Update from Cookiecutter Template

.github/workflows/github-actions.yml

@@ -19,30 +19,6 @@ jobs:
             toxpython: 'python3.11'
             tox_env: 'docs'
             os: 'ubuntu-latest'
-          - name: 'py38 (ubuntu/x86_64)'
-            python: '3.8'
-            toxpython: 'python3.8'
-            python_arch: 'x64'
-            tox_env: 'py38'
-            cibw_arch: 'x86_64'
-            cibw_build: false
-            os: 'ubuntu-latest'
-          - name: 'py38 (windows/AMD64)'
-            python: '3.8'
-            toxpython: 'python3.8'
-            python_arch: 'x64'
-            tox_env: 'py38'
-            cibw_arch: 'AMD64'
-            cibw_build: false
-            os: 'windows-latest'
-          - name: 'py38 (macos/x86_64)'
-            python: '3.8'
-            toxpython: 'python3.8'
-            python_arch: 'x64'
-            tox_env: 'py38'
-            cibw_arch: 'x86_64'
-            cibw_build: false
-            os: 'macos-latest'
           - name: 'py39 (ubuntu/x86_64)'
             python: '3.9'
             toxpython: 'python3.9'
@@ -66,7 +42,7 @@ jobs:
             tox_env: 'py39'
             cibw_arch: 'x86_64'
             cibw_build: false
-            os: 'macos-latest'
+            os: 'macos-13'
           - name: 'py310 (ubuntu/x86_64)'
             python: '3.10'
             toxpython: 'python3.10'
@@ -90,7 +66,7 @@ jobs:
             tox_env: 'py310'
             cibw_arch: 'x86_64'
             cibw_build: false
-            os: 'macos-latest'
+            os: 'macos-13'
           - name: 'py311 (ubuntu/x86_64)'
             python: '3.11'
             toxpython: 'python3.11'
@@ -139,78 +115,6 @@ jobs:
             cibw_arch: 'x86_64'
             cibw_build: false
             os: 'macos-latest'
-          - name: 'pypy38 (ubuntu/x86_64)'
-            python: 'pypy-3.8'
-            toxpython: 'pypy3.8'
-            python_arch: 'x64'
-            tox_env: 'pypy38'
-            cibw_arch: 'x86_64'
-            cibw_build: false
-            os: 'ubuntu-latest'
-          - name: 'pypy38 (windows/AMD64)'
-            python: 'pypy-3.8'
-            toxpython: 'pypy3.8'
-            python_arch: 'x64'
-            tox_env: 'pypy38'
-            cibw_arch: 'AMD64'
-            cibw_build: false
-            os: 'windows-latest'
-          - name: 'pypy38 (macos/x86_64)'
-            python: 'pypy-3.8'
-            toxpython: 'pypy3.8'
-            python_arch: 'x64'
-            tox_env: 'pypy38'
-            cibw_arch: 'x86_64'
-            cibw_build: false
-            os: 'macos-latest'
-          - name: 'pypy39 (ubuntu/x86_64)'
-            python: 'pypy-3.9'
-            toxpython: 'pypy3.9'
-            python_arch: 'x64'
-            tox_env: 'pypy39'
-            cibw_arch: 'x86_64'
-            cibw_build: false
-            os: 'ubuntu-latest'
-          - name: 'pypy39 (windows/AMD64)'
-            python: 'pypy-3.9'
-            toxpython: 'pypy3.9'
-            python_arch: 'x64'
-            tox_env: 'pypy39'
-            cibw_arch: 'AMD64'
-            cibw_build: false
-            os: 'windows-latest'
-          - name: 'pypy39 (macos/x86_64)'
-            python: 'pypy-3.9'
-            toxpython: 'pypy3.9'
-            python_arch: 'x64'
-            tox_env: 'pypy39'
-            cibw_arch: 'x86_64'
-            cibw_build: false
-            os: 'macos-latest'
-          - name: 'pypy310 (ubuntu/x86_64)'
-            python: 'pypy-3.10'
-            toxpython: 'pypy3.10'
-            python_arch: 'x64'
-            tox_env: 'pypy310'
-            cibw_arch: 'x86_64'
-            cibw_build: false
-            os: 'ubuntu-latest'
-          - name: 'pypy310 (windows/AMD64)'
-            python: 'pypy-3.10'
-            toxpython: 'pypy3.10'
-            python_arch: 'x64'
-            tox_env: 'pypy310'
-            cibw_arch: 'AMD64'
-            cibw_build: false
-            os: 'windows-latest'
-          - name: 'pypy310 (macos/x86_64)'
-            python: 'pypy-3.10'
-            toxpython: 'pypy3.10'
-            python_arch: 'x64'
-            tox_env: 'pypy310'
-            cibw_arch: 'x86_64'
-            cibw_build: false
-            os: 'macos-latest'
     steps:
     - uses: docker/setup-qemu-action@v3
       if: matrix.cibw_arch == 'aarch64'
@@ -274,4 +178,4 @@ jobs:
     steps:
     - uses: codecov/codecov-action@v3
       with:
-        CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
+        CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}

