Merge branch 'main' into lane/vis-todos

.github/PULL_REQUEST_TEMPLATE.md

@@ -0,0 +1,38 @@
+# WIP Steps
+
+_This section is optional if the PR is fully ready for review_
+
+-   Create the PR as a "draft" PR
+-   Add [WIP] to the title
+-   Use the template below to ask for specific feedback
+-   [ ] @name: Could you look at \_\_\_? I'm trying to do... (etc.)
+
+# What
+
+Replace this with 1-2 line Description of what feature, bugfix, chore does the PR contain the code for.
+
+# How
+
+Replace this txt describing what kind of technical overlaying code changes were introduced here.
+
+# Screenshots
+
+_This section is optional if there are no visible changes_
+
+-   If possible add screenshots of the visible additions in the UI.
+-   If there are changes in the UI, add **Before** and **After** Screenshots for quick overview.
+-   If there was a Figma design, add a link to that here as well.
+-   Hint : Drag and Drop any images you want to add to the PR. Also you can create a gif of an interactive version and add that!
+
+# PR Checklist
+
+-   [ ] Is your PR title following our conventional commit naming recommendations?
+-   [ ] Have you filled in the PR Description Template?
+-   [ ] Is your branch up to date with the latest in `main`?
+-   [ ] Do the CI checks pass successfully?
+-   [ ] Have you smoke tested the example applications?
+-   [ ] Did you check that the changes meet accessibility standards?
+-   [ ] Have you tested the application on these browsers?
+    -   [ ] Chrome (Fully supported)
+    -   [ ] Firefox (Major bug fixes supported)
+    -   [ ] Safari (Major bug fixes supported)

.github/workflows/ci.yml

@@ -0,0 +1,129 @@
+name: CI
+
+on: [pull_request]
+
+concurrency:
+    # Cancels workflows that are already running when a new one is triggered for a branch
+    group: ${{ github.workflow }}-${{ github.ref }}
+    cancel-in-progress: true
+
+jobs:
+    build:
+        name: Build
+        runs-on: ubuntu-latest
+
+        steps:
+            - uses: actions/checkout@v4
+
+            - name: Install pnpm
+              uses: pnpm/action-setup@v4
+              with:
+                  version: 9
+
+            - name: Use Node.js
+              uses: actions/setup-node@v4
+              with:
+                  node-version: '22'
+
+            - name: Install dependencies
+              run: pnpm install --frozen-lockfile
+
+            - name: Build
+              run: pnpm build
+
+    format:
+        name: Format
+        runs-on: ubuntu-latest
+
+        steps:
+            - uses: actions/checkout@v4
+
+            - name: Install pnpm
+              uses: pnpm/action-setup@v4
+              with:
+                  version: 9
+
+            - name: Use Node.js
+              uses: actions/setup-node@v4
+              with:
+                  node-version: '22'
+
+            - name: Install dependencies
+              run: pnpm install --frozen-lockfile
+
+            - name: Format
+              run: pnpm fmt:check
+
+    lint:
+        name: Lint
+        runs-on: ubuntu-latest
+        # Skip job until we get a linter added
+        if: false
+
+        steps:
+            - uses: actions/checkout@v4
+
+            - name: Install pnpm
+              uses: pnpm/action-setup@v4
+              with:
+                  version: 9
+
+            - name: Use Node.js
+              uses: actions/setup-node@v4
+              with:
+                  node-version: '22'
+
+            - name: Install dependencies
+              run: pnpm install --frozen-lockfile
+
+            - name: Lint
+              run: echo "Add pnpm lint command here"
+
+    test:
+        name: Test
+        runs-on: ubuntu-latest
+
+        steps:
+            - uses: actions/checkout@v4
+
+            - name: Install pnpm
+              uses: pnpm/action-setup@v4
+              with:
+                  version: 9
+
+            - name: Use Node.js
+              uses: actions/setup-node@v4
+              with:
+                  node-version: '22'
+
+            - name: Install dependencies
+              run: pnpm install --frozen-lockfile
+
+            - name: Test
+              run: pnpm test
+
+    typecheck:
+        name: Typecheck
+        runs-on: ubuntu-latest
+
+        steps:
+            - uses: actions/checkout@v4
+
+            - name: Install pnpm
+              uses: pnpm/action-setup@v4
+              with:
+                  version: 9
+
+            - name: Use Node.js
+              uses: actions/setup-node@v4
+              with:
+                  node-version: '22'
+
+            - name: Install dependencies
+              run: pnpm install --frozen-lockfile
+
+            - name: Build
+              run: pnpm build
+
+            - name: Typecheck
+              run: pnpm typecheck

