Bump codespell from 2.4.1 to 2.4.2 by dependabot[bot] · Pull Request #213 · alpha-unito/streamflow-postgresql

dependabot · 2026-03-06T10:56:12Z

Bumps codespell from 2.4.1 to 2.4.2.

Release notes

v2.4.2

Highlights

Fixed compatibility with chardet 7+

What's Changed

Fix and clarify cases in ignore patterns by @DanielYang59 in codespell-project/codespell#3583

codespell-private.yml: Do not codespell digital signature files by @cclauss in codespell-project/codespell#3623

[pre-commit.ci] pre-commit autoupdate by @pre-commit-ci[bot] in codespell-project/codespell#3634

numbes->numbers and numbesr->numbers by @skshetry in codespell-project/codespell#3635

Add spelling corrections for disclose and variables. by @cfi-gb in codespell-project/codespell#3622

Add spelling correction for Vulnererability and variants. by @cfi-gb in codespell-project/codespell#3625

Remove lets->let's by @Piedone in codespell-project/codespell#3633

Add corrections for "dictate" by @jdufresne in codespell-project/codespell#3636

Add specicification (and pl) typo by @yarikoptic in codespell-project/codespell#3639

Remove "blueish" correction by @hadess in codespell-project/codespell#3510

Add "lighting" as an option to fix "lighning" by @yarikoptic in codespell-project/codespell#3648

Revert adding lien to the rare dictionary by @nikolaik in codespell-project/codespell#3631

"ane" could have been "one" by @yarikoptic in codespell-project/codespell#3645

Add spelling correction for "priort" by @cfi-gb in codespell-project/codespell#3647

Remove "fix" of "deques" - it is quite legit by @yarikoptic in codespell-project/codespell#3649

Several new suggestions by @mdeweerd in codespell-project/codespell#3621

Add proposal constraints to containts by @mdeweerd in codespell-project/codespell#3652

Additions dleay,infp,practive,utiliy by @mdeweerd in codespell-project/codespell#3643

Add calncelled and its variations by @mdeweerd in codespell-project/codespell#3650

Use raw strings for regex by @DimitriPapadopoulos in codespell-project/codespell#3654

Allow multiple spaces before codespell:ignore by @DimitriPapadopoulos in codespell-project/codespell#3653

Added correction from timeour to timeout by @jamesbraza in codespell-project/codespell#3656

Add typos found in various software projects by @luzpaz in codespell-project/codespell#3640

[pre-commit.ci] pre-commit autoupdate by @pre-commit-ci[bot] in codespell-project/codespell#3659

Add codespell suggestions for enabke and friends by @mdeweerd in codespell-project/codespell#3657

END: add "queues" (plural from queue) as possible fix for ques by @yarikoptic in codespell-project/codespell#3591

agreegate, lesda, realod, colouer by @mdeweerd in codespell-project/codespell#3665

Update pre-commit version in documentation by @prchoward in codespell-project/codespell#3666

MAINT: Rename CI file and run name by @larsoner in codespell-project/codespell#3667

preoccuption->preoccupation; occuption->occupation by @TheGiraffe3 in codespell-project/codespell#3668

Suggestions for: checkto, diminsion, waitfor by @mdeweerd in codespell-project/codespell#3670

Typos found in sigstore-python by @DimitriPapadopoulos in codespell-project/codespell#3664

usgin->using by @ydah in codespell-project/codespell#3672

Add typos found in various software projects by @luzpaz in codespell-project/codespell#3669

Add coered -> coerced by @effigies in codespell-project/codespell#3680

backwward(s)->backward(s), onwward(s)->onward(s) by @cjwatson in codespell-project/codespell#3682

[pre-commit.ci] pre-commit autoupdate by @pre-commit-ci[bot] in codespell-project/codespell#3685

telemetery->telemetry by @august-soderberg in codespell-project/codespell#3686

Add hexedacimal and similar typos by @Akuli in codespell-project/codespell#3692

Add rounted->routed, rounded and friends by @peternewman in codespell-project/codespell#3693

Add symmectric and similar typos by @Akuli in codespell-project/codespell#3694

Fix CI on Windows: pip upgrade pip by @DimitriPapadopoulos in codespell-project/codespell#3698

... (truncated)

