stisim 1.4.0__tar.gz

stisim-1.4.0/.github/workflows/README.md

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+# GitHub workflows
+
+The continuous integration tests (`tests.yml`) run with every push on a pull request.
+
+The PyPI workflow (`publish_pypi.yml`) runs when a tag is pushed to GitHub, e.g.
+
+```
+git tag v1.2.3
+git push origin v1.2.3
+```
+
+Make sure the git tag matches the STIsim version.

stisim-1.4.0/.github/workflows/pypi_release.yaml

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+name: Publish STIsim to PyPI (manual)
+
+on: workflow_dispatch
+
+jobs:
+  build:
+    name: Build STIsim
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v4
+      with:
+        persist-credentials: false
+    - name: Set up Python
+      uses: actions/setup-python@v5
+      with:
+        python-version: "3.x"
+    - name: Install pypa/build
+      run: python3 -m pip install build --user
+    - name: Build a binary wheel and a source tarball
+      run: python3 -m build
+    - name: Store the distribution packages
+      uses: actions/upload-artifact@v4
+      with:
+        name: python-package-distributions
+        path: dist/
+
+  publish-to-pypi:
+    name: Publish STIsim
+    needs:
+    - build
+    runs-on: ubuntu-latest
+    environment:
+      name: pypi
+      url: https://pypi.org/p/stisim
+    permissions:
+      id-token: write
+
+    steps:
+    - name: Download all the dists
+      uses: actions/download-artifact@v4
+      with:
+        name: python-package-distributions
+        path: dist/
+    - name: Publish distribution 📦 to PyPI
+      uses: pypa/gh-action-pypi-publish@release/v1

stisim-1.4.0/.github/workflows/tests.yaml

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+name: STIsim CI tests
+on:
+  push:
+    branches:
+      - main
+    tags: v*
+  pull_request:
+
+jobs:
+  test:
+    timeout-minutes: 8
+    strategy:
+      fail-fast: false
+      max-parallel: 8
+      matrix:
+        os: ['ubuntu-latest']
+        python-version: ['3.12']
+    runs-on: ${{ matrix.os }}
+    name: Install and test
+    steps:
+      - name: Checkout sources
+        uses: actions/checkout@v4
+      - uses: actions/setup-python@master
+        with:
+          python-version: ${{ matrix.python-version }}
+          architecture: x64
+      - name: Install STIsim
+        run: pip install -e .
+      - name: Install tests
+        working-directory: ./tests
+        run: pip install -r requirements.txt
+      - name: Run tests
+        working-directory: ./tests
+        run: pytest test_*.py -n auto --durations=0 --junitxml=test-results.xml
+      - name: Publish Test Report
+        uses: mikepenz/action-junit-report@v4
+        if: always()
+        with:
+          report_paths: './tests/test-results.xml'

stisim-1.4.0/.gitignore

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+supervisord.log
+
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+env/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+.hypothesis/
+junit
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+docs/api/
+docs/modules.rst
+docs/stisim.*.rst
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# pyenv
+.python-version
+
+# celery beat schedule file
+celerybeat-schedule
+
+# SageMath parsed files
+*.sage.py
+
+# dotenv
+.env
+
+# virtualenv
+.venv
+venv/
+ENV/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.DS_Store
+*.iml
+*.xml
+
+# other stuff
+package-lock.json
+temp
+vueapp
+
+# Excel temp files
+~$*
+
+# VIM
+*.sw*
+
+# flake8
+flake8.txt
+flake8_junit.xml
+
+.ipython
+.matplotlib
+.idea
+*.png
+*.obj

stisim-1.4.0/.readthedocs.yaml

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+# .readthedocs.yaml
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Set the version of Python and other tools you might need
+build:
+  os: ubuntu-20.04
+  tools:
+    python: "3.9"
+
+# Build documentation in the docs/ directory with Sphinx
+sphinx:
+   configuration: docs/conf.py
+
+# If using Sphinx, optionally build your docs in additional formats such as PDF
+# formats:
+
+# Optionally declare the Python requirements required to build your docs
+python:
+  install:
+    - requirements: docs/requirements.txt
+    - method: pip
+      path: .

