[WIP] Cookie

[alanlujan91]

This pull request includes a variety of changes to improve the project's configuration, documentation, and continuous integration workflows. The most important changes include adding detailed contribution guidelines, setting up continuous integration and continuous deployment workflows, and updating pre-commit hooks.

Configuration and Documentation Improvements:

• .github/CONTRIBUTING.md: Added detailed contribution guidelines, including instructions for setting up a development environment, running tests, and building documentation.
• .readthedocs.yaml: Added a configuration file for Read the Docs to specify the build environment and commands for generating documentation.

Continuous Integration and Deployment:

• .github/workflows/ci.yml: Added a CI workflow to run pre-commit hooks, linting, and tests on multiple operating systems and Python versions.
• .github/workflows/cd.yml: Added a CD workflow to build and publish the package to PyPI upon release.
• .github/dependabot.yml: Configured Dependabot to maintain dependencies for GitHub Actions.

Pre-commit Hooks:

• .pre-commit-config.yaml: Updated and added new pre-commit hooks for code formatting, linting, and validation.

Documentation Updates:

• .github/workflows/documentation.yml: Updated paths and commands to reflect the new documentation structure. [1] [2] [3] [4]
• Documentation/overview/index.rst: Removed outdated documentation structure.

Please ensure your pull request adheres to the following guidelines:

• Tests for new functionality/models or Tests to reproduce the bug-fix in code.
• Updated documentation of features that add new functionality.
• Update CHANGELOG.md with major/minor changes.

[codecov-commenter]

Codecov Report

✅ All modified and coverable lines are covered by tests.
⚠️ Please upload report for BASE (main@ce59965). Learn more about missing BASE report.

Additional details and impacted files

@@           Coverage Diff           @@
##             main    #1514   +/-   ##
=======================================
  Coverage        ?   60.89%           
=======================================
  Files           ?       54           
  Lines           ?    14017           
  Branches        ?        0           
=======================================
  Hits            ?     8535           
  Misses          ?     5482           
  Partials        ?        0           

☔ View full report in Codecov by Harness.
📢 Have feedback on the report? Share it here.

🚀 New features to boost your workflow:

• ❄️ Test Analytics: Detect flaky tests, report on failures, and find test suite problems.

[Copilot]

Pull request overview

This PR migrates the repository toward a Scientific Python “cookiecutter” style project layout, with updated packaging, docs structure, and CI/CD, while adding/relocating a large set of tests and support modules.

Changes:

• Switched packaging/build configuration to Hatch (dynamic VCS versioning), added Nox sessions, and updated dev/test/doc dependency sets.
• Reworked documentation layout under docs/ (Sphinx config + API reference scaffolding) and adjusted notebook execution + docs workflows accordingly.
• Added multiple new modules and extensive test suite additions/updates, plus new CI/CD workflows and Dependabot config.

Reviewed changes

Copilot reviewed 61 out of 279 changed files in this pull request and generated 3 comments.

Show a summary per file

File	Description
pyproject.toml	Moves build system to Hatch, adds Ruff/Mypy/PyLint/Coverage/Pytest config and env metadata.
noxfile.py	Adds Nox automation for lint/tests/docs/build.
.pre-commit-config.yaml	Expands pre-commit hooks (formatting/linting/schema checks).
.github/workflows/ci.yml	Adds multi-OS/multi-Python CI, coverage upload, pre-commit + pylint.
.github/workflows/cd.yml	Adds distribution build and (test-)PyPI publish on release.
.readthedocs.yaml	Adds RTD build steps using uv and Sphinx.
docs/conf.py	Updates Sphinx configuration for new docs layout and type-hints extension.
docs/index.rst	Updates top-level docs navigation to new docs/ structure.
docs/reference/**	Adds API reference scaffolding for tools and models.
docs/overview/**, docs/guides/**	Adds/updates overview and contributor/user guides.
docs/license.md	Adds a license page in docs (needs alignment with repo license).
src/HARK/helpers.py	Introduces filesystem/environment helpers (currently broken due to missing imports/dead code).
src/HARK/parser.py	Adds initial YAML/sympy parsing utilities (currently contains a constructor bug).
src/HARK/parallel.py	Adds Joblib-based parallel command execution helpers.
src/HARK/validators.py	Adds a non_empty argument validator decorator.
src/HARK/models/**	Adds example block-based model definitions and YAML configs (one YAML block has structural indentation issues).
tests/**	Adds/updates a broad unittest/pytest-based test suite (several tests currently won’t behave as intended).

---

💡 Add Copilot custom instructions for smarter, more guided reviews. Learn how to get started.

[Copilot]

In the portfolio_choice block, dynamics: is indented under shocks:, so YAML will treat it as another shock entry rather than a sibling section. Fix the indentation so dynamics is at the same level as shocks and reward.

[Copilot]

CD is configured to run on pushes to main, but other workflows still target master. Align the branch filters so releases/builds run from the repo’s default branch consistently.

[Copilot]

CI is configured to run on pushes to main, but other workflows in this repo (e.g. .github/workflows/examples.yml) still target master. Align the branch filters so CI/CD reliably run on the default branch.