Claude/add beta disclaimers n xi ai

.claude/settings.local.json

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+{
+  "permissions": {
+    "allow": [
+      "Bash(rm:*)",
+      "Bash(.venv/bin/python -m pytest:*)",
+      "Bash(~/.local/bin/uv venv:*)",
+      "Bash(~/.local/bin/uv pip install:*)"
+    ]
+  }
+}

.gitattributes

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+# Auto detect text files and perform LF normalization
+* text=auto
+
+# Force LF for all text files
+*.py text eol=lf
+*.md text eol=lf
+*.yml text eol=lf
+*.yaml text eol=lf
+*.json text eol=lf
+*.toml text eol=lf
+*.txt text eol=lf
+*.rst text eol=lf
+*.R text eol=lf
+*.Rd text eol=lf
+*.Rnw text eol=lf
+*.bib text eol=lf
+
+# Binary files
+*.png binary
+*.jpg binary
+*.gif binary
+*.ico binary
+*.pdf binary

.github/ISSUE_TEMPLATE/bug_report.md

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+---
+name: Bug Report
+about: Create a report to help us improve sensPy
+---
+
+**Describe the bug**
+A clear and concise description of what the bug is.
+
+**To Reproduce**
+Steps to reproduce the behavior.
+
+**Expected behavior**
+A clear and concise description of what you expected to happen.

.github/pull_request_template.md

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+## Summary
+Describe the changes in this pull request.
+
+## Testing
+- [ ] `pytest`

.github/workflows/auto-comment-gemini-review.yml

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+# Place this file in: .github/workflows/auto-comment-gemini-review.yml
+
+name: Auto Comment Gemini Review
+
+on:
+  push:
+    branches:
+      - '**'  # Trigger on push to any branch
+
+jobs:
+  comment-gemini-review:
+    runs-on: ubuntu-latest
+    permissions:
+      pull-requests: write  # Required to comment on pull requests
+      contents: read       # Required to access repository contents
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+
+      - name: Get branch name
+        id: branch
+        run: echo "branch=${GITHUB_REF#refs/heads/}" >> $GITHUB_OUTPUT
+
+      - name: Check for open pull requests
+        id: check-pr
+        env:
+          GITHUB_TOKEN: ${{ secrets.GEMINI_REVIEW_TOKEN }}  # Use organization secret
+        run: |
+          PR_JSON=$(gh api \
+            -H "Accept: application/vnd.github+json" \
+            "/repos/${{ github.repository }}/pulls?head=${{ github.repository_owner }}:${{ steps.branch.outputs.branch }}&state=open")
+          PR_COUNT=$(echo "$PR_JSON" | jq length)
+          if [ "$PR_COUNT" -gt 0 ]; then
+            PR_NUMBER=$(echo "$PR_JSON" | jq -r '.[0].number')
+            echo "Found open PR #$PR_NUMBER"
+            echo "pr_number=$PR_NUMBER" >> $GITHUB_OUTPUT
+          else
+            echo "No open PR found for branch ${{ steps.branch.outputs.branch }}"
+            echo "pr_number=" >> $GITHUB_OUTPUT
+          fi
+
+      - name: Comment on pull request
+        if: steps.check-pr.outputs.pr_number != ''
+        env:
+          GITHUB_TOKEN: ${{ secrets.GEMINI_REVIEW_TOKEN }}  # Use organization secret
+        run: |
+          gh api \
+            -H "Accept: application/vnd.github+json" \
+            "/repos/${{ github.repository }}/issues/${{ steps.check-pr.outputs.pr_number }}/comments" \
+            -f body='/gemini review'

.github/workflows/claude-code-review.yml

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+name: Claude Code Review
+
+on:
+  pull_request:
+    types: [opened, synchronize]
+    # Optional: Only run on specific file changes
+    # paths:
+    #   - "src/**/*.ts"
+    #   - "src/**/*.tsx"
+    #   - "src/**/*.js"
+    #   - "src/**/*.jsx"
+
+jobs:
+  claude-review:
+    # Optional: Filter by PR author
+    # if: |
+    #   github.event.pull_request.user.login == 'external-contributor' ||
+    #   github.event.pull_request.user.login == 'new-developer' ||
+    #   github.event.pull_request.author_association == 'FIRST_TIME_CONTRIBUTOR'
+
+    runs-on: ubuntu-latest
+    permissions:
+      contents: read
+      pull-requests: read
+      issues: read
+      id-token: write
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 1
+
+      - name: Run Claude Code Review
+        id: claude-review
+        uses: anthropics/claude-code-action@v1
+        with:
+          claude_code_oauth_token: ${{ secrets.CLAUDE_CODE_OAUTH_TOKEN }}
+          prompt: |
+            REPO: ${{ github.repository }}
+            PR NUMBER: ${{ github.event.pull_request.number }}
+
+            Please review this pull request and provide feedback on:
+            - Code quality and best practices
+            - Potential bugs or issues
+            - Performance considerations
+            - Security concerns
+            - Test coverage
+
+            Use the repository's CLAUDE.md for guidance on style and conventions. Be constructive and helpful in your feedback.
+
+            Use `gh pr comment` with your Bash tool to leave your review as a comment on the PR.
+
+          # See https://github.com/anthropics/claude-code-action/blob/main/docs/usage.md
+          # or https://code.claude.com/docs/en/cli-reference for available options
+          claude_args: '--allowed-tools "Bash(gh issue view:*),Bash(gh search:*),Bash(gh issue list:*),Bash(gh pr comment:*),Bash(gh pr diff:*),Bash(gh pr view:*),Bash(gh pr list:*)"'
+