Commits

2ccb47f Compat with chardet 7 (#3886)
4ec53bf [pre-commit.ci] pre-commit autoupdate
2a4acba Bump actions/download-artifact from 7 to 8
be17cac Bump actions/upload-artifact from 6 to 7
04a0712 Bump ruff (#3879)
583d879 avoide->avoid, avoided, avoids,
1f59f34 Add correction for 'foudation' to 'foundation'
e047fda Add spelling correction for gather and variants.
b5cd66d respondant->respondent
92125a3 Add detection of ivoice and variants.
Additional commits viewable in compare view

codecov · 2026-03-06T11:11:14Z

❌ 1 Tests Failed:

Tests completed	Failed	Passed	Skipped
409	1	408	3

View the top 3 failed test(s) by shortest run time

cwl-v1.3-2063e9095f421f2a2ce12abaf196b2ba06ca5aae/conformance_tests.cwltest.yaml::conformance_tests::cwltest::yaml::clt_any_input_with_file_provided

Stack Traces | 0.101s run time

CWL test execution failed. 
Returned non-zero but it should be zero
Test: job: 
  file:.../streamflow-postgresql/streamflow-postgresql/cwl-v1.3-2063e9095f421f2a2ce12abaf196b2ba06ca5aae/tests/io-any-file.json
output:
  t1: File
tool: 
  file:.../streamflow-postgresql/streamflow-postgresql/cwl-v1.3-2063e9095f421f2a2ce12abaf196b2ba06ca5aae/tests/io-any-1.cwl
id: 
  file:.../streamflow-postgresql/streamflow-postgresql/cwl-v1.3-2063e9095f421f2a2ce12abaf196b2ba06ca5aae/conformance_tests.cwltest.yaml#clt_any_input_with_file_provided
doc: Test Any parameter with file input to a tool
tags:
- command_line_tool
- inline_javascript
line: '2100'

cwl-v1.3-2063e9095f421f2a2ce12abaf196b2ba06ca5aae/conformance_tests.cwltest.yaml::conformance_tests::cwltest::yaml::workflow_any_input_with_string_provided

Stack Traces | 0.108s run time

CWL test execution failed. 
Returned non-zero but it should be zero
Test: job: 
  file:.../streamflow-postgresql/streamflow-postgresql/cwl-v1.3-2063e9095f421f2a2ce12abaf196b2ba06ca5aae/tests/io-any-string.json
output:
  t1: '7'
tool: 
  file:.../streamflow-postgresql/streamflow-postgresql/cwl-v1.3-2063e9095f421f2a2ce12abaf196b2ba06ca5aae/tests/io-any-wf-1.cwl
id: 
  file:.../streamflow-postgresql/streamflow-postgresql/cwl-v1.3-2063e9095f421f2a2ce12abaf196b2ba06ca5aae/conformance_tests.cwltest.yaml#workflow_any_input_with_string_provided
doc: Test Any parameter with string input to a workflow
tags:
- workflow
- inline_javascript
line: '2128'

cwl-v1.3-2063e9095f421f2a2ce12abaf196b2ba06ca5aae/conformance_tests.cwltest.yaml::conformance_tests::cwltest::yaml::clt_any_input_with_mixed_array_provided

Stack Traces | 0.139s run time

CWL test execution failed. 
Returned non-zero but it should be zero
Test: job: 
  file:.../streamflow-postgresql/streamflow-postgresql/cwl-v1.3-2063e9095f421f2a2ce12abaf196b2ba06ca5aae/tests/io-any-array.json
output:
  t1:
  - 1
  - moocow
tool: 
  file:.../streamflow-postgresql/streamflow-postgresql/cwl-v1.3-2063e9095f421f2a2ce12abaf196b2ba06ca5aae/tests/io-any-1.cwl
id: 
  file:.../streamflow-postgresql/streamflow-postgresql/cwl-v1.3-2063e9095f421f2a2ce12abaf196b2ba06ca5aae/conformance_tests.cwltest.yaml#clt_any_input_with_mixed_array_provided
doc: Test Any parameter with array input to a tool
tags:
- command_line_tool
- inline_javascript
line: '2107'

cwl-v1.3-2063e9095f421f2a2ce12abaf196b2ba06ca5aae/conformance_tests.cwltest.yaml::conformance_tests::cwltest::yaml::clt_any_input_with_record_provided

