[C] Upgrade packages (#203)

* [C] Upgrade packages
- Upgrade all packages
- Move from JS to Typescript
- Move Sass and Styled Components to PostCSS
- Update swizzled templates as needed
- Update markdown files, fix markdown errors
- Upgrade from Yarn 1 to Yarn 4
- Update docusaurus config
- Update github actions
- Fix anchor links

.github/workflows/documentation.yml

@@ -11,33 +11,28 @@ jobs:
     if: github.event_name != 'push'
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v1
-      - uses: actions/setup-node@v1
+      - uses: actions/checkout@v4
+      - uses: actions/setup-node@v4
         with:
-          node-version: "12.x"
+          node-version-file: "package.json"
+          cache: "yarn"
+      - name: Install dependencies
+        run: yarn install --immutable
       - name: Test Build
         env:
           ALGOLIA_API_KEY: ${{ secrets.ALGOLIA_API_KEY }}
           ALGOLIA_APP_ID: ${{ secrets.ALGOLIA_APP_ID }}
           ALGOLIA_INDEX_NAME: ${{ secrets.ALGOLIA_INDEX_NAME }}
           GOOGLE_ANALYTICS: ${{ secrets.GOOGLE_ANALYTICS }}
-        run: |
-          if [ -e yarn.lock ]; then
-          yarn install --frozen-lockfile
-          elif [ -e package-lock.json ]; then
-          npm ci
-          else
-          npm i
-          fi
-          npm run build
+        run: yarn build
   gh-release:
     if: github.event_name != 'pull_request'
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v1
-      - uses: actions/setup-node@v1
+      - uses: actions/checkout@v4
+      - uses: actions/setup-node@v4
         with:
-          node-version: "12.x"
+          node-version: "21.x"
       - name: Add key to allow access to repository
         env:
           SSH_AUTH_SOCK: /tmp/ssh_agent.sock
@@ -62,11 +57,6 @@ jobs:
         run: |
           git config --global user.email "[email protected]"
           git config --global user.name "gh-actions"
-          if [ -e yarn.lock ]; then
-          yarn install --frozen-lockfile
-          elif [ -e package-lock.json ]; then
-          npm ci
-          else
-          npm i
-          fi
+          yarn install --immutable
+          yarn build
           npx docusaurus deploy

.gitignore

@@ -16,6 +16,14 @@
 .env.test.local
 .env.production.local
 
+# Yarn
+.pnp.*
+.yarn/*
+!.yarn/patches
+!.yarn/plugins
+!.yarn/releases
+!.yarn/sdks
+!.yarn/versions
 npm-debug.log*
 yarn-debug.log*
 yarn-error.log*

.node-version

@@ -0,0 +1 @@
+21.1.0

.yarnrc.yml

@@ -0,0 +1,3 @@
+nodeLinker: node-modules
+
+yarnPath: .yarn/releases/yarn-4.5.1.cjs

babel.config.js

@@ -1,4 +1,3 @@
 module.exports = {
   presets: [require.resolve('@docusaurus/core/lib/babel/preset')],
-  plugins: ["babel-plugin-styled-components"]
 };

blog/2021-09-08-version6.md

@@ -11,6 +11,8 @@ The Manifold Team is proud to announce the release of version 6.0.
 
 Our [complete list of release notes](https://manifoldscholar.github.io/manifold-docusaurus/docs/administering/release_notes/v6x) for this version details all of the new additions, but here are some of the highlights, with links to the corresponding sections of our documentation.
 
+<!--truncate-->
+
 [Analytics](https://manifoldscholar.github.io/manifold-docusaurus/docs/backend/analytics). Built from the ground up, our analytics tools provide usage data at the site, project, text, and text-section levels. We are committed to protecting our users’ privacy, so all reported data is anonymized.
 
 [Word Ingestion](https://manifoldscholar.github.io/manifold-docusaurus/docs/administering/configuring/ingestion_settings). With version 6, we’ve transitioned from PanDoc to [Mammoth](https://www.npmjs.com/package/mammoth) to power our Word to HTML conversion. The Mammoth engine produces better results and allows us to map Word styles to HTML styles. This means that if you use a custom style in Word, it will persist into Manifold, where you can assign it a specific type of rendering using a stylesheet.

blog/2021-10-14-accessibility-sprint.md

@@ -6,6 +6,8 @@ title: "Fall 2021 Accessibility Sprint!"
 
