less random files left over after tests

Author: mr-c

tests/test_cuda.py

@@ -1,3 +1,5 @@
+from unittest.mock import MagicMock
+
 import mock
 import pytest
 from schema_salad.avro import schema
@@ -17,8 +19,6 @@
 
 from .util import get_data, needs_docker, needs_singularity_3_or_newer
 
-from unittest.mock import MagicMock
-
 cuda_version = cuda_version_and_device_count()
 
 

tests/test_dependencies.py

@@ -18,20 +18,22 @@
 
 @needs_docker
 @pytest.mark.skipif(not deps, reason="galaxy-tool-util is not installed")
-def test_biocontainers() -> None:
+def test_biocontainers(tmp_path: Path) -> None:
     wflow = get_data("tests/seqtk_seq.cwl")
     job = get_data("tests/seqtk_seq_job.json")
-    error_code, _, _ = get_main_output(["--beta-use-biocontainers", wflow, job])
+    error_code, _, _ = get_main_output(
+        ["--outdir", str(tmp_path), "--beta-use-biocontainers", wflow, job]
+    )
 
     assert error_code == 0
 
 
 @pytest.mark.skipif(not deps, reason="galaxy-tool-util is not installed")
-def test_bioconda() -> None:
+def test_bioconda(tmp_path: Path) -> None:
     wflow = get_data("tests/seqtk_seq.cwl")
     job = get_data("tests/seqtk_seq_job.json")
     error_code, _, stderr = get_main_output(
-        ["--beta-conda-dependencies", "--debug", wflow, job]
+        ["--outdir", str(tmp_path), "--beta-conda-dependencies", "--debug", wflow, job]
     )
 
     assert error_code == 0, stderr

tests/test_docker.py

@@ -73,12 +73,14 @@ def test_docker_file_mount() -> None:
 
 
 @needs_docker
-def test_docker_strict_cpu_limit() -> None:
+def test_docker_strict_cpu_limit(tmp_path: Path) -> None:
     result_code, stdout, stderr = get_main_output(
         [
             "--strict-cpu-limit",
             "--default-container",
             "docker.io/debian:stable-slim",
+            "--outdir",
+            str(tmp_path),
             get_data("tests/wf/cores_float.cwl"),
         ]
     )
@@ -88,12 +90,14 @@ def test_docker_strict_cpu_limit() -> None:
 
 
 @needs_docker
-def test_docker_strict_memory_limit() -> None:
+def test_docker_strict_memory_limit(tmp_path: Path) -> None:
     result_code, stdout, stderr = get_main_output(
         [
             "--strict-memory-limit",
             "--default-container",
             "docker.io/debian:stable-slim",
+            "--outdir",
+            str(tmp_path),
             get_data("tests/wf/storage_float.cwl"),
         ]
     )
@@ -103,11 +107,13 @@ def test_docker_strict_memory_limit() -> None:
 
 
 @needs_docker
-def test_docker_strict_cpu_limit_warning() -> None:
+def test_docker_strict_cpu_limit_warning(tmp_path: Path) -> None:
     result_code, stdout, stderr = get_main_output(
         [
             "--default-container",
             "docker.io/debian:stable-slim",
+            "--outdir",
+            str(tmp_path),
             get_data("tests/wf/cores_float.cwl"),
         ]
     )
@@ -117,11 +123,13 @@ def test_docker_strict_cpu_limit_warning() -> None:
 
 
 @needs_docker
-def test_docker_strict_memory_limit_warning() -> None:
+def test_docker_strict_memory_limit_warning(tmp_path: Path) -> None:
     result_code, stdout, stderr = get_main_output(
         [
             "--default-container",
             "docker.io/debian:stable-slim",
+            "--outdir",
+            str(tmp_path),
             get_data("tests/wf/storage_float.cwl"),
         ]
     )

tests/test_examples.py

@@ -1188,7 +1188,7 @@ def test_cid_file_w_prefix(tmp_path: Path, factor: str) -> None:
 