Stack Traces | 0.146s run time

CWL test execution failed. 
Returned non-zero but it should be zero
Test: job: 
  file:.../streamflow-postgresql/streamflow-postgresql/cwl-v1.3-2063e9095f421f2a2ce12abaf196b2ba06ca5aae/tests/io-any-record.json
output:
  t1:
    moo: 1
    cow: 5
tool: 
  file:.../streamflow-postgresql/streamflow-postgresql/cwl-v1.3-2063e9095f421f2a2ce12abaf196b2ba06ca5aae/tests/io-any-1.cwl
id: 
  file:.../streamflow-postgresql/streamflow-postgresql/cwl-v1.3-2063e9095f421f2a2ce12abaf196b2ba06ca5aae/conformance_tests.cwltest.yaml#clt_any_input_with_record_provided
doc: Test Any parameter with record input to a tool
tags:
- command_line_tool
- inline_javascript
line: '2114'

cwl-v1.3-2063e9095f421f2a2ce12abaf196b2ba06ca5aae/conformance_tests.cwltest.yaml::conformance_tests::cwltest::yaml::clt_any_input_with_string_provided

Stack Traces | 0.26s run time

CWL test execution failed. 
Returned non-zero but it should be zero
Test: job: 
  file:.../streamflow-postgresql/streamflow-postgresql/cwl-v1.3-2063e9095f421f2a2ce12abaf196b2ba06ca5aae/tests/io-any-string.json
output:
  t1: '7'
tool: 
  file:.../streamflow-postgresql/streamflow-postgresql/cwl-v1.3-2063e9095f421f2a2ce12abaf196b2ba06ca5aae/tests/io-any-1.cwl
id: 
  file:.../streamflow-postgresql/streamflow-postgresql/cwl-v1.3-2063e9095f421f2a2ce12abaf196b2ba06ca5aae/conformance_tests.cwltest.yaml#clt_any_input_with_string_provided
doc: Test Any parameter with string input to a tool
tags:
- command_line_tool
- inline_javascript
line: '2093'

cwl-v1.3-2063e9095f421f2a2ce12abaf196b2ba06ca5aae/conformance_tests.cwltest.yaml::conformance_tests::cwltest::yaml::workflow_any_input_with_integer_provided

Stack Traces | 1.99s run time

CWL test execution failed. 
Returned non-zero but it should be zero
Test: job: 
  file:.../streamflow-postgresql/streamflow-postgresql/cwl-v1.3-2063e9095f421f2a2ce12abaf196b2ba06ca5aae/tests/io-any-int.json
output:
  t1: 7
tool: 
  file:.../streamflow-postgresql/streamflow-postgresql/cwl-v1.3-2063e9095f421f2a2ce12abaf196b2ba06ca5aae/tests/io-any-wf-1.cwl
id: 
  file:.../streamflow-postgresql/streamflow-postgresql/cwl-v1.3-2063e9095f421f2a2ce12abaf196b2ba06ca5aae/conformance_tests.cwltest.yaml#workflow_any_input_with_integer_provided
doc: Test Any parameter with integer input to a workflow
tags:
- workflow
- inline_javascript
line: '2121'

cwl-v1.3-2063e9095f421f2a2ce12abaf196b2ba06ca5aae/conformance_tests.cwltest.yaml::conformance_tests::cwltest::yaml::clt_any_input_with_integer_provided

Stack Traces | 11801s run time

CWL test execution failed. 
Returned non-zero but it should be zero
Test: job: 
  file:.../streamflow-postgresql/streamflow-postgresql/cwl-v1.3-2063e9095f421f2a2ce12abaf196b2ba06ca5aae/tests/io-any-int.json
output:
  t1: 7
tool: 
  file:.../streamflow-postgresql/streamflow-postgresql/cwl-v1.3-2063e9095f421f2a2ce12abaf196b2ba06ca5aae/tests/io-any-1.cwl
id: 
  file:.../streamflow-postgresql/streamflow-postgresql/cwl-v1.3-2063e9095f421f2a2ce12abaf196b2ba06ca5aae/conformance_tests.cwltest.yaml#clt_any_input_with_integer_provided
doc: Test Any parameter with integer input to a tool
tags:
- command_line_tool
- inline_javascript
line: '2086'