.pre-commit-config.yaml

@@ -6,13 +6,13 @@ 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: main
+    rev: v0.7.0
     hooks:
       - id: ruff
         args: [--fix, --exit-non-zero-on-fix, --show-fixes]
       - id: ruff-format
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: main
+    rev: v5.0.0
     hooks:
       - id: trailing-whitespace
       - id: end-of-file-fixer

.readthedocs.yml

@@ -12,3 +12,8 @@ python:
     - requirements: docs/requirements.txt
     - method: pip
       path: .
+
+# Optionally build your docs in additional formats such as PDF and ePub
+# formats:
+#    - pdf
+#    - epub

LICENSE

@@ -1,9 +1,9 @@
 MIT License
 
-Copyright (c) 2024, Christopher Lorton
+Copyright (c) 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.
+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.

README.MD

@@ -0,0 +1,8 @@
+# LASIK - LASER based SImulation of Kolera
+
+- template created with `cookiecutter --verbose -f -o laser-cholera gh:ionelmc/cookiecutter-pylibrary`
+- `uv` package and project manager: `python3 -m pip install uv`
+  - `uv python install 3.9 3.10 3.11 3.12`
+  - in the `laser-cholera` directory:
+  - `uv venv` optionally specify `--python #` to use a particular versin of Python in the virtual environment
+  - `uv pip install -e .`

README.rst

@@ -14,7 +14,7 @@ Overview
     * - package
       - |version| |wheel| |supported-versions| |supported-implementations| |commits-since|
 .. |docs| image:: https://readthedocs.org/projects/laser-cholera/badge/?style=flat
-    :target: https://readthedocs.org/projects/laser-cholera/
+    :target: https://laser-cholera.readthedocs.org/en/latest/
     :alt: Documentation Status
 
 .. |github-actions| image:: https://github.com/InstituteforDiseaseModeling/laser-cholera/actions/workflows/github-actions.yml/badge.svg
@@ -27,23 +27,23 @@ Overview
 
 .. |version| image:: https://img.shields.io/pypi/v/laser-cholera.svg
     :alt: PyPI Package latest release
-    :target: https://pypi.org/project/laser-cholera
+    :target: https://test.pypi.org/project/laser-cholera
 
 .. |wheel| image:: https://img.shields.io/pypi/wheel/laser-cholera.svg
     :alt: PyPI Wheel
-    :target: https://pypi.org/project/laser-cholera
+    :target: https://test.pypi.org/project/laser-cholera
 
 .. |supported-versions| image:: https://img.shields.io/pypi/pyversions/laser-cholera.svg
     :alt: Supported versions
-    :target: https://pypi.org/project/laser-cholera
+    :target: https://test.pypi.org/project/laser-cholera
 
 .. |supported-implementations| image:: https://img.shields.io/pypi/implementation/laser-cholera.svg
     :alt: Supported implementations
-    :target: https://pypi.org/project/laser-cholera
+    :target: https://test.pypi.org/project/laser-cholera
 
