chore: GitHub Actions (#15)

* Backend: linting, formatting
* Frontend: linting, formatting
* Runner: Docker image build

.github/workflows/backend.yaml

@@ -0,0 +1,66 @@
+name: backend
+
+on:
+  workflow_dispatch:
+  push:
+    paths:
+      - 'packages/backend/**'
+    branches:
+      - main
+    tags:
+      - "v*.*.*"
+  pull_request:
+    paths:
+      - 'packages/backend/**'
+    branches:
+      - main
+
+jobs:
+  lint:
+    runs-on: ubuntu-latest
+    name: Check for Linting Errors
+    defaults:
+      run:
+        working-directory: packages/backend
+    steps:
+      - name: Checkout Repository
+        uses: actions/checkout@v3
+        with:
+          ref: ${{ github.event.pull_request.head.ref }}
+
+      - name: Setup NodeJS
+        uses: actions/setup-node@v3
+        with:
+          node-version: 22
+
+      - name: NPM Install
+        run: npm install --only=dev
+        shell: bash
+
+      - name: Check for Formatting Issues
+        run: npm run format
+
+      - name: Check for Linting Issues
+        run: npm run lint
+
+  build:
+    runs-on: ubuntu-latest
+    name: Build Code
+    defaults:
+      run:
+        working-directory: packages/backend
+    steps:
+      - name: Checkout Repository
+        uses: actions/checkout@v3
+
+      - name: Setup NodeJS
+        uses: actions/setup-node@v3
+        with:
+          node-version: 22
+
+      - name: NPM Install
+        run: npm install
+        shell: bash
+
+      - name: Build
+        run: npm run build

.github/workflows/frontend.yaml

@@ -0,0 +1,66 @@
+name: frontend
+
+on:
+  workflow_dispatch:
+  push:
+    paths:
+      - 'packages/frontend/**'
+    branches:
+      - main
+    tags:
+      - "v*.*.*"
+  pull_request:
+    paths:
+      - 'packages/frontend/**'
+    branches:
+      - main
+
+jobs:
+  lint:
+    runs-on: ubuntu-latest
+    name: Check for Linting Errors
+    defaults:
+      run:
+        working-directory: packages/frontend
+    steps:
+      - name: Checkout Repository
+        uses: actions/checkout@v3
+        with:
+          ref: ${{ github.event.pull_request.head.ref }}
+
+      - name: Setup NodeJS
+        uses: actions/setup-node@v3
+        with:
+          node-version: 22
+
+      - name: NPM Install
+        run: npm install --only=dev
+        shell: bash
+
+      - name: Check for Formatting Issues
+        run: npm run format
+
+      - name: Check for Linting Issues
+        run: npm run lint
+
+  build:
+    runs-on: ubuntu-latest
+    name: Build Code
+    defaults:
+      run:
+        working-directory: packages/frontend
+    steps:
+      - name: Checkout Repository
+        uses: actions/checkout@v3
+
+      - name: Setup NodeJS
+        uses: actions/setup-node@v3
+        with:
+          node-version: 22
+
+      - name: NPM Install
+        run: npm install
+        shell: bash
+
+      - name: Build
+        run: npm run build

.github/workflows/runner.yaml

@@ -0,0 +1,60 @@
+name: runner
+
+on:
+  workflow_dispatch:
+  push:
+    paths:
+      - 'packages/runner/**'
+    branches:
+      - main
+    tags:
+      - "v*.*.*"
+  pull_request:
+    paths:
+      - 'packages/runner/**'
+    branches:
+      - main
+
+jobs:
+  docker:
+      name: Docker Build and Push
+      runs-on: ubuntu-latest
+      defaults:
+        run:
+          working-directory: packages/runner
+      steps:
+        - uses: docker/setup-qemu-action@v2
+        - uses: docker/setup-buildx-action@v2
+
+        - name: Checkout repository
+          uses: actions/checkout@v3
+
+        - name: Docker Tags
+          id: meta
+          uses: docker/metadata-action@v4
+          with:
+            images: |
+              hicsail/comets-runner
+            tags: |
+              type=ref,event=branch
+              type=semver,pattern={{version}}
+              type=semver,pattern={{major}}
+              type=semver,pattern={{major}}.{{minor}}
+
+        - name: Login to Docker Hub
+          if: github.ref == 'refs/heads/main' || startsWith(github.ref, 'refs/tags/v')
+          uses: docker/login-action@v2
+          with:
+            username: ${{ secrets.DOCKERHUB_USERNAME }}
+            password: ${{ secrets.DOCKERHUB_TOKEN }}
+
+        - name: Build & Push Docker Build
+          uses: docker/build-push-action@v4
+          with:
+            push: ${{ github.event_name != 'pull_request' }}
+            context: ./packages/runner
+            file: ./packages/runner/Dockerfile
+            tags: ${{ steps.meta.outputs.tags }}
+            labels: ${{ steps.meta.outputs.labels }}
+            cache-from: type=gha,scope=gateway
+            cache-to: type=gha,mode=max,scope=gateway

