Mesa 2.3.0__tar.gz → 3.4.0__tar.gz

mesa-3.4.0/.coderabbit.yaml

@@ -0,0 +1,137 @@
+language: en-US
+tone_instructions: ''
+early_access: false
+enable_free_tier: true
+reviews:
+  profile: chill
+  request_changes_workflow: false
+  high_level_summary: true
+  high_level_summary_placeholder: '@coderabbitai summary'
+  high_level_summary_in_walkthrough: false
+  auto_title_placeholder: '@coderabbitai'
+  auto_title_instructions: ''
+  review_status: false
+  commit_status: true
+  fail_commit_status: false
+  collapse_walkthrough: false
+  changed_files_summary: true
+  sequence_diagrams: true
+  assess_linked_issues: true
+  related_issues: true
+  related_prs: true
+  suggested_labels: true
+  auto_apply_labels: false
+  suggested_reviewers: true
+  auto_assign_reviewers: false
+  poem: true
+  labeling_instructions: []
+  path_filters: []
+  path_instructions: []
+  abort_on_close: true
+  disable_cache: false
+  auto_review:
+    enabled: false
+    auto_incremental_review: false
+    ignore_title_keywords: []
+    labels: []
+    drafts: false
+    base_branches: []
+  finishing_touches:
+    docstrings:
+      enabled: true
+  tools:
+    ast-grep:
+      rule_dirs: []
+      util_dirs: []
+      essential_rules: true
+      packages: []
+    shellcheck:
+      enabled: true
+    ruff:
+      enabled: true
+    markdownlint:
+      enabled: true
+    github-checks:
+      enabled: true
+      timeout_ms: 180000
+    languagetool:
+      enabled: true
+      enabled_rules: []
+      disabled_rules: []
+      enabled_categories: []
+      disabled_categories: []
+      enabled_only: false
+      level: default
+    biome:
+      enabled: true
+    hadolint:
+      enabled: true
+    swiftlint:
+      enabled: true
+    phpstan:
+      enabled: true
+      level: default
+    golangci-lint:
+      enabled: true
+    yamllint:
+      enabled: true
+    gitleaks:
+      enabled: true
+    checkov:
+      enabled: true
+    detekt:
+      enabled: true
+    eslint:
+      enabled: true
+    rubocop:
+      enabled: true
+    buf:
+      enabled: true
+    regal:
+      enabled: true
+    actionlint:
+      enabled: true
+    pmd:
+      enabled: true
+    cppcheck:
+      enabled: true
+    semgrep:
+      enabled: true
+    circleci:
+      enabled: true
+    sqlfluff:
+      enabled: true
+    prismaLint:
+      enabled: true
+    oxc:
+      enabled: true
+    shopifyThemeCheck:
+      enabled: true
+chat:
+  auto_reply: true
+  create_issues: true
+  integrations:
+    jira:
+      usage: auto
+    linear:
+      usage: auto
+knowledge_base:
+  opt_out: false
+  web_search:
+    enabled: true
+  learnings:
+    scope: auto
+  issues:
+    scope: auto
+  jira:
+    usage: auto
+    project_keys: []
+  linear:
+    usage: auto
+    team_keys: []
+  pull_requests:
+    scope: auto
+code_generation:
+  docstrings:
+    language: en-US
+    path_instructions: []

{mesa-2.3.0 → mesa-3.4.0}/.github/ISSUE_TEMPLATE/bug-report.md

@@ -11,7 +11,8 @@ about: Let us know if something is broken on Mesa
 <!-- A clear and concise description of what you expected to happen -->
 
 **To Reproduce**
-<!-- Steps to reproduce the bug, or a link to a project where the bug is visible -->
+<!-- Steps to reproduce the bug, or a link to a project where the bug is visible
+Include a Minimal reproducible example: https://stackoverflow.com/help/minimal-reproducible-example -->
 
