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5 changes: 5 additions & 0 deletions .github/ISSUE_TEMPLATE/config.yml
Original file line number Diff line number Diff line change
@@ -0,0 +1,5 @@
blank_issues_enabled: true
contact_links:
- name: Phenotype org
url: https://github.com/KooshaPari
about: Other Phenotype-ecosystem repos and discussions
7 changes: 5 additions & 2 deletions .github/workflows/alert-sync-issues.yml
Original file line number Diff line number Diff line change
@@ -1,16 +1,19 @@
name: Alert sync issues
on:
push:
branches: [main, master, develop]
pull_request:
branches: [main, master, develop]
schedule:
- cron: '17 * * * *'
workflow_dispatch:

permissions:
contents: read
issues: write

jobs:
sync:
uses: KooshaPari/phenoShared/.github/workflows/alert-sync-issues.yml@main
uses: KooshaPari/phenoShared/.github/workflows/alert-sync-issues.yml@4b820a6d1eca7884e692e4ec4edf2b59732809cd
with:
auto-label: auto-alert-sync
min_severity: high
8 changes: 6 additions & 2 deletions .github/workflows/auto-merge.yml
Original file line number Diff line number Diff line change
@@ -1,8 +1,11 @@
name: Auto Merge Gate

on:
push:
branches: [main, master, develop]
pull_request:
branches: [main, master, develop]
workflow_dispatch:

permissions:
contents: read
pull-requests: write
Expand All @@ -18,6 +21,7 @@ jobs:
if: |
contains(github.event.pull_request.labels.*.name, 'automerge') &&
!contains(github.event.pull_request.labels.*.name, 'do-not-merge')
uses: peter-evans/enable-pull-request-automerge@a660677d5469627102a1c1e11409dd063606628d # v3with:
uses: peter-evans/enable-pull-request-automerge@a660677d5469627102a1c1e11409dd063606628d # v3
with:
github-token: ${{ secrets.GITHUB_TOKEN }}
merge-method: squash
8 changes: 6 additions & 2 deletions .github/workflows/ci-rerun-flaky.yml
Original file line number Diff line number Diff line change
@@ -1,8 +1,11 @@
name: ci-rerun-flaky

on:
push:
branches: [main, master, develop]
pull_request:
branches: [main, master, develop]
workflow_dispatch:

permissions:
actions: write
contents: read
Expand All @@ -15,7 +18,8 @@ jobs:
runs-on: ubuntu-latest
steps:
- name: Rerun failed CI jobs and remove rerun label
uses: actions/github-script@f28e40c7f34bde8b3046d885e986cb6290c5673b # v7with:
uses: actions/github-script@f28e40c7f34bde8b3046d885e986cb6290c5673b # v7
with:
script: |
const label = 'ci:rerun-flaky';
const { owner, repo } = context.repo;
Expand Down
18 changes: 13 additions & 5 deletions .github/workflows/ci.yml
Original file line number Diff line number Diff line change
@@ -1,4 +1,8 @@
name: CI
concurrency:
group: ${{ github.workflow }}-${{ github.ref }}
cancel-in-progress: true


on:
push:
Expand All @@ -18,18 +22,21 @@ jobs:
go-version: ['1.21', '1.22']

steps:
- uses: actions/checkout@34e114876b0b11c390a56381ad16ebd13914f8d5@11bd71901bbe5b1630ceea73d27597364c9af683 # v4- name: Refresh models catalog
run: |
- uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
name: Refresh models catalog
- run: |
git fetch --depth 1 https://github.com/router-for-me/models.git main
mkdir -p pkg/llmproxy/registry/models
git show FETCH_HEAD:models.json > pkg/llmproxy/registry/models/models.json

- name: Setup Go
uses: actions/setup-go@40f1582b2485089dde7abd97c1529aa768e1baff # v5with:
uses: actions/setup-go@40f1582b2485089dde7abd97c1529aa768e1baff # v5
with:
go-version: ${{ matrix.go-version }}

