Merge branch 'neurobagel:main' into newWork

.autorc

@@ -0,0 +1,118 @@
+{
+    "onlyPublishWithReleaseLabel": true,
+    "noDefaultLabels": true,
+    "baseBranch": "main",
+    "author": "Chef Bot <[email protected]>",
+    "noVersionPrefix": false,
+    "plugins": [
+        "git-tag",
+        "released",
+        "protected-branch",
+        "first-time-contributor",
+        [
+            "omit-commits",
+            {
+                "username": "dependabot[bot]",
+                "subject": "[pre-commit.ci]",
+                "labels": "_bot"
+            }
+        ]
+    ],
+    "labels": [
+        {
+            "name": "pr-major-breaking",
+            "changelogTitle": "💥 Breaking Changes",
+            "description": "Significant behaviour change that breaks compatibility, will increment major version (+1.0.0)",
+            "releaseType": "major",
+            "overwrite": true,
+            "color": "#C5000B"
+        },
+        {
+            "name": "pr-minor-breaking",
+            "changelogTitle": "💥 Breaking Changes",
+            "description": "Feature or enhancement that breaks compatibility, will increment minor version (0.+1.0)",
+            "releaseType": "minor",
+            "overwrite": true,
+            "color": "#F1A60E"
+        },
+        {
+            "name": "pr-minor",
+            "changelogTitle": "🚀 Enhancements",
+            "description": "Non-breaking feature or enhancement, will increment minor version (0.+1.0)",
+            "releaseType": "minor",
+            "overwrite": true,
+            "color": "#F1A60E"
+        },
+        {
+            "name": "pr-patch",
+            "changelogTitle": "🚀 Enhancements",
+            "description": "Incremental feature improvement, will increment patch version when merged (0.0.+1)",
+            "releaseType": "patch",
+            "overwrite": true,
+            "default": true,
+            "color": "#870048"
+        },
+        {
+            "name": "pr-bug-fix",
+            "changelogTitle": "🐛 Bug Fixes",
+            "description": "Bug fix, will increment patch version when merged (0.0.+1)",
+            "releaseType": "patch",
+            "overwrite": true,
+            "color": "#870048"
+        },
+        {
+            "name": "pr-internal",
+            "changelogTitle": "🏠 Internal",
+            "description": "Non-user-facing code improvement, will increment patch version when merged (0.0.+1)",
+            "releaseType": "patch",
+            "overwrite": true,
+            "color": "#696969"
+        },
+        {
+            "name": "pr-performance",
+            "changelogTitle": "🏎 Performance Improvements",
+            "description": "Improve performance of an existing feature, will increment patch version when merged (0.0.+1)",
+            "releaseType": "patch",
+            "overwrite": true,
+            "color": "#f4b2d8"
+        },
+        {
+            "name": "pr-documentation",
+            "changelogTitle": "📝 Documentation",
+            "description": "Change that only affects user documentation",
+            "releaseType": "none",
+            "overwrite": true,
+            "color": "#cfd3d7"
+        },
+        {
+            "name": "pr-tests",
+            "changelogTitle": " 🧪 Tests",
+            "description": "Add or improve existing tests",
+            "releaseType": "none",
+            "overwrite": true,
+            "color": "#ffd3cc"
+        },
+        {
+            "name": "pr-dependencies",
+            "changelogTitle": "🔩 Dependency Updates",
+            "description": "Update one or more dependencies version",
+            "releaseType": "none",
+            "overwrite": true,
+            "color": "#8732bc"
+        },
+        {
+            "name": "skip-release",
+            "description": "PR doesn't appear in the changelog and preserves current version when merged",
+            "releaseType": "skip",
+            "overwrite": true,
+            "color": "#bf5416"
+        },
+        {
+            "name": "release",
+            "description": "Create a release when this PR is merged",
+            "releaseType": "release",
+            "overwrite": true,
+            "color": "#007f70"
+        }
+    ]
+}

.dockerignore

@@ -0,0 +1 @@
+node_modules

.github/pull_request_template.md

@@ -0,0 +1,47 @@
+<!--- 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/add_iss2project.yml

@@ -0,0 +1,16 @@
+name: Add new issues to project
+
+on:
+  issues:
+    types:
+      - opened
+
+jobs:
+  add-to-project:
+    name: Add issue to project
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/add-to-project@main
+        with:
+          project-url: https://github.com/orgs/neurobagel/projects/1
+          github-token: ${{ secrets.NB_PROJECT_PAT }}

