Use prettier to word wrap markdown prose (#3396)

* Update docs with word wrapping using prettier

* Format rest of codebase

.prettierrc.json

@@ -2,5 +2,6 @@
   "semi": false,
   "singleQuote": true,
   "trailingComma": "all",
-  "arrowParens": "avoid"
+  "arrowParens": "avoid",
+  "proseWrap": "always"
 }

CODE_OF_CONDUCT.md

@@ -5,9 +5,9 @@
 In the interest of fostering an open and welcoming environment, we as
 contributors and maintainers pledge to making participation in our project and
 our community a harassment-free experience for everyone, regardless of age, body
-size, disability, ethnicity, sex characteristics, gender identity and expression,
-level of experience, education, socio-economic status, nationality, personal
-appearance, race, religion, or sexual identity and orientation.
+size, disability, ethnicity, sex characteristics, gender identity and
+expression, level of experience, education, socio-economic status, nationality,
+personal appearance, race, religion, or sexual identity and orientation.
 
 ## Our Standards
 
@@ -37,11 +37,11 @@ Project maintainers are responsible for clarifying the standards of acceptable
 behavior and are expected to take appropriate and fair corrective action in
 response to any instances of unacceptable behavior.
 
-Project maintainers have the right and responsibility to remove, edit, or
-reject comments, commits, code, wiki edits, issues, and other contributions
-that are not aligned to this Code of Conduct, or to ban temporarily or
-permanently any contributor for other behaviors that they deem inappropriate,
-threatening, offensive, or harmful.
+Project maintainers have the right and responsibility to remove, edit, or reject
+comments, commits, code, wiki edits, issues, and other contributions that are
+not aligned to this Code of Conduct, or to ban temporarily or permanently any
+contributor for other behaviors that they deem inappropriate, threatening,
+offensive, or harmful.
 
 ## Scope
 
@@ -55,20 +55,22 @@ a project may be further defined and clarified by project maintainers.
 ## Enforcement
 
 Instances of abusive, harassing, or otherwise unacceptable behavior may be
-reported by contacting the project team at jbrowse-conduct@lists.berkeley.edu. All
-complaints will be reviewed and investigated and will result in a response that
-is deemed necessary and appropriate to the circumstances. The project team is
-obligated to maintain confidentiality with regard to the reporter of an incident.
-Further details of specific enforcement policies may be posted separately.
+reported by contacting the project team at jbrowse-conduct@lists.berkeley.edu.
+All complaints will be reviewed and investigated and will result in a response
+that is deemed necessary and appropriate to the circumstances. The project team
+is obligated to maintain confidentiality with regard to the reporter of an
+incident. Further details of specific enforcement policies may be posted
+separately.
 
 Project maintainers who do not follow or enforce the Code of Conduct in good
 faith may face temporary or permanent repercussions as determined by other
 members of the project's leadership.
 
 ## Attribution
 
-This Code of Conduct is adapted from the [Contributor Covenant][homepage], version 1.4,
-available at https://www.contributor-covenant.org/version/1/4/code-of-conduct.html
+This Code of Conduct is adapted from the [Contributor Covenant][homepage],
+version 1.4, available at
+https://www.contributor-covenant.org/version/1/4/code-of-conduct.html
 
 [homepage]: https://www.contributor-covenant.org
 

CONTRIBUTING.md

@@ -41,8 +41,8 @@ yarn
 yarn start
 ```
 
-You can edit the markdown by hand. The documentation is built into a website
-and a PDF using latex here http://jbrowse.org/jb2/jbrowse2.pdf
+You can edit the markdown by hand. The documentation is built into a website and
+a PDF using latex here http://jbrowse.org/jb2/jbrowse2.pdf
 
 ### Adding images to the docs
 
@@ -55,16 +55,16 @@ line in the markdown
 Your caption of the image here
 ```
 
-This creates a caption of the image properly in the PDF, and just shows the
-text below the image on the website
+This creates a caption of the image properly in the PDF, and just shows the text
+below the image on the website
 
 ## Developers
 
 ### Releasing/publishing
 
 There is a script `scripts/release.sh` that will publish the public packages in
-the monorepo to NPM and trigger the creation of a release on GitHub. To run
-this script:
+the monorepo to NPM and trigger the creation of a release on GitHub. To run this
+script:
 
 - Ensure that there is an announcement file for this release in
   `website/release_announcement_drafts/<tag>.md` containing an overview of the
@@ -78,12 +78,12 @@ this script:
   need to generate an access token.
 
