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@@ -0,0 +1 @@ +/summerepi-3.6.4.tar.gz diff --git a/python-summerepi.spec b/python-summerepi.spec new file mode 100644 index 0000000..22548de --- /dev/null +++ b/python-summerepi.spec @@ -0,0 +1,594 @@ +%global _empty_manifest_terminate_build 0 +Name: python-summerepi +Version: 3.6.4 +Release: 1 +Summary: Summer is a compartmental disease modelling framework, written in Python. It provides a high-level API to build and run models. +License: BSD-2-Clause +URL: http://summerepi.com/ +Source0: https://mirrors.nju.edu.cn/pypi/web/packages/3a/d0/3d645964dedc8a2766e385ef894c7184d78f62e5606361bb0eac35095234/summerepi-3.6.4.tar.gz +BuildArch: noarch + +Requires: python3-numpy +Requires: python3-networkx +Requires: python3-scipy +Requires: python3-numba +Requires: python3-setuptools +Requires: python3-pandas +Requires: python3-sphinx-rtd-theme +Requires: python3-recommonmark +Requires: python3-nbsphinx +Requires: python3-sphinxcontrib-napoleon +Requires: python3-ipykernel +Requires: python3-matplotlib + +%description +# Summer: compartmental disease modelling in Python + +[](https://github.com/monash-emu/summer/actions/workflows/tests.yml) + +Summer is a Python-based framework for the creation and execution of [compartmental](https://en.wikipedia.org/wiki/Compartmental_models_in_epidemiology) (or "state-based") epidemiological models of infectious disease transmission. + +It provides a range of structures for easily implementing compartmental models, including structure for some of the most common features added to basic compartmental frameworks, including: + +- A variety of inter-compartmental flows (infections, transitions, births, deaths, imports) +- Force of infection multipliers (frequency, density) +- Post-processing of compartment sizes into derived outputs +- Stratification of compartments, including: + - Adjustments to flow rates based on strata + - Adjustments to infectiousness based on strata + - Heterogeneous mixing between strata + - Multiple disease strains + +Some helpful links to learn more: + +- [Rationale](http://summerepi.com/rationale.html) for why we are building Summer +- **[Documentation](http://summerepi.com/)** with [code examples](http://summerepi.com/examples) +- [Available on PyPi](https://pypi.org/project/summerepi/) as `summerepi`. +- [Performance benchmarks](https://monash-emu.github.io/summer/) + +## Installation and Quickstart + +This project requires at least Python 3.7 (and is actively targeted at 3.9) +Install the `summerepi` package from PyPI + +```bash +pip install summerepi +``` + +Then you can use the library to build and run models. See [here](http://summerepi.com/examples) for some code examples. + +## Development + +[Poetry](https://python-poetry.org/) is used for packaging and dependency management. + +Initial project setup is documented [here](./docs/dev-setup.md) and should work for Windows or Ubuntu, maybe for MacOS. + +Some common things to do as a developer working on this codebase: + +```bash +# Activate summer conda environment prior to doing other stuff (see setup docs) +conda activate summer + +# Install latest requirements +poetry install + +# Publish to PyPI - use your PyPI credentials +poetry publish --build + +# Add a new package +poetry add + +# Run tests +pytest -vv + +# Format Python code +black . +isort . --profile black +``` + +## Releases + +Releases are numbered using [Semantic Versioning](https://semver.org/) + +- 1.0.0/1: + - Initial release +- 1.1.0: + - Add stochastic integrator +- 2.0.2: + - Rename fractional flow to transition flow + - Remove sojourn flow + - Add vectorized backend and other performance improvements +- 2.0.3: + - Set default IVP solver to use a maximum step size of 1 timestep +- 2.0.4: + - Add runtime derived values +- 2.0.5: + - Remove legacy Summer implementation +- 2.1.0: + - Add AdjustmentSystems + - Improve vectorization of flows + - Add computed_values inputs to flow and adjustment parameters +- 2.1.1: + - Fix for invalid/unused package imports (cachetools) +- 2.2.0 + - Add validation and compartment caching optimizations +- 2.2.1 + - Derived output index caching + - Optimized fast-tracks for infectious multipliers +- 2.2.2 + - JIT infectiousness calculations + - Various micro-optimizations +- 2.2.3 + - Bugfix release (clamp outputs to 0.0) +- 2.2.4 + - Datetime awareness, DataFrame outputs +- 2.2.5 + - Performance improvements (frozenset), no API changes +- 2.2.6 + - Verify strata in flow adjustments (prevent unexpected behaviour) +- 2.2.7 + - Rename add_flow_adjustments -> set_flow_adjustments +- 2.2.8 + - Split imports functionality (add_importation_flow now requires split_imports arg) +- 2.2.9 + - Post-stratification