com/pints-team/pints/pull/1503) Stopped showing time units in controller logs, because the units change depending on the output type (see #1467).
+- [#1699](https://github.com/pints-team/pints/pull/1699) PINTS is no longer tested on Python 3.7. Testing for Python 3.12 and 3.13 has been added.
 ### Deprecated
 ### Removed
 ### Fixed

diff --git a/docs/source/boundaries.rst b/docs/source/boundaries.rst
@@ -12,12 +12,15 @@ implementation of the :class:`Boundaries` interface.
 Overview:
 
 - :class:`Boundaries`
+- :class:`ComposedBoundaries`
 - :class:`LogPDFBoundaries`
 - :class:`RectangularBoundaries`
 
 
 .. autoclass:: Boundaries
 
+.. autoclass:: ComposedBoundaries
+
 .. autoclass:: LogPDFBoundaries
 
 .. autoclass:: RectangularBoundaries
diff --git a/docs/source/log_likelihoods.rst b/docs/source/log_likelihoods.rst
@@ -19,6 +19,7 @@ Overview:
 - :class:`AR1LogLikelihood`
 - :class:`ARMA11LogLikelihood`
 - :class:`CauchyLogLikelihood`
+- :class:`CensoredGaussianLogLikelihood`
 - :class:`ConstantAndMultiplicativeGaussianLogLikelihood`
 - :class:`GaussianIntegratedLogUniformLogLikelihood`
 - :class:`GaussianIntegratedUniformLogLikelihood`
@@ -38,6 +39,8 @@ Overview:
 
 .. autoclass:: CauchyLogLikelihood
 
+.. autoclass:: CensoredGaussianLogLikelihood
+
 .. autoclass:: ConstantAndMultiplicativeGaussianLogLikelihood
 
 .. autoclass:: GaussianIntegratedLogUniformLogLikelihood

diff --git a/examples/README.md b/examples/README.md
@@ -150,3 +150,4 @@ relevant code.
 
 ## Miscellaneous
 - [The example shown on the landing page](./sampling/readme-example.ipynb)
+- [Rt estimation Renewal Equation model](./miscellaneous/model-rt-estimation-renewal-equation.ipynb)
Original file line number	Diff line number	Diff line change
Expand Up		@@ -150,3 +150,4 @@ relevant code.

		## Miscellaneous
		- [The example shown on the landing page](./sampling/readme-example.ipynb)
		- [Rt estimation Renewal Equation model](./miscellaneous/model-rt-estimation-renewal-equation.ipynb)