docs.quilt.bio (#4373)

drernie · web-flow · commit 75b547a89844 · 2025-04-15T15:07:42.000Z
Co-authored-by: Dr. Ernie Prabhakar &lt;19791+drernie@users.noreply.github.com&gt;
diff --git a/.github/pull_request_template.md b/.github/pull_request_template.md
@@ -12,6 +12,6 @@
     - [ ] run `optipng` on any new PNGs
     - [ ] [Python: Run `build.py`](../tree/master/gendocs/build.py) for new docstrings
     - [ ] JavaScript: basic explanation and screenshot of new features
-    - [ ] Markdown somewhere in docs/**/*.md that explains the feature to end users (said .md files should be linked from SUMMARY.md so they appear on https://docs.quiltdata.com)
+    - [ ] Markdown somewhere in docs/**/*.md that explains the feature to end users (said .md files should be linked from SUMMARY.md so they appear on https://docs.quilt.bio)
     - [ ] Markdown docs for developers
 - [ ] [Changelog](../tree/master/docs/CHANGELOG.md) entry (skip if change is not significant to end users, e.g. docs only)
diff --git a/api/python/quilt3/packages.py b/api/python/quilt3/packages.py
@@ -100,7 +100,7 @@ def f(wrapped):
 _WORKFLOW_PARAM_DOCSTRING = (
     'workflow: workflow ID or `None` to skip workflow validation.\n'
     '        If not specified, the default workflow will be used.\n'
-    '        For details see: https://docs.quiltdata.com/advanced-usage/workflows\n'
+    '        For details see: https://docs.quilt.bio/advanced-usage/workflows\n'
 )
 
 
diff --git a/api/python/setup.py b/api/python/setup.py
@@ -15,7 +15,7 @@ def readme():
 biotech, and other data-driven domains.
 
 The `quilt3` PyPI package allows you to build, push, and install data packages.
-Visit the `documentation quickstart <https://docs.quiltdata.com/quickstart>`_
+Visit the `documentation quickstart <https://docs.quilt.bio/quickstart>`_
 to learn more.
 """
 
diff --git a/catalog/app/components/Assistant/Model/Conversation.ts b/catalog/app/components/Assistant/Model/Conversation.ts
@@ -335,7 +335,7 @@ const TASK_CONTEXT = XML.tag(
 const TASK_DESCRIPTION = XML.tag(
   'task-description',
   {},
-  'When asked a question about Quilt or Quilt Data, refer to the documentation at https://docs.quiltdata.com.',
+  'When asked a question about Quilt or Quilt Data, refer to the documentation at https://docs.quilt.bio.',
 ).toString()
 
 const CONVERSATION_START = `
diff --git a/catalog/app/components/FileEditor/QuiltConfigEditor/BucketPreferences/__snapshots__/BucketPreferences.spec.tsx.snap b/catalog/app/components/FileEditor/QuiltConfigEditor/BucketPreferences/__snapshots__/BucketPreferences.spec.tsx.snap
@@ -11,7 +11,7 @@ exports[`components/FileEditor/QuiltConfigEditor/BucketPreferences/BucketPrefere
      
     <a
       className="root"
-      href="https://docs.quiltdata.com/quilt-platform-administrator/preferences"
+      href="https://docs.quilt.bio/quilt-platform-administrator/preferences"
       target="_blank"
     >
       Learn more
@@ -712,7 +712,7 @@ exports[`components/FileEditor/QuiltConfigEditor/BucketPreferences/BucketPrefere
      
     <a
       className="root"
-      href="https://docs.quiltdata.com/quilt-platform-administrator/preferences"
+      href="https://docs.quilt.bio/quilt-platform-administrator/preferences"
       target="_blank"
     >
       Learn more
diff --git a/catalog/app/components/FileEditor/QuiltConfigEditor/QuiltSummarize/__snapshots__/QuiltSummarize.spec.tsx.snap b/catalog/app/components/FileEditor/QuiltConfigEditor/QuiltSummarize/__snapshots__/QuiltSummarize.spec.tsx.snap
@@ -133,7 +133,7 @@ exports[`QuiltSummarize Render columns 1`] = `
      