.prettierignore

@@ -0,0 +1,81 @@
+### dependencies
+node_modules
+
+### production
+build
+dist
+
+### boilerplate below ###
+
+# Visual Studio Code
+.vscode/*
+!.vscode/settings.json
+!.vscode/tasks.json
+!.vscode/launch.json
+!.vscode/extensions.json
+*.code-workspace
+
+# Local History for Visual Studio Code
+.history/
+
+# Jet Brains
+.idea
+
+### macos
+# General
+.DS_Store
+.AppleDouble
+.LSOverride
+
+# Icon must end with two \r
+Icon
+
+# Thumbnails
+._*
+
+# Files that might appear in the root of a volume
+.DocumentRevisions-V100
+.fseventsd
+.Spotlight-V100
+.TemporaryItems
+.Trashes
+.VolumeIcon.icns
+.com.apple.timemachine.donotpresent
+
+# Directories potentially created on remote AFP share
+.AppleDB
+.AppleDesktop
+Network Trash Folder
+Temporary Items
+.apdisk
+
+# Logs
+logs
+*.log
+npm-debug.log*
+
+# Diagnostic reports (https://nodejs.org/api/report.html)
+report.[0-9]*.[0-9]*.[0-9]*.[0-9]*.json
+
+# Runtime data
+pids
+*.pid
+*.seed
+*.pid.lock
+
+# TypeScript cache
+*.tsbuildinfo
+
+# Output of 'npm pack'
+*.tgz
+
+# dotenv environment variables file
+.env
+.env.test
+
+# code coverage
+coverage
+
+# Lock files
+package-lock.json
+pnpm-lock.yaml

LICENSE.md

@@ -1,4 +1,4 @@
-Copyright 2024 Allen Institute 
+Copyright 2024 Allen Institute
 
 Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:
 
@@ -8,4 +8,4 @@ Redistribution and use in source and binary forms, with or without modification,
 
 3. Neither the name of the copyright holder nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission.
 
-THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS “AS IS” AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS “AS IS” AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

README.md

@@ -14,6 +14,12 @@ See the `example` directory for example projects using the packages. Over time,
 
 For details on running or adding new examples, see the `docs/examples.md` file.s
 
+# Installation for Development
+
+This project uses [Node.js](https://nodejs.org) and [pnpm](https://pnpm.io/). We use [Volta](https://volta.sh/) to manage the versions of each. If you're not using Volta, check the "volta" key in the root `package.json` for the Node and pnpm versions we're using when developing.
+
+Volta has experimental support for pnpm, so [follow the steps on their docs](https://docs.volta.sh/advanced/pnpm) to get it enabled.
+
 # Using the Libraries
 
 See the `docs/using-packages.md` file for information on how to use the packages in your own projects.

examples/index.html

@@ -5,6 +5,7 @@
         <br />
         <ul>
             <li><a href="/dzi">Deep Zoom Image</a><br /></li>
+            <li><a href="/omezarr">OMEZARR</a><br /></li>
             <li><a href="/layers">Layers</a><br /></li>
         </ul>
     </body>

examples/omezarr.html

@@ -0,0 +1,17 @@
+<!doctype html>
+<html>
+    <body>
+        <div
+            id="sidebar"
+            style="top: 0; left: 0; width: 15%; height: 100%; position: absolute"
+        ></div>
+        <div
+            id="main"
+            style="top: 0; left: 15%; width: 85%; height: 100%; position: absolute"
+        />
+    </body>
+</html>
+<script
+    type="module"
+    src="./src/omezarr/omezarr.ts"
+></script>

examples/package.json

@@ -46,6 +46,7 @@
         "@alleninstitute/vis-geometry": "workspace:*",
         "@alleninstitute/vis-scatterbrain": "workspace:*",
         "@alleninstitute/vis-dzi": "workspace:*",
+        "@alleninstitute/vis-omezarr": "workspace:*",
         "@czi-sds/components": "^20.0.1",
         "@emotion/css": "^11.11.2",
         "@emotion/react": "^11.11.4",
@@ -64,4 +65,4 @@
         "regl": "^2.1.0",
         "zarrita": "0.4.0-next.14"
     }
-}
+}

