simplify env handling

Author: mr-c

tests/test_pack.py

@@ -154,7 +154,7 @@ def test_packed_workflow_execution(wf_path, job_path, namespaced, tmpdir):
     packed_output = StringIO()
 
     normal_params = ['--outdir', str(tmpdir), get_data(wf_path), get_data(job_path)]
-    packed_params = ['--outdir', str(tmpdir), '--debug', get_data(wf_packed_path), get_data(job_path)]
+    packed_params = ['--outdir', str(tmpdir), '--debug', wf_packed_path, get_data(job_path)]
 
     assert main(normal_params, stdout=normal_output) == 0
     assert main(packed_params, stdout=packed_output) == 0

tests/test_singularity.py

@@ -1,4 +1,5 @@
 import sys
+import copy
 import os
 import pytest
 
@@ -16,34 +17,17 @@
 
 @needs_singularity
 def test_singularity_pullfolder(tmp_path):
-
-    if "SINGULARITY_PULLFOLDER" in os.environ:
-        del os.environ["SINGULARITY_PULLFOLDER"]
-        workdir = tmp_path / "working_dir_new"
-        workdir.mkdir()
-        os.chdir(str(workdir))
-        pullfolder = tmp_path / "pull_folder"
-        pullfolder.mkdir()
-        os.environ["SINGULARITY_PULLFOLDER"] = str(pullfolder)
-        if "SINGULARITY_PULLFOLDER" in os.environ:
-            result_code, stdout, stderr = get_main_output(
-                ['--singularity', get_data("tests/sing_pullfolder_test.cwl"), "--message", "hello"])
-            assert result_code == 0
-        else:
-            assert result_code != 0
-    else:
-        workdir = tmp_path / "working_dir_new"
-        workdir.mkdir()
-        os.chdir(str(workdir))
-        pullfolder = tmp_path / "pullfolder"
-        pullfolder.mkdir()
-        os.environ["SINGULARITY_PULLFOLDER"] = str(pullfolder)
-        if "SINGULARITY_PULLFOLDER" in os.environ:
-            result_code, stdout, stderr = get_main_output(
-                ['--singularity', get_data("tests/sing_pullfolder_test.cwl"), "--message", "hello"])
-            assert result_code == 0
-        else:
-            assert result_code != 0
+    workdir = tmp_path / "working_dir_new"
+    workdir.mkdir()
+    os.chdir(str(workdir))
+    pullfolder = tmp_path / "pullfolder"
+    pullfolder.mkdir()
+    env = copy.deepcopy(os.environ)
+    env["SINGULARITY_PULLFOLDER"] = str(pullfolder)
+    result_code, stdout, stderr = get_main_output(
+        ['--singularity', get_data("tests/sing_pullfolder_test.cwl"), "--message", "hello"], env=env)
+    assert result_code == 0
+    # TODO, confirm that the image is in the pullfolder
 
 @needs_singularity
 def test_singularity_workflow(tmpdir):

tests/util.py

@@ -64,10 +64,10 @@ def get_data(filename):
     reason="Running this test on MS Windows requires the docker executable "
     "on the system path.")
 
-def get_main_output(args):
+def get_main_output(args, env=None):
     process = subprocess.Popen(
         [sys.executable, "-m", "cwltool"] + args,
-        stdout=subprocess.PIPE, stderr=subprocess.PIPE)
+        stdout=subprocess.PIPE, stderr=subprocess.PIPE, env=env)
 
     stdout, stderr = process.communicate()
     return process.returncode, stdout.decode(), stderr.decode()