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Draft implementation of proposed syntax changes (feedback requested) #766

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Draft implementation of proposed syntax changes (feedback requested) #766

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@tclose tclose commented Nov 19, 2024

NB: This is just a draft PR at this stage, but demonstrates the new "design" syntax I had in mind. It isn't connected up to the internals of the Task logic so everything will be broken outside of pydra/design/tests, but if you have a look at those tests you should be able to see what they would look like.

Types of changes

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

Summary

Attempts to streamline the public API for defining tasks and workflow as per #692

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
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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
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all python and shell design tests pass
e606459
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added initialization tests to test_python
b38ced6
tclose added 30 commits December 28, 2024 18:33
@tclose
finished workflow tutorial and reworked some of the docs structure
a8ed05e
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finished off the workflow tutorial for now
8e88ed2
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restructuring new docs
6f1c8e3
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more restructuring of new docs
03546ed
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writing getting-starting notebook
35641b1
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renamed Spec and specification to Def and definition
ffdfce1
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finished getting-started (apart from debugging) tutorial
e317e8e
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imported examples from tutorials
720efdb
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touched up errors in first-level-glm
7a7cffd
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reinstated changes to getting-started
edd682f
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touched up getting-started
f5276b9
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converted two-level glm to new syntax
8170777
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more touching up of documentation
02f6a1c
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finished python task and canonical form tuts
4502260
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added dependencies required for examples
d71542f
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touching up tutorials
70edf85
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renamed spec to definition across the board
9594e75
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fixed mrtrix import
940f004
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finished playing with tutorials for now
e15cb35
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fixed doc dependency
96e0b92
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download tags to docs build
3495b50
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more fixes to docs CI
ec669e1
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commented out pydra-mrtrix3 dep for docs until new release
e95e8ff
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combined typing and hashing
b5b95d3
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renamed help_string to help
1e81774
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renamed make_task_spec to make_task_def
ac7ab7f
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touch up docs
7c47eef
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touching up docs
83cbbb6
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renamed tutorials to give natural order
e6c488f
@tclose
filled out explanation sections with subheadings
88a05bb
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@satra satra satra left review comments

@effigies effigies effigies left review comments

@djarecka djarecka Awaiting requested review from djarecka

@yibeichan yibeichan Awaiting requested review from yibeichan

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@tclose @effigies @satra