 - Make sure you have a GitHub access token with public_repo scope. To generate
-  one, go to https://github.com/settings/tokens, click "Generate new token,"
-  add a note describing what you want the token to be for, select the
-  "public_repo" checkbox (under "repo"), and then click "Generate token." Make
-  sure to save this token in a safe place to use for future releases as you
-  won't be able to see it again. If you do lose your token, delete/revoke the
-  token you lost and generate a new one.
+  one, go to https://github.com/settings/tokens, click "Generate new token," add
+  a note describing what you want the token to be for, select the "public_repo"
+  checkbox (under "repo"), and then click "Generate token." Make sure to save
+  this token in a safe place to use for future releases as you won't be able to
+  see it again. If you do lose your token, delete/revoke the token you lost and
+  generate a new one.
 
 - Decide if the release should have a major, minor, or patch level version
   increase. All packages that are published will get the same version number.
@@ -96,15 +96,15 @@ If you don't provide `versionIncreaseLevel`, it will default to "patch".
 
 This will trigger a GitHub workflow that will create a draft release on GitHub,
 build JBrowse Web, and upload the build to that release. It will also trigger
-workflows that will build JBrowse Desktop for Windows, Mac, and Linux and
-upload those to the release as well.
+workflows that will build JBrowse Desktop for Windows, Mac, and Linux and upload
+those to the release as well.
 
 Once the draft release has been created (you can look for it
 [here](https://github.com/GMOD/jbrowse-components/releases)), go to the release
 and click "Edit," then add a description to the release. Usually you can copy
-the content of the blog post that was generated (it will be named something
-like `website/blog/${DATE}-${RELEASE_TAG}-release.md`), removing the
-"Downloads" section.
+the content of the blog post that was generated (it will be named something like
+`website/blog/${DATE}-${RELEASE_TAG}-release.md`), removing the "Downloads"
+section.
 
 Note that it is very helpful to run the release from a computer with a stable
 and fast internet connection. One option for this is to run it from a AWS
@@ -124,8 +124,8 @@ uploaded, the workflows will refuse to add them to the published release since
 it looks for draft releases)
 
 Finally, run the update_demos.sh script from within the demos folder of the
-monorepo after the packages have been published. This will update the `demos`
-to use the latest version, and then publish them to our S3 bucket e.g. at
+monorepo after the packages have been published. This will update the `demos` to
+use the latest version, and then publish them to our S3 bucket e.g. at
 https://jbrowse.org/demos/lgv
 
 ## Monorepo code organization
@@ -188,8 +188,8 @@ Provides variant features including
 - VCF tabix parser
 - VCF non-tabix parser
 - VariantFeatureWidget
-- VariantTrack that is basically just a normal track, but has logic to popup
-  the VariantFeatureWidget on feature click
+- VariantTrack that is basically just a normal track, but has logic to popup the
+  VariantFeatureWidget on feature click
 
 #### plugins/hic
 
@@ -227,8 +227,8 @@ General usage of this involves referencing the SvgFeatureRenderer
 
 #### plugins/spreadsheet-view
 
-This provides a spreadsheet-in-the-browser that can be used as a data backend
-to power other views
+This provides a spreadsheet-in-the-browser that can be used as a data backend to
+power other views
 
 #### plugins/circular-view
 
@@ -246,14 +246,14 @@ Plugins may be built as separate packages that can be distributed on NPM. In
 order to streamline development and avoid having to build every plugin before
 developing on e.g. JBrowse Web, however, the `package.json`'s "main" entry for
 plugins in this monorepo by default points to the un-built code (e.g.
-`src/index.ts`). JBrowse Web then takes care of building the plugins itself
-(see `products/jbrowse-web/rescripts/yarnWorkspacesRescript.js`).
+`src/index.ts`). JBrowse Web then takes care of building the plugins itself (see
+`products/jbrowse-web/rescripts/yarnWorkspacesRescript.js`).
 