stisim-1.4.0/CHANGELOG.rst

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+==========
+What's new
+==========
+
+.. currentmodule:: stisim
+
+All notable changes to the codebase are documented in this file.
+
+
+Version 1.4 (2025-08-12)
+--------------------------
+- Add location arg and Sim class
+- Update to work with Starsim v3.
+- *GitHub info*: PR `148 <https://github.com/starsimhub/stisim/pull/148>`_
+
+
+Version 1.3 (2025-06-27)
+--------------------------
+- Fixes to the pair-matching algorithm within the sexual network to better align partner ages 
+- Improvements to networks, including analyzers for debut age and partner age differences
+- *GitHub info*: PR `143 <https://github.com/starsimhub/stisim/pull/143>`_
+
+
+Version 1.2 (2025-06-10)
+--------------------------
+- Improvements to networks, including analyzers for relationship duration and network degree
+- Adds a `PriorPartners` network for recalling past relationships - for use in partner notification
+- *GitHub info*: PR `135 <https://github.com/starsimhub/stisim/pull/135>`_
+
+
+Version 1.1.2 (2025-06-03)
+--------------------------
+- Bugfix to calibration class for multisims
+- *GitHub info*: PR `138 <https://github.com/starsimhub/stisim/pull/138>`_
+
+
+Version 1.1.1 (2025-05-23)
+--------------------------
+- Bugfixes to calibration class and BV connector
+- Replaces the `match_pairs` method of the `StructuredSexual` network with the faster option that was previously in the `FastStructuredSexual` network (now removed).
+- *GitHub info*: PR `https://github.com/starsimhub/stisim/pull/124`_
+
+
+Version 1.1.0 (2025-05-13)
+--------------------------
+- Improvements to the Calibration class: this class now inherits directly from the Starsim calibration class, so users will have access to easier parameter constraints, plotting, flexible fit functions, etc
+- Generalization of the coinfection class to handle any two diseases
+- Addition of a more detailed BV model
+- *GitHub info*: PR `119 <https://github.com/starsimhub/stisim/pull/119>`_
+
+
+Version 1.0.5 (2025-05-08)
+--------------------------
+- Adds results for syphilis transmission by disease stage
+- *GitHub info*: PR `112 <https://github.com/starsimhub/stisim/pull/112>`_
+
+Version 1.0.4 (2025-05-07)
+--------------------------
+- Adds results for overtreatment among pregnant women
+- *GitHub info*: PR `111 <https://github.com/starsimhub/stisim/pull/111>`_
+
+Version 1.0.3 (2025-04-30)
+--------------------------
+- Bugfixes for congenital syphilis
+- *GitHub info*: PR `85 <https://github.com/starsimhub/stisim/pull/85>`_
+
+Version 1.0.2 (2025-04-14)
+--------------------------
+- Bugfixes for syphilis and GUD
+- *GitHub info*: PR `83 <https://github.com/starsimhub/stisim/pull/83>`_
+
+Version 1.0.1 (2025-03-31)
+--------------------------
+- Track HIV prevalence for 15-49 year olds
+- *GitHub info*: PR `79 <https://github.com/starsimhub/stisim/pull/79>`_
+
+Version 1.0.0 (2024-12-11)
+--------------------------
+- Updates to work with Starsim v2.2.1
+- *GitHub info*: PR `63 <https://github.com/starsimhub/stisim/pull/63>`_
+
+
+Version 0.2.0 (2024-11-01)
+--------------------------
+- Updates to work with Starsim v2.0
+- *GitHub info*: PR `62 <https://github.com/starsimhub/stisim/pull/62>`_
+
+
+Version 0.1.0 (2024-10-02)
+--------------------------
+- Collection of updates related to the NG/CT/TV work
+- *GitHub info*: PR `59 <https://github.com/starsimhub/stisim/pull/59>`_
+
+
+Version 0.0.2 (2024-06-07)
+--------------------------
+- Initial version of STIsim with structured sexual networks, models of HIV and syphilis, worksflows for model calibration, and interventions for testing and treatment.
+- *GitHub info*: PR `22 <https://github.com/starsimhub/stisim/pull/22>`_
+
+
+Version 0.0.1 (2024-05-15)
+--------------------------
+- Pre-release version
+