population restribution +- 2.3.0 + - First official version to support only Python 3.7 +- 2.5.0 + - Support Python 3.9 +- 2.6.0 + - Merge 3.9/master branches +- 2.7.0 + - Include Python 3.10 support and update requirements +- 3.6.0 + - Summer 'classic' end-of-line release +- 3.6.3 + - Small compatibility fixed for numpy deprecations + +## Release process + +To do a release: + +- Commit any code changes and push them to GitHub +- Choose a new release number accoridng to [Semantic Versioning](https://semver.org/) +- Add a release note above +- Edit the `version` key in `pyproject.toml` to reflect the release number +- Publish the package to [PyPI](https://pypi.org/project/summerepi/) using Poetry, you will need a PyPI login and access to the project +- Commit the release changes and push them to GitHub (Use a commit message like "Release 1.1.0") +- Update `requirements.txt` in Autumn to use the new version of Summer + +```bash +poetry build +poetry publish +``` + +## Documentation + +Sphinx is used to automatically build reference documentation for this library. +The documentation is automatically built and deployed to [summerepi.com](http://summerepi.com/) whenever code is pushed to `master`. + +To run or edit the code examples in the documentation, start a jupyter notebook server as follows: + +```bash +jupyter notebook --config docs/jupyter_notebook_config.py +# Go to http://localhost:8888/tree/docs/examples in your web browser. +``` + +You can clean outputs from all the example notbooks with + +```bash +./docs/scripts/clean.sh +``` + +To build and deploy + +```bash +./docs/scripts/build.sh +./docs/scripts/deploy.sh +``` + +To work on docs locally + +```bash +./docs/scripts/watch.sh +``` + + +%package -n python3-summerepi +Summary: Summer is a compartmental disease modelling framework, written in Python. It provides a high-level API to build and run models. +Provides: python-summerepi +BuildRequires: python3-devel +BuildRequires: python3-setuptools +BuildRequires: python3-pip +%description -n python3-summerepi +# Summer: compartmental disease modelling in Python + +[](https://github.com/monash-emu/summer/actions/workflows/tests.yml) + +Summer is a Python-based framework for the creation and execution of [compartmental](https://en.wikipedia.org/wiki/Compartmental_models_in_epidemiology) (or "state-based") epidemiological models of infectious disease transmission. + +It provides a range of structures for easily implementing compartmental models, including structure for some of the most common features added to basic compartmental frameworks, including: + +- A variety of inter-compartmental flows (infections, transitions, births, deaths, imports) +- Force of infection multipliers (frequency, density) +- Post-processing of compartment sizes into derived outputs +- Stratification of compartments, including: + - Adjustments to flow rates based on strata + - Adjustments to infectiousness based on strata + - Heterogeneous mixing between strata + - Multiple disease strains + +Some helpful links to learn more: + +- [Rationale](http://summerepi.com/rationale.html) for why we are building Summer +- **[Documentation](http://summerepi.com/)** with [code examples](http://summerepi.com/examples) +- [Available on PyPi](https://pypi.org/project/summerepi/) as `summerepi`. +- [Performance benchmarks](https://monash-emu.github.io/summer/) + +## Installation and Quickstart + +This project requires at least Python 3.7 (and is actively targeted at 3.9) +Install the `summerepi` package from PyPI + +```bash +pip install summerepi +``` + +Then you can use the library to build and run models. See [here](http://summerepi.com/examples) for some code examples. + +## Development + +[Poetry](https://python-poetry.org/) is used for packaging and dependency management. + +Initial project setup is documented [here](./docs/dev-setup.md) and should work for Windows or Ubuntu, maybe for MacOS. + +Some common things to do as a developer working on this codebase: + +```bash +# Activate summer conda environment prior to doing other stuff (see setup docs) +conda activate summer + +# Install latest requirements +poetry install + +# Publish to PyPI - use your PyPI credentials +poetry publish --build + +# Add a new package +poetry add + +# Run tests +pytest -vv + +# Format Python code +black . +isort . --profile black +``` + +## Releases + +Releases are numbered using [Semantic Versioning](https://semver.org/) + +- 1.0.0/1: + - Initial release +- 1.1.0: + - Add stochastic integrator +- 2.0.2: + - Rename fractional flow to transition flow + - Remove sojourn flow + - Add vectorized backend and other performance improvements +- 2.0.3: + - Set default IVP solver to use a maximum step size of 1 