examples/src/common/loaders/ome-zarr/fetchSlice.worker.ts

@@ -1,6 +1,6 @@
 // a web-worker which fetches slices of data, decodes them, and returns the result as a flat float32 array, using transferables
 import type { Chunk } from 'zarrita';
-import { getSlice, type ZarrDataset, type ZarrRequest } from './zarr-data';
+import { type ZarrDataset, type ZarrRequest, getSlice } from '@alleninstitute/vis-omezarr';
 
 const ctx = self;
 type ZarrSliceRequest = {

examples/src/common/loaders/ome-zarr/sliceWorkerPool.ts

@@ -1,5 +1,5 @@
 import { uniqueId } from 'lodash';
-import type { ZarrDataset, ZarrRequest } from './zarr-data';
+import type { ZarrDataset, ZarrRequest } from '@alleninstitute/vis-omezarr';
 
 type PromisifiedMessage = {
     requestCacheKey: string;

examples/src/dzi/render-server-provider.tsx → examples/src/common/react/render-server-provider.tsx

@@ -7,7 +7,8 @@ export function RenderServerProvider(props: PropsWithChildren<{}>) {
     const server = useRef<RenderServer>();
     const { children } = props;
     useEffect(() => {
-        server.current = new RenderServer([2048, 2048], []);
+        server.current = new RenderServer([2048, 2048], ['oes_texture_float']);
+        console.log('server started...');
     }, []);
     return <renderServerContext.Provider value={server.current ?? null}>{children}</renderServerContext.Provider>;
 }

examples/src/data-renderers/versa-renderer.ts

@@ -7,7 +7,7 @@ import {
     sizeInUnits,
     type ZarrDataset,
     type ZarrRequest,
-} from '~/common/loaders/ome-zarr/zarr-data';
+} from '@alleninstitute/vis-omezarr';
 import { getSlicePool } from '~/common/loaders/ome-zarr/sliceWorkerPool';
 import type { Camera } from '~/common/camera';
 

examples/src/data-renderers/volumeSliceRenderer.ts

@@ -12,7 +12,7 @@ import {
     sizeInVoxels,
     sliceDimensionForPlane,
     uvForPlane,
-} from '~/common/loaders/ome-zarr/zarr-data';
+} from '@alleninstitute/vis-omezarr';
 import {
     cacheKeyFactory,
     getVisibleTiles,

examples/src/data-sources/ome-zarr/planar-slice.ts

@@ -1,4 +1,4 @@
-import { type ZarrDataset, load } from '~/common/loaders/ome-zarr/zarr-data';
+import { loadMetadata, type ZarrDataset } from '@alleninstitute/vis-omezarr';
 import type { AxisAlignedPlane } from '~/data-renderers/versa-renderer';
 import type { ColorMapping } from '../../data-renderers/types';
 import type { OptionalTransform, Simple2DTransform } from '../types';
@@ -32,7 +32,7 @@ function assembleZarrSlice(config: ZarrSliceConfig, dataset: ZarrDataset): AxisA
 }
 export function createZarrSlice(config: ZarrSliceConfig): Promise<AxisAlignedZarrSlice> {
     const { url } = config;
-    return load(url).then((dataset) => {
+    return loadMetadata(url).then((dataset) => {
         return assembleZarrSlice(config, dataset);
     });
 }

examples/src/data-sources/ome-zarr/slice-grid.ts

@@ -1,4 +1,4 @@
-import { type ZarrDataset, load } from '~/common/loaders/ome-zarr/zarr-data';
+import { loadMetadata, type ZarrDataset } from '@alleninstitute/vis-omezarr';
 import type { AxisAlignedPlane } from '~/data-renderers/versa-renderer';
 import type { ColorMapping } from '../../data-renderers/types';
 import type { OptionalTransform, Simple2DTransform } from '../types';
@@ -33,7 +33,7 @@ function assembleZarrSliceGrid(config: ZarrSliceGridConfig, dataset: ZarrDataset
 }
 export function createZarrSliceGrid(config: ZarrSliceGridConfig): Promise<AxisAlignedZarrSliceGrid> {
     const { url } = config;
-    return load(url).then((dataset) => {
+    return loadMetadata(url).then((dataset) => {
         return assembleZarrSliceGrid(config, dataset);
     });
 }

examples/src/dzi/double.tsx

@@ -1,5 +1,5 @@
 import { useContext, useEffect, useMemo, useRef, useState } from 'react';
-import { RenderServerProvider } from './render-server-provider';
+import { RenderServerProvider } from '../common/react/render-server-provider';
 import React from 'react';
 import { DziView } from './dziView';
 import type { DziImage, DziRenderSettings } from '@alleninstitute/vis-dzi';