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software dependencies: allow newer versions of galaxy-tool-util
Skip the known broken versions (23.0.1 - 23.0.5)
1 parent 3d61ffb commit 4337bee

6 files changed

+13
-7
lines changed

cwltool/software_requirements.py

Lines changed: 3 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -12,6 +12,7 @@
1212
import string
1313
from typing import (
1414
TYPE_CHECKING,
15+
Any,
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Dict,
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List,
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MutableMapping,
@@ -109,7 +110,7 @@ def build_job_script(self, builder: "Builder", command: List[str]) -> str:
109110

110111
def get_dependencies(builder: HasReqsHints) -> ToolRequirements:
111112
(software_requirement, _) = builder.get_requirement("SoftwareRequirement")
112-
dependencies: List["ToolRequirement"] = []
113+
dependencies: List[Union["ToolRequirement", Dict[str, Any]]] = []
113114
if software_requirement and software_requirement.get("packages"):
114115
packages = cast(
115116
MutableSequence[MutableMapping[str, Union[str, MutableSequence[str]]]],
@@ -158,7 +159,7 @@ def get_container_from_software_requirements(
158159
[DOCKER_CONTAINER_TYPE], tool_info
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)
160161
if container_description:
161-
return cast(Optional[str], container_description.identifier)
162+
return container_description.identifier
162163

163164
return None
164165

mypy-requirements.txt

Lines changed: 2 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -5,3 +5,5 @@ types-requests
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types-setuptools
66
types-psutil
77
types-mock
8+
galaxy-tool-util>=22.1.2,<23.2,!=23.0.1,!=23.0.2,!=23.0.3,!=23.0.4,!=23.0.5
9+
galaxy-util<23.2

pyproject.toml

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -8,8 +8,8 @@ requires = [
88
"importlib_resources>=1.4", # equivalent to Python 3.9
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"ruamel.yaml>=0.16.0,<0.18",
1010
"schema-salad>=8.4.20230426093816,<9",
11-
"packaging<22",
1211
"cwl-utils>=0.19",
12+
"galaxy-tool-util>=22.1.2,<23.2,!=23.0.1,!=23.0.2,!=23.0.3,!=23.0.4,!=23.0.5",
1313
"toml",
1414
"argcomplete>=1.12.0",
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]

setup.py

Lines changed: 4 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -117,7 +117,10 @@
117117
"cwl-utils >= 0.22",
118118
],
119119
extras_require={
120-
"deps": ["galaxy-tool-util >= 22.1.2, <23", "galaxy-util <23"],
120+
"deps": [
121+
"galaxy-tool-util>=22.1.2,<23.2,!=23.0.1,!=23.0.2,!=23.0.3,!=23.0.4,!=23.0.5",
122+
"galaxy-util <23.2",
123+
],
121124
},
122125
python_requires=">=3.8, <4",
123126
use_scm_version=True,

test-requirements.txt

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -7,5 +7,5 @@ pytest-mock>=1.10.0
77
pytest-cov
88
arcp>=0.2.0
99
-rrequirements.txt
10-
galaxy-tool-util>=22.1.2,<23
11-
galaxy-util<23
10+
galaxy-tool-util>=22.1.2,<23.2,!=23.0.1,!=23.0.2,!=23.0.3,!=23.0.4,!=23.0.5
11+
galaxy-util<23.2

tests/test_dependencies.py

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -17,7 +17,7 @@
1717

1818
deps: Optional[ModuleType] = None
1919
try:
20-
from galaxy.tool_util import deps # type: ignore[no-redef]
20+
from galaxy.tool_util import deps
2121
except ImportError:
2222
pass
2323

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