Merge branch 'projectmesa:main' into Schelling

.github/workflows/benchmarks.yml

@@ -29,7 +29,7 @@ jobs:
       - name: Add project directory to PYTHONPATH
         run: echo "PYTHONPATH=$PYTHONPATH:$(pwd)" >> $GITHUB_ENV
       - name: Install dependencies
-        run: pip install numpy pandas tqdm tabulate
+        run: pip install numpy pandas tqdm tabulate matplotlib solara networkx
       # Benchmarks on the projectmesa main branch
       - name: Checkout main branch
         uses: actions/checkout@v4

.github/workflows/build_lint.yml

@@ -73,7 +73,7 @@ jobs:
     - name: Install Mesa
       run: pip install --no-deps .
     - name: Test with pytest
-      run: pytest --cov=mesa tests/ --cov-report=xml
+      run: pytest --durations=10 --cov=mesa tests/ --cov-report=xml
     - if: matrix.os == 'ubuntu'
       name: Codecov
       uses: codecov/codecov-action@v4

.pre-commit-config.yaml

@@ -24,3 +24,11 @@ repos:
     -   id: trailing-whitespace
     -   id: check-toml
     -   id: check-yaml
+- repo: https://github.com/codespell-project/codespell
+  rev: v2.2.6
+  hooks:
+    - id: codespell
+      args: [
+        "--ignore-words",
+        ".codespellignore",
+      ]

CODE_OF_CONDUCT.md

@@ -1,46 +1,131 @@
-#  Contributor Covenant Code of Conduct
+# Contributor Covenant 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, gender identity and expression, level of experience, nationality, personal appearance, race, religion, or sexual identity and orientation.
+We as members, contributors, and leaders pledge to make participation in our
+community a harassment-free experience for everyone, regardless of age, body
+size, visible or invisible disability, ethnicity, sex characteristics, gender
+identity and expression, level of experience, education, socio-economic status,
+nationality, personal appearance, race, caste, color, religion, or sexual
+identity and orientation.
+
+We pledge to act and interact in ways that contribute to an open, welcoming,
+diverse, inclusive, and healthy community.
 
 ## Our Standards
 
-Examples of behavior that contributes to creating a positive environment include:
+Examples of behavior that contributes to a positive environment for our
+community 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
+* Demonstrating empathy and kindness toward other people
+* Being respectful of differing opinions, viewpoints, and experiences
+* Giving and gracefully accepting constructive feedback
+* Accepting responsibility and apologizing to those affected by our mistakes,
+  and learning from the experience
+* Focusing on what is best not just for us as individuals, but for the overall
+  community
 
-Examples of unacceptable behavior by participants include:
+Examples of unacceptable behavior include:
 
-* The use of sexualized language or imagery and unwelcome sexual attention or advances
-* Trolling, insulting/derogatory comments, and personal or political attacks
+* The use of sexualized language or imagery, and sexual attention or advances of
+  any kind
+* Trolling, insulting or 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
+* Publishing others' private information, such as a physical or email address,
+  without their explicit permission
+* Other conduct which could reasonably be considered inappropriate in a
+  professional setting
 
-## Our Responsibilities
+## Enforcement 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.
+Community leaders are responsible for clarifying and enforcing our standards of
+acceptable behavior and will take appropriate and fair corrective action in
+response to any behavior that they deem inappropriate, threatening, offensive,
+or harmful.
 
-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.
+Community leaders 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, and will communicate reasons for moderation
+decisions when appropriate.
 
 ## 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.
+This Code of Conduct applies within all community spaces, and also applies when
+an individual is officially representing the community in public spaces.
+Examples of representing our community include using an official email address,
+posting via an official social media account, or acting as an appointed
+representative at an online or offline event.
 