     <a
       className="root"
-      href="https://docs.quiltdata.com/quilt-platform-catalog-user/visualizationdashboards#quilt_summarize.json"
+      href="https://docs.quilt.bio/quilt-platform-catalog-user/visualizationdashboards#quilt_summarize.json"
       target="_blank"
     >
       the docs
@@ -226,7 +226,7 @@ exports[`QuiltSummarize Render empty placeholders 1`] = `
      
     <a
       className="root"
-      href="https://docs.quiltdata.com/quilt-platform-catalog-user/visualizationdashboards#quilt_summarize.json"
+      href="https://docs.quilt.bio/quilt-platform-catalog-user/visualizationdashboards#quilt_summarize.json"
       target="_blank"
     >
       the docs
@@ -319,7 +319,7 @@ exports[`QuiltSummarize Render row 1`] = `
      
     <a
       className="root"
-      href="https://docs.quiltdata.com/quilt-platform-catalog-user/visualizationdashboards#quilt_summarize.json"
+      href="https://docs.quilt.bio/quilt-platform-catalog-user/visualizationdashboards#quilt_summarize.json"
       target="_blank"
     >
       the docs
diff --git a/catalog/app/components/FileEditor/__snapshots__/HelpLinks.spec.tsx.snap b/catalog/app/components/FileEditor/__snapshots__/HelpLinks.spec.tsx.snap
@@ -12,7 +12,7 @@ exports[`components/FileEditor/HelpLinks MissingSourceBucket should render 1`] =
      is empty.
      
     <a
-      href="https://docs.quiltdata.com/catalog/preferences"
+      href="https://docs.quilt.bio/catalog/preferences"
     >
       Learn more
     </a>
diff --git a/catalog/app/constants/urls.js b/catalog/app/constants/urls.js
@@ -1,7 +1,7 @@
 /* Constants are a developer's best friend
  * convention: camelcase, no terminating slash */
 export const blog = 'https://blog.quiltdata.com'
-export const docs = 'https://docs.quiltdata.com'
+export const docs = 'https://docs.quilt.bio'
 export const gitWeb = 'https://github.com/quiltdata/quilt'
 export const homeMarketing = 'https://quiltdata.com'
 export const instagram = 'https://www.instagram.com/quiltdata/'
diff --git a/catalog/app/containers/Bucket/Download/__snapshots__/PackageCodeSamples.spec.tsx.snap b/catalog/app/containers/Bucket/Download/__snapshots__/PackageCodeSamples.spec.tsx.snap
@@ -3,7 +3,7 @@
 exports[`containers/Bucket/CodeSamples/Package renders catalog property 1`] = `
 <div>
   <dl
-    data-help="https://docs.quiltdata.com/quilt-python-sdk-developers/api-reference/package#package.browse"
+    data-help="https://docs.quilt.bio/quilt-python-sdk-developers/api-reference/package#package.browse"
   >
     <dt>
       Browse using Quilt3 Python API
@@ -17,7 +17,7 @@ exports[`containers/Bucket/CodeSamples/Package renders catalog property 1`] = `
     </dd>
   </dl>
   <dl
-    data-help="https://docs.quiltdata.com/quilt-python-sdk-developers/api-reference/package#package.install"
+    data-help="https://docs.quilt.bio/quilt-python-sdk-developers/api-reference/package#package.install"
   >
     <dt>
       Install using Quilt3 Python API
@@ -31,7 +31,7 @@ exports[`containers/Bucket/CodeSamples/Package renders catalog property 1`] = `
     </dd>
   </dl>
   <dl
-    data-help="https://docs.quiltdata.com/quilt-python-sdk/api-reference/cli#install"
+    data-help="https://docs.quilt.bio/quilt-python-sdk/api-reference/cli#install"
   >
     <dt>
       Install using Quilt3 CLI
diff --git a/catalog/app/containers/Bucket/PackageList/PackageList.tsx b/catalog/app/containers/Bucket/PackageList/PackageList.tsx
@@ -36,7 +36,7 @@ import { displayError } from '../errors'
 import PACKAGE_COUNT_QUERY from './gql/PackageCount.generated'
 import PACKAGE_LIST_QUERY from './gql/PackageList.generated'
 