- name: Cache Go modules
uses: actions/cache@0057852bfaa89a56745cba8c7296529d2fc39830 # v4with:
uses: actions/cache@0057852bfaa89a56745cba8c7296529d2fc39830 # v4
with:
path: ~/go/pkg/mod
key: ${{ runner.os }}-go-${{ hashFiles('**/go.sum') }}
restore-keys: |
Expand All @@ -45,7 +52,8 @@ jobs:
run: go test ./... -v -race -coverprofile=coverage.out

- name: Upload coverage
uses: codecov/codecov-action@ab904c41d6ece82784817410c45d8b8c02684457 # v3with:
uses: codecov/codecov-action@ab904c41d6ece82784817410c45d8b8c02684457 # v3
with:
files: ./coverage.out


Expand Down
14 changes: 10 additions & 4 deletions .github/workflows/codeql.yml
Original file line number Diff line number Diff line change
@@ -1,8 +1,11 @@
name: codeql

on:
push:
branches: [main, master, develop]
pull_request:
branches: [main, master, develop]
workflow_dispatch:

permissions:
actions: read
contents: read
Expand All @@ -19,12 +22,15 @@ jobs:
language: [go]
steps:
- name: Checkout
uses: actions/checkout@34e114876b0b11c390a56381ad16ebd13914f8d5@11bd71901bbe5b1630ceea73d27597364c9af683 # v4- name: Initialize CodeQL
uses: github/codeql-action/init@95e58e9a2cdfd71adc6e0353d5c52f41a045d225 # v4with:
uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
name: Initialize CodeQL
uses: github/codeql-action/init@95e58e9a2cdfd71adc6e0353d5c52f41a045d225 # v4
with:
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Checkout and CodeQL init merged into single step

High Severity

The Checkout step and Initialize CodeQL step have been merged into a single YAML mapping with duplicate name: and uses: keys. YAML uses the last value for duplicate keys, so only github/codeql-action/init runs — the actions/checkout step is silently dropped. CodeQL analysis will fail because no code is checked out.

Fix in Cursor Fix in Web

Reviewed by Cursor Bugbot for commit b00b205. Configure here.

languages: ${{ matrix.language }}
config-file: .github/codeql/codeql-config.yml
- name: Set up Go
uses: actions/setup-go@40f1582b2485089dde7abd97c1529aa768e1baff # v5with:
uses: actions/setup-go@40f1582b2485089dde7abd97c1529aa768e1baff # v5
with:
go-version-file: go.mod
cache: true
- name: Build
Expand Down
10 changes: 7 additions & 3 deletions .github/workflows/coderabbit-rate-limit-retry.yml
Original file line number Diff line number Diff line change
@@ -1,8 +1,11 @@
name: coderabbit-rate-limit-retry

on:
push:
branches: [main, master, develop]
pull_request:
branches: [main, master, develop]
workflow_dispatch:

permissions:
checks: write
contents: read
Expand All @@ -15,7 +18,8 @@ jobs:
runs-on: ubuntu-latest
steps:
- name: Re-request CodeRabbit when backlog is high and check is stale
uses: actions/github-script@f28e40c7f34bde8b3046d885e986cb6290c5673b # v7with:
uses: actions/github-script@f28e40c7f34bde8b3046d885e986cb6290c5673b # v7
with:
script: |
const owner = context.repo.owner;
const repo = context.repo.repo;
Expand Down Expand Up @@ -166,7 +170,7 @@ jobs:
status: "completed",
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CRITICAL: JavaScript syntax error - ternary expression incorrectly wrapped in quotes

The entire ternary expression has been wrapped in quotes, making it a string literal instead of executable code. This will cause a JavaScript syntax error.

Suggested change
status: "completed",
title: pass ? "CodeRabbit gate passed" : "CodeRabbit gate blocked",

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CRITICAL: JavaScript syntax error - ternary expression incorrectly wrapped in quotes

The entire ternary expression has been wrapped in quotes, making it a string literal instead of executable code. This will cause a JavaScript syntax error.