.github/workflows/claude.yml

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+name: Claude Code
+
+on:
+  issue_comment:
+    types: [created]
+  pull_request_review_comment:
+    types: [created]
+  issues:
+    types: [opened, assigned]
+  pull_request_review:
+    types: [submitted]
+
+jobs:
+  claude:
+    if: |
+      (github.event_name == 'issue_comment' && contains(github.event.comment.body, '@claude')) ||
+      (github.event_name == 'pull_request_review_comment' && contains(github.event.comment.body, '@claude')) ||
+      (github.event_name == 'pull_request_review' && contains(github.event.review.body, '@claude')) ||
+      (github.event_name == 'issues' && (contains(github.event.issue.body, '@claude') || contains(github.event.issue.title, '@claude')))
+    runs-on: ubuntu-latest
+    permissions:
+      contents: read
+      pull-requests: read
+      issues: read
+      id-token: write
+      actions: read # Required for Claude to read CI results on PRs
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 1
+
+      - name: Run Claude Code
+        id: claude
+        uses: anthropics/claude-code-action@v1
+        with:
+          claude_code_oauth_token: ${{ secrets.CLAUDE_CODE_OAUTH_TOKEN }}
+
+          # This is an optional setting that allows Claude to read CI results on PRs
+          additional_permissions: |
+            actions: read
+
+          # Optional: Give a custom prompt to Claude. If this is not specified, Claude will perform the instructions specified in the comment that tagged it.
+          # prompt: 'Update the pull request description to include a summary of changes.'
+
+          # Optional: Add claude_args to customize behavior and configuration
+          # See https://github.com/anthropics/claude-code-action/blob/main/docs/usage.md
+          # or https://code.claude.com/docs/en/cli-reference for available options
+          # claude_args: '--allowed-tools Bash(gh pr:*)'
+

.github/workflows/docs.yml

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+name: Deploy Docs
+
+on:
+  push:
+    branches: [master]
+  workflow_dispatch:
+
+permissions:
+  contents: read
+  pages: write
+  id-token: write
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.11'
+
+      - name: Install dependencies
+        run: |
+          pip install mkdocs mkdocs-material mkdocstrings[python]
+
+      - name: Build docs
+        run: mkdocs build
+
+      - name: Upload artifact
+        uses: actions/upload-pages-artifact@v3
+        with:
+          path: site/
+
+  deploy:
+    needs: build
+    runs-on: ubuntu-latest
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+    steps:
+      - name: Deploy to GitHub Pages
+        id: deployment
+        uses: actions/deploy-pages@v4

.github/workflows/publish.yml

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+name: Publish to PyPI
+
+on:
+  release:
+    types: [published]
+  workflow_dispatch:  # Manual trigger
+
+jobs:
+  publish:
+    runs-on: ubuntu-latest
+    environment: pypi
+    permissions:
+      id-token: write  # For trusted publishing
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v4
+
+      - name: Set up Python
+        run: uv python install 3.11
+
+      - name: Build package
+        run: |
+          uv venv .venv
+          uv pip install build
+          uv run python -m build
+
+      - name: Publish to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          # For trusted publishing (no token needed if configured on PyPI)
+          # Or use: password: ${{ secrets.PYPI_API_TOKEN }}
+          packages-dir: dist/

.github/workflows/pytest.yml

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+name: CI
+
+on:
+  push:
+    branches: [master, main]
+  pull_request:
+    branches: [master, main]
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    timeout-minutes: 10
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ['3.10', '3.11', '3.12']
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v4
+
+      - name: Set up Python ${{ matrix.python-version }}
+        run: uv python install ${{ matrix.python-version }}
+
+      - name: Create venv and install dependencies
+        run: |
+          uv venv .venv --python ${{ matrix.python-version }}
+          uv pip install -e .
+          uv pip install pytest pytest-cov
+
+      - name: Run tests with coverage
+        run: uv run pytest tests/ -v --tb=short --cov=senspy --cov-report=xml --cov-report=term-missing
+
+      - name: Upload coverage reports to Codecov
+        if: matrix.python-version == '3.11'
+        uses: codecov/codecov-action@v5
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
+          fail_ci_if_error: false

.gitignore

@@ -1,9 +1,28 @@
-.Rproj.user
-.Rhistory
-.RData
-.Ruserdata
-# Ignore all files ending with a 'tilde' (autogenerated by some
-# programs, e.g. emacs):
-*~
-/doc/
-/Meta/
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*.so
+
+# Virtual environments
+venv/
+.env
+
+# Distribution / packaging
+build/
+dist/
+*.egg-info/
+
+# Misc
+.DS_Store
+
+# Build outputs
+site/
+
+# Test/cache
+.pytest_cache/
+.coverage
+coverage.xml
+htmlcov/
+
+# Virtual environments
+.venv/