807 delete lapis 1 and clean up

.commitlintrc.js

@@ -11,9 +11,9 @@ const Configuration = {
             RuleConfigSeverity.Error,
             "always",
             [
-                "lapis2",
-                "lapis2-docs",
-                "siloLapisTests",
+                "lapis",
+                "lapis-docs",
+                "lapis-e2e",
                 "github-actions",
                 "root", // used by dependabot to update the root package.json
             ]

.github/dependabot.yml

@@ -7,7 +7,7 @@ updates:
     commit-message:
       prefix: "chore(github-actions)"
   - package-ecosystem: gradle
-    directory: lapis2/
+    directory: lapis/
     schedule:
       interval: weekly
     groups:
@@ -16,9 +16,9 @@ updates:
           - "minor"
           - "patch"
     commit-message:
-      prefix: "chore(lapis2)"
+      prefix: "chore(lapis)"
   - package-ecosystem: npm
-    directory: siloLapisTests/
+    directory: lapis-e2e/
     schedule:
       interval: weekly
     groups:
@@ -27,9 +27,9 @@ updates:
           - "minor"
           - "patch"
     commit-message:
-      prefix: "chore(siloLapisTests)"
+      prefix: "chore(lapis-e2e)"
   - package-ecosystem: npm
-    directory: lapis2-docs/
+    directory: lapis-docs/
     schedule:
       interval: weekly
     groups:
@@ -38,7 +38,7 @@ updates:
           - "minor"
           - "patch"
     commit-message:
-      prefix: "chore(lapis2-docs)"
+      prefix: "chore(lapis-docs)"
   - package-ecosystem: npm
     directory: /
     schedule:

.github/workflows/lapis2-docs.yml → .github/workflows/lapis-docs.yml

@@ -1,13 +1,13 @@
-name: LAPIS v2 Docs
+name: LAPIS Docs
 
 on: [push]
 
 env:
-  DOCKER_IMAGE_NAME: ghcr.io/genspectrum/lapis-v2-docs
+  DOCKER_IMAGE_NAME: ghcr.io/genspectrum/lapis-docs
 
 defaults:
   run:
-    working-directory: ./lapis2-docs
+    working-directory: ./lapis-docs
 
 jobs:
   checks:
@@ -21,7 +21,7 @@ jobs:
       - uses: actions/cache@v4
         with:
           path: ~/.npm
-          key: ${{ runner.os }}-node-${{ hashFiles('lapis2-docs/**/package-lock.json') }}
+          key: ${{ runner.os }}-node-${{ hashFiles('lapis-docs/**/package-lock.json') }}
       - run: npm ci
       - run: npm run check-format
       - run: npm run check-types
@@ -56,7 +56,7 @@ jobs:
       - name: Build and push image
         uses: docker/build-push-action@v5
         with:
-          context: ./lapis2-docs
+          context: ./lapis-docs
           push: true
           tags: ${{ steps.dockerMetadata.outputs.tags }}
 
@@ -95,5 +95,5 @@ jobs:
         if: ${{ failure() }}
         with:
           name: playwright-report
-          path: lapis2-docs/playwright-report/
+          path: lapis-docs/playwright-report/
           retention-days: 7

.github/workflows/lapis2.yml → .github/workflows/lapis.yml

@@ -1,9 +1,9 @@
-name: LAPIS v2
+name: LAPIS
 
 on: [ push ]
 
 env:
-  DOCKER_IMAGE_NAME: ghcr.io/genspectrum/lapis-v2
+  DOCKER_IMAGE_NAME: ghcr.io/genspectrum/lapis
 
 jobs:
   Tests:
@@ -19,12 +19,12 @@ jobs:
         uses: gradle/actions/setup-gradle@v3
         with:
           arguments: test
-          build-root-directory: lapis2
+          build-root-directory: lapis
       - name: Check Format And Lint
         uses: gradle/actions/setup-gradle@v3
         with:
           arguments: ktlintCheck
-          build-root-directory: lapis2
+          build-root-directory: lapis
 
   dockerImage:
     name: Build Docker Image
@@ -56,10 +56,10 @@ jobs:
       - name: Build and push image
         uses: docker/build-push-action@v5
         with:
-          context: ./lapis2
+          context: ./lapis
           tags: ${{ steps.dockerMetadata.outputs.tags }}
-          cache-from: type=gha,scope=lapis2-${{ github.ref }}
-          cache-to: type=gha,mode=max,scope=lapis2-${{ github.ref }}
+          cache-from: type=gha,scope=lapis-${{ github.ref }}
+          cache-to: type=gha,mode=max,scope=lapis-${{ github.ref }}
           platforms: ${{ github.ref == 'refs/heads/main' && 'linux/amd64,linux/arm64' || 'linux/amd64' }}
           push: true
 