 At Manifold, we treat accessibility as a top-tier concern. Our developers at [Cast Iron Coding](https://castironcoding.com/) are accessibility experts who design and develop the application with accessible functionality foremost in mind. In addition to the extensive testing they do in-house using screen-readers and browser add-ons, we’ve had the benefit of collaborating with the University of Washington’s [library](https://www.lib.washington.edu/), [press](https://uwapress.uw.edu/), and [accessibility office](https://www.washington.edu/doit/accessible-technology-services-0) over the past three years. The Washington team has performed an ongoing audit of Manifold over that time, and our two groups meet regularly to discuss new ideas and strategies for making the application even more performant for readers and content creators using assistive technologies. 
 
+<!--truncate-->
+
 Born out of this collaboration, we have recently been engaged in an accessibility sprint that has involved the following:
 
 1. We reworked the user notification preferences interface for better screen reader UX. Dana’s [extended commit message](https://github.com/ManifoldScholar/manifold/pull/3079/commits/0aad0424cd0235f7fe6346775f9d3b02339258cf) on this issue is indicative the care and expertise we bring to accessibility concerns.

blog/2021-10-26-OA-week-spotlight1.md

@@ -6,6 +6,8 @@ title: "OA Week 2021 Project Spotlight 1"
 
 As part of [Open Access Week](http://www.openaccessweek.org/), Manifold is featuring interviews with the creators of exemplary projects that use Manifold's capabilities to the fullest. Our first installment in this series is [Race &/ in America](https://digitalpublications.brown.edu/projects/project-collection/race-and-in-america). We interviewed Allison Levy from [Brown University Library Center for Digital Scholarship](https://library.brown.edu/create/cds/) about this impressive project. 
 
+<!--truncate-->
+
 ## How did the project come together? Who was involved?
 
 Over the 2020-21 academic year, the Center for the Study of Race and Ethnicity in America at Brown University, in partnership with the Office of the Provost, undertook a systematic investigation of the foundational and enduring contemporary effects of anti-Black racism via a pioneering panel discussion series featuring Brown faculty on the role that racism plays in American public health, democracy, punishment, and more.

blog/2021-10-27-OA-week-spotlight2.md

@@ -7,6 +7,8 @@ title: "OA Week 2021 Project Spotlight 2"
 
 As part of [Open Access Week](http://www.openaccessweek.org/), Manifold is featuring interviews with the creators of exemplary projects that use Manifold's capabilities to the fullest. Our second installment in this series is [The Greater Chaco Landscape](http://read.upcolorado.com/projects/the-greater-chaco-landscape). We interviewed Darrin Pratt, director of the University Press of Colorado, about this amazing project. 
 
+<!--truncate-->
+
 ## How did the project come together? Who was involved?
 
 The Greater Chaco Landscape originated with a seminar held at Crow Canyon Archaeological Center in August 2017. This seminar brought together academics and Native scholars from the tribal communities who have a vested interest in Chaco Canyon to address "potential conflicts between energy development and Chacoan archaeology across the San Juan Basin.” Individual seminar presentations, which provided the underpinnings for the volume’s written chapters, were filmed, and after the initial seminar, Durango filmmaker Larry Ruiz recorded additional footage—at Chaco Canyon itself—of Acoma (Haaku), Diné (Navajo), Hopi, and A:shiwi (Zuni) tribal elders and scholars talking about the significance of Chaco to their people. The seminar, filmmaking, and book production were funded by the National Park Service and organized by Steve Lekson (University of Colorado Boulder), Ruth Van Dyke (University of Binghamton) and Carrie Heitman (University of Nebraska). Ruth Van Dyke and Carrie Heitman served as the volume editors for both the online and print editions of the book.

blog/2021-10-28-OA-week-spotlight3.md

@@ -7,6 +7,8 @@ title: "OA Week 2021 Project Spotlight 3"
 
 As part of [Open Access Week](http://www.openaccessweek.org/), Manifold is featuring interviews with the creators of exemplary projects that use Manifold's capabilities to the fullest. Our third installment in this series is [The Negro and The Nation](https://cuny.manifoldapp.org/projects/hubert-harrison-the-negro-and-the-nation). We interviewed Justin Rogers-Cooper, a Professor at CUNY LaGuardia and the Graduate Center, about this collaborative project. 
 
+<!--truncate-->
+
 ## How did the project come together? Who was involved?
 
