cgmpy 0.5.2__tar.gz

cgmpy-0.5.2/.editorconfig

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+root = true
+
+# Universal defaults for all files
+[*]
+charset = utf-8
+end_of_line = lf
+insert_final_newline = true
+trim_trailing_whitespace = true
+
+# Python source code
+[*.py]
+indent_style = space
+indent_size = 4
+max_line_length = 100
+
+# Python config files
+[{pyproject.toml,setup.cfg,tox.ini}]
+indent_style = space
+indent_size = 4
+
+# JSON and config files
+[*.{json,jsonc}]
+indent_style = space
+indent_size = 2
+
+# YAML / TOML
+[*.{yml,yaml,toml}]
+indent_style = space
+indent_size = 2
+
+# Markdown — preserve trailing whitespace (significant in some dialects)
+[*.md]
+trim_trailing_whitespace = false
+max_line_length = off
+
+# Shell scripts
+[*.{sh,bash}]
+indent_style = space
+indent_size = 2
+
+# Windows batch files — LF for cross-platform CI/Docker
+[*.{bat,cmd}]
+end_of_line = lf
+
+# PowerShell scripts — LF enforced
+[*.ps1]
+end_of_line = lf
+
+# Makefile — tabs are semantic
+[{Makefile,makefile,*.mk}]
+indent_style = tab
+
+# Lock files — generated, minimize diff noise
+[{uv.lock,package-lock.json,package-lock.yaml,poetry.lock}]
+indent_style = space
+insert_final_newline = true

cgmpy-0.5.2/.gitattributes

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+# GitAttributes — Line Ending & Diff Governance
+# https://git-scm.com/docs/gitattributes
+#
+# CGMPy enforces LF for all text files to ensure consistent
+# cross-platform behavior in CI/CD, packaging, and tooling.
+
+# ------------------------------------------------------------------
+# Default: auto-detect text, force LF
+# ------------------------------------------------------------------
+* text=auto eol=lf
+
+# ------------------------------------------------------------------
+# Source code — explicit text declaration
+# ------------------------------------------------------------------
+*.py       text eol=lf
+*.toml     text eol=lf
+*.json     text eol=lf
+*.jsonc    text eol=lf
+*.yml      text eol=lf
+*.yaml     text eol=lf
+*.md       text eol=lf
+*.rst      text eol=lf
+*.txt      text eol=lf
+*.cfg      text eol=lf
+*.ini      text eol=lf
+
+# Windows scripts — LF enforced for cross-platform CI/Docker
+# (PowerShell and modern cmd.exe handle LF correctly)
+*.bat      text eol=lf
+*.cmd      text eol=lf
+*.ps1      text eol=lf
+
+# ------------------------------------------------------------------
+# Binary assets — do not modify, do not diff as text
+# ------------------------------------------------------------------
+*.png      binary
+*.jpg      binary
+*.jpeg     binary
+*.gif      binary
+*.ico      binary
+*.icns     binary
+*.svg      text eol=lf
+*.woff     binary
+*.woff2    binary
+*.ttf      binary
+*.eot      binary
+*.pdf      binary
+*.pkl      binary
+*.db       binary
+*.parquet  binary
+*.h5       binary
+*.hdf5     binary
+*.feather  binary
+*.zip      binary
+*.tar      binary
+*.gz       binary
+*.7z       binary
+*.whl      binary
+*.egg      binary
+*.exe      binary
+*.dll      binary
+*.so       binary
+*.dylib    binary
+
+# ------------------------------------------------------------------
+# Lock files — generated, minimize diff noise on GitHub
+# ------------------------------------------------------------------
+uv.lock            linguist-generated=true
+poetry.lock        linguist-generated=true
+package-lock.json  linguist-generated=true

