Migrate to monorepo with higlass-schema subpackage

.github/dependabot.yml

@@ -9,7 +9,7 @@ updates:
         patterns:
           - "*"
 
-  - package-ecosystem: "pip"
+  - package-ecosystem: "uv"
     directory: "/"
     schedule:
       interval: "weekly"

.github/workflows/ci.yml

@@ -14,9 +14,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
-      - uses: astral-sh/setup-uv@v5
-        with:
-          version: "0.5.x"
+      - uses: astral-sh/setup-uv@v6
       - run: |
           uv run ruff check .
 
@@ -27,9 +25,7 @@ jobs:
         python-version: ["3.8", "3.9", "3.10", "3.11"]
     steps:
       - uses: actions/checkout@v4
-      - uses: astral-sh/setup-uv@v5
-        with:
-          version: "0.5.x"
+      - uses: astral-sh/setup-uv@v6
       - run: uv run pytest
         env:
           UV_PYTHON: ${{ matrix.python-version }}
@@ -57,6 +53,20 @@ jobs:
       - run: |
           deno check src/higlass/widget.js
 
+  Schema:
+    name: Check higlass-schema against viewconfs
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: astral-sh/setup-uv@v6
+      - run: |
+          uv run --package higlass-schema higlass-schema export > schema.json
+      - uses: actions/setup-node@v4
+        with:
+          node-version: "20.x"
+      - run: npm install -g ajv-cli
+      - run: ajv validate --spec=draft2020 -s schema.json -d "packages/higlass-schema/tests/fixtures/{docs/examples/viewconfs,test/{view-configs,view-configs-more}}/*.json"
+
   Release:
     needs: [Lint, Test]
     runs-on: ubuntu-latest
@@ -66,9 +76,7 @@ jobs:
       contents: read
     steps:
       - uses: actions/checkout@v4
-      - uses: astral-sh/setup-uv@v5
-        with:
-          version: "0.5.x"
+      - uses: astral-sh/setup-uv@v6
       - run: uv build
       - name: Publish distribution 📦 to PyPI
         uses: pypa/gh-action-pypi-publish@release/v1

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                        |

deno.json

@@ -10,6 +10,6 @@
     }
   },
   "fmt": {
-    "exclude": ["examples"]
+    "exclude": ["examples", "docs", "packages/higlass-schema/tests/fixtures"]
   }
 }

packages/higlass-schema/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2022 Trevor James Manz
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

packages/higlass-schema/README.md

@@ -0,0 +1,27 @@
+# higlass-schema
+
+[![PyPI](https://img.shields.io/pypi/v/higlass-schema.svg?color=green)](https://pypi.org/project/higlass-schema)
+[![License](https://img.shields.io/pypi/l/gosling.svg?color=green)](https://github.com/higlass/higlass-schema/raw/main/LICENSE)
+
+Pydantic models for HiGlass
+
+```bash
+pip install higlass-schema
+```
+
+## Development
+
+Try it out:
+
+```bash
+$ 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:
+
+```sh
+uv run pytest # tests
+uv run ruff check # linting
+uv run ruff format --check # formatting (remove --check to apply)
+```

packages/higlass-schema/pyproject.toml

@@ -0,0 +1,23 @@
+[project]
+name = "higlass-schema"
+version = "0.2.1"
+description = "Pydantic models for HiGlass"
+readme = "README.md"
+requires-python = ">=3.8"
+license = { text = "MIT" }
+authors = [{ name = "Trevor Manz", email = "trevor.j.manz@gmail.com" }]
+dependencies = ["pydantic>=2.0", "rich>=13.0.0"]
+
+[project.urls]
+homepage = "https://github.com/higlass/higlass-schema"
+
+[project.scripts]
+higlass-schema = "higlass_schema.cli:main"
+
+[build-system]
+requires = ["uv_build>=0.8.0,<0.9"]
+build-backend = "uv_build"
+
+[tool.ruff]
+extend = "../../pyproject.toml"
+src = ["src", "tests"]

packages/higlass-schema/src/higlass_schema/__init__.py

@@ -0,0 +1,12 @@
+try:
+    from importlib.metadata import PackageNotFoundError, version
+except ImportError:
+    from importlib_metadata import PackageNotFoundError, version  # type: ignore
+
+try:
+    __version__ = version("higlass-schema")
+except PackageNotFoundError:
+    __version__ = "uninstalled"
+
+
+from .schema import *

packages/higlass-schema/src/higlass_schema/cli.py

@@ -0,0 +1,57 @@
+import argparse
+import sys
+
+from pydantic import ValidationError
+from rich.console import Console
+
+from .schema import Track, View, Viewconf, schema_json
+
+console = Console()
+
+
+def export(args: argparse.Namespace) -> None:
+    print(schema_json(indent=args.indent))
+
+
+def check(args: argparse.Namespace) -> None:
+    try:
+        if args.path == "-":
+            raw = "\n".join(sys.stdin.readlines())
+            Viewconf[View[Track]].model_validate_json(raw)
+        else:
+            with open(args.path) as file:
+                raw = file.read()
+            Viewconf[View[Track]].model_validate_json(raw)
+        console.print("✅ valid viewconf.", style="green")
+    except ValidationError:
+        msg = "❌ Invalid viewconf."
+        if args.verbose:
+            console.print(msg, style="yellow")
+            console.print_exception()
+
+        console.print(
+            f"{msg} Run [white]`higlass-schema check --verbose`[/white] for "
+            "more details.",
+            style="yellow",
+        )
+        sys.exit(1)
+
+
+def main():
+    parser = argparse.ArgumentParser()
+    subparsers = parser.add_subparsers(dest="command")
+    subparsers.required = True
+
+    # export
+    parser_export = subparsers.add_parser("export")
+    parser_export.add_argument("--indent", type=int)
+    parser_export.set_defaults(func=export)
+
+    # check
+    parser_check = subparsers.add_parser("check")
+    parser_check.add_argument("path")
+    parser_check.add_argument("--verbose", action="store_true")
+    parser_check.set_defaults(func=check)
+
+    ns = parser.parse_args(sys.argv[1:])
+    ns.func(ns)