laser-core 0.1.1__tar.gz

laser_core-0.1.1/.cookiecutterrc

@@ -0,0 +1,61 @@
+# This file exists so you can easily regenerate your project.
+#
+# `cookiepatcher` is a convenient shim around `cookiecutter`
+# for regenerating projects (it will generate a .cookiecutterrc
+# automatically for any template). To use it:
+#
+#    pip install cookiepatcher
+#    cookiepatcher gh:ionelmc/cookiecutter-pylibrary laser
+#
+# See:
+#    https://pypi.org/project/cookiepatcher
+#
+# Alternatively, you can run:
+#
+#    cookiecutter --overwrite-if-exists --config-file=laser/.cookiecutterrc gh:ionelmc/cookiecutter-pylibrary
+
+default_context:
+    allow_tests_inside_package: "no"
+    c_extension_function: "longest"
+    c_extension_module: "_lasercore"
+    c_extension_optional: "no"
+    c_extension_support: "no"
+    codacy: "no"
+    codacy_projectid: "[Get ID from https://app.codacy.com/gh/InstituteforDiseaseModeling/laser/settings]"
+    codeclimate: "no"
+    codecov: "yes"
+    command_line_interface: "click"
+    command_line_interface_bin_name: "idmlaser"
+    coveralls: "no"
+    distribution_name: "idmlaser"
+    email: "christopher.lorton@gatesfoundation.org"
+    formatter_quote_style: "double"
+    full_name: "Christopher Lorton"
+    github_actions: "yes"
+    github_actions_osx: "yes"
+    github_actions_windows: "yes"
+    license: "MIT license"
+    package_name: "idmlaser"
+    pre_commit: "yes"
+    project_name: "LASER"
+    project_short_description: "Light Agent Spatial modeling for ERadication."
+    pypi_badge: "yes"
+    pypi_disable_upload: "no"
+    release_date: "today"
+    repo_hosting: "github.com"
+    repo_hosting_domain: "github.com"
+    repo_main_branch: "main"
+    repo_name: "laser"
+    repo_username: "InstituteforDiseaseModeling"
+    scrutinizer: "no"
+    setup_py_uses_setuptools_scm: "no"
+    sphinx_docs: "yes"
+    sphinx_docs_hosting: "https://docs.idmod.org/projects/laser/en/latest/"
+    sphinx_doctest: "no"
+    sphinx_theme: "sphinx-rtd-theme"
+    test_matrix_separate_coverage: "no"
+    version: "0.1.1"
+    version_manager: "bump2version"
+    website: "https://www.idmod.org"
+    year_from: "2023"
+    year_to: "2023"

laser_core-0.1.1/.coveragerc

@@ -0,0 +1,16 @@
+[paths]
+source =
+   src
+   */site-packages
+
+[run]
+branch = true
+source =
+    laser_core
+    tests
+parallel = true
+
+[report]
+show_missing = true
+precision = 2
+omit = *migrations*

laser_core-0.1.1/.editorconfig

@@ -0,0 +1,20 @@
+# see https://editorconfig.org/
+root = true
+
+[*]
+# Use Unix-style newlines for most files (except Windows files, see below).
+end_of_line = lf
+trim_trailing_whitespace = true
+indent_style = space
+insert_final_newline = true
+indent_size = 4
+charset = utf-8
+
+[*.{bat,cmd,ps1}]
+end_of_line = crlf
+
+[*.{yml,yaml}]
+indent_size = 2
+
+[*.tsv]
+indent_style = tab