Suggested change
status: "completed",
conclusion: pass ? "success" : "failure",

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CRITICAL: JavaScript syntax error - ternary expression incorrectly wrapped in quotes

The entire ternary expression has been wrapped in quotes, making it a string literal instead of executable code. This will cause a JavaScript syntax error.

Suggested change
status: "completed",
conclusion: pass ? "success" : "failure",

conclusion: pass ? "success" : "failure",
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CRITICAL: JavaScript syntax error - mismatched quotes in title string

The line has invalid JavaScript due to quote mismatch. It should be:

Suggested change
conclusion: pass ? "success" : "failure",
title: pass ? "CodeRabbit gate passed" : "CodeRabbit gate blocked",

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CRITICAL: JavaScript syntax error - mismatched quotes in title string

The line has invalid JavaScript due to quote mismatch. It should be:

Suggested change
conclusion: pass ? "success" : "failure",
title: pass ? "CodeRabbit gate passed" : "CodeRabbit gate blocked",

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CRITICAL: JavaScript syntax error - mismatched quotes in title string

The line has invalid JavaScript due to quote mismatch. It should be:

Suggested change
conclusion: pass ? "success" : "failure",
title: pass ? "CodeRabbit gate passed" : "CodeRabbit gate blocked",

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CRITICAL: JavaScript syntax error - mismatched quotes in title string

The line has invalid JavaScript due to quote mismatch. It should be:

Suggested change
conclusion: pass ? "success" : "failure",
title: pass ? "CodeRabbit gate passed" : "CodeRabbit gate blocked",

output: {
title: pass ? "CodeRabbit gate passed" : "CodeRabbit gate blocked",
title: "pass ? "CodeRabbit gate passed" : "CodeRabbit gate blocked","
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JavaScript ternary expression corrupted into broken string literal

High Severity

The title field was changed from a valid JavaScript ternary expression pass ? "CodeRabbit gate passed" : "CodeRabbit gate blocked" into a malformed string "pass ? "CodeRabbit gate passed" : "CodeRabbit gate blocked",". The outer double quotes cause the inner double quotes to prematurely terminate the string, resulting in a JavaScript syntax error that will crash the publishGate function every time it runs.

Fix in Cursor Fix in Web

Reviewed by Cursor Bugbot for commit b00b205. Configure here.

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CRITICAL: JavaScript syntax error - ternary expression incorrectly wrapped in quotes

The entire ternary expression has been wrapped in quotes, making it a string literal instead of executable code. This will cause a JavaScript syntax error.

Suggested change
title: "pass ? "CodeRabbit gate passed" : "CodeRabbit gate blocked","
title: pass ? "CodeRabbit gate passed" : "CodeRabbit gate blocked",

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CRITICAL: JavaScript syntax error - ternary expression incorrectly wrapped in quotes

The entire ternary expression has been wrapped in quotes, making it a string literal instead of executable code. This will cause a JavaScript syntax error.

Suggested change
title: "pass ? "CodeRabbit gate passed" : "CodeRabbit gate blocked","
conclusion: pass ? "success" : "failure",

summary,
Comment on lines +173 to 174
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🔴 Architect Review — CRITICAL

Inside the GitHub Script step, output.title is set to a malformed JavaScript string literal ("pass ? "CodeRabbit gate passed" : "CodeRabbit gate blocked","), which has unbalanced quotes and is syntactically invalid. This causes the github.rest.checks.create call to throw at runtime so the CodeRabbit gate check cannot be published.

Suggestion: Restore a valid expression for output.title (for example title: pass ? "CodeRabbit gate passed" : "CodeRabbit gate blocked",) and optionally assert that checks.create succeeds (e.g., by catching and failing on errors) to ensure the gate status is reliably reported.