cgmpy-0.5.2/.github/ISSUE_TEMPLATE/bug_report.md

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+---
+name: Bug report
+about: Report a bug to help CGMPy improve
+title: "[Bug]: "
+labels: ["bug", "needs-triage"]
+assignees: []
+---
+
+## 🐛 Bug Description
+
+A clear and concise description of what the bug is.
+
+## 📋 Reproduction
+
+Minimal, complete example to reproduce the issue:
+
+```python
+# Paste your code here
+```
+
+## 📊 Data (anonymized!)
+
+If the bug requires specific data:
+
+- **Is the data synthetic or anonymized?** (required — see [SECURITY.md](../SECURITY.md))
+- **What format is it in?** (CSV, Parquet, DataFrame)
+- **How many rows / time span?**
+- **What device does it come from?** (Dexcom, Libre, ...)
+
+> ⚠️ **DO NOT paste real CGM data, even if you think it's anonymous.** Use `python scripts/anonymize_cgm.py` first.
+
+## ✅ Expected Behavior
+
+What you expected to happen.
+
+## ❌ Actual Behavior
+
+What actually happened. Include the full traceback:
+
+```
+Paste the full traceback here
+```
+
+## 🖥️ Environment
+
+- **OS**: (e.g., Windows 11, macOS 14, Ubuntu 22.04)
+- **Python version**: (output of `python --version`)
+- **CGMPy version**: (output of `pip show cgmpy`)
+- **Install method**: (pip, uv, from source)
+- **Optional dependencies installed**: (e.g., `agata`, `pyarrow` version)
+
+## 📝 Additional Context
+
+Add any other context, screenshots, or links here.
+
+## ✅ Checklist
+
+- [ ] I have searched the [existing issues](../../issues) for this bug.
+- [ ] I have read [SECURITY.md](../SECURITY.md) and will **not** include real patient data.
+- [ ] I am using the latest released version of CGMPy (or the latest `main`).

cgmpy-0.5.2/.github/ISSUE_TEMPLATE/feature_request.md

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+---
+name: Feature request
+about: Suggest a new feature for CGMPy
+title: "[Feature]: "
+labels: ["enhancement", "needs-triage"]
+assignees: []
+---
+
+## 🚀 Feature Description
+
+A clear and concise description of the feature you want.
+
+## 💡 Motivation
+
+What problem does this solve? Why is it useful for clinical or research workflows?
+
+## 📐 Proposed API
+
+If you have an idea of the API, sketch it out:
+
+```python
+# Example usage
+from cgmpy.metrics import ...
+
+result = ...
+```
+
+## 🔗 References
+
+- Clinical / academic reference (paper, DOI, URL)
+- Similar feature in another library (e.g., R's `iglu`, Python's `agata`)
+- Related issue or discussion
+
+## 🎯 Acceptance Criteria
+
+- [ ] The metric / loader / plot is implemented.
+- [ ] Unit tests are added (with a known-answer dataset).
+- [ ] Clinical regression test is added (if a published reference exists).
+- [ ] Documentation is updated (`docs/user-guide/...`).
+- [ ] `CHANGELOG.md` `[Unreleased]` is updated.
+- [ ] AGATA parity is checked (if applicable).
+
+## 📊 Priority
+
+How important is this for your work?
+
+- [ ] Blocking my work / study.
+- [ ] Would significantly improve my workflow.
+- [ ] Nice to have.
+
+## ✅ Checklist
+
+- [ ] I have searched the [existing issues](../../issues) for a similar request.
+- [ ] I am willing to submit a PR for this feature (or a draft of it).

cgmpy-0.5.2/.github/ISSUE_TEMPLATE/question.md

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+---
+name: Question
+about: Ask a question about CGMPy
+title: "[Question]: "
+labels: ["question"]
+assignees: []
+---
+
+## ❓ Question
+
+A clear, focused question. If you have multiple, please open multiple issues.
+
+## 📖 What I've Tried
+
+- [ ] Read the [README](../README.md)
+- [ ] Read the [docs/](../docs/)
+- [ ] Searched [existing issues](../../issues) and [discussions](../../discussions)
+- [ ] Searched the [CHANGELOG](../CHANGELOG.md) for breaking changes
+
+## 🖥️ Environment (if relevant)
+
+- **OS**: ...
+- **Python version**: ...
+- **CGMPy version**: ...
+
+## 📝 Additional Context
+
+Code snippets, screenshots, or links that help explain the question.

