[med-svn] [Git][med-team/cwltool][master] 7 commits: d/rules: use DEB_BUILD_OPTION_PARALLEL instead of "auto" for setting the...
Michael R. Crusoe (@crusoe)
gitlab at salsa.debian.org
Thu Jan 30 12:36:38 GMT 2025
Michael R. Crusoe pushed to branch master at Debian Med / cwltool
Commits:
d09d2835 by Michael R. Crusoe at 2025-01-30T10:57:45+01:00
d/rules: use DEB_BUILD_OPTION_PARALLEL instead of "auto" for setting the amount of parallel testing.
- - - - -
0df97243 by Michael R. Crusoe at 2025-01-30T11:06:06+01:00
d/rules: clean up extra license files.
- - - - -
6f6021c6 by Michael R. Crusoe at 2025-01-30T12:23:52+01:00
d/cwltool.lintian-overrides: update syntax
- - - - -
576d7e06 by Michael R. Crusoe at 2025-01-30T13:22:00+01:00
New patch to better mark the included CWL files as executable.
- - - - -
a0650667 by Michael R. Crusoe at 2025-01-30T13:22:00+01:00
New patch to improve user privacy by removing externally hosted badge images from the README.
- - - - -
dde5b5c0 by Michael R. Crusoe at 2025-01-30T13:22:00+01:00
Simplify test invocation and switch to autopkgtest-pkg-pybuild
- - - - -
31c7864a by Michael R. Crusoe at 2025-01-30T13:36:00+01:00
routine-update: Ready to upload to unstable
- - - - -
11 changed files:
- debian/changelog
- debian/control
- debian/cwltool.lintian-overrides
- + debian/patches/0003-Add-missing-cwl-runner-refs.patch
- debian/patches/disable_prov
- debian/patches/intersphinx
- + debian/patches/privacy
- debian/patches/series
- debian/rules
- − debian/tests/control
- − debian/tests/run-tests
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,16 @@
+cwltool (3.1.20250110105449-3) unstable; urgency=medium
+
+ * d/rules: use DEB_BUILD_OPTION_PARALLEL instead of "auto" for setting
+ the amount of parallel testing.
+ * d/rules: clean up extra license files.
+ * d/cwltool.lintian-overrides: update syntax
+ * New patch to better mark the included CWL files as executable.
+ * New patch to improve user privacy by removing externally hosted
+ badge images from the README.
+ * Simplify test invocation and switch to autopkgtest-pkg-pybuild
+
+ -- Michael R. Crusoe <crusoe at debian.org> Thu, 30 Jan 2025 13:22:50 +0100
+
cwltool (3.1.20250110105449-2) unstable; urgency=medium
* Team upload.
=====================================
debian/control
=====================================
@@ -27,6 +27,7 @@ Build-Depends: debhelper-compat (= 13),
python3-keepalive <!nocheck>,
python3-ruamel.yaml <!nocheck>,
python3-pytest (>> 6.2) <!nocheck>,
+ python3-pytest-httpserver <!nocheck>,
python3-pytest-xdist <!nocheck>,
python3-pytest-runner <!nocheck>,
python3-pytest-mock <!nocheck>,
@@ -47,6 +48,7 @@ Vcs-Browser: https://salsa.debian.org/med-team/cwltool
Vcs-Git: https://salsa.debian.org/med-team/cwltool.git
Homepage: https://cwltool.readthedocs.io/
Rules-Requires-Root: no
+Testsuite: autopkgtest-pkg-pybuild
Package: cwltool
Architecture: all
=====================================
debian/cwltool.lintian-overrides
=====================================
@@ -1,5 +1,4 @@
package-contains-documentation-outside-usr-share-doc [usr/lib/python3/dist-packages/cwltool/schemas/*]
-package-contains-documentation-outside-usr-share-doc [usr/lib/python3/dist-packages/cwltool/tests/wf/hello.txt]
-package-contains-documentation-outside-usr-share-doc [usr/lib/python3/dist-packages/cwltool/tests/wf/whale.txt]
-cwltool: unusual-interpreter usr/lib/python3/dist-packages/cwltool/hello.simg run-singularity
-cwltool: executable-not-elf-or-script [usr/lib/python3/dist-packages/cwltool/tests/wf/expect_trick_packed.cwl]
+package-contains-documentation-outside-usr-share-doc [usr/lib/python3/dist-packages/cwltool/tests/*.txt]
+unusual-interpreter run-singularity [usr/lib/python3/dist-packages/cwltool/hello.simg]
+executable-not-elf-or-script [usr/lib/python3/dist-packages/cwltool/tests/wf/expect_trick_packed.cwl]
=====================================
debian/patches/0003-Add-missing-cwl-runner-refs.patch
=====================================
@@ -0,0 +1,1261 @@
+From: "Michael R. Crusoe" <crusoe at debian.org>
+Date: Thu, 30 Jan 2025 11:15:09 +0100
+Subject: Add missing cwl-runner refs
+
+Forwarded: https://github.com/common-workflow-language/cwltool/pull/2095
+
+And mark executable
+---
+ cwltool/schemas/v1.1.0-dev1/cwl-runner.cwl | 0
+ cwltool/schemas/v1.1/cwl-runner.cwl | 0
+ cwltool/schemas/v1.2.0-dev1/cwl-runner.cwl | 0
+ cwltool/schemas/v1.2.0-dev2/cwl-runner.cwl | 0
+ cwltool/schemas/v1.2.0-dev3/cwl-runner.cwl | 0
+ cwltool/schemas/v1.2.0-dev4/cwl-runner.cwl | 0
+ cwltool/schemas/v1.2.0-dev5/cwl-runner.cwl | 0
+ cwltool/schemas/v1.3.0-dev1/cwl-runner.cwl | 0
+ tests/CometAdapter.cwl | 1 +
+ tests/arg-empty-prefix-separate-false.cwl | 0
+ tests/checker_wf/optional_array_mismatch.cwl | 1 +
+ tests/default_values_list.cwl | 0
+ tests/echo-badposition-expr.cwl | 0
+ tests/echo-position-expr.cwl | 0
+ tests/echo-stdout-log-dir.cwl | 0
+ tests/env.cwl | 0
+ tests/env2.cwl | 0
+ tests/env3.cwl | 0
+ tests/env4.cwl | 0
+ tests/input_deps/docker-array-secondaryfiles.cwl | 0
+ tests/iwdr_bad_expr.cwl | 0
+ tests/iwdr_dir_literal_real_file.cwl | 0
+ tests/load_contents-array.cwl | 1 +
+ tests/loop-ext/all-output-loop-no-iteration.cwl | 0
+ tests/loop-ext/all-output-loop.cwl | 0
+ tests/loop-ext/default-value-loop.cwl | 0
+ tests/loop-ext/invalid-loop-command-line-tool.cwl | 0
+ tests/loop-ext/invalid-loop-expression-tool.cwl | 0
+ tests/loop-ext/invalid-loop-hint.cwl | 0
+ tests/loop-ext/invalid-loop-scatter.cwl | 0
+ tests/loop-ext/invalid-loop-when-exception.cwl | 0
+ tests/loop-ext/invalid-loop-when.cwl | 0
+ tests/loop-ext/invalid-loop-workflow.cwl | 0
+ tests/loop-ext/invalid-multi-source-loop-no-requirement.cwl | 0
+ tests/loop-ext/invalid-no-loopWhen.cwl | 0
+ tests/loop-ext/invalid-non-boolean-loopWhen.cwl | 0
+ tests/loop-ext/invalid-non-boolean-loopWhen2.cwl | 0
+ tests/loop-ext/invalid-value-from-loop-no-requirement.cwl | 0
+ tests/loop-ext/loop-inside-loop-all.cwl | 0
+ tests/loop-ext/loop-inside-loop.cwl | 0
+ tests/loop-ext/loop-inside-scatter.cwl | 0
+ tests/loop-ext/multi-source-loop.cwl | 0
+ tests/loop-ext/opt-var-loop.cwl | 0
+ tests/loop-ext/scatter-inside-loop.cwl | 0
+ tests/loop-ext/single-var-loop-no-iteration.cwl | 0
+ tests/loop-ext/single-var-loop.cwl | 0
+ tests/loop-ext/two-vars-loop-2.cwl | 0
+ tests/loop-ext/two-vars-loop.cwl | 0
+ tests/loop-ext/value-from-loop.cwl | 0
+ tests/loop/all-output-loop-no-iteration.cwl | 0
+ tests/loop/all-output-loop.cwl | 0
+ tests/loop/default-value-loop.cwl | 0
+ tests/loop/invalid-loop-scatter.cwl | 0
+ tests/loop/invalid-loop-when-exception.cwl | 0
+ tests/loop/invalid-loop-when-exception2.cwl | 0
+ tests/loop/invalid-multi-source-loop-no-requirement.cwl | 0
+ tests/loop/invalid-no-loopWhen.cwl | 0
+ tests/loop/invalid-non-boolean-loopWhen.cwl | 0
+ tests/loop/invalid-non-boolean-loopWhen2.cwl | 0
+ tests/loop/invalid-value-from-loop-no-requirement.cwl | 0
+ tests/loop/loop-inside-loop-all.cwl | 0
+ tests/loop/loop-inside-loop.cwl | 0
+ tests/loop/loop-inside-scatter.cwl | 0
+ tests/loop/multi-source-loop.cwl | 0
+ tests/loop/opt-var-loop.cwl | 0
+ tests/loop/scatter-inside-loop.cwl | 0
+ tests/loop/single-var-loop-no-iteration.cwl | 0
+ tests/loop/single-var-loop.cwl | 0
+ tests/loop/two-vars-loop-2.cwl | 0
+ tests/loop/two-vars-loop.cwl | 0
+ tests/loop/value-from-loop.cwl | 0
+ tests/nested-array.cwl | 1 +
+ tests/non_portable.cwl | 0
+ tests/non_portable2.cwl | 0
+ tests/override/env-tool.cwl | 0
+ tests/override/env-tool_v1.1.0-dev1.cwl | 0
+ tests/override/env-tool_v1.1.cwl | 0
+ tests/portable.cwl | 0
+ tests/reloc/test.cwl | 1 +
+ tests/scatter_numbers.cwl | 0
+ tests/secondary-files-bad.cwl | 0
+ tests/secondary-files-required-container.cwl | 0
+ tests/secondary-files-required-missing-container.cwl | 0
+ tests/secondary-files-string-v1.cwl | 0
+ tests/secondary-files.cwl | 0
+ tests/sing_pullfolder_test.cwl | 0
+ tests/subgraph/1432.cwl | 1 +
+ tests/subgraph/env-tool2.cwl | 1 +
+ tests/subgraph/env-tool2_no_env.cwl | 1 +
