fixes

snakemake · Sep 8, 2023 · b31a2b5 · b31a2b5
1 parent 22ec978
commit b31a2b5
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diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -55,9 +55,19 @@ jobs:
 
   testing:
     runs-on: ubuntu-latest
+    services:
+      mysql:
+        image: mysql:8.0
+        env:
+          MYSQL_ROOT_PASSWORD: root
+        ports:
+          - "8888:3306"
+        options: --health-cmd="mysqladmin ping" --health-interval=10s --health-timeout=5s --health-retries=3
     steps:
       - uses: actions/checkout@v3
 
+      - uses: koesterlab/setup-slurm-action@v1
+
       - name: Install poetry
         run: pipx install poetry
 

diff --git a/pyproject.toml b/pyproject.toml
@@ -15,7 +15,7 @@ black = "^23.7.0"
 flake8 = "^6.1.0"
 coverage = "^7.3.1"
 pytest = "^7.4.2"
-snakemake = "^7.32.3"
+snakemake = {git = "https://github.com/snakemake/snakemake.git", branch = "feat/api-rewrite"}
 
 [build-system]
 requires = ["poetry-core"]