View the full list of 1 ❄️ flaky test(s)

cwl-v1.3-2063e9095f421f2a2ce12abaf196b2ba06ca5aae/conformance_tests.cwltest.yaml::conformance_tests::cwltest::yaml::initial_workdir_secondary_files_expr

Flake rate in main: 10.00% (Passed 9 times, Failed 1 times)

Stack Traces | 142s run time

CWL test execution failed. 
expected: {
    "indexedfile": {
        "checksum": "sha1$327fc7aedf4f6b69a42a7c8b808dc5a7aff61376",
        "class": "File",
        "location": "input.txt",
        "secondaryFiles": [
            {
                "checksum": "sha1$1f6fe811644355974cdd06d9eb695d6e859f3b44",
                "class": "File",
                "location": "input.txt.idx1",
                "size": 1500
            },
            {
                "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",
                "class": "File",
                "location": "input.idx2",
                "size": 0
            },
            {
                "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",
                "class": "File",
                "location": "input.txt.idx3",
                "size": 0
            },
            {
                "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",
                "class": "File",
                "location": "input.txt.idx4",
                "size": 0
            },
            {
                "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",
                "class": "File",
                "location": "input.txt.idx5",
                "size": 0
            },
            {
                "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",
                "class": "File",
                "location": "input.idx6.txt",
                "size": 0
            },
            {
                "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",
                "class": "File",
                "location": "input.txt.idx7",
                "size": 0
            },
            {
                "checksum": "sha1$47a013e660d408619d894b20806b1d5086aab03b",
                "class": "File",
                "location": "hello.txt",
                "size": 13
            },
            {
                "class": "Directory",
                "listing": [
                    {
                        "basename": "index",
                        "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",
                        "class": "File",
                        "location": "index",
                        "size": 0
                    }
                ],
                "location": "input.txt_idx8"
            }
        ],
        "size": 1111
    },
    "outfile": {
        "checksum": "sha1$e2dc9daaef945ac15f01c238ed2f1660f60909a0",
        "class": "File",
        "location": "result.txt",
        "size": 142
    }
}
got: {
    "indexedfile": {
        "basename": "input.txt",
        "checksum": "sha1$327fc7aedf4f6b69a42a7c8b808dc5a7aff61376",
        "class": "File",
        "dirname": ".../pytest-0/popen-gw2/unlabled_test5",
        "location": "file://.../pytest-0/popen-gw2/unlabled_test5/input.txt",
        "nameext": ".txt",
        "nameroot": "input",
        "path": ".../pytest-0/popen-gw2/unlabled_test5/input.txt",
        "secondaryFiles": [
            {
                "basename": "input.txt.idx1",
                "checksum": "sha1$1f6fe811644355974cdd06d9eb695d6e859f3b44",
                "class": "File",
                "dirname": ".../pytest-0/popen-gw2/unlabled_test5",
                "location": "file://.../pytest-0/popen-gw2/unlabled_test5/input.txt.idx1",
                "nameext": ".idx1",
                "nameroot": "input.txt",
                "path": ".../pytest-0/popen-gw2/unlabled_test5/input.txt.idx1",
                "size": 1500
            },
            {
                "basename": "input.idx2",
                "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",
                "class": "File",
                "dirname": ".../pytest-0/popen-gw2/unlabled_test5",
                "location": "file://.../pytest-0/popen-gw2/unlabled_test5/input.idx2",
                "nameext": ".idx2",
                "nameroot": "input",
                "path": ".../pytest-0/popen-gw2/unlabled_test5/input.idx2",
                "size": 0
            },
            {
                "basename": "input.txt.idx3",
                "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",
                "class": "File",
                "dirname": ".../pytest-0/popen-gw2/unlabled_test5",
                "location": "file://.../pytest-0/popen-gw2/unlabled_test5/input.txt.idx3",
                "nameext": ".idx3",
                "nameroot": "input.txt",
