tests: no more files written to the working directory.

Author: mr-c

.github/workflows/ci-tests.yml

@@ -69,6 +69,9 @@ jobs:
           path: .mypy_cache/${{ env.py-semver }}
           key: mypy-${{ env.py-semver }}
 
+      - name: make working directory read-only
+        run: chmod a-w .
+
       - name: Test with tox
         run: tox
 

tests/test_examples.py

@@ -1291,6 +1291,8 @@ def test_cache_relative_paths(tmp_path: Path, factor: str) -> None:
     commands = factor.split()
     commands.extend(
         [
+            "--out",
+            str(tmp_path / "out"),
             "--cachedir",
             cache_dir,
             get_data(f"tests/{test_file}"),
@@ -1306,6 +1308,8 @@ def test_cache_relative_paths(tmp_path: Path, factor: str) -> None:
     commands = factor.split()
     commands.extend(
         [
+            "--out",
+            str(tmp_path / "out2"),
             "--cachedir",
             cache_dir,
             get_data(f"tests/{test_file}"),
@@ -1324,6 +1328,8 @@ def test_cache_relative_paths(tmp_path: Path, factor: str) -> None:
 def test_write_summary(tmp_path: Path) -> None:
     """Test --write-summary."""
     commands = [
+        "--out",
+        str(tmp_path / "out1"),
         get_data("tests/wf/no-parameters-echo.cwl"),
     ]
     error_code, stdout, stderr = get_main_output(commands)
@@ -1332,6 +1338,8 @@ def test_write_summary(tmp_path: Path) -> None:
 
     final_output_path = str(tmp_path / "final-output.json")
     commands_no = [
+        "--out",
+        str(tmp_path / "out2"),
         "--write-summary",
         final_output_path,
         get_data("tests/wf/no-parameters-echo.cwl"),
@@ -1347,10 +1355,11 @@ def test_write_summary(tmp_path: Path) -> None:
 
 
 @needs_docker
-def test_compute_checksum() -> None:
+def test_compute_checksum(tmp_path: Path) -> None:
     runtime_context = RuntimeContext()
     runtime_context.compute_checksum = True
     runtime_context.use_container = False
+    runtime_context.outdir = str(tmp_path)
     factory = cwltool.factory.Factory(runtime_context=runtime_context)
     echo = factory.make(get_data("tests/wf/cat-tool.cwl"))
     output = echo(
@@ -1413,10 +1422,12 @@ def test_bad_stdout_expr_error() -> None:
 
 
 @needs_docker
-def test_stdin_with_id_preset() -> None:
+def test_stdin_with_id_preset(tmp_path: Path) -> None:
     """Confirm that a type: stdin with a preset id does not give an error."""
     error_code, _, stderr = get_main_output(
         [
+            "--out",
+            str(tmp_path),
             get_data("tests/wf/1590.cwl"),
             "--file1",
             get_data("tests/wf/whale.txt"),
@@ -1590,7 +1601,7 @@ def test_v1_0_arg_empty_prefix_separate_false() -> None:
 
 def test_scatter_output_filenames(tmp_path: Path) -> None:
     """Confirm that the final output is renamed correctly from identically named scatter outputs."""
-    cwd = Path.cwd()
+    cwd = tmp_path
     with working_directory(tmp_path):
         rtc = RuntimeContext()
         rtc.outdir = str(cwd)
@@ -1726,10 +1737,10 @@ def test_command_line_tool_class() -> None:
     assert str(expression_tool) == f"CommandLineTool: file://{tool_path}"
 
 
-def test_record_default_with_long() -> None:
+def test_record_default_with_long(tmp_path: Path) -> None:
     """Confirm that record defaults are respected."""
     tool_path = get_data("tests/wf/paramref_arguments_roundtrip.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)["same_record"]
     assert result["first"] == "y"

tests/test_iwdr.py

@@ -10,6 +10,8 @@
 
 from .util import get_data, get_main_output, needs_docker, needs_singularity
 
+import pytest
+
 
 def test_newline_in_entry() -> None:
     """Files in a InitialWorkingDirectory are created with a newline character."""
@@ -246,7 +248,9 @@ def test_iwdr_permutations_inplace(tmp_path_factory: Any) -> None:
 
