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Updates Nipype2Pydra so that it generates new Pydra syntax #25

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Merged
merged 44 commits into from
Aug 1, 2025
Merged

Updates Nipype2Pydra so that it generates new Pydra syntax #25

merged 44 commits into from
Aug 1, 2025

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@tclose tclose commented Jul 28, 2025

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tclose added 30 commits May 29, 2024 15:26
@tclose
debugging running tests
c97e489
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fixing defaults for function interfaces
caee1bc
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set mandatory to False when there is a valid default
5e8da87
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added support for _format_arg and _parse_inputs methods
843a83a
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debugging reworked _list_outputs handling
07700f2
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handled super methods properly
985ab46
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added callables to outputs
1bcc2ec
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touching up format_arg super handling
68e09c7
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handling special super methods
b550966
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fixed handling of super methods, added supported for aggregate_output…
28659bc 
…s and fix bug with inputs handling in _list_outputs
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debugged changes so that all packages build successfully again
1e92a40
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finally got all packages to convert again!
63a4077
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debugging updates to conversions to handle function task super methods
0aa80aa
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all packages build again after refactor
3591c7b
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moved constants to bottom of file just in case they rely on a local f…
23ebaa4 
…unction
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disabled return dict unwrapping (used in _list_outputs) by default. A…
dc3214f 
…dded copyfile to python functions
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added option to explicitly route connections from/to explicit inputs …
0cac4cd 
…and outputs
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debugged workflows and spatial normalisation monster interface
955e6c8
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unwrapped super methods in shell helper methods
abf3551
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debugging mriqc/niworkflows conversions
8c696fd
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debugging switch to class-symbols
3d0e218
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debugging class symbol detection
596f5ff
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converting to generate new syntax
96274bf
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updated worker from serial to debug
f5b078a
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updated locations in generated imports
f49482e
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removed stray reference to serial worker
b952dde
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updated to use get_fields instead of task_fields (old function name)
83f2bf6
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updated yaml specs
8ddebc3
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commented out mriqc dep
8d723b8
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debugging interface conversions
5992a20
tclose added 14 commits June 2, 2025 09:21
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fixed up handling of union types
78690fc
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Got python and shell interface conversions to work for new syntax
ae60b07
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fixed up the inclusion of local functions and classes
a4c92ad
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dropped special "ported" module name from output dir clearance
c4eae3b
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debugging mriqc and qsmxt conversions
f0b03f2
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refreshed the example specs generated from package gen
251cd20
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debugging interface converter
fb38d6c
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debugging interface conversions
c1136a3
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removed fileformat version files from repo
3144f50
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check that xor is not a single string in code generation
f2814de
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upped python versions in ci-cd to >=3.11
54f6f44
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use venv in github actions
d44f643
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replaced auto with specifiable "target_version" for target of interfa…
700e818 
…ce only packages
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added target versions to package gen specs and skip mriqc and qsmxt t…
552a6b6 
…ests
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codecov-commenter commented Aug 1, 2025 •
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Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 69.05%. Comparing base (dc9fe56) to head (552a6b6).

❗ There is a different number of reports uploaded between BASE (dc9fe56) and HEAD (552a6b6). Click for more details.

HEAD has 4 uploads less than BASE
Flag BASE (dc9fe56) HEAD (552a6b6)
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Additional details and impacted files 
@@             Coverage Diff             @@
##             main      #25       +/-   ##
===========================================
- Coverage   88.48%   69.05%   -19.43%     
===========================================
  Files          33       29        -4     
  Lines        4454     5083      +629     
===========================================
- Hits         3941     3510      -431     
- Misses        513     1573     +1060

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@tclose tclose merged commit 959eaf6 into main Aug 1, 2025
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@tclose @codecov-commenter