                "path": ".../pytest-0/popen-gw2/unlabled_test5/input.txt.idx3",
                "size": 0
            },
            {
                "basename": "input.txt.idx4",
                "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",
                "class": "File",
                "dirname": ".../pytest-0/popen-gw2/unlabled_test5",
                "location": "file://.../pytest-0/popen-gw2/unlabled_test5/input.txt.idx4",
                "nameext": ".idx4",
                "nameroot": "input.txt",
                "path": ".../pytest-0/popen-gw2/unlabled_test5/input.txt.idx4",
                "size": 0
            },
            {
                "basename": "input.txt.idx5",
                "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",
                "class": "File",
                "dirname": ".../pytest-0/popen-gw2/unlabled_test5",
                "location": "file://.../pytest-0/popen-gw2/unlabled_test5/input.txt.idx5",
                "nameext": ".idx5",
                "nameroot": "input.txt",
                "path": ".../pytest-0/popen-gw2/unlabled_test5/input.txt.idx5",
                "size": 0
            },
            {
                "basename": "input.idx6.txt",
                "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",
                "class": "File",
                "dirname": ".../pytest-0/popen-gw2/unlabled_test5",
                "location": "file://.../pytest-0/popen-gw2/unlabled_test5/input.idx6.txt",
                "nameext": ".txt",
                "nameroot": "input.idx6",
                "path": ".../pytest-0/popen-gw2/unlabled_test5/input.idx6.txt",
                "size": 0
            },
            {
                "basename": "input.txt.idx7",
                "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",
                "class": "File",
                "dirname": ".../pytest-0/popen-gw2/unlabled_test5",
                "location": "file://.../pytest-0/popen-gw2/unlabled_test5/input.txt.idx7",
                "nameext": ".idx7",
                "nameroot": "input.txt",
                "path": ".../pytest-0/popen-gw2/unlabled_test5/input.txt.idx7",
                "size": 0
            },
            {
                "basename": "hello.txt",
                "checksum": "sha1$47a013e660d408619d894b20806b1d5086aab03b",
                "class": "File",
                "dirname": ".../pytest-0/popen-gw2/unlabled_test5",
                "location": "file://.../pytest-0/popen-gw2/unlabled_test5/hello.txt",
                "nameext": ".txt",
                "nameroot": "hello",
                "path": ".../pytest-0/popen-gw2/unlabled_test5/hello.txt",
                "size": 13
            },
            {
                "basename": "input.txt_idx8",
                "class": "Directory",
                "dirname": ".../pytest-0/popen-gw2/unlabled_test5",
                "location": "file://.../pytest-0/popen-gw2/unlabled_test5/input.txt_idx8",
                "path": ".../pytest-0/popen-gw2/unlabled_test5/input.txt_idx8"
            }
        ],
        "size": 1111
    },
    "outfile": {
        "basename": "result.txt",
        "checksum": "sha1$e2dc9daaef945ac15f01c238ed2f1660f60909a0",
        "class": "File",
        "dirname": ".../pytest-0/popen-gw2/unlabled_test5",
        "location": "file://.../pytest-0/popen-gw2/unlabled_test5/result.txt",
        "nameext": ".txt",
        "nameroot": "result",
        "path": ".../pytest-0/popen-gw2/unlabled_test5/result.txt",
        "size": 142
    }
}
caused by: failed comparison for key 'indexedfile': expected: {
    "checksum": "sha1$327fc7aedf4f6b69a42a7c8b808dc5a7aff61376",
    "class": "File",
    "location": "input.txt",
    "secondaryFiles": [
        {
            "checksum": "sha1$1f6fe811644355974cdd06d9eb695d6e859f3b44",
            "class": "File",
            "location": "input.txt.idx1",
            "size": 1500
        },
        {
            "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",
            "class": "File",
            "location": "input.idx2",
            "size": 0
        },
        {
            "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",
            "class": "File",
            "location": "input.txt.idx3",
            "size": 0
        },
        {
            "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",
            "class": "File",
            "location": "input.txt.idx4",
            "size": 0
        },
        {
            "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",
            "class": "File",
            "location": "input.txt.idx5",
            "size": 0
        },
