Merge branch 'common-workflow-language:main' into ResourceRequirement-MinMax

Author: Stellatsuu

.github/workflows/wheels.yml

@@ -44,7 +44,7 @@ jobs:
       #     platforms: all
 
       - name: Build wheels
-        uses: pypa/cibuildwheel@v3.2
+        uses: pypa/cibuildwheel@v3.3
         env:
           CIBW_BUILD: ${{ matrix.build }}
           CIBW_MANYLINUX_X86_64_IMAGE: quay.io/pypa/${{ matrix.image }}
@@ -86,8 +86,8 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        # macos-13 is an intel runner, macos-14 is apple silicon
-        os: [macos-13, macos-14]
+        # macos-15-intel is an intel runner, macos-14 is apple silicon
+        os: [macos-15-intel, macos-14, macos-15]
     steps:
       - uses: actions/checkout@v5
         if: ${{ github.event_name != 'repository_dispatch' }}
@@ -100,7 +100,7 @@ jobs:
           ref: ${{ github.event.client_payload.ref }}
 
       - name: Build wheels
-        uses: pypa/cibuildwheel@v3.2
+        uses: pypa/cibuildwheel@v3.3
 
       - uses: actions/upload-artifact@v5
         with:

cwltool/command_line_tool.py

@@ -26,7 +26,7 @@
 
 from mypy_extensions import mypyc_attr
 from ruamel.yaml.comments import CommentedMap, CommentedSeq
-from schema_salad.avro.schema import Schema
+from schema_salad.avro.schema import RecordSchema
 from schema_salad.exceptions import ValidationException
 from schema_salad.ref_resolver import file_uri, uri_file_path
 from schema_salad.sourceline import SourceLine
@@ -1221,6 +1221,7 @@ def collect_output_ports(
         if cwl_version != "v1.0":
             builder.resources["exitCode"] = rcode
         try:
+            expected_schema = cast(RecordSchema, self.names.get_name("outputs_record_schema", None))
             fs_access = builder.make_fs_access(outdir)
             custom_output = fs_access.join(outdir, "cwl.output.json")
             if fs_access.exists(custom_output):
@@ -1232,6 +1233,20 @@ def collect_output_ports(
                         custom_output,
                         json_dumps(ret, indent=4),
                     )
+                if ORDERED_VERSIONS.index(cast(str, cwl_version)) >= ORDERED_VERSIONS.index(
+                    "v1.3.0-dev1"
+                ):
+                    for k in list(ret):
+                        found = False
+                        for field in expected_schema.fields:
+                            if k == field.name:
+                                found = True
+                                break
+                        if not found:
+                            _logger.warning(
+                                f"Discarded undeclared output named {k!r} from {custom_output}."
+                            )
+                            ret.pop(k)
             else:
                 for i, port in enumerate(ports):
                     with SourceLine(
@@ -1262,7 +1277,6 @@ def collect_output_ports(
 
                 if compute_checksum:
                     adjustFileObjs(ret, partial(compute_checksums, fs_access))
-            expected_schema = cast(Schema, self.names.get_name("outputs_record_schema", None))
             validate_ex(
                 expected_schema,
                 ret,

setup.py

@@ -176,7 +176,7 @@ def _find_package_data(base: str, globs: list[str], root: str = "cwltool") -> li
     test_suite="tests",
     tests_require=[
         "bagit >= 1.6.4, < 1.10",
-        "pytest >= 6.2, < 8.5",
+        "pytest >= 6.2, < 9.1",
         "mock >= 2.0.0",
         "pytest-mock >= 1.10.0",
         "pytest-httpserver",

test-requirements.txt

@@ -1,5 +1,5 @@
 bagit>=1.6.4,<1.10
-pytest>= 6.2,< 8.5
+pytest>= 6.2,< 9.1
 pytest-xdist>=3.2.0 # for the worksteal scheduler
 psutil # enhances pytest-xdist to allow "-n logical"
 pytest-httpserver

tests/test-cwl-out-v1.0.cwl

@@ -0,0 +1,15 @@
+class: CommandLineTool
+cwlVersion: v1.0
+
+inputs: []
+
+baseCommand: sh
+
+arguments:
+   - -c
+   - |
+     echo '{"foo": 5 }'
+
+stdout: cwl.output.json
+
+outputs: {}

tests/test-cwl-out-v1.1.cwl

@@ -0,0 +1,15 @@
+class: CommandLineTool
+cwlVersion: v1.1
+
+inputs: []
+
+baseCommand: sh
+
+arguments:
+   - -c
+   - |
+     echo '{"foo": 5 }'
+
+stdout: cwl.output.json
+
+outputs: {}

tests/test-cwl-out-v1.2.cwl

@@ -0,0 +1,15 @@
+class: CommandLineTool
+cwlVersion: v1.2
+
+inputs: []
+
+baseCommand: sh
+
+arguments:
+   - -c
+   - |
+     echo '{"foo": 5 }'
+
+stdout: cwl.output.json
+
+outputs: {}

tests/test-cwl-out-v1.3.cwl

@@ -0,0 +1,15 @@
+class: CommandLineTool
+cwlVersion: v1.3.0-dev1
+
+inputs: []
+
+baseCommand: sh
+
+arguments:
+   - -c
+   - |
+     echo '{"foo": 5 }'
+
+stdout: cwl.output.json
+
+outputs: {}

tests/test_cwl_output_json.py

@@ -0,0 +1,34 @@
+import json
+
+from .util import get_data, get_main_output
+
+
+def test_cwl_output_json_missing_field_v1_0() -> None:
+    """Confirm that unknown outputs are propagated from cwl.output.json in CWL v1.0."""
+    err_code, stdout, _ = get_main_output([get_data("tests/test-cwl-out-v1.0.cwl")])
+    assert err_code == 0
+    assert "foo" in json.loads(stdout)
+
+
+def test_cwl_output_json_missing_field_v1_1() -> None:
+    """Confirm that unknown outputs are propagated from cwl.output.json in CWL v1.1."""
+    err_code, stdout, _ = get_main_output([get_data("tests/test-cwl-out-v1.1.cwl")])
+    assert err_code == 0
+    assert "foo" in json.loads(stdout)
+
+
+def test_cwl_output_json_missing_field_v1_2() -> None:
+    """Confirm that unknown outputs are propagated from cwl.output.json in CWL v1.2."""
+    err_code, stdout, _ = get_main_output([get_data("tests/test-cwl-out-v1.2.cwl")])
+    assert err_code == 0
+    assert "foo" in json.loads(stdout)
+
+
+def test_cwl_output_json_missing_field_v1_3() -> None:
+    """Confirm that unknown outputs are propagated from cwl.output.json in CWL v1.3."""
+    err_code, stdout, stderr = get_main_output(
+        ["--enable-dev", get_data("tests/test-cwl-out-v1.3.cwl")]
+    )
+    assert err_code == 0
+    assert "foo" not in json.loads(stdout)
+    assert "Discarded undeclared output named 'foo' from" in stderr