[skip ci] Merge origin/main

.eslintignore

@@ -13,7 +13,7 @@ products/jbrowse-web/scripts/**
 /products/jbrowse-web/config/
 products/jbrowse-desktop/public/electron.js
 products/jbrowse-desktop/public/generateFastaIndex.js
-/demos/
+/embedded_demos/
 webpack.config.js
 craco.config.js
 packages/core/util/QuickLRU.js

.eslintrc.json

@@ -25,10 +25,9 @@
     "@typescript-eslint/explicit-module-boundary-types": "off",
     "@typescript-eslint/no-empty-function": "off",
     "@typescript-eslint/no-unused-vars": ["warn"],
+    "@typescript-eslint/no-floating-promises": "error",
     "@typescript-eslint/no-unused-expressions": "off",
-    "@typescript-eslint/no-use-before-define": "off",
     "@typescript-eslint/no-var-requires": "off",
-    "@typescript-eslint/no-redeclare": "off",
 
     "no-use-before-define": "off",
     "curly": "error",

.github/workflows/desktop_build_linux.yml

@@ -18,7 +18,7 @@ jobs:
         uses: bahmutov/npm-install@v1
       - name: Install build deps
         run: |
-          sudo apt install -y python make gcc libcairo2-dev libpango1.0-dev libjpeg-dev libgif-dev librsvg2-dev
+          sudo apt install -y python3 make gcc libcairo2-dev libpango1.0-dev libjpeg-dev libgif-dev librsvg2-dev
       - name: Build app
         env:
           GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/desktop_build_win.yml

@@ -22,7 +22,7 @@ jobs:
           apt install --yes wine wine32 wine64 libwine libwine:i386 fonts-wine
       - name: Install build deps
         run: |
-          apt install --yes python make gcc libcairo2-dev libpango1.0-dev libjpeg-dev libgif-dev librsvg2-dev
+          apt install --yes python3 make gcc libcairo2-dev libpango1.0-dev libjpeg-dev libgif-dev librsvg2-dev
       - name: Build app
         env:
           WIN_CSC_LINK: ${{ secrets.WIN_CSC_LINK }}

.github/workflows/pull_request.yml

@@ -30,3 +30,12 @@ jobs:
         uses: bahmutov/npm-install@v1
       - name: Check codebase format
         run: yarn prettier --check .
+
+  spellcheck:
+    name: Spell check
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v2
+      - name: Check spelling
+        uses: crate-ci/typos@master

.github/workflows/push.yml

@@ -91,8 +91,8 @@ jobs:
           aws-region: us-east-1
       - name: Copy branch build to S3
         run: |
-          cp products/jbrowse-web/build/test_data/config.json products/jbrowse-web/build/config.json
           cd products/jbrowse-web/build && zip -r "jbrowse-web-$(echo ${{github.ref}} | cut -d '/' -f3-).zip" . && cd -
+          cp products/jbrowse-web/build/test_data/config.json products/jbrowse-web/build/config.json
           aws s3 sync --delete products/jbrowse-web/build s3://jbrowse.org/code/jb2/$(echo ${{github.ref}} | cut -d "/" -f3-)
   storybook_lgv:
     name: Build and deploy static linear genome view Storybook site to AWS S3

.ignore

@@ -0,0 +1,21 @@
+*.ix
+test_data/large.chrom.sizes
+packages/core/ui/react-colorful.js
+plugins/legacy-jbrowse/test_data
+plugins/data-management/src/ucsc-trackhub/ucscAssemblies.ts
+plugins/circular-view/test_data/circos_example_content.txt
+plugins/circular-view/test_data/circos_example.svg
+products/jbrowse-web/src/tests/Loader.test.tsx
+test_data/yeast_synteny/
+test_data/hg38_aliases.txt
+test_data/config_honeybee.json
+test_data/amel_hav3.1.chrom.sizes
+plugins/wiggle/src/util.ts
+plugins/protein/src/ProteinReferenceSequenceRenderer/aminoAcids.js
+plugins/spreadsheet-view/src/SpreadsheetView/test_data/starfusion_example.fusion_predictions.tsv
+products/jbrowse-aws-lambda-functions/
+products/jbrowse-desktop/src/JBrowse.test.tsx
+test_data/volvox/names/
+products/jbrowse-web/src/sessionSharing.ts
+website/docs/models/
+*.snap

.prettierignore

@@ -15,3 +15,4 @@
 # JSON files we don't want to format
 **/*nclist*/**/*.json
 **/ensembl_genes/**/*.json
+**/storybook-static/*

.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 [email protected]. 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 [email protected].
+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
 
@@ -55,8 +55,8 @@ 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
 
@@ -78,21 +78,19 @@ 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.
 
 Run the script like this:
 
-```
-scripts/release.sh myGitHubAuthToken versionIncreaseLevel
-```
+`scripts/release.sh myGitHubAuthToken versionIncreaseLevel`
 
 If you don't provide `versionIncreaseLevel`, it will default to "patch".
 
