diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 743667d7..8989ff9f 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -14,6 +14,7 @@ concurrency: env: PYTHONUNBUFFERED: "1" FORCE_COLOR: "1" + SKIP_DENO_BUILD: "1" jobs: diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml index 8a6dde2f..4b957676 100644 --- a/.github/workflows/docs.yml +++ b/.github/workflows/docs.yml @@ -14,6 +14,9 @@ concurrency: group: "pages" cancel-in-progress: true +env: + SKIP_DENO_BUILD: "1" + jobs: Deploy: diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml index 39817f79..1a5de078 100644 --- a/.github/workflows/release.yml +++ b/.github/workflows/release.yml @@ -20,6 +20,9 @@ jobs: - uses: actions/checkout@v4 with: fetch-depth: 0 + - uses: denoland/setup-deno@v1 + with: + deno-version: v2.x - uses: astral-sh/setup-uv@v3 with: version: "0.5.x" diff --git a/.gitignore b/.gitignore index 565369c5..ca4735f1 100644 --- a/.gitignore +++ b/.gitignore @@ -16,3 +16,4 @@ node_modules/ _build/ generated/ gallery/ +gosling/static/ diff --git a/deno.json b/deno.json new file mode 100644 index 00000000..7eb4a5e0 --- /dev/null +++ b/deno.json @@ -0,0 +1,20 @@ +{ + "lock": false, + "nodeModulesDir": "auto", + "tasks": { + "dev": "deno run -A --node-modules-dir npm:esbuild --bundle --minify --loader:.css=text --format=esm --outfile=gosling/static/widget.js frontend/widget.ts --sourcemap=inline --watch", + "build": "deno run -A --node-modules-dir npm:esbuild --bundle --minify --loader:.css=text --format=esm --outfile=gosling/static/widget.js frontend/widget.ts" + }, + "imports": { + "@anywidget/types": "npm:@anywidget/types@^0.2.0", + "gosling.js": "npm:gosling.js@^0.17.0" + }, + "fmt": { + "useTabs": true + }, + "lint": { + "rules": { + "exclude": ["prefer-const"] + } + } +} diff --git a/frontend/widget.ts b/frontend/widget.ts new file mode 100644 index 00000000..cd9220e6 --- /dev/null +++ b/frontend/widget.ts @@ -0,0 +1,23 @@ +import * as gosling from "gosling.js"; + +interface Model { + _viewconf: string; +} + +export default { + async render({ model, el }: import("@anywidget/types").RenderProps) { + const viewconf = JSON.parse(model.get("_viewconf")); + const api = await gosling.embed(el, viewconf, { padding: 0 }); + model.on("msg:custom", (msg) => { + msg = JSON.parse(msg); + console.log(msg); + try { + const [fn, ...args] = msg; + // @ts-expect-error - This is a dynamic call + api[fn](...args); + } catch (e) { + console.error(e); + } + }); + }, +}; diff --git a/gosling/_widget.py b/gosling/_widget.py new file mode 100644 index 00000000..26bb848f --- /dev/null +++ b/gosling/_widget.py @@ -0,0 +1,27 @@ +import json +import pathlib +from typing import Any, Dict +import warnings + +import anywidget +import traitlets as t + +_esm = pathlib.Path(__file__).parent / "static" / "widget.js" + +if not _esm.exists(): + warnings.warn("Widget front-end code not found. Assuming running in CI.") + _esm = None + + +class GoslingWidget(anywidget.AnyWidget): + _esm = _esm + _viewconf = t.Unicode("null").tag(sync=True) + + location = t.List(t.Union([t.Float(), t.Tuple()]), read_only=True).tag(sync=True) + + def __init__(self, viewconf: Dict[str, Any], **kwargs): + super().