 
 @needs_singularity
-def test_iwdr_permutations_singularity(tmp_path_factory: Any) -> None:
+def test_iwdr_permutations_singularity(
+    tmp_path_factory: pytest.TempPathFactory, monkeypatch: pytest.MonkeyPatch
+) -> None:
     misc = tmp_path_factory.mktemp("misc")
     fifth = misc / "fifth"
     fifth.mkdir()
@@ -269,6 +273,8 @@ def test_iwdr_permutations_singularity(tmp_path_factory: Any) -> None:
     twelfth = misc / "twelfth"
     twelfth.touch()
     outdir = str(tmp_path_factory.mktemp("outdir"))
+    singularity_dir = str(tmp_path_factory.mktemp("singularity"))
+    monkeypatch.setenv("CWL_SINGULARITY_CACHE", singularity_dir)
     err_code, stdout, _ = get_main_output(
         [
             "--outdir",
@@ -306,7 +312,9 @@ def test_iwdr_permutations_singularity(tmp_path_factory: Any) -> None:
 
 
 @needs_singularity
-def test_iwdr_permutations_singularity_inplace(tmp_path_factory: Any) -> None:
+def test_iwdr_permutations_singularity_inplace(
+    tmp_path_factory: pytest.TempPathFactory, monkeypatch: pytest.MonkeyPatch
+) -> None:
     """IWDR tests using --singularity and a forced InplaceUpdateRequirement."""
     misc = tmp_path_factory.mktemp("misc")
     fifth = misc / "fifth"
@@ -330,6 +338,8 @@ def test_iwdr_permutations_singularity_inplace(tmp_path_factory: Any) -> None:
     twelfth = misc / "twelfth"
     twelfth.touch()
     outdir = str(tmp_path_factory.mktemp("outdir"))
+    singularity_dir = str(tmp_path_factory.mktemp("singularity"))
+    monkeypatch.setenv("CWL_SINGULARITY_CACHE", singularity_dir)
     assert (
         main(
             [

tests/test_provenance.py

@@ -591,8 +591,8 @@ def check_prov(
 
 
 @pytest.fixture
-def research_object() -> Generator[ResearchObject, None, None]:
-    re_ob = ResearchObject(StdFsAccess(""))
+def research_object(tmp_path: Path) -> Generator[ResearchObject, None, None]:
+    re_ob = ResearchObject(StdFsAccess(str(tmp_path / "ro")), temp_prefix_ro=str(tmp_path / "tmp"))
     yield re_ob
     re_ob.close()
 

tests/test_singularity.py

@@ -5,6 +5,8 @@
 
 from cwltool.main import main
 
+import pytest
+
 from .util import (
     get_data,
     get_main_output,
@@ -58,7 +60,10 @@ def test_singularity_workflow(tmp_path: Path) -> None:
     assert error_code == 0
 
 
-def test_singularity_iwdr() -> None:
+def test_singularity_iwdr(tmp_path: Path, monkeypatch: pytest.MonkeyPatch) -> None:
+    singularity_dir = tmp_path / "singularity"
+    singularity_dir.mkdir()
+    monkeypatch.setenv("CWL_SINGULARITY_CACHE", str(singularity_dir))
     result_code = main(
         [
             "--singularity",

tests/test_subgraph.py

@@ -219,10 +219,12 @@ def test_single_process_packed_subwf_step(tmp_path: Path) -> None:
 
 
 @needs_docker
-def test_single_process_subwf_subwf_inline_step() -> None:
+def test_single_process_subwf_subwf_inline_step(tmp_path: Path) -> None:
     """Test --single-process on an inline sub-sub-workflow step."""
     err_code, stdout, stderr = get_main_output(
         [
+            "--outdir",
+            str(tmp_path),
             "--single-process",
             "step1/stepX/stepY",
             get_data("tests/subgraph/count-lines17-wf.cwl.json"),

tox.ini

@@ -11,7 +11,7 @@ envlist =
 skip_missing_interpreters = True
 
 [pytest]
-addopts=--ignore cwltool/schemas --basetemp ./tmp -n auto
+addopts=--ignore cwltool/schemas -n auto
 testpaths = tests
 
 [gh-actions]