From f6c9a62871e51dd8d20ab88ebea4d5adfb84ae9b Mon Sep 17 00:00:00 2001 From: Trevor Manz Date: Sat, 19 Jul 2025 11:35:57 -0400 Subject: [PATCH 1/4] Migrate higlass-schema to uv workspace monorepo Uses uv's native workspace support to manage dependencies. --- packages/higlass-schema/LICENSE | 21 + packages/higlass-schema/README.md | 37 + packages/higlass-schema/pyproject.toml | 26 + .../src/higlass_schema/__init__.py | 12 + .../higlass-schema/src/higlass_schema/cli.py | 57 + .../src/higlass_schema/schema.py | 512 +++ .../src/higlass_schema/utils.py | 113 + .../higlass-schema/tests/fixtures/README.md | 1 + .../examples/viewconfs/1d-annotations.json | 298 ++ .../viewconfs/1d-constant-indicators.json | 130 + .../viewconfs/1d-heatmap-track-2.json | 101 + .../examples/viewconfs/1d-heatmap-track.json | 223 ++ .../docs/examples/viewconfs/axis-margin.json | 242 ++ .../viewconfs/bar-track-color-range.json | 138 + .../docs/examples/viewconfs/bar-track.json | 42 + .../examples/viewconfs/bar-zero-line.json | 180 + .../examples/viewconfs/bedlike-track.json | 74 + .../viewconfs/bigwig-aggregation-modes.json | 77 + .../examples/viewconfs/chromosome-labels.json | 141 + .../docs/examples/viewconfs/default.json | 316 ++ .../viewconfs/diagonal-split-heatmap.json | 250 ++ .../examples/viewconfs/fancy-overlays.json | 133 + .../viewconfs/genbank-data-fetcher.json | 82 + .../examples/viewconfs/gene-annotations.json | 120 + .../docs/examples/viewconfs/label-margin.json | 226 ++ .../examples/viewconfs/lots-of-locks.json | 177 + .../overlay-chromosome-grid-track.json | 121 + .../examples/viewconfs/overlay-track.json | 119 + .../examples/viewconfs/overlay-tracks.json | 266 ++ .../invalidTrackConfig.json | 56 + .../annotationsTilesView.json | 62 + .../divergentTrackConfig.json | 92 + .../view-configs-more/divisionViewConfig.json | 112 + .../test/view-configs-more/emptyConf.json | 29 + .../view-configs-more/exportDataConfig.json | 173 + .../test/view-configs-more/fritzBug1.json | 1720 ++++++++ .../test/view-configs-more/fritzBug2.json | 3457 +++++++++++++++++ .../geneAnnotationsOnly.json | 122 + .../geneAnnotationsOnly1.json | 74 + .../horizontalAndVerticalMultivec.json | 115 + .../horizontalDiagonalTrackViewConf.json | 50 + .../view-configs-more/horizontalLineEnd.json | 111 + .../horizontalMultivecWithAggregation.json | 67 + .../horizontalMultivecWithFilteredRows.json | 65 + ...rizontalMultivecWithSmallerDimensions.json | 109 + ...ontalMultivecWithZeroValueColorOption.json | 174 + .../local-tiles-viewconf.json | 285 ++ .../test/view-configs-more/noGPSB.json | 89 + .../view-configs-more/oneTrackConfig.json | 72 + .../test/view-configs-more/oneViewConfig.json | 130 + .../oneZoomedOutViewConf.json | 124 + .../test/view-configs-more/onlyGPSB.json | 34 + .../test/view-configs-more/osmConf.json | 71 + .../test/view-configs-more/paperFigure1.json | 540 +++ .../test/view-configs-more/project1D.json | 216 + .../view-configs-more/rectangleDomains.json | 100 + .../view-configs-more/restrictedZoom.json | 206 + .../simple1And2dAnnotations.json | 68 + .../simpleCenterViewConfig.json | 83 + .../test/view-configs-more/smallViewconf.json | 179 + .../view-configs-more/stacked-top-tracks.json | 349 ++ .../view-configs-more/stacked-top-views.json | 951 +++++ .../view-configs-more/testViewConfX1.json | 163 + .../view-configs-more/testViewConfX2.json | 136 + .../test/view-configs-more/threeViews.json | 166 + .../test/view-configs-more/topAxisOnly.json | 49 + .../test/view-configs-more/twoViewConfig.json | 175 + .../valueIntervalTrackViewConf.json | 127 + ...iewportProjectionsWithoutFromViewUids.json | 158 + .../view-configs-tracks/chromInfoTrack.json | 10 + .../chromosomeGridTrack.json | 16 + .../view-configs-tracks/heatmapTrack.json | 25 + .../horizontalHeatmapTrack.json | 23 + .../largeHorizontalHeatmapTrack.json | 21 + .../verticalHeatmapTrack.json | 24 + .../view-configs/adjust-view-spacing.json | 40 + .../axis-specific-location-locks.json | 247 ++ .../fixtures/test/view-configs/axis.json | 74 + .../tests/fixtures/test/view-configs/bar.json | 167 + .../continuous-scaling-1D-horizontal.json | 311 ++ .../continuous-scaling-1D-vertical.json | 149 + .../view-configs/continuous-scaling-2D.json | 97 + .../test/view-configs/dummy-data-fetcher.json | 36 + .../test/view-configs/dummy-track.json | 33 + .../view-configs/global-mouse-position.json | 55 + .../horizontal-1d-line-track-with-const.json | 58 + .../test/view-configs/label-margin.json | 115 + .../view-configs/label-split-heatmaps.json | 153 + .../test/view-configs/loop-annotations.json | 93 + .../overlay-annotations-1d-2d.json | 60 + .../test/view-configs/overlay-chrom-grid.json | 51 + ...horizontal-vertical-and-2d-data-track.json | 58 + .../simple-heatmap-gene-annotations.json | 41 + .../test/view-configs/simple-heatmap.json | 32 + .../view-configs/two-bars-and-a-heatmap.json | 164 + .../view-configs/viewport-projection.json | 255 ++ packages/higlass-schema/tests/test_schema.py | 32 + packages/higlass-schema/uv.lock | 307 ++ pyproject.toml | 77 +- 99 files changed, 18078 insertions(+), 40 deletions(-) create mode 100644 packages/higlass-schema/LICENSE