Updated lychee and README

.context/research.md

@@ -15,7 +15,7 @@ Track technical solutions, explored approaches, and references during developmen
 
 ## References
 
-- [HED Specification](https://hed-specification.readthedocs.io)
+- [HED Specification](https://www.hedtags.org/hed-specification)
 - [HED Python API Docs](https://www.hedtags.org/hed-python/)
-- [HED Resources](https://www.hed-resources.org)
+- [HED Resources](https://www.hedtags.org/hed-resources)
 - [BIDS Specification](https://bids-specification.readthedocs.io)

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

@@ -50,7 +50,7 @@ jobs:
             3. For suggestions: only mention if they clearly improve code quality
 
             Follow the project's code style: ruff formatting, Google-style docstrings,
-            127-char line length, PEP 8. Check for correctness, test coverage, and
+            120-char line length, PEP 8. Check for correctness, test coverage, and
             backward compatibility.
 
             Do not flag stylistic preferences or false positives.

.github/workflows/links.yaml

@@ -38,10 +38,9 @@ jobs:
         run: |
           sphinx-build -b html docs docs/_build/html
 
-      - name: Link Checker on built documentation
+      - name: Link Checker
         id: lychee
         uses: lycheeverse/lychee-action@v2.8.0
         with:
-          # Check the built HTML files recursively (includes internal links)
-          args: --config lychee.toml --verbose --no-progress --max-redirects 10 'docs/_build/html/**/*.html'
+          args: --config lychee.toml --verbose --no-progress --max-redirects 10 'docs/_build/html/**/*.html' README.md RELEASE_GUIDE.md CONTRIBUTING.md
           fail: true

.github/workflows/codespell.yaml → .github/workflows/typos.yaml

@@ -1,5 +1,5 @@
 ---
-name: Codespell
+name: Typos
 
 on:
   push:
@@ -11,7 +11,7 @@ permissions:
   contents: read
 
 jobs:
-  codespell:
+  typos:
     name: Check for spelling errors
     runs-on: ubuntu-latest
 
@@ -25,5 +25,5 @@ jobs:
           enable-cache: true
           cache-dependency-glob: "**/pyproject.toml"
 
-      - name: Run Codespell
-        run: uvx --with tomli codespell .
+      - name: Run typos
+        run: uvx typos

.gitignore

@@ -137,7 +137,6 @@ Desktop.ini
 # Project specific
 schema_cache_test/
 hed_cache/
-spec_tests/hed-specification/tests
 spec_tests/*.json
 
 # GitHub Copilot instructions (project-specific)

.rules/ci_cd.md

@@ -14,12 +14,11 @@
 
 ### Code Quality
 
-| Workflow         | Triggers                 | Python | Description                                  |
-| ---------------- | ------------------------ | ------ | -------------------------------------------- |
-| `ruff.yaml`      | Push + PR to main        | 3.12   | Ruff linter (>=0.8.0)                        |
-| `black.yaml`     | Push + PR (all branches) | 3.12   | Black formatter check (>=24.0.0)             |
-| `codespell.yaml` | Push + PR to main        | 3.10   | Spelling check                               |
-| `mdformat.yaml`  | Push + PR to main        | 3.12   | Markdown format check (docs/ and root \*.md) |
+| Workflow        | Triggers          | Python | Description                                  |
+| --------------- | ----------------- | ------ | -------------------------------------------- |
+| `ruff.yaml`     | Push + PR to main | 3.12   | Ruff linter and formatter check (>=0.8.0)    |
+| `typos.yaml`    | Push + PR to main | 3.10   | Spelling check (typos)                       |
+| `mdformat.yaml` | Push + PR to main | 3.12   | Markdown format check (docs/ and root \*.md) |
 
 ### Documentation
 
@@ -36,6 +35,6 @@
 ## All CI Must Pass Before Merge
 
 - Tests across Python 3.10-3.14
-- Linting (ruff), formatting (black), spelling (codespell), markdown (mdformat)
+- Linting and formatting (ruff check + ruff format), spelling (typos), markdown (mdformat)
 - Documentation builds successfully
 - Package installs correctly in fresh environment

