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WIP: Implement Pydra code-generators #2665

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WIP: Implement Pydra code-generators #2665

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Commits on Feb 22, 2024

  1. implemented print_pydra_usage for C++ commands

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  2. touch up imports in pydra_usage_print output

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  3. implementing type-aware output_file_template

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  4. fixed up output_file_template

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  5. added return statement to make gcc happy

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  6. implemented python __print_usage_pydra__ option

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  7. cleaned up pylint issues in app.py

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  8. debugged handling of type printing in python __print_usage_pydra__

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  9. started to add in pydra-package to be auto-generated as nested direct… 

    …ory of repo
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  10. preparing pydra directory for auto-genned code

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  11. fixed up gitignore

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  12. fixed handling of choices

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  13. removed debugging statements from code gen

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  14. debugged remaining issues with python pydra export

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  15. escaped 5tt* cmd names with "filetissuetype" prefix

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  16. renamed auto-gen script

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  17. added DS_store to gitignore

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  18. configured pydra pyproject.toml

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  19. replaced 5tt with five_tissue_type in pydra module names

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  20. added github action to build pydra package

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  21. fixed error in gh action

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  22. expanded pydra github action to trigger on pull requests to dev

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  23. added requirements file

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  24. fixed up auto-gen call in GHA

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  25. added mrtrix build to pydra deploy GHA

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  26. reinstated checkout actions in other pydra GHA steps

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  27. added log-errors option to pydra-auto-gen.py script

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  28. added separate licence file for pydra

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  29. added separate licence for pydra, really this time

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  30. added artifacts to GHA build/deploy workflow

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  31. fixed up shared lib upload artifact in GHA

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  32. removed upload of build script

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  33. renamed pydra GHA

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  34. set path and ld_library_path in gha

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  35. escaped all help_strings in triple quotes in pydra auto gen

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  36. set execute perms on bin dir of pydra GHA

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  37. combined build and generate into single step

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  38. added flake8 opts to pydra package toml

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  39. added support for pydra usage for python cmd with algorithm

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  40. added return statement after generating pydra tasks for python algori… 

    …thm sub-commands
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  41. reverted debugging statements

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  42. handle the case of nested commands i.e. algorithms

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  43. reverted auto formatting in algorithm.py

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  44. escape python keywords in pydra print in c++ cmds

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  45. bug fixes to pydra-usage printing: escape python keyword args and add… 

    … file templates to output file options (e.g. --export_grad*)
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  46. added pydra handling for options with multiple file args

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  47. added test generation code to pydra generate

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  48. escaped cmd_name

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  49. added fileformats-mrtrix package

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  50. added MGH and MGZ to supported file-formats

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  51. added in mrtrix formats into fileformats-mrtrix

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  52. updated Mgh format name

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  53. renamed TrackFile format to Tracks

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  54. removed mistakenly staged generated file

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  55. fixed up dwi fileformats

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  56. debugging automatic test generation

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  57. added auto-generated tests

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  58. added in fileformats-mrtrix3-extras package

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  59. touched up fileformats extras readme

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  60. added in more fileformats-mrtrix3 extras

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  61. fixing up fileformats packages before initial release

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  62. added in mrconvert converter to fileformats-mrtrix3

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  63. getting fileformats-extras tests to pass

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  64. added in_file/out_file kwargs to converter

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  65. split converters so they aren't wrapped twice

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  66. Pydra gen: added task name to input and output specs to aid debugging

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  67. debugged pydra autotest generation

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  68. debugged pydra untittest structure

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  69. renamed directions argument so it doesn't clash with 'directions' option

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  70. renamed fileformats-mrtrix to fileformats-medimage-mrtrix

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  71. renamed fileformats.mrtrix package name

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  72. renamed fileformats.mrtrix package name in extras package

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  73. renamed pydra-auto-gen.py to generate.py

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  74. changed import path for fileformats mrtrix3

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  75. renamed fileformats.mrtrix3 to fileformats.medimage_mrtrix3

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  76. added some pydra-specific keywords to PYTHON_KEYWORDS

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  77. added back in pydra_usage function to app.cpp

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  78. added __print_usage_pydra__ special option back in

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  79. removed generated _version files

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  80. updated dicom import location

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  81. updated Mgz format name

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  82. added mif.gz format

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  83. touched up pydra test fixtures to set the right paths and env vars

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  84. added comment to start of generated pydra commands from pythong

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  85. debugging unittests

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  86. updated generated sample data args

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  87. updated syntax to latest version of fileformats

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  88. fixed up extras signatures

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  89. added separate b-file formats for MIF/