+ tests/subgraph/env-tool2_req.cwl | 1 +
+ tests/subgraph/env-wf2.cwl | 0
+ tests/subgraph/env-wf2_hint_collision.cwl | 0
+ tests/subgraph/env-wf2_hint_req_collision.cwl | 0
+ tests/subgraph/env-wf2_long.cwl | 0
+ tests/subgraph/env-wf2_only_hint.cwl | 0
+ tests/subgraph/env-wf2_req_collision.cwl | 0
+ tests/subgraph/env-wf2_subwf-packed.cwl | 3 ++-
+ tests/subgraph/env-wf2_subwf.cwl | 0
+ tests/subgraph/env-wf2_subwf_b.cwl | 0
+ tests/subgraph/steplevel-resreq.cwl | 0
+ tests/subgraph/timelimit2-wf.cwl | 0
+ tests/test_examples.py | 2 +-
+ tests/test_validate.py | 8 ++++----
+ tests/trs/Dockstore.cwl | 0
+ tests/trs/md5sum-tool.cwl | 0
+ tests/trs/md5sum-workflow.cwl | 0
+ tests/utf_doc_example.cwl | 0
+ tests/wc-tool-bad-hints.cwl | 0
+ tests/wc-tool-bad-reqs.cwl | 0
+ tests/wf/1496.cwl | 1 +
+ tests/wf/1590.cwl | 1 +
+ tests/wf/1st-workflow.cwl | 0
+ tests/wf/811-12.cwl | 1 +
+ tests/wf/811.cwl | 1 +
+ tests/wf/816_tool.cwl | 1 +
+ tests/wf/816_wf.cwl | 1 +
+ tests/wf/910.cwl | 0
+ tests/wf/arguments.cwl | 0
+ tests/wf/bad-stderr-expr.cwl | 0
+ tests/wf/bad-stdin-expr.cwl | 0
+ tests/wf/bad-stdout-expr.cwl | 0
+ tests/wf/bad_networkaccess.cwl | 0
+ tests/wf/bad_timelimit.cwl | 0
+ tests/wf/cache_test_workflow.cwl | 0
+ tests/wf/cat-tool.cwl | 0
+ tests/wf/conditional_step_no_inputs.cwl | 0
+ tests/wf/conflict.cwl | 0
+ tests/wf/cores_float.cwl | 0
+ tests/wf/default-dir5.cwl | 0
+ tests/wf/default-wf5.cwl | 0
+ tests/wf/double-nested.cwl | 0
+ tests/wf/expect_trick_packed.cwl | 0
+ tests/wf/extract_region_specs.cwl | 1 +
+ tests/wf/floats_small_and_large.cwl | 1 +
+ tests/wf/generator/pytoolgen.cwl | 0
+ tests/wf/input_named_id.cwl | 1 +
+ tests/wf/iwd-passthrough1.cwl | 0
+ tests/wf/iwdr-empty.cwl | 0
+ tests/wf/iwdr-entry.cwl | 0
+ tests/wf/iwdr-passthrough-successive.cwl | 0
+ tests/wf/literalfile.cwl | 0
+ tests/wf/malformed_outputs.cwl | 0
+ tests/wf/missing-tool.cwl | 0
+ tests/wf/mpi_env.cwl | 0
+ tests/wf/mpi_expr.cwl | 0
+ tests/wf/mpi_line_count.cwl | 0
+ tests/wf/mpi_simple.cwl | 0
+ tests/wf/mpi_simple_wf.cwl | 0
+ tests/wf/nested.cwl | 0
+ tests/wf/networkaccess-fail.cwl | 0
+ tests/wf/networkaccess.cwl | 0
+ tests/wf/no-parameters-echo.cwl | 0
+ tests/wf/nvidia-smi-cc.cwl | 1 +
+ tests/wf/nvidia-smi-container.cwl | 1 +
+ tests/wf/nvidia-smi-max.cwl | 1 +
+ tests/wf/nvidia-smi-range.cwl | 1 +
+ tests/wf/nvidia-smi.cwl | 1 +
+ tests/wf/operation/abstract-cosifer.cwl | 1 +
+ tests/wf/operation/operation-single.cwl | 1 +
+ tests/wf/optional-numerical-output-0.cwl | 0
+ tests/wf/optional_src_mandatory_sink.cwl | 0
+ tests/wf/packed-with-loadlisting.cwl | 0
+ tests/wf/packed_no_main.cwl | 1 +
+ tests/wf/paramref_arguments_roundtrip.cwl | 0
+ tests/wf/paramref_arguments_self.cwl | 0
+ tests/wf/record_outputeval.cwl | 1 +
+ tests/wf/resreq_expr_float_v1_0.cwl | 1 +
+ tests/wf/resreq_expr_float_v1_2.cwl | 1 +
+ tests/wf/scatter2.cwl | 0
+ tests/wf/scatter2_subwf.cwl | 0
+ tests/wf/schemadef-bug-1473.cwl | 1 +
+ tests/wf/schemadef-tool-12.cwl | 0
+ tests/wf/schemadef-tool.cwl | 0
+ tests/wf/sec-tool.cwl | 0
+ tests/wf/sec-wf-out.cwl | 0
+ tests/wf/sec-wf.cwl | 0
+ tests/wf/secret_job.cwl | 0
+ tests/wf/secret_wf.cwl | 0
+ tests/wf/separate_without_prefix.cwl | 0
+ tests/wf/shm_size.cwl | 0
+ tests/wf/storage_float.cwl | 0
+ tests/wf/tar-param.cwl | 0
+ tests/wf/three_step_color.cwl | 0
+ tests/wf/timelimit-fail.cwl | 0
+ tests/wf/timelimit.cwl | 0
+ tests/wf/touch_tool.cwl | 0
+ tests/wf/trick_defaults.cwl | 0
+ tests/wf/trick_defaults2.cwl | 0
+ tests/wf/vf-concat.cwl | 0
+ tests/wf/workreuse-fail.cwl | 0
+ tests/wf/workreuse.cwl | 0
+ tests/with_doc.cwl | 0
+ tests/without_doc.cwl | 0
+ 193 files changed, 37 insertions(+), 6 deletions(-)
+ mode change 100644 => 100755 cwltool/schemas/v1.1.0-dev1/cwl-runner.cwl
+ mode change 100644 => 100755 cwltool/schemas/v1.1/cwl-runner.cwl
+ mode change 100644 => 100755 cwltool/schemas/v1.2.0-dev1/cwl-runner.cwl
+ mode change 100644 => 100755 cwltool/schemas/v1.2.0-dev2/cwl-runner.cwl
+ mode change 100644 => 100755 cwltool/schemas/v1.2.0-dev3/cwl-runner.cwl
+ mode change 100644 => 100755 cwltool/schemas/v1.2.0-dev4/cwl-runner.cwl
+ mode change 100644 => 100755 cwltool/schemas/v1.2.0-dev5/cwl-runner.cwl
+ mode change 100644 => 100755 cwltool/schemas/v1.3.0-dev1/cwl-runner.cwl
+ mode change 100644 => 100755 tests/CometAdapter.cwl
+ mode change 100644 => 100755 tests/arg-empty-prefix-separate-false.cwl
+ mode change 100644 => 100755 tests/checker_wf/optional_array_mismatch.cwl
+ mode change 100644 => 100755 tests/default_values_list.cwl
+ mode change 100644 => 100755 tests/echo-badposition-expr.cwl
+ mode change 100644 => 100755 tests/echo-position-expr.cwl
+ mode change 100644 => 100755 tests/echo-stdout-log-dir.cwl
+ mode change 100644 => 100755 tests/env.cwl
+ mode change 100644 => 100755 tests/env2.cwl
+ mode change 100644 => 100755 tests/env3.cwl
+ mode change 100644 => 100755 tests/env4.cwl
+ mode change 100644 => 100755 tests/input_deps/docker-array-secondaryfiles.cwl
+ mode change 100644 => 100755 tests/iwdr_bad_expr.cwl
+ mode change 100644 => 100755 tests/iwdr_dir_literal_real_file.cwl
+ mode change 100644 => 100755 tests/load_contents-array.cwl
+ mode change 100644 => 100755 tests/loop-ext/all-output-loop-no-iteration.cwl
+ mode change 100644 => 100755 tests/loop-ext/all-output-loop.cwl
+ mode change 100644 => 100755 tests/loop-ext/default-value-loop.cwl
+ mode change 100644 => 100755 tests/loop-ext/invalid-loop-command-line-tool.cwl
+ mode change 100644 => 100755 tests/loop-ext/invalid-loop-expression-tool.cwl
+ mode change 100644 => 100755 tests/loop-ext/invalid-loop-hint.cwl
+ mode change 100644 => 100755 tests/loop-ext/invalid-loop-scatter.cwl
+ mode change 100644 => 100755 tests/loop-ext/invalid-loop-when-exception.cwl
+ mode change 100644 => 100755 tests/loop-ext/invalid-loop-when.cwl
+ mode change 100644 => 100755 tests/loop-ext/invalid-loop-workflow.cwl
+ mode change 100644 => 100755 tests/loop-ext/invalid-multi-source-loop-no-requirement.cwl
+ mode change 100644 => 100755 tests/loop-ext/invalid-no-loopWhen.cwl
+ mode change 100644 => 100755 tests/loop-ext/invalid-non-boolean-loopWhen.cwl
+ mode change 100644 => 100755 tests/loop-ext/invalid-non-boolean-loopWhen2.cwl
+ mode change 100644 => 100755 tests/loop-ext/invalid-value-from-loop-no-requirement.cwl
+ mode change 100644 => 100755 tests/loop-ext/loop-inside-loop-all.cwl
+ mode change 100644 => 100755 tests/loop-ext/loop-inside-loop.cwl
+ mode change 100644 => 100755 tests/loop-ext/loop-inside-scatter.cwl
+ mode change 100644 => 100755 tests/loop-ext/multi-source-loop.cwl
+ mode change 100644 => 100755 tests/loop-ext/opt-var-loop.cwl
+ mode change 100644 => 100755 tests/loop-ext/scatter-inside-loop.cwl
+ mode change 100644 => 100755 tests/loop-ext/single-var-loop-no-iteration.cwl
+ mode change 100644 => 100755 tests/loop-ext/single-var-loop.cwl
+ mode change 100644 => 100755 tests/loop-ext/two-vars-loop-2.cwl
+ mode change 100644 => 100755 tests/loop-ext/two-vars-loop.cwl
+ mode change 100644 => 100755 tests/loop-ext/value-from-loop.cwl
+ mode change 100644 => 100755 tests/loop/all-output-loop-no-iteration.cwl
+ mode change 100644 => 100755 tests/loop/all-output-loop.cwl
+ mode change 100644 => 100755 tests/loop/default-value-loop.cwl
+ mode change 100644 => 100755 tests/loop/invalid-loop-scatter.cwl
+ mode change 100644 => 100755 tests/loop/invalid-loop-when-exception.cwl
+ mode change 100644 => 100755 tests/loop/invalid-loop-when-exception2.cwl
+ mode change 100644 => 100755 tests/loop/invalid-multi-source-loop-no-requirement.cwl
+ mode change 100644 => 100755 tests/loop/invalid-no-loopWhen.cwl
+ mode change 100644 => 100755 tests/loop/invalid-non-boolean-loopWhen.cwl
+ mode change 100644 => 100755 tests/loop/invalid-non-boolean-loopWhen2.cwl
+ mode change 100644 => 100755 tests/loop/invalid-value-from-loop-no-requirement.cwl
+ mode change 100644 => 100755 tests/loop/loop-inside-loop-all.cwl