packages/backend/.eslintrc.js

@@ -2,7 +2,7 @@ module.exports = {
   parser: '@typescript-eslint/parser',
   parserOptions: {
     project: 'tsconfig.json',
-    tsconfigRootDir : __dirname, 
+    tsconfigRootDir : __dirname,
     sourceType: 'module',
   },
   plugins: ['@typescript-eslint/eslint-plugin'],
@@ -21,5 +21,16 @@ module.exports = {
     '@typescript-eslint/explicit-function-return-type': 'off',
     '@typescript-eslint/explicit-module-boundary-types': 'off',
     '@typescript-eslint/no-explicit-any': 'off',
+    '@typescript-eslint/no-empty-interface': 'off',
+    '@typescript-eslint/no-non-null-assertion': 'off',
+    "no-unused-vars": "off",
+    "@typescript-eslint/no-unused-vars": [
+      "warn", // or "error"
+      {
+        "argsIgnorePattern": "^_",
+        "varsIgnorePattern": "^_",
+        "caughtErrorsIgnorePattern": "^_"
+      }
+    ]
   },
 };

packages/backend/.prettierrc

@@ -1,4 +1,5 @@
 {
   "singleQuote": true,
-  "trailingComma": "all"
-}
+  "trailingComma": "none",
+  "printWidth": 120
+}

packages/backend/package.json

@@ -8,12 +8,14 @@
   "scripts": {
     "prebuild": "rimraf dist",
     "build": "nest build",
-    "format": "prettier --write \"src/**/*.ts\" \"test/**/*.ts\"",
+    "format": "prettier \"src/**/*.ts\" \"test/**/*.ts\"",
+    "format:fix": "prettier --write \"src/**/*.ts\" \"test/**/*.ts\"",
     "start": "nest start",
     "start:dev": "nest start --watch",
     "start:debug": "nest start --debug --watch",
     "start:prod": "node dist/main",
-    "lint": "eslint \"{src,apps,libs,test}/**/*.ts\" --fix",
+    "lint:fix": "eslint \"{src,apps,libs,test}/**/*.ts\" --fix",
+    "lint": "eslint \"{src,apps,libs,test}/**/*.ts\"",
     "test": "jest",
     "test:watch": "jest --watch",
     "test:cov": "jest --coverage",

packages/backend/src/app.module.ts

@@ -12,7 +12,6 @@ import { ExpressAdapter } from '@bull-board/express';
 import { S3Module } from './s3/s3.module';
 import { EmailModule } from './email/email.module';
 
-
 @Module({
   imports: [
     GraphQLModule.forRoot<ApolloDriverConfig>({
@@ -49,6 +48,6 @@ import { EmailModule } from './email/email.module';
     JobModule,
     S3Module,
     EmailModule
-  ],
+  ]
 })
 export class AppModule {}

packages/backend/src/email/email.service.ts

@@ -21,7 +21,7 @@ export class EmailService {
       to: email,
       subject: 'Your COMETS SI simulation has been completed successfully',
       text: `Click here to view the results of your simulation: ${this.frontendURL}/results/${id}`
-    }
+    };
     await this.transporter.sendMail(mailOptions);
   }
 
@@ -39,7 +39,7 @@ export class EmailService {
       to: email,
       subject: 'COMETS Simulation Failed to Run',
       text: `Unfortunately your requested simulation has failed to run. We are looking into the issue now!`
-    }
+    };
     await this.transporter.sendMail(mailOptions);
   }
 