timestep +- 2.0.4: + - Add runtime derived values +- 2.0.5: + - Remove legacy Summer implementation +- 2.1.0: + - Add AdjustmentSystems + - Improve vectorization of flows + - Add computed_values inputs to flow and adjustment parameters +- 2.1.1: + - Fix for invalid/unused package imports (cachetools) +- 2.2.0 + - Add validation and compartment caching optimizations +- 2.2.1 + - Derived output index caching + - Optimized fast-tracks for infectious multipliers +- 2.2.2 + - JIT infectiousness calculations + - Various micro-optimizations +- 2.2.3 + - Bugfix release (clamp outputs to 0.0) +- 2.2.4 + - Datetime awareness, DataFrame outputs +- 2.2.5 + - Performance improvements (frozenset), no API changes +- 2.2.6 + - Verify strata in flow adjustments (prevent unexpected behaviour) +- 2.2.7 + - Rename add_flow_adjustments -> set_flow_adjustments +- 2.2.8 + - Split imports functionality (add_importation_flow now requires split_imports arg) +- 2.2.9 + - Post-stratification population restribution +- 2.3.0 + - First official version to support only Python 3.7 +- 2.5.0 + - Support Python 3.9 +- 2.6.0 + - Merge 3.9/master branches +- 2.7.0 + - Include Python 3.10 support and update requirements +- 3.6.0 + - Summer 'classic' end-of-line release +- 3.6.3 + - Small compatibility fixed for numpy deprecations + +## Release process + +To do a release: + +- Commit any code changes and push them to GitHub +- Choose a new release number accoridng to [Semantic Versioning](https://semver.org/) +- Add a release note above +- Edit the `version` key in `pyproject.toml` to reflect the release number +- Publish the package to [PyPI](https://pypi.org/project/summerepi/) using Poetry, you will need a PyPI login and access to the project +- Commit the release changes and push them to GitHub (Use a commit message like "Release 1.1.0") +- Update `requirements.txt` in Autumn to use the new version of Summer + +```bash +poetry build +poetry publish +``` + +## Documentation + +Sphinx is used to automatically build reference documentation for this library. +The documentation is automatically built and deployed to [summerepi.com](http://summerepi.com/) whenever code is pushed to `master`. + +To run or edit the code examples in the documentation, start a jupyter notebook server as follows: + +```bash +jupyter notebook --config docs/jupyter_notebook_config.py +# Go to http://localhost:8888/tree/docs/examples in your web browser. +``` + +You can clean outputs from all the example notbooks with + +```bash +./docs/scripts/clean.sh +``` + +To build and deploy + +```bash +./docs/scripts/build.sh +./docs/scripts/deploy.sh +``` + +To work on docs locally + +```bash +./docs/scripts/watch.sh +``` + + +%package help +Summary: Development documents and examples for summerepi +Provides: python3-summerepi-doc +%description help +# Summer: compartmental disease modelling in Python + +[](https://github.com/monash-emu/summer/actions/workflows/tests.yml) + +Summer is a Python-based framework for the creation and execution of [compartmental](https://en.wikipedia.org/wiki/Compartmental_models_in_epidemiology) (or "state-based") epidemiological models of infectious disease transmission. + +It provides a range of structures for easily implementing compartmental models, including structure for some of the most common features added to basic compartmental frameworks, including: + +- A variety of inter-compartmental flows (infections, transitions, births, deaths, imports) +- Force of infection multipliers (frequency, density) +- Post-processing of compartment sizes into derived outputs +- Stratification of compartments, including: + - Adjustments to flow rates based on strata + - Adjustments to infectiousness based on strata + - Heterogeneous mixing between strata + - Multiple disease strains + +Some helpful links to learn more: + +- [Rationale](http://summerepi.com/rationale.html) for why we are building Summer +- **[Documentation](http://summerepi.com/)** with [code examples](http://summerepi.com/examples) +- [Available on PyPi](https://pypi.org/project/summerepi/) as `summerepi`. +- [Performance benchmarks](https://monash-emu.github.io/summer/) + +## Installation and Quickstart + +This project requires at least Python 3.7 (and is actively targeted at 3.9) +Install the `summerepi` package from PyPI + +```bash +pip install summerepi +``` + +Then you can use the library to build and run models. See [here](http://summerepi.com/examples) for some code examples. + +## Development + +[Poetry](https://python-poetry.org/) is used for packaging and dependency management. + +Initial project setup is documented [here](./docs/dev-setup.md) and should work for Windows or Ubuntu, maybe for MacOS. + +Some common things to do as a