From a0e60804eadd37adcf4a8424c808e206e04ff95b Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Mon, 13 Nov 2023 07:37:47 +0000
Subject: [PATCH 1/2] Bump mypy from 1.6.1 to 1.7.1

Bumps [mypy](https://github.com/python/mypy) from 1.6.1 to 1.7.1.
- [Changelog](https://github.com/python/mypy/blob/master/CHANGELOG.md)
- [Commits](https://github.com/python/mypy/compare/v1.6.1...v1.7.1)

---
updated-dependencies:
- dependency-name: mypy
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 mypy-requirements.txt | 2 +-
 pyproject.toml        | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/mypy-requirements.txt b/mypy-requirements.txt
index 3be7ea1c9..b9a1904a6 100644
--- a/mypy-requirements.txt
+++ b/mypy-requirements.txt
@@ -1,4 +1,4 @@
-mypy==1.6.1  # also update pyproject.toml
+mypy==1.7.1  # also update pyproject.toml
 ruamel.yaml>=0.16.0,<0.19
 cwl-utils>=0.22,!=0.30
 types-requests
diff --git a/pyproject.toml b/pyproject.toml
index 3a787209e..7729cbc57 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -2,7 +2,7 @@
 requires = [
     "setuptools>=45",
     "setuptools_scm[toml]>=8.0.4,<9",
-    "mypy==1.6.0",  # also update mypy-requirements.txt
+    "mypy==1.7.1",  # also update mypy-requirements.txt
     "types-requests",
     "types-psutil",
     "importlib_resources>=1.4",  # equivalent to Python 3.9

From a366a0727d6953b52ab8678e605d9eb81c765e97 Mon Sep 17 00:00:00 2001
From: "Michael R. Crusoe" <michael.crusoe@gmail.com>
Date: Mon, 13 Nov 2023 10:15:46 +0100
Subject: [PATCH 2/2] type updates for mypy 1.7.x

---
 cwltool/job.py                     | 10 ++++++----
 mypy.ini                           |  1 -
 tests/test_singularity_versions.py |  2 +-
 3 files changed, 7 insertions(+), 6 deletions(-)

diff --git a/cwltool/job.py b/cwltool/job.py
index d1950154b..4011641cd 100644
--- a/cwltool/job.py
+++ b/cwltool/job.py
@@ -66,6 +66,11 @@
     from .cwlprov.provenance_profile import (
         ProvenanceProfile,  # pylint: disable=unused-import
     )
+
+    CollectOutputsType = Union[
+        Callable[[str, int], CWLObjectType], functools.partial[CWLObjectType]
+    ]
+
 needs_shell_quoting_re = re.compile(r"""(^$|[\s|&;()<>\'"$@])""")
 
 FORCE_SHELLED_POPEN = os.getenv("CWLTOOL_FORCE_SHELL_POPEN", "0") == "1"
@@ -112,9 +117,6 @@ def neverquote(string: str, pos: int = 0, endpos: int = 0) -> Optional[Match[str
     return None
 
 
-CollectOutputsType = Union[Callable[[str, int], CWLObjectType], functools.partial]
-
-
 class JobBase(HasReqsHints, metaclass=ABCMeta):
     def __init__(
         self,
@@ -144,7 +146,7 @@ def __init__(
         self.generatemapper: Optional[PathMapper] = None
 
         # set in CommandLineTool.job(i)
-        self.collect_outputs = cast(CollectOutputsType, None)
+        self.collect_outputs = cast("CollectOutputsType", None)
         self.output_callback: Optional[OutputCallbackType] = None
         self.outdir = ""
         self.tmpdir = ""
diff --git a/mypy.ini b/mypy.ini
index b99f97b82..bac992869 100644
--- a/mypy.ini
+++ b/mypy.ini
@@ -5,7 +5,6 @@ show_column_numbers = true
 show_error_codes = true
 pretty = true
 warn_unreachable = True
-new_type_inference = True
 
 [mypy-galaxy.tool_util.*]
 ignore_missing_imports = True
diff --git a/tests/test_singularity_versions.py b/tests/test_singularity_versions.py
index 61b16177b..f9e841706 100644
--- a/tests/test_singularity_versions.py
+++ b/tests/test_singularity_versions.py
@@ -21,7 +21,7 @@ def reset_singularity_version_cache() -> None:
 def set_dummy_check_output(name: str, version: str) -> None:
     """Mock out subprocess.check_output."""
     cwltool.singularity.check_output = (  # type: ignore[attr-defined]
-        lambda c, text: name + " version " + version
+        lambda c, text: name + " version " + version  # type: ignore[assignment]
     )