Initial commit

.codespellrc

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+[codespell]
+# Ref: https://github.com/codespell-project/codespell#using-a-config-file
+skip = .git,package-lock.json,*.css,.codespellrc
+check-hidden = true
+# ignore-regex = 
+# ignore-words-list =

.eslintrc.cjs

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+module.exports = {
+  root: true,
+  env: { browser: true, es2020: true },
+  extends: [
+    'eslint:recommended',
+    'plugin:@typescript-eslint/recommended',
+    'plugin:react-hooks/recommended',
+    'plugin:cypress/recommended',
+    'airbnb',
+    'airbnb/hooks',
+    'airbnb-typescript',
+    'prettier',
+  ],
+  ignorePatterns: ['dist', '.eslintrc.cjs', 'lint-staged.config.js'],
+  parser: '@typescript-eslint/parser',
+  parserOptions: {
+    project: ['./tsconfig.*json'],
+  },
+  settings: {
+    'import/parsers': {
+      '@typescript-eslint/parser': ['.ts', '.tsx'],
+    },
+    'import/resolver': {
+      typescript: {
+        alwaysTryTypes: true,
+      },
+    },
+  },
+  plugins: ['react-refresh', 'cypress', 'eslint-plugin-tsdoc'],
+  rules: {
+    'react-refresh/only-export-components': ['warn', { allowConstantExport: true }],
+    'react/react-in-jsx-scope': 'off',
+    'tsdoc/syntax': 'warn',
+    // Disabling this rule allows us to use blanket exports from components
+    'import/prefer-default-export': 'off',
+  },
+};

.github/dependabot.yml

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+# To get started with Dependabot version updates, you'll need to specify which
+# package ecosystems to update and where the package manifests are located.
+# Please see the documentation for all configuration options:
+# https://docs.github.com/code-security/dependabot/dependabot-version-updates/configuration-options-for-the-dependabot.yml-file
+
+version: 2
+updates:
+  - package-ecosystem: 'github-actions'
+    directory: '/'
+    schedule:
+      interval: 'weekly'
+    labels:
+      - '_bot'
+      - 'maint:dependency'
+      - 'type:maintenance'
+
+  - package-ecosystem: 'gitsubmodule'
+    directory: '/'
+    schedule:
+      interval: 'weekly'
+
+  - package-ecosystem: 'npm'
+    directory: '/'
+    schedule:
+      interval: 'weekly'
+    labels:
+      - '_bot'
+      - 'maint:dependency'
+      - 'type:maintenance'

.github/pull_request_template.md

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+<!--- Until this PR is ready for review, you can include [WIP] in the title, or create a draft PR. -->
+
+
+<!---
+Below is a suggested pull request template. Feel free to add more details you feel are relevant/necessary.
+
+For more info on the Neurobagel PR process and other contributing guidelines, see https://neurobagel.org/contributing/CONTRIBUTING/.
+-->
+
+<!-- 
+Please indicate after the # which issue you're closing with this PR, if applicable.
+If the PR closes multiple issues, include "closes" before each one is listed.
+You can also link to other issues if necessary, e.g. "See also #1234".
+
+https://help.github.com/articles/closing-issues-using-keywords
+-->
+- Closes #
+
+<!-- 
+Please give a brief overview of what has changed or been added in the PR.
+This can include anything specific the maintainers should be looking for when they review the PR.
+-->
+Changes proposed in this pull request:
+
+-
+-
+
+<!-- To be checked off by reviewers -->
+## Checklist
+_This section is for the PR reviewer_
+
+- [ ] PR has an interpretable title with a prefix (`[ENH]`, `[FIX]`, `[REF]`, `[TST]`, `[CI]`, `[MNT]`, `[INF]`, `[MODEL]`, `[DOC]`) _(see our [Contributing Guidelines](https://neurobagel.org/contributing/CONTRIBUTING#pull-request-guidelines) for more info)_
+- [ ] PR has a label for the release changelog or `skip-release` (to be applied by maintainers only)
+- [ ] PR links to GitHub issue with mention `Closes #XXXX`
+- [ ] Tests pass
+- [ ] Checks pass
+
+For new features:
+- [ ] Tests have been added
+
+For bug fixes:
+- [ ] There is at least one test that would fail under the original bug conditions.