+ mode change 100644 => 100755 tests/loop/loop-inside-loop.cwl
+ mode change 100644 => 100755 tests/loop/loop-inside-scatter.cwl
+ mode change 100644 => 100755 tests/loop/multi-source-loop.cwl
+ mode change 100644 => 100755 tests/loop/opt-var-loop.cwl
+ mode change 100644 => 100755 tests/loop/scatter-inside-loop.cwl
+ mode change 100644 => 100755 tests/loop/single-var-loop-no-iteration.cwl
+ mode change 100644 => 100755 tests/loop/single-var-loop.cwl
+ mode change 100644 => 100755 tests/loop/two-vars-loop-2.cwl
+ mode change 100644 => 100755 tests/loop/two-vars-loop.cwl
+ mode change 100644 => 100755 tests/loop/value-from-loop.cwl
+ mode change 100644 => 100755 tests/nested-array.cwl
+ mode change 100644 => 100755 tests/non_portable.cwl
+ mode change 100644 => 100755 tests/non_portable2.cwl
+ mode change 100644 => 100755 tests/override/env-tool.cwl
+ mode change 100644 => 100755 tests/override/env-tool_v1.1.0-dev1.cwl
+ mode change 100644 => 100755 tests/override/env-tool_v1.1.cwl
+ mode change 100644 => 100755 tests/portable.cwl
+ mode change 100644 => 100755 tests/reloc/test.cwl
+ mode change 100644 => 100755 tests/scatter_numbers.cwl
+ mode change 100644 => 100755 tests/secondary-files-bad.cwl
+ mode change 100644 => 100755 tests/secondary-files-required-container.cwl
+ mode change 100644 => 100755 tests/secondary-files-required-missing-container.cwl
+ mode change 100644 => 100755 tests/secondary-files-string-v1.cwl
+ mode change 100644 => 100755 tests/secondary-files.cwl
+ mode change 100644 => 100755 tests/sing_pullfolder_test.cwl
+ mode change 100644 => 100755 tests/subgraph/1432.cwl
+ mode change 100644 => 100755 tests/subgraph/env-tool2.cwl
+ mode change 100644 => 100755 tests/subgraph/env-tool2_no_env.cwl
+ mode change 100644 => 100755 tests/subgraph/env-tool2_req.cwl
+ mode change 100644 => 100755 tests/subgraph/env-wf2.cwl
+ mode change 100644 => 100755 tests/subgraph/env-wf2_hint_collision.cwl
+ mode change 100644 => 100755 tests/subgraph/env-wf2_hint_req_collision.cwl
+ mode change 100644 => 100755 tests/subgraph/env-wf2_long.cwl
+ mode change 100644 => 100755 tests/subgraph/env-wf2_only_hint.cwl
+ mode change 100644 => 100755 tests/subgraph/env-wf2_req_collision.cwl
+ mode change 100644 => 100755 tests/subgraph/env-wf2_subwf-packed.cwl
+ mode change 100644 => 100755 tests/subgraph/env-wf2_subwf.cwl
+ mode change 100644 => 100755 tests/subgraph/env-wf2_subwf_b.cwl
+ mode change 100644 => 100755 tests/subgraph/steplevel-resreq.cwl
+ mode change 100644 => 100755 tests/subgraph/timelimit2-wf.cwl
+ mode change 100644 => 100755 tests/trs/Dockstore.cwl
+ mode change 100644 => 100755 tests/trs/md5sum-tool.cwl
+ mode change 100644 => 100755 tests/trs/md5sum-workflow.cwl
+ mode change 100644 => 100755 tests/utf_doc_example.cwl
+ mode change 100644 => 100755 tests/wc-tool-bad-hints.cwl
+ mode change 100644 => 100755 tests/wc-tool-bad-reqs.cwl
+ mode change 100644 => 100755 tests/wf/1496.cwl
+ mode change 100644 => 100755 tests/wf/1590.cwl
+ mode change 100644 => 100755 tests/wf/1st-workflow.cwl
+ mode change 100644 => 100755 tests/wf/811-12.cwl
+ mode change 100644 => 100755 tests/wf/811.cwl
+ mode change 100644 => 100755 tests/wf/816_tool.cwl
+ mode change 100644 => 100755 tests/wf/816_wf.cwl
+ mode change 100644 => 100755 tests/wf/910.cwl
+ mode change 100644 => 100755 tests/wf/arguments.cwl
+ mode change 100644 => 100755 tests/wf/bad-stderr-expr.cwl
+ mode change 100644 => 100755 tests/wf/bad-stdin-expr.cwl
+ mode change 100644 => 100755 tests/wf/bad-stdout-expr.cwl
+ mode change 100644 => 100755 tests/wf/bad_networkaccess.cwl
+ mode change 100644 => 100755 tests/wf/bad_timelimit.cwl
+ mode change 100644 => 100755 tests/wf/cache_test_workflow.cwl
+ mode change 100644 => 100755 tests/wf/cat-tool.cwl
+ mode change 100644 => 100755 tests/wf/conditional_step_no_inputs.cwl
+ mode change 100644 => 100755 tests/wf/conflict.cwl
+ mode change 100644 => 100755 tests/wf/cores_float.cwl
+ mode change 100644 => 100755 tests/wf/default-dir5.cwl
+ mode change 100644 => 100755 tests/wf/default-wf5.cwl
+ mode change 100644 => 100755 tests/wf/double-nested.cwl
+ mode change 100644 => 100755 tests/wf/expect_trick_packed.cwl
+ mode change 100644 => 100755 tests/wf/extract_region_specs.cwl
+ mode change 100644 => 100755 tests/wf/floats_small_and_large.cwl
+ mode change 100644 => 100755 tests/wf/generator/pytoolgen.cwl
+ mode change 100644 => 100755 tests/wf/input_named_id.cwl
+ mode change 100644 => 100755 tests/wf/iwd-passthrough1.cwl
+ mode change 100644 => 100755 tests/wf/iwdr-empty.cwl
+ mode change 100644 => 100755 tests/wf/iwdr-entry.cwl
+ mode change 100644 => 100755 tests/wf/iwdr-passthrough-successive.cwl
+ mode change 100644 => 100755 tests/wf/literalfile.cwl
+ mode change 100644 => 100755 tests/wf/malformed_outputs.cwl
+ mode change 100644 => 100755 tests/wf/missing-tool.cwl
+ mode change 100644 => 100755 tests/wf/mpi_env.cwl
+ mode change 100644 => 100755 tests/wf/mpi_expr.cwl
+ mode change 100644 => 100755 tests/wf/mpi_line_count.cwl
+ mode change 100644 => 100755 tests/wf/mpi_simple.cwl
+ mode change 100644 => 100755 tests/wf/mpi_simple_wf.cwl
+ mode change 100644 => 100755 tests/wf/nested.cwl
+ mode change 100644 => 100755 tests/wf/networkaccess-fail.cwl
+ mode change 100644 => 100755 tests/wf/networkaccess.cwl
+ mode change 100644 => 100755 tests/wf/no-parameters-echo.cwl
+ mode change 100644 => 100755 tests/wf/nvidia-smi-cc.cwl
+ mode change 100644 => 100755 tests/wf/nvidia-smi-container.cwl
+ mode change 100644 => 100755 tests/wf/nvidia-smi-max.cwl
+ mode change 100644 => 100755 tests/wf/nvidia-smi-range.cwl
+ mode change 100644 => 100755 tests/wf/nvidia-smi.cwl
+ mode change 100644 => 100755 tests/wf/operation/abstract-cosifer.cwl
+ mode change 100644 => 100755 tests/wf/operation/operation-single.cwl
+ mode change 100644 => 100755 tests/wf/optional-numerical-output-0.cwl
+ mode change 100644 => 100755 tests/wf/optional_src_mandatory_sink.cwl
+ mode change 100644 => 100755 tests/wf/packed-with-loadlisting.cwl
+ mode change 100644 => 100755 tests/wf/packed_no_main.cwl
+ mode change 100644 => 100755 tests/wf/paramref_arguments_roundtrip.cwl
+ mode change 100644 => 100755 tests/wf/paramref_arguments_self.cwl
+ mode change 100644 => 100755 tests/wf/record_outputeval.cwl
+ mode change 100644 => 100755 tests/wf/resreq_expr_float_v1_0.cwl
+ mode change 100644 => 100755 tests/wf/resreq_expr_float_v1_2.cwl
+ mode change 100644 => 100755 tests/wf/scatter2.cwl
+ mode change 100644 => 100755 tests/wf/scatter2_subwf.cwl
+ mode change 100644 => 100755 tests/wf/schemadef-bug-1473.cwl
+ mode change 100644 => 100755 tests/wf/schemadef-tool-12.cwl
+ mode change 100644 => 100755 tests/wf/schemadef-tool.cwl
+ mode change 100644 => 100755 tests/wf/sec-tool.cwl
+ mode change 100644 => 100755 tests/wf/sec-wf-out.cwl
+ mode change 100644 => 100755 tests/wf/sec-wf.cwl
+ mode change 100644 => 100755 tests/wf/secret_job.cwl
+ mode change 100644 => 100755 tests/wf/secret_wf.cwl
+ mode change 100644 => 100755 tests/wf/separate_without_prefix.cwl
+ mode change 100644 => 100755 tests/wf/shm_size.cwl
+ mode change 100644 => 100755 tests/wf/storage_float.cwl
+ mode change 100644 => 100755 tests/wf/tar-param.cwl
+ mode change 100644 => 100755 tests/wf/three_step_color.cwl
+ mode change 100644 => 100755 tests/wf/timelimit-fail.cwl
+ mode change 100644 => 100755 tests/wf/timelimit.cwl
+ mode change 100644 => 100755 tests/wf/touch_tool.cwl
+ mode change 100644 => 100755 tests/wf/trick_defaults.cwl
+ mode change 100644 => 100755 tests/wf/trick_defaults2.cwl
+ mode change 100644 => 100755 tests/wf/vf-concat.cwl
+ mode change 100644 => 100755 tests/wf/workreuse-fail.cwl
+ mode change 100644 => 100755 tests/wf/workreuse.cwl
+ mode change 100644 => 100755 tests/with_doc.cwl
+ mode change 100644 => 100755 tests/without_doc.cwl
+
+diff --git a/cwltool/schemas/v1.1.0-dev1/cwl-runner.cwl b/cwltool/schemas/v1.1.0-dev1/cwl-runner.cwl
+old mode 100644
+new mode 100755
+diff --git a/cwltool/schemas/v1.1/cwl-runner.cwl b/cwltool/schemas/v1.1/cwl-runner.cwl