laser_core-0.1.1/.github/workflows/github-actions.yml

@@ -0,0 +1,137 @@
+name: build
+on: [push, pull_request]
+jobs:
+  test:
+    name: ${{ matrix.name }}
+    runs-on: ${{ matrix.os }}
+    timeout-minutes: 30
+    strategy:
+      fail-fast: false
+      matrix:
+        include:
+          - name: 'check'
+            python: '3.11'
+            toxpython: 'python3.11'
+            tox_env: 'check'
+            os: 'ubuntu-latest'
+          - name: 'docs'
+            python: '3.11'
+            toxpython: 'python3.11'
+            tox_env: 'docs'
+            os: 'ubuntu-latest'
+          - name: 'py39 (ubuntu)'
+            python: '3.9'
+            toxpython: 'python3.9'
+            python_arch: 'x64'
+            tox_env: 'py39'
+            os: 'ubuntu-latest'
+          - name: 'py39 (windows)'
+            python: '3.9'
+            toxpython: 'python3.9'
+            python_arch: 'x64'
+            tox_env: 'py39'
+            os: 'windows-latest'
+          - name: 'py39 (macos x64)'
+            python: '3.9'
+            toxpython: 'python3.9'
+            python_arch: 'x64'
+            tox_env: 'py39'
+            os: 'macos-13'
+          - name: 'py310 (ubuntu)'
+            python: '3.10'
+            toxpython: 'python3.10'
+            python_arch: 'x64'
+            tox_env: 'py310'
+            os: 'ubuntu-latest'
+          - name: 'py310 (windows)'
+            python: '3.10'
+            toxpython: 'python3.10'
+            python_arch: 'x64'
+            tox_env: 'py310'
+            os: 'windows-latest'
+          - name: 'py310 (macos x64)'
+            python: '3.10'
+            toxpython: 'python3.10'
+            python_arch: 'x64'
+            tox_env: 'py310'
+            os: 'macos-13'
+          - name: 'py311 (ubuntu)'
+            python: '3.11'
+            toxpython: 'python3.11'
+            python_arch: 'x64'
+            tox_env: 'py311'
+            os: 'ubuntu-latest'
+          - name: 'py311 (windows)'
+            python: '3.11'
+            toxpython: 'python3.11'
+            python_arch: 'x64'
+            tox_env: 'py311'
+            os: 'windows-latest'
+          - name: 'py311 (macos x64 rosetta)'
+            python: '3.11'
+            toxpython: 'python3.11'
+            python_arch: 'x64'
+            tox_env: 'py311'
+            os: 'macos-latest'
+          - name: 'py312 (ubuntu)'
+            python: '3.12'
+            toxpython: 'python3.12'
+            python_arch: 'x64'
+            tox_env: 'py312'
+            os: 'ubuntu-latest'
+          - name: 'py312 (windows)'
+            python: '3.12'
+            toxpython: 'python3.12'
+            python_arch: 'x64'
+            tox_env: 'py312'
+            os: 'windows-latest'
+          - name: 'py312 (macos x64 rosetta)'
+            python: '3.12'
+            toxpython: 'python3.12'
+            python_arch: 'x64'
+            tox_env: 'py312'
+            os: 'macos-latest'
+          - name: 'py39 (macos arm64 apple silicon)'
+            python: '3.9'
+            toxpython: 'python3.9'
+            python_arch: 'arm64'
+            tox_env: 'py39'
+            os: 'macos-latest'
+          - name: 'py310 (macos arm64 apple silicon)'
+            python: '3.10'
+            toxpython: 'python3.10'
+            python_arch: 'arm64'
+            tox_env: 'py310'
+            os: 'macos-latest'
+          - name: 'py311 (macos arm64 apple silicon)'
+            python: '3.11'
+            toxpython: 'python3.11'
+            python_arch: 'arm64'
+            tox_env: 'py311'
+            os: 'macos-latest'
+          - name: 'py312 (macos arm64 apple silicon)'
+            python: '3.12'
+            toxpython: 'python3.12'
+            python_arch: 'arm64'
+            tox_env: 'py312'
+            os: 'macos-latest'
+    steps:
+    - uses: actions/checkout@v4
+      with:
+        fetch-depth: 0
+    - uses: actions/setup-python@v5
+      with:
+        python-version: ${{ matrix.python }}
+        architecture: ${{ matrix.python_arch }}
+    - name: install dependencies
+      run: |
+        python -mpip install --progress-bar=off -r ci/requirements.txt
+        virtualenv --version
+        pip --version
+        tox --version
+        pip list --format=freeze
+    - name: test
+      env:
+        TOXPYTHON: '${{ matrix.toxpython }}'
+      run: >
+        tox -e ${{ matrix.tox_env }} -v

laser_core-0.1.1/.pre-commit-config.yaml

@@ -0,0 +1,22 @@
+# To install the git pre-commit hooks run:
+#   pre-commit install --install-hooks
+# To update the versions:
+#   pre-commit autoupdate
+exclude: '^(\.tox|ci/templates|\.bumpversion\.cfg)(/|$)'
+# Note the order is intentional to avoid multiple passes of the hooks
+repos:
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.1.6
+    hooks:
+      - id: ruff
+        args: [--fix, --exit-non-zero-on-fix, --show-fixes]
+  - repo: https://github.com/psf/black
+    rev: 23.11.0
+    hooks:
+      - id: black
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.5.0
+    hooks:
+      - id: trailing-whitespace
+      - id: end-of-file-fixer
+      - id: debug-statements

laser_core-0.1.1/.readthedocs.yml

@@ -0,0 +1,28 @@
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+version: 2
+
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.12"
+
+sphinx:
+  configuration: docs/conf.py
+  fail_on_warning: true
+
+formats:
+  - htmlzip
+  - pdf
+
+python:
+  install:
+    - requirements: docs/requirements.txt
+    - method: pip
+      path: .
+      extra_requirements:
+        - test
+
+search:
+  ranking:
+    installation.html: 3
+    laser_core.html: 2

laser_core-0.1.1/AUTHORS.rst

@@ -0,0 +1,8 @@
+
+Authors
+=======
+
+* Christopher Lorton - https://www.idmod.org
+* Jonathan Bloedow - https://www.idmod.org
+* Katherine Rosenfeld - https://www.idmod.org
+* Kevin McCarthy - https://www.idmod.org

laser_core-0.1.1/CHANGELOG.rst

@@ -0,0 +1,8 @@
+
+Changelog
+=========
+
+0.0.1 (2023-11-18)
+------------------
+
+* First release on PyPI.