        {
            "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",
            "class": "File",
            "location": "input.idx6.txt",
            "size": 0
        },
        {
            "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",
            "class": "File",
            "location": "input.txt.idx7",
            "size": 0
        },
        {
            "checksum": "sha1$47a013e660d408619d894b20806b1d5086aab03b",
            "class": "File",
            "location": "hello.txt",
            "size": 13
        },
        {
            "class": "Directory",
            "listing": [
                {
                    "basename": "index",
                    "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",
                    "class": "File",
                    "location": "index",
                    "size": 0
                }
            ],
            "location": "input.txt_idx8"
        }
    ],
    "size": 1111
}
got: {
    "basename": "input.txt",
    "checksum": "sha1$327fc7aedf4f6b69a42a7c8b808dc5a7aff61376",
    "class": "File",
    "dirname": ".../pytest-0/popen-gw2/unlabled_test5",
    "location": "file://.../pytest-0/popen-gw2/unlabled_test5/input.txt",
    "nameext": ".txt",
    "nameroot": "input",
    "path": ".../pytest-0/popen-gw2/unlabled_test5/input.txt",
    "secondaryFiles": [
        {
            "basename": "input.txt.idx1",
            "checksum": "sha1$1f6fe811644355974cdd06d9eb695d6e859f3b44",
            "class": "File",
            "dirname": ".../pytest-0/popen-gw2/unlabled_test5",
            "location": "file://.../pytest-0/popen-gw2/unlabled_test5/input.txt.idx1",
            "nameext": ".idx1",
            "nameroot": "input.txt",
            "path": ".../pytest-0/popen-gw2/unlabled_test5/input.txt.idx1",
            "size": 1500
        },
        {
            "basename": "input.idx2",
            "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",
            "class": "File",
            "dirname": ".../pytest-0/popen-gw2/unlabled_test5",
            "location": "file://.../pytest-0/popen-gw2/unlabled_test5/input.idx2",
            "nameext": ".idx2",
            "nameroot": "input",
            "path": ".../pytest-0/popen-gw2/unlabled_test5/input.idx2",
            "size": 0
        },
        {
            "basename": "input.txt.idx3",
            "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",
            "class": "File",
            "dirname": ".../pytest-0/popen-gw2/unlabled_test5",
            "location": "file://.../pytest-0/popen-gw2/unlabled_test5/input.txt.idx3",
            "nameext": ".idx3",
            "nameroot": "input.txt",
            "path": ".../pytest-0/popen-gw2/unlabled_test5/input.txt.idx3",
            "size": 0
        },
        {
            "basename": "input.txt.idx4",
            "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",
            "class": "File",
            "dirname": ".../pytest-0/popen-gw2/unlabled_test5",
            "location": "file://.../pytest-0/popen-gw2/unlabled_test5/input.txt.idx4",
            "nameext": ".idx4",
            "nameroot": "input.txt",
            "path": ".../pytest-0/popen-gw2/unlabled_test5/input.txt.idx4",
            "size": 0
        },
        {
            "basename": "input.txt.idx5",
            "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",
            "class": "File",
            "dirname": ".../pytest-0/popen-gw2/unlabled_test5",
            "location": "file://.../pytest-0/popen-gw2/unlabled_test5/input.txt.idx5",
            "nameext": ".idx5",
            "nameroot": "input.txt",
            "path": ".../pytest-0/popen-gw2/unlabled_test5/input.txt.idx5",
            "size": 0
        },
        {
            "basename": "input.idx6.txt",
            "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",
            "class": "File",
            "dirname": ".../pytest-0/popen-gw2/unlabled_test5",
            "location": "file://.../pytest-0/popen-gw2/unlabled_test5/input.idx6.txt",
            "nameext": ".txt",
            "nameroot": "input.idx6",
            "path": ".../pytest-0/popen-gw2/unlabled_test5/input.idx6.txt",
            "size": 0
        },
        {
            "basename": "input.txt.idx7",
            "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",
            "class": "File",
            "dirname": ".../pytest-0/popen-gw2/unlabled_test5",
            "location": "file://.../pytest-0/popen-gw2/unlabled_test5/input.txt.idx7",
            "nameext": ".idx7",
            "nameroot": "input.txt",
            "path": ".../pytest-0/popen-gw2/unlabled_test5/input.txt.idx7",
            "size": 0
