Update README with unified documentation

Author: manzt

README.md

@@ -70,11 +70,12 @@ and understanding are greatly appreciated.
 
 ## Development
 
-**higlass-python** is primarily a Python project, but it includes JavaScript for
-the anywidget-based front-end code (`src/higlass/widget.js`). We use
-[uv](https://github.com/astral-sh/uv) for Python development and
-[deno](https://github.com/denoland/deno) for linting and type-checking
-JavaScript.
+**higlass-python** is a uv workspace monorepo that includes the main library
+and additional packages (e.g., **higlass-schema**). It's primarily a Python
+project, but includes JavaScript for the anywidget-based front-end code
+(`src/higlass/widget.js`). We use [uv](https://github.com/astral-sh/uv) for
+Python development and [deno](https://github.com/denoland/deno) for linting and
+type-checking JavaScript.
 
 All formatting, linting, and tests are enforced in CI.
 
@@ -84,15 +85,25 @@ All commands are run from the root of the project, from a terminal:
 
 #### Python
 
+**Workspace-wide commands** (runs across all packages):
+
 | Command                                         | Action                                        |
 | ----------------------------------------------- | --------------------------------------------- |
 | `uv run jupyter lab`                            | Run Jupyter lab with current package state    |
-| `uv run ruff check --fix && uv run ruff format` | Lint and apply formatting                     |
-| `uv run check`                                  | Check linting rules                           |
-| `uv run ruff format --check`                    | Check formatting                              |
-| `uv run pytest`                                 | Run unit tests                                |
+| `uv run ruff check --fix && uv run ruff format` | Lint and apply formatting across all packages |
+| `uv run ruff format --check`                    | Check formatting across all packages          |
+| `uv run pytest`                                 | Run unit tests across all packages            |
 | `uv run docs/build.py`                          | Build the documentation in `docs/_build/html` |
 
+**Package-specific commands** (run a command within a specific package):
+
+| Command                                          | Action                               |
+| ------------------------------------------------ | ------------------------------------ |
+| `uv run --package higlass-schema pytest`         | Run tests for higlass-schema package |
+| `uv run --package higlass-schema ruff check`     | Lint higlass-schema package          |
+| `uv run --package higlass-schema ruff format`    | Format higlass-schema package        |
+| `uv run --package higlass-schema higlass-schema` | Run higlass-schema CLI               |
+
 #### JavaScript
 
 | Command                            | Action                        |

packages/higlass-schema/README.md

@@ -9,16 +9,13 @@ Pydantic models for HiGlass
 pip install higlass-schema
 ```
 
-🚧 👷
-
-
 ## Development
 
 Try it out:
 
 ```bash
-$ uvx --no-cache --from . higlass-schema check ./example.json # [--verbose]
-$ uvx --no-cache --from . higlass-schema export # prints JSON schema to stdout
+$ uv run higlass-schema check ./example.json # [--verbose]
+$ uv run higlass-schema export # prints JSON schema to stdout
 ```
 
 Testing, linting, & formatting are enforced in CI. Locally, you can run:
@@ -28,10 +25,3 @@ uv run pytest # tests
 uv run ruff check # linting
 uv run ruff format --check # formatting (remove --check to apply)
 ```
-
-## Release
-
-```bash
-git tag -a v0.0.0 -m "v0.0.0"
-git push --follow-tags
-```

packages/higlass-schema/pyproject.toml

@@ -14,9 +14,6 @@ homepage = "https://github.com/higlass/higlass-schema"
 [project.scripts]
 higlass-schema = "higlass_schema.cli:main"
 
-[dependency-groups]
-dev = ["pytest", "ruff"]
-
 [build-system]
 requires = ["uv_build>=0.8.0,<0.9"]
 build-backend = "uv_build"

pyproject.toml

@@ -60,5 +60,14 @@ extend-select = [
   "F811",  # redefintion
 ]
 
+[tool.uv]
+required-version = ">=0.8.0,<0.9.0"
+
+[tool.uv.build-backend]
+module-name = "higlass"
+
 [tool.uv.workspace]
 members = ["packages/*"]
+
+[tool.uv.sources]
+higlass-schema = { workspace = true }