Merge pull request #7 from snakemake/feat--refactor

feat: refactor

Author: jakevc

.github/workflows/ci_mocked_api.yml

@@ -9,6 +9,10 @@ on:
 env:
   PYTHON_VERSION: 3.11
 
+permissions:
+  id-token: write
+  contents: read
+
 jobs:
   formatting:
     runs-on: ubuntu-latest
@@ -84,10 +88,37 @@ jobs:
           python-version: ${{ env.PYTHON_VERSION }}
           cache: poetry
 
+      - name: Set up Docker Compose
+        run: |
+          sudo apt-get update
+          sudo apt-get install docker-compose
+      - name: Start MinIO service
+        run: docker-compose -f tests/docker-compose.yml up -d
+
+      - name: Install MinIO Client CLI
+        run: |
+          curl -O https://dl.min.io/client/mc/release/linux-amd64/mc
+          chmod +x mc
+          sudo mv mc /usr/local/bin/
+      - name: Configure MinIO client
+        run: |
+          mc alias set minio http://localhost:9000 minio minio123
+
       - name: Install dependencies
         run: poetry install
 
+      - name: Configure AWS Credentials
+        uses: aws-actions/configure-aws-credentials@v4
+        with:
+          aws-region: "${{ secrets.SNAKEMAKE_AWS_BATCH_REGION }}"
+          role-to-assume: "${{ secrets.GH_AWS_ROLE_ARN }}"
+          role-session-name: "GitHubActions"
+
       - name: Run pytest
+        env:
+          SNAKEMAKE_AWS_BATCH_REGION: "${{ secrets.SNAKEMAKE_AWS_BATCH_REGION }}"
+          SNAKEMAKE_AWS_BATCH_JOB_QUEUE: "${{ secrets.SNAKEMAKE_AWS_BATCH_JOB_QUEUE }}"
+          SNAKEMAKE_AWS_BATCH_JOB_ROLE: "${{ secrets.SNAKEMAKE_AWS_BATCH_JOB_ROLE }}"
         run: poetry run coverage run -m pytest tests/tests_mocked_api.py -v
 
       - name: Run Coverage

.github/workflows/ci_true_api.yml

@@ -6,6 +6,10 @@ on:
 env:
   PYTHON_VERSION: "3.11"
 
+permissions:
+  id-token: write
+  contents: read
+
 jobs:
   testing-true-api:
     runs-on: ubuntu-latest
@@ -30,6 +34,17 @@ jobs:
       - name: Install Dependencies using Poetry
         run: poetry install
 
+      - name: Configure AWS Credentials
+        uses: aws-actions/configure-aws-credentials@v4
+        with:
+          aws-region: "${{ secrets.SNAKEMAKE_AWS_BATCH_REGION }}"
+          role-to-assume: "${{ secrets.GH_AWS_ROLE_ARN }}"
+          role-session-name: "GitHubActions"
+
       - name: Run pytest
+        env:
+          SNAKEMAKE_AWS_BATCH_REGION: "${{ secrets.SNAKEMAKE_AWS_BATCH_REGION }}"
+          SNAKEMAKE_AWS_BATCH_JOB_QUEUE: "${{ secrets.SNAKEMAKE_AWS_BATCH_JOB_QUEUE }}"
+          SNAKEMAKE_AWS_BATCH_JOB_ROLE: "${{ secrets.SNAKEMAKE_AWS_BATCH_JOB_ROLE }}"
         run: 
           poetry run pytest tests/tests_true_api.py -v

.gitignore

@@ -159,4 +159,7 @@ cython_debug/
 #  option (not recommended) you can uncomment the following to ignore the entire idea folder.
 #.idea/
 
-poetry.lock
+poetry.lock
+
+.terraform*
+terraform.tfstate*

.vscode/settings.json

@@ -0,0 +1,9 @@
+{
+    "black-formatter.interpreter": [
+        "./.venv/bin/python"
+    ],
+    "flake8.interpreter": [
+        "./.venv/bin/python"
+    ],
+    "files.saveConflictResolution": "overwriteFileOnDisk"
+}

pyproject.toml

@@ -10,9 +10,9 @@ keywords = ["snakemake", "plugin", "executor", "aws-batch"]
 
 [tool.poetry.dependencies]
 python = "^3.11"
-snakemake-interface-common = "^1.15.0"
-snakemake-interface-executor-plugins = "^9.0.0"
-boto3 = "^1.33.11"
+snakemake-interface-common = "^1.17.4"
+snakemake-interface-executor-plugins = "^9.3.2"
+boto3 = "^1.36.5"
 
 [tool.poetry.group.dev.dependencies]
 black = "^23.11.0"