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Update dependencies (#269)
* Update dependencies * Update dev dependencies * Update `@lumino` packages * Switch to ESLint * Prettier * Fix ESLint errors * Lint staged * Fix geojson build * Fix mathjax3 * Fix vega3 * Fix fasta and vega2 * More updates * More updates * Add lint workflow on CI * Fix prettier check
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-2654
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‎.eslintignore‎

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node_modules
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dist
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coverage
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**/*.d.ts
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tests

‎.eslintrc.js‎

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module.exports = {
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extends: [
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'eslint:recommended',
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'plugin:@typescript-eslint/eslint-recommended',
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'plugin:@typescript-eslint/recommended',
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'plugin:prettier/recommended',
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],
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parser: '@typescript-eslint/parser',
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parserOptions: {
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project: 'tsconfig.eslint.json',
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sourceType: 'module',
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},
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plugins: ['@typescript-eslint'],
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rules: {
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'@typescript-eslint/naming-convention': [
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'error',
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{
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selector: 'interface',
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format: ['PascalCase'],
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custom: {
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regex: '^I[A-Z]',
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match: true,
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},
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},
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],
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'@typescript-eslint/no-unused-vars': ['warn', { args: 'none' }],
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'@typescript-eslint/no-explicit-any': 'off',
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'@typescript-eslint/no-namespace': 'off',
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'@typescript-eslint/no-use-before-define': 'off',
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'@typescript-eslint/quotes': [
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'error',
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'single',
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{ avoidEscape: true, allowTemplateLiterals: false },
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],
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curly: ['error', 'all'],
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eqeqeq: 'error',
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'prefer-arrow-callback': 'error',
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},
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};

‎.github/workflows/lint.yaml‎

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name: Lint
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on:
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push:
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branches:
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- '*'
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pull_request:
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branches:
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- '*'
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jobs:
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lint:
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runs-on: ubuntu-latest
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steps:
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- name: Checkout
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uses: actions/checkout@v2
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- name: Base Setup
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uses: jupyterlab/maintainer-tools/.github/actions/base-setup@v1
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- name: Install dependencies
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run: |
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python -m pip install -U jupyterlab~=3.2
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- name: Lint
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run: |
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jlpm
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jlpm run eslint:check
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jlpm run prettier:check

‎.gitignore‎

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.ipynb_checkpoints
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*.tsbuildinfo
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**/labextension
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_temp_extension
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**/_temp_extension/
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# Created by https://www.gitignore.io/api/python
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# Edit at https://www.gitignore.io/?templates=python

‎.prettierignore‎

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node_modules
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**/node_modules
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**/lib
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**/package.json
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**/static
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**/labextension
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build
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ipynb_checkpoints
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notebooks/

‎lint-staged.config.js‎

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const escape = require('shell-quote').quote;
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const fs = require('fs');
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const isWin = process.platform === 'win32';
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const escapeFileNames = (filenames) =>
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filenames
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.filter((filename) => fs.existsSync(filename))
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.map((filename) => `"${isWin ? filename : escape([filename])}"`)
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.join(' ');
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module.exports = {
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'**/*{.css,.json,.md}': (filenames) => {
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const escapedFileNames = escapeFileNames(filenames);
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return [
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`prettier --write ${escapedFileNames}`,
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`git add -f ${escapedFileNames}`,
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];
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},
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'**/*{.ts,.tsx}': (filenames) => {
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const escapedFileNames = escapeFileNames(filenames);
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return [
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`prettier --write ${escapedFileNames}`,
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`eslint --fix ${escapedFileNames}`,
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`git add -f ${escapedFileNames}`,
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];
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},
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};