@@ -83,35 +83,35 @@ jobs:
         uses: gradle/actions/setup-gradle@v3
         with:
           arguments: generateOpenApiDocs
-          build-root-directory: lapis2
+          build-root-directory: lapis
 
       - name: Build OpenAPI Spec Protected
         uses: gradle/actions/setup-gradle@v3
         with:
           arguments: generateOpenApiDocs -PopennessLevel=protected
-          build-root-directory: lapis2
+          build-root-directory: lapis
 
       - name: Cache .npm
         uses: actions/cache@v4
         with:
           path: ~/.npm
-          key: ${{ runner.os }}-node-${{ hashFiles('siloLapisTests/**/package-lock.json') }}
+          key: ${{ runner.os }}-node-${{ hashFiles('lapis-e2e/**/package-lock.json') }}
 
       - name: Prepare Tests
         run: npm ci
-        working-directory: siloLapisTests
+        working-directory: lapis-e2e
 
       - name: Generate Lapis Client
         run: npm run generateLapisClient
-        working-directory: siloLapisTests
+        working-directory: lapis-e2e
 
       - name: Generate Lapis Client Protected
         run: npm run generateLapisClientProtected
-        working-directory: siloLapisTests
+        working-directory: lapis-e2e
 
       - name: Check Format
         run: npm run check-format
-        working-directory: siloLapisTests
+        working-directory: lapis-e2e
 
       - name: Docker metadata
         id: dockerMetadata
@@ -137,17 +137,17 @@ jobs:
 
       - name: Start SILO and LAPIS and Run Tests
         run: |
-          docker compose -f lapis2/docker-compose.yml pull
-          docker compose -f lapis2/docker-compose.yml up -d --wait
-          cd siloLapisTests && npm run test
+          docker compose -f lapis/docker-compose.yml pull
+          docker compose -f lapis/docker-compose.yml up -d --wait
+          cd lapis-e2e && npm run test
         env:
           SILO_TAG: latest
           LAPIS_TAG: ${{ steps.lapisBranchTag.outputs.lapisTag }}
 
       - name: Store Logs
         if: ${{ always() }}
         run: |
-          cd lapis2
+          cd lapis
           mkdir p e2e-logs
           docker compose logs silo > e2e-logs/silo.log
           docker compose logs lapisOpen > e2e-logs/lapisOpen.log
@@ -161,4 +161,4 @@ jobs:
         uses: actions/upload-artifact@v4
         with:
           name: logs
-          path: lapis2/e2e-logs
+          path: lapis/e2e-logs

.github/workflows/release-lapis2.yml → .github/workflows/release-lapis.yml

@@ -1,14 +1,14 @@
-name: Release LAPIS 2
+name: Release LAPIS
 
 on:
   workflow_run:
-    workflows: [LAPIS v2]
+    workflows: [LAPIS]
     types: [completed]
     branches: [main]
 
 env:
-  LAPIS_DOCKER_IMAGE_NAME: ghcr.io/genspectrum/lapis-v2
-  DOCS_DOCKER_IMAGE_NAME: ghcr.io/genspectrum/lapis-v2-docs
+  LAPIS_DOCKER_IMAGE_NAME: ghcr.io/genspectrum/lapis
+  DOCS_DOCKER_IMAGE_NAME: ghcr.io/genspectrum/lapis-docs
 
 jobs:
   release-please:
@@ -50,7 +50,7 @@ jobs:
           username: ${{ github.actor }}
           password: ${{ secrets.GITHUB_TOKEN }}
 
-      - name: Wait for Lapis 2 Docs Docker Image
+      - name: Wait for Lapis Docs Docker Image
         if: ${{ steps.release.outputs.release_created }}
         uses: lewagon/[email protected]
         with:

.gitignore

@@ -6,8 +6,6 @@
 # Personal preference
 playground/
 
-docker-compose.override.yml
-
 log/
 logs/