 ## Enforcement
 
-Instances of abusive, harassing, or otherwise unacceptable behavior may be reported by using Matrix to direct message a [Mesa administrator](@edgeofchaos:matrix.org). The project team will review and investigate all complaints, and will respond in a way that it deems 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.
+Instances of abusive, harassing, or otherwise unacceptable behavior may be
+reported to the community leaders responsible for enforcement at [@jackiekazil](https://matrix.to/#/@jackiekazil:matrix.org) and/or [@edgeofchaos](https://matrix.to/#/@edgeofchaos:matrix.org). Violations posted as Github comments, discussion, etc maybe also be reported via the [report functionality](https://docs.github.com/en/communities/maintaining-your-safety-on-github/reporting-abuse-or-spam)
+All complaints will be reviewed and investigated promptly and fairly.
+
+All community leaders are obligated to respect the privacy and security of the
+reporter of any incident.
+
+## Enforcement Guidelines
+
+Community leaders will follow these Community Impact Guidelines in determining
+the consequences for any action they deem in violation of this Code of Conduct:
+
+### 1. Correction
+
+**Community Impact**: Use of inappropriate language or other behavior deemed
+unprofessional or unwelcome in the community.
+
+**Consequence**: A private, written warning from community leaders, providing
+clarity around the nature of the violation and an explanation of why the
+behavior was inappropriate. A public apology may be requested.
+
+### 2. Warning
+
+**Community Impact**: A violation through a single incident or series of
+actions.
 
-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.
+**Consequence**: A warning with consequences for continued behavior. No
+interaction with the people involved, including unsolicited interaction with
+those enforcing the Code of Conduct, for a specified period of time. This
+includes avoiding interactions in community spaces as well as external channels
+like social media. Violating these terms may lead to a temporary or permanent
+ban.
+
+### 3. Temporary Ban
+
+**Community Impact**: A serious violation of community standards, including
+sustained inappropriate behavior.
+
+**Consequence**: A temporary ban from any sort of interaction or public
+communication with the community for a specified period of time. No public or
+private interaction with the people involved, including unsolicited interaction
+with those enforcing the Code of Conduct, is allowed during this period.
+Violating these terms may lead to a permanent ban.
+
+### 4. Permanent Ban
+
+**Community Impact**: Demonstrating a pattern of violation of community
+standards, including sustained inappropriate behavior, harassment of an
+individual, or aggression toward or disparagement of classes of individuals.
+
+**Consequence**: A permanent ban from any sort of public interaction within the
+community.
 
 ## Attribution
 
-This Code of Conduct is adapted from the [Contributor Covenant][homepage], version 1.4, available at [http://contributor-covenant.org/version/1/4][version]
+This Code of Conduct is adapted from the [Contributor Covenant][homepage],
+version 2.1, available at
+[https://www.contributor-covenant.org/version/2/1/code_of_conduct.html][v2.1].
+
+Community Impact Guidelines were inspired by
+[Mozilla's code of conduct enforcement ladder][Mozilla CoC].
+
+For answers to common questions about this code of conduct, see the FAQ at
+[https://www.contributor-covenant.org/faq][FAQ]. Translations are available at
+[https://www.contributor-covenant.org/translations][translations].
 
-[homepage]: http://contributor-covenant.org
-[version]: http://contributor-covenant.org/version/1/4/
+[homepage]: https://www.contributor-covenant.org
+[v2.1]: https://www.contributor-covenant.org/version/2/1/code_of_conduct.html
+[Mozilla CoC]: https://github.com/mozilla/diversity
+[FAQ]: https://www.contributor-covenant.org/faq
+[translations]: https://www.contributor-covenant.org/translations