 This project is partly a story about the network effects of the CUNY Graduate Center, where I got my PhD in English and was later appointed as a faculty member in the Master of Liberal Studies (MALS) program. 

blog/2021-10-29-OA-week-spotlight4.md

@@ -7,6 +7,8 @@ title: "OA Week 2021 Project Spotlight 4"
 
 As part of [Open Access Week](http://www.openaccessweek.org/), Manifold is featuring interviews with the creators of exemplary projects that use Manifold's capabilities to the fullest. Our fourth installment in this series is an "Anthropocene Edition" of [The Mill on The Floss](https://uw.manifoldapp.org/projects/the-mill-on-the-floss). We interviewed its creators, Megan Butler, Francesca Colonnese, and Mara Minion, about this exciting project. 
 
+<!--truncate-->
+
 ## How did the project come together? Who was involved?
 
 Our Manifold project around George Eliot’s The Mill on the Floss grew out of a suggestion from our professor, Jesse Oak Taylor, for an alternative to the classic quarter-end seminar paper. The project allowed us to flip the script: instead of incorporating the novel into our essays, we incorporated our research into the novel. This also gave us a useful perspective on what is involved in creating a scholarly edition of a text. What and how much should we include? How do we frame our edition as an ecocritical intervention into the novel? How can we bring to the novel a new understanding of the role of nature, including how that fits with modern concerns about the Anthropocene?

docs/accessibility.md

@@ -70,6 +70,6 @@ Manifold is distributed software that is used by many different publishers and g
 
 ## Contact Us
 
-If you need accessibility-related help with a Manifold publication, please contact us at <[email protected]>.
+If you need accessibility-related help with a Manifold publication, please contact us at [[email protected]](mailto:[email protected]).
 
-If you would like to report an issue with the Manifold platform, please [email us](mailto:[email protected]) or submit an [issue](https://github.com/ManifoldScholar/manifold/issues) or start a [discussion](https://github.com/ManifoldScholar/manifold/discussions) in our GitHub repository. We are also widely available on [Twitter](https://twitter.com/ManifoldScholar) and [Slack](https://manifold-slackin.herokuapp.com/) for help.
+If you would like to report an issue with the Manifold platform, please [email us](mailto:[email protected]) or submit an [issue](https://github.com/ManifoldScholar/manifold/issues) or start a [discussion](https://github.com/ManifoldScholar/manifold/discussions) in our GitHub repository. We are also widely available on [Twitter](https://twitter.com/ManifoldScholar) and [Slack](https://manifold-slackin.herokuapp.com/) for help.

docs/administering/configuring/integration_settings.md

@@ -41,7 +41,7 @@ The Facebook callback route is located at `/auth/facebook/callback`. The callbac
 
 Once your Facebook app is created, enter your Facebook App ID and App Secret values in Manifold, using the **Facebook App ID** and **Facebook App Secret** fields respectively.
 
-These settings can also be [managed from environment variables](/docs/administering/configuring/managing_settings#managing-settings-with-environment-variables).
+These settings can also be [managed from environment variables](/docs/administering/configuring/managing_settings#from-the-environment).
 </TabItem>
 
 <TabItem value="twitter">
@@ -50,7 +50,7 @@ The Twitter callback route is located at `/auth/twitter/callback`. The callback
 
 After the callback URL has been supplied to the Twitter app, save the Consumer Key (API Key), Consumer Secret (API Secret), Access Token, and Access Token Secret the app generates into Manifold in the **Twitter Consumer Key**, **Twitter Consumer Secret**, **Twitter Access Token**, and **Twitter Access Token Secret** fields, respectively.
 
-These settings can also be [managed from environment variables](/docs/administering/configuring/managing_settings#managing-settings-with-environment-variables).
+These settings can also be [managed from environment variables](/docs/administering/configuring/managing_settings#from-the-environment).
 
 As you complete your Twitter app, it should be configured to be **Read Only**, **Request email addresses from users**, with **3-legged OAuth enabled**.
 
@@ -75,7 +75,7 @@ The **Console** tab in Google’s step-by-step docs refers to the Google Cloud w
 
 When the Service Account Key has been saved to your system, you can load it into the **Google Service Config File** field in Manifold, which will automatically populate the rest of the required fields to complete the Google integration.
 
-These settings can also be [managed from environment variables](/docs/administering/configuring/managing_settings#managing-settings-with-environment-variables).
+These settings can also be [managed from environment variables](/docs/administering/configuring/managing_settings#from-the-environment).
 