.rules/code_review.md

@@ -2,10 +2,10 @@
 
 ## Before Creating a PR
 
-1. All tests pass: `pytest tests/ --cov` and `pytest spec_tests/`
-2. Linting clean: `ruff check hed/ tests/`
-3. Formatting clean: `black --check hed/ tests/`
-4. Spelling clean: `codespell`
+1. All tests pass: `python -m unittest discover tests -v` and `python -m unittest discover spec_tests -v`
+2. Linting clean: `ruff check . --fix`
+3. Formatting clean: `ruff format --check .`
+4. Spelling clean: `typos`
 5. New functionality has tests (real data, no mocks)
 
 ## PR Review with pr-review-toolkit

.rules/git.md

@@ -3,17 +3,17 @@
 ## Branch Strategy
 
 - `stable`: Released versions on PyPI
-- `main`/`master`: Most recent usable version
-- `develop`: Experimental, evolving features
+- `main`: Most recent usable version on `hed-standard/hed-python`
 - Feature branches: `feature/<issue-number>-short-description`
-- PRs target `develop` branch
+- Development happens on a personal fork of `hed-standard/hed-python`
+- Push feature branches to the forked repository, then open a PR targeting `main` on `hed-standard/hed-python`
 
 ## Commits
 
 - Atomic, focused changes
 - Messages \<50 chars, no emojis
 - No AI attribution in commits or PRs
-- Pre-commit hook runs ruff check + format on staged .py files
+- Precommit: Should run ruff check and format and mdformat locally before to eliminate format errors
 
 ## Submodules
 
@@ -26,20 +26,21 @@ Three submodules under `spec_tests/`, all tracking `main`:
 
 ## PR Process
 
-1. Create issue (except for minor fixes)
-2. Use `gh issue develop` to create branch from `develop`
-3. Implement with atomic commits
-4. Run tests: `pytest tests/ --cov` and `pytest spec_tests/`
-5. Run linting: `ruff check hed/ tests/` and `black --check hed/ tests/`
-6. Create PR targeting `develop`
-7. Run `/review-pr` for code review
-8. Address all critical/important findings
-9. Merge when all CI (12 workflows) is green
+01. Create issue on `hed-standard/hed-python` (except for minor fixes)
+02. Create a feature branch on your fork: `git checkout -b feature/<issue-number>-short-description`
+03. Implement with atomic commits
+04. Run tests: `python -m unittest discover tests -v` and `python -m unittest discover spec_tests -v`
+05. Run linting and formatting check: `ruff check hed/ tests/` and `ruff format --check hed/ tests/`
+06. Push the feature branch to your fork: `git push origin feature/<issue-number>-short-description`
+07. Open a PR from your fork's feature branch targeting `main` on `hed-standard/hed-python`
+08. Run `/review-pr` for code review
+09. Address all critical/important findings
+10. Merge by a maintainer
 
 ## Release Process (see RELEASE_GUIDE.md)
 
 1. Update CHANGELOG.md
-2. Run code quality checks (black, ruff, codespell)
+2. Run code quality checks (ruff check, ruff format, typos)
 3. Run all tests (unit + spec)
 4. Push CHANGELOG PR, merge to main
 5. Create git tag (semantic versioning: MAJOR.MINOR.PATCH)

.rules/python.md

@@ -2,7 +2,7 @@
 
 ## Style
 
-- PEP 8 compliant with 127-char line length (configured in pyproject.toml)
+- PEP 8 compliant with 120-char line length (configured in pyproject.toml)
 - Google-style docstrings for all public classes and functions
 - Type hints where appropriate
 
@@ -13,8 +13,8 @@
   - Max McCabe complexity: 10
   - Excludes: .git, .venv, __pycache__, build, dist, hed/\_version.py, spec_tests submodules
   - Per-file: F401 ignored in `__init__.py` (unused imports are re-exports)
-- **black:** Format (`black hed/ tests/`); 127-char line, targets py310-py314
-- **codespell:** Spell checking; skips binary/data files, ignores domain-specific words (hed, parms, etc.)
+- **ruff format:** Format (`ruff format hed/ tests/`); 120-char line, matches ruff lint config
+- **typos:** Spell checking; skips binary/data files, ignores domain-specific words (hed, parms, etc.)
 