 **Additional context**
 <!--

mesa-3.4.0/.github/ISSUE_TEMPLATE/config.yml

@@ -0,0 +1,5 @@
+blank_issues_enabled: true
+contact_links:
+  - name: Questions, ideas, showcases and more
+    url: https://github.com/mesa/mesa/discussions
+    about: Discuss Mesa, ask questions, share ideas, and showcase your projects

mesa-3.4.0/.github/PULL_REQUEST_TEMPLATE/bug.md

@@ -0,0 +1,16 @@
+### Summary
+<!-- Provide a brief summary of the bug and its impact. -->
+
+### Bug / Issue
+<!-- Link to the related issue(s) and describe the bug. Include details like the context, what was expected, and what actually happened. -->
+
+### Implementation
+<!-- Describe the changes made to resolve the issue. Highlight any important parts of the code that were modified. -->
+
+### Testing
+<!-- Detail the testing performed to verify the fix. Include information on test cases, steps taken, and any relevant results.
+
+If you're fixing the visualisation, add before/after screenshots. -->
+
+### Additional Notes
+<!-- Add any additional information that may be relevant for the reviewers, such as potential side effects, dependencies, or related work.

mesa-3.4.0/.github/PULL_REQUEST_TEMPLATE/feature.md

@@ -0,0 +1,16 @@
+### Summary
+<!-- Provide a concise summary of the feature and its purpose. -->
+
+### Motive
+<!-- Explain the reasoning behind this feature. Include details on the problem it addresses or the enhancement it provides. -->
+
+### Implementation
+<!-- Describe how the feature was implemented. Include details on the approach taken, important decisions made, and code changes. -->
+
+### Usage Examples
+<!-- Provide code snippets or examples demonstrating how to use the new feature. Highlight key scenarios where this feature will be beneficial.
+
+If you're modifying the visualisation, add before/after screenshots. -->
+
+### Additional Notes
+<!-- Add any additional information that may be relevant for the reviewers, such as potential side effects, dependencies, or related work. -->

mesa-3.4.0/.github/pull_request_template.md

@@ -0,0 +1,4 @@
+Thanks for opening a PR! Please click the `Preview` tab and select a PR template:
+
+- [🐛 Bug fix](?expand=1&template=bug.md)
+- [🛠 Feature/enhancement](?expand=1&template=feature.md)

{mesa-2.3.0 → mesa-3.4.0}/.github/release.yml

@@ -7,6 +7,9 @@ changelog:
     - title: ⚠️ Breaking changes
       labels:
         - breaking
+    - title: ⏳ Deprecations
+      labels:
+        - deprecation
     - title: 🧪 Experimental features
       labels:
         - experimental
@@ -19,6 +22,9 @@ changelog:
     - title: 🐛 Bugs fixed
       labels:
         - bug
+    - title: 🔍 Examples updated
+      labels:
+        - example
     - title: 📜 Documentation improvements
       labels:
         - docs

{mesa-2.3.0 → mesa-3.4.0}/.github/workflows/benchmarks.yml

@@ -23,19 +23,21 @@ jobs:
     steps:
       # Python and dependency setup
       - name: Set up Python
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@v6
         with:
-          python-version: '3.12'
+          python-version: '3.14'
       - name: Add project directory to PYTHONPATH
         run: echo "PYTHONPATH=$PYTHONPATH:$(pwd)" >> $GITHUB_ENV
+      - name: Install uv
+        run: pip install uv
       - name: Install dependencies
-        run: pip install numpy pandas tqdm tabulate matplotlib solara networkx
-      # Benchmarks on the projectmesa main branch
+        run: uv pip install --system numpy pandas tqdm tabulate matplotlib solara networkx scipy
+      # Benchmarks on the mesa main branch
       - name: Checkout main branch
-        uses: actions/checkout@v4
+        uses: actions/checkout@v6
         with:
           ref: main
-          repository: projectmesa/mesa
+          repository: mesa/mesa
       - name: Install Mesa
         run: pip install --no-deps .
       - name: Run benchmarks on main branch
@@ -43,12 +45,12 @@ jobs:
         run: python global_benchmark.py
       # Upload benchmarks, checkout PR branch, download benchmarks
       - name: Upload benchmark results
-        uses: actions/upload-artifact@v4
+        uses: actions/upload-artifact@v6
         with:
           name: timings-main
           path: benchmarks/timings_1.pickle
       - name: Checkout PR branch
-        uses: actions/checkout@v4
+        uses: actions/checkout@v6
         if: github.event_name == 'pull_request_target'
         with:
           ref: ${{ github.event.pull_request.head.ref }}
@@ -59,7 +61,7 @@ jobs:
       - name: Install Mesa of the PR branch
         run: pip install --no-deps .
       - name: Download benchmark results
-        uses: actions/download-artifact@v4
+        uses: actions/download-artifact@v7
         with:
           name: timings-main
           path: benchmarks
@@ -74,7 +76,7 @@ jobs:
           TIMING_COMPARISON=$(python compare_timings.py | base64 -w 0)  # Base64 encode the output
           echo "TIMING_COMPARISON=$TIMING_COMPARISON" >> $GITHUB_ENV
       - name: Comment PR
-        uses: actions/github-script@v7
+        uses: actions/github-script@v8
         with:
           script: |
             const output = Buffer.from(process.env.TIMING_COMPARISON, 'base64').toString('utf-8');