laser_core-0.1.1/CONTRIBUTING.rst

@@ -0,0 +1,85 @@
+============
+Contributing
+============
+
+Contributions are welcome, and they are greatly appreciated! Every
+little bit helps, and credit will always be given.
+
+Bug reports
+===========
+
+When `reporting a bug <https://github.com/InstituteforDiseaseModeling/laser/issues>`_ please include:
+
+    * Your operating system name and version.
+    * Any details about your local setup that might be helpful in troubleshooting.
+    * Detailed steps to reproduce the bug.
+
+Documentation improvements
+==========================
+
+LASER could always use more documentation, whether as part of the
+official LASER docs, in docstrings, or even on the web in blog posts,
+articles, and such.
+
+Feature requests and feedback
+=============================
+
+The best way to send feedback is to file an issue at https://github.com/InstituteforDiseaseModeling/laser/issues.
+
+If you are proposing a feature:
+
+* Explain in detail how it would work.
+* Keep the scope as narrow as possible, to make it easier to implement.
+* Remember that this is a volunteer-driven project, and that code contributions are welcome :)
+
+Development
+===========
+
+To set up `laser` for local development:
+
+1. Fork `laser <https://github.com/InstituteforDiseaseModeling/laser>`_
+   (look for the "Fork" button).
+2. Clone your fork locally::
+
+    git clone git@github.com:YOURGITHUBNAME/laser.git
+
+3. Create a branch for local development::
+
+    git checkout -b name-of-your-bugfix-or-feature
+
+   Now you can make your changes locally.
+
+4. When you're done making changes run all the checks and docs builder with one command::
+
+    tox
+
+5. Commit your changes and push your branch to GitHub::
+
+    git add .
+    git commit -m "Your detailed description of your changes."
+    git push origin name-of-your-bugfix-or-feature
+
+6. Submit a pull request through the GitHub website.
+
+Pull Request Guidelines
+-----------------------
+
+If you need some code review or feedback while you're developing the code just make the pull request.
+
+For merging, you should:
+
+1. Include passing tests (run ``tox``).
+2. Update documentation when there's new API, functionality etc.
+3. Add a note to ``CHANGELOG.rst`` about the changes.
+4. Add yourself to ``AUTHORS.rst``.
+
+Tips
+----
+
+To run a subset of tests::
+
+    tox -e envname -- pytest -k test_myfeature
+
+To run all the test environments in *parallel*::
+
+    tox -p auto

laser_core-0.1.1/LICENSE

@@ -0,0 +1,9 @@
+MIT License
+
+Copyright (c) 2023 - 2024 Bill & Melinda Gates Foundation
+
+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 (including the next paragraph) 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.

laser_core-0.1.1/MANIFEST.in

@@ -0,0 +1,24 @@
+graft docs
+graft src
+graft ci
+graft tests
+
+include .bumpversion.cfg
+include .cookiecutterrc
+include .coveragerc
+include .editorconfig
+include .github/workflows/github-actions.yml
+include .pre-commit-config.yaml
+include .readthedocs.yml
+include pytest.ini
+include tox.ini
+
+include AUTHORS.rst
+include CHANGELOG.rst
+include CONTRIBUTING.rst
+include LICENSE
+include README.rst
+
+include *.md
+
+global-exclude *.py[cod] __pycache__/* *.so *.dylib .DS_Store