Fix in Cursor | Fix in VSCode Claude

(Use Cmd/Ctrl + Click for best experience)

Prompt for AI Agent 🤖
This is an **Architect / Logical Review** comment left during a code review. These reviews are first-class, important findings — not optional suggestions. Do NOT dismiss this as a 'big architectural change' just because the title says architect review; most of these can be resolved with a small, localized fix once the intent is understood.

**Path:** .github/workflows/coderabbit-rate-limit-retry.yml
**Line:** 173:174
**Comment:**
	*CRITICAL: Inside the GitHub Script step, `output.title` is set to a malformed JavaScript string literal (`"pass ? "CodeRabbit gate passed" : "CodeRabbit gate blocked","`), which has unbalanced quotes and is syntactically invalid. This causes the `github.rest.checks.create` call to throw at runtime so the CodeRabbit gate check cannot be published.

Validate the correctness of the flagged issue. If correct, How can I resolve this? If you propose a fix, implement it and please make it concise.
If a suggested approach is provided above, use it as the authoritative instruction. If no explicit code suggestion is given, you MUST still draft and apply your own minimal, localized fix — do not punt back with 'no suggestion provided, review manually'. Keep the change as small as possible: add a guard clause, gate on a loading state, reorder an await, wrap in a conditional, etc. Do not refactor surrounding code or expand scope beyond the finding.
Once fix is implemented, also check other comments on the same PR, and ask user if the user wants to fix the rest of the comments as well. if said yes, then fetch all the comments validate the correctness and implement a minimal fix

},
});
Expand Down
40 changes: 27 additions & 13 deletions .github/workflows/docker-image.yml
Original file line number Diff line number Diff line change
@@ -1,8 +1,11 @@
name: docker-image

on:
push:
branches: [main, master, develop]
pull_request:
branches: [main, master, develop]
workflow_dispatch:

env:
APP_NAME: CLIProxyAPI
DOCKERHUB_REPO: ${{ secrets.DOCKERHUB_USERNAME }}/cli-proxy-api-plus
Expand All @@ -15,13 +18,16 @@ jobs:
runs-on: ubuntu-latest
steps:
- name: Checkout
uses: actions/checkout@34e114876b0b11c390a56381ad16ebd13914f8d5@11bd71901bbe5b1630ceea73d27597364c9af683 # v4- name: Refresh models catalog
uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
- name: Refresh models catalog
run: |
git fetch --depth 1 https://github.com/router-for-me/models.git main
git show FETCH_HEAD:models.json > internal/registry/models/models.json
- name: Set up Docker Buildx
uses: docker/setup-buildx-action@8d2750c68a42422c14e847fe6c8ac0403b4cbd6f # v3- name: Login to DockerHub
uses: docker/login-action@c94ce9fb468520275223c153574b00df6fe4bcc9 # v3with:
uses: docker/setup-buildx-action@8d2750c68a42422c14e847fe6c8ac0403b4cbd6f # v3
- name: Login to DockerHub
uses: docker/login-action@c94ce9fb468520275223c153574b00df6fe4bcc9 # v3
with:
username: ${{ secrets.DOCKERHUB_USERNAME }}
password: ${{ secrets.DOCKERHUB_TOKEN }}
- name: Generate Build Metadata
Expand All @@ -30,7 +36,8 @@ jobs:
echo COMMIT=`git rev-parse --short HEAD` >> $GITHUB_ENV
echo BUILD_DATE=`date -u +%Y-%m-%dT%H:%M:%SZ` >> $GITHUB_ENV
- name: Build and push (amd64)
uses: docker/build-push-action@10e90e3645eae34f1e60eeb005ba3a3d33f178e8 # v6with:
uses: docker/build-push-action@10e90e3645eae34f1e60eeb005ba3a3d33f178e8 # v6
with:
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Docker push on PRs

High Severity

docker-image.yml now runs on pull_request while build steps still use push: true to Docker Hub. PR CI can publish :latest and version tags from unmerged code.

