miscore-sim 0.0.998__tar.gz

miscore_sim-0.0.998/.coveragerc

@@ -0,0 +1,3 @@
+[run]
+plugins = Cython.Coverage
+source = miscore

miscore_sim-0.0.998/.flake8

@@ -0,0 +1,27 @@
+[flake8]
+# W503: Line break occurred before a binary operator
+ignore = W503
+per-file-ignores =
+    # F401: Module imported but unused
+    # I100: Import statements are in the wrong order
+    # I101: Imported names are in the wrong order
+    __init__.py: F401
+    miscore/__init__.py: F401, I100, I101
+max-line-length = 99
+max-doc-length = 99
+exclude =
+    .git,
+    __pycache__,
+    venv,
+    doc/conf.py,
+    doc/_build,
+    build,
+    dist,
+    examples/article.py,
+doctests = True
+import-order-style = google
+application_import_names =
+    miscore,
+    version
+strictness = short
+docstring_style = sphinx

miscore_sim-0.0.998/.gitignore

@@ -0,0 +1,136 @@
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+pip-wheel-metadata/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# 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/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+doc/_build/
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+.python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# idea
+/.idea
+
+# Mac .DS_Store files
+.DS_Store

miscore_sim-0.0.998/.gitlab-ci.yml

@@ -0,0 +1,212 @@
+variables:
+  PIP_CACHE_DIR: "$CI_PROJECT_DIR/.cache/pip"
+
+cache:
+  paths:
+    - .cache/pip
+
+stages:
+  - test
+  - coverage
+  - deploy
+  - build
+  - release
+
+test_functionality:
+  stage: test
+  parallel:
+    matrix:
+      - VERSION: ["3.9", "3.14"]
+  image: python:$VERSION
+  script:
+    - python -V
+    - python -m pip install pip --upgrade
+    - python -m pip install -r requirements.txt
+    - python -m build
+    - python -m pip install dist/*.whl
+    - cd tests
+    - python -m unittest discover -s unit -v
+    - python -m unittest discover -s integration -v
+    - cd ../examples
+    - find . -name "*.py" -type f -print0 | xargs -t -0 -n1 python
+    - cd ../doc
+    - find . -name "*.py" ! -name "conf.py" -type f -print0 | xargs -t -0 -n1 python
+
+test_documentation:
+  stage: test
+  # Using Python 3.11 instead of 3.9 here so that pandas 3.0.0 is used and intersphinx works correctly
+  image: python:3.11
+  script:
+    - python -V
+    - python -m pip install pip --upgrade
+    - python -m pip install -r requirements.txt
+    - (cd doc && make doctest)
+    - sphinx-build doc html -n -W --keep-going
+  artifacts:
+    paths:
+      - html
+    expire_in: 2 weeks
+
+test_style:
+  stage: test
+  image: python:3.9
+  script:
+    - python -V
+    - python -m pip install pip --upgrade
+    - python -m pip install -r requirements.txt
+    - python -m flake8
+    - python -m pydocstyle miscore
+
+# test coverage with Python 3.13 instead of 3.14 because of cython issues
+test_coverage:
+  stage: coverage
+  image: python:3.13
+  variables:
+    CYTHON_COVERAGE: "all"
+  script:
+    - python -V
+    - python -m pip install pip --upgrade
+    - python -m pip install -r requirements.txt
+    - python setup.py build_ext --inplace
+    - python -m pytest tests/unit -v --cov=miscore
+    - python -m pytest tests/integration -v --cov=miscore --cov-append
+    - coverage report --precision=1
+    - coverage xml
+    - coverage html
+  artifacts:
+    expose_as: "coverage"
+    name: "coverage"
+    paths:
+      - coverage.xml
+      - htmlcov/
+    reports:
+      coverage_report:
+          coverage_format: cobertura
+          path: coverage.xml