-const EXAMPLE_PACKAGE_URL = 'https://docs.quiltdata.com/walkthrough/editing-a-package'
+const EXAMPLE_PACKAGE_URL = 'https://docs.quilt.bio/walkthrough/editing-a-package'
 
 const PER_PAGE = 30
 
diff --git a/catalog/app/containers/Bucket/Queries/Athena/Athena.tsx b/catalog/app/containers/Bucket/Queries/Athena/Athena.tsx
@@ -25,7 +25,7 @@ const CreatePackage = React.lazy(() => import('./CreatePackage'))
 function SeeDocsForCreatingPackage() {
   return (
     <M.Tooltip title="You can create packages from the query results. Click to see the docs.">
-      <a href="https://docs.quiltdata.com/advanced/athena" target="_blank">
+      <a href="https://docs.quilt.bio/advanced/athena" target="_blank">
         <M.IconButton size="small">
           <M.Icon>help_outline</M.Icon>
         </M.IconButton>
diff --git a/catalog/app/utils/AWS/Bedrock/History.ts b/catalog/app/utils/AWS/Bedrock/History.ts
@@ -5,7 +5,7 @@ import {
   Message,
 } from './Message'
 
-const SYSTEM_PROMPT = `You are a conservative and creative scientist. When asked a question about Quilt, refer to the documentation at https://docs.quiltdata.com. For cross-account bucket policies, see https://docs.quiltdata.com/advanced/crossaccount. Use GitHub flavored Markdown syntax for formatting when appropriate.`
+const SYSTEM_PROMPT = `You are a conservative and creative scientist. When asked a question about Quilt, refer to the documentation at https://docs.quilt.bio. For cross-account bucket policies, see https://docs.quilt.bio/advanced/crossaccount. Use GitHub flavored Markdown syntax for formatting when appropriate.`
 
 export interface History {
   messages: Message[]
diff --git a/catalog/app/website/pages/Install/Install.js b/catalog/app/website/pages/Install/Install.js
@@ -11,7 +11,7 @@ import mp from './mp.png'
 const MP_LINK =
   'https://aws.amazon.com/marketplace/pp/Quilt-Data-Quilt-Business/B07QF1VXFQ'
 const PREREQ_LINK =
-  'https://docs.quiltdata.com/references/technical-reference#before-you-install-quilt'
+  'https://docs.quilt.bio/references/technical-reference#before-you-install-quilt'
 const MAILTO = 'mailto:contact@quiltdata.com'
 
 const useStyles = M.makeStyles((t) => ({
diff --git a/catalog/app/website/pages/Landing/LocalMode/LocalMode.js b/catalog/app/website/pages/Landing/LocalMode/LocalMode.js
@@ -71,7 +71,7 @@ export default function Showcase() {
               </M.Typography>
             </M.Box>
             <M.Box mt={4}>
-              <ChevronLink href="https://docs.quiltdata.com/v/master/catalog/localmode">
+              <ChevronLink href="https://docs.quilt.bio/v/master/catalog/localmode">
                 Read more about local mode
               </ChevronLink>
             </M.Box>
diff --git a/docs/CHANGELOG.md b/docs/CHANGELOG.md
@@ -696,7 +696,7 @@ Python
 
 # 3.1.4 - 2019-10-17
 
-* [`delete_package`](https://docs.quiltdata.com/api-reference/api#delete\_package) for a specific version via `top_hash=`
+* [`delete_package`](https://docs.quilt.bio/api-reference/api#delete\_package) for a specific version via `top_hash=`
 
 # 3.1.3 - 2019-10-11
 
@@ -711,7 +711,7 @@ Python
 
 # 3.0.0 - 2019-05-24 - Quilt 3 (formerly Quilt T4) Initial Release
 
-This is the initial release of the new and improved Quilt 3 ([formerly Quilt T4](https://github.com/quiltdata/t4)). For more information [refer to the documentation](https://docs.quiltdata.com/).
+This is the initial release of the new and improved Quilt 3 ([formerly Quilt T4](https://github.com/quiltdata/t4)). For more information [refer to the documentation](https://docs.quilt.bio/).
 