 When you want to use a built plugin, you can run `yarn useDist` in the plugin's
-`package.json`, and then run `yarn useSrc` to restore it when you're done. As
-an example, the root-level `yarn build` that builds all the packages does this
-to build all the plugins and then build JBrowse Web and JBrowse Desktop using
-the built plugins.
+`package.json`, and then run `yarn useSrc` to restore it when you're done. As an
+example, the root-level `yarn build` that builds all the packages does this to
+build all the plugins and then build JBrowse Web and JBrowse Desktop using the
+built plugins.
 
 ## Preparing sample data sets
 
@@ -277,8 +277,8 @@ jbrowse text-index -a hg19 --tracks ncbi_gff_hg19 --out config_demo.json --force
 Our setup for the monorepo takes notes from the material-ui repository. Some
 particular notes include
 
-1. The use of the "flat" packages/core package, where you can import from
-   nested subpaths like '@jbrowse/core/util'
+1. The use of the "flat" packages/core package, where you can import from nested
+   subpaths like '@jbrowse/core/util'
 2. The use of tsconfig.build.json to generate types in the final release
 3. The use of referring to the src directory at development time
 

component_tests/cgv/README.md

@@ -1,6 +1,7 @@
 # Demo of `@jbrowse/react-linear-genome-view`
 
-This module uses "packed" builds of the repo, and runs an e2e test using cypress.
+This module uses "packed" builds of the repo, and runs an e2e test using
+cypress.
 
 It is most similar to a test that a user would get from installing the module
 from NPM. Note that these `packed` builds can be heavily cached by the yarn

component_tests/lgv/README.md

@@ -1,6 +1,7 @@
 # Demo of `@jbrowse/react-linear-genome-view`
 
-This module uses "packed" builds of the repo, and runs an e2e test using cypress.
+This module uses "packed" builds of the repo, and runs an e2e test using
+cypress.
 
 It is most similar to a test that a user would get from installing the module
 from NPM. Note that these `packed` builds can be heavily cached by the yarn

demos/jbrowse-react-circular-genome-view-cra5/README.md

@@ -1,14 +1,17 @@
 # jbrowse-react-circular-genome-view-cra5
 
-This is a demo of using the circular genome view with create-react-app v5 (which uses webpack 5)
+This is a demo of using the circular genome view with create-react-app v5 (which
+uses webpack 5)
 
-It uses craco to add the webpack NodePolyfillPlugin (used for Buffer polyfill, etc)
+It uses craco to add the webpack NodePolyfillPlugin (used for Buffer polyfill,
+etc)
 
 # Demo of `@jbrowse/react-circular-genome-view` with CRA 5
 
 See this app running at https://jbrowse.org/demos/cgv-cra5/.
 
-Download this directory from the monorepo using https://download-directory.github.io/?url=https%3A%2F%2Fgithub.com%2FGMOD%2Fjbrowse-components%2Ftree%2Fmain%2Fdemos%2Fjbrowse-react-circular-genome-view-cra5
+Download this directory from the monorepo using
+https://download-directory.github.io/?url=https%3A%2F%2Fgithub.com%2FGMOD%2Fjbrowse-components%2Ftree%2Fmain%2Fdemos%2Fjbrowse-react-circular-genome-view-cra5
 
 ## Usage
 

demos/jbrowse-react-circular-genome-view-vanillajs/README.md

@@ -2,7 +2,8 @@
 
 See this app running at https://jbrowse.org/demos/cgv-vanillajs/.
 