developer working on this codebase: + +```bash +# Activate summer conda environment prior to doing other stuff (see setup docs) +conda activate summer + +# Install latest requirements +poetry install + +# Publish to PyPI - use your PyPI credentials +poetry publish --build + +# Add a new package +poetry add + +# Run tests +pytest -vv + +# Format Python code +black . +isort . --profile black +``` + +## Releases + +Releases are numbered using [Semantic Versioning](https://semver.org/) + +- 1.0.0/1: + - Initial release +- 1.1.0: + - Add stochastic integrator +- 2.0.2: + - Rename fractional flow to transition flow + - Remove sojourn flow + - Add vectorized backend and other performance improvements +- 2.0.3: + - Set default IVP solver to use a maximum step size of 1 timestep +- 2.0.4: + - Add runtime derived values +- 2.0.5: + - Remove legacy Summer implementation +- 2.1.0: + - Add AdjustmentSystems + - Improve vectorization of flows + - Add computed_values inputs to flow and adjustment parameters +- 2.1.1: + - Fix for invalid/unused package imports (cachetools) +- 2.2.0 + - Add validation and compartment caching optimizations +- 2.2.1 + - Derived output index caching + - Optimized fast-tracks for infectious multipliers +- 2.2.2 + - JIT infectiousness calculations + - Various micro-optimizations +- 2.2.3 + - Bugfix release (clamp outputs to 0.0) +- 2.2.4 + - Datetime awareness, DataFrame outputs +- 2.2.5 + - Performance improvements (frozenset), no API changes +- 2.2.6 + - Verify strata in flow adjustments (prevent unexpected behaviour) +- 2.2.7 + - Rename add_flow_adjustments -> set_flow_adjustments +- 2.2.8 + - Split imports functionality (add_importation_flow now requires split_imports arg) +- 2.2.9 + - Post-stratification population restribution +- 2.3.0 + - First official version to support only Python 3.7 +- 2.5.0 + - Support Python 3.9 +- 2.6.0 + - Merge 3.9/master branches +- 2.7.0 + - Include Python 3.10 support and update requirements +- 3.6.0 + - Summer 'classic' end-of-line release +- 3.6.3 + - Small compatibility fixed for numpy deprecations + +## Release process + +To do a release: + +- Commit any code changes and push them to GitHub +- Choose a new release number accoridng to [Semantic Versioning](https://semver.org/) +- Add a release note above +- Edit the `version` key in `pyproject.toml` to reflect the release number +- Publish the package to [PyPI](https://pypi.org/project/summerepi/) using Poetry, you will need a PyPI login and access to the project +- Commit the release changes and push them to GitHub (Use a commit message like "Release 1.1.0") +- Update `requirements.txt` in Autumn to use the new version of Summer + +```bash +poetry build +poetry publish +``` + +## Documentation + +Sphinx is used to automatically build reference documentation for this library. +The documentation is automatically built and deployed to [summerepi.com](http://summerepi.com/) whenever code is pushed to `master`. + +To run or edit the code examples in the documentation, start a jupyter notebook server as follows: + +```bash +jupyter notebook --config docs/jupyter_notebook_config.py +# Go to http://localhost:8888/tree/docs/examples in your web browser. +``` + +You can clean outputs from all the example notbooks with + +```bash +./docs/scripts/clean.sh +``` + +To build and deploy + +```bash +./docs/scripts/build.sh +./docs/scripts/deploy.sh +``` + +To work on docs locally + +```bash +./docs/scripts/watch.sh +``` + + +%prep +%autosetup -n summerepi-3.6.4 + +%build +%py3_build + +%install +%py3_install +install -d -m755 %{buildroot}/%{_pkgdocdir} +if [ -d doc ]; then cp -arf doc %{buildroot}/%{_pkgdocdir}; fi +if [ -d docs ]; then cp -arf docs %{buildroot}/%{_pkgdocdir}; fi +if [ -d example ]; then cp -arf example %{buildroot}/%{_pkgdocdir}; fi +if [ -d examples ]; then cp -arf examples %{buildroot}/%{_pkgdocdir}; fi +pushd %{buildroot} +if [ -d usr/lib ]; then + find usr/lib -type f -printf "/%h/%f\n" >> filelist.lst +fi +if [ -d usr/lib64 ]; then + find usr/lib64 -type f -printf "/%h/%f\n" >> filelist.lst +fi +if [ -d usr/bin ]; then + find usr/bin -type f -printf "/%h/%f\n" >> filelist.lst +fi +if [ -d usr/sbin ]; then + find usr/sbin -type f -printf "/%h/%f\n" >> filelist.lst +fi +touch doclist.lst +if [ -d usr/share/man ]; then + find usr/share/man -type f -printf "/%h/%f.gz\n" >> doclist.lst +fi +popd +mv %{buildroot}/filelist.lst . +mv %{buildroot}/doclist.lst . + +%files -n python3-summerepi -f filelist.lst +%dir %{python3_sitelib}/* + +%files help -f doclist.lst +%{_docdir}/* + +%changelog +* Wed May 10 2023 Python_Bot <Python_Bot@openeuler.org> - 3.6.4-1 +- Package Spec generated @@ -0,0 +1 @@ +336a8b0741ecc5a7afae7550af926cfd summerepi-3.6.4.tar.gz |