 # 2.9.15 - 2019-01-09 - Teams Config
 
@@ -937,19 +937,19 @@ Data fragments can now be downloaded in parallel leading to much faster package
 
 ## Quilt packages live in a centralized location on your machine
 
-Quilt data packages are now available wherever you run Python. We recommend that users **quilt push all local packages to the registry before upgrading**. Further details on migration are [here](https://docs.quiltdata.com/troubleshooting.html).
+Quilt data packages are now available wherever you run Python. We recommend that users **quilt push all local packages to the registry before upgrading**. Further details on migration are [here](https://docs.quilt.bio/troubleshooting.html).
 
 ## Faster builds with build cache
 
 Quilt now caches build intermediates. So if you wish to update the README of a multi-gigabyte package, you can rebuild the entire package in one second.
 
 ## Group-level build parameters
 
-You can now specify build parameters (like transform) for all children of a group in one shot. The updated syntax and docs are [here](https://docs.quiltdata.com/buildyml.html).
+You can now specify build parameters (like transform) for all children of a group in one shot. The updated syntax and docs are [here](https://docs.quilt.bio/buildyml.html).
 
 ## quilt.yml is like requirements.txt but for data
 
-You can now express dependencies on multiple packages in a single file. Docs [here](https://docs.quiltdata.com/cli.html#installing-via-requirements-file).
+You can now express dependencies on multiple packages in a single file. Docs [here](https://docs.quilt.bio/cli.html#installing-via-requirements-file).
 
 ## Experimental: build a package from a GitHub repo
 
diff --git a/docs/FAQ.md b/docs/FAQ.md
@@ -8,7 +8,7 @@ p.push("USR/PKG", message="MSG", registry="s3://BUCKET")
 ```
 
 > Use a [.quiltignore
-file](https://docs.quiltdata.com/advanced-usage/.quiltignore) for more control
+file](https://docs.quilt.bio/advanced-usage/.quiltignore) for more control
 over which files `set_dir()` includes.
 
 ## How does Quilt versioning relate to S3 object versioning?
@@ -171,7 +171,7 @@ export AWS_PROFILE=your_profile
 
 The S3 permissions needed by `quilt3` are similar to
 <!-- markdownlint-disable-next-line line-length -->
-[this bucket policy](https://docs.quiltdata.com/advanced/crossaccount#bucket-policies)                                                                                                  but `quilt3` does not need either `s3:GetBucketNotification` or `s3:PutBucketNotification`.
+[this bucket policy](https://docs.quilt.bio/advanced/crossaccount#bucket-policies)                                                                                                  but `quilt3` does not need either `s3:GetBucketNotification` or `s3:PutBucketNotification`.
 
 ## How complex can my Athena queries be?
 
@@ -243,7 +243,7 @@ in the Amazon S3 documentation.
 ## How many IPs does a standard Quilt stack require?
 
 Currently, a full size, multi-Availability Zone deployment (without
-[Voila](https://docs.quiltdata.com/catalog/visualizationdashboards#voila))
+[Voila](https://docs.quilt.bio/catalog/visualizationdashboards#voila))
 requires at least 256 IPs. This means a minimum CIDR block of `/24`.
 
 Optional additional features (such as automated data packaging) require
diff --git a/docs/Troubleshooting.md b/docs/Troubleshooting.md
@@ -36,7 +36,7 @@ p.push(
 )
 ```
 
-- [Reference](https://docs.quiltdata.com/api-reference/package#package.set_dir).
+- [Reference](https://docs.quilt.bio/api-reference/package#package.set_dir).
 
 ## User creation and log in
 
diff --git a/docs/Troubleshooting_SSO.md b/docs/Troubleshooting_SSO.md
@@ -14,7 +14,7 @@ Incorrect redirect URIs are a common cause of SSO loops.
 - **Okta**: Go to **Okta Admin > Applications > [Your App] > Sign On**.
 