+old mode 100644
+new mode 100755
+diff --git a/cwltool/schemas/v1.2.0-dev1/cwl-runner.cwl b/cwltool/schemas/v1.2.0-dev1/cwl-runner.cwl
+old mode 100644
+new mode 100755
+diff --git a/cwltool/schemas/v1.2.0-dev2/cwl-runner.cwl b/cwltool/schemas/v1.2.0-dev2/cwl-runner.cwl
+old mode 100644
+new mode 100755
+diff --git a/cwltool/schemas/v1.2.0-dev3/cwl-runner.cwl b/cwltool/schemas/v1.2.0-dev3/cwl-runner.cwl
+old mode 100644
+new mode 100755
+diff --git a/cwltool/schemas/v1.2.0-dev4/cwl-runner.cwl b/cwltool/schemas/v1.2.0-dev4/cwl-runner.cwl
+old mode 100644
+new mode 100755
+diff --git a/cwltool/schemas/v1.2.0-dev5/cwl-runner.cwl b/cwltool/schemas/v1.2.0-dev5/cwl-runner.cwl
+old mode 100644
+new mode 100755
+diff --git a/cwltool/schemas/v1.3.0-dev1/cwl-runner.cwl b/cwltool/schemas/v1.3.0-dev1/cwl-runner.cwl
+old mode 100644
+new mode 100755
+diff --git a/tests/CometAdapter.cwl b/tests/CometAdapter.cwl
+old mode 100644
+new mode 100755
+index ed1b24b..3d70835
+--- a/tests/CometAdapter.cwl
++++ b/tests/CometAdapter.cwl
+@@ -1,3 +1,4 @@
++#!/usr/bin/env cwl-runner
+ # Copyright (c) 2002-present, The OpenMS Team -- EKU Tuebingen, ETH Zurich, and FU Berlin
+ # SPDX-License-Identifier: Apache-2.0
+ label: CometAdapter
+diff --git a/tests/arg-empty-prefix-separate-false.cwl b/tests/arg-empty-prefix-separate-false.cwl
+old mode 100644
+new mode 100755
+diff --git a/tests/checker_wf/optional_array_mismatch.cwl b/tests/checker_wf/optional_array_mismatch.cwl
+old mode 100644
+new mode 100755
+index d6f0527..a557927
+--- a/tests/checker_wf/optional_array_mismatch.cwl
++++ b/tests/checker_wf/optional_array_mismatch.cwl
+@@ -1,3 +1,4 @@
++#!/usr/bin/env cwl-runner
+ cwlVersion: v1.0
+ class: Workflow
+ inputs:
+diff --git a/tests/default_values_list.cwl b/tests/default_values_list.cwl
+old mode 100644
+new mode 100755
+diff --git a/tests/echo-badposition-expr.cwl b/tests/echo-badposition-expr.cwl
+old mode 100644
+new mode 100755
+diff --git a/tests/echo-position-expr.cwl b/tests/echo-position-expr.cwl
+old mode 100644
+new mode 100755
+diff --git a/tests/echo-stdout-log-dir.cwl b/tests/echo-stdout-log-dir.cwl
+old mode 100644
+new mode 100755
+diff --git a/tests/env.cwl b/tests/env.cwl
+old mode 100644
+new mode 100755
+diff --git a/tests/env2.cwl b/tests/env2.cwl
+old mode 100644
+new mode 100755
+diff --git a/tests/env3.cwl b/tests/env3.cwl
+old mode 100644
+new mode 100755
+diff --git a/tests/env4.cwl b/tests/env4.cwl
+old mode 100644
+new mode 100755
+diff --git a/tests/input_deps/docker-array-secondaryfiles.cwl b/tests/input_deps/docker-array-secondaryfiles.cwl
+old mode 100644
+new mode 100755
+diff --git a/tests/iwdr_bad_expr.cwl b/tests/iwdr_bad_expr.cwl
+old mode 100644
+new mode 100755
+diff --git a/tests/iwdr_dir_literal_real_file.cwl b/tests/iwdr_dir_literal_real_file.cwl
+old mode 100644
+new mode 100755
+diff --git a/tests/load_contents-array.cwl b/tests/load_contents-array.cwl
+old mode 100644
+new mode 100755
+index f6b786e..eaad624
+--- a/tests/load_contents-array.cwl
++++ b/tests/load_contents-array.cwl
+@@ -1,3 +1,4 @@
++#!/usr/bin/env cwl-runner
+ cwlVersion: "v1.2"
+ class: CommandLineTool
+ baseCommand: echo
+diff --git a/tests/loop-ext/all-output-loop-no-iteration.cwl b/tests/loop-ext/all-output-loop-no-iteration.cwl
+old mode 100644
+new mode 100755
+diff --git a/tests/loop-ext/all-output-loop.cwl b/tests/loop-ext/all-output-loop.cwl
+old mode 100644
+new mode 100755
+diff --git a/tests/loop-ext/default-value-loop.cwl b/tests/loop-ext/default-value-loop.cwl
+old mode 100644
+new mode 100755
+diff --git a/tests/loop-ext/invalid-loop-command-line-tool.cwl b/tests/loop-ext/invalid-loop-command-line-tool.cwl
+old mode 100644
+new mode 100755
+diff --git a/tests/loop-ext/invalid-loop-expression-tool.cwl b/tests/loop-ext/invalid-loop-expression-tool.cwl
+old mode 100644
+new mode 100755
+diff --git a/tests/loop-ext/invalid-loop-hint.cwl b/tests/loop-ext/invalid-loop-hint.cwl
+old mode 100644
+new mode 100755
+diff --git a/tests/loop-ext/invalid-loop-scatter.cwl b/tests/loop-ext/invalid-loop-scatter.cwl
+old mode 100644
+new mode 100755
+diff --git a/tests/loop-ext/invalid-loop-when-exception.cwl b/tests/loop-ext/invalid-loop-when-exception.cwl
+old mode 100644
+new mode 100755
+diff --git a/tests/loop-ext/invalid-loop-when.cwl b/tests/loop-ext/invalid-loop-when.cwl
+old mode 100644
+new mode 100755
+diff --git a/tests/loop-ext/invalid-loop-workflow.cwl b/tests/loop-ext/invalid-loop-workflow.cwl
+old mode 100644
+new mode 100755
+diff --git a/tests/loop-ext/invalid-multi-source-loop-no-requirement.cwl b/tests/loop-ext/invalid-multi-source-loop-no-requirement.cwl
+old mode 100644
+new mode 100755
+diff --git a/tests/loop-ext/invalid-no-loopWhen.cwl b/tests/loop-ext/invalid-no-loopWhen.cwl
+old mode 100644
+new mode 100755
+diff --git a/tests/loop-ext/invalid-non-boolean-loopWhen.cwl b/tests/loop-ext/invalid-non-boolean-loopWhen.cwl
+old mode 100644
+new mode 100755
+diff --git a/tests/loop-ext/invalid-non-boolean-loopWhen2.cwl b/tests/loop-ext/invalid-non-boolean-loopWhen2.cwl
+old mode 100644
+new mode 100755
+diff --git a/tests/loop-ext/invalid-value-from-loop-no-requirement.cwl b/tests/loop-ext/invalid-value-from-loop-no-requirement.cwl
+old mode 100644
+new mode 100755
+diff --git a/tests/loop-ext/loop-inside-loop-all.cwl b/tests/loop-ext/loop-inside-loop-all.cwl
+old mode 100644
+new mode 100755
+diff --git a/tests/loop-ext/loop-inside-loop.cwl b/tests/loop-ext/loop-inside-loop.cwl
+old mode 100644
+new mode 100755
+diff --git a/tests/loop-ext/loop-inside-scatter.cwl b/tests/loop-ext/loop-inside-scatter.cwl
+old mode 100644
+new mode 100755
+diff --git a/tests/loop-ext/multi-source-loop.cwl b/tests/loop-ext/multi-source-loop.cwl
+old mode 100644
+new mode 100755
+diff --git a/tests/loop-ext/opt-var-loop.cwl b/tests/loop-ext/opt-var-loop.cwl
+old mode 100644
+new mode 100755
+diff --git a/tests/loop-ext/scatter-inside-loop.cwl b/tests/loop-ext/scatter-inside-loop.cwl
+old mode 100644
+new mode 100755
+diff --git a/tests/loop-ext/single-var-loop-no-iteration.cwl b/tests/loop-ext/single-var-loop-no-iteration.cwl
+old mode 100644
+new mode 100755
+diff --git a/tests/loop-ext/single-var-loop.cwl b/tests/loop-ext/single-var-loop.cwl
+old mode 100644
+new mode 100755
+diff --git a/tests/loop-ext/two-vars-loop-2.cwl b/tests/loop-ext/two-vars-loop-2.cwl
+old mode 100644
+new mode 100755
+diff --git a/tests/loop-ext/two-vars-loop.cwl b/tests/loop-ext/two-vars-loop.cwl
+old mode 100644
+new mode 100755
+diff --git a/tests/loop-ext/value-from-loop.cwl b/tests/loop-ext/value-from-loop.cwl
+old mode 100644
+new mode 100755
+diff --git a/tests/loop/all-output-loop-no-iteration.cwl b/tests/loop/all-output-loop-no-iteration.cwl
+old mode 100644
+new mode 100755
+diff --git a/tests/loop/all-output-loop.cwl b/tests/loop/all-output-loop.cwl
+old mode 100644
+new mode 100755
+diff --git a/tests/loop/default-value-loop.cwl b/tests/loop/default-value-loop.cwl
+old mode 100644
+new mode 100755
+diff --git a/tests/loop/invalid-loop-scatter.cwl b/tests/loop/invalid-loop-scatter.cwl
+old mode 100644
+new mode 100755
+diff --git a/tests/loop/invalid-loop-when-exception.cwl b/tests/loop/invalid-loop-when-exception.cwl
+old mode 100644
+new mode 100755
+diff --git a/tests/loop/invalid-loop-when-exception2.cwl b/tests/loop/invalid-loop-when-exception2.cwl
+old mode 100644
+new mode 100755
+diff --git a/tests/loop/invalid-multi-source-loop-no-requirement.cwl b/tests/loop/invalid-multi-source-loop-no-requirement.cwl
+old mode 100644
+new mode 100755
+diff --git a/tests/loop/invalid-no-loopWhen.cwl b/tests/loop/invalid-no-loopWhen.cwl
+old mode 100644
+new mode 100755
+diff --git a/tests/loop/invalid-non-boolean-loopWhen.cwl b/tests/loop/invalid-non-boolean-loopWhen.cwl
+old mode 100644
+new mode 100755
+diff --git a/tests/loop/invalid-non-boolean-loopWhen2.cwl b/tests/loop/invalid-non-boolean-loopWhen2.cwl
+old mode 100644
+new mode 100755