mesa-3.4.0/.github/workflows/build_lint.yml

@@ -0,0 +1,106 @@
+name: build
+
+on:
+  push:
+    branches:
+      - main
+      - release**
+    paths-ignore:
+      - "**.md"
+  pull_request:
+    paths-ignore:
+      - "**.md"
+  workflow_dispatch:
+  schedule:
+    - cron: "0 6 * * 1"
+
+# This will cancel previous run if a newer job that obsoletes the said previous
+# run, is started.
+# Based on https://github.com/zulip/zulip/commit/4a11642cee3c8aec976d305d51a86e60e5d70522
+concurrency:
+  group: "${{ github.workflow }}-${{ github.head_ref || github.run_id }}"
+  cancel-in-progress: true
+
+jobs:
+  build:
+    runs-on: ${{ matrix.os }}-latest
+    # We need an explicit timeout because sometimes the batch_runner test never
+    # completes.
+    timeout-minutes: 6
+    strategy:
+      fail-fast: False
+      matrix:
+        os: [windows, ubuntu, macos]
+        python-version: ["3.14"]
+        pip-pre: [""]
+        include:
+          - os: ubuntu
+            python-version: "3.13"
+          - os: ubuntu
+            python-version: "3.12"
+          - os: ubuntu
+            python-version: "3.14"
+            pip-pre: "--pre"
+          # Disabled for now. See https://github.com/mesa/mesa/issues/1253
+          #- os: ubuntu
+          #  python-version: 'pypy-3.8'
+
+    steps:
+      - uses: actions/checkout@v6
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v6
+        with:
+          python-version: ${{ matrix.python-version }}
+          allow-prereleases: true
+          cache: "pip"
+      - name: Install uv
+        run: pip install uv
+      - name: Install Mesa and dependencies
+        run: uv pip install --system .[dev] ${{ matrix.pip-pre }}
+      - name: Setup Playwright
+        run: playwright install chromium-headless-shell
+      - name: Test with pytest
+        run: pytest --durations=10 tests/ -Werror -Wdefault::PendingDeprecationWarning
+
+  coverage:
+    runs-on: ubuntu-latest
+    timeout-minutes: 6
+    steps:
+      - uses: actions/checkout@v6
+      - uses: actions/setup-python@v6
+        with:
+          python-version: "3.14"
+      - run: pip install uv
+      - run: uv pip install --system .[dev]
+      - run: playwright install chromium-headless-shell
+      - run: |
+          coverage run -m pytest tests/
+          coverage xml
+      - uses: codecov/codecov-action@v5
+        with:
+          fail_ci_if_error: true
+          token: ${{ secrets.CODECOV_TOKEN }}
+
+  examples:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v6
+      - name: Set up Python
+        uses: actions/setup-python@v6
+        with:
+          python-version: "3.13"
+          allow-prereleases: true
+          cache: "pip"
+      - name: Install uv
+        run: pip install uv
+      - name: Install Mesa
+        run: uv pip install --system .[examples]
+      - name: Checkout mesa-examples
+        uses: actions/checkout@v6
+        with:
+          repository: mesa/mesa-examples
+          path: mesa-examples
+      - name: Test examples
+        run: |
+          cd mesa-examples
+          pytest -rA -Werror -Wdefault::PendingDeprecationWarning test_examples.py