create mode 100644 packages/higlass-schema/README.md create mode 100644 packages/higlass-schema/pyproject.toml create mode 100644 packages/higlass-schema/src/higlass_schema/__init__.py create mode 100644 packages/higlass-schema/src/higlass_schema/cli.py create mode 100644 packages/higlass-schema/src/higlass_schema/schema.py create mode 100644 packages/higlass-schema/src/higlass_schema/utils.py create mode 100644 packages/higlass-schema/tests/fixtures/README.md create mode 100644 packages/higlass-schema/tests/fixtures/docs/examples/viewconfs/1d-annotations.json create mode 100644 packages/higlass-schema/tests/fixtures/docs/examples/viewconfs/1d-constant-indicators.json create mode 100644 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create mode 100644 packages/higlass-schema/tests/fixtures/test/view-configs/simple-1d-horizontal-vertical-and-2d-data-track.json create mode 100644 packages/higlass-schema/tests/fixtures/test/view-configs/simple-heatmap-gene-annotations.json create mode 100644 packages/higlass-schema/tests/fixtures/test/view-configs/simple-heatmap.json create mode 100644 packages/higlass-schema/tests/fixtures/test/view-configs/two-bars-and-a-heatmap.json create mode 100644 packages/higlass-schema/tests/fixtures/test/view-configs/viewport-projection.json create mode 100644 packages/higlass-schema/tests/test_schema.py create mode 100644 packages/higlass-schema/uv.lock diff --git a/packages/higlass-schema/LICENSE b/packages/higlass-schema/LICENSE new file mode 100644 index 0000000..86f8e8f --- /dev/null +++ b/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. diff --git a/packages/higlass-schema/README.md b/packages/higlass-schema/README.md new file mode 100644 index 0000000..4e6d361 --- /dev/null +++ b/packages/higlass-schema/README.md @@ -0,0 +1,37 @@ +# 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 +$ uvx --no-cache --from . higlass-schema check ./example.json # [--verbose] +$ uvx --no-cache --from . 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) +``` + +## Release + +```bash +git tag -a v0.0.0 -m "v0.0.0" +git push --follow-tags +``` diff --git a/packages/higlass-schema/pyproject.toml b/packages/higlass-schema/pyproject.toml new file mode 100644 index 0000000..72c1ec2 --- /dev/null +++ b/packages/higlass-schema/pyproject.toml @@ -0,0 +1,26 @@ +[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" + +[dependency-groups] +dev = ["pytest", "ruff"] + +[build-system] +requires = ["uv_build>=0.8.0,<0.9"] +build-backend = "uv_build" + +[tool.ruff] +extend = "../../pyproject.toml" +src = ["src", "tests"] diff --git a/packages/higlass-schema/src/higlass_schema/__init__.py b/packages/higlass-schema/src/higlass_schema/__init__.py new file mode 100644 index 0000000..157a52b --- /dev/null +++ b/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 * diff --git a/packages/higlass-schema/src/higlass_schema/cli.py b/packages/higlass-schema/src/higlass_schema/cli.py new file mode 100644 index 0000000..717b2dc --- /dev/null +++ b/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) diff --git a/packages/higlass-schema/src/higlass_schema/schema.py b/packages/higlass-schema/src/higlass_schema/schema.py new file mode 100644 index 0000000..56f3bf8 --- /dev/null +++ b/packages/higlass-schema/src/higlass_schema/schema.py @@ -0,0 +1,512 @@ +import json +from typing import ( + Any, + Dict, + Generator, + Generic, + List, + Optional, + Tuple, + TypeVar, + Union, +) + +from pydantic import BaseModel as PydanticBaseModel +from pydantic import ConfigDict, Field, RootModel, model_validator +from typing_extensions import Annotated, Literal, TypedDict + +from .utils import _GenerateJsonSchema, get_schema_of + + +# Override Basemodel +class BaseModel(PydanticBaseModel): + model_config = ConfigDict(validate_assignment=True) + + # nice repr if printing with rich + def __rich_repr__(self): + return iter(self) + + def json(self, exclude_none: bool = True, **kwargs): + return super().json(exclude_none=exclude_none, **kwargs) + + def dict(self, exclude_none: bool = True, **kwargs): + return super().dict(exclude_none=exclude_none, **kwargs) + + def model_dump(self, exclude_none: bool = True, **kwargs): + return super().model_dump(exclude_none=exclude_none, **kwargs) + + def model_dump_json(self, exclude_none: bool = True, **kwargs): + return super().model_dump_json(exclude_none=exclude_none, **kwargs) + + +################################################## +# General # +################################################## + +Domain = Tuple[float, float] + + +class OverlayOptions(BaseModel): + extent: Optional[List[List[int]]] = None + minWidth: Optional[float] = None + fill: Optional[str] = None + fillOpacity: Optional[float] = None + stroke: Optional[str] = None + strokeOpacity: Optional[float] = None + strokeWidth: Optional[float] = None + strokePos: Optional[Union[str, List[str]]] = None + outline: Optional[str] = None + outlineOpacity: Optional[float] = None + outlineWidth: Optional[float] = None + outlinePos: Optional[Union[str, List[str]]] = None + + +class Overlay(BaseModel): + type: Optional[str] = None + uid: Optional[str] = None + chromInfoPath: Optional[str] = None + includes: Optional[List[str]] = None + options: Optional[OverlayOptions] = None + + +################################################## +# Locks # +################################################## + + +# Locks are tricky to describe with python's type system +# because _some_ keys are static (e.g., the lock `uid`) while +# the rest of the keys are dynamic (the view uids) and +# satisfy a different type constraint. +# +# In JSON schema, this is type can be described using an "object" +# "type" with "additionalProperties" or "patternProperties" field. +# +# ```json +# { +# "type": "object", +# "properties": { +# "uid": { "type: "string" } +# }, +# "additionalProperties": { +# "type": "array", +# "minLength": 3, +# "maxLength": 3, +# "items": [ +# { "type": "number" }, +# { "type": "number" }, +# { "type": "number" } +# ] +# } +# } +# ``` +# +# The lock classes implement pydantic Models which: +# +# (1) Performs the appropriate validation/serde for this object +# +# (2) Exports the appropriate JSON schema using "additionalProperties" +# field via a custom `schema_extra` extension. +# +# This could probably be implemented generally with +# pydantic.generics.Generic/typing.Generic, but we implement +# concretely for the different lock types. + + +LockEntry = Tuple[float, float, float] + + +# We'd rather have tuples in our final model, because a +# RootModel is clunky from a python user perspective. +# We create this class to get validation for free in `root_validator` +class _LockEntryModel(RootModel[LockEntry]): + pass + + +def _lock_schema_extra(schema: Dict[str, Any], _: Any) -> None: + schema["additionalProperties"] = get_schema_of(LockEntry) + + +class Lock(BaseModel): + uid: Optional[str] = None + + model_config = ConfigDict(extra="allow", json_schema_extra=_lock_schema_extra) + + def __iter__(self) -> Generator[Tuple[str, LockEntry], None, None]: + for key, val in super().__iter__(): + if key not in self.model_fields: + yield key, val + + # can only validate on creation for "extra" fields + @model_validator(mode="before") + @classmethod + def validate_locks(cls, values: Dict[str, Any]): + for k in values: + if k not in cls.model_fields: + # validate using our custom validator + model = _LockEntryModel.model_validate(values[k]) + # get back the root type + values[k] = model.model_dump() + return values + + +class ValueScaleLockEntry(TypedDict): + view: str + track: str + + +class _ValueScaleLockEntryModel(RootModel[ValueScaleLockEntry]): + pass + + +def _value_scale_lock_schema_extra(schema: Dict[str, Any], _: Any) -> None: + schema["additionalProperties"] = get_schema_of(ValueScaleLockEntry) + + +class ValueScaleLock(BaseModel): + uid: Optional[str] = None + ignoreOffScreenValues: Optional[bool] = None + + model_config = ConfigDict( + extra="allow", + json_schema_extra=_value_scale_lock_schema_extra, + ) + + def __iter__(self) -> Generator[Tuple[str, ValueScaleLockEntry], None, None]: + for key, val in super().__iter__(): + if key not in self.model_fields: + yield key, val + + # can only validate on creation for "extra" fields + @model_validator(mode="before") + @classmethod + def validate_locks(cls, values: Dict[str, Any]): + for k in values: + if k not in cls.model_fields: + # validate using our custom validator + model = _ValueScaleLockEntryModel.model_validate(values[k]) + # read back as a regular dict + values[k] = model.model_dump() + return values + + +class AxisSpecificLock(BaseModel): + axis: Literal["x", "y"] + lock: str + + +class AxisSpecificLocks(BaseModel): + x: Optional[AxisSpecificLock] = None + y: Optional[AxisSpecificLock] = None + + +class LocationLocks(BaseModel): + locksByViewUid: Dict[str, Union[str, AxisSpecificLocks]] = Field( + default_factory=dict + ) + locksDict: Dict[str, Lock] = Field(default_factory=dict) + + +class ZoomLocks(BaseModel): + model_config = ConfigDict(extra="forbid") + + locksByViewUid: Dict[str, str] = Field(default_factory=dict) + locksDict: Dict[str, Lock] = Field(default_factory=dict) + + +class ValueScaleLocks(BaseModel): + model_config = ConfigDict(extra="forbid") + + locksByViewUid: Dict[str, str] = Field(default_factory=dict) + locksDict: Dict[str, ValueScaleLock] = Field(default_factory=dict) + + +################################################## +# Tracks # +################################################## + +TrackTypeT = TypeVar("TrackTypeT", bound=str) +TrackOptions = Dict[str, Any] +TilesetInfo = Dict[str, Any] +Tile = Dict[str, Any] + + +class Data(BaseModel): + type: Optional[str] = None + url: Optional[str] = None + server: Optional[str] = None + filetype: Optional[str] = None + children: Optional[List] = None + tilesetInfo: Optional[TilesetInfo] = None + tiles: Optional[Tile] = None + + +class BaseTrack(BaseModel, Generic[TrackTypeT]): + model_config = ConfigDict(extra="allow") + + type: TrackTypeT + uid: Optional[str] = None + width: Optional[int] = None + height: Optional[int] = None + options: Optional[TrackOptions] = None + + +class Tileset(BaseModel): + tilesetUid: Optional[str] = None + server: Optional[str] = None + + +ViewportProjectionTrackType = Literal[ + "viewport-projection-center", + "viewport-projection-vertical", + "viewport-projection-horizontal", +] + +EnumTrackType = Union[ + ViewportProjectionTrackType, + Literal[ + "multivec", + "1d-heatmap", + "line", + "point", + "bar", + "divergent-bar", + "stacked-interval", + "gene-annotations", + "linear-2d-rectangle-domains", + "chromosome-labels", + "linear-heatmap", + "1d-value-interval", + "2d-annotations", + "2d-chromosome-annotations", + "2d-chromosome-grid", + "2d-chromosome-labels", + "2d-rectangle-domains", + "2d-tiles", + "arrowhead-domains", + "bedlike", + "cross-rule", + "dummy", + "horizontal-1d-annotations", + "horizontal-1d-heatmap", + "horizontal-1d-tiles", + "horizontal-1d-value-interval", + "horizontal-2d-rectangle-domains", + "horizontal-bar", + "horizontal-chromosome-grid", + "horizontal-chromosome-labels", + "horizontal-divergent-bar", + "horizontal-gene-annotations", + "horizontal-heatmap", + "horizontal-line", + "horizontal-multivec", + "horizontal-point", + "horizontal-rule", + "horizontal-vector-heatmap", + "image-tiles", + "left-axis", + "left-stacked-interval", + "mapbox-tiles", + "osm-2d-tile-ids", + "osm-tiles", + "raster-tiles", + "simple-svg", + "square-markers", + "top-axis", + "top-stacked-interval", + "vertical-1d-annotations", + "vertical-1d-heatmap", + "vertical-1d-tiles", + "vertical-1d-value-interval", + "vertical-2d-rectangle-domains", + "vertical-bar", + "vertical-bedlike", + "vertical-chromosome-grid", + "vertical-chromosome-labels", + "vertical-gene-annotations", + "vertical-heatmap", + "vertical-line", + "vertical-multivec", + "vertical-point", + "vertical-rule", + "vertical-vector-heatmap", + ], +] + + +class EnumTrack(BaseTrack[EnumTrackType], Tileset): + model_config = ConfigDict(extra="ignore") + + data: Optional[Data] = None + chromInfoPath: Optional[str] = None + fromViewUid: Optional[str] = None + x: Optional[float] = None + y: Optional[float] = None + + +class HeatmapTrack(BaseTrack[Literal["heatmap"]], Tileset): + model_config = ConfigDict(extra="ignore") + + data: Optional[Data] = None + position: Optional[str] = None + transforms: Optional[List] = None + + +class IndependentViewportProjectionTrack(BaseTrack[ViewportProjectionTrackType]): + model_config = ConfigDict(extra="ignore") + + fromViewUid: None = None + projectionXDomain: Optional[Domain] = None + projectionYDomain: Optional[Domain] = None + transforms: Optional[List] = None + x: Optional[float] = None + y: Optional[float] = None + + +class CombinedTrack(BaseTrack[Literal["combined"]]): + model_config = ConfigDict(extra="ignore") + + contents: List["Track"] + position: Optional[str] = None + + +Track = Union[ + EnumTrack, + CombinedTrack, + HeatmapTrack, + IndependentViewportProjectionTrack, + BaseTrack, +] + +# CombinedTrack is recursive and needs delayed evaluation of annoations +CombinedTrack.model_rebuild() + + +################################################## +# View # +################################################## + + +TrackT = TypeVar("TrackT", bound=Track) + +TrackPosition = Literal["left", "right", "top", "bottom", "center", "whole", "gallery"] + + +class Tracks(BaseModel, Generic[TrackT]): + """Track layout within a View.""" + + model_config = ConfigDict(extra="ignore") + + left: Optional[List[TrackT]] = None + right: Optional[List[TrackT]] = None + top: Optional[List[TrackT]] = None + bottom: Optional[List[TrackT]] = None + center: Optional[List[TrackT]] = None + whole: Optional[List[TrackT]] = None + gallery: Optional[List[TrackT]] = None + + def __iter__(self) -> Generator[Tuple[TrackPosition, TrackT], None, None]: + for pos, tlist in super().__iter__(): + if tlist is None: + continue + for track in tlist: + yield pos, track # type: ignore + + +class Layout(BaseModel): + """Size and position of a View.""" + + model_config = ConfigDict(extra="ignore") + + x: int = Field(default=0, description="The X Position") + y: int = Field(default=0, description="The Y Position") + w: int = Field(default=12, description="Width") + h: int = Field(default=12, description="Height") + moved: Optional[bool] = None + static: Optional[bool] = None + + +class GenomePositionSearchBox(BaseModel): + """Locations to search within a View.""" + + autocompleteServer: Optional[str] = Field( + default=None, + examples=["//higlass.io/api/v1"], + description="The Autocomplete Server URL", + ) + autocompleteId: Optional[str] = Field( + default=None, + examples=["OHJakQICQD6gTD7skx4EWA"], + description="The Autocomplete ID", + ) + chromInfoServer: Optional[str] = Field( + default=None, + examples=["//higlass.io/api/v1"], + description="The Chrominfo Server URL", + ) + chromInfoId: Optional[str] = Field( + default=None, + examples=["hg19"], + description="The Chromosome Info ID", + ) + visible: Optional[bool] = Field( + default=None, + description="The Visible Schema", + ) + + +class View(BaseModel, Generic[TrackT]): + """An arrangment of Tracks to display within a given Layout.""" + + model_config = ConfigDict(extra="ignore") + + layout: Layout + tracks: Tracks[TrackT] + uid: Optional[str] = None + autocompleteSource: Optional[str] = None + chromInfoPath: Optional[str] = None + genomePositionSearchBox: Optional[GenomePositionSearchBox] = None + genomePositionSearchBoxVisible: Optional[bool] = None + initialXDomain: Optional[Domain] = None + initialYDomain: Optional[Domain] = None + overlays: Optional[List[Overlay]] = None + selectionView: Optional[bool] = None + zoomFixed: Optional[bool] = None + zoomLimits: Tuple[float, Optional[float]] = (1, None) + + +################################################## +# Viewconf # +################################################## + +ViewT = TypeVar("ViewT", bound=View) + + +class Viewconf(BaseModel, Generic[ViewT]): + """Root object describing a HiGlass visualization.""" + + model_config = ConfigDict(extra="forbid") + + editable: Optional[bool] = True + viewEditable: Optional[bool] = True + tracksEditable: Optional[bool] = True + zoomFixed: Optional[bool] = None + compactLayout: Optional[bool] = None + exportViewUrl: Optional[str] = None + trackSourceServers: Optional[List[str]] = None + views: Optional[Annotated[List[ViewT], Field(min_length=1)]] = None + zoomLocks: Optional[ZoomLocks] = None + locationLocks: Optional[LocationLocks] = None + valueScaleLocks: Optional[ValueScaleLocks] = None + chromInfoPath: Optional[str] = None + + +def schema(): + json_schema = Viewconf.model_json_schema(schema_generator=_GenerateJsonSchema) + json_schema["$schema"] = _GenerateJsonSchema.schema_dialect + json_schema["title"] = "HiGlass viewconf" + return json_schema + + +def schema_json(**kwargs): + return json.dumps(schema(), **kwargs) diff --git a/packages/higlass-schema/src/higlass_schema/utils.py b/packages/higlass-schema/src/higlass_schema/utils.py new file mode 100644 index 0000000..a9ad83f --- /dev/null +++ b/packages/higlass-schema/src/higlass_schema/utils.py @@ -0,0 +1,113 @@ +from __future__ import annotations + +from typing import TYPE_CHECKING, Any, TypeVar, Union + +import pydantic_core.core_schema as core_schema +from pydantic import BaseModel, TypeAdapter +from pydantic.json_schema import GenerateJsonSchema, JsonSchemaMode, JsonSchemaValue + +if TYPE_CHECKING: + from typing import TypeGuard + +### Vendored from pydantic._internal._core_utils + +CoreSchemaField = Union[ + core_schema.ModelField, + core_schema.DataclassField, + core_schema.TypedDictField, + core_schema.ComputedField, +] + +CoreSchemaOrField = Union[core_schema.CoreSchema, CoreSchemaField] + +_CORE_SCHEMA_FIELD_TYPES = { + "typed-dict-field", + "dataclass-field", + "model-field", + "computed-field", +} + + +def is_core_schema( + schema: CoreSchemaOrField, +) -> TypeGuard[core_schema.CoreSchema]: + return schema["type"] not in _CORE_SCHEMA_FIELD_TYPES + + +### End vendored code + + +class _GenerateJsonSchema(GenerateJsonSchema): + def field_title_should_be_set(self, schema: CoreSchemaOrField) -> bool: + """Check if the title should be set for a field. + + Override the default implementation to not set the title for core + schemas. Makes the final schema more readable by removing + redundant titles. Explicit Field(title=...) can still be used. + """ + return_value = super().field_title_should_be_set(schema) + if return_value and is_core_schema(schema): + return False + return return_value + + def nullable_schema(self, schema: core_schema.NullableSchema) -> JsonSchemaValue: + """Generate a JSON schema for a nullable schema. + + This overrides the default implementation to ignore the nullable + and generate a more simple schema. All the Optional[T] fields + are converted to T (instead of the + default {"anyOf": [{"type": "null"}, {"type": "T"}]}). + """ + return self.generate_inner(schema["schema"]) + + def default_schema(self, schema: core_schema.WithDefaultSchema) -> JsonSchemaValue: + """Generate a JSON schema for a schema with a default value. + + Similar to above, this overrides the default implementation to + not explicity set {"default": null} in the schema when the field + is Optional[T] = None. + """ + if schema.get("default") is None: + return self.generate_inner(schema["schema"]) + return super().default_schema(schema) + + def generate( + self, schema: core_schema.CoreSchema, mode: JsonSchemaMode = "validation" + ) -> JsonSchemaValue: + """Generate a JSON schema. + + This overrides the default implementation to remove the titles + from the definitions. This makes the final schema more readable. + """ + + json_schema = super().generate(schema, mode=mode) + # clear the titles from the definitions + for d in json_schema.get("$defs", {}).values(): + d.pop("title", None) + return json_schema + + +# Schema modifiers +ModelT = TypeVar("ModelT", bound=BaseModel) + + +def get_schema_of(type_: object): + return TypeAdapter(type_).json_schema(schema_generator=_GenerateJsonSchema) + + +def simplify_enum_schema(schema: dict[str, Any]): + # reduce union of enums into single enum + if "anyOf" in schema: + enum = [] + for entry in schema["anyOf"]: + assert "enum" in entry + enum.extend(entry["enum"]) + return {"enum": enum} + + enum = schema["enum"] + + # if there is only one enum entry, make it a const + if len(enum) == 1: + return {"const": enum[0]} + + return {"enum": enum} diff --git a/packages/higlass-schema/tests/fixtures/README.md b/packages/higlass-schema/tests/fixtures/README.md new file mode 100644 index 0000000..ec464b3 --- /dev/null +++ b/packages/higlass-schema/tests/fixtures/README.md @@ -0,0 +1 @@ +These files are copied from the root of https://github.com/higlass/higlass. diff --git a/packages/higlass-schema/tests/fixtures/docs/examples/viewconfs/1d-annotations.json b/packages/higlass-schema/tests/fixtures/docs/examples/viewconfs/1d-annotations.json new file mode 100644 index 0000000..82ca843 --- /dev/null +++ b/packages/higlass-schema/tests/fixtures/docs/examples/viewconfs/1d-annotations.json @@ -0,0 +1,298 @@ +{ + "editable": true, + "zoomFixed": false, + "trackSourceServers": ["http://higlass.io/api/v1"], + "exportViewUrl": "http://higlass.io/api/v1/viewconfs/", + "views": [ + { + "uid": "aa", + "initialXDomain": [7595655.0000270605, 2507738795.9999733], + "initialYDomain": [-545671929.4383738, 3061006380.438374], + "autocompleteSource": "http://higlass.io/api/v1/suggest/?d=OHJakQICQD6gTD7skx4EWA&", + "chromInfoPath": "//s3.amazonaws.com/pkerp/data/hg19/chromSizes.tsv", + "tracks": { + "top": [ + { + "uid": "tc1a", + "type": "combined", + "height": 20, + "contents": [ + { + "uid": "selection-a", + "type": "horizontal-1d-annotations", + "options": { + "regions": [[230000000, 561000000]], + "minRectWidth": 3, + "fillOpacity": 0.1, + "stroke": "blue", + "strokePos": ["left", "right"], + "strokeWidth": 2, + "strokeOpacity": 0.6 + } + }, + { + "server": "http://higlass.io/api/v1", + "tilesetUid": "b6qFe7fOSnaX-YkP2kzN1w", + "uid": "WCGssXHmQTGOkdRgweYKkQ", + "type": "horizontal-bar", + "options": { + "labelColor": "black", + "labelPosition": "hidden", + "axisPositionHorizontal": "right", + "barFillColor": "darkgreen", + "valueScaling": "linear", + "trackBorderWidth": 0, + "trackBorderColor": "black", + "labelTextOpacity": 0.4, + "barOpacity": 1, + "name": "wgEncodeSydhTfbsGm12878Ctcfsc15914c20StdSig" + }, + "height": 20 + } + ] + }, + { + "uid": "tc1b", + "type": "combined", + "height": 60, + "contents": [ + { + "uid": "selection-b", + "type": "horizontal-1d-annotations", + "options": { + "regions": [[230000000, 561000000]], + "minRectWidth": 3, + "fillOpacity": 0.1, + "stroke": "blue", + "strokePos": ["left", "right"], + "strokeWidth": 2, + "strokeOpacity": 0.6 + } + }, + { + "server": "http://higlass.io/api/v1", + "tilesetUid": "OHJakQICQD6gTD7skx4EWA", + "uid": "BEEMEjU7QCa2krDO9C0yOQ", + "type": "horizontal-gene-annotations", + "options": { + "labelPosition": "hidden", + "name": "Gene Annotations (hg19)", + "labelColor": "black", + "plusStrandColor": "blue", + "minusStrandColor": "red", + "trackBorderWidth": 0, + "trackBorderColor": "black", + "showMousePosition": false, + "mousePositionColor": "#999999" + }, + "height": 60 + } + ] + }, + { + "uid": "tc1c", + "type": "combined", + "contents": [ + { + "uid": "selection-c", + "type": "horizontal-1d-annotations", + "options": { + "regions": [[230000000, 561000000]], + "minRectWidth": 3, + "fillOpacity": 0, + "stroke": "fuchsia", + "strokePos": "around", + "strokeWidth": 4, + "strokeOpacity": 0.6 + } + }, + { + "chromInfoPath": "//s3.amazonaws.com/pkerp/data/hg19/chromSizes.tsv", + "type": "horizontal-chromosome-labels", + "height": 30, + "uid": "I1QUF22JQJuJ38j9PS4iqw", + "options": { + "showMousePosition": false, + "mousePositionColor": "#999999" + } + } + ] + } + ], + "left": [ + { + "uid": "tc2a", + "type": "combined", + "width": 20, + "contents": [ + { + "uid": "selection-2a", + "type": "vertical-1d-annotations", + "options": { + "regions": [[230000000, 561000000]], + "minRectWidth": 3, + "fillOpacity": 0.1, + "stroke": "blue", + "strokePos": ["left", "right"], + "strokeWidth": 2, + "strokeOpacity": 0.6 + } + }, + { + "server": "http://higlass.io/api/v1", + "tilesetUid": "b6qFe7fOSnaX-YkP2kzN1w", + "uid": "WCGssXHmQTGOkdRgweYKkQ2", + "type": "vertical-bar", + "options": { + "labelColor": "black", + "labelPosition": "topLeft", + "axisPositionHorizontal": "right", + "barFillColor": "darkgreen", + "valueScaling": "linear", + "trackBorderWidth": 0, + "trackBorderColor": "black", + "labelTextOpacity": 0.4, + "barOpacity": 1, + "name": "wgEncodeSydhTfbsGm12878Ctcfsc15914c20StdSig" + } + } + ] + }, + { + "uid": "tc2b", + "type": "combined", + "width": 60, + "contents": [ + { + "uid": "selection-2b", + "type": "vertical-1d-annotations", + "options": { + "regions": [[230000000, 561000000]], + "minRectWidth": 3, + "fillOpacity": 0.1, + "stroke": "blue", + "strokePos": ["left", "right"], + "strokeWidth": 2, + "strokeOpacity": 0.6 + } + }, + { + "server": "http://higlass.io/api/v1", + "tilesetUid": "OHJakQICQD6gTD7skx4EWA", + "uid": "BEEMEjU7QCa2krDO9C0yOQ2", + "type": "vertical-gene-annotations", + "options": { + "labelPosition": "outerTop", + "name": "Gene Annotations (hg19)", + "labelColor": "black", + "plusStrandColor": "blue", + "minusStrandColor": "red", + "trackBorderWidth": 0, + "trackBorderColor": "black", + "showMousePosition": false, + "mousePositionColor": "#999999" + } + } + ] + }, + { + "uid": "tc2c", + "type": "combined", + "width": 