stisim-1.4.0/LICENSE

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+MIT License
+
+Copyright (c) 2023 by the Starsim Development Team
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

stisim-1.4.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: stisim
+Version: 1.4.0
+Summary: STI modelling toolbox built on the Starsim platform
+Author: Alina Muellenmeister, Romesh Abeysuriya, Ryan Hull, Cliff Kerr, Jamie Cohen
+Author-email: Robyn Stuart <info@starsim.org>
+License: MIT License
+        
+        Copyright (c) 2023 by the Starsim Development Team
+        
+        Permission is hereby granted, free of charge, to any person obtaining a copy
+        of this software and associated documentation files (the "Software"), to deal
+        in the Software without restriction, including without limitation the rights
+        to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+        copies of the Software, and to permit persons to whom the Software is
+        furnished to do so, subject to the following conditions:
+        
+        The above copyright notice and this permission notice shall be included in all
+        copies or substantial portions of the Software.
+        
+        THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+        IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+        FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+        AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+        LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+        OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+        SOFTWARE.
+        
+Project-URL: Website, https://stisim.org
+Project-URL: Source, https://github.com/starsimhub/stisim/
+Keywords: agent-based model,simulation,disease,epidemiology,sexually transmitted infections,STIs,STDs
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python
+Classifier: Topic :: Software Development :: Libraries :: Python Modules
+Classifier: Development Status :: 5 - Production/Stable
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Requires-Python: >=3.9
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: starsim>=3.0.1
+Requires-Dist: optuna
+Requires-Dist: requests
+Dynamic: license-file

stisim-1.4.0/README.rst

@@ -0,0 +1,51 @@
+STIsim
+======
+
+.. |tests| image:: https://github.com/starsimhub/stisim/actions/workflows/tests.yaml/badge.svg
+
+.. |pypi| image:: https://img.shields.io/pypi/v/stisim?label=PyPI
+    :target: https://pypi.org/project/stisim/
+
+|tests| |pypi|
+
+**Warning! STIsim is still in the early stages of development. It is being shared solely for transparency and to facilitate collaborative development. It is not ready to be used for real research or policy questions.**
+
+STIsim is an agent-based modeling framework in which users can design and configure simulations of sexually-transmitted diseases. STIsim uses the `Starsim <https://starsim.org>`_ architecture, and belongs to the Starsim model suite which also includes `Covasim <https://covasim.org>`_, `HPVsim <https://hpvsim.org>`_, and `FPsim <https://fpsim.org>`_.
+
+
+Requirements
+------------
+
+Python 3.9-3.13.
+
+We recommend, but do not require, installing STIsim in a virtual environment, such as `Anaconda <https://www.anaconda.com/products>`__.
+
+
+Installation
+------------
+
+STIsim is most easily installed via PyPI: ``pip install stisim``.
+
+STIsim can also be installed locally. To do this, clone first this repository, then run ``pip install -e .`` (don't forget the dot at the end!).
+
+
+Usage and documentation
+-----------------------
+
+Documentation is available at https://docs.idmod.org/projects/stisim. 
+
+
+Contributing
+------------
+
+Questions or comments can be directed to `info@starsim.org <mailto:info@starsim.org>`__ , or on this project’s `GitHub <https://github.com/starsimhub/stisim>`__ page.
+
+See `.github/workflows/README.md` for details on publishing new releases of STIsim.
+
+
+Disclaimer
+----------
+
+The code in this repository was developed by IDM, the Burnet Institute, and other collaborators to support our joint research on flexible agent-based modeling. We've made it publicly available under the MIT License to provide others with a better understanding of our research and an opportunity to build upon it for their own work. We make no representations that the code works as intended or that we will provide support, address issues that are found, or accept pull requests. You are welcome to create your own fork and modify the code to suit your own modeling needs as permitted under the MIT License.
+
+

