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Merge branch 'main' into 1691-pints-logpdf-storage
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MichaelClerx authored Dec 18, 2024
2 parents 3d16d1a + 89fd597 commit 61c47df
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2 changes: 1 addition & 1 deletion .github/workflows/copyright-test.yml
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Expand Up @@ -25,7 +25,7 @@ jobs:
- name: Set up Python
uses: actions/setup-python@v5
with:
python-version: '3.11'
python-version: '3.13'

- name: install pints
run: |
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3 changes: 2 additions & 1 deletion .github/workflows/coverage-test.yml
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Expand Up @@ -25,7 +25,8 @@ jobs:
- name: Set up Python
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: |
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2 changes: 1 addition & 1 deletion .github/workflows/docs-test.yml
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Expand Up @@ -25,7 +25,7 @@ jobs:
- name: Set up Python
uses: actions/setup-python@v5
with:
python-version: '3.11'
python-version: '3.13'

- name: install pints
run: |
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2 changes: 1 addition & 1 deletion .github/workflows/notebook-interfaces-test.yml
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Expand Up @@ -17,7 +17,7 @@ jobs:
- name: Set up Python
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
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2 changes: 1 addition & 1 deletion .github/workflows/notebook-test.yml
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Expand Up @@ -17,7 +17,7 @@ jobs:
- name: Set up Python
uses: actions/setup-python@v5
with:
python-version: '3.11'
python-version: '3.13'

- name: install pints
run: |
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2 changes: 1 addition & 1 deletion .github/workflows/style-test.yml
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Expand Up @@ -25,7 +25,7 @@ jobs:
- name: Set up Python
uses: actions/setup-python@v5
with:
python-version: '3.11'
python-version: '3.13'


- name: install pints
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2 changes: 1 addition & 1 deletion .github/workflows/unit-test-os-coverage.yml
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Expand Up @@ -30,7 +30,7 @@ jobs:
- name: Set up Python
uses: actions/setup-python@v5
with:
python-version: '3.11'
python-version: '3.13'

- name: install pints
run: |
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4 changes: 2 additions & 2 deletions .github/workflows/unit-test-python-coverage.yml
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Expand Up @@ -21,7 +21,7 @@ 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:
Expand All @@ -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
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3 changes: 3 additions & 0 deletions CHANGELOG.md
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Expand Up @@ -10,14 +10,17 @@ All notable changes to this project will be documented in this file.
- [#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
- [#1698](https://github.com/pints-team/pints/pull/1698) CMA-ES now raises a more informative exception when an unsupported 1-d optimisation is attempted.
- [#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
- [#1517](https://github.com/pints-team/pints/pull/1517) Fixed a major bug in the covariance matrix update for xNES.
- [#1505](https://github.com/pints-team/pints/pull/1505) Fixed issues with toy problems that accept invalid inputs.



## [0.5.0] - 2023-07-27

### Added
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1 change: 1 addition & 0 deletions examples/README.md
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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)
1,973 changes: 1,973 additions & 0 deletions examples/miscellaneous/model-rt-estimation-renewal-equation.ipynb

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101 changes: 101 additions & 0 deletions examples/miscellaneous/negbin_rt.csv
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