+diff --git a/tests/loop/invalid-value-from-loop-no-requirement.cwl b/tests/loop/invalid-value-from-loop-no-requirement.cwl
+old mode 100644
+new mode 100755
+diff --git a/tests/loop/loop-inside-loop-all.cwl b/tests/loop/loop-inside-loop-all.cwl
+old mode 100644
+new mode 100755
+diff --git a/tests/loop/loop-inside-loop.cwl b/tests/loop/loop-inside-loop.cwl
+old mode 100644
+new mode 100755
+diff --git a/tests/loop/loop-inside-scatter.cwl b/tests/loop/loop-inside-scatter.cwl
+old mode 100644
+new mode 100755
+diff --git a/tests/loop/multi-source-loop.cwl b/tests/loop/multi-source-loop.cwl
+old mode 100644
+new mode 100755
+diff --git a/tests/loop/opt-var-loop.cwl b/tests/loop/opt-var-loop.cwl
+old mode 100644
+new mode 100755
+diff --git a/tests/loop/scatter-inside-loop.cwl b/tests/loop/scatter-inside-loop.cwl
+old mode 100644
+new mode 100755
+diff --git a/tests/loop/single-var-loop-no-iteration.cwl b/tests/loop/single-var-loop-no-iteration.cwl
+old mode 100644
+new mode 100755
+diff --git a/tests/loop/single-var-loop.cwl b/tests/loop/single-var-loop.cwl
+old mode 100644
+new mode 100755
+diff --git a/tests/loop/two-vars-loop-2.cwl b/tests/loop/two-vars-loop-2.cwl
+old mode 100644
+new mode 100755
+diff --git a/tests/loop/two-vars-loop.cwl b/tests/loop/two-vars-loop.cwl
+old mode 100644
+new mode 100755
+diff --git a/tests/loop/value-from-loop.cwl b/tests/loop/value-from-loop.cwl
+old mode 100644
+new mode 100755
+diff --git a/tests/nested-array.cwl b/tests/nested-array.cwl
+old mode 100644
+new mode 100755
+index 8272614..6aa3650
+--- a/tests/nested-array.cwl
++++ b/tests/nested-array.cwl
+@@ -1,3 +1,4 @@
++#!/usr/bin/env cwl-runner
+ cwlVersion: v1.2
+ class: CommandLineTool
+ baseCommand: echo
+diff --git a/tests/non_portable.cwl b/tests/non_portable.cwl
+old mode 100644
+new mode 100755
+diff --git a/tests/non_portable2.cwl b/tests/non_portable2.cwl
+old mode 100644
+new mode 100755
+diff --git a/tests/override/env-tool.cwl b/tests/override/env-tool.cwl
+old mode 100644
+new mode 100755
+diff --git a/tests/override/env-tool_v1.1.0-dev1.cwl b/tests/override/env-tool_v1.1.0-dev1.cwl
+old mode 100644
+new mode 100755
+diff --git a/tests/override/env-tool_v1.1.cwl b/tests/override/env-tool_v1.1.cwl
+old mode 100644
+new mode 100755
+diff --git a/tests/portable.cwl b/tests/portable.cwl
+old mode 100644
+new mode 100755
+diff --git a/tests/reloc/test.cwl b/tests/reloc/test.cwl
+old mode 100644
+new mode 100755
+index 41d3747..c88cf48
+--- a/tests/reloc/test.cwl
++++ b/tests/reloc/test.cwl
+@@ -1,3 +1,4 @@
++#!/usr/bin/env cwl-runner
+ cwlVersion: v1.2
+ class: CommandLineTool
+ inputs:
+diff --git a/tests/scatter_numbers.cwl b/tests/scatter_numbers.cwl
+old mode 100644
+new mode 100755
+diff --git a/tests/secondary-files-bad.cwl b/tests/secondary-files-bad.cwl
+old mode 100644
+new mode 100755
+diff --git a/tests/secondary-files-required-container.cwl b/tests/secondary-files-required-container.cwl
+old mode 100644
+new mode 100755
+diff --git a/tests/secondary-files-required-missing-container.cwl b/tests/secondary-files-required-missing-container.cwl
+old mode 100644
+new mode 100755
+diff --git a/tests/secondary-files-string-v1.cwl b/tests/secondary-files-string-v1.cwl
+old mode 100644
+new mode 100755
+diff --git a/tests/secondary-files.cwl b/tests/secondary-files.cwl
+old mode 100644
+new mode 100755
+diff --git a/tests/sing_pullfolder_test.cwl b/tests/sing_pullfolder_test.cwl
+old mode 100644
+new mode 100755
+diff --git a/tests/subgraph/1432.cwl b/tests/subgraph/1432.cwl
+old mode 100644
+new mode 100755
+index 54d5538..41283ab
+--- a/tests/subgraph/1432.cwl
++++ b/tests/subgraph/1432.cwl
+@@ -1,3 +1,4 @@
++#!/usr/bin/env cwl-runner
+ class: Workflow
+ cwlVersion: v1.2
+ inputs:
+diff --git a/tests/subgraph/env-tool2.cwl b/tests/subgraph/env-tool2.cwl
+old mode 100644
+new mode 100755
+index f568e54..14c8a68
+--- a/tests/subgraph/env-tool2.cwl
++++ b/tests/subgraph/env-tool2.cwl
+@@ -1,3 +1,4 @@
++#!/usr/bin/env cwl-runner
+ class: CommandLineTool
+ cwlVersion: v1.2
+ inputs:
+diff --git a/tests/subgraph/env-tool2_no_env.cwl b/tests/subgraph/env-tool2_no_env.cwl
+old mode 100644
+new mode 100755
+index c4a6f63..2b3711b
+--- a/tests/subgraph/env-tool2_no_env.cwl
++++ b/tests/subgraph/env-tool2_no_env.cwl
+@@ -1,3 +1,4 @@
++#!/usr/bin/env cwl-runner
+ class: CommandLineTool
+ cwlVersion: v1.2
+ inputs:
+diff --git a/tests/subgraph/env-tool2_req.cwl b/tests/subgraph/env-tool2_req.cwl
+old mode 100644
+new mode 100755
+index 96b0bc3..9431080
+--- a/tests/subgraph/env-tool2_req.cwl
++++ b/tests/subgraph/env-tool2_req.cwl
+@@ -1,3 +1,4 @@
++#!/usr/bin/env cwl-runner
+ class: CommandLineTool
+ cwlVersion: v1.2
+ inputs:
+diff --git a/tests/subgraph/env-wf2.cwl b/tests/subgraph/env-wf2.cwl
+old mode 100644
+new mode 100755
+diff --git a/tests/subgraph/env-wf2_hint_collision.cwl b/tests/subgraph/env-wf2_hint_collision.cwl
+old mode 100644
+new mode 100755
+diff --git a/tests/subgraph/env-wf2_hint_req_collision.cwl b/tests/subgraph/env-wf2_hint_req_collision.cwl
+old mode 100644
+new mode 100755
+diff --git a/tests/subgraph/env-wf2_long.cwl b/tests/subgraph/env-wf2_long.cwl
+old mode 100644
+new mode 100755
+diff --git a/tests/subgraph/env-wf2_only_hint.cwl b/tests/subgraph/env-wf2_only_hint.cwl
+old mode 100644
+new mode 100755
+diff --git a/tests/subgraph/env-wf2_req_collision.cwl b/tests/subgraph/env-wf2_req_collision.cwl
+old mode 100644
+new mode 100755
+diff --git a/tests/subgraph/env-wf2_subwf-packed.cwl b/tests/subgraph/env-wf2_subwf-packed.cwl
+old mode 100644
+new mode 100755
+index ed119f0..e1c0964
+--- a/tests/subgraph/env-wf2_subwf-packed.cwl
++++ b/tests/subgraph/env-wf2_subwf-packed.cwl
+@@ -1,3 +1,4 @@
++#!/usr/bin/env cwl-runner
+ {
+ "$graph": [
+ {
+@@ -127,4 +128,4 @@
+ }
+ ],
+ "cwlVersion": "v1.2"
+-}
+\ No newline at end of file
++}
+diff --git a/tests/subgraph/env-wf2_subwf.cwl b/tests/subgraph/env-wf2_subwf.cwl
+old mode 100644
+new mode 100755
+diff --git a/tests/subgraph/env-wf2_subwf_b.cwl b/tests/subgraph/env-wf2_subwf_b.cwl
+old mode 100644
+new mode 100755
+diff --git a/tests/subgraph/steplevel-resreq.cwl b/tests/subgraph/steplevel-resreq.cwl
+old mode 100644
+new mode 100755
+diff --git a/tests/subgraph/timelimit2-wf.cwl b/tests/subgraph/timelimit2-wf.cwl
+old mode 100644
+new mode 100755
+diff --git a/tests/test_examples.py b/tests/test_examples.py
+index f413976..b78965b 100644
+--- a/tests/test_examples.py
++++ b/tests/test_examples.py
+@@ -1878,7 +1878,7 @@ def test_invalid_nested_array() -> None:
+ stdout = re.sub(r"\s\s+", " ", stdout)
+ assert "Tool definition failed validation:" in stdout
+ assert (
+- "tests/nested-array.cwl:6:5: Field 'type' references unknown identifier 'string[][]'"
++ "tests/nested-array.cwl:7:5: Field 'type' references unknown identifier 'string[][]'"
+ ) in stdout
+
+
+diff --git a/tests/test_validate.py b/tests/test_validate.py
+index f2d89e4..8e664d9 100644
+--- a/tests/test_validate.py
++++ b/tests/test_validate.py
+@@ -70,7 +70,7 @@ def test_validate_quiet() -> None:
+ stdout = re.sub(r"\s\s+", " ", stdout)
+ assert "INFO" not in stdout
+ assert "INFO" not in stderr
+- assert "tests/CometAdapter.cwl:9:3: object id" in stdout
++ assert "tests/CometAdapter.cwl:10:3: object id" in stdout
+ assert "tests/CometAdapter.cwl#out' previously defined" in stdout
+
+
+@@ -119,9 +119,9 @@ def test_validate_custom_logger() -> None:
+ assert "WARNING" not in stdout
+ assert "WARNING" not in stderr
+ assert "WARNING" in custom_log_text
+- assert "tests/CometAdapter.cwl:9:3: object id" not in stdout
+- assert "tests/CometAdapter.cwl:9:3: object id" not in stderr
+- assert "tests/CometAdapter.cwl:9:3: object id" in custom_log_text
++ assert "tests/CometAdapter.cwl:10:3: object id" not in stdout
++ assert "tests/CometAdapter.cwl:10:3: object id" not in stderr
++ assert "tests/CometAdapter.cwl:10:3: object id" in custom_log_text
+ assert "tests/CometAdapter.cwl#out' previously defined" not in stdout