stisim-1.4.0/code_of_conduct.rst

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+===============
+Code of conduct
+===============
+
+Our pledge
+==========
+
+In the interest of fostering an open and welcoming environment, we as
+contributors and maintainers pledge to making participation in our project and
+our community a harassment-free experience for everyone, regardless of age, body
+size, disability, ethnicity, sex characteristics, gender identity and expression,
+level of experience, education, socio-economic status, nationality, personal
+appearance, race, religion, or sexual identity and orientation.
+
+Our standards
+=============
+
+Examples of behavior that contributes to creating a positive environment
+include:
+
+*   Using welcoming and inclusive language
+*   Being respectful of differing viewpoints and experiences
+*   Gracefully accepting constructive criticism
+*   Focusing on what is best for the community
+*   Showing empathy towards other community members
+
+Examples of unacceptable behavior by participants include:
+
+*   The use of sexualized language or imagery and unwelcome sexual attention or
+    advances
+*   Trolling, insulting/derogatory comments, and personal or political attacks
+*   Public or private harassment
+*   Publishing others' private information, such as a physical or electronic
+    address, without explicit permission
+*   Other conduct which could reasonably be considered inappropriate in a
+    professional setting
+
+Our responsibilities
+====================
+
+Project maintainers are responsible for clarifying the standards of acceptable
+behavior and are expected to take appropriate and fair corrective action in
+response to any instances of unacceptable behavior.
+
+Project maintainers have the right and responsibility to remove, edit, or
+reject comments, commits, code, wiki edits, issues, and other contributions
+that are not aligned to this Code of Conduct, or to ban temporarily or
+permanently any contributor for other behaviors that they deem inappropriate,
+threatening, offensive, or harmful.
+
+Scope
+=====
+
+This Code of Conduct applies both within project spaces and in public spaces
+when an individual is representing the project or its community. Examples of
+representing a project or community include using an official project e-mail
+address, posting via an official social media account, or acting as an appointed
+representative at an online or offline event. Representation of a project may be
+further defined and clarified by project maintainers.
+
+Enforcement
+===========
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be
+reported by contacting the project team at info@starsim.org. All
+complaints will be reviewed and investigated and will result in a response that
+is deemed necessary and appropriate to the circumstances. The project team is
+obligated to maintain confidentiality with regard to the reporter of an incident.
+Further details of specific enforcement policies may be posted separately.
+
+Project maintainers who do not follow or enforce the Code of Conduct in good
+faith may face temporary or permanent repercussions as determined by other
+members of the project's leadership.
+
+Attribution
+===========
+
+This Code of Conduct is adapted from the `Contributor Covenant`_, version 1.4,
+available at https://www.contributor-covenant.org/version/1/4/code-of-conduct.html.
+
+.. _Contributor Covenant: https://www.contributor-covenant.org
+
+For answers to common questions about this code of conduct, see the FAQ_.
+
+.. _FAQ: https://www.contributor-covenant.org/faq

stisim-1.4.0/contributing.rst

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+============
+Contributing
+============
+
+Welcome! We are thrilled you are interested in contributing to STIsim. This
+document will help you get started.
+
+- We are serious about inclusion and believe the open-source software community still has a long way to go. The STIsim community follows a `code of conduct`_. By participating in this project, you agree to abide by its terms.
+- Take a look at our house `style guide`_. STIsim more or less follows Google's Python style guide, but with some exceptions. 
+- Feel free to `open an issue`_ on more or less anything! This project is small enough that we don't need a formal triage system.
+- Pull requests should be made against ``main``. In addition to following the `style guide`_, please make sure the tests pass (``run_tests`` in the ``tests`` folder; they also run via GitHub actions).
+
+If you have any other questions, please reach out to us: info@starsim.org. Thank you!
+
+.. _code of conduct: https://docs.idmod.org/projects/starsim/en/stable/conduct.html
+.. _style guide: https://github.com/starsimhub/styleguide
+.. _open an issue: https://github.com/starsimhub/starsim/issues/new/choose