Fix in Cursor Fix in Web

Reviewed by Cursor Bugbot for commit 9b2d42d. Configure here.

context: .
platforms: linux/amd64
push: true
Expand All @@ -46,13 +53,16 @@ jobs:
runs-on: ubuntu-24.04-arm
steps:
- name: Checkout
uses: actions/checkout@34e114876b0b11c390a56381ad16ebd13914f8d5@11bd71901bbe5b1630ceea73d27597364c9af683 # v4- name: Refresh models catalog
uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
- name: Refresh models catalog
run: |
git fetch --depth 1 https://github.com/router-for-me/models.git main
git show FETCH_HEAD:models.json > internal/registry/models/models.json
- name: Set up Docker Buildx
uses: docker/setup-buildx-action@8d2750c68a42422c14e847fe6c8ac0403b4cbd6f # v3- name: Login to DockerHub
uses: docker/login-action@c94ce9fb468520275223c153574b00df6fe4bcc9 # v3with:
uses: docker/setup-buildx-action@8d2750c68a42422c14e847fe6c8ac0403b4cbd6f # v3
- name: Login to DockerHub
uses: docker/login-action@c94ce9fb468520275223c153574b00df6fe4bcc9 # v3
with:
username: ${{ secrets.DOCKERHUB_USERNAME }}
password: ${{ secrets.DOCKERHUB_TOKEN }}
- name: Generate Build Metadata
Expand All @@ -61,7 +71,8 @@ jobs:
echo COMMIT=`git rev-parse --short HEAD` >> $GITHUB_ENV
echo BUILD_DATE=`date -u +%Y-%m-%dT%H:%M:%SZ` >> $GITHUB_ENV
- name: Build and push (arm64)
uses: docker/build-push-action@10e90e3645eae34f1e60eeb005ba3a3d33f178e8 # v6with:
uses: docker/build-push-action@10e90e3645eae34f1e60eeb005ba3a3d33f178e8 # v6
with:
context: .
platforms: linux/arm64
push: true
Expand All @@ -80,9 +91,12 @@ jobs:
- docker_arm64
steps:
- name: Checkout
uses: actions/checkout@34e114876b0b11c390a56381ad16ebd13914f8d5@11bd71901bbe5b1630ceea73d27597364c9af683 # v4- name: Set up Docker Buildx
uses: docker/setup-buildx-action@8d2750c68a42422c14e847fe6c8ac0403b4cbd6f # v3- name: Login to DockerHub
uses: docker/login-action@c94ce9fb468520275223c153574b00df6fe4bcc9 # v3with:
uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
- name: Set up Docker Buildx
uses: docker/setup-buildx-action@8d2750c68a42422c14e847fe6c8ac0403b4cbd6f # v3
- name: Login to DockerHub
uses: docker/login-action@c94ce9fb468520275223c153574b00df6fe4bcc9 # v3
with:
username: ${{ secrets.DOCKERHUB_USERNAME }}
password: ${{ secrets.DOCKERHUB_TOKEN }}
- name: Generate Build Metadata
Expand All @@ -102,7 +116,7 @@ jobs:
"${DOCKERHUB_REPO}:${VERSION}-arm64"
- name: Cleanup temporary tags
continue-on-error: true
env:
- env:
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Docker cleanup step split from its name and config

Medium Severity

The "Cleanup temporary tags" step was split into two steps: one with just name: and continue-on-error: true (an empty step with no action), and another unnamed step starting with - env: that contains the actual cleanup logic. The continue-on-error: true no longer applies to the cleanup script, so a failure in tag deletion will now fail the entire workflow.

Fix in Cursor Fix in Web

Reviewed by Cursor Bugbot for commit b00b205. Configure here.

