Enable warn_unreachable mypy option
#17365
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mvdbeek
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lib/galaxy/tool_util/toolbox/base.py
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| @@ -758,7 +758,7 @@ def get_tool(self, tool_id, tool_version=None, get_all_versions=False, exact=Fal | |||
| def has_tool(self, tool_id: str, tool_version: Optional[str] = None, exact: bool = False): | |||
| return self.get_tool(tool_id, tool_version=tool_version, exact=exact) is not None | |||
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|
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| def is_missing_shed_tool(self, tool_id: str) -> bool: | |||
| def is_missing_shed_tool(self, tool_id: Optional[str]) -> bool: | |||
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In the only place from which this is called ( lib/galaxy/webapps/galaxy/services/workflows.py ), the tool_id passed is never None, so maybe keep the previous annotation and drop lines 763-765?
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step.tool_id can be None, I don't think this is safe
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We check that it's not None in https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/managers/workflows.py#L1954 ?
| args = [] | ||
| args = [RuntimeContext(job_args)] | ||
| kwargs: Dict[str, str] = {} | ||
| if RuntimeContext is not None: | ||
| args.append(RuntimeContext(job_args)) | ||
| else: | ||
| kwargs = job_args |
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I think the previous code should be restored with a # type: ignore[unreachable] added to this last line, as RuntimeContext can be None in the tool-util package if the cwl extra is not specified.
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I can do that, but tool parsing would fail in https://github.com/mvdbeek/galaxy/blob/c713b37c588bba50ad7d7897632e36bc16215e4d/lib/galaxy/tool_util/cwl/parser.py#L342 too ... idk if this partial support approach makes sense ?
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how about
diff --git a/lib/galaxy/tool_util/cwl/parser.py b/lib/galaxy/tool_util/cwl/parser.py
index 3207eea965..ac71393c61 100644
--- a/lib/galaxy/tool_util/cwl/parser.py
+++ b/lib/galaxy/tool_util/cwl/parser.py
@@ -293,6 +293,7 @@ class ExpressionToolProxy(CommandLineToolProxy):
class JobProxy:
def __init__(self, tool_proxy, input_dict, output_dict, job_directory):
+ assert RuntimeContext is not None, "cwltool is not installed, cannot run CWL jobs"
self._tool_proxy = tool_proxy
self._input_dict = input_dict
self._output_dict = output_dictinstead ?
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Sounds good for me. @jmchilton ?
Not going to do further work on upload1, so not fixing this.
mvdbeek
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Haven't fixed all cases, see mypy.ini.
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