Merge branch 'release_24.1' into dev

.github/workflows/lint.yaml

@@ -55,4 +55,6 @@ jobs:
       - name: Run mypy checks
         run: tox -e mypy
       - uses: psf/black@stable
+        with:
+          version: "24.8.0"  # last version supporting Python 3.8
       - uses: isort/isort-action@v1

lib/galaxy/tool_util/cwl/__init__.py

@@ -1,7 +1,4 @@
-from .cwltool_deps import (
-    needs_shell_quoting,
-    shellescape,
-)
+from .cwltool_deps import needs_shell_quoting
 from .parser import (
     tool_proxy,
     tool_proxy_from_persistent_representation,
@@ -21,5 +18,4 @@
     "to_cwl_job",
     "to_galaxy_parameters",
     "needs_shell_quoting",
-    "shellescape",
 )

lib/galaxy/tool_util/cwl/cwltool_deps.py

@@ -71,11 +71,6 @@
     visit_class = None  # type: ignore[assignment]
     normalizeFilesDirs = None  # type: ignore[assignment]
 
-try:
-    import shellescape
-except ImportError:
-    shellescape = None
-
 try:
     import schema_salad
     from schema_salad import (
@@ -105,16 +100,14 @@ def ensure_cwltool_available():
 
     Throw an ImportError with a description of the problem if they do not exist.
     """
-    if main is None or workflow is None or shellescape is None:
+    if main is None or workflow is None:
         message = "This feature requires cwltool and dependencies to be available, they are not."
         if main is None:
             message += " cwltool is not unavailable."
         elif resolve_and_validate_document is None:
             message += " cwltool.load_tool.resolve_and_validate_document is unavailable - cwltool version is too old."
         if requests is None:
             message += " Library 'requests' unavailable."
-        if shellescape is None:
-            message += " Library 'shellescape' unavailable."
         if schema_salad is None:
             message += " Library 'schema_salad' unavailable."
         raise ImportError(message)
@@ -137,7 +130,6 @@ def ensure_cwltool_available():
     "resolve_and_validate_document",
     "RuntimeContext",
     "schema_salad",
-    "shellescape",
     "sourceline",
     "StdFsAccess",
     "visit_class",