.github/workflows/build_docker_on_release.yml

@@ -0,0 +1,26 @@
+name: build Docker image on release
+
+on:
+  release:
+    types: [published]
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+      - name: Login to Docker Hub
+        uses: docker/login-action@v3
+        with:
+          username: ${{ secrets.DOCKERHUB_USERNAME }}
+          password: ${{ secrets.DOCKERHUB_TOKEN }}
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v3
+      - name: Build and push
+        uses: docker/build-push-action@v5
+        with:
+          context: .
+          file: ./Dockerfile
+          push: true
+          tags: ${{ secrets.DOCKERHUB_USERNAME }}/query_tool:latest, ${{ secrets.DOCKERHUB_USERNAME }}/query_tool:${{ github.event.release.tag_name }}

.github/workflows/deploy.yaml

@@ -0,0 +1,49 @@
+# Adapted from sample vite workflow file: https://vitejs.dev/guide/static-deploy#github-pages
+name: deploy
+
+on:
+  release:
+    types: [published]
+  workflow_dispatch:
+
+# Sets the GITHUB_TOKEN permissions to allow deployment to GitHub Pages
+permissions:
+  contents: read
+  pages: write
+  id-token: write
+
+# Allow one concurrent deployment
+concurrency:
+  group: 'pages'
+  cancel-in-progress: true
+
+jobs:
+  deploy:
+    # See docs: https://docs.github.com/en/actions/deployment/targeting-different-environments/using-environments-for-deployment#using-an-environment
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+      - name: Set up Node
+        uses: actions/setup-node@v3
+        with:
+          cache: 'npm'
+      - name: Create .env file
+        run: |
+          echo -e "NB_API_QUERY_URL=${{ vars.NB_API_QUERY_URL }}\nNB_IS_FEDERATION_API=${{ vars.NB_IS_FEDERATION_API }}" > .env
+      - name: Install dependencies
+        run: npm ci
+      - name: Build
+        run: npm run build
+      - name: Setup Pages
+        uses: actions/configure-pages@v4
+      - name: Upload artifact
+        uses: actions/upload-pages-artifact@v3
+        with:
+          path: './dist'
+      - name: Deploy to GitHub Pages
+        id: deployment
+        uses: actions/deploy-pages@v4

.github/workflows/lint.yaml

@@ -18,4 +18,4 @@ jobs:
         run: npm ci
 
       - name: Run ESLint
-        run: npm run lint
+        run: npm run lint:check

.github/workflows/release.yaml

@@ -0,0 +1,28 @@
+name: auto release
+
+on:
+  push:
+    branches:
+      - main
+
+jobs:
+  auto-release:
+    runs-on: ubuntu-latest
+    if: "!contains(github.event.head_commit.message, 'ci skip') && !contains(github.event.head_commit.message, 'skip ci')"
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - name: Download latest auto
+        run: |
+          auto_download_url="$(curl -fsSL https://api.github.com/repos/intuit/auto/releases/latest | jq -r '.assets[] | select(.name == "auto-linux.gz") | .browser_download_url')"
+          wget -O- "$auto_download_url" | gunzip > ~/auto
+          chmod a+x ~/auto
+
+      - name: Release
+        run: ~/auto shipit -vv
+        env:
+          GH_TOKEN: ${{ secrets.NB_PAT_RELEASE }}
+          PROTECTED_BRANCH_REVIEWER_TOKEN: ${{ secrets.NB_PAT_RELEASE_PROTECTED }}

.github/workflows/stale.yml

@@ -0,0 +1,24 @@
+name: 'Close stale issues and PRs'
+on:
+  schedule:
+    - cron: '30 1 * * *'
+
+jobs:
+  stale:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/stale@v8
+        with:
+          stale-issue-message: |
+            We want to keep our issues up to date and active. This issue hasn't seen any activity in the last 75 days.
+            We have applied the `_flag:stale` label to indicate that this issue should be reviewed again.
+            When you review, please reread the spec and then apply one of these three options:
+            - prioritize: apply the `flag:schedule` label to suggest moving this issue into the backlog now
+            - close: if the issue is no longer relevant, explain why (give others a chance to reply) and then close.
+            - archive: sometimes an issue has important information or ideas but we won't work on it soon. In this case
+            apply the `someday` label to show that this won't be prioritized. The stalebot will ignore issues with this
+            label in the future. Use sparingly!
+          days-before-stale: 75
+          days-before-close: -1
+          stale-issue-label: '_flag:stale'
+          exempt-issue-labels: 'Roadmap,Milestone,Epic,someday'

.husky/post-merge

@@ -0,0 +1,4 @@
+#!/bin/sh
+. "$(dirname "$0")/_/husky.sh"
+
+git diff HEAD^ HEAD --exit-code -- ./package.json || npm ci

.husky/pre-commit

@@ -2,3 +2,4 @@
 . "$(dirname -- "$0")/_/husky.sh"
 
 npx lint-staged
+

.lintstagedrc.json

@@ -1,3 +1,3 @@
 {
-  "*.{ts,tsx}": ["npm run lint", "npm run format"]
+  "*.{ts,tsx}": ["npm run lint:check", "npm run format:check"]
 }