__init__(_viewconf=json.dumps(viewconf), **kwargs) + + def zoom_to(self, view_id: str, pos: str, padding: float = 0, duration: int = 1000): + msg = json.dumps(["zoomTo", view_id, pos, padding, duration]) + self.send(msg) diff --git a/gosling/api.py b/gosling/api.py index ccd8b654..7546b073 100644 --- a/gosling/api.py +++ b/gosling/api.py @@ -218,7 +218,7 @@ def save( def widget(self): try: - from gosling_widget import GoslingWidget + from ._widget import GoslingWidget except ImportError: raise ImportError( "The 'gosling-widget' package is required to use the widget() method." diff --git a/notebooks/example.ipynb b/notebooks/example.ipynb index 8605d4d8..cdd84bb2 100644 --- a/notebooks/example.ipynb +++ b/notebooks/example.ipynb @@ -2,7 +2,7 @@ "cells": [ { "cell_type": "code", - "execution_count": 1, + "execution_count": null, "id": "2a014a14-3d7c-4288-8534-df01d7bf2432", "metadata": {}, "outputs": [], @@ -12,57 +12,10 @@ }, { "cell_type": "code", - "execution_count": 2, + "execution_count": null, "id": "61233841", "metadata": {}, - "outputs": [ - { - "data": { - "text/plain": [ - "Track({\n", - " color: Color({\n", - " shorthand: 's1:N'\n", - " }),\n", - " data: {'type': 'csv', 'url': 'https://raw.githubusercontent.com/sehilyi/gemini-datasets/master/data/circos-segdup-edited.txt', 'chromosomeField': 'c2', 'genomicFields': ['s1', 'e1', 's2', 'e2']},\n", - " height: 130,\n", - " mark: 'withinLink',\n", - " opacity: OpacityValue({\n", - " value: 0.2\n", - " }),\n", - " stroke: StrokeValue({\n", - " value: 'black'\n", - " }),\n", - " strokeWidth: StrokeWidthValue({\n", - " value: 0.5\n", - " }),\n", - " width: 600,\n", - " x: X({\n", - " domain: GenomicDomain({\n", - " chromosome: '1',\n", - " interval: [103900000, 104100000]\n", - " }),\n", - " shorthand: 's1:G'\n", - " }),\n", - " x1: X1({\n", - " domain: GenomicDomain({\n", - " chromosome: '1'\n", - " }),\n", - " shorthand: 's2:G'\n", - " }),\n", - " x1e: X1e({\n", - " shorthand: 'e2:G'\n", - " }),\n", - " xe: Xe({\n", - " shorthand: 'e1:G'\n", - " })\n", - "})" - ] - }, - "execution_count": 2, - "metadata": {}, - "output_type": "execute_result" - } - ], + "outputs": [], "source": [ "csvData = gos.csv(\n", " url=\"https://raw.githubusercontent.com/sehilyi/gemini-datasets/master/data/circos-segdup-edited.txt\",\n", @@ -87,141 +40,15 @@ }, { "cell_type": "code", - "execution_count": 3, + "execution_count": null, "id": "88f3a522", - "metadata": { - "scrolled": true - }, - "outputs": [ - { - "data": { - "text/html": [ - "\n", - "\n", - "\n", - "\n", - " \n", - " \n", - "\n", - "\n", - "
\n", - " \n", - "\n", - "" - ], - "text/plain": [ - "View({\n", - " subtitle: 'Tutorial Examples',\n", - " title: 'Basic Marks: Bar',\n", - " tracks: [Track({\n", - " color: Color({\n", - " field: 's1',\n", - " type: 'nominal'\n", - " }),\n", - " data: {'type': 'csv', 'url': 'https://raw.githubusercontent.com/sehilyi/gemini-datasets/master/data/circos-segdup-edited.txt', 'chromosomeField': 'c2', 'genomicFields': ['s1', 'e1', 's2', 'e2']},\n", - " height: 130,\n", - " mark: 'withinLink',\n", - " opacity: OpacityValue({\n", - " value: 0.2\n", - " }),\n", - " stroke: StrokeValue({\n", - " value: 'black'\n", - " }),\n", - " strokeWidth: StrokeWidthValue({\n", - " value: 0.5\n", - " }),\n", - " width: 600,\n", - " x: X({\n", - " domain: GenomicDomain({\n", - " chromosome: '1',\n", - " interval: [103900000, 104100000]\n", - " }),\n", - " field: 's1',\n", - " type: 'genomic'\n", - " }),\n", - " x1: X1({\n", - " domain: GenomicDomain({\n", - " chromosome: '1'\n", - " }),\n", - " field: 's2',\n", - " type: 'genomic'\n", - " }),\n", - " x1e: X1e({\n", - " field: 'e2',\n", - " type: 'genomic'\n", - " }),\n", - " xe: Xe({\n", - " field: 'e1',\n", - " type: 'genomic'\n", - " })\n", - " })]\n", - "})" - ] - }, - "execution_count": 3, - "metadata": {}, - "output_type": "execute_result" - } - ], + "metadata": {}, + "outputs": [], "source": [ "# just render a view (not a mutable object)\n", - "track.view(title=\"Basic Marks: Bar\", subtitle=\"Tutorial Examples\")" + "view = track.view(title=\"Basic Marks: Bar\", subtitle=\"Tutorial Examples\", id=\"aa\")\n", + "w = view.widget()\n", + "w" ] }, { @@ -230,6 +57,16 @@ "id": "7a82cfcc", "metadata": {}, "outputs": [], + "source": [ + "view.id" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "05d7ecf9-d336-4daa-8d49-447d062f7236", + "metadata": {}, + "outputs": [], "source": [] } ], @@ -249,7 +86,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.9.7" + "version": "3.12.7" } }, "nbformat": 4, diff --git a/notebooks/multiple-coordinated-views.ipynb b/notebooks/multiple-coordinated-views.ipynb index 6be89bc8..ce28fb02 100644 --- a/notebooks/multiple-coordinated-views.ipynb +++ b/notebooks/multiple-coordinated-views.ipynb @@ -2,7 +2,7 @@ "cells": [ { "cell_type": "code", - "execution_count": 1, + "execution_count": null, "id": "c8988b10", "metadata": {}, "outputs": [], @@ -21,7 +21,7 @@ }, { "cell_type": "code", - "execution_count": 2, + "execution_count": null, "id": "252487de", "metadata": {}, "outputs": [], @@ -56,201 +56,10 @@ }, { "cell_type": "code", - "execution_count": 3, + "execution_count": null, "id": "8e125ba2", "metadata": {}, - "outputs": [ - { - "data": { - "text/html": [ - "\n", - "\n", - "\n", - "\n", - " \n", - " \n", - "\n", - "\n", - "
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b/pyproject.toml index 89fdc5f8..2f525548 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -11,15 +11,15 @@ license = { text = "MIT" } readme = "README.md" dynamic = ["version"] urls = { homepage = "https://github.com/gosling-lang/gos" } -dependencies = ["jsonschema>=3.0", "jinja2", "pandas"] +dependencies = ["jsonschema>=3.0", "jinja2", "pandas", "anywidget>=0.9.13"] [project.optional-dependencies] -all = ["servir>=0.2.1", "gosling-widget>=0.0.2", "clodius>=0.20.1"] +all = ["servir>=0.2.1", "clodius>=0.20.1"] -[tool.uv] -dev-dependencies = [ +[dependency-groups] +dev = [ "clodius>=0.20.1", - "gosling-widget>=0.0.2", + "jupyterlab>=4.3.1", "pytest>=6.0", "requests>=2.0", "servir>=0.2.1", @@ -28,7 +28,9 @@ dev-dependencies = [ ] [tool.hatch.build] +only-packages = true include = ["/gosling", "/tests"] +artifacts = ["gosling/static/widget.js", "scripts/hatch_build.py"] [tool.hatch.version] source = "vcs" @@ -36,9 +38,13 @@ source = "vcs" [tool.hatch.build.hooks.vcs] version-file = 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