Merge pull request #22 from percyfal/fix-slurm-utils

Update test architecture

.github/workflows/slurm.yaml

@@ -1,6 +1,6 @@
 name: Test SnakemakeProfiles/slurm
 env:
-  SNAKEMAKE_IMAGE: quay.io/biocontainers/snakemake:7.3.2--hdfd78af_0
+  SNAKEMAKE_IMAGE: quay.io/biocontainers/snakemake:7.30.1--hdfd78af_0
   SLURM_IMAGE: giovtorres/docker-centos7-slurm:20.11.8
   DOCKER_COMPOSE: tests/docker-compose.yaml
 
@@ -12,17 +12,21 @@ jobs:
     runs-on: ubuntu-latest
     timeout-minutes: 30
     steps:
-      - uses: actions/checkout@v2
+      - name: Checkout repository
+        uses: actions/checkout@v3
+
       - run: mkdir -p ~/image-cache
-      - name: cache-conda
-        uses: actions/cache@v2
+
+      - name: cache conda environment
+        uses: actions/cache@v3
         env:
           CACHE_NUMBER: 0
         with:
           path: ~/conda_pkgs_dir
-          key: ${{ runner.os }}-conda-${{ env.CACHE_NUMBER }}-${{ hashFiles('test-environment.yml') }}
+          key: ${{ runner.os }}-conda-${{ env.CACHE_NUMBER }}-${{ hashFiles('conda-linux-64.lock') }}
 
-      - uses: actions/cache@v2
+      - name: cache images
+        uses: actions/cache@v3
         id: cache-images
         env:
           CACHE_NUMBER: 0
@@ -33,10 +37,8 @@ jobs:
       - name: install miniconda
         uses: conda-incubator/setup-miniconda@v2
         with:
-          mamba-version: "*"
-          channels: conda-forge,bioconda,default
-          channel-priority: true
-          environment-file: test-environment.yml
+          miniconda-version: "latest"
+          environment-file: conda-linux-64.lock
           use-only-tar-bz2: true
 
       - name: docker swarm init

pytest.ini

@@ -0,0 +1,2 @@
+[pytest]
+addopts = --keep-baked-projects -v -s

test-environment.yml

@@ -15,4 +15,4 @@ dependencies:
   - pyflakes
   - snakemake
   - urllib3
-  - cryptography <=37.0.0
+  - cryptography

tests/deploystack.sh

@@ -6,7 +6,7 @@
 DOCKER_COMPOSE=${DOCKER_COMPOSE:=docker-compose.yaml}
 
 # Images
-SNAKEMAKE_IMAGE=${SNAKEMAKE_IMAGE:=quay.io/biocontainers/snakemake:7.3.2--hdfd78af_0}
+SNAKEMAKE_IMAGE=${SNAKEMAKE_IMAGE:=quay.io/biocontainers/snakemake:7.30.1--hdfd78af_0}
 SLURM_IMAGE=${SLURM_IMAGE:=giovtorres/docker-centos7-slurm:20.11.8}
 
 docker pull $SNAKEMAKE_IMAGE

tests/docker-compose.yaml

@@ -1,7 +1,7 @@
 version: '3'
 services:
   snakemake:
-    image: quay.io/biocontainers/snakemake:7.3.2--hdfd78af_0
+    image: quay.io/biocontainers/snakemake:7.30.1--hdfd78af_0
     hostname: slurmctl
     command: /bin/bash
     deploy:

tests/test_cookie.py

@@ -1,6 +1,7 @@
 #!/usr/bin/env python3
 import sys
 import pytest
+from unittest.mock import patch
 
 
 @pytest.mark.parametrize("sidecar", ["yes", "no"])
@@ -20,24 +21,38 @@ def test_bake_project(cookies, sidecar):
 
 def test_cookiecutter(cookies, monkeypatch):
     result = cookies.bake(template=str(pytest.cookie_template))
-    monkeypatch.syspath_prepend(str(result.project_path))
-    from CookieCutter import CookieCutter
-    assert CookieCutter.SBATCH_DEFAULTS == ""
-    assert CookieCutter.CLUSTER_NAME == ""
-    assert CookieCutter.CLUSTER_CONFIG == ""
-    assert CookieCutter.get_cluster_option() == ""
-    sys.modules.pop("CookieCutter")
+    assert result.exit_code == 0
+    assert result.exception is None
+
+    assert result.project_path.name == "slurm"
+    assert result.project_path.is_dir()
+    with patch.dict(sys.modules):
+        if "CookieCutter" in sys.modules:
+            del sys.modules["CookieCutter"]
+        monkeypatch.syspath_prepend(str(result.project_path))
+        from CookieCutter import CookieCutter
+        assert CookieCutter.SBATCH_DEFAULTS == ""
+        assert CookieCutter.CLUSTER_NAME == ""
+        assert CookieCutter.CLUSTER_CONFIG == ""
+        assert CookieCutter.get_cluster_option() == ""
 
 
 def test_cookiecutter_extra_context(cookies, monkeypatch):
     result = cookies.bake(template=str(pytest.cookie_template),
                           extra_context={"sbatch_defaults": "account=foo",
                                          "cluster_name": "dusk",
                                          "cluster_config": "slurm.yaml"})
-    monkeypatch.syspath_prepend(str(result.project_path))
-    from CookieCutter import CookieCutter
-    assert CookieCutter.SBATCH_DEFAULTS == "account=foo"
-    assert CookieCutter.CLUSTER_NAME == "dusk"
-    assert CookieCutter.CLUSTER_CONFIG == "slurm.yaml"
-    assert CookieCutter.get_cluster_option() == "--cluster=dusk"
-    sys.modules.pop("CookieCutter")
+    assert result.exit_code == 0
+    assert result.exception is None
+
+    assert result.project_path.name == "slurm"
+    assert result.project_path.is_dir()
+    with patch.dict(sys.modules):
+        if "CookieCutter" in sys.modules:
+            del sys.modules["CookieCutter"]
+        monkeypatch.syspath_prepend(str(result.project_path))
+        from CookieCutter import CookieCutter
+        assert CookieCutter.SBATCH_DEFAULTS == "account=foo"
+        assert CookieCutter.CLUSTER_NAME == "dusk"
+        assert CookieCutter.CLUSTER_CONFIG == "slurm.yaml"
+        assert CookieCutter.get_cluster_option() == "--cluster=dusk"