modelly-abm 1.0.0__tar.gz

modelly_abm-1.0.0/.coderabbit.yaml

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+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: []

modelly_abm-1.0.0/.gitattributes

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+# Normalise line endings so a checkout on Windows never dirties the tree.
+* text=auto eol=lf
+*.bat text eol=crlf
+*.png binary
+*.ico binary
+
+# Notebooks are text; keep tutorial notebooks output-free so their diffs stay reviewable.
+*.ipynb text
+
+# Generated files: collapsed in pull-request diffs and excluded from language statistics.
+docs/images/branding/*.svg linguist-generated
+docs/examples/** linguist-generated
+pelloux-baseline.json linguist-generated
+
+# Documentation and examples should not skew the repository's language breakdown.
+docs/** linguist-documentation
+benchmarks/** linguist-vendored=false
+
+# Keep local-only material out of release archives (git archive, GitHub source zips).
+benchmarks/mesa_baseline/ export-ignore
+benchmarks/mesaVSmodelly/ export-ignore
+.github/ export-ignore
+.pre-commit-config.yaml export-ignore

modelly_abm-1.0.0/.github/CODEOWNERS

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+# Review requests are routed to these owners automatically.
+# The last matching pattern wins.
+
+*                       @RemiPelloux
+
+/modelly/               @RemiPelloux
+/docs/                  @RemiPelloux
+/.github/               @RemiPelloux
+/pyproject.toml         @RemiPelloux
+/pelloux-guidelines.md  @RemiPelloux
+/pelloux-baseline.json  @RemiPelloux

modelly_abm-1.0.0/.github/ISSUE_TEMPLATE/bug-report.md

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+---
+name: Bug report
+about: Let us know if something is broken on Modelly
+
+---
+
+**Describe the bug**
+<!-- A clear and concise description the bug -->
+
+**Expected behavior**
+<!-- 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
+Include a Minimal reproducible example: https://stackoverflow.com/help/minimal-reproducible-example -->
+
+**Additional context**
+<!--
+    Add any other context here.
+    Any details about your specific platform:
+    * If the problem is in the browser, what browser, version, and OS?
+-->

modelly_abm-1.0.0/.github/ISSUE_TEMPLATE/config.yml

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+blank_issues_enabled: true
+contact_links:
+  - name: Questions, ideas, showcases and more
+    url: https://github.com/RemiPelloux/Modelly/discussions
+    about: Discuss Modelly, ask questions, share ideas, and showcase your projects

modelly_abm-1.0.0/.github/ISSUE_TEMPLATE/feature-request.md

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+---
+name: Feature request
+about: Suggest a new feature for Modelly
+
+---
+
+**What's the problem this feature will solve?**
+<!-- A clear and concise description of what the problem is. -->
+
+**Describe the solution you'd like**
+<!-- A clear and concise description of what you want to happen. -->
+
+**Are you planning to open a PR for this?**
+<!-- For enhancements/new features, please wait for maintainer approval on this issue/discussion before opening a PR. -->
+
+**Additional context**
+<!-- Add any other context, links, etc. about the feature here. -->

modelly_abm-1.0.0/.github/PULL_REQUEST_TEMPLATE/bug.md

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+> [!NOTE]
+> Use this template for bug fixes only. For enhancements/new features, use the feature template and get maintainer approval in an issue/discussion before opening a PR.
+
+### Pre-PR Checklist
+- [ ] This PR is a bug fix, not a new feature or enhancement.
+
+### 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.
+-->

modelly_abm-1.0.0/.github/PULL_REQUEST_TEMPLATE/feature.md

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+> [!IMPORTANT]
+> For enhancements and new features, include the issue/discussion where a maintainer approved this work before opening a PR. Unapproved feature/enhancement PRs may be closed.
+
+### Pre-PR Checklist
+- [ ] I linked an issue/discussion where a maintainer approved this enhancement/feature for implementation.
+
+### Approval Link
+<!-- Link to the issue/discussion comment where a maintainer confirmed this is ready for a PR. -->
+
+### 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. -->

modelly_abm-1.0.0/.github/dependabot.yml

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+version: 2
+updates:
+  # Maintain dependencies for GitHub Actions
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      # Check for updates to GitHub Actions every week
+      interval: "weekly"

modelly_abm-1.0.0/.github/pull_request_template.md

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+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)
+
+Feature/enhancement PRs require prior maintainer approval in an issue or discussion before they are accepted.