‎package.json‎

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"build": "lerna run --parallel build",
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"build-py": "rimraf dist && mkdir -p dist && lerna run --parallel clean:all && lerna exec --concurrency 4 -- python setup.py sdist bdist_wheel && lerna exec --concurrency 4 -- mv dist/* ../../dist/",
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"build:prod": "lerna run --parallel build:prod",
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"install-py": "lerna exec --concurrency 4 -- python -m pip install -e .",
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"eslint": "eslint . --ext .ts,.tsx --fix",
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"eslint:check": "eslint . --ext .ts,.tsx",
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"install-ext": "lerna run install:extension",
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"install-py": "lerna exec --concurrency 4 -- python -m pip install -e .",
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"link": "lerna exec --parallel -- jupyter labextension link . --no-build",
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"precommit": "lint-staged",
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"prettier": "prettier --write '{!(package),packages/*/!(package),packages/*/!(lib)/**}{.js,.jsx,.ts,.tsx,.css,.json,.md}'",
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"prettier": "prettier --write \"**/*{.ts,.tsx,.js,.jsx,.css,.json,.md}\"",
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"prettier:check": "prettier --list-different \"**/*{.ts,.tsx,.js,.jsx,.css,.json,.md}\"",
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"update-dependency": "update-dependency --lerna",
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"watch": "lerna run --parallel watch"
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},
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"lint-staged": {
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"{!(package),packages/*/!(package),packages/*/!(lib)/**}{.js,.jsx,.ts,.tsx,.css,.json,.md}": [
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"prettier --write",
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"git add"
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]
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"husky": {
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"hooks": {
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"pre-commit": "lint-staged"
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}
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},
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"devDependencies": {
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"@jupyterlab/buildutils": "^3.0.0",
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"husky": "^0.14.3",
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"@jupyterlab/buildutils": "^3.2.8",
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"@typescript-eslint/eslint-plugin": "^5.9.1",
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"@typescript-eslint/parser": "^5.9.1",
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"eslint": "^8.7.0",
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"eslint-config-prettier": "^8.3.0",
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"eslint-plugin-prettier": "^4.0.0",
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"husky": "^7.0.4",
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"lerna": "^4.0.0",
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"lint-staged": "^7.1.0",
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"prettier": "^1.11.1",
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"rimraf": "^3.0.2",
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"tslint": "^5.9.1",
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"tslint-config-prettier": "^1.9.0",
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"tslint-plugin-prettier": "^1.3.0"
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"lint-staged": "^12.1.7",
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"prettier": "^2.5.1",
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"rimraf": "^3.0.2"
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}
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}

‎packages/fasta-extension/package.json‎

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"build:prod": "jlpm run build:lib && jlpm run build:labextension",
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"clean": "jlpm run clean:lib",
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"clean:all": "jlpm run clean:lib && jlpm run clean:labextension && jlpm run clean:dist",
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"clean:dist": "rimraf dist",
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"clean:labextension": "rimraf ./jupyterlab-fasta/labextension",
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"clean:lib": "rimraf lib tsconfig.tsbuildinfo",
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"clean:dist": "rimraf dist",
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"eslint": "eslint . --ext .ts,.tsx --fix",
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"eslint:check": "eslint . --ext .ts,.tsx",
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"install:extension": "jupyter labextension develop --overwrite .",
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"watch:src": "tsc -w"
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},
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"dependencies": {
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"@jupyterlab/rendermime-interfaces": "^3.0.5",
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"@lumino/messaging": "^1.4.3",
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"@lumino/widgets": "^1.16.1",
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"@jlab-contrib/msa": "^1.1.2"
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"@jlab-contrib/msa": "^1.1.2",
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"@jupyterlab/rendermime-interfaces": "^3.2.8",
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"@lumino/messaging": "^1.10.1",
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"@lumino/widgets": "^1.31.1"
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},
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"devDependencies": {
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"@jupyterlab/builder": "^3.0.0",
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"@jupyterlab/builder": "^3.2.8",
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"npm-run-all": "^4.1.5",
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"rimraf": "^3.0.2",
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"typescript": "~4.1.3"