 @needs_docker
 @pytest.mark.parametrize("factor", test_factors)
-def test_secondary_files_v1_1(factor: str) -> None:
+def test_secondary_files_v1_1(factor: str, tmp_path: Path) -> None:
     test_file = "secondary-files.cwl"
     test_job_file = "secondary-files-job.yml"
     try:
@@ -1197,14 +1197,16 @@ def test_secondary_files_v1_1(factor: str) -> None:
         commands.extend(
             [
                 "--debug",
+                "--outdir",
+                str(tmp_path),
                 get_data(os.path.join("tests", test_file)),
                 get_data(os.path.join("tests", test_job_file)),
             ]
         )
         error_code, _, stderr = get_main_output(commands)
     finally:
         # 664 in octal, '-rw-rw-r--'
-        assert stat.S_IMODE(os.stat("lsout").st_mode) == 436
+        assert stat.S_IMODE(os.stat(tmp_path / "lsout").st_mode) == 436
         os.umask(old_umask)  # revert back to original umask
     stderr = re.sub(r"\s\s+", " ", stderr)
     assert "completed success" in stderr
@@ -1213,13 +1215,15 @@ def test_secondary_files_v1_1(factor: str) -> None:
 
 @needs_docker
 @pytest.mark.parametrize("factor", test_factors)
-def test_secondary_files_bad_v1_1(factor: str) -> None:
+def test_secondary_files_bad_v1_1(factor: str, tmp_path: Path) -> None:
     """Affirm the correct error message for a bad secondaryFiles expression."""
     test_file = "secondary-files-bad.cwl"
     test_job_file = "secondary-files-job.yml"
     commands = factor.split()
     commands.extend(
         [
+            "--outdir",
+            str(tmp_path),
             get_data(os.path.join("tests", test_file)),
             get_data(os.path.join("tests", test_job_file)),
         ]
@@ -1706,10 +1710,10 @@ def test_record_default_with_long() -> None:
     )
 
 
-def test_record_outputeval() -> None:
+def test_record_outputeval(tmp_path: Path) -> None:
     """Confirm that record types can be populated from outputEval."""
     tool_path = get_data("tests/wf/record_outputeval.cwl")
-    err_code, stdout, stderr = get_main_output([tool_path])
+    err_code, stdout, stderr = get_main_output(["--outdir", str(tmp_path), tool_path])
     assert err_code == 0
     result = json.loads(stdout)["references"]
     assert "genome_fa" in result

tests/test_procgenerator.py

@@ -1,5 +1,6 @@
 """ProcessGenerator related tests."""
 
+from pathlib import Path
 
 import pytest
 
@@ -8,21 +9,34 @@
 from .util import get_data
 
 
-def test_missing_enable_ext(monkeypatch: pytest.MonkeyPatch) -> None:
+def test_missing_enable_ext(monkeypatch: pytest.MonkeyPatch, tmp_path: Path) -> None:
     """Test missing enable-ext option fails.
 
     Check that a workflow that needs `--enable-ext` and
     `--enable-dev` fails without those options and passes with them.
     """
     monkeypatch.delenv("CWLTOOL_OPTIONS", raising=False)
-    assert main([get_data("tests/wf/generator/zing.cwl"), "--zing", "zipper"]) == 1
+    assert (
+        main(
+            [
+                "--outdir",
+                str(tmp_path),
+                get_data("tests/wf/generator/zing.cwl"),
+                "--zing",
+                "zipper",
+            ]
+        )
+        == 1
+    )
 
     assert (
         main(
             [
                 "--debug",
                 "--enable-ext",
                 "--enable-dev",
+                "--outdir",
+                str(tmp_path),
                 get_data("tests/wf/generator/zing.cwl"),
                 "--zing",
                 "zipper",
@@ -32,4 +46,15 @@ def test_missing_enable_ext(monkeypatch: pytest.MonkeyPatch) -> None:
     )
 
     monkeypatch.setenv("CWLTOOL_OPTIONS", "--enable-ext --enable-dev")
-    assert main([get_data("tests/wf/generator/zing.cwl"), "--zing", "zipper"]) == 0
+    assert (
+        main(
+            [
+                "--outdir",
+                str(tmp_path),
+                get_data("tests/wf/generator/zing.cwl"),
+                "--zing",
+                "zipper",
+            ]
+        )
+        == 0
+    )

tests/test_relocate.py

@@ -13,9 +13,9 @@
 
 
 @needs_docker
-def test_for_910() -> None:
-    assert main([get_data("tests/wf/910.cwl")]) == 0
-    assert main([get_data("tests/wf/910.cwl")]) == 0
+def test_for_910(tmp_path: Path) -> None:
+    assert main(["--outdir", str(tmp_path), get_data("tests/wf/910.cwl")]) == 0
+    assert main(["--outdir", str(tmp_path), get_data("tests/wf/910.cwl")]) == 0
 
 
 @needs_docker