Merge pull request CCBR#115 from CCBR/iss-113

test: show that sif images are cached correctly

.github/workflows/main.yaml

@@ -17,7 +17,7 @@ jobs:
       - name: Dry-run pipeline
         run: |
           docker run -v $PWD:/opt2 -w /opt2 snakemake/snakemake:v5.24.2 \
-            python ./src/renee/__main__.py run \
+            python src/renee/__main__.py run \
               --input .tests/KO_S3.R1.fastq.gz .tests/KO_S3.R2.fastq.gz .tests/KO_S4.R1.fastq.gz .tests/KO_S4.R2.fastq.gz .tests/WT_S1.R1.fastq.gz .tests/WT_S1.R2.fastq.gz .tests/WT_S2.R1.fastq.gz .tests/WT_S2.R2.fastq.gz \
               --output output \
               --genome config/genomes/biowulf/hg38_30.json \
@@ -35,23 +35,34 @@ jobs:
     strategy:
       matrix:
         python-version: ["3.11"]
+        snakemake-version: ["7.32.3"]
     steps:
       - uses: actions/checkout@v4
-      - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v4
+      - uses: mamba-org/setup-micromamba@v1
         with:
-          python-version: ${{ matrix.python-version }}
-          cache: "pip"
-      - name: pip
-        run: |
-          python -m pip install --upgrade pip setuptools pytest
+          environment-name: test
+          cache-environment: true
+          condarc: |
+            channels:
+              - conda-forge
+              - bioconda
+          create-args: >-
+            python=${{ matrix.python-version }}
+            snakemake=${{ matrix.snakemake-version }}
+            setuptools
+            pip
+            pytest
       - name: check CLI basics
         run: |
           ./bin/renee --help
           ./bin/renee --version
+        shell: micromamba-shell {0}
       - name: Test
         run: |
           python -m pytest
+        env:
+          TMPDIR: ${{ runner.temp }}
+        shell: micromamba-shell {0}
 
   build-status: # https://github.com/orgs/community/discussions/4324#discussioncomment-3477871
     runs-on: ubuntu-latest

src/renee/__main__.py

@@ -812,7 +812,6 @@ def setup(sub_args, ifiles, repo_path, output_path):
         ),
         end="",
     )
-    # print(json.dumps(config, indent = 4, sort_keys=True))
     with open(os.path.join(output_path, "config.json"), "w") as fh:
         json.dump(config, fh, indent=4, sort_keys=True)
     print("Done!")

tests/test_cache.py

@@ -0,0 +1,48 @@
+import tempfile
+import json
+import os.path
+import subprocess
+
+renee_run = (
+    "src/renee/__main__.py run "
+    "--mode local --runmode init --dry-run "
+    "--input .tests/*.fastq.gz "
+    "--genome config/genomes/biowulf/hg38_30.json "
+)
+
+
+def run_in_temp(command_str):
+    with tempfile.TemporaryDirectory() as tmp_dir:
+        outdir = os.path.join(tmp_dir, "testout")
+        output = subprocess.run(
+            f"{command_str} --output {outdir}",
+            capture_output=True,
+            shell=True,
+            text=True,
+        )
+        if os.path.exists(os.path.join(outdir, "config.json")):
+            with open(os.path.join(outdir, "config.json"), "r") as infile:
+                config = json.load(infile)
+        else:
+            config = None
+    return output, config
+
+
+def test_cache_sif():
+    output, config = run_in_temp(f"{renee_run} --sif-cache tests/data/sifs/")
+    assertions = [
+        config["images"]["arriba"].endswith(
+            "tests/data/sifs/ccbr_arriba_2.0.0_v0.0.1.sif"
+        ),
+        "does not exist in singularity cache" in output.stderr,
+    ]
+    assert all(assertions)
+
+
+def test_cache_nosif():
+    output, config = run_in_temp(f"{renee_run}")
+    assertions = [
+        config["images"]["arriba"] == "docker://nciccbr/ccbr_arriba_2.0.0:v0.0.1",
+        "The singularity command has to be available" in output.stderr,
+    ]
+    assert all(assertions)

tests/test_cli.py

@@ -1,6 +1,12 @@
 import pytest
 import subprocess
-from src.renee.__main__ import exists
+
+renee_run = (
+    "src/renee/__main__.py run "
+    "--mode local --runmode init --dry-run "
+    "--input .tests/*.fastq.gz "
+    "--genome config/genomes/biowulf/hg38_30.json "
+)
 
 
 def test_help():
@@ -15,3 +21,12 @@ def test_version():
         "src/renee/__main__.py --version", capture_output=True, shell=True, text=True
     ).stdout
     assert "renee v" in output
+
+
+def test_run_error():
+    assert (
+        "the following arguments are required: --output"
+        in subprocess.run(
+            f"{renee_run}", capture_output=True, shell=True, text=True
+        ).stderr
+    )