helices 0.1.0__tar.gz

helices-0.1.0/.github/ISSUE_TEMPLATE/bug_report.md

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+---
+name: 🐛 Bug Report
+about: Report a bug to help us improve the project
+title: '[BUG] '
+labels: 'bug'
+assignees: ''
+
+---
+
+## Bug Description
+
+<!-- A clear and concise description of what the bug is -->
+
+## Steps to Reproduce
+
+1.
+2.
+3.
+
+**Code snippet (if applicable):**
+```python
+# Your code here
+```
+
+## Expected Behavior
+
+<!-- A clear description of what you expected to happen -->
+
+## Actual Behavior
+
+<!-- A clear description of what actually happened -->
+
+## Environment
+
+- **OS:** [Windows | MacOS | Linux]
+- **Python Version:**
+- **helices Version:**
+
+## Screenshots/Logs
+
+<!-- If applicable, add screenshots or error logs -->
+
+## Additional Context
+
+<!-- Add any other context about the problem here -->
+
+## Possible Solution
+
+<!-- If you have suggestions on how to fix the bug, please describe them here -->

helices-0.1.0/.github/ISSUE_TEMPLATE/config.yml

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+blank_issues_enabled: false
+contact_links:
+  - name: 💬 Discussion
+    url: https://github.com/VectorInstitute/helix/discussions
+    about: Ask questions or discuss ideas with the community
+  - name: 📖 Documentation
+    url: https://github.com/VectorInstitute/helix#readme
+    about: Check the documentation for setup and usage guides

helices-0.1.0/.github/ISSUE_TEMPLATE/feature_request.md

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+---
+name: ✨ Feature Request
+about: Suggest a new feature or enhancement
+title: '[FEATURE] '
+labels: 'enhancement'
+assignees: ''
+
+---
+
+## Problem Statement
+
+<!-- Is your feature request related to a problem? Describe the problem or use case -->
+
+## Proposed Solution
+
+<!-- A clear description of what you want to happen -->
+
+## Alternative Solutions
+
+<!-- Describe any alternative solutions or features you've considered -->
+
+## Use Cases
+
+<!-- Describe specific use cases where this feature would be valuable -->
+-
+-
+-
+
+## Implementation Ideas
+
+<!-- If you have ideas about how this could be implemented, describe them here -->
+
+## Component Impact
+
+<!-- Which parts of the system would this feature affect? -->
+- [ ] CLI (`helix init` / `helix run` / `helix status`)
+- [ ] Runner / agent loop
+- [ ] Config schema (`helix.yaml`)
+- [ ] Templates
+- [ ] Documentation
+- [ ] Other
+
+## Additional Context
+
+<!-- Add any other context, mockups, or screenshots about the feature request here -->
+
+## Priority
+
+<!-- How important is this feature to you? -->
+- [ ] Nice to have
+- [ ] Would be helpful
+- [ ] Important for my use case
+- [ ] Critical/blocking

helices-0.1.0/.github/dependabot.yml

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+# https://docs.github.com/code-security/dependabot/dependabot-version-updates/configuration-options-for-the-dependabot.yml-file
+
+version: 2
+updates:
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "daily"
+
+  # Keep uv dependencies (uv.lock) up to date
+  - package-ecosystem: "uv"
+    directory: "/"
+    schedule:
+      interval: "daily"

helices-0.1.0/.github/pull_request_template.md

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+## Summary
+
+<!-- Provide a brief description of what this PR does -->
+
+## Type of Change
+
+- [ ] 🐛 Bug fix (non-breaking change that fixes an issue)
+- [ ] ✨ New feature (non-breaking change that adds functionality)
+- [ ] 💥 Breaking change (fix or feature that would cause existing functionality to not work as expected)
+- [ ] 📝 Documentation update
+- [ ] 🔧 Refactoring (no functional changes)
+- [ ] ⚡ Performance improvement
+- [ ] 🧪 Test improvements
+- [ ] 🔒 Security fix
+
+## Changes Made
+
+<!-- List the main changes made in this PR -->
+-
+-
+-
+
+## Testing
+
+<!-- Describe how you tested these changes -->
+- [ ] Tests pass locally (`uv run pytest tests/`)
+- [ ] Type checking passes (`uv run mypy src/helix/`)
+- [ ] Linting passes (`uv run ruff check src/helix/`)
+- [ ] Manual testing performed (describe below)
+
+**Manual testing details:**
+<!-- Describe any manual testing performed -->
+
+## Screenshots/Recordings
+
+<!-- If applicable, add screenshots or recordings to demonstrate the changes -->
+
+## Related Issues
+
+<!-- Link any related issues using "Closes #123" or "Relates to #123" -->
+
+## Checklist
+
+- [ ] Code follows the project's style guidelines
+- [ ] Self-review of code completed
+- [ ] Documentation updated (if applicable)
+- [ ] No sensitive information (API keys, credentials) exposed

