Add workaround for snakemake#1550 in tests

The new auto `--default-resources` was causing test failures, so we
manually set the default mem_mb to 0.

Ran formatting with black

snakemake/dag.py

@@ -1476,12 +1476,12 @@ def handle_pipes_and_services(self):
             # All pipe groups should be contained within one user-defined group
             if len(user_groups) > 1:
                 raise WorkflowError(
-                        "An output file is marked as "
-                        "pipe or service, but consuming jobs "
-                        "are part of conflicting "
-                        "groups.",
-                        rule=job.rule,
-                    )
+                    "An output file is marked as "
+                    "pipe or service, but consuming jobs "
+                    "are part of conflicting "
+                    "groups.",
+                    rule=job.rule,
+                )
 
             if len(candidate_groups) > 1:
                 # Merge multiple pipe groups together

snakemake/executors/__init__.py

@@ -767,7 +767,6 @@ def get_resource_declarations(self, job):
         ]
         return format_cli_arg("--resources", resources)
 
-
     def get_python_executable(self):
         return sys.executable if self.assume_shared_fs else "python"
 

tests/tests.py

@@ -9,6 +9,8 @@
 import subprocess as sp
 from pathlib import Path
 
+from snakemake.resources import DefaultResources
+
 sys.path.insert(0, os.path.dirname(__file__))
 
 from .common import *
@@ -947,6 +949,7 @@ def test_group_jobs_resources(mocker):
         cores=6,
         resources={"typo": 23, "mem_mb": 60000},
         group_components={0: 5},
+        default_resources=DefaultResources(["mem_mb=0"]),
     )
     assert set(spy.spy_return.items()) == {
         ("_nodes", 1),
@@ -955,6 +958,7 @@ def test_group_jobs_resources(mocker):
         ("tmpdir", "/tmp"),
         ("mem_mb", 60000),
         ("fake_res", 400),
+        ("disk_mb", 2000),
     }
 
 
@@ -968,6 +972,7 @@ def test_group_jobs_resources_with_max_threads(mocker):
         resources={"mem_mb": 60000},
         max_threads=1,
         group_components={0: 5},
+        default_resources=DefaultResources(["mem_mb=0"]),
     )
     assert set(spy.spy_return.items()) == {
         ("_nodes", 1),
@@ -976,6 +981,7 @@ def test_group_jobs_resources_with_max_threads(mocker):
         ("tmpdir", "/tmp"),
         ("mem_mb", 60000),
         ("fake_res", 1200),
+        ("disk_mb", 3000),
     }
 
 
@@ -989,6 +995,7 @@ def test_group_jobs_resources_with_limited_resources(mocker):
         resources={"mem_mb": 10000},
         max_threads=1,
         group_components={0: 5},
+        default_resources=DefaultResources(["mem_mb=0"]),
     )
     assert set(spy.spy_return.items()) == {
         ("_nodes", 1),
@@ -997,8 +1004,10 @@ def test_group_jobs_resources_with_limited_resources(mocker):
         ("tmpdir", "/tmp"),
         ("mem_mb", 10000),
         ("fake_res", 400),
+        ("disk_mb", 1000),
     }
 
+
 @skip_on_windows
 def test_multiple_group_jobs_submit_ignoring_resource_constraints():
     tmp = run(
@@ -1011,13 +1020,15 @@ def test_multiple_group_jobs_submit_ignoring_resource_constraints():
         resources={"typo": 23, "mem_mb": 50000},
         group_components={0: 5, 1: 5},
         overwrite_groups={"a": 0, "a_1": 1, "b": 2, "c": 2},
+        default_resources=DefaultResources(["mem_mb=0"]),
         shouldfail=True,
     )
-    with (Path(tmp)/'qsub.log').open('r') as f:
+    with (Path(tmp) / "qsub.log").open("r") as f:
         lines = [l for l in f.readlines() if not l == "\n"]
     assert len(lines) == 2
     shutil.rmtree(tmp)
 
+
 @skip_on_windows
 def test_group_job_resources_with_pipe(mocker):
     spy = mocker.spy(GroupJob, "_calculate_resources")
@@ -1029,13 +1040,15 @@ def test_group_job_resources_with_pipe(mocker):
             "mem_mb": 60000,
         },
         group_components={0: 5},
+        default_resources=DefaultResources(["mem_mb=0"]),
     )
     assert set(spy.spy_return.items()) == {
         ("_nodes", 1),
         ("_cores", 4),
         ("runtime", 280),
         ("tmpdir", "/tmp"),
         ("mem_mb", 50000),
+        ("disk_mb", 1000),
     }
 
 
@@ -1050,6 +1063,7 @@ def test_group_job_resources_with_pipe_with_too_much_constraint():
         },
         group_components={0: 5},
         shouldfail=True,
+        default_resources=DefaultResources(["mem_mb=0"]),
     )