+  coverage: /(?i)total.*? (100(?:\.0+)?\%|[1-9]?\d(?:\.\d+)?\%)$/
+
+pages:
+  stage: deploy
+  only:
+    - main
+  # Using Python 3.11 instead of 3.9 here so that pandas 3.0.0 is used and intersphinx works correctly
+  image: python:3.11
+  script:
+    - python -V
+    - python -m pip install pip --upgrade
+    - python -m pip install -r requirements.txt
+    - cd doc
+    - make dirhtml
+    - mv _build/dirhtml/ ../public/
+  artifacts:
+    paths:
+      - public
+    expire_in: 2 weeks
+  allow_failure: true
+
+build_source:
+  stage: build
+  when: manual
+  dependencies: []
+  image: python:3.9
+  script:
+    - python -V
+    - python -m pip install pip setuptools twine --upgrade
+    - python -m pip install -r requirements.txt
+    - python -m build --sdist
+    - python -m twine check dist/*
+  artifacts:
+    paths:
+      - dist/
+    expire_in: 2 weeks
+  allow_failure: true
+
+build_mac:
+  stage: build
+  when: manual
+  parallel:
+    matrix:
+      - VERSION: ["10", "11", "12", "13", "14"]
+        IMAGE: ["macos-15-xcode-16", "macos-26-xcode-26"]
+  # This makes sure artifacts from other build jobs are not downloaded
+  dependencies: []
+  tags:
+    - saas-macos-medium-m1
+  image: $IMAGE
+  script:
+    - brew install python@3.$VERSION
+    - python3.$VERSION -m venv .venv
+    - source .venv/bin/activate
+    - python3.$VERSION -V
+    - python3.$VERSION -m pip install pip setuptools wheel twine --upgrade
+    - python3.$VERSION -m pip install -r requirements.txt
+    - python3.$VERSION -m build
+    - python3.$VERSION -m twine check dist/*
+  artifacts:
+    paths:
+      - dist/
+    expire_in: 2 weeks
+  allow_failure: true
+
+build_linux:
+  stage: build
+  when: manual
+  parallel:
+    matrix:
+      - VERSION: ["9", "10", "11", "12", "13", "14"]
+  # This makes sure artifacts from other build jobs are not downloaded
+  dependencies: []
+  image: quay.io/pypa/manylinux_2_28_x86_64
+  script:
+    - PYBIN=/opt/python/cp3${VERSION}-cp3${VERSION}/bin/python
+    - $PYBIN -m pip install pip build Cython auditwheel twine --upgrade
+    - $PYBIN -m pip install -r requirements.txt
+
+    # First build linux wheels in temporary folder
+    - mkdir tmp-linux-dist
+    - $PYBIN -m build --wheel --outdir tmp-linux-dist
+
+    # Then repair them and move to the dist folder
+    - auditwheel repair tmp-linux-dist/*.whl -w dist
+    - $PYBIN -m twine check dist/*
+  artifacts:
+    paths:
+      - dist/
+    expire_in: 2 weeks
+  allow_failure: true
+
+build_windows:
+    stage: build
+    when: manual
+    parallel:
+      matrix:
+        - VERSION: ["9", "10", "11", "12", "13", "14"]
+    # This makes sure artifacts from other build jobs are not downloaded
+    dependencies: []
+    tags:
+      - saas-windows-medium-amd64
+    script:
+      - choco install python3$VERSION -yes --no-progress --allow-downgrade
+      - Import-Module "$env:ChocolateyInstall\helpers\chocolateyProfile.psm1"
+      - refreshenv
+      - py -3.$VERSION -V
+      - py -3.$VERSION -m pip install pip twine setuptools wheel --upgrade
+      - py -3.$VERSION -m pip install -r requirements.txt
+      - py -3.$VERSION -m build
+      - py -3.$VERSION -m twine check dist/*
+    artifacts:
+      paths:
+        - dist/
+      expire_in: 2 weeks
+    allow_failure: true
+
+release-real:
+  stage: release
+#  only:
+#    - tags
+  when: manual
+  image: python:3.9
+  script:
+    - python -V
+    - python -m pip install twine
+    - TWINE_PASSWORD=${PYPI_TOKEN} TWINE_USERNAME=__token__ python -m twine upload dist/* --verbose

