sweep: add a panel to toggle individual annotations #35

theosanderson · 2023-11-24T13:12:24Z

Checklist

Create src/components/AnnotationTogglePanel.js ✓ 5aeb01b
Ran sandbox for src/components/AnnotationTogglePanel.js. ✓ 9b0a7c8
Modify src/App.js ✓ f876222
Ran sandbox for src/App.js. ✗
Modify src/App.js ✓ ec1ce71
Ran sandbox for src/App.js. ✓ 44ecd3f
Ran sandbox for src/App.js. ✓
Create src/components/GenomeDisplay.js ✓ f79b976
Ran sandbox for src/components/GenomeDisplay.js. ✓ 60e8d7a

The text was updated successfully, but these errors were encountered:

sweep-ai · 2023-11-24T13:12:34Z

Here's the PR! #36.

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Sandbox Execution ✓

Here are the sandbox execution logs prior to making any changes:

Sandbox logs for 12a9ff3

pre-commit install 1/6 ✓

pre-commit installed at .git/hooks/pre-commit

yarn install 2/6 ✓

yarn install v1.22.19
warning package-lock.json found. Your project contains lock files generated by tools other than Yarn. It is advised not to mix package managers in order to avoid resolution inconsistencies caused by unsynchronized lock files. To clear this warning, remove package-lock.json.
[1/4] Resolving packages...
[2/4] Fetching packages...
[3/4] Linking dependencies...
warning " > @testing-library/[email protected]" has unmet peer dependency "@testing-library/dom@>=7.21.4".
warning "react-scripts > eslint-config-react-app > [email protected]" has unmet peer dependency "@babel/plugin-syntax-flow@^7.14.5".
warning "react-scripts > eslint-config-react-app > [email protected]" has unmet peer dependency "@babel/plugin-transform-react-jsx@^7.14.9".
warning "react-scripts > react-dev-utils > [email protected]" has unmet peer dependency "typescript@>= 2.7".
warning "react-scripts > eslint-config-react-app > @typescript-eslint/eslint-plugin > [email protected]" has unmet peer dependency "typescript@>=2.8.0 || >= 3.2.0-dev || >= 3.3.0-dev || >= 3.4.0-dev || >= 3.5.0-dev || >= 3.6.0-dev || >= 3.6.0-beta || >= 3.7.0-dev || >= 3.7.0-beta".
[4/4] Building fresh packages...
Done in 37.67s.

npm i 3/6 ✓

added 300 packages, removed 82 packages, changed 56 packages, and audited 1548 packages in 19s
238 packages are looking for funding
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14 vulnerabilities (6 moderate, 6 high, 2 critical)
To address issues that do not require attention, run:
  npm audit fix
To address all issues (including breaking changes), run:
  npm audit fix --force
Run `npm audit` for details.
npm notice 
npm notice New major version of npm available! 9.6.7 -> 10.2.4
npm notice Changelog: 
npm notice Run `npm install -g [email protected]` to update!
npm notice

trunk init 4/6 ✓

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✔ 10 linters were enabled (.trunk/trunk.yaml)
  checkov 3.1.9 (3 json, 2 yaml files)
  git-diff-check (29 files)
  markdownlint 0.37.0 (1 markdown file) (created .markdownlint.yaml)
  osv-scanner 1.4.3 (2 lockfile files)
  oxipng 9.0.0 (1 png file)
  prettier 3.1.0 (2 css, 1 html, 14 javascript, 2 json, 1 markdown, 2 yaml files)
  svgo 3.0.4 (1 svg file) (created svgo.config.js)
  trivy 0.47.0 (2 yaml files)
  trufflehog 3.63.2-rc0 (31 files)
  yamllint 1.33.0 (2 yaml files) (created .yamllint.yaml)
Next Steps
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    Join the Trunk community at https://slack.trunk.io

trunk fmt src/App.js || exit 0 5/6 ✓

Checked 1 file
✔ No issues

trunk check --fix --print-failures src/App.js 6/6 ✓

Checked 1 file
✔ No issues

Sandbox passed on the latest main, so sandbox checks will be enabled for this issue.

Install Sweep Configs: Pull Request

Step 1: 🔎 Searching

I found the following snippets in your repository. I will now analyze these snippets and come up with a plan.