laser_core-0.1.1/PKG-INFO

@@ -0,0 +1,155 @@
+Metadata-Version: 2.1
+Name: laser-core
+Version: 0.1.1
+Summary: Core functionality for the Light Agent Spatial modeling for ERadication toolkit (LASER).
+Author-email: Christopher Lorton <christopher.lorton@gatesfoundation.org>, Jonathan Bloedow <jonathan.bloedow@gatesfoundation.org>, Katherine Rosenfeld <katherine.rosenfeld@gatesfoundation.org>, Kevin McCarthy <kevin.mccarthy@gatesfoundation.org>
+Maintainer-email: Christopher Lorton <christopher.lorton@gatesfoundation.org>, Jonathan Bloedow <jonathan.bloedow@gatesfoundation.org>
+License: MIT License
+        
+        Copyright (c) 2023 - 2024 Bill & Melinda Gates Foundation
+        
+        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 (including the next paragraph) 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: Homepage, https://github.com/InstituteforDiseaseModeling/laser
+Project-URL: Issues, https://github.com/InstituteforDiseaseModeling/laser/issues
+Project-URL: Documentation, https://docs.idmod.org/projects/laser/en/latest/
+Project-URL: Changelog, https://docs.idmod.org/projects/laser/en/latest/changelog.html
+Keywords: spatial modeling,disease eradication,agent-based modeling
+Classifier: Programming Language :: Python :: 3
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python
+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 :: Implementation :: CPython
+Requires-Python: >=3.9
+Description-Content-Type: text/x-rst
+License-File: LICENSE
+License-File: AUTHORS.rst
+Requires-Dist: click
+Requires-Dist: numpy<2.0.0,>=1.26.4
+Requires-Dist: numba~=0.59.1
+Requires-Dist: polars
+Requires-Dist: tqdm
+Requires-Dist: matplotlib
+Requires-Dist: pandas
+Requires-Dist: pytest
+Provides-Extra: dev
+Requires-Dist: pytest>=6.0; extra == "dev"
+Requires-Dist: black; extra == "dev"
+Requires-Dist: flake8; extra == "dev"
+Provides-Extra: docs
+Requires-Dist: sphinx>=1.3; extra == "docs"
+Requires-Dist: sphinx-rtd-theme; extra == "docs"
+Requires-Dist: furo; extra == "docs"
+Provides-Extra: test
+Requires-Dist: pytest>=6.0; extra == "test"
+Requires-Dist: pytest-cov; extra == "test"
+Requires-Dist: scipy; extra == "test"
+
+========
+Overview
+========
+
+.. start-badges
+
+.. list-table::
+    :stub-columns: 1
+
+    * - docs
+      - |docs|
+    * - tests
+      - | |github-actions|
+        | |codecov|
+    * - package
+      - | |version| |wheel| |supported-versions| |supported-implementations|
+        | |commits-since|
+.. |docs| image:: https://readthedocs.org/projects/idmlaser/badge/?style=flat
+    :target: https://docs.idmod.org/projects/laser/en/latest/
+    :alt: Documentation Status
+
+.. |github-actions| image:: https://github.com/InstituteforDiseaseModeling/laser/actions/workflows/github-actions.yml/badge.svg
+    :alt: GitHub Actions Build Status
+    :target: https://github.com/InstituteforDiseaseModeling/laser/actions
+
+.. |codecov| image:: https://codecov.io/gh/InstituteforDiseaseModeling/laser/branch/main/graphs/badge.svg?branch=main
+    :alt: Coverage Status
+    :target: https://app.codecov.io/github/InstituteforDiseaseModeling/laser
+
+.. |version| image:: https://img.shields.io/pypi/v/idmlaser.svg
+    :alt: PyPI Package latest release
+    :target: https://test.pypi.org/project/laser-core/
+
+.. |wheel| image:: https://img.shields.io/pypi/wheel/idmlaser.svg
+    :alt: PyPI Wheel
+    :target: https://test.pypi.org/project/laser-core/
+
+.. |supported-versions| image:: https://img.shields.io/pypi/pyversions/idmlaser.svg
+    :alt: Supported versions
+    :target: https://test.pypi.org/project/laser-core/
+
+.. |supported-implementations| image:: https://img.shields.io/pypi/implementation/idmlaser.svg
+    :alt: Supported implementations
+    :target: https://test.pypi.org/project/laser-core/
+
+.. |commits-since| image:: https://img.shields.io/github/commits-since/InstituteforDiseaseModeling/laser/v0.1.1.svg
+    :alt: Commits since latest release
+    :target: https://github.com/InstituteforDiseaseModeling/laser/compare/v0.1.1...main
+
+
+
+.. end-badges
+
+Light Agent Spatial modeling for ERadication.
+
+* Free software: MIT license
+
+Installation
+============
+
+::
+
+    pip install laser-core
+
+You can also install the in-development version with::
+
+    pip install https://github.com/InstituteforDiseaseModeling/laser/archive/main.zip
+
+
+Documentation
+=============
+
+
+https://docs.idmod.org/projects/laser/en/latest/
+
+
+Development
+===========
+
+To run all the tests run::
+
+    tox
+
+Note, to combine the coverage data from all the tox environments run:
+
+.. list-table::
+    :widths: 10 90
+    :stub-columns: 1
+
+    - - Windows
+      - ::
+
+            set PYTEST_ADDOPTS=--cov-append
+            tox
+
+    - - Other
+      - ::
+
+            PYTEST_ADDOPTS=--cov-append tox