‎packages/fasta-extension/src/index.ts‎

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'application/vnd.fasta.fasta': {
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name: 'Fasta',
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extensions: ['.fasta', '.fa'],
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reader: msa.io.fasta
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reader: msa.io.fasta,
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},
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'application/vnd.clustal.clustal': {
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name: 'Clustal',
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extensions: ['.clustal', '.aln'],
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reader: msa.io.clustal
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}
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reader: msa.io.clustal,
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},
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};
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/**
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this._mimeType = options.mimeType;
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this._parser = TYPES[this._mimeType].reader;
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this.addClass('jp-RenderedMSA');
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let msaDiv = document.createElement('div');
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const msaDiv = document.createElement('div');
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this.msa = new msa.msa({
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el: msaDiv,
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vis: {
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overviewbox: true,
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seqlogo: false,
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gapHeader: false,
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leftHeader: true
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}
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leftHeader: true,
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},
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});
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// The menu doesn't work correctly in the absolutely positioned panel, so
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*/
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renderModel(model: IRenderMime.IMimeModel): Promise<void> {
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return new Promise<void>((resolve, reject) => {
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let data = model.data[this._mimeType];
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let seqs = this._parser.parse(data);
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const data = model.data[this._mimeType];
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const seqs = this._parser.parse(data);
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this.msa.seqs.reset(seqs);
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this.msa.render();
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this.update();
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protected onUpdateRequest(msg: Message): void {
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// Update size after update
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if (this.isVisible) {
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let newWidth =
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const newWidth =
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this.node.getBoundingClientRect().width -
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this.msa.g.zoomer.getLeftBlockWidth();
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this.msa.g.zoomer.set('alignmentWidth', newWidth);
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export const rendererFactory: IRenderMime.IRendererFactory = {
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safe: false,
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mimeTypes: Object.keys(TYPES),
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createRenderer: options => new RenderedData(options)
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createRenderer: (options) => new RenderedData(options),
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};
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const extensions = Object.keys(TYPES).map(k => {
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const extensions = Object.keys(TYPES).map((k) => {
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const { name } = TYPES[k];
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return {
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id: `jupyterlab-fasta:${name}`,
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name,
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extensions: TYPES[k].extensions,
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mimeTypes: [k],
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iconClass: 'jp-MaterialIcon jp-MSAIcon'
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}
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iconClass: 'jp-MaterialIcon jp-MSAIcon',
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},
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],
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documentWidgetFactoryOptions: {
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name,
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primaryFileType: name,
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fileTypes: [name],
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defaultFor: [name]
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}
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defaultFor: [name],
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},
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} as IRenderMime.IExtension;
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});
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‎packages/geojson-extension/package.json‎

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"build:prod": "jlpm run build:lib && jlpm run build:labextension",
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"clean": "jlpm run clean:lib",
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"clean:all": "jlpm run clean:lib && jlpm run clean:labextension && jlpm run clean:dist",
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"clean:dist": "rimraf dist",
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"clean:labextension": "rimraf ./jupyterlab-geojson/labextension",
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"clean:lib": "rimraf lib tsconfig.tsbuildinfo",
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"clean:dist": "rimraf dist",
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"eslint": "eslint . --ext .ts,.tsx --fix",
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"eslint:check": "eslint . --ext .ts,.tsx",
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"install:extension": "jupyter labextension develop --overwrite .",
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"watch:src": "tsc -w"
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},
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"dependencies": {
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"@jupyterlab/apputils": "^3.0.5",
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"@jupyterlab/rendermime-interfaces": "^3.0.5",
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"@lumino/messaging": "^1.4.3",
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"@lumino/widgets": "^1.16.1",
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"@jupyterlab/apputils": "^3.2.8",
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"@jupyterlab/rendermime-interfaces": "^3.2.8",
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"@lumino/messaging": "^1.10.1",
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"@lumino/widgets": "^1.31.1",
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"leaflet": "^1.5.0"
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},
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"devDependencies": {
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"@jupyterlab/builder": "^3.0.0",
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"@jupyterlab/builder": "^3.2.8",
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"@types/leaflet": "^1.4.0",
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"npm-run-all": "^4.1.5",
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"rimraf": "^3.0.2",

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