miscore_sim-0.0.998/.pydocstyle

@@ -0,0 +1,11 @@
+[pydocstyle]
+convention = pep257
+add-ignore =
+    D107, # Missing docstring in __init__
+    D200, # One-line docstring should fit on one line with quotes
+    D205, # 1 blank line required between summary line and description
+    D400, # First line should end with a period
+    D401, # First line should be in imperative mood
+    D402, # First line should not be the function’s signature
+    D403, # First word of the first line should be properly capitalized
+    D412, # No blank lines allowed between a section header and its content

miscore_sim-0.0.998/LICENSE

@@ -0,0 +1,108 @@
+MISCAN/MISCore License
+
+These terms of use (hereinafter: “Terms and Conditions”) have been drawn up by Erasmus University Medical Center
+Rotterdam, address kept at Dr. Molewaterplein 40, 3015 GD Rotterdam, the Netherlands (“Erasmus MC”) .
+
+By using the Software, you (hereinafter "You" or "Your") agree to these terms.
+
+Article 1 The Software
+
+1.1 Erasmus MC is the author and copyright holder of the software described as “MISCAN: MIcrosimulation SCreening
+ANalysis” and “MICore: MISCAN Core”, including software and related documentation made available through the repository
+(hereinafter: "Software").
+
+1.2 Erasmus MC allows You to use the Software under the following conditions.
+
+Article 2 The License
+
+2.1 Erasmus MC, after making the Software available, grants You a non-exclusive, non-sublicensable, non-transferable
+right to use the Software at your public institution for academic and non-commercial research and/or educational
+purposes (hereinafter: “the Use”). By using the Software, you agree to the terms and conditions as described below.
+
+2.2 Access to Software includes the following modules or parts thereof:
+
+MISCAN models of disease natural history and intervention effectiveness, defined as any and all code defined in the
+“miscore/processes/ec” and "miscore/processes/ec_screening" subfolders in the publicly available repository.
+
+MISCore, defined as any and all code in the publicly available repository that facilitates microsimulation modeling and
+the processing of results obtained from running the software. This includes all code in the repository, except the code
+that falls under the MISCAN models.
+
+2.3 Your use is subject to the following terms:
+
+A. You are authorized to use the Software only for academic research and educational purposes only at your institution.
+
+B. You may not use the Software for commercial purposes without a prior written consent from Erasmus MC and without
+entering into a separate license agreement regarding such commercial use.
+
+C. Your Use of the Software is at your own expense and risk.
+
+D. The Software must be used ethically and responsibly.
+
+E. Erasmus MC reserves the right to continue using the Software in the broadest sense of the word.
+
+F. The use of MISCore only does not constitute the use of MISCAN, and may not be published as such. For the use of
+MISCAN, condition 2.3G applies.
+
+G. The use of MISCAN, as defined in article 2.2, implies adherence to the MISCAN parameters specified in the “data”
+subfolder of each individual model. Any deviation from the supplied parameters does not constitute the use of MISCAN
+model, and may not be published as such. Some parameters are exempted from this condition, as specified in the data
+file.
+
+H. The use of the MISCAN parameters outside the MISCAN and MISCore code does not constitute the use of the MISCAN model,
+and may not be published as such.
+
+2.3 Permission is hereby granted, free of charge, to any person obtaining a license to this Software, to deal in the
+Software  without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute
+the Software, subject to the following conditions:
+
+(a) the Software is used, copied, modified or distributed only for academic research and trainings purposes in
+accordance with section 2.2 of the Agreement and;
+
+(b) if You create any derivate Software using or containing Software or any parts thereof You will apply only public
+license and make the code available for public review and require that all derivative Software have the same license
+and;
+
+2.4 Erasmus MC has the right at all times to deny You the Use of the Software by terminating the license, terminating
+the Use of the Software or denying access to the Software in whole or in part, temporarily or permanently.
+
+Article 3 Cooperation and Publication
+
+3.1 If you want to collaborate with Erasmus MC regarding the Software, with a view to further development and
+validation, you can contribute to the members of the MISCAN core team, as listed in the MISCAN documentation, or to
+MISCAN@erasmusmc.nl
+
+3.2 If you are going to publish the results of the Use of the Software, you must make an appropriate reference to the
+Software. This reference is as follows:
+
+a) Academic reference: TODO
+
+3.3 You will also observe the academic authoring standards of the ICMJE, so that the authors of the Software may also be
+included as co-authors in such publication.
+
+Article 4 Guarantee and liability
+
+4.1 Erasmus MC does not guarantee that the Software is correct or complete, or free of errors.
+
+4.2 Erasmus MC is not liable for any direct or indirect damages resulting from or related to the Use of the Software
+and/or the inability to Use it. Indirect damages includes, but is not limited to, consequential damage, reputational
+damage, damage as a result of business interruption and loss of profit and turnover.
+
+4.3 You indemnify Erasmus MC against all possible claims from third parties as a result of the Use of (the content of)
+the Software. You will compensate Erasmus MC for all damages and costs (including but not limited to judicial and extra
+judicial costs) that Erasmus MC suffers as a result of such claims.
+
+Article 5 Duration & Termination
+
+5.1 These Terms are effective from the date that the Software is available to You.
+
+5.2 If the license is terminated pursuant to Article 2.4, You will stop using the Software and if requested by Erasmus
+MC, destroy the Software and any copies thereof and will issue a certificate of destruction and provide it to Erasmus
+MC.
+
+Article 6 Applicable law and dispute resolution
+
+6.1 These Terms and Conditions are governed by law of the Netherlands.
+
+6.2 All disputes that may arise as a result of the Conditions or their implementation will be submitted exclusively to
+the competent court in Rotterdam, the Netherlands.