DOCKERHUB_USERNAME: ${{ secrets.DOCKERHUB_USERNAME }}
DOCKERHUB_TOKEN: ${{ secrets.DOCKERHUB_TOKEN }}
run: |
Expand Down
27 changes: 19 additions & 8 deletions .github/workflows/docs.yml
Original file line number Diff line number Diff line change
@@ -1,6 +1,10 @@
name: VitePress Pages

on:
push:
branches: [main, master, develop]
pull_request:
branches: [main, master, develop]
workflow_dispatch:

concurrency:
Expand All @@ -8,9 +12,9 @@
cancel-in-progress: true

permissions:
contents: read

Check warning on line 15 in .github/workflows/docs.yml

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SonarQubeCloud / SonarCloud Code Analysis

Move this read permission from workflow level to job level.

See more on https://sonarcloud.io/project/issues?id=KooshaPari_cliproxyapi-plusplus&issues=AZ4AfC1ibvIMb_8uaRhW&open=AZ4AfC1ibvIMb_8uaRhW&pullRequest=1004
pages: write

Check warning on line 16 in .github/workflows/docs.yml

View check run for this annotation

SonarQubeCloud / SonarCloud Code Analysis

Move this write permission from workflow level to job level.

See more on https://sonarcloud.io/project/issues?id=KooshaPari_cliproxyapi-plusplus&issues=AZ4AfC1ibvIMb_8uaRhX&open=AZ4AfC1ibvIMb_8uaRhX&pullRequest=1004
id-token: write

Check warning on line 17 in .github/workflows/docs.yml

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SonarQubeCloud / SonarCloud Code Analysis

Move this write permission from workflow level to job level.

See more on https://sonarcloud.io/project/issues?id=KooshaPari_cliproxyapi-plusplus&issues=AZ4AfC1ibvIMb_8uaRhY&open=AZ4AfC1ibvIMb_8uaRhY&pullRequest=1004

jobs:
build:
Expand All @@ -19,14 +23,18 @@
runs-on: ubuntu-latest
steps:
- name: Checkout
uses: actions/checkout@34e114876b0b11c390a56381ad16ebd13914f8d5@11bd71901bbe5b1630ceea73d27597364c9af683 # v4- name: Setup Node
uses: actions/setup-node@49933ea5288caeca8642d1e84afbd3f7d6820020@8f152de45cc393bb48ce5d89d36b731f54556e65 # v4with:
uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4

- name: Setup Node
uses: actions/setup-node@8f152de45cc393bb48ce5d89d36b731f54556e65 # v4
with:
node-version: "20"
cache: "npm"
cache-dependency-path: docs/package.json

- name: Setup Bun
uses: oven-sh/setup-bun@0c5077e51419868618aeaa5fe8019c62421857d6 # v2with:
uses: oven-sh/setup-bun@0c5077e51419868618aeaa5fe8019c62421857d6 # v2
with:
bun-version: latest

- name: Install OXC dependencies
Expand All @@ -36,21 +44,22 @@
run: bun run lint

- name: Check docs TS/JS formatting with OXC
run: bun run format:check
run: "bun run format:check"

- name: Install dependencies
working-directory: docs
run: npm install --frozen-lockfile

- name: Build docs
working-directory: docs
run: npm run docs:build
run: "npm run docs:build"

- name: Verify built docs
run: test -f docs/.vitepress/dist/index.html

- name: Upload pages artifact
uses: actions/upload-pages-artifact@56afc609e74202658d3ffba0e8f6dda462b719fa # v3with:
uses: actions/upload-pages-artifact@56afc609e74202658d3ffba0e8f6dda462b719fa # v3
with:
path: docs/.vitepress/dist/

build-skip-branch-ci-unblock:
Expand All @@ -71,6 +80,8 @@
url: ${{ steps.deployment.outputs.page_url }}
steps:
- name: Configure Pages
uses: actions/configure-pages@983d7736d9b0ae728b81ab479565c72886d7745b # v5- name: Deploy
uses: actions/configure-pages@983d7736d9b0ae728b81ab479565c72886d7745b # v5

- name: Deploy
id: deployment
uses: actions/deploy-pages@d6db90164ac5ed86f2b6aed7e0febac5b3c0c03e # v4
uses: actions/deploy-pages@d6db90164ac5ed86f2b6aed7e0febac5b3c0c03e # v4
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