-Download this directory from the monorepo using https://download-directory.github.io/?url=https%3A%2F%2Fgithub.com%2FGMOD%2Fjbrowse-components%2Ftree%2Fmain%2Fdemos%2Fjbrowse-react-circular-genome-view-vanillajs
+Download this directory from the monorepo using
+https://download-directory.github.io/?url=https%3A%2F%2Fgithub.com%2FGMOD%2Fjbrowse-components%2Ftree%2Fmain%2Fdemos%2Fjbrowse-react-circular-genome-view-vanillajs
 
 ## Usage
 

demos/jbrowse-react-linear-genome-view-cra5/README.md

@@ -1,14 +1,17 @@
 # jbrowse-react-linear-genome-view-cra5
 
-This is a demo of using the linear genome view with create-react-app v5 (which uses webpack 5)
+This is a demo of using the linear genome view with create-react-app v5 (which
+uses webpack 5)
 
-It uses craco to add the webpack NodePolyfillPlugin (used for Buffer polyfill, etc)
+It uses craco to add the webpack NodePolyfillPlugin (used for Buffer polyfill,
+etc)
 
 # Demo of `@jbrowse/react-linear-genome-view` with CRA 5
 
 See this app running at https://jbrowse.org/demos/lgv-cra5/.
 
-Download this directory from the monorepo using https://download-directory.github.io/?url=https%3A%2F%2Fgithub.com%2FGMOD%2Fjbrowse-components%2Ftree%2Fmain%2Fdemos%2Fjbrowse-react-linear-genome-view-cra5
+Download this directory from the monorepo using
+https://download-directory.github.io/?url=https%3A%2F%2Fgithub.com%2FGMOD%2Fjbrowse-components%2Ftree%2Fmain%2Fdemos%2Fjbrowse-react-linear-genome-view-cra5
 
 ## Usage
 

demos/jbrowse-react-linear-genome-view-nextjs/README.md

@@ -1,12 +1,14 @@
 # jbrowse-react-linear-genome-view-nextjs
 
-This is a demo of using the linear genome view with next.js 11 (which uses webpack 5)
+This is a demo of using the linear genome view with next.js 11 (which uses
+webpack 5)
 
 # Demo of `@jbrowse/react-linear-genome-view` with next.js
 
 See this app running at https://jbrowse.org/demos/lgv-nextjs/.
 
-Download this directory from the monorepo using https://download-directory.github.io/?url=https%3A%2F%2Fgithub.com%2FGMOD%2Fjbrowse-components%2Ftree%2Fmain%2Fdemos%2Fjbrowse-react-linear-genome-view-nextjs
+Download this directory from the monorepo using
+https://download-directory.github.io/?url=https%3A%2F%2Fgithub.com%2FGMOD%2Fjbrowse-components%2Ftree%2Fmain%2Fdemos%2Fjbrowse-react-linear-genome-view-nextjs
 
 ## Getting Started
 
@@ -20,4 +22,5 @@ yarn dev
 
 ## Deploy
 
-This page is deployed to https://jbrowse.org/demos/lgv-nextjs (uses `yarn build && yarn export` to create static build with no server side)
+This page is deployed to https://jbrowse.org/demos/lgv-nextjs (uses
+`yarn build && yarn export` to create static build with no server side)

demos/jbrowse-react-linear-genome-view-vanillajs/README.md

@@ -2,7 +2,8 @@
 
 See this app running at https://jbrowse.org/demos/lgv-vanillajs/.
 