 .. |commits-since| image:: https://img.shields.io/github/commits-since/InstituteforDiseaseModeling/laser-cholera/v0.0.1.svg
     :alt: Commits since latest release
-    :target: https://github.com/InstituteforDiseaseModeling/laser-cholera/compare/v0.0.1...main
+    :target: https://github.com/InstituteforDiseaseModeling/laser-cholera/compare/301d0d2...main
 
 
 
@@ -69,7 +69,7 @@ Documentation
 =============
 
 
-https://laser-cholera.readthedocs.io/
+https://laser-cholera.readthedocs.io/en/latest/
 
 
 Development

docs/conf.py

@@ -26,7 +26,7 @@
 
 html_theme = "furo"
 html_theme_options = {
-    "githuburl": "https://github.com/InstituteforDiseaseModeling/laser-cholera/",
+    # "githuburl": "https://github.com/InstituteforDiseaseModeling/laser-cholera/",
 }
 
 html_use_smartypants = True

pyproject.toml

@@ -7,7 +7,7 @@ requires = [
 extend-exclude = ["static", "ci/templates"]
 line-length = 140
 src = ["src", "tests"]
-target-version = "py38"
+target-version = "py39"
 
 [tool.ruff.lint.per-file-ignores]
 "ci/*" = ["S"]

setup.py

@@ -94,28 +94,27 @@ def read(*names, **kwargs):
         "Programming Language :: Python",
         "Programming Language :: Python :: 3",
         "Programming Language :: Python :: 3 :: Only",
-        "Programming Language :: Python :: 3.8",
         "Programming Language :: Python :: 3.9",
         "Programming Language :: Python :: 3.10",
         "Programming Language :: Python :: 3.11",
         "Programming Language :: Python :: 3.12",
         "Programming Language :: Python :: Implementation :: CPython",
-        "Programming Language :: Python :: Implementation :: PyPy",
         # uncomment if you test on these interpreters:
+        # "Programming Language :: Python :: Implementation :: PyPy",
         # "Programming Language :: Python :: Implementation :: IronPython",
         # "Programming Language :: Python :: Implementation :: Jython",
         # "Programming Language :: Python :: Implementation :: Stackless",
         "Topic :: Utilities",
     ],
     project_urls={
-        "Documentation": "https://laser-cholera.readthedocs.io/",
+        "Documentation": "https://laser-cholera.readthedocs.io/en/latest/",
         "Changelog": "https://laser-cholera.readthedocs.io/en/latest/changelog.html",
         "Issue Tracker": "https://github.com/InstituteforDiseaseModeling/laser-cholera/issues",
     },
     keywords=[
         # eg: "keyword1", "keyword2", "keyword3",
     ],
-    python_requires=">=3.8",
+    python_requires=">=3.9",
     install_requires=[
         "click",
         # eg: "aspectlib==1.1.1", "six>=1.7",
@@ -124,6 +123,7 @@ def read(*names, **kwargs):
         # eg:
         #   "rst": ["docutils>=0.11"],
         #   ":python_version=='3.8'": ["backports.zoneinfo"],
+        "dev": ["tox"],
     },
     entry_points={
         "console_scripts": [

tox.ini

@@ -14,16 +14,12 @@ envlist =
     clean,
     check,
     docs,
-    {py38,py39,py310,py311,py312,pypy38,pypy39,pypy310},
+    {py39,py310,py311,py312},
     report
 ignore_basepython_conflict = true
 
 [testenv]
 basepython =
-    pypy38: {env:TOXPYTHON:pypy3.8}
-    pypy39: {env:TOXPYTHON:pypy3.9}
-    pypy310: {env:TOXPYTHON:pypy3.10}
-    py38: {env:TOXPYTHON:python3.8}
     py39: {env:TOXPYTHON:python3.9}
     py310: {env:TOXPYTHON:python3.10}
     py311: {env:TOXPYTHON:python3.11}
@@ -55,6 +51,7 @@ skip_install = true
 commands =
     python setup.py check --strict --metadata --restructuredtext
     check-manifest .
+    pre-commit autoupdate
     pre-commit run --all-files --show-diff-on-failure
 
 [testenv:docs]