.github/workflows/checks.yaml

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+name: checks
+
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+  # Enables GH merge queues
+  # https://docs.github.com/en/actions/using-workflows/events-that-trigger-workflows#merge_group
+  merge_group:
+
+jobs:
+  tsc:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+
+      - name: Set up Node.js
+        uses: actions/setup-node@v4
+        with:
+          node-version: '20'
+
+      - name: Install dependencies
+        run: npm ci
+
+      - name: Run TSC
+        run: npm run typecheck
+
+  eslint:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+
+      - name: Set up Node.js
+        uses: actions/setup-node@v4
+        with:
+          node-version: '20'
+
+      - name: Install dependencies
+        run: npm ci
+
+      - name: Run ESLint
+        run: npm run lint:check
+
+  prettier:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+
+      - name: Set up Node.js
+        uses: actions/setup-node@v4
+        with:
+          node-version: '20'
+
+      - name: Install dependencies
+        run: npm ci
+
+      - name: Run Prettier Check
+        run: npm run format:check
+
+  codespell:
+    name: Check for spelling errors
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+      - name: Codespell
+        uses: codespell-project/actions-codespell@v2

.github/workflows/tests.yaml

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+name: tests
+
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+  merge_group:
+
+jobs:
+  e2e:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+
+      - name: Set up node env
+        uses: actions/setup-node@v4
+        with:
+          node-version: 20
+
+      - name: build
+        run: npm install && npm run build
+
+      - name: Run end to end tests
+        uses: cypress-io/github-action@v6
+        with:
+          wait-on: http://localhost:5173
+          start: npm run preview
+          component: false
+
+      - name: Upload e2e coverage artifact
+        uses: actions/upload-artifact@v4
+        with:
+          name: e2eCov
+          path: coverage
+
+  component:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+
+      - name: build
+        run: npm install && npm run build
+
+      - name: Run component tests
+        uses: cypress-io/github-action@v6
+        with:
+          component: true
+
+      - name: Upload component coverage artifact
+        uses: actions/upload-artifact@v4
+        with:
+          name: compCov
+          path: coverage
+
+  unit:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+
+      - name: Set up Node.js
+        uses: actions/setup-node@v4
+        with:
+          node-version: '20'
+
+      - name: Install dependencies
+        run: npm ci
+
+      - name: Run unit tests
+        run: npm run test:unit
+
+      - name: Upload unit coverage artifact
+        uses: actions/upload-artifact@v4
+        with:
+          name: unitCov
+          path: coverage
+
+  merge-coverage:
+    # Run this job only if both e2e and component tests passed
+    needs: [e2e, component, unit]
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+
+      - name: Set up Node.js
+        uses: actions/setup-node@v4
+        with:
+          node-version: '20'
+
+      - name: Setup
+        run: npm install
+
+      - name: Download e2e coverage artifacts
+        uses: actions/download-artifact@v4
+        with:
+          name: e2eCov
+          path: e2eCov
+
+      - name: Download component coverage artifacts
+        uses: actions/download-artifact@v4
+        with:
+          name: compCov
+          path: compCov
+
+      - name: Download unit coverage artifacts
+        uses: actions/download-artifact@v4
+        with:
+          name: unitCov
+          path: unitCov
+
+      - name: Install nyc
+        run: npm install -g nyc
+
+      - name: Merge coverage reports
+        run: |
+          mkdir -p combined_coverage final_coverage
+          nyc merge e2eCov combined_coverage/e2e.json 
+          nyc merge compCov combined_coverage/component.json
+          nyc merge unitCov combined_coverage/unit.json
+          nyc merge combined_coverage final_coverage/combined-coverage.json
+
+      - name: Generate final coverage report
+        run: nyc report --reporter=lcov --temp-dir final_coverage --report-dir ./coverage
+
+      - name: Upload coverage to Codecov
+        uses: codecov/codecov-action@v4
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
+          file: ./coverage/lcov.info
+          flags: tests
+          name: codecov-combined  
+          fail_ci_if_error: true
+

.gitignore

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+# Logs
+logs
+*.log
+npm-debug.log*
+yarn-debug.log*
+yarn-error.log*
+pnpm-debug.log*
+lerna-debug.log*
+
+node_modules
+dist
+dist-ssr
+*.local
+
+# Editor directories and files
+.vscode/*
+!.vscode/extensions.json
+.idea
+.DS_Store
+*.suo
+*.ntvs*
+*.njsproj
+*.sln
+*.sw?
+
+# Environment files
+.env
+
+# Cypress
+cypress/screenshots
+cypress/downloads
+
+# Code coverage reports
+coverage
+.nyc_output
+

.husky/post-merge

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+#!/bin/sh
+. "$(dirname "$0")/_/husky.sh"
+
+git diff HEAD^ HEAD --exit-code -- ./package.json || npm ci

.husky/pre-commit

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+#!/usr/bin/env sh
+. "$(dirname -- "$0")/_/husky.sh"
+
+npx lint-staged
+