@@ -66,7 +66,7 @@ export class EmailService {
       to: this.internalEmail,
       subject: 'COMETS Simulation Failed',
       text: message
-    }
+    };
     await this.transporter.sendMail(mailOptions);
   }
 }

packages/backend/src/email/transport.provider.ts

@@ -2,7 +2,6 @@ import { Provider } from '@nestjs/common';
 import { ConfigService } from '@nestjs/config';
 import { Transporter, createTransport } from 'nodemailer';
 
-
 export const TRANSPORT_PROVIDER = 'TRANSPORT_PROVIDER';
 
 export const transportProvider: Provider<Transporter> = {

packages/backend/src/job/converter.service.ts

@@ -8,10 +8,8 @@ import {
 } from './comets-paramters.dto';
 import { LayoutType, SimulationRequest } from '../simulation/models/request.model';
 
-
 @Injectable()
 export class RequestConverter {
-
   private readonly GRID_SIZE = 61;
   private readonly PETRI_DISH_DIAMETER = 3.0;
 
@@ -23,7 +21,7 @@ export class RequestConverter {
       globalParams: await this.getGlobalParams(request),
       s3Folder: await this.getS3Folder(request),
       requestID: await this.getRequestID(request)
-    }
+    };
   }
 
   private async getLayoutParams(request: SimulationRequest): Promise<CometsLayoutParameters> {
@@ -39,7 +37,7 @@ export class RequestConverter {
       type: request.layoutParams.type,
       spaceWidth: spaceWidth,
       gridSize: gridSize
-    }
+    };
   }
 
   private async getMetaboliteParams(request: SimulationRequest): Promise<CometsMetaboliteParameters> {
@@ -48,15 +46,15 @@ export class RequestConverter {
       metaboliteAmount = request.layoutParams.volume * request.metaboliteParams.concentration;
     } else {
       const spaceWidth = this.PETRI_DISH_DIAMETER / this.GRID_SIZE;
-      const area = Math.PI * Math.pow(0.5 * this.PETRI_DISH_DIAMETER, 2)
-      metaboliteAmount = request.metaboliteParams.concentration * request.layoutParams.volume *
-                         Math.pow(spaceWidth, 2) / area;
+      const area = Math.PI * Math.pow(0.5 * this.PETRI_DISH_DIAMETER, 2);
+      metaboliteAmount =
+        (request.metaboliteParams.concentration * request.layoutParams.volume * Math.pow(spaceWidth, 2)) / area;
     }
 
     return {
       type: request.metaboliteParams.type,
       amount: metaboliteAmount
-    }
+    };
   }
 
   private async getModelParams(request: SimulationRequest): Promise<CometsModelParamters[]> {

packages/backend/src/job/job.service.ts

@@ -70,7 +70,8 @@ export class JobService {
     this.jobTemplate.spec.template.spec.restartPolicy = 'Never';
     this.jobTemplate.spec.backoffLimit = 0;
     this.jobTemplate.spec.template.spec.imagePullSecrets = [new V1LocalObjectReference()];
-    this.jobTemplate.spec.template.spec.imagePullSecrets![0].name = this.configService.getOrThrow<string>('runner.imagePullSecret')
+    this.jobTemplate.spec.template.spec.imagePullSecrets[0].name =
+      this.configService.getOrThrow<string>('runner.imagePullSecret');
   }
 
   async triggerJob(request: SimulationRequest): Promise<string> {
@@ -111,8 +112,14 @@ export class JobService {
   }
 
   async getPodLogs(jobName: string): Promise<string> {
-    const pods = await this.coreClient.listNamespacedPod(this.namespace,
-      undefined, undefined, undefined, undefined, `batch.kubernetes.io/job-name=${jobName}`);
+    const pods = await this.coreClient.listNamespacedPod(
+      this.namespace,
+      undefined,
+      undefined,
+      undefined,
+      undefined,
+      `batch.kubernetes.io/job-name=${jobName}`
+    );
     const podName = pods.body!.items[0].metadata!.name;
 
     const logs = await this.coreClient.readNamespacedPodLog(podName!, this.namespace);
@@ -154,6 +161,6 @@ export class JobService {
       `--default-v-max=${parameters.globalParams.defaultVMax}`,
       `--default-km=${parameters.globalParams.defaultKm}`,
       `--max-cycles=${parameters.globalParams.maxCycles}`
-    ]
+    ];
   }
 }