{mesa-2.3.0 → mesa-3.4.0}/.github/workflows/release.yml

@@ -14,6 +14,8 @@ on:
       - '**.md'
       - '**.rst'
   workflow_dispatch:
+  schedule:
+    - cron: '0 6 * * 1'
 
 permissions:
   id-token: write
@@ -26,19 +28,20 @@ jobs:
       id-token: write
     steps:
       - name: Checkout source
-        uses: actions/checkout@v4
+        uses: actions/checkout@v6
       - name: Set up Python
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@v6
         with:
-          python-version: "3.12"
+          python-version: "3.14"
+          allow-prereleases: true
           cache: 'pip'
       - name: Install dependencies
         run: pip install -U pip hatch
       - name: Build distributions
         run: hatch build
       - name: Upload package as artifact to GitHub
-        if: github.repository == 'projectmesa/mesa' && startsWith(github.ref, 'refs/tags')
-        uses: actions/upload-artifact@v4
+        if: github.repository == 'mesa/mesa' && startsWith(github.ref, 'refs/tags')
+        uses: actions/upload-artifact@v6
         with:
           name: package
           path: dist/

{mesa-2.3.0 → mesa-3.4.0}/.gitignore

@@ -1,6 +1,10 @@
 # Benchmarking
 benchmarks/**/*.pickle
 
+# exampledocs
+docs/examples/*
+docs/example.md
+
 # Byte-compiled / optimized / DLL files
 __pycache__/
 *.py[cod]
@@ -15,6 +19,8 @@ __pycache__/
 .Python
 env/
 venv/
+pythonenv*/
+.venv/
 build/
 develop-eggs/
 dist/
@@ -63,6 +69,7 @@ target/
 
 # Jupyter and iPython notebook checkpoints
 *.ipynb_checkpoints
+*.virtual_documents
 
 # Spyder app workspace config file
 .spyderworkspace
@@ -83,10 +90,6 @@ target/
 .dmypy.json
 dmypy.json
 
-# pythonenv
-pythonenv*/
-
 # JS dependencies
 mesa/visualization/templates/external/
 mesa/visualization/templates/js/external/
-

{mesa-2.3.0 → mesa-3.4.0}/.pre-commit-config.yaml

@@ -4,7 +4,7 @@ ci:
 repos:
 - repo: https://github.com/astral-sh/ruff-pre-commit
   # Ruff version.
-  rev: v0.3.5
+  rev: v0.14.7
   hooks:
     # Run the linter.
     - id: ruff
@@ -14,21 +14,17 @@ repos:
     - id: ruff-format
       types_or: [ python, pyi, jupyter ]
 -   repo: https://github.com/asottile/pyupgrade
-    rev: v3.15.2
+    rev: v3.21.2
     hooks:
     -   id: pyupgrade
-        args: [--py38-plus]
+        args: [--py312-plus]
 -   repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.5.0  # Use the ref you want to point at
+    rev: v6.0.0  # Use the ref you want to point at
     hooks:
     -   id: trailing-whitespace
     -   id: check-toml
     -   id: check-yaml
 - repo: https://github.com/codespell-project/codespell
-  rev: v2.2.6
+  rev: v2.4.1
   hooks:
     - id: codespell
-      args: [
-        "--ignore-words",
-        ".codespellignore",
-      ]

{mesa-2.3.0 → mesa-3.4.0}/.readthedocs.yml

@@ -1,5 +1,5 @@
 # Read the Docs configuration file
-# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+# See https://docs.readthedocs.io/stable/config-file/v2.html for details
 