CONTRIBUTING.md

@@ -0,0 +1,110 @@
+# Contributing
+
+As an open source project, Mesa welcomes contributions of many forms, and from beginners to experts. If you are
+curious or just want to see what is happening, we post our development session agendas
+and development session notes on [Mesa discussions]. We also have a threaded discussion forum on [Matrix]
+for casual conversation.
+
+In no particular order, examples include:
+
+- Code patches
+- Bug reports and patch reviews
+- New features
+- Documentation improvements
+- Tutorials
+
+No contribution is too small. Although, contributions can be too big, so let's
+discuss via [Matrix] OR via [an issue].
+
+**To submit a contribution**
+
+- Create a ticket for the item that you are working on.
+- Fork the Mesa repository.
+- [Clone your repository] from Github to your machine.
+- Create a new branch in your fork: `git checkout -b BRANCH_NAME`
+- Run `git config pull.rebase true`. This prevents messy merge commits when updating your branch on top of Mesa main branch.
+- Install an editable version with developer requirements locally: `pip install -e ".[dev]"`
+- Edit the code. Save.
+- Git add the new files and files with changes: `git add FILE_NAME`
+- Git commit your changes with a meaningful message: `git commit -m "Fix issue X"`
+- If implementing a new feature, include some documentation in docs folder.
+- Make sure that your submission works with a few of the examples in the examples repository. If adding a new feature to mesa, please illustrate usage by implementing it in an example.
+- Make sure that your submission passes the [GH Actions build]. See "Testing and Standards below" to be able to run these locally.
+- Make sure that your code is formatted according to [the black] standard (you can do it via [pre-commit]).
+- Push your changes to your fork on Github: `git push origin NAME_OF_BRANCH`.
+- [Create a pull request].
+- Describe the change w/ ticket number(s) that the code fixes.
+- Format your commit message as per [Tim Pope's guideline].
+
+## Testing and Code Standards
+
+```{image} https://codecov.io/gh/projectmesa/mesa/branch/main/graph/badge.svg
+:target: https://codecov.io/gh/projectmesa/mesa
+```
+
+```{image} https://img.shields.io/badge/code%20style-black-000000.svg
+:target: https://github.com/psf/black
+```
+
+As part of our contribution process, we practice continuous integration and use GH Actions to help enforce best practices.
+
+If you're changing previous Mesa features, please make sure of the following:
+
+- Your changes pass the current tests.
+- Your changes pass our style standards.
+- Your changes don't break the models or your changes include updated models.
+- Additional features or rewrites of current features are accompanied by tests.
+- New features are demonstrated in a model, so folks can understand more easily.
+
+To ensure that your submission will not break the build, you will need to install Ruff and pytest.
+
+```bash
+pip install ruff pytest pytest-cov
+```
+
+We test by implementing simple models and through traditional unit tests in the tests/ folder. The following only covers unit tests coverage. Ensure that your test coverage has not gone down. If it has and you need help, we will offer advice on how to structure tests for the contribution.
+
+```bash
+py.test --cov=mesa tests/
+```
+
+With respect to code standards, we follow [PEP8] and the [Google Style Guide]. We use [ruff format] (a more performant alternative to `black`) as an automated code formatter. You can automatically format your code using [pre-commit], which will prevent `git commit` of unstyled code and will automatically apply black style so you can immediately re-run `git commit`. To set up pre-commit run the following commands:
+
+```bash
+pip install pre-commit
+pre-commit install
+```
+
+You should no longer have to worry about code formatting. If still in doubt you may run the following command. If the command generates errors, fix all errors that are returned.
+
+```bash
+ruff .
+```
+
+## Licensing
+
+The license of this project is located in [LICENSE].  By submitting a contribution to this project, you are agreeing that your contribution will be released under the terms of this license.
+
+## Special Thanks
+
+A special thanks to the following projects who offered inspiration for this contributing file.
+
+- [Django]
+- [18F's FOIA]
+- [18F's Midas]
+
+[18f's foia]: https://github.com/18F/foia-hub/blob/master/CONTRIBUTING.md
+[18f's midas]: https://github.com/18F/midas/blob/devel/CONTRIBUTING.md
+[an issue]: https://github.com/projectmesa/mesa/issues
+[black]: https://github.com/psf/black
+[clone your repository]: https://help.github.com/articles/cloning-a-repository/
+[create a pull request]: https://help.github.com/articles/creating-a-pull-request/
+[django]: https://github.com/django/django/blob/master/CONTRIBUTING.rst
+[gh actions build]: https://github.com/projectmesa/mesa/actions/workflows/build_lint.yml
+[google style guide]: https://google.github.io/styleguide/pyguide.html
+[license]: https://github.com/projectmesa/mesa/blob/main/LICENSE
+[matrix]: https://matrix.to/#/#project-mesa:matrix.org`
+[mesa discussions]: https://github.com/projectmesa/mesa/discussions
+[pep8]: https://www.python.org/dev/peps/pep-0008
+[pre-commit]: https://github.com/pre-commit/pre-commit
+[tim pope's guideline]: https://tbaggery.com/2008/04/19/a-note-about-git-commit-messages.html