+ assert "tests/CometAdapter.cwl#out' previously defined" not in stderr
+ assert "tests/CometAdapter.cwl#out' previously defined" in custom_log_text
+diff --git a/tests/trs/Dockstore.cwl b/tests/trs/Dockstore.cwl
+old mode 100644
+new mode 100755
+diff --git a/tests/trs/md5sum-tool.cwl b/tests/trs/md5sum-tool.cwl
+old mode 100644
+new mode 100755
+diff --git a/tests/trs/md5sum-workflow.cwl b/tests/trs/md5sum-workflow.cwl
+old mode 100644
+new mode 100755
+diff --git a/tests/utf_doc_example.cwl b/tests/utf_doc_example.cwl
+old mode 100644
+new mode 100755
+diff --git a/tests/wc-tool-bad-hints.cwl b/tests/wc-tool-bad-hints.cwl
+old mode 100644
+new mode 100755
+diff --git a/tests/wc-tool-bad-reqs.cwl b/tests/wc-tool-bad-reqs.cwl
+old mode 100644
+new mode 100755
+diff --git a/tests/wf/1496.cwl b/tests/wf/1496.cwl
+old mode 100644
+new mode 100755
+index 74f6ef4..d5da025
+--- a/tests/wf/1496.cwl
++++ b/tests/wf/1496.cwl
+@@ -1,3 +1,4 @@
++#!/usr/bin/env cwl-runner
+ cwlVersion: v1.2
+ class: CommandLineTool
+
+diff --git a/tests/wf/1590.cwl b/tests/wf/1590.cwl
+old mode 100644
+new mode 100755
+index 19c8ad3..de602a5
+--- a/tests/wf/1590.cwl
++++ b/tests/wf/1590.cwl
+@@ -1,3 +1,4 @@
++#!/usr/bin/env cwl-runner
+ {
+ "baseCommand": [
+ "cat"
+diff --git a/tests/wf/1st-workflow.cwl b/tests/wf/1st-workflow.cwl
+old mode 100644
+new mode 100755
+diff --git a/tests/wf/811-12.cwl b/tests/wf/811-12.cwl
+old mode 100644
+new mode 100755
+index f4403f4..ab0b2bd
+--- a/tests/wf/811-12.cwl
++++ b/tests/wf/811-12.cwl
+@@ -1,3 +1,4 @@
++#!/usr/bin/env cwl-runner
+ cwlVersion: v1.2
+ class: Workflow
+
+diff --git a/tests/wf/811.cwl b/tests/wf/811.cwl
+old mode 100644
+new mode 100755
+index 16a4c82..8ef826f
+--- a/tests/wf/811.cwl
++++ b/tests/wf/811.cwl
+@@ -1,3 +1,4 @@
++#!/usr/bin/env cwl-runner
+ cwlVersion: v1.0
+ class: Workflow
+
+diff --git a/tests/wf/816_tool.cwl b/tests/wf/816_tool.cwl
+old mode 100644
+new mode 100755
+index 00395ab..c48d3e3
+--- a/tests/wf/816_tool.cwl
++++ b/tests/wf/816_tool.cwl
+@@ -1,3 +1,4 @@
++#!/usr/bin/env cwl-runner
+ cwlVersion: v1.0
+ class: CommandLineTool
+ requirements:
+diff --git a/tests/wf/816_wf.cwl b/tests/wf/816_wf.cwl
+old mode 100644
+new mode 100755
+index a64b130..9db1439
+--- a/tests/wf/816_wf.cwl
++++ b/tests/wf/816_wf.cwl
+@@ -1,3 +1,4 @@
++#!/usr/bin/env cwl-runner
+ class: Workflow
+ cwlVersion: v1.0
+ inputs:
+diff --git a/tests/wf/910.cwl b/tests/wf/910.cwl
+old mode 100644
+new mode 100755
+diff --git a/tests/wf/arguments.cwl b/tests/wf/arguments.cwl
+old mode 100644
+new mode 100755
+diff --git a/tests/wf/bad-stderr-expr.cwl b/tests/wf/bad-stderr-expr.cwl
+old mode 100644
+new mode 100755
+diff --git a/tests/wf/bad-stdin-expr.cwl b/tests/wf/bad-stdin-expr.cwl
+old mode 100644
+new mode 100755
+diff --git a/tests/wf/bad-stdout-expr.cwl b/tests/wf/bad-stdout-expr.cwl
+old mode 100644
+new mode 100755
+diff --git a/tests/wf/bad_networkaccess.cwl b/tests/wf/bad_networkaccess.cwl
+old mode 100644
+new mode 100755
+diff --git a/tests/wf/bad_timelimit.cwl b/tests/wf/bad_timelimit.cwl
+old mode 100644
+new mode 100755
+diff --git a/tests/wf/cache_test_workflow.cwl b/tests/wf/cache_test_workflow.cwl
+old mode 100644
+new mode 100755
+diff --git a/tests/wf/cat-tool.cwl b/tests/wf/cat-tool.cwl
+old mode 100644
+new mode 100755
+diff --git a/tests/wf/conditional_step_no_inputs.cwl b/tests/wf/conditional_step_no_inputs.cwl
+old mode 100644
+new mode 100755
+diff --git a/tests/wf/conflict.cwl b/tests/wf/conflict.cwl
+old mode 100644
+new mode 100755
+diff --git a/tests/wf/cores_float.cwl b/tests/wf/cores_float.cwl
+old mode 100644
+new mode 100755
+diff --git a/tests/wf/default-dir5.cwl b/tests/wf/default-dir5.cwl
+old mode 100644
+new mode 100755
+diff --git a/tests/wf/default-wf5.cwl b/tests/wf/default-wf5.cwl
+old mode 100644
+new mode 100755
+diff --git a/tests/wf/double-nested.cwl b/tests/wf/double-nested.cwl
+old mode 100644
+new mode 100755
+diff --git a/tests/wf/expect_trick_packed.cwl b/tests/wf/expect_trick_packed.cwl
+old mode 100644
+new mode 100755
+diff --git a/tests/wf/extract_region_specs.cwl b/tests/wf/extract_region_specs.cwl
+old mode 100644
+new mode 100755
+index 279fa44..437222a
+--- a/tests/wf/extract_region_specs.cwl
++++ b/tests/wf/extract_region_specs.cwl
+@@ -1,3 +1,4 @@
++#!/usr/bin/env cwl-runner
+ {
+ "cwlVersion": "v1.0",
+ "class": "CommandLineTool",
+diff --git a/tests/wf/floats_small_and_large.cwl b/tests/wf/floats_small_and_large.cwl
+old mode 100644
+new mode 100755
+index 4343273..1637bd9
+--- a/tests/wf/floats_small_and_large.cwl
++++ b/tests/wf/floats_small_and_large.cwl
+@@ -1,3 +1,4 @@
++#!/usr/bin/env cwl-runner
+ cwlVersion: v1.0
+ class: CommandLineTool
+ baseCommand: echo
+diff --git a/tests/wf/generator/pytoolgen.cwl b/tests/wf/generator/pytoolgen.cwl
+old mode 100644
+new mode 100755
+diff --git a/tests/wf/input_named_id.cwl b/tests/wf/input_named_id.cwl
+old mode 100644
+new mode 100755
+index e559f96..82a0353
+--- a/tests/wf/input_named_id.cwl
++++ b/tests/wf/input_named_id.cwl
+@@ -1,3 +1,4 @@
++#!/usr/bin/env cwl-runner
+ label: FeatureFinderIdentification
+ doc: ""
+ inputs:
+diff --git a/tests/wf/iwd-passthrough1.cwl b/tests/wf/iwd-passthrough1.cwl
+old mode 100644
+new mode 100755
+diff --git a/tests/wf/iwdr-empty.cwl b/tests/wf/iwdr-empty.cwl
+old mode 100644
+new mode 100755
+diff --git a/tests/wf/iwdr-entry.cwl b/tests/wf/iwdr-entry.cwl
+old mode 100644
+new mode 100755
+diff --git a/tests/wf/iwdr-passthrough-successive.cwl b/tests/wf/iwdr-passthrough-successive.cwl
+old mode 100644
+new mode 100755
+diff --git a/tests/wf/literalfile.cwl b/tests/wf/literalfile.cwl
+old mode 100644
+new mode 100755
+diff --git a/tests/wf/malformed_outputs.cwl b/tests/wf/malformed_outputs.cwl
+old mode 100644
+new mode 100755
+diff --git a/tests/wf/missing-tool.cwl b/tests/wf/missing-tool.cwl
+old mode 100644
+new mode 100755
+diff --git a/tests/wf/mpi_env.cwl b/tests/wf/mpi_env.cwl
+old mode 100644
+new mode 100755
+diff --git a/tests/wf/mpi_expr.cwl b/tests/wf/mpi_expr.cwl
+old mode 100644
+new mode 100755
+diff --git a/tests/wf/mpi_line_count.cwl b/tests/wf/mpi_line_count.cwl
+old mode 100644
+new mode 100755
+diff --git a/tests/wf/mpi_simple.cwl b/tests/wf/mpi_simple.cwl
+old mode 100644
+new mode 100755
+diff --git a/tests/wf/mpi_simple_wf.cwl b/tests/wf/mpi_simple_wf.cwl
+old mode 100644
+new mode 100755
+diff --git a/tests/wf/nested.cwl b/tests/wf/nested.cwl
+old mode 100644
+new mode 100755
+diff --git a/tests/wf/networkaccess-fail.cwl b/tests/wf/networkaccess-fail.cwl
+old mode 100644
+new mode 100755
+diff --git a/tests/wf/networkaccess.cwl b/tests/wf/networkaccess.cwl
+old mode 100644
+new mode 100755
+diff --git a/tests/wf/no-parameters-echo.cwl b/tests/wf/no-parameters-echo.cwl
+old mode 100644
+new mode 100755
+diff --git a/tests/wf/nvidia-smi-cc.cwl b/tests/wf/nvidia-smi-cc.cwl
+old mode 100644
+new mode 100755
+index a4f315b..92e781d
+--- a/tests/wf/nvidia-smi-cc.cwl
++++ b/tests/wf/nvidia-smi-cc.cwl
+@@ -1,3 +1,4 @@
++#!/usr/bin/env cwl-runner
+ cwlVersion: v1.2
+ class: CommandLineTool
+ $namespaces:
+diff --git a/tests/wf/nvidia-smi-container.cwl b/tests/wf/nvidia-smi-container.cwl
+old mode 100644
+new mode 100755
+index 84fd72d..22092fa
+--- a/tests/wf/nvidia-smi-container.cwl
++++ b/tests/wf/nvidia-smi-container.cwl
+@@ -1,3 +1,4 @@
++#!/usr/bin/env cwl-runner
+ cwlVersion: v1.2
+ class: CommandLineTool
+ $namespaces:
+diff --git a/tests/wf/nvidia-smi-max.cwl b/tests/wf/nvidia-smi-max.cwl
+old mode 100644
+new mode 100755
+index d3d4d5e..1f8687d
+--- a/tests/wf/nvidia-smi-max.cwl
++++ b/tests/wf/nvidia-smi-max.cwl
+@@ -1,3 +1,4 @@
++#!/usr/bin/env cwl-runner
+ cwlVersion: v1.2
+ class: CommandLineTool
+ $namespaces:
+diff --git a/tests/wf/nvidia-smi-range.cwl b/tests/wf/nvidia-smi-range.cwl
+old mode 100644
+new mode 100755
+index 19d3ea4..2e131a3
+--- a/tests/wf/nvidia-smi-range.cwl
++++ b/tests/wf/nvidia-smi-range.cwl
+@@ -1,3 +1,4 @@
++#!/usr/bin/env cwl-runner
