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Bump mypy from 1.13.0 to 1.14.0 #347

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merged 4 commits into from
Dec 25, 2024
Merged

Bump mypy from 1.13.0 to 1.14.0 #347

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ade03b4
Bump mypy from 1.13.0 to 1.14.0
dependabot[bot] Dec 23, 2024
cca605f
regenerate parsers using https://github.com/common-workflow-language/…
mr-c Dec 25, 2024
a179318
expression refactor: always set the ID for ExpressionTools
mr-c Dec 25, 2024
613102c
more type fixes
mr-c Dec 25, 2024
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5 changes: 4 additions & 1 deletion cwl_utils/cwl_v1_0_expression_refactor.py
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Original file line number Diff line number Diff line change
Expand Up @@ -4,6 +4,7 @@
"""CWL Expression refactoring tool for CWL v1.0 ."""
import copy
import hashlib
import uuid
from collections.abc import Mapping, MutableSequence, Sequence
from typing import Any, Optional, Union, cast

Expand Down Expand Up @@ -395,6 +396,7 @@
find_expressionLib(extra_processes) if extra_processes else None
)
return cwl.ExpressionTool(
id="_:" + str(uuid.uuid4()),
inputs=inputs,
outputs=outputs,
expression=expression,
Expand Down Expand Up @@ -1423,7 +1425,7 @@
new_clt_step = copy.copy(
step
) # a deepcopy would be convenient, but params2.cwl gives it problems
new_clt_step.id = cast(str, new_clt_step.id).split("#")[-1]
new_clt_step.id = new_clt_step.id.split("#")[-1]

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cwl_utils/cwl_v1_0_expression_refactor.py#L1428 

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new_clt_step.run = copy.copy(step.run)
new_clt_step.run.id = None
remove_JSReq(new_clt_step.run, skip_command_line1)
Expand Down Expand Up @@ -1741,6 +1743,7 @@
x for x in reqs if not isinstance(x, cwl.InitialWorkDirRequirement)
]
return cwl.ExpressionTool(
id="_:" + str(uuid.uuid4()),
inputs=inputs,
outputs=outputs,
expression=expression,
Expand Down
5 changes: 4 additions & 1 deletion cwl_utils/cwl_v1_1_expression_refactor.py
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Original file line number Diff line number Diff line change
Expand Up @@ -4,6 +4,7 @@
"""CWL Expression refactoring tool for CWL v1.1 ."""
import copy
import hashlib
import uuid
from collections.abc import Mapping, MutableSequence, Sequence
from typing import Any, Optional, Union, cast

Expand Down Expand Up @@ -393,6 +394,7 @@
find_expressionLib(extra_processes) if extra_processes else None
)
return cwl.ExpressionTool(
id="_:" + str(uuid.uuid4()),
inputs=inputs,
outputs=outputs,
expression=expression,
Expand Down Expand Up @@ -1423,7 +1425,7 @@
new_clt_step = copy.copy(
step
) # a deepcopy would be convenient, but params2.cwl gives it problems
new_clt_step.id = cast(str, new_clt_step.id).split("#")[-1]
new_clt_step.id = new_clt_step.id.split("#")[-1]

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cwl_utils/cwl_v1_1_expression_refactor.py#L1428 

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new_clt_step.run = copy.copy(step.run)
new_clt_step.run.id = None
remove_JSReq(new_clt_step.run, skip_command_line1)
Expand Down Expand Up @@ -1741,6 +1743,7 @@
x for x in reqs if not isinstance(x, cwl.InitialWorkDirRequirement)
]
return cwl.ExpressionTool(
id="_:" + str(uuid.uuid4()),
inputs=inputs,
outputs=outputs,
expression=expression,
Expand Down
7 changes: 5 additions & 2 deletions cwl_utils/cwl_v1_2_expression_refactor.py
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Original file line number Diff line number Diff line change
Expand Up @@ -4,6 +4,7 @@
"""CWL Expression refactoring tool for CWL v1.2 ."""
import copy
import hashlib
import uuid
from collections.abc import Mapping, MutableSequence, Sequence
from typing import Any, Optional, Union, cast

Expand Down Expand Up @@ -393,6 +394,7 @@
find_expressionLib(extra_processes) if extra_processes else None
)
return cwl.ExpressionTool(
id="_:" + str(uuid.uuid4()),
inputs=inputs,
outputs=outputs,
expression=expression,
Expand Down Expand Up @@ -694,7 +696,7 @@
)
target_type = copy.deepcopy(param2.type_)
if isinstance(target_type, cwl.OutputArraySchema):
target_type.name = None
target_type.name = ""

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cwl_utils/cwl_v1_2_expression_refactor.py#L699 

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target = cwl.WorkflowInputParameter(id=None, type_=target_type)
if not isinstance(param2.outputSource, list):
sources = param2.outputSource.split("#")[-1]
Expand Down Expand Up @@ -1518,7 +1520,7 @@
new_clt_step = copy.copy(
step
) # a deepcopy would be convenient, but params2.cwl gives it problems
new_clt_step.id = cast(str, new_clt_step.id).split("#")[-1]
new_clt_step.id = new_clt_step.id.split("#")[-1]

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cwl_utils/cwl_v1_2_expression_refactor.py#L1523 

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new_clt_step.run = copy.copy(step.run)
new_clt_step.run.id = None
remove_JSReq(new_clt_step.run, skip_command_line1)
Expand Down Expand Up @@ -1836,6 +1838,7 @@
x for x in reqs if not isinstance(x, cwl.InitialWorkDirRequirement)
]
return cwl.ExpressionTool(
id="_:" + str(uuid.uuid4()),
inputs=inputs,
outputs=outputs,
expression=expression,
Expand Down
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