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Prevent VARCHAR round-trip auto cast, check for duplicate primary keys and add preprocessing tests #279

Prevent VARCHAR round-trip auto cast, check for duplicate primary keys and add preprocessing tests

Prevent VARCHAR round-trip auto cast, check for duplicate primary keys and add preprocessing tests #279

Workflow file for this run

name: Run Linter
on:
pull_request:
concurrency:
group: linter-${{ github.ref }}
cancel-in-progress: true
env:
DOCKER_LINTER_DEPENDENCY_IMAGE_NAME: ghcr.io/genspectrum/lapis-silo-linter-dependencies
jobs:
linterDependencies:
name: Build linter dependencies
runs-on: ubuntu-latest
permissions:
packages: write
steps:
- uses: actions/checkout@v4
- name: Generate dependency files hash
id: files-hash
run: |
DIR_HASH=$(echo -n ${{ hashFiles('conanfile.py', 'conanprofile.docker', '.github/workflows/linter.yml', './Dockerfile_linter_dependencies') }})
echo "DIR_HASH=$DIR_HASH" >> $GITHUB_ENV
- name: Docker metadata
id: dockerMetadata
uses: docker/metadata-action@v5
with:
images: ${{ env.DOCKER_LINTER_DEPENDENCY_IMAGE_NAME }}
tags: |
type=ref,event=branch
type=raw,value=latest,enable=${{ github.ref == 'refs/heads/main' }}
type=raw,value=${{ env.DIR_HASH }}
type=sha,format=long,prefix=commit-
- name: Login to GitHub Container Registry
uses: docker/login-action@v3
with:
registry: ghcr.io
username: ${{ github.actor }}
password: ${{ secrets.GITHUB_TOKEN }}
- name: Check if image exists
id: check-image
run: |
EXISTS=$(docker manifest inspect ${{ env.DOCKER_LINTER_DEPENDENCY_IMAGE_NAME }}:${{ env.DIR_HASH }} > /dev/null 2>&1 && echo "true" || echo "false")
echo "CACHE_HIT=$EXISTS" >> $GITHUB_ENV
- name: Set up Docker Buildx
if: env.CACHE_HIT == 'false'
uses: docker/setup-buildx-action@v3
- name: Build linter dependencies image
if: env.CACHE_HIT == 'false'
uses: docker/build-push-action@v6
with:
context: .
push: true
tags: ${{ steps.dockerMetadata.outputs.tags }}
file: ./Dockerfile_linter_dependencies
cache-from: type=gha,ref=linter-dependencies-image-cache-${{ hashFiles('conanfile.py', 'Dockerfile_linter') }}
cache-to: type=gha,mode=min,ref=linter-dependencies-image-cache-${{ hashFiles('conanfile.py', 'Dockerfile_linter') }}
- name: Retag and push existing image if cache hit
if: env.CACHE_HIT == 'true'
run: |
TAGS=(${{ steps.dockerMetadata.outputs.tags }})
for TAG in "${TAGS[@]}"; do
docker buildx imagetools create --tag $TAG ${{ env.DOCKER_LINTER_DEPENDENCY_IMAGE_NAME }}:${{ env.DIR_HASH }}
done
linter:
name: Build And Run linter
needs: linterDependencies
runs-on: ubuntu-latest
env:
PR_NUMBER: ${{ github.event.number }}
container:
image: ghcr.io/genspectrum/lapis-silo-linter-dependencies:commit-${{ github.sha }}
steps:
- uses: actions/checkout@v4
- shell: bash
name: Configure and run clang-tidy on changed files
run: |
mv /src/build .
cmake -DBUILD_WITH_CLANG_TIDY=on -D CMAKE_BUILD_TYPE=Debug -B build/Debug
echo "Successfully configured cmake"
files=""
PAGE=1
while true; do
page_files=$(curl -s \
"https://api.github.com/repos/${{ github.repository }}/pulls/${PR_NUMBER}/files?per_page=100&page=$PAGE" \
| jq -r '.[] | select(.status != "removed") | .filename')
# If there are no more files, break the loop
if [[ -z "$page_files" ]]; then
break
fi
files+="$page_files"$'\n'
PAGE=$((PAGE + 1))
done
echo "Changed files of this PR:"
echo "$files"
IFS=$'\n'
for file in $files; do
echo "Check ending for file: $file"
if [[ $file == *.cpp ]]; then
echo "Now linting the file: $file"
echo "cmake --build build/Debug --target ${file%.cpp}.o"
cmake --build build/Debug --target ${file%.cpp}.o
fi
done