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Implementation of proposed syntax changes #768

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Implementation of proposed syntax changes #768

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@tclose tclose commented Feb 17, 2025 •
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Types of changes

  • Bug fix (non-breaking change which fixes an issue)
  • New feature (non-breaking change which adds functionality)
  • Breaking change (fix or feature that would cause existing functionality to change)

Summary

Implements proposed syntax changes in #692

Test modules (to fix)

  • test_python (design)
  • test_shell (design)
  • test_workflow (design)
  • test_boutiques
  • test_dockertask
  • test_environments
  • test_functions
  • test_graph
  • test_helpers_file
  • test_helpers_state
  • test_helpers
  • test_nipype1_convert
  • test_node_task
  • test_numpy_examples
  • test_profiles
  • test_shelltask_inputspec
  • test_shelltask
  • test_singularity
  • test_specs
  • test_state
  • test_submitter
  • test_task
  • test_tasks_files
  • test_workflow (engine)
  • test_hash
  • test_messenger
  • test_typing

Checklist

  • I have added tests to cover my changes (if necessary)
  • I have updated documentation (if necessary)

tclose added 30 commits June 4, 2024 08:20
@tclose
reworked collect outputs so callable's are used over simply copying v…
8f06ac4 
…alue from input
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if bool field argstr includes a string template, do templating instea…
f06171d 
…d of just argstr
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bugfix for argstr formatting for bool types
2b33473
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wrote cmd_out arg and unittest based on "ls" for shell_cmd
b177091
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added small note to docs
5758eb3
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renamed cmd_arg and cmd_out to shell_arg and shell_out
0f0485c
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touched up docs
16cecf1
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pass through kwargs to attrs.field in shell_arg and shell_out
6ee5b86
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added shell_task decorator
47806ff
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implemented shell_task and basic unittests. Generated tasks do not wo…
c0d7011 
…rk as need to determine best way to map onto input_spec
@tclose
shell command unittests pass
0da3b46
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renamed pydra.mark.shell_commands to pydra.mark.shell
c4d1875
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fixed up inheritance of Inputs and Outputs
d25eab0
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added tests for output_file_template/output_field_name and various un…
e4095a7 
…covered cases in shell_task decorator
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converted to hatch build system and made proper namespace package
e9a58bc
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initial structure of 'design' sub-package
e8bce86
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implementing new decorator syntax
e1b677e
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got all new python interface unittests to pass
1a0ffff
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fixed up checking of wrapped type in python.task decorator
3a159bb
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added shell.task decorator implementation and working through tests
dabe2ef
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debugging shell interface syntax
0aa12cf
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debugging type hints
8581f55
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debugged test_shell unittests
4b408a3
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added tests for shell command templates
6cf4e1b
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cleaning up shell tests
8cbeade
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capture defaults in pydra.design
79e98f6
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added function to python.interface fields instead of static
bba8be7
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reworked and debugged shell design tests
7ab7713
@tclose
all python and shell design tests pass
e606459
@tclose
added initialization tests to test_python
b38ced6
tclose added 19 commits February 14, 2025 09:03
@tclose
debugged advanced execution tutorial
6f60ae1
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fixed up docs cd
6237368
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debugging tutorials
072fae6
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added medimage-extras to tutorial deps
9481f30
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re-implementing docker/singularity environments after refactor
b0b45b9
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fixed up toy environments example, all docs should build now
d4ce1d3
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fixed bug in multi-input typing
b55ef24
@tclose
upped fileformats dep versions
1488ccc
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debugging environments unittests
377ab07
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upped requirement on pydra-mrtrix to 3.0.4a17
dddf8a2
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more dep version changes
b9221d7
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cleaned up deps and added ipywidgets to docs build
c8e25b1
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upped fileformats dep version
dc9e638
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added favicon to conf.py
799a384
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relaxed fileformats dep version
8c62ea7
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setup virtual desktop to accept notifications
bbdf072
@tclose
trying to get desktop notifications to work
8f1623c
@tclose
added additional comment to toymedianThreshold example
76feb69
@tclose
attempting to get virtual desktop notifications to work
de83727
@tclose tclose mentioned this pull request Feb 17, 2025
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@tclose tclose mentioned this pull request Feb 17, 2025
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