 # Required
 version: 2
@@ -13,9 +13,9 @@ formats:
   - pdf
 
 build:
-  os: "ubuntu-22.04"
+  os: ubuntu-lts-latest
   tools:
-    python: "3"
+    python: latest
 
 # Optionally set the version of Python and requirements required to build your docs
 python:

mesa-3.4.0/CITATION.cff

@@ -0,0 +1,62 @@
+cff-version: "1.2.0"
+authors:
+- family-names: Hoeven
+  given-names: Ewout
+  name-particle: ter
+  orcid: "https://orcid.org/0009-0002-0805-3425"
+- family-names: Kwakkel
+  given-names: Jan
+  orcid: "https://orcid.org/0000-0001-9447-2954"
+- family-names: Hess
+  given-names: Vincent
+  orcid: "https://orcid.org/0000-0002-9242-8500"
+- family-names: Pike
+  given-names: Thomas
+  orcid: "https://orcid.org/0000-0003-1576-0283"
+- family-names: Wang
+  given-names: Boyu
+  orcid: "https://orcid.org/0000-0001-9879-2138"
+- family-names: rht
+  orcid: "https://orcid.org/0009-0002-6902-111X"
+- family-names: Kazil
+  given-names: Jackie
+  orcid: "https://orcid.org/0000-0002-8300-7384"
+doi: 10.5281/zenodo.15090710
+message: If you use this software, please cite our article in the
+  Journal of Open Source Software.
+preferred-citation:
+  authors:
+  - family-names: Hoeven
+    given-names: Ewout
+    name-particle: ter
+    orcid: "https://orcid.org/0009-0002-0805-3425"
+  - family-names: Kwakkel
+    given-names: Jan
+    orcid: "https://orcid.org/0000-0001-9447-2954"
+  - family-names: Hess
+    given-names: Vincent
+    orcid: "https://orcid.org/0000-0002-9242-8500"
+  - family-names: Pike
+    given-names: Thomas
+    orcid: "https://orcid.org/0000-0003-1576-0283"
+  - family-names: Wang
+    given-names: Boyu
+    orcid: "https://orcid.org/0000-0001-9879-2138"
+  - family-names: rht
+    orcid: "https://orcid.org/0009-0002-6902-111X"
+  - family-names: Kazil
+    given-names: Jackie
+    orcid: "https://orcid.org/0000-0002-8300-7384"
+  date-published: 2025-03-28
+  doi: 10.21105/joss.07668
+  issn: 2475-9066
+  issue: 107
+  journal: Journal of Open Source Software
+  publisher:
+    name: Open Journals
+  start: 7668
+  title: "Mesa 3: Agent-based modeling with Python in 2025"
+  type: article
+  url: "https://joss.theoj.org/papers/10.21105/joss.07668"
+  volume: 10
+title: "Mesa 3: Agent-based modeling with Python in 2025"

{mesa-2.3.0 → mesa-3.4.0}/CODE_OF_CONDUCT.md

@@ -5,7 +5,7 @@
 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,
+identity and expression, level of experience, education, socioeconomic status,
 nationality, personal appearance, race, caste, color, religion, or sexual
 identity and orientation.
 
@@ -36,6 +36,16 @@ Examples of unacceptable behavior include:
 * Other conduct which could reasonably be considered inappropriate in a
   professional setting
 
+### AI and LLM Use
+
+AI tools can be valuable for learning, exploring ideas, and accelerating work. We welcome their thoughtful use. To ensure contributions remain meaningful and contributors continue to grow, we ask that you:
+
+* Understand what you submit. Be able to explain and defend any contribution you make. If you cannot, it is not ready to submit.
+* Stay in the driver's seat. Use AI to support your learning and work, not to replace the effort and critical thinking that make you a better developer.
+* Engage meaningfully. Low-effort, AI-generated submissions (issues, PRs, or proposals) without genuine personal engagement are not acceptable.
+
+Maintainers may ask contributors to explain their work. This is part of our commitment to learning and quality—not a test of whether you used AI, but whether you understood and own what you contributed.
+
 ## Enforcement Responsibilities
 
 Community leaders are responsible for clarifying and enforcing our standards of