Some code snippets I looked at (click to expand). If some file is missing from here, you can mention the path in the ticket description.

gensplore/README.md

Lines 1 to 10 in 12a9ff3

    
           # Gensplore 
        
           A simple genome browser for smallish genomes (e.g. viruses and bacteria) 
        
           ![image](https://user-images.githubusercontent.com/19732295/219011538-43b9b66b-0227-4171-87c6-08b496a7bf2e.png) 
        
           ## https://gensplore.theo.io/ 
        
           ### Adding custom genomes

gensplore/package.json

Lines 1 to 55 in 12a9ff3

    
           { 
        
             "name": "genbank_view", 
        
             "version": "0.1.0", 
        
             "private": true, 
        
             "dependencies": { 
        
               "@headlessui/react": "^1.7.16", 
        
               "@tanstack/react-virtual": "^3.0.0-beta.48", 
        
               "@testing-library/jest-dom": "^5.16.5", 
        
               "@testing-library/react": "^13.4.0", 
        
               "@testing-library/user-event": "^13.5.0", 
        
               "autoprefixer": "^10.4.13", 
        
               "bio-parsers": "^9.3.0", 
        
               "color-hash": "^2.0.2", 
        
               "postcss": "^8.4.21", 
        
               "qs": "^6.11.0", 
        
               "rc-slider": "^10.1.1", 
        
               "react": "^18.2.0", 
        
               "react-debounce-input": "^3.3.0", 
        
               "react-dom": "^18.2.0", 
        
               "react-icons": "^4.7.1", 
        
               "react-router-dom": "^6.8.1", 
        
               "react-scripts": "5.0.1", 
        
               "react-spinners": "^0.13.8", 
        
               "react-toastify": "^9.1.1", 
        
               "react-tooltip": "^5.7.5", 
        
               "react-use": "^17.4.0", 
        
               "tailwindcss": "^3.2.6", 
        
               "ve-range-utils": "^2.6.6", 
        
               "ve-sequence-utils": "^5.2.9", 
        
               "web-vitals": "^2.1.4" 
        
             }, 
        
             "scripts": { 
        
               "start": "react-scripts start", 
        
               "build": "react-scripts build", 
        
               "test": "react-scripts test", 
        
               "eject": "react-scripts eject" 
        
             }, 
        
             "eslintConfig": { 
        
               "extends": [ 
        
                 "react-app", 
        
                 "react-app/jest" 
        
               ] 
        
             }, 
        
             "browserslist": { 
        
               "production": [ 
        
                 ">0.2%", 
        
                 "not dead", 
        
                 "not op_mini all" 
        
               ], 
        
               "development": [ 
        
                 "last 1 chrome version", 
        
                 "last 1 firefox version", 
        
                 "last 1 safari version" 
        
               ] 
        
             }

gensplore/postcss.config.js

Lines 1 to 5 in 12a9ff3

    
           module.exports = { 
        
             plugins: { 
        
               tailwindcss: {}, 
        
               autoprefixer: {}, 
        
             },

gensplore/tailwind.config.js

Lines 1 to 7 in 12a9ff3

    
           /** @type {import('tailwindcss').Config} */ 
        
           module.exports = { 
        
             content: ["./src/**/*.{html,js}"], 
        
             theme: { 
        
               extend: {}, 
        
             }, 
        
             plugins: [],

Step 2: ⌨️ Coding

Create src/components/AnnotationTogglePanel.js ✓ 5aeb01b

Create src/components/AnnotationTogglePanel.js with contents:
• Create a new file `src/components/AnnotationTogglePanel.js`.
• In this file, define a new React component `AnnotationTogglePanel`. This component should maintain a state object that tracks the toggle state for each annotation.
• The render method of this component should iterate over the available annotations and for each one, render a toggle switch. The state of this switch should be bound to the corresponding entry in the state object.
• Export this component as the default export of the file.

Ran sandbox for src/components/AnnotationTogglePanel.js. ✓ 9b0a7c8

Sandbox logs for https://github.com/theosanderson/gensplore/commit/9b0a7c89ed58c9211e460184de093f820b095536
trunk fmt src/components/AnnotationTogglePanel.js || exit 0 1/2 ✓
 ✔ Formatted src/components/AnnotationTogglePanel.js
Re-checking autofixed files...


Checked 1 file
✔ No issues
trunk check --fix --print-failures src/components/AnnotationTogglePanel.js 2/2 ✓
Checked 1 file
✔ No issues

Modify src/App.js ✓ f876222

Modify src/App.js with contents:
• In `src/App.js`, import the `AnnotationTogglePanel` component from `src/components/AnnotationTogglePanel.js`.
• Modify the render method of the `App` component to include the `AnnotationTogglePanel`. This should be placed in a suitable location in the layout, such as in a sidebar or a modal dialog.
• Pass a callback to the `AnnotationTogglePanel` that allows it to update the parent component's state with the current toggle states.