        },
        {
            "basename": "hello.txt",
            "checksum": "sha1$47a013e660d408619d894b20806b1d5086aab03b",
            "class": "File",
            "dirname": ".../pytest-0/popen-gw2/unlabled_test5",
            "location": "file://.../pytest-0/popen-gw2/unlabled_test5/hello.txt",
            "nameext": ".txt",
            "nameroot": "hello",
            "path": ".../pytest-0/popen-gw2/unlabled_test5/hello.txt",
            "size": 13
        },
        {
            "basename": "input.txt_idx8",
            "class": "Directory",
            "dirname": ".../pytest-0/popen-gw2/unlabled_test5",
            "location": "file://.../pytest-0/popen-gw2/unlabled_test5/input.txt_idx8",
            "path": ".../pytest-0/popen-gw2/unlabled_test5/input.txt_idx8"
        }
    ],
    "size": 1111
}
caused by: field 'secondaryFiles' failed comparison: expected: [
    {
        "checksum": "sha1$1f6fe811644355974cdd06d9eb695d6e859f3b44",
        "class": "File",
        "location": "input.txt.idx1",
        "size": 1500
    },
    {
        "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",
        "class": "File",
        "location": "input.idx2",
        "size": 0
    },
    {
        "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",
        "class": "File",
        "location": "input.txt.idx3",
        "size": 0
    },
    {
        "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",
        "class": "File",
        "location": "input.txt.idx4",
        "size": 0
    },
    {
        "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",
        "class": "File",
        "location": "input.txt.idx5",
        "size": 0
    },
    {
        "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",
        "class": "File",
        "location": "input.idx6.txt",
        "size": 0
    },
    {
        "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",
        "class": "File",
        "location": "input.txt.idx7",
        "size": 0
    },
    {
        "checksum": "sha1$47a013e660d408619d894b20806b1d5086aab03b",
        "class": "File",
        "location": "hello.txt",
        "size": 13
    },
    {
        "class": "Directory",
        "listing": [
            {
                "basename": "index",
                "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",
                "class": "File",
                "location": "index",
                "size": 0
            }
        ],
        "location": "input.txt_idx8"
    }
]
got: [
    {
        "basename": "input.txt.idx1",
        "checksum": "sha1$1f6fe811644355974cdd06d9eb695d6e859f3b44",
        "class": "File",
        "dirname": ".../pytest-0/popen-gw2/unlabled_test5",
        "location": "file://.../pytest-0/popen-gw2/unlabled_test5/input.txt.idx1",
        "nameext": ".idx1",
        "nameroot": "input.txt",
        "path": ".../pytest-0/popen-gw2/unlabled_test5/input.txt.idx1",
        "size": 1500
    },
    {
        "basename": "input.idx2",
        "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",
        "class": "File",
        "dirname": ".../pytest-0/popen-gw2/unlabled_test5",
        "location": "file://.../pytest-0/popen-gw2/unlabled_test5/input.idx2",
        "nameext": ".idx2",
        "nameroot": "input",
        "path": ".../pytest-0/popen-gw2/unlabled_test5/input.idx2",
        "size": 0
    },
    {
        "basename": "input.txt.idx3",
        "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",
        "class": "File",
        "dirname": ".../pytest-0/popen-gw2/unlabled_test5",
        "location": "file://.../pytest-0/popen-gw2/unlabled_test5/input.txt.idx3",
        "nameext": ".idx3",
        "nameroot": "input.txt",
        "path": ".../pytest-0/popen-gw2/unlabled_test5/input.txt.idx3",
        "size": 0
    },
    {
        "basename": "input.txt.idx4",
        "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",
        "class": "File",
        "dirname": ".../pytest-0/popen-gw2/unlabled_test5",
        "location": "file://.../pytest-0/popen-gw2/unlabled_test5/input.txt.idx4",
        "nameext": ".idx4",
        "nameroot": "input.txt",
        "path": ".../pytest-0/popen-gw2/unlabled_test5/input.txt.idx4",
        "size": 0
    },
    {
        "basename": "input.txt.idx5",
        "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",
        "class": "File",
        "dirname": ".../pytest-0/popen-gw2/unlabled_test5",
        "location": "file://.../pytest-0/popen-gw2/unlabled_test5/input.txt.idx5",
        "nameext": ".idx5",
        "nameroot": "input.txt",
        "path": ".../pytest-0/popen-gw2/unlabled_test5/input.txt.idx5",
        "size": 0
    },