modelly_abm-1.0.0/.github/release.yml

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+# Docs: https://docs.github.com/en/repositories/releasing-projects-on-github/automatically-generated-release-notes
+changelog:
+  exclude:
+    labels:
+      - ignore-for-release
+  categories:
+    - title: ⚠️ Breaking changes
+      labels:
+        - breaking
+    - title: ⏳ Deprecations
+      labels:
+        - deprecation
+    - title: 🧪 Experimental
+      labels:
+        - experimental
+    - title: 🎉 New features added
+      labels:
+        - feature
+    - title: 🛠 Enhancements made
+      labels:
+        - enhancement
+    - title: 🐛 Bugs fixed
+      labels:
+        - bug
+    - title: ⚡ Performance improvements
+      labels:
+        - performance
+    - title: 🔍 Examples updated
+      labels:
+        - example
+    - title: 📜 Documentation improvements
+      labels:
+        - docs
+    - title: 🔧 Maintenance
+      labels:
+        - ci
+        - testing
+        - dependency
+        - maintenance
+        - packaging
+    - title: Other changes
+      labels:
+        - "*"

modelly_abm-1.0.0/.github/styles/Modelly/README.md

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+# Vale Configuration for Modelly
+
+Vale is a syntax-aware prose linter that helps maintain consistent, high-quality documentation across Modelly's markdown and reStructuredText files.
+
+## How Vale is Configured for Modelly
+
+### Base Style: Google Developer Style Guide
+
+Modelly uses the Google style guide as its foundation because it prioritizes technical clarity and developer documentation over corporate/marketing tone. This aligns well with Modelly's technical, academic audience.
+
+### Configuration Files
+
+- **`.vale.ini`**: Main configuration at repository root
+- **`.github/styles/Modelly/modelly.yml`**: Custom Modelly-specific terminology rules (e.g., "Modelly" vs "modelly", "NumPy" vs "numpy")
+- **`.github/workflows/vale.yml`**: CI workflow that runs on documentation changes
+
+### Alert Levels
+
+Modelly uses a tiered approach:
+
+- **`suggestion`** (default): Google style recommendations are informational only, non-blocking
+- **`warning`**: Important issues shown in CI (via `--minAlertLevel=warning`)
+- **`error`**: Modelly branding rules that must be enforced (e.g., correct capitalization)
+
+### Disabled Google Rules
+
+Many Google rules are disabled for technical documentation:
+
+- **Acronyms, Passive Voice, Semicolons**: Common and acceptable in technical writing
+- **First Person, Contractions**: "We" and formal tone are appropriate for tutorials
+- **Headings, Spacing**: Can have false positives with code examples and formulas
+- **Spelling**: Modelly already uses `codespell` to avoid redundancy
+
+See [`.vale.ini`](../../.vale.ini) for the complete list and rationale.
+
+### Excluded Files
+
+
+## CI Integration
+
+Vale runs automatically on:
+- Pull requests modifying `*.md`, `*.rst`, `*.txt`, or `docs/**`
+- Pushes to `main` branch
+- Manual workflow dispatch from Actions tab
+
+The workflow checks documentation with `--minAlertLevel=warning`, meaning only warnings and errors are reported (suggestions are hidden in CI).
+
+## Understanding Vale Output
+
+### Alert Levels
+
+- 🔵 **suggestion**: Style recommendations (informational, hidden in CI)
+- 🟡 **warning**: Important style issues
+- 🔴 **error**: Critical issues (e.g., incorrect branding)
+
+### Example Output
+
+```
+docs/tutorials/intro.md
+ 15:23  warning  Use 'for example' instead of 'e.g.'.    Google.Latin
+ 28:1   error    'modelly' should be 'Modelly'.                Modelly.Branding
+```
+
+**Reading:**
+- `15:23` = Line 15, Column 23
+- `warning`/`error` = Alert level
+- Middle column = Fix suggestion
+- Right column = Rule that triggered
+
+## Resources
+
+- **Vale Documentation**: https://vale.sh/docs/
+- **Google Style Guide**: https://developers.google.com/style
+- **Installation**: See Vale's [installation guide](https://vale.sh/docs/vale-cli/installation/)
+- **Running locally**: `vale sync` (first time), then `vale *.md docs/`

modelly_abm-1.0.0/.github/styles/Modelly/modelly.yml

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+# styles/Modelly/Branding.yml
+extends: substitution
+message: "Use '%s' instead of '%s'."
+level: error
+ignorecase: true
+swap:
+  # modelly: Modelly
+  # MODELLY: MODELLY
+  # numpy: NumPy
+  # matplotlib: Matplotlib
+  # pytorch: PyTorch
+  # scikit-learn: scikit-learn
+  # dataframe: DataFrame
+  # python: Python

modelly_abm-1.0.0/.github/workflows/benchmarks-comment.yml

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+name: Comment benchmark results
+
+on:
+  workflow_run:
+    workflows: ["Performance benchmarks"]
+    types:
+      - completed
+
+permissions:
+  issues: write
+  pull-requests: write
+
+jobs:
+  comment:
+    if: github.event.workflow_run.conclusion == 'success'
+    runs-on: ubuntu-latest
+    steps:
+      - name: Download benchmark results
+        uses: actions/download-artifact@v8
+        with:
+          name: benchmark-results
+          run-id: ${{ github.event.workflow_run.id }}
+          github-token: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Comment PR
+        uses: actions/github-script@v9
+        with:
+          script: |
+            const fs = require('fs');
+            const prNumber = parseInt(fs.readFileSync('pr_number.txt', 'utf8').trim());
+            const output = fs.readFileSync('benchmark_output.txt', 'utf8');
+            await github.rest.issues.createComment({
+              issue_number: prNumber,
+              owner: context.repo.owner,
+              repo: context.repo.repo,
+              body: 'Performance benchmarks:\n\n' + output
+            });