+ cwlVersion: v1.2
+ class: CommandLineTool
+ $namespaces:
+diff --git a/tests/wf/nvidia-smi.cwl b/tests/wf/nvidia-smi.cwl
+old mode 100644
+new mode 100755
+index 8e227d0..8a17f8e
+--- a/tests/wf/nvidia-smi.cwl
++++ b/tests/wf/nvidia-smi.cwl
+@@ -1,3 +1,4 @@
++#!/usr/bin/env cwl-runner
+ cwlVersion: v1.2
+ class: CommandLineTool
+ $namespaces:
+diff --git a/tests/wf/operation/abstract-cosifer.cwl b/tests/wf/operation/abstract-cosifer.cwl
+old mode 100644
+new mode 100755
+index 0576208..2a50cde
+--- a/tests/wf/operation/abstract-cosifer.cwl
++++ b/tests/wf/operation/abstract-cosifer.cwl
+@@ -1,3 +1,4 @@
++#!/usr/bin/env cwl-runner
+ class: Operation
+ cwlVersion: v1.2
+
+diff --git a/tests/wf/operation/operation-single.cwl b/tests/wf/operation/operation-single.cwl
+old mode 100644
+new mode 100755
+index 2119bf0..63b6a6b
+--- a/tests/wf/operation/operation-single.cwl
++++ b/tests/wf/operation/operation-single.cwl
+@@ -1,3 +1,4 @@
++#!/usr/bin/env cwl-runner
+ class: Workflow
+ cwlVersion: v1.2
+ id: abstract_cosifer_workflow
+diff --git a/tests/wf/optional-numerical-output-0.cwl b/tests/wf/optional-numerical-output-0.cwl
+old mode 100644
+new mode 100755
+diff --git a/tests/wf/optional_src_mandatory_sink.cwl b/tests/wf/optional_src_mandatory_sink.cwl
+old mode 100644
+new mode 100755
+diff --git a/tests/wf/packed-with-loadlisting.cwl b/tests/wf/packed-with-loadlisting.cwl
+old mode 100644
+new mode 100755
+diff --git a/tests/wf/packed_no_main.cwl b/tests/wf/packed_no_main.cwl
+old mode 100644
+new mode 100755
+index 8307a08..aafd0de
+--- a/tests/wf/packed_no_main.cwl
++++ b/tests/wf/packed_no_main.cwl
+@@ -1,3 +1,4 @@
++#!/usr/bin/env cwl-runner
+ cwlVersion: v1.2
+ $graph:
+ - id: echo
+diff --git a/tests/wf/paramref_arguments_roundtrip.cwl b/tests/wf/paramref_arguments_roundtrip.cwl
+old mode 100644
+new mode 100755
+diff --git a/tests/wf/paramref_arguments_self.cwl b/tests/wf/paramref_arguments_self.cwl
+old mode 100644
+new mode 100755
+diff --git a/tests/wf/record_outputeval.cwl b/tests/wf/record_outputeval.cwl
+old mode 100644
+new mode 100755
+index 45daf9b..e7b59cb
+--- a/tests/wf/record_outputeval.cwl
++++ b/tests/wf/record_outputeval.cwl
+@@ -1,3 +1,4 @@
++#!/usr/bin/env cwl-runner
+ cwlVersion: v1.2
+ class: CommandLineTool
+ requirements:
+diff --git a/tests/wf/resreq_expr_float_v1_0.cwl b/tests/wf/resreq_expr_float_v1_0.cwl
+old mode 100644
+new mode 100755
+index d5ea08c..a36877c
+--- a/tests/wf/resreq_expr_float_v1_0.cwl
++++ b/tests/wf/resreq_expr_float_v1_0.cwl
+@@ -1,3 +1,4 @@
++#!/usr/bin/env cwl-runner
+ cwlVersion: v1.0
+ class: CommandLineTool
+ requirements:
+diff --git a/tests/wf/resreq_expr_float_v1_2.cwl b/tests/wf/resreq_expr_float_v1_2.cwl
+old mode 100644
+new mode 100755
+index cfb1b2a..ca72364
+--- a/tests/wf/resreq_expr_float_v1_2.cwl
++++ b/tests/wf/resreq_expr_float_v1_2.cwl
+@@ -1,3 +1,4 @@
++#!/usr/bin/env cwl-runner
+ cwlVersion: v1.2
+ class: CommandLineTool
+ requirements:
+diff --git a/tests/wf/scatter2.cwl b/tests/wf/scatter2.cwl
+old mode 100644
+new mode 100755
+diff --git a/tests/wf/scatter2_subwf.cwl b/tests/wf/scatter2_subwf.cwl
+old mode 100644
+new mode 100755
+diff --git a/tests/wf/schemadef-bug-1473.cwl b/tests/wf/schemadef-bug-1473.cwl
+old mode 100644
+new mode 100755
+index ad87ae0..beab321
+--- a/tests/wf/schemadef-bug-1473.cwl
++++ b/tests/wf/schemadef-bug-1473.cwl
+@@ -1,3 +1,4 @@
++#!/usr/bin/env cwl-runner
+ {
+ "$graph": [
+ {
+diff --git a/tests/wf/schemadef-tool-12.cwl b/tests/wf/schemadef-tool-12.cwl
+old mode 100644
+new mode 100755
+diff --git a/tests/wf/schemadef-tool.cwl b/tests/wf/schemadef-tool.cwl
+old mode 100644
+new mode 100755
+diff --git a/tests/wf/sec-tool.cwl b/tests/wf/sec-tool.cwl
+old mode 100644
+new mode 100755
+diff --git a/tests/wf/sec-wf-out.cwl b/tests/wf/sec-wf-out.cwl
+old mode 100644
+new mode 100755
+diff --git a/tests/wf/sec-wf.cwl b/tests/wf/sec-wf.cwl
+old mode 100644
+new mode 100755
+diff --git a/tests/wf/secret_job.cwl b/tests/wf/secret_job.cwl
+old mode 100644
+new mode 100755
+diff --git a/tests/wf/secret_wf.cwl b/tests/wf/secret_wf.cwl
+old mode 100644
+new mode 100755
+diff --git a/tests/wf/separate_without_prefix.cwl b/tests/wf/separate_without_prefix.cwl
+old mode 100644
+new mode 100755
+diff --git a/tests/wf/shm_size.cwl b/tests/wf/shm_size.cwl
+old mode 100644
+new mode 100755
+diff --git a/tests/wf/storage_float.cwl b/tests/wf/storage_float.cwl
+old mode 100644
+new mode 100755
+diff --git a/tests/wf/tar-param.cwl b/tests/wf/tar-param.cwl
+old mode 100644
+new mode 100755
+diff --git a/tests/wf/three_step_color.cwl b/tests/wf/three_step_color.cwl
+old mode 100644
+new mode 100755
+diff --git a/tests/wf/timelimit-fail.cwl b/tests/wf/timelimit-fail.cwl
+old mode 100644
+new mode 100755
+diff --git a/tests/wf/timelimit.cwl b/tests/wf/timelimit.cwl
+old mode 100644
+new mode 100755
+diff --git a/tests/wf/touch_tool.cwl b/tests/wf/touch_tool.cwl
+old mode 100644
+new mode 100755
+diff --git a/tests/wf/trick_defaults.cwl b/tests/wf/trick_defaults.cwl
+old mode 100644
+new mode 100755
+diff --git a/tests/wf/trick_defaults2.cwl b/tests/wf/trick_defaults2.cwl
+old mode 100644
+new mode 100755
+diff --git a/tests/wf/vf-concat.cwl b/tests/wf/vf-concat.cwl
+old mode 100644
+new mode 100755
+diff --git a/tests/wf/workreuse-fail.cwl b/tests/wf/workreuse-fail.cwl
+old mode 100644
+new mode 100755
+diff --git a/tests/wf/workreuse.cwl b/tests/wf/workreuse.cwl
+old mode 100644
+new mode 100755
+diff --git a/tests/with_doc.cwl b/tests/with_doc.cwl
+old mode 100644
+new mode 100755
+diff --git a/tests/without_doc.cwl b/tests/without_doc.cwl
+old mode 100644
+new mode 100755
=====================================
debian/patches/disable_prov
=====================================
@@ -4,15 +4,17 @@ Subject: Disable --provance until python3-prov issue is resolved
Forwarded: not-needed
---
- cwltool/argparser.py | 60 +---
+ cwltool/argparser.py | 58 +--
setup.py | 2 +-
- tests/test_main_parsed_args.py | 19 --
- tests/test_provenance.py | 757 -----------------------------------------
- 4 files changed, 2 insertions(+), 836 deletions(-)
+ tests/test_main_parsed_args.py | 19 -
+ tests/test_provenance.py | 845 -----------------------------------------
+ 4 files changed, 2 insertions(+), 922 deletions(-)
---- cwltool.orig/cwltool/argparser.py
-+++ cwltool/cwltool/argparser.py
-@@ -145,63 +145,7 @@
+diff --git a/cwltool/argparser.py b/cwltool/argparser.py
+index 3622b62..8e7b427 100644
+--- a/cwltool/argparser.py
++++ b/cwltool/argparser.py
+@@ -145,63 +145,7 @@ def arg_parser() -> argparse.ArgumentParser:
default=60,
)
@@ -77,9 +79,11 @@ Forwarded: not-needed
non_exec_group = parser.add_argument_group(title="Non-execution options")
printgroup = non_exec_group.add_mutually_exclusive_group()
---- cwltool.orig/setup.py
-+++ cwltool/setup.py
-@@ -126,7 +126,7 @@
+diff --git a/setup.py b/setup.py
+index d3fef7b..879e9a2 100644
+--- a/setup.py
++++ b/setup.py
+@@ -126,7 +126,7 @@ setup(
"ruamel.yaml >= 0.16, < 0.19",
"rdflib >= 4.2.2, < 7.2.0",
"schema-salad >= 8.7, < 9",
@@ -88,9 +92,11 @@ Forwarded: not-needed
"mypy-extensions",
"psutil >= 5.6.6",
"coloredlogs",
---- cwltool.orig/tests/test_main_parsed_args.py
-+++ cwltool/tests/test_main_parsed_args.py
-@@ -19,22 +19,3 @@
+diff --git a/tests/test_main_parsed_args.py b/tests/test_main_parsed_args.py
+index 7a94d92..278d864 100644
+--- a/tests/test_main_parsed_args.py
++++ b/tests/test_main_parsed_args.py
+@@ -19,22 +19,3 @@ def test_main_parsed_args(tmp_path: Path) -> None:
assert main(args=parsed_args, stdout=stdout, stderr=stderr) == 0
except SystemExit as err:
assert err.code == 0
@@ -113,9 +119,11 @@ Forwarded: not-needed
-
- manifest_file = prov_folder / "metadata" / "manifest.json"
- assert manifest_file.is_file(), f"Can't find RO-Crate manifest {manifest_file}"
---- cwltool.orig/tests/test_provenance.py
-+++ cwltool/tests/test_provenance.py
-@@ -8,7 +8,6 @@
+diff --git a/tests/test_provenance.py b/tests/test_provenance.py