-Download this directory from the monorepo using https://download-directory.github.io/?url=https%3A%2F%2Fgithub.com%2FGMOD%2Fjbrowse-components%2Ftree%2Fmain%2Fdemos%2Fjbrowse-react-linear-genome-view-vanillajs
+Download this directory from the monorepo using
+https://download-directory.github.io/?url=https%3A%2F%2Fgithub.com%2FGMOD%2Fjbrowse-components%2Ftree%2Fmain%2Fdemos%2Fjbrowse-react-linear-genome-view-vanillajs
 
 ## Usage
 

demos/jbrowse-react-linear-genome-view-vite/README.md

@@ -1,18 +1,23 @@
 # vite with @jbrowse/react-linear-genome-view
 
-Based on https://codesandbox.io/s/ylt4t?file=/vite.config.ts:478-540 by @garrettjstevens
+Based on https://codesandbox.io/s/ylt4t?file=/vite.config.ts:478-540 by
+@garrettjstevens
 
-This is a demo of using the linear genome view with vite (see https://vitejs.dev/)
+This is a demo of using the linear genome view with vite (see
+https://vitejs.dev/)
 
-Vite is a build system that is very fast and becoming more popular, using esbuild and rollup instead of webpack
+Vite is a build system that is very fast and becoming more popular, using
+esbuild and rollup instead of webpack
 
-This particular demo includes several polyfills that are needed for JBrowse including the Buffer polyfill
+This particular demo includes several polyfills that are needed for JBrowse
+including the Buffer polyfill
 
 # Demo of `@jbrowse/react-linear-genome-view` with vite
 
 See this app running at https://jbrowse.org/demos/lgv-vite/.
 
-Download this directory from the monorepo using https://download-directory.github.io/?url=https%3A%2F%2Fgithub.com%2FGMOD%2Fjbrowse-components%2Ftree%2Fmain%2Fdemos%2Fjbrowse-react-linear-genome-view-vite
+Download this directory from the monorepo using
+https://download-directory.github.io/?url=https%3A%2F%2Fgithub.com%2FGMOD%2Fjbrowse-components%2Ftree%2Fmain%2Fdemos%2Fjbrowse-react-linear-genome-view-vite
 
 ## Usage
 

docs/README.md

@@ -34,7 +34,8 @@ and
  */
 ```
 
-it is not able to document a single variable, so in some places, a dummy function is put below the `#config/#stateModel` comments
+it is not able to document a single variable, so in some places, a dummy
+function is put below the `#config/#stateModel` comments
 
 ```
 function x(){}

packages/core/README.md

@@ -1,7 +1,8 @@
 # jbrowse-core
 
 [![NPM version](https://img.shields.io/npm/v/@jbrowse/core.svg?style=flat-square)](https://npmjs.org/package/@jbrowse/core)
-[![Build Status](https://img.shields.io/travis/GMOD/jbrowse-components/main.svg?style=flat-square)](https://travis-ci.org/GMOD/jbrowse-components) [![Coverage Status](https://img.shields.io/codecov/c/github/GMOD/jbrowse-components/main.svg?style=flat-square)](https://codecov.io/gh/GMOD/jbrowse-components/branch/main)
+[![Build Status](https://img.shields.io/travis/GMOD/jbrowse-components/main.svg?style=flat-square)](https://travis-ci.org/GMOD/jbrowse-components)
+[![Coverage Status](https://img.shields.io/codecov/c/github/GMOD/jbrowse-components/main.svg?style=flat-square)](https://codecov.io/gh/GMOD/jbrowse-components/branch/main)
 
 Core JBrowse libraries used by most JBrowse plugins.
 
@@ -11,7 +12,10 @@ See [docs](docs/README.md)
 
 ## Academic Use
 
-This package was written with funding from the [NHGRI](http://genome.gov) as part of the [JBrowse](http://jbrowse.org) project. If you use it in an academic project that you publish, please cite the most recent JBrowse paper, which will be linked from [jbrowse.org](http://jbrowse.org).
+This package was written with funding from the [NHGRI](http://genome.gov) as
+part of the [JBrowse](http://jbrowse.org) project. If you use it in an academic
+project that you publish, please cite the most recent JBrowse paper, which will
+be linked from [jbrowse.org](http://jbrowse.org).
 
 ## License