cgmpy-0.5.2/.github/PULL_REQUEST_TEMPLATE.md

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+---
+name: Pull Request
+about: Submit changes to CGMPy
+title: "[<type>(<scope>)]: <description>"
+---
+
+## 📋 Summary
+
+<!-- Replace this line with a one-paragraph summary of what this PR does. -->
+
+## 🎯 Motivation
+
+<!-- Why is this change needed? What problem does it solve? -->
+
+## 🔧 Changes
+
+<!-- Bullet list of the main changes. -->
+
+- ...
+
+## 📸 Screenshots / Outputs
+
+<!-- If the change affects plots, reports, or UI, include a screenshot or paste the relevant output. -->
+
+## 🧪 Testing
+
+- [ ] I have added or updated unit tests.
+- [ ] I have added a clinical regression test (if a published reference exists).
+- [ ] I have checked AGATA parity (if applicable).
+- [ ] I have run `make lint` and `make test` locally — all pass.
+
+## 📚 Documentation
+
+Per the [Documentation Golden Rule](../AGENTS.md) §3:
+
+- [ ] `docs/user-guide/...` updated (if user-facing).
+- [ ] `docs/api/...` regenerated (auto, on next build).
+- [ ] `CHANGELOG.md` `[Unreleased]` updated (if user-facing).
+- [ ] Docstrings added / updated for new public symbols.
+
+## 🔒 Security
+
+- [ ] No PHI in code, tests, examples, or fixtures.
+- [ ] No hardcoded credentials or secrets.
+- [ ] No new dependencies without justification.
+
+## ⚠️ Breaking Changes
+
+<!-- If this PR introduces breaking changes, describe the migration path. -->
+
+- [ ] No breaking changes.
+- [ ] Breaking change described above, with migration notes.
+
+## 📎 Related Issues
+
+<!-- Use keywords to auto-close: Closes #N, Fixes #N, Relates to #N -->
+
+Closes #
+
+## ✅ Pre-Submit Checklist
+
+- [ ] I have read [CONTRIBUTING.md](../CONTRIBUTING.md).
+- [ ] My branch is up to date with `main` (`git fetch && git rebase origin/main`).
+- [ ] My commit messages follow [Conventional Commits](https://www.conventionalcommits.org/).
+- [ ] The PR title follows Conventional Commits (verified by CI).
+- [ ] I have run `make pre-commit-all` — all hooks pass.
+- [ ] I have updated relevant tests and documentation.

cgmpy-0.5.2/.github/dependabot.yml

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+version: 2
+updates:
+  # Python dependencies (pyproject.toml)
+  - package-ecosystem: "pip"
+    directory: "/"
+    schedule:
+      interval: "weekly"
+      day: "monday"
+      time: "06:00"
+    open-pull-requests-limit: 10
+    labels:
+      - "dependencies"
+      - "python"
+    groups:
+      # Group patch + minor updates into one PR
+      python-minor:
+        patterns:
+          - "*"
+        update-types:
+          - "minor"
+          - "patch"
+      # Major updates are surfaced separately
+      python-major:
+        patterns:
+          - "*"
+        update-types:
+          - "major"
+    commit-message:
+      prefix: "chore(deps)"
+
+  # GitHub Actions
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "weekly"
+      day: "tuesday"
+    open-pull-requests-limit: 5
+    labels:
+      - "dependencies"
+      - "ci"
+    commit-message:
+      prefix: "ci(actions)"

cgmpy-0.5.2/.github/labeler.yml

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+"area/data":
+  - cgmpy/data/**
+"area/metrics":
+  - cgmpy/metrics/**
+"area/plotting":
+  - cgmpy/plotting/**
+"area/analysis":
+  - cgmpy/analysis/**
+"area/agata":
+  - cgmpy/agata/**
+
+"docs":
+  - docs/**
+  - "**/*.md"
+  - "**/*.rst"
+
+"tests":
+  - tests/**
+
+"examples":
+  - examples/**
+
+"ci":
+  - .github/**
+  - .pre-commit-config.yaml
+  - Makefile
+
+"tooling":
+  - pyproject.toml
+  - commitlint.config.cjs
+  - .editorconfig
+  - .gitattributes
+  - .gitignore
+  - .gitmessage
+
+"agents":
+  - .opencode/**
+  - AGENTS.md
+  - .geminiignore

cgmpy-0.5.2/.github/workflows/check-line-endings.yml

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+name: Check Line Endings
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+  workflow_dispatch:
+
+permissions:
+  contents: read
+
+jobs:
+  check-line-endings:
+    name: Enforce LF
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v6
+        with:
+          fetch-depth: 0
+
+      - name: Check for CRLF
+        run: |
+          echo "Checking for CRLF line endings in tracked files..."
+          # Find any tracked file that contains CRLF.
+          # `|| true` masks xargs's exit 123 when no sub-sh returns 0 (i.e. no
+          # files match). The real failure is decided by [ -n "$BAD" ] below.
+          BAD=$(git ls-files -z | xargs -0 -I {} sh -c 'file "{}" 2>/dev/null | grep -q CRLF && echo "{}"' 2>/dev/null || true)
+          if [ -n "$BAD" ]; then
+            echo "::error::The following files have CRLF line endings (should be LF):"
+            echo "$BAD"
+            exit 1
+          fi
+          echo "✅ All tracked files use LF line endings."
+
+      - name: Check for BOM
+        run: |
+          echo "Checking for UTF-8 BOM in tracked files..."
+          # See CRLF step above for the `|| true` rationale.
+          BAD=$(git ls-files -z | xargs -0 -I {} sh -c 'head -c 3 "{}" 2>/dev/null | xxd | grep -q "efbbbf" && echo "{}"' 2>/dev/null || true)
+          if [ -n "$BAD" ]; then
+            echo "::error::The following files have a UTF-8 BOM (should not):"
+            echo "$BAD"
+            exit 1
+          fi
+          echo "✅ No tracked files have a UTF-8 BOM."