    {
        "basename": "input.idx6.txt",
        "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",
        "class": "File",
        "dirname": ".../pytest-0/popen-gw2/unlabled_test5",
        "location": "file://.../pytest-0/popen-gw2/unlabled_test5/input.idx6.txt",
        "nameext": ".txt",
        "nameroot": "input.idx6",
        "path": ".../pytest-0/popen-gw2/unlabled_test5/input.idx6.txt",
        "size": 0
    },
    {
        "basename": "input.txt.idx7",
        "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",
        "class": "File",
        "dirname": ".../pytest-0/popen-gw2/unlabled_test5",
        "location": "file://.../pytest-0/popen-gw2/unlabled_test5/input.txt.idx7",
        "nameext": ".idx7",
        "nameroot": "input.txt",
        "path": ".../pytest-0/popen-gw2/unlabled_test5/input.txt.idx7",
        "size": 0
    },
    {
        "basename": "hello.txt",
        "checksum": "sha1$47a013e660d408619d894b20806b1d5086aab03b",
        "class": "File",
        "dirname": ".../pytest-0/popen-gw2/unlabled_test5",
        "location": "file://.../pytest-0/popen-gw2/unlabled_test5/hello.txt",
        "nameext": ".txt",
        "nameroot": "hello",
        "path": ".../pytest-0/popen-gw2/unlabled_test5/hello.txt",
        "size": 13
    },
    {
        "basename": "input.txt_idx8",
        "class": "Directory",
        "dirname": ".../pytest-0/popen-gw2/unlabled_test5",
        "location": "file://.../pytest-0/popen-gw2/unlabled_test5/input.txt_idx8",
        "path": ".../pytest-0/popen-gw2/unlabled_test5/input.txt_idx8"
    }
]
caused by: expected: {
    "class": "Directory",
    "listing": [
        {
            "basename": "index",
            "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",
            "class": "File",
            "location": "index",
            "size": 0
        }
    ],
    "location": "input.txt_idx8"
}
got: {
    "basename": "input.txt_idx8",
    "class": "Directory",
    "dirname": ".../pytest-0/popen-gw2/unlabled_test5",
    "location": "file://.../pytest-0/popen-gw2/unlabled_test5/input.txt_idx8",
    "path": ".../pytest-0/popen-gw2/unlabled_test5/input.txt_idx8"
}
caused by: 'listing' is mandatory field in Directory object
Test: job: 
  file:.../streamflow-postgresql/streamflow-postgresql/cwl-v1.3-2063e9095f421f2a2ce12abaf196b2ba06ca5aae/tests/search-job.json
output:
  outfile:
    class: File
    checksum: sha1$e2dc9daaef945ac15f01c238ed2f1660f60909a0
    location: result.txt
    size: 142
  indexedfile:
    location: input.txt
    class: File
    checksum: sha1$327fc7aedf4f6b69a42a7c8b808dc5a7aff61376
    secondaryFiles:
    - location: input.txt.idx1
      class: File
      checksum: sha1$1f6fe811644355974cdd06d9eb695d6e859f3b44
      size: 1500
    - location: input.idx2
      class: File
      checksum: sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709
      size: 0
    - location: input.txt.idx3
      class: File
      checksum: sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709
      size: 0
    - location: input.txt.idx4
      class: File
      checksum: sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709
      size: 0
    - location: input.txt.idx5
      class: File
      checksum: sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709
      size: 0
    - location: input.idx6.txt
      class: File
      checksum: sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709
      size: 0
    - checksum: sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709
      class: File
      location: input.txt.idx7
      size: 0
    - checksum: sha1$47a013e660d408619d894b20806b1d5086aab03b
      class: File
      location: hello.txt
      size: 13
    - class: Directory
      listing:
      - basename: index
        checksum: sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709
        class: File
        location: index
        size: 0
      location: input.txt_idx8
    size: 1111
tool: 
  file:.../streamflow-postgresql/streamflow-postgresql/cwl-v1.3-2063e9095f421f2a2ce12abaf196b2ba06ca5aae/tests/search.cwl#main
id: 
  file:.../streamflow-postgresql/streamflow-postgresql/cwl-v1.3-2063e9095f421f2a2ce12abaf196b2ba06ca5aae/conformance_tests.cwltest.yaml#initial_workdir_secondary_files_expr
doc: Test InitialWorkDirRequirement linking input files and capturing 
  secondaryFiles on input and output. Also tests the use of a variety of 
  parameter references and expressions in the secondaryFiles field.
tags:
- initial_work_dir
- inline_javascript
- workflow
line: '512'

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Bump codespell from 2.4.1 to 2.4.2#213

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