 ## Naming Conventions
 
@@ -33,7 +33,7 @@
 ## Dependencies
 
 - **Core:** click, click-option-group, pandas (\<3.0), numpy (>=2.0.2), openpyxl, defusedxml, inflect, semantic-version, portalocker
-- **Dev:** ruff (>=0.8.0), codespell, black[jupyter], mdformat, mdformat-myst
+- **Dev:** ruff (>=0.8.0), typos (>=1.29.0), mdformat, mdformat-myst
 - **Docs:** sphinx (\<10), furo, sphinx-copybutton, myst-parser, sphinx-autodoc-typehints, linkify-it-py
 - **Test:** coverage
 - **Examples:** jupyter, notebook, nbformat, nbconvert, ipykernel

.rules/testing.md

@@ -2,11 +2,10 @@
 
 ## Framework
 
-- **unittest** is the project standard for writing tests
-- **pytest** as the test runner (supports unittest natively)
+- **unittest** is the project standard for writing and running tests
 - Test files mirror `hed/` package structure under `tests/`
 - Test file naming: `test_<module>.py`
-- No conftest.py or pytest fixtures; uses unittest's `setUp`/`setUpClass`
+- Uses unittest's `setUp`/`setUpClass` (no pytest fixtures or conftest.py)
 
 ## Test Organization (60 test files)
 
@@ -42,13 +41,10 @@ tests/
 
 ```bash
 # All unit tests
-pytest tests/ --cov
-
-# Unittest discovery (alternative)
-python -m unittest discover tests
+python -m unittest discover tests -v
 
 # Spec tests (require submodule init)
-pytest spec_tests/
+python -m unittest discover spec_tests -v
 
 # Specific test file
 python -m unittest tests/models/test_hed_string.py
@@ -57,7 +53,7 @@ python -m unittest tests/models/test_hed_string.py
 python -m unittest tests.models.test_hed_string.TestHedString.test_constructor
 
 # Notebook tests
-pytest tests/test_notebooks.py
+python -m unittest tests.test_notebooks
 ```
 
 ## Test Patterns

CHANGELOG.md

@@ -121,7 +121,7 @@ The main purpose of this release is to clean up the CLI for the hedtools and to
 - `hed/scripts/extract_tabular_summary.py` - Non-BIDS tabular summarization
 - `hed/scripts/script_utils.py` - Shared utility functions for scripts
 
-**Script uilities:**
+**Script utilities:**
 
 - Centralized logging setup across all scripts
 - Standardized validation result formatting

CLAUDE.md

@@ -37,23 +37,22 @@ examples/      - 10 Jupyter notebooks (validation, extraction, summarization wor
 
 ```bash
 # Tests
-pytest tests/ --cov
-python -m unittest discover tests
+python -m unittest discover tests -v
 
 # Spec tests (require submodule init)
-pytest spec_tests/
+python -m unittest discover spec_tests -v
 
 # Linting and formatting
 ruff check --fix --unsafe-fixes hed/ tests/
-black hed/ tests/
-codespell
+ruff format hed/ tests/
+typos
 
 # Documentation
 cd docs && sphinx-build -b html . _build/html
 
 # CLI
 hedpy --help
-hedpy validate string --hed-string "Event" --schema-version 8.3.0
+hedpy validate string --hed-string "Event" --schema-version 8.4.0
 hedpy validate bids-dataset --bids-path /path/to/bids
 hedpy schema convert --input schema.xml --output schema.json
 ```
@@ -62,16 +61,16 @@ hedpy schema convert --input schema.xml --output schema.json
 
 ### Testing: Real Data Only
 
-- unittest framework (project standard); pytest as runner
+- unittest framework (project standard) for both writing and running tests
 - No mocks; real schemas, real HED strings, real files
 - Spec tests via git submodules for official HED test suites
 - Details: `.rules/testing.md`
 
 ### Code Style
 
-- PEP 8; 127-char line length
+- PEP 8; 120-char line length
 - Google-style docstrings for public APIs
-- ruff (E, W, F, N, B, C4 rules), black for formatting, codespell for spelling
+- ruff (E, W, F, N, B, C4 rules + ruff format for formatting), typos for spelling
 - Details: `.rules/python.md`
 
 ### Git and PRs

CONTRIBUTING.md

@@ -93,20 +93,17 @@ This project adheres to a code of conduct that we expect all contributors to fol
 
 We use several tools to maintain code quality:
 
-- **black:** For automatic code formatting
+- **ruff format:** For automatic code formatting
 