30, + "contents": [ + { + "uid": "selection-2", + "type": "vertical-1d-annotations", + "options": { + "regions": [[230000000, 561000000]], + "minRectWidth": 3, + "fillOpacity": 0.1, + "stroke": "blue", + "strokePos": ["left", "right"], + "strokeWidth": 2, + "strokeOpacity": 0.6 + } + }, + { + "chromInfoPath": "//s3.amazonaws.com/pkerp/data/hg19/chromSizes.tsv", + "type": "vertical-chromosome-labels", + "uid": "I1QUF22JQJuJ38j9PS4iqw2", + "options": { + "showMousePosition": false, + "mousePositionColor": "#999999" + } + } + ] + } + ], + "center": [ + { + "uid": "c1", + "type": "combined", + "contents": [ + { + "server": "http://higlass.io/api/v1", + "tilesetUid": "CQMd6V_cRw6iCI_-Unl3PQ", + "type": "heatmap", + "options": { + "colorRange": ["#FFFFFF", "#F8E71C", "#F5A623", "#D0021B"], + "colorbarPosition": "topRight", + "colorbarLabelsPosition": "outside", + "maxZoom": null, + "labelPosition": "bottomLeft", + "name": "Rao et al. (2014) GM12878 MboI (allreps) 1kb", + "trackBorderWidth": 0, + "trackBorderColor": "black", + "heatmapValueScaling": "log", + "scaleStartPercent": "0.00000", + "scaleEndPercent": "1.00000", + "backgroundColor": "#eeeeee", + "showMousePosition": false, + "mousePositionColor": "#999999", + "showTooltip": false + }, + "uid": "heatmap1", + "width": 479, + "height": 691 + }, + { + "uid": "selection-c1", + "type": "horizontal-1d-annotations", + "options": { + "regions": [[230000000, 561000000]], + "minRectWidth": 3, + "fillOpacity": 0.1, + "stroke": "green", + "strokePos": "right", + "strokeWidth": 4, + "strokeOpacity": 0.6 + } + }, + { + "uid": "selection-c2", + "type": "vertical-1d-annotations", + "options": { + "regions": [[230000000, 561000000]], + "minRectWidth": 3, + "fillOpacity": 0.1, + "stroke": "blue", + "strokePos": ["left", "right"], + "strokeWidth": 2, + "strokeOpacity": 0.6 + } + } + ] + } + ], + "right": [], + "bottom": [] + }, + "layout": { + "w": 12, + "h": 12, + "x": 0, + "y": 0 + } + } + ] +} diff --git a/packages/higlass-schema/tests/fixtures/docs/examples/viewconfs/1d-constant-indicators.json b/packages/higlass-schema/tests/fixtures/docs/examples/viewconfs/1d-constant-indicators.json new file mode 100644 index 0000000..9651471 --- /dev/null +++ b/packages/higlass-schema/tests/fixtures/docs/examples/viewconfs/1d-constant-indicators.json @@ -0,0 +1,130 @@ +{ + "editable": false, + "zoomFixed": false, + "views": [{ + "initialXDomain": [1500000, 3000000], + "initialYDomain": [1500000, 3000000], + "tracks": { + "top": [{ + "uid": "chroms", + "chromInfoPath": "//s3.amazonaws.com/pkerp/data/hg19/chromSizes.tsv", + "type": "horizontal-chromosome-labels" + }, { + "uid": "genes", + "tilesetUid": "OHJakQICQD6gTD7skx4EWA", + "server": "http://higlass.io/api/v1", + "type": "horizontal-gene-annotations" + }, { + "uid": "lines", + "tilesetUid": "PjIJKXGbSNCalUZO21e_HQ", + "height": 200, + "server": "http://higlass.io/api/v1", + "type": "horizontal-line", + "options": { + "constIndicators": [{ + "color": "#000000", + "opacity": 0.33, + "label": "Max", + "labelPosition": "leftBottom", + "labelColor": "#000000", + "labelOpacity": 0.25, + "value": 60000 + }, { + "color": "#000000", + "opacity": 0.33, + "label": "Mean", + "labelPosition": "left", + "labelColor": "#000000", + "labelOpacity": 0.25, + "value": 30000 + }, { + "color": "#000000", + "opacity": 0.33, + "label": "Min", + "labelPosition": "leftTop", + "labelColor": "#000000", + "labelOpacity": 0.25, + "value": 10000 + }], + "showTooltip": true + } + }, { + "uid": "bars", + "tilesetUid": "PjIJKXGbSNCalUZO21e_HQ", + "height": 200, + "server": "http://higlass.io/api/v1", + "type": "horizontal-bar", + "options": { + "barFillColor": "orange", + "axisPositionHorizontal": "left", + "constIndicators": [{ + "color": "#000000", + "opacity": 0.33, + "label": "Max", + "labelPosition": "rightBottom", + "labelColor": "#000000", + "labelOpacity": 0.25, + "value": 60000 + }, { + "color": "#000000", + 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b/packages/higlass-schema/tests/fixtures/test/view-configs-tracks/heatmapTrack.json new file mode 100644 index 0000000..cc133ed --- /dev/null +++ b/packages/higlass-schema/tests/fixtures/test/view-configs-tracks/heatmapTrack.json @@ -0,0 +1,25 @@ +{ + "filetype": "cooler", + "name": "Dixon et al. 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b/pyproject.toml @@ -1,46 +1,40 @@ -[build-system] -requires = ["hatchling", "hatch-vcs"] -build-backend = "hatchling.build" - [project] name = "higlass-python" +version = "1.3.3" description = "Python bindings for HiGlass" +readme = "README.md" +requires-python = ">=3.8" +license = { text = "MIT" } authors = [ - { name = "Fritz Lekschas", email = "code@lekschas.de" }, - { name = "Nezar Abdennur", email = "nabdennur@gmail.com" }, - { name = "Peter Kerpdjiev", email = "pkerpedjiev@gmail.com" }, - { name = "Trevor Manz", email = "trevor.j.manz@gmail.com" }, + { name = "Fritz Lekschas", email = "code@lekschas.de" }, + { name = "Nezar Abdennur", email = "nabdennur@gmail.com" }, + { name = "Peter Kerpdjiev", email = "pkerpedjiev@gmail.com" }, + { name = "Trevor Manz", email = "trevor.j.manz@gmail.com" }, ] classifiers = [ - "Development Status :: 3 - Alpha", - "Intended Audience :: Developers", - "Programming Language :: Python", - "Programming Language :: Python :: 3", - "Programming Language :: Python :: 3.8", - "Programming Language :: Python :: 3.9", - "Programming Language :: Python :: 3.10", - "Programming Language :: Python :: 3.11", - "Operating System :: OS Independent", + "Development Status :: 3 - Alpha", + "Intended Audience :: Developers", + "Operating System :: OS Independent", + "Programming Language :: Python", + "Programming Language :: Python :: 3", + "Programming Language :: Python :: 3.8", + "Programming Language :: Python :: 3.9", + "Programming Language :: Python :: 3.10", + "Programming Language :: Python :: 3.11", ] -license = { text = "MIT" } -dynamic = ["version"] -readme = "README.md" +urls = { homepage = "https://github.com/higlass/higlass-python" } dependencies = [ - "higlass-schema>=0.2.0", - "anywidget>=0.9.0", - "typing-extensions ; python_version<'3.9'", + "anywidget>=0.9.0", + "higlass-schema>=0.2.0", + "typing-extensions ; python_version<'3.9'", ] -requires-python = ">=3.8" -urls = { homepage = "https://github.com/higlass/higlass-python" } [dependency-groups] dev = ["anywidget[dev]", "jupyterlab", "pytest", "ruff"] -[tool.hatch.build.targets.wheel] -packages = ["src/higlass"] - -[tool.hatch.version] -source = "vcs" +[build-system] +requires = ["uv_build>=0.8.0,<0.9"] +build-backend = "uv_build" [tool.ruff] line-length = 88 @@ -48,20 +42,23 @@ target-version = "py38" [tool.ruff.lint] extend-select = [ - "E", # style errors - # "D", # pydocstyle - "F", # pyflakes - "I", # isort - "RUF", # ruff-specific rules - "UP", # pyupgrade - "W", # style warnings + "E", # style errors + # "D", # pydocstyle + "F", # pyflakes + "I", # isort + "RUF", # ruff-specific rules + "UP", # pyupgrade + "W", # style warnings ] [tool.ruff.lint.per-file-ignores] "__init__.py" = [ - "F403", # unused-star-used - "F401", # unused import + "F403", # unused-star-used + "F401", # unused import ] "examples/*.ipynb" = [ - "F811", # redefintion + "F811", # redefintion ] + +[tool.uv.workspace] +members = ["packages/*"] From 69aa6554a4ae4725c527cfcf31dad325f76aeb1e Mon Sep 17 00:00:00 2001 From: Trevor Manz Date: Sat, 19 Jul 2025 14:00:36 -0400 Subject: [PATCH 2/4] Update GitHub Actions --- .github/dependabot.yml | 2 +- .github/workflows/ci.yml | 26 +++++++++++++++++--------- 2 files changed, 18 insertions(+), 10 deletions(-) diff --git a/.github/dependabot.yml b/.github/dependabot.yml index 88d68cf..8f6cbd7 100644 --- a/.github/dependabot.yml +++ b/.github/dependabot.yml @@ -9,7 +9,7 @@ updates: patterns: - "*" - - package-ecosystem: "pip" + - package-ecosystem: "uv" directory: "/" schedule: interval: "weekly" diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index d58334f..40575a6 100644 --- a/.github/workflows/ci.yml +++ b/.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: JS viewconf validation with generated JSON Schema + 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 From b146655120856e523fd997dd51dfb0e626242757 Mon Sep 17 00:00:00 2001 From: Trevor Manz Date: Sat, 19 Jul 2025 14:00:47 -0400 Subject: [PATCH 3/4] Update README with unified documentation --- README.md | 29 +- packages/higlass-schema/README.md | 14 +- packages/higlass-schema/pyproject.toml | 3 - pyproject.toml | 9 + uv.lock | 2632 ++++++++++++------------ 5 files changed, 1352 insertions(+), 1335 deletions(-) diff --git a/README.md b/README.md index 5d00592..e4d8559 100644 --- a/README.md +++ b/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 | diff --git a/packages/higlass-schema/README.md b/packages/higlass-schema/README.md index 4e6d361..6e7e90c 100644 --- a/packages/higlass-schema/README.md +++ b/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. 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Trevor Manz Date: Sat, 19 Jul 2025 14:20:19 -0400 Subject: [PATCH 4/4] Fix linting --- .github/workflows/ci.yml | 4 ++-- README.md | 6 +++--- deno.json | 2 +- 3 files changed, 6 insertions(+), 6 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 40575a6..69ac685 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -54,7 +54,7 @@ jobs: deno check src/higlass/widget.js Schema: - name: JS viewconf validation with generated JSON Schema + name: Check higlass-schema against viewconfs runs-on: ubuntu-latest steps: - uses: actions/checkout@v4 @@ -63,7 +63,7 @@ jobs: uv run --package higlass-schema higlass-schema export > schema.json - uses: actions/setup-node@v4 with: - node-version: '20.x' + 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" diff --git a/README.md b/README.md index e4d8559..68e4cff 100644 --- a/README.md +++ b/README.md @@ -70,9 +70,9 @@ and understanding are greatly appreciated. ## Development -**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 +**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. diff --git a/deno.json b/deno.json index b78de0c..3c3eb09 100644 --- a/deno.json +++ b/deno.json @@ -10,6 +10,6 @@ } }, "fmt": { - "exclude": ["examples"] + "exclude": ["examples", "docs", "packages/higlass-schema/tests/fixtures"] } }