@@ -104,9 +102,9 @@ 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
@@ -126,8 +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
@@ -179,10 +177,8 @@ This package provides the "alignments" related features including
 
 - BamAdapter - our BAM parser that wraps @gmod/bam NPM module
 - CramAdapter - our CRAM parser that wraps the @gmod/cram NPM module
-- PileupTrack type - draws alignments as boxes in a "pileup" style view
-- SNPCoverageTrack - draws calculated coverage with mismatches drawn over the coverage
-- AlignmentsTrack - a "supertrack" which contains a PileupTrack and
-  SNPCoverageTrack "subtracks"
+- AlignmentsTrack - a "supertrack" which contains a PileupDisplay and
+  SNPCoverageDisplay "subtracks"
 - AlignmentsFeatureWidget for alignments features
 
 #### plugins/variants/
@@ -192,8 +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
 
@@ -231,8 +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
 
@@ -278,8 +274,22 @@ jbrowse text-index -a hg19 --tracks ncbi_gff_hg19 --out config_demo.json --force
 
 ## Notes about monorepo setup
 
-Our setup for the monorepo takes notes from the material-ui repository. Some particular notes include
+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
+
+## Notes about yarn
+
+Using `yarn upgrade` or `yarn upgrade-interactive --latest` can produce errors
+with the latest version of yarn. This is commonly cited around the web, but
+using npx to one-off run an older version of yarn can fix this issues
+
+Example:
+
+```
+npx [email protected] upgrade-interactive --latest
+```

README.md

@@ -1,4 +1,4 @@
-[![Build Status](https://img.shields.io/github/workflow/status/GMOD/jbrowse-components/Push/main?logo=github&style=for-the-badge)](https://github.com/GMOD/jbrowse-components/actions?query=branch%3Amain+workflow%3APush+)
+[![Build Status](https://img.shields.io/github/actions/workflow/status/GMOD/jbrowse-components/push.yml?branch=main&logo=github&style=for-the-badge)](https://github.com/GMOD/jbrowse-components/actions)
 [![Coverage Status](https://img.shields.io/codecov/c/github/GMOD/jbrowse-components/main.svg?logo=codecov&style=for-the-badge)](https://codecov.io/gh/GMOD/jbrowse-components/branch/main)
 [![Contributor Covenant](https://img.shields.io/badge/Contributor%20Covenant-v1.4%20adopted-ff69b4.svg?style=for-the-badge&logo=data:image/svg+xml;base64,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)](CODE_OF_CONDUCT.md)
 
@@ -61,15 +61,19 @@ cd products/jbrowse-web
 yarn start
 ```
 
-For jbrowse-desktop
+For jbrowse-desktop, launch two tabs
 
 ```sh
+# starts webpack dev server
 cd products/jbrowse-desktop
 yarn start
+
+# starts electron window
+cd products/jbrowse-desktop
+yarn electron
 ```
 
-For running like jbrowse-react-linear-genome-view you can use
-storybook
+For running e.g. jbrowse-react-linear-genome-view you can use storybook
 
 ```sh
 cd products/jbrowse-react-linear-genome-view

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/cgv/package.json

@@ -1,5 +1,5 @@
 {
-  "name": "jbrowse-react-circular-genome-view-demo",
+  "name": "jbrowse-react-circular-genome-view-demo-integration",
   "version": "0.1.0",
   "private": true,
   "dependencies": {
@@ -27,10 +27,12 @@
   "resolutions": {
     "@jbrowse/core": "file:./packed/jbrowse-core.tgz",
     "@jbrowse/plugin-alignments": "file:./packed/jbrowse-plugin-alignments.tgz",
+    "@jbrowse/plugin-authentication": "file:./packed/jbrowse-plugin-authentication.tgz",
     "@jbrowse/plugin-bed": "file:./packed/jbrowse-plugin-bed.tgz",
     "@jbrowse/plugin-circular-view": "file:./packed/jbrowse-plugin-circular-view.tgz",
     "@jbrowse/plugin-config": "file:./packed/jbrowse-plugin-config.tgz",
     "@jbrowse/plugin-data-management": "file:./packed/jbrowse-plugin-data-management.tgz",
+    "@jbrowse/plugin-gccontent": "file:./packed/jbrowse-plugin-gccontent.tgz",
     "@jbrowse/plugin-gff3": "file:./packed/jbrowse-plugin-gff3.tgz",
     "@jbrowse/plugin-linear-genome-view": "file:./packed/jbrowse-plugin-linear-genome-view.tgz",
     "@jbrowse/plugin-sequence": "file:./packed/jbrowse-plugin-sequence.tgz",

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

component_tests/lgv/cypress/integration/basic.spec.ts

@@ -1,5 +1,11 @@
 describe('JBrowse embedded view', () => {
   it('page loads', () => {
+    Cypress.on(
+      // from https://github.com/cypress-io/cypress/issues/8418
+      'uncaught:exception',
+      // @ts-ignore thinks we are es5 and don't have includes, may be able to update
+      err => !err.message.includes('ResizeObserver loop limit exceeded'),
+    )
     cy.visit('/')
     cy.contains('JBrowse 2 React Linear Genome View Demo')
   })
@@ -8,7 +14,7 @@ describe('JBrowse embedded view', () => {
 
     // eslint-disable-next-line testing-library/await-async-query,testing-library/prefer-screen-queries
     cy.findByTestId('Blockset-pileup', { timeout: 30000 }).findByTestId(
-      'prerendered_canvas_{GRCh38}10:29,838,637..29,838,705-0_done',
+      'prerendered_canvas_{GRCh38}10:29838637..29838705-0_done',
       { timeout: 30000 },
     )
   })