Ran sandbox for src/App.js. ✗

Sandbox logs for

trunk fmt src/App.js || exit 0 1/2 ✓

  FAILURES  
 prettier  src/App.js  .trunk/out/oJO6G.yaml
  NOTICES  
 A tool failed to run. You can open the details yaml file for more information.
Checked 0 files
✖ No issues, 1 failure

trunk check --fix --print-failures src/App.js 2/2 ❌ (`1`)

  FAILURES  
 prettier  src/App.js  .trunk/out/MlCBs.yaml
  NOTICES  
 A tool failed to run. You can open the details yaml file for more information.
Checked 1 file
✖ No issues, 1 failure
# .trunk/out/MlCBs.yaml
trunk_cli_version: 1.17.2
title: prettier exited with exit_code=2
report:
  - prettier exited with exit_code=2
  - linter:
      command: |
        /root/.cache/trunk/tools/prettier/3.1.0-a552fdee5ef3daae1274e7dca8183c14/node_modules/.bin/prettier -w src/App.js
      stdin_path: (none)
      run_from: /tmp/trunk-0/sFQXXY/SR2Ryp
      timeout: 10m
      rerun: (cd /tmp/trunk-0/sFQXXY/SR2Ryp; env -i PATH=/root/.cache/trunk/tools/prettier/3.1.0-a552fdee5ef3daae1274e7dca8183c14/node_modules/.bin:/root/.cache/trunk/tools/node/18.12.1-00ae74f39ac4de3ff3c7e3686016ebf3/bin:/root/.cache/trunk/tools/node/18.12.1-00ae74f39ac4de3ff3c7e3686016ebf3:/root/.nvm/versions/node/v18.17.0/bin/:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin NODE_PATH=/root/.cache/trunk/tools/prettier/3.1.0-a552fdee5ef3daae1274e7dca8183c14/node_modules HOME=/root /root/.cache/trunk/tools/prettier/3.1.0-a552fdee5ef3daae1274e7dca8183c14/node_modules/.bin/prettier -w src/App.js)
      affects_cache:
        - package.json
      direct_configs:
        []
      exit_status: exited
      exit_code: 2
      stdout: (none)
      stderr: |
        [error] src/App.js: SyntaxError: Unexpected token (472:11)
        [error]   470 |        472 |           
        [error]       |           ^
        [error]   473 |       >
        [error]   474 |         Customize appearance
        [error]   475 |       
    parser: |
      (none)

Modify src/App.js ✓ ec1ce71

Modify src/App.js with contents: Move the AnnotationTogglePanel component out of the Dialog.Description opening tag. Place it above the Dialog.Description tag, so it remains within the Dialog.Panel but is not a child of the Dialog.Description tag.

Ran sandbox for src/App.js. ✓ 44ecd3f

Sandbox logs for https://github.com/theosanderson/gensplore/commit/44ecd3f565d6d219efbf343f6f1dd76532886fc2
trunk fmt src/App.js || exit 0 1/2 ✓
 ✔ Formatted src/App.js
Re-checking autofixed files...


Checked 1 file
✔ No issues
trunk check --fix --print-failures src/App.js 2/2 ✓
Checked 1 file
✔ No issues

Ran sandbox for src/App.js. ✓

Sandbox logs for
trunk fmt src/App.js || exit 0 1/2 ✓
Checked 1 file
✔ No issues
trunk check --fix --print-failures src/App.js 2/2 ✓
Checked 1 file
✔ No issues

Create src/components/GenomeDisplay.js ✓ f79b976

Create src/components/GenomeDisplay.js with contents:
• In `src/components/GenomeDisplay.js`, modify the component to accept a new prop that contains the annotation toggle states.
• In the render method, filter the displayed annotations based on the toggle states.
• This will ensure that only the annotations with their corresponding toggle switched on in the `AnnotationTogglePanel` are displayed.

Ran sandbox for src/components/GenomeDisplay.js. ✓ 60e8d7a

Sandbox logs for https://github.com/theosanderson/gensplore/commit/60e8d7afa39791c2b0537b6b5b738adf4cff895d
trunk fmt src/components/GenomeDisplay.js || exit 0 1/2 ✓
 ✔ Formatted src/components/GenomeDisplay.js
Re-checking autofixed files...


Checked 1 file
✔ No issues
trunk check --fix --print-failures src/components/GenomeDisplay.js 2/2 ✓
Checked 1 file
✔ No issues

Step 3: 🔁 Code Review

I have finished reviewing the code for completeness. I did not find errors for sweep/annotation-toggle-panel.

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sweep-ai bot added the sweep Assigns Sweep to an issue or pull request. label Nov 24, 2023

sweep-ai bot linked a pull request Nov 24, 2023 that will close this issue

Add Annotation Toggle Panel #36

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sweep: add a panel to toggle individual annotations #35

sweep: add a panel to toggle individual annotations #35

theosanderson commented Nov 24, 2023 •

edited by sweep-ai bot

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sweep-ai bot commented Nov 24, 2023 •

edited

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sweep: add a panel to toggle individual annotations #35

sweep: add a panel to toggle individual annotations #35

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theosanderson commented Nov 24, 2023 • edited by sweep-ai bot Loading

sweep-ai bot commented Nov 24, 2023 • edited Loading

Here's the PR! #36.

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Sandbox Execution ✓

Step 1: 🔎 Searching

Step 2: ⌨️ Coding

Step 3: 🔁 Code Review

🎉 Latest improvements to Sweep:

theosanderson commented Nov 24, 2023 •

edited by sweep-ai bot

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sweep-ai bot commented Nov 24, 2023 •

edited

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