Merge branch 'main' into shm-size#1821

.git-blame-ignore-revs

@@ -6,3 +6,6 @@
 
 # upgrade to black 23.1, longer lines (100)
 7fe8c0739b0515d00daabc7db87bc5fad926d345
+
+# upgrade to black 24
+80c9ec01b4602fc51ac1f53744f98df8baba3c31

cwltool/builder.py

@@ -1,4 +1,5 @@
 """Command line builder."""
+
 import copy
 import logging
 import math

cwltool/checker.py

@@ -1,4 +1,5 @@
 """Static checking of CWL workflow connectivity."""
+
 from collections import namedtuple
 from typing import (
     Any,

cwltool/context.py

@@ -1,4 +1,5 @@
 """Shared context objects that replace use of kwargs."""
+
 import copy
 import os
 import shutil

cwltool/cwlviewer.py

@@ -1,4 +1,5 @@
 """Visualize a CWL workflow."""
+
 from pathlib import Path
 from typing import Iterator, List, cast
 from urllib.parse import urlparse

cwltool/executors.py

@@ -1,4 +1,5 @@
 """Single and multi-threaded executors."""
+
 import datetime
 import functools
 import logging

cwltool/loghandler.py

@@ -1,4 +1,5 @@
 """Shared logger for cwltool."""
+
 import logging
 
 import coloredlogs

cwltool/mpi.py

@@ -1,4 +1,5 @@
 """Experimental support for MPI."""
+
 import inspect
 import os
 import re

cwltool/process.py

@@ -1,4 +1,5 @@
 """Classes and methods relevant for all CWL Process types."""
+
 import abc
 import copy
 import functools

cwltool/run_job.py

@@ -1,4 +1,5 @@
 """Only used when there is a job script or CWLTOOL_FORCE_SHELL_POPEN=1."""
+
 import json
 import os
 import subprocess  # nosec

cwltool/secrets.py

@@ -1,4 +1,5 @@
 """Minimal in memory storage of secrets."""
+
 import uuid
 from typing import Dict, List, MutableMapping, MutableSequence, Optional, cast
 

cwltool/utils.py

@@ -1,4 +1,5 @@
 """Shared functions and other definitions."""
+
 import collections
 
 try:

lint-requirements.txt

@@ -1,3 +1,3 @@
 flake8-bugbear<23.13
-black~=23.12
+black~=24.1
 codespell

mypy-stubs/prov/model.pyi

@@ -223,10 +223,9 @@ class ProvBundle:
     ) -> QualifiedName | None: ...
     def get_records(
         self,
-        class_or_type_or_tuple: type
-        | type[int | str]
-        | Tuple[type | type[int | str] | Tuple[Any, ...], ...]
-        | None = ...,
+        class_or_type_or_tuple: (
+            type | type[int | str] | Tuple[type | type[int | str] | Tuple[Any, ...], ...] | None
+        ) = ...,
     ) -> List[ProvRecord]: ...
     def get_record(self, identifier: Identifier | None) -> ProvRecord | List[ProvRecord] | None: ...
     def is_document(self) -> bool: ...

tests/cwl-conformance/cwltool-conftest.py

@@ -3,6 +3,7 @@
 
 Calls cwltool via Python, instead of a subprocess via `--cwl-runner cwltool`.
 """
+
 import json
 from io import StringIO
 from typing import Any, Dict, List, Optional, Tuple

tests/test_check.py

@@ -1,4 +1,5 @@
 """Confirm some known-bad CWL descriptions."""
+
 import pytest
 
 from cwltool.main import main

tests/test_dependencies.py

@@ -1,4 +1,5 @@
 """Tests of satisfying SoftwareRequirement via dependencies."""
+
 import os
 import tempfile
 from getpass import getuser

tests/test_docker.py

@@ -1,4 +1,5 @@
 """Tests for docker engine."""
+
 import json
 import re
 from pathlib import Path

tests/test_environment.py

@@ -1,4 +1,5 @@
 """Test passing of environment variables to tools."""
+
 import os
 from abc import ABC, abstractmethod
 from pathlib import Path

tests/test_iwdr.py

@@ -1,4 +1,5 @@
 """InitialWorkDirRequirement related tests."""
+
 import json
 import re
 from pathlib import Path

tests/test_js_sandbox.py

@@ -1,4 +1,5 @@
 """Test sandboxjs.py and related code."""
+
 import logging
 import os
 import shutil

tests/test_load_tool.py

@@ -1,4 +1,5 @@
 """Tests for cwltool.load_tool."""
+
 import logging
 import urllib.parse
 from pathlib import Path

tests/test_loop.py

@@ -1,4 +1,5 @@
 """Test the prototype loop extension."""
+
 import json
 from io import StringIO
 from typing import MutableMapping, MutableSequence

tests/test_mpi.py

@@ -1,4 +1,5 @@
 """Tests of the experimental MPI extension."""
+
 import json
 import os.path
 import sys

tests/test_recursive_validation.py

@@ -1,4 +1,5 @@
 """Test the recursive validation feature (validate document and try to build tool)."""
+
 from cwltool.load_tool import fetch_document, recursive_resolve_and_validate_document
 
 from .util import get_data

tests/test_singularity.py

@@ -1,4 +1,5 @@
 """Tests to find local Singularity image."""
+
 import shutil
 from pathlib import Path
 from typing import Any

tests/test_singularity_versions.py

@@ -1,4 +1,5 @@
 """Test singularity{,-ce} & apptainer versions."""
+
 from subprocess import check_output  # nosec
 
 import cwltool.singularity

tests/test_streaming.py

@@ -1,4 +1,5 @@
 """Test that files marked as 'streamable' when 'streaming_allowed' can be named pipes."""
+
 import os
 from pathlib import Path
 from typing import cast

tests/test_tmpdir.py

@@ -1,4 +1,5 @@
 """Test that all temporary directories respect the --tmpdir-prefix and --tmp-outdir-prefix options."""
+
 import os
 import re
 import shutil

tests/test_udocker.py

@@ -1,4 +1,5 @@
 """Test optional udocker feature."""
+
 import copy
 import os
 import subprocess

tests/test_validate.py

@@ -1,4 +1,5 @@
 """Tests --validation."""
+
 import re
 
 from .util import get_data, get_main_output

tests/util.py

@@ -1,4 +1,5 @@
 """Test functions."""
+
 import atexit
 import contextlib
 import io