helices-0.1.0/.github/workflows/code_checks.yml

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+name: code checks
+permissions:
+  contents: read
+  pull-requests: write
+
+on:
+  push:
+    branches:
+      - main
+    paths:
+      - .pre-commit-config.yaml
+      - .github/workflows/code_checks.yml
+      - '**.py'
+      - uv.lock
+      - pyproject.toml
+  pull_request:
+    branches:
+      - main
+    paths:
+      - .pre-commit-config.yaml
+      - .github/workflows/code_checks.yml
+      - '**.py'
+      - uv.lock
+      - pyproject.toml
+
+jobs:
+  code-checks:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v6.0.2
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v7.6.0
+        with:
+          version: "0.9.11"
+          enable-cache: true
+
+      - name: Set up Python
+        uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405
+        with:
+          python-version-file: ".python-version"
+
+      - name: Install the project
+        run: uv sync --all-extras --dev
+
+      - name: Run pre-commit checks
+        run: |
+          source .venv/bin/activate
+          pre-commit run --all-files
+
+      - name: Seed pip into venv
+        run: uv pip install pip
+
+      - name: pip-audit
+        uses: pypa/gh-action-pip-audit@v1.1.0
+        with:
+          virtual-environment: .venv/
+          ignore-vulns: |
+            CVE-2026-4539

helices-0.1.0/.github/workflows/publish.yml

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+name: publish package
+permissions:
+  contents: read
+  pull-requests: write
+
+on:
+  push:
+    tags:
+      - "v*"
+
+jobs:
+  deploy:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v6.0.2
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v7.6.0
+        with:
+          version: "0.9.11"
+          enable-cache: true
+
+      - name: Set up Python
+        uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405
+        with:
+          python-version-file: ".python-version"
+
+      - name: Install the project
+        run: uv sync --all-extras --dev
+
+      - name: Build package
+        run: uv build
+
+      - name: Publish to PyPI
+        uses: pypa/gh-action-pypi-publish@ed0c53931b1dc9bd32cbe73a98c7f6766f8a527e
+        with:
+          user: __token__
+          password: ${{ secrets.PYPI_API_TOKEN }}
+
+      - name: Create GitHub Release
+        uses: ncipollo/release-action@339a81892b84b4eeb0f6e744e4574d79d0d9b8dd
+        with:
+          artifacts: "dist/*"
+          generateReleaseNotes: true

helices-0.1.0/.github/workflows/unit_tests.yml

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+name: unit tests
+permissions:
+  contents: read
+  pull-requests: write
+
+on:
+  push:
+    branches:
+      - main
+    paths:
+      - .pre-commit-config.yaml
+      - .github/workflows/unit_tests.yml
+      - .github/workflows/code_checks.yml
+      - '**.py'
+      - uv.lock
+      - pyproject.toml
+  pull_request:
+    branches:
+      - main
+    paths:
+      - .pre-commit-config.yaml
+      - .github/workflows/unit_tests.yml
+      - .github/workflows/code_checks.yml
+      - '**.py'
+      - uv.lock
+      - pyproject.toml
+
+jobs:
+  unit-tests:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v6.0.2
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v7.6.0
+        with:
+          version: "0.9.11"
+          enable-cache: true
+
+      - name: Set up Python
+        uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405
+        with:
+          python-version-file: ".python-version"
+
+      - name: Install the project
+        run: uv sync --all-extras --dev
+
+      - name: Run unit tests
+        run: |
+          uv run pytest --cov src/helix --cov-report=xml tests
+
+      - name: Upload coverage to Codecov
+        uses: codecov/codecov-action@57e3a136b779b570ffcdbf80b3bdc90e7fab3de2
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
+          slug: VectorInstitute/helix
+          fail_ci_if_error: false
+          verbose: true