modelly_abm-1.0.0/.github/workflows/benchmarks.yml

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+name: Performance benchmarks
+
+on:
+  pull_request:
+    types: [opened, ready_for_review, labeled]
+    branches:
+      - main
+    paths:
+      - '**.py'
+      - '.github/workflows/benchmarks.yml'
+
+permissions:
+  contents: read
+
+jobs:
+  run-benchmarks:
+    if: >
+      github.event.action == 'labeled' && contains(github.event.pull_request.labels.*.name, 'trigger-benchmarks') ||
+      github.event.action == 'opened' ||
+      github.event.action == 'ready_for_review'
+    runs-on: ubuntu-latest
+    steps:
+      - name: Set up Python
+        uses: actions/setup-python@v7
+        with:
+          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: uv pip install --system numpy pandas tqdm tabulate matplotlib solara networkx scipy
+
+      # Benchmarks on main
+      - name: Checkout main branch
+        uses: actions/checkout@v7
+        with:
+          ref: main
+          repository: RemiPelloux/Modelly
+      - name: Install Modelly
+        run: pip install --no-deps .
+      - name: Run benchmarks on main branch
+        working-directory: benchmarks
+        run: python global_benchmark.py
+
+      # Upload main benchmarks, then checkout PR
+      - name: Upload benchmark results
+        uses: actions/upload-artifact@v7
+        with:
+          name: timings-main
+          path: benchmarks/timings_1.pickle
+      - name: Checkout PR branch
+        uses: actions/checkout@v7
+        with:
+          ref: ${{ github.event.pull_request.head.ref }}
+          repository: ${{ github.event.pull_request.head.repo.full_name }}
+          fetch-depth: 0
+          persist-credentials: false
+          clean: false
+      - name: Install Modelly of the PR branch
+        run: pip install --no-deps .
+      - name: Download benchmark results
+        uses: actions/download-artifact@v8
+        with:
+          name: timings-main
+          path: benchmarks
+
+      # Run benchmarks on PR and compare
+      - name: Run benchmarks on PR branch
+        working-directory: benchmarks
+        run: python global_benchmark.py
+      - name: Run compare timings
+        working-directory: benchmarks
+        run: python compare_timings.py > benchmark_output.txt
+
+      # Save PR number and results for the comment workflow
+      - name: Save PR number
+        run: echo "${{ github.event.pull_request.number }}" > benchmarks/pr_number.txt
+      - name: Upload benchmark comparison
+        uses: actions/upload-artifact@v7
+        with:
+          name: benchmark-results
+          path: |
+            benchmarks/benchmark_output.txt
+            benchmarks/pr_number.txt

modelly_abm-1.0.0/.github/workflows/build_lint.yml

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+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
+    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/RemiPelloux/Modelly/issues/1253
+          #- os: ubuntu
+          #  python-version: 'pypy-3.8'
+
+    steps:
+      - uses: actions/checkout@v7
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v7
+        with:
+          python-version: ${{ matrix.python-version }}
+          allow-prereleases: true
+          cache: "pip"
+      - name: Install uv
+        run: pip install uv
+      - name: Install Modelly and dependencies
+        run: uv pip install --system .[dev] ${{ matrix.pip-pre }}
+      - name: Setup Playwright
+        run: playwright install chromium-headless-shell
+      - name: Test with pytest
+        run: pytest --durations=10 tests/ -Werror -Wdefault::PendingDeprecationWarning
+
+  coverage:
+    runs-on: ubuntu-latest
+    timeout-minutes: 6
+    steps:
+      - uses: actions/checkout@v7
+      - uses: actions/setup-python@v7
+        with:
+          python-version: "3.14"
+      - run: pip install uv
+      - run: uv pip install --system .[dev]
+      - run: playwright install chromium-headless-shell
+      - run: python -Im pytest -p pytest_cov --cov --cov-report=xml --cov-report=markdown-append:"${GITHUB_STEP_SUMMARY}" --cov-context=test tests/
+      - uses: codecov/codecov-action@v7
+        with:
+          fail_ci_if_error: true
+          token: ${{ secrets.CODECOV_TOKEN }}
+
+  examples:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v7
+      - name: Set up Python
+        uses: actions/setup-python@v7
+        with:
+          python-version: "3.13"
+          allow-prereleases: true
+          cache: "pip"
+      - name: Install uv
+        run: pip install uv
+      - name: Install Modelly
+        run: uv pip install --system .[examples]
+      - name: Checkout modelly-examples
+        uses: actions/checkout@v7
+        with:
+          repository: RemiPelloux/Modelly-examples
+          path: modelly-examples
+      - name: Test examples
+        run: |
+          cd modelly-examples
+          pytest -rA -Werror -Wdefault::PendingDeprecationWarning test_examples.py