 Ensure the **redirect URI** matches exactly what is expected,
-as documented in the Quilt [technical reference](https://docs.quiltdata.com/quilt-platform-administrator/technical-reference#single-sign-on-sso).
+as documented in the Quilt [technical reference](https://docs.quilt.bio/quilt-platform-administrator/technical-reference#single-sign-on-sso).
 This includes:
 
 - Case sensitivity (Azure and Okta are case-sensitive!)
@@ -57,7 +57,7 @@ Incorrect claims or missing attributes can cause authentication failures.
 
 ## Step 5: Collect CloudWatch Logs for ECS
 
-Follow the usual [troubleshooting steps](https://docs.quiltdata.com/quilt-python-sdk/more/troubleshooting#elastic-container-service-ecs) to collect the ECS logs for the registry service:
+Follow the usual [troubleshooting steps](https://docs.quilt.bio/quilt-python-sdk/more/troubleshooting#elastic-container-service-ecs) to collect the ECS logs for the registry service:
 
 - Look for authentication-related errors or unexpected redirects.
 - Verify that the expected redirect URIs are being returned.
diff --git a/docs/advanced-features/athena.md b/docs/advanced-features/athena.md
@@ -11,7 +11,7 @@ using predicates based on package or object-level metadata.
 Packages can be created from the resulting tabular data.
 To be able to create a package,
 the table must contain the columns `logical_key`, `physical_keys` (or `physical_key`) and `size`.
-(See also [Mental Model](https://docs.quiltdata.com/mentalmodel))
+(See also [Mental Model](https://docs.quilt.bio/mentalmodel))
 
 ![Athena page with results ready to be packaged](../imgs/athena-package.png)
 
diff --git a/docs/api-reference/Package.md b/docs/api-reference/Package.md
@@ -205,7 +205,7 @@ __Arguments__
 * __message__:  the commit message of the package
 * __workflow__:  workflow ID or `None` to skip workflow validation.
     If not specified, the default workflow will be used.
-* __For details see__:  https://docs.quiltdata.com/advanced-usage/workflows
+* __For details see__:  https://docs.quilt.bio/advanced-usage/workflows
 
 
 __Returns__
@@ -314,7 +314,7 @@ __Arguments__
     push the local file to s3 (instead of pushing all data to the destination bucket).
 * __workflow__:  workflow ID or `None` to skip workflow validation.
     If not specified, the default workflow will be used.
-* __For details see__:  https://docs.quiltdata.com/advanced-usage/workflows
+* __For details see__:  https://docs.quilt.bio/advanced-usage/workflows
 
 * __force__:  skip the top hash check and overwrite any existing package
 * __dedupe__:  don't push if the top hash matches the existing package top hash; return the current package
diff --git a/docs/examples/nextflow.md b/docs/examples/nextflow.md
@@ -8,7 +8,7 @@ share data-intensive, highly scalable, workflows on any infrastructure.
 - `nf-quilt` is a [Nextflow
 plugin](https://www.nextflow.io/docs/latest/plugins.html) developed by Quilt
 Data that enables you read and write directly to [Quilt data
-packages](https://docs.quiltdata.com) instead of just S3 locations.
+packages](https://docs.quilt.bio) instead of just S3 locations.
 
 ## Quick Start
 

Original file line number	Diff line number	Diff line change
`@@ -100,7 +100,7 @@ def f(wrapped):`
`100`	`100`	`_WORKFLOW_PARAM_DOCSTRING = (`
`101`	`101`	'workflow: workflow ID or `None` to skip workflow validation.\n'
`102`	`102`	`' If not specified, the default workflow will be used.\n'`
`103`		`- ' For details see: https://docs.quiltdata.com/advanced-usage/workflows\n'`
	`103`	`+ ' For details see: https://docs.quilt.bio/advanced-usage/workflows\n'`
`104`	`104`	`)`
`105`	`105`
`106`	`106`
Original file line number	Diff line number	Diff line change
@@ -12,7 +12,7 @@ exports[`components/FileEditor/HelpLinks MissingSourceBucket should render 1`] =
`12`	`12`	`is empty.`
`13`	`13`
`14`	`14`	`<a`
`15`		`- href="https://docs.quiltdata.com/catalog/preferences"`
	`15`	`+ href="https://docs.quilt.bio/catalog/preferences"`
`16`	`16`	`>`
`17`	`17`	`Learn more`
`18`	`18`	`</a>`