cgmpy-0.5.2/.github/workflows/ci.yml

@@ -0,0 +1,149 @@
+name: CI
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+  workflow_dispatch:
+
+# Cancel in-progress runs for the same branch on new pushes
+concurrency:
+  group: ci-${{ github.ref }}
+  cancel-in-progress: true
+
+permissions:
+  contents: read
+
+jobs:
+  # ------------------------------------------------------------------
+  # Lint & format (fast feedback)
+  # ------------------------------------------------------------------
+  lint:
+    name: Lint & format
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v6
+
+      - name: Setup Python
+        uses: actions/setup-python@v6
+        with:
+          python-version: "3.12"
+
+      - name: Install ruff + mypy
+        run: pip install "ruff>=0.6" mypy
+
+      - name: ruff check
+        run: ruff check .
+
+      - name: ruff format check
+        run: ruff format --check .
+
+      - name: mypy
+        run: mypy cgmpy
+
+  # ------------------------------------------------------------------
+  # Security audit + pre-commit
+  # ------------------------------------------------------------------
+  security:
+    name: Security audit
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v6
+
+      - name: Setup Python
+        uses: actions/setup-python@v6
+        with:
+          python-version: "3.12"
+
+      - name: Install bandit + pip-audit + pre-commit
+        run: pip install "bandit[toml]>=1.7" pip-audit pre-commit
+
+      - name: Bandit
+        run: bandit -r cgmpy/ -ll
+
+      - name: pip-audit
+        # Block on known-vulnerable dependencies. CGMPy handles medical
+        # data; a "warning" here is not a soft signal. If a transitive
+        # dependency is flagged, fix it (pin a safe version, replace,
+        # or open an issue) — do not silence the failure.
+        run: pip-audit
+
+      - name: pre-commit
+        run: pre-commit run --all-files --show-diff-on-failure
+
+  # ------------------------------------------------------------------
+  # Test matrix (multi-OS, multi-Python)
+  # ------------------------------------------------------------------
+  test:
+    name: Tests (${{ matrix.os }} · py${{ matrix.python-version }})
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest, windows-latest, macos-latest]
+        python-version: ["3.10", "3.11", "3.12"]
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v6
+
+      - name: Setup Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v6
+        with:
+          python-version: ${{ matrix.python-version }}
+          cache: pip
+
+      - name: Install package + dev deps
+        run: |
+          python -m pip install --upgrade pip
+          pip install -e ".[dev,agata]"
+
+      - name: Run tests
+        run: pytest -v --color=yes
+
+      - name: Upload coverage (Linux only)
+        if: matrix.os == 'ubuntu-latest' && matrix.python-version == '3.12'
+        uses: codecov/codecov-action@v6
+        with:
+          files: ./coverage.xml
+          flags: unittests
+          name: codecov-${{ matrix.os }}-py${{ matrix.python-version }}
+          fail_ci_if_error: false
+        env:
+          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
+
+  # ------------------------------------------------------------------
+  # Test with coverage (Linux + py3.12, generates coverage.xml)
+  # ------------------------------------------------------------------
+  coverage:
+    name: Coverage report
+    runs-on: ubuntu-latest
+    needs: [lint, test]
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v6
+
+      - name: Setup Python
+        uses: actions/setup-python@v6
+        with:
+          python-version: "3.12"
+          cache: pip
+
+      - name: Install package + dev deps
+        run: |
+          python -m pip install --upgrade pip
+          pip install -e ".[dev,agata]"
+
+      - name: Run tests with coverage
+        run: pytest --cov=cgmpy --cov-report=xml --cov-report=term-missing
+
+      - name: Upload coverage to Codecov
+        uses: codecov/codecov-action@v6
+        with:
+          file: ./coverage.xml
+          fail_ci_if_error: false
+        env:
+          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}

cgmpy-0.5.2/.github/workflows/codeql.yml

@@ -0,0 +1,43 @@
+name: CodeQL
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+  schedule:
+    # Run weekly on Mondays at 04:00 UTC
+    - cron: "0 4 * * 1"
+  workflow_dispatch:
+
+permissions:
+  actions: read
+  contents: read
+  security-events: write
+
+jobs:
+  analyze:
+    name: CodeQL (${{ matrix.language }})
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        include:
+          - language: python
+            build-mode: none
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v6
+
+      - name: Initialize CodeQL
+        uses: github/codeql-action/init@v4
+        with:
+          languages: ${{ matrix.language }}
+          build-mode: ${{ matrix.build-mode }}
+          queries: security-and-quality
+
+      - name: Perform CodeQL Analysis
+        uses: github/codeql-action/analyze@v4
+        with:
+          category: "/language:${{ matrix.language }}"