helices-0.1.0/.gitignore

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+# Python
+__pycache__/
+*.py[cod]
+*.pyo
+*.pyd
+*.so
+*.egg
+*.egg-info/
+dist/
+build/
+.eggs/
+
+# Virtual environments
+.venv/
+venv/
+env/
+
+# uv
+.uv/
+
+# Testing
+.pytest_cache/
+.coverage
+htmlcov/
+
+# Mypy
+.mypy_cache/
+
+# Ruff
+.ruff_cache/
+
+# Helix session files (untracked by design)
+run.log
+run.pid
+results.tsv
+
+# Editor
+.vscode/
+.idea/
+*.swp
+*.swo
+coverage.xml

helices-0.1.0/.pre-commit-config.yaml

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+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v6.0.0
+    hooks:
+      - id: trailing-whitespace
+      - id: check-ast
+      - id: check-builtin-literals
+      - id: check-docstring-first
+      - id: check-executables-have-shebangs
+      - id: debug-statements
+      - id: end-of-file-fixer
+      - id: mixed-line-ending
+        args: [--fix=lf]
+      - id: fix-byte-order-marker
+      - id: check-merge-conflict
+      - id: check-symlinks
+      - id: detect-private-key
+      - id: check-yaml
+        args: [--unsafe]
+      - id: check-toml
+
+  - repo: https://github.com/astral-sh/uv-pre-commit
+    rev: 0.9.26
+    hooks:
+      - id: uv-lock
+
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: 'v0.15.8'
+    hooks:
+      - id: ruff-check
+        args: [--fix, --exit-non-zero-on-fix]
+        types_or: [python, jupyter]
+      - id: ruff-format
+        types_or: [python, jupyter]
+
+  - repo: https://github.com/pre-commit/mirrors-mypy
+    rev: v1.19.1
+    hooks:
+      - id: mypy
+        entry: python3 -m mypy --config-file pyproject.toml
+        language: system
+        types: [python]
+        exclude: "tests|examples"
+
+  - repo: https://github.com/crate-ci/typos
+    rev: v1.32.0
+    hooks:
+      - id: typos
+
+ci:
+  autofix_commit_msg: |
+    [pre-commit.ci] Add auto fixes from pre-commit.com hooks
+
+    for more information, see https://pre-commit.ci
+  autofix_prs: true
+  autoupdate_branch: ''
+  autoupdate_commit_msg: '[pre-commit.ci] pre-commit autoupdate'
+  autoupdate_schedule: weekly
+  skip: [mypy]
+  submodules: false

helices-0.1.0/.python-version

@@ -0,0 +1 @@
+3.12.8

helices-0.1.0/CODE_OF_CONDUCT.md

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+# Contributor Covenant Code of Conduct
+
+## Our Pledge
+
+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, 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 a positive environment for our
+community include:
+
+* 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 include:
+
+* 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 email
+  address, without their explicit permission
+* Other conduct which could reasonably be considered inappropriate in a
+  professional setting
+
+## Enforcement Responsibilities
+
+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.
+
+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 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 e-mail 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 to the community leaders responsible for enforcement at
+ai_engineering@vectorinstitute.ai.
+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.
+
+**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 2.0, available at
+https://www.contributor-covenant.org/version/2/0/code_of_conduct.html.
+
+Community Impact Guidelines were inspired by [Mozilla's code of conduct
+enforcement ladder](https://github.com/mozilla/diversity).
+
+[homepage]: https://www.contributor-covenant.org
+
+For answers to common questions about this code of conduct, see the FAQ at
+https://www.contributor-covenant.org/faq. Translations are available at
+https://www.contributor-covenant.org/translations.

helices-0.1.0/CONTRIBUTING.md

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+# Contributing to helix
+
+Thanks for your interest in contributing to helix!
+
+To submit PRs, please fill out the PR template along with the PR. If the PR
+fixes an issue, don't forget to link the PR to the issue!
+
+## Pre-commit hooks
+
+Once the Python virtual environment is set up, you can run pre-commit hooks using:
+
+```bash
+pre-commit run --all-files
+```
+
+## Coding guidelines
+
+For code style, we follow the [PEP 8 style guide](https://peps.python.org/pep-0008/).
+
+For docstrings we use [numpy format](https://numpydoc.readthedocs.io/en/latest/format.html).
+
+We use [ruff](https://docs.astral.sh/ruff/) for code formatting and static analysis,
+and [mypy](https://mypy.readthedocs.io/en/stable/) for type checking. The pre-commit
+hooks will catch errors before you submit a PR.