 ## Google OAuth
 
@@ -87,12 +87,12 @@ The Manifold API handles OAuth callbacks. For Google, the callback route is loca
 
 Manifold Google OAuth requires **Setup Consent** configured with your email, your authorized Manifold domain, and the callback URL entered in the **Authorized redirect URIs** field. The Manifold Integration page has fields to input both **Client ID** and **Client secret**.
 
-These settings can also be [managed from environment variables](/docs/administering/configuring/managing_settings#managing-settings-with-environment-variables).
+These settings can also be [managed from environment variables](/docs/administering/configuring/managing_settings#from-the-environment).
 
 ## Google Analytics
 
 Manifold ships with its own [built-in analytics reporting tool](../../backend/analytics.md), independent of third party systems. However, if you would like to secure usage data from Google as well, you can set up an analytics property in the Google Console. That property will enable Google to return usage information about your instance in the Google Analytics interface.
 
 To enable this functionality, you will first need to complete the Google Services Integration described above. Once that is complete, [set up a Universal Authorization property](https://support.google.com/analytics/answer/10269537). The Tracking ID that results from that process should be saved to the **Google Analytics Tracking ID** field in Manifold, complete with the the `UA-` prefix.
 
-These settings can also be [managed from environment variables](/docs/administering/configuring/managing_settings#managing-settings-with-environment-variables).
+These settings can also be [managed from environment variables](/docs/administering/configuring/managing_settings#from-the-environment).

docs/administering/configuring/theme_settings.md

@@ -5,7 +5,7 @@ sidebar_label: Theme Settings
 ---
 
 import Spec from "@theme/Spec";
-const defaultImageFormats = "GIF, JPEG, JPG, PNG";
+export const defaultImageFormats = "GIF, JPEG, JPG, PNG";
 
 :::location
 The fields discussed in this section can be accessed from the Manifold backend by selecting **Settings** from the main menu and then **Theme** in the submenu.

docs/administering/installation.md

@@ -46,7 +46,7 @@ Shell into the server as root and download the most recent package.
 
 <Tabs
   groupId="install-type"
-  defaultValue="ubuntu18"
+  defaultValue="ubuntu22"
   values={[
     {label: "Ubuntu22", value: "ubuntu22"},
     {label: "Ubuntu20", value: "ubuntu20"},
@@ -83,7 +83,7 @@ curl -O ${getData("installUrlFor", "centos7")}
 
 <Tabs
   groupId="install-type"
-  defaultValue="ubuntu18"
+  defaultValue="ubuntu22"
   values={[
     {label: "Ubuntu22", value: "ubuntu22"},
     {label: "Ubuntu20", value: "ubuntu20"},

docs/backend/entitlements.md

@@ -60,7 +60,7 @@ If a project is still in Draft, having an entitlement alone will not allow a use
 
 When the **Add Entitlement** button is selected a drawer will slide open from the right of the screen exposing three fields and three dropdowns separated into two different categories.
 
-Beneath the **User Details** category, you can enter the email address, first name, and last name of the person for whom you want to create the entitlement. The email address entered here will be the one the intended user will use to activate their pending account and log into the system. Once they have established their account, they will have the option to change their email address by [editing their profile](../docs/using/your_account.md).
+Beneath the **User Details** category, you can enter the email address, first name, and last name of the person for whom you want to create the entitlement. The email address entered here will be the one the intended user will use to activate their pending account and log into the system. Once they have established their account, they will have the option to change their email address by [editing their profile]../using/your_account.md).
 
 The **Entitlement Details** section that follows is where you will specify which restricted-access project, journal, or journal issue you want to make available through the entitlement, using the three available dropdown menus.
 

docs/backend/features.md

@@ -3,10 +3,13 @@ id: features
 title: Features
 sidebar_label: Features
 ---
+
 import Tabs from '@theme/Tabs';
 import TabItem from '@theme/TabItem';
 import Spec from "@theme/Spec";
 
+# Features
+
 :::location
 The Features detail views discussed in this section are accessed by selecting Records from the main menu and then Features in the submenu while in the Manifold backend.
 

docs/backend/journals.md

@@ -7,7 +7,7 @@ sidebar_label: Journals
 import Tabs from '@theme/Tabs';
 import TabItem from '@theme/TabItem';
 import Spec from "@theme/Spec";
-const defaultImageFormats = "GIF, JPEG, JPG, PNG";
+export const defaultImageFormats = "GIF, JPEG, JPG, PNG";
 
 :::location
 The Journals detail views discussed in this section are accessed from the Manifold backend by selecting **Journals** from the main menu.