miscore_sim-0.0.998/PKG-INFO

@@ -0,0 +1,33 @@
+Metadata-Version: 2.4
+Name: miscore-sim
+Version: 0.0.998
+Summary: A Python framework for discrete-event microsimulation of diseases and interventions
+Author: Niels Dunnewind et al.
+Maintainer-email: "MISCAN Core team, Department of Public Health, Erasmus University Medical Center" <miscan@erasmusmc.nl>
+Project-URL: Documentation, https://miscore.io
+Project-URL: Source, https://gitlab.com/erasmusmc-public-health/early-detection-and-screening/miscore
+Project-URL: Issues, https://gitlab.com/erasmusmc-public-health/early-detection-and-screening/miscore/-/issues
+Classifier: Development Status :: 5 - Production/Stable
+Classifier: Intended Audience :: Science/Research
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Programming Language :: Python :: 3.14
+Requires-Python: >=3.9
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: numpy>=2.0.0
+Requires-Dist: pandas!=1.3.0,>=1
+Requires-Dist: tqdm>=4.40
+Requires-Dist: matplotlib>=3
+Requires-Dist: scipy>=1
+Dynamic: license-file
+
+# MISCore
+
+The MISCAN Core, or MISCore, is a Python modelling platform for discrete-event microsimulation. 
+
+Please read the documentation at https://miscore.io

miscore_sim-0.0.998/README.md

@@ -0,0 +1,5 @@
+# MISCore
+
+The MISCAN Core, or MISCore, is a Python modelling platform for discrete-event microsimulation. 
+
+Please read the documentation at https://miscore.io

miscore_sim-0.0.998/doc/Makefile

@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = .
+BUILDDIR      = _build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)