   ```bash
   # Check if code is formatted correctly
-  black --check .
+  ruff format --check .
 
   # Automatically format all code
-  black .
+  ruff format .
 
   # Format specific files or directories
-  black hed/ tests/
-
-  # Windows: Use --workers 1 if you encounter file I/O errors
-  black --workers 1 .
+  ruff format hed/ tests/
   ```
 
 - **ruff:** For linting, style checking, and import sorting
@@ -121,10 +118,10 @@ We use several tools to maintain code quality:
   ruff check --fix hed/ tests/
   ```
 
-- **codespell:** For spell checking
+- **typos:** For spell checking
 
   ```bash
-  codespell
+  typos
   ```
 
 ### Documentation Style

README.md

@@ -61,7 +61,7 @@ cd hed-python
 pip install -e .
 
 # Install with optional dependency groups
-pip install -e ".[dev]"       # Development tools (ruff, black, codespell)
+pip install -e ".[dev]"       # Development tools (ruff, typos)
 pip install -e ".[docs]"      # Documentation tools (sphinx, furo)
 pip install -e ".[test]"      # Testing tools (coverage)
 pip install -e ".[examples]"  # Jupyter notebook support
@@ -72,7 +72,7 @@ pip install -e ".[dev,docs,test,examples]"
 
 **Optional dependency groups:**
 
-- `dev` - Code quality tools: ruff (linter), black (formatter), codespell, mdformat
+- `dev` - Code quality tools: ruff (linter + formatter), typos, mdformat
 - `docs` - Documentation generation: sphinx, furo theme, myst-parser
 - `test` - Code coverage reporting: coverage
 - `examples` - Jupyter notebook support: jupyter, notebook, ipykernel
@@ -180,39 +180,32 @@ cd docs
 sphinx-build -b html . _build/html
 ```
 
-To iew the built documentation open `docs/_build/html/index.html` in your browser
+To view the built documentation open `docs/_build/html/index.html` in your browser
 
-### Formatting with Black
+### Code Formatting
 
-This project uses [Black](https://black.readthedocs.io/) for consistent code formatting.
+This project uses [ruff format](https://docs.astral.sh/ruff/formatter/) for consistent code formatting.
 
 ```bash
 # Check if code is properly formatted (without making changes)
-black --check .
+ruff format --check .
 
 # Check and show what would change
-black --check --diff .
+ruff format --check --diff .
 
 # Format all Python code in the repository
-black .
+ruff format .
 
 # Format specific files or directories
-black hed/
-black tests/
+ruff format hed/
+ruff format tests/
 ```
 
-**Windows Users:** If you encounter "I/O operation on closed file" errors, use the `--workers 1` flag:
+**Configuration:** Formatter settings are in `pyproject.toml` under `[tool.ruff.format]` with a line length of 120 characters.
 
-```bash
-black --workers 1 --check .
-black --workers 1 .
-```
-
-**Configuration:** Black settings are in `pyproject.toml` with a line length of 127 characters (matching our ruff configuration).
+**Exclusions:** Ruff automatically excludes `.venv/`, `__pycache__/`, auto-generated files (`hed/_version.py`), and external repos (`spec_tests/hed-examples/`, `spec_tests/hed-schemas/`).
 
-**Exclusions:** Black automatically excludes `.venv/`, `__pycache__/`, auto-generated files (`hed/_version.py`), and external repos (`spec_tests/hed-examples/`, `spec_tests/hed-specification/`).
-
-**CI integration:** All code is automatically checked for Black formatting in GitHub Actions. Run `black .` before committing to ensure your code passes CI checks.
+**CI integration:** All code is automatically checked for formatting in GitHub Actions. Run `ruff format .` before committing to ensure your code passes CI checks.
 
 ## Related repositories
 
@@ -303,3 +296,7 @@ HEDTools is licensed under the MIT License. See [LICENSE](LICENSE) for details.
 - GitHub issues: [https://github.com/hed-standard/hed-python/issues](https://github.com/hed-standard/hed-python/issues)
 - Questions or ideas: [HED discussions](https://github.com/orgs/hed-standard/discussions)
 - Contact: [hed-maintainers@gmail.com](mailto:hed-maintainers@gmail.com)
+
+## Funding
+
+Partial support for this project was provided by [NIH 1R01MH126700-01A1](https://reporter.nih.gov/project-details/10480619).