+index d7a2a69..d11c261 100644
+--- a/tests/test_provenance.py
++++ b/tests/test_provenance.py
+@@ -8,7 +8,6 @@ from pathlib import Path
from typing import IO, Any, cast
import arcp
@@ -123,7 +131,7 @@ Forwarded: not-needed
import pytest
from rdflib import Graph, Namespace, URIRef
from rdflib.namespace import DC, DCTERMS, RDF
-@@ -36,847 +35,3 @@
+@@ -36,847 +35,3 @@ FOAF = Namespace("http://xmlns.com/foaf/0.1/")
TEST_ORCID = "https://orcid.org/0000-0003-4862-3349"
=====================================
debian/patches/intersphinx
=====================================
@@ -1,9 +1,17 @@
-Author: Michael R. Crusoe <crusoe at debian.org>
-Description: link to the packaged docs
+From: "Michael R. Crusoe" <crusoe at debian.org>
+Date: Thu, 30 Jan 2025 11:09:18 +0100
+Subject: link to the packaged docs
+
Forwarded: not-needed
---- cwltool.orig/docs/conf.py
-+++ cwltool/docs/conf.py
-@@ -49,9 +49,9 @@
+---
+ docs/conf.py | 6 +++---
+ 1 file changed, 3 insertions(+), 3 deletions(-)
+
+diff --git a/docs/conf.py b/docs/conf.py
+index 6e04b5d..af813af 100644
+--- a/docs/conf.py
++++ b/docs/conf.py
+@@ -49,9 +49,9 @@ extensions = [
autosectionlabel_prefix_document = True
intersphinx_mapping = {
=====================================
debian/patches/privacy
=====================================
@@ -0,0 +1,56 @@
+Author: Michael R. Crusoe <crusoe at debian.org>
+Description: Remove externally-hosted badges from the README
+Forwarded: not-needed
+--- cwltool.orig/README.rst
++++ cwltool/README.rst
+@@ -2,50 +2,6 @@
+ ``cwltool``: The reference implementation of the Common Workflow Language standards
+ #############################################################################################
+
+-|Linux Status| |Coverage Status| |Docs Status|
+-
+-PyPI: |PyPI Version| |PyPI Downloads Month| |Total PyPI Downloads|
+-
+-Conda: |Conda Version| |Conda Installs|
+-
+-Debian: |Debian Testing package| |Debian Stable package|
+-
+-Quay.io (Docker): |Quay.io Container|
+-
+-.. |Linux Status| image:: https://github.com/common-workflow-language/cwltool/actions/workflows/ci-tests.yml/badge.svg?branch=main
+- :target: https://github.com/common-workflow-language/cwltool/actions/workflows/ci-tests.yml
+-
+-.. |Debian Stable package| image:: https://badges.debian.net/badges/debian/stable/cwltool/version.svg
+- :target: https://packages.debian.org/stable/cwltool
+-
+-.. |Debian Testing package| image:: https://badges.debian.net/badges/debian/testing/cwltool/version.svg
+- :target: https://packages.debian.org/testing/cwltool
+-
+-.. |Coverage Status| image:: https://img.shields.io/codecov/c/github/common-workflow-language/cwltool.svg
+- :target: https://codecov.io/gh/common-workflow-language/cwltool
+-
+-.. |PyPI Version| image:: https://badge.fury.io/py/cwltool.svg
+- :target: https://badge.fury.io/py/cwltool
+-
+-.. |PyPI Downloads Month| image:: https://pepy.tech/badge/cwltool/month
+- :target: https://pepy.tech/project/cwltool
+-
+-.. |Total PyPI Downloads| image:: https://static.pepy.tech/personalized-badge/cwltool?period=total&units=international_system&left_color=black&right_color=orange&left_text=Total%20PyPI%20Downloads
+- :target: https://pepy.tech/project/cwltool
+-
+-.. |Conda Version| image:: https://anaconda.org/conda-forge/cwltool/badges/version.svg
+- :target: https://anaconda.org/conda-forge/cwltool
+-
+-.. |Conda Installs| image:: https://anaconda.org/conda-forge/cwltool/badges/downloads.svg
+- :target: https://anaconda.org/conda-forge/cwltool
+-
+-.. |Quay.io Container| image:: https://quay.io/repository/commonwl/cwltool/status
+- :target: https://quay.io/repository/commonwl/cwltool
+-
+-.. |Docs Status| image:: https://readthedocs.org/projects/cwltool/badge/?version=latest
+- :target: https://cwltool.readthedocs.io/en/latest/?badge=latest
+- :alt: Documentation Status
+-
+ This is the reference implementation of the `Common Workflow Language open
+ standards <https://www.commonwl.org/>`_. It is intended to be feature complete
+ and provide comprehensive validation of CWL
=====================================
debian/patches/series
=====================================
@@ -1,2 +1,4 @@
disable_prov
intersphinx
+0003-Add-missing-cwl-runner-refs.patch
+privacy
=====================================
debian/rules
=====================================
@@ -3,9 +3,10 @@
DH_VERBOSE := 1
include /usr/share/dpkg/default.mk
export PYBUILD_DESTDIR=$(CURDIR)/debian/cwltool
-export PYBUILD_TEST_ARGS=-n=auto
export PYBUILD_AFTER_TEST=rm -Rf {build_dir}/tmp/ {build_dir}/main.cwl {build_dir}/output.txt*
-export HOME=$(shell echo $$PWD"/fakehome")
+export PYBUILD_TEST_ARGS=-k 'not (test_http_path_mapping or test_get_subgraph or test_udocker_usage_should_not_write_cid_file or test_udocker_should_display_memory_usage or test_content_types or test_get_step or test_udocker_nobanner)' $(DEB_BUILD_OPTION_PARALLEL:%=-n %) --ignore cwltool/schemas/ -rs --pyargs cwltool
+# test_http_path_mapping requires internet access (could be mocked?)
+# test_get_{subgraph,step} embedded local path isn't being cleaned properlyexport HOME=$(shell echo $$PWD"/fakehome")
%:
dh $@ --buildsystem=pybuild
@@ -14,7 +15,7 @@ execute_after_dh_auto_build:
PYTHONPATH=$(CURDIR)/cwltool $(MAKE) docs
debian/cwltool.1: debian/rules debian/cwltool.help2man
- python3 setup.py develop --user
+ export HOME=$(shell echo $$PWD"/fakehome") ; python3 setup.py develop --user ; \
help2man --version-string $(DEB_VERSION_EPOCH_UPSTREAM) -I debian/cwltool.help2man -N \
-o debian/cwltool.1 'python3 -m cwltool'
sed -i 's/__main__.py/cwltool/g' debian/cwltool.1
@@ -27,19 +28,5 @@ override_dh_installman:
endif
execute_after_dh_auto_install:
- find debian -name '*.cwl' -exec chmod a+x {} \;
find debian -name '*.json' -exec chmod a-x {} \;
-
-override_dh_auto_test:
-ifeq (,$(filter nocheck,$(DEB_BUILD_PROFILES)))
- dh_auto_install
- PYBUILD_SYSTEM=custom \
- PYBUILD_TEST_ARGS="cd {dir}; export PATH={destdir}/usr/bin:$$PATH ; \
- cd {build_dir}; export PYTHONPATH=$$(pwd); {interpreter} -m pytest \
- --ignore-glob "*test_http_input.py" \
- -k 'not (test_http_path_mapping or test_get_subgraph or test_udocker_usage_should_not_write_cid_file or test_udocker_should_display_memory_usage or test_content_types or test_get_step or test_udocker_nobanner)' \
- -n auto --ignore cwltool/schemas/ -rs --pyargs cwltool" dh_auto_test
- find .pybuild -name "out" -type f -delete
-endif
-# test_http_path_mapping requires internet access (could be mocked?)
-# test_get_{subgraph,step} embedded local path isn't being cleaned properly
+ find debian -name LICENSE.txt -delete
=====================================
debian/tests/control deleted
=====================================
@@ -1,3 +0,0 @@
-Tests: run-tests
-Depends: @, python3-pytest-xdist, python3-pytest-mock, python3-pytest-runner, nodejs, curl, procps, python3-pytest (>> 6.2), jq
-Restrictions: allow-stderr
=====================================
debian/tests/run-tests deleted
=====================================
@@ -1,19 +0,0 @@
-#!/bin/bash
-set -ex
-
-pkg=cwltool
-
-export LC_ALL=C.UTF-8
-if [ "${AUTOPKGTEST_TMP}" = "" ] ; then
- AUTOPKGTEST_TMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX)
- # shellcheck disable=SC2064
- trap "rm -rf ${AUTOPKGTEST_TMP}" 0 INT QUIT ABRT PIPE TERM
-fi
-cd "$AUTOPKGTEST_TMP"
-
-export HOME=${AUTOPKGTEST_TMP}
-
-py.test-3 -vvv --numprocesses=auto --ignore=cwltool/schemas -rs \
- --ignore=/usr/lib/python3/dist-packages/cwltool/tests/test_http_input.py \
- -k 'not (test_udocker_usage_should_not_write_cid_file or test_udocker_should_display_memory_usage or test_udocker_nobanner)' \
- --pyargs cwltool
View it on GitLab: https://salsa.debian.org/med-team/cwltool/-/compare/f10e9be585aaf5abc3df219e6eeba41a28b7cfad...31c7864a185f6ca6c280ac14da56b5dd7dd060fc
--
View it on GitLab: https://salsa.debian.org/med-team/cwltool/-/compare/f10e9be585aaf5abc3df219e6eeba41a28b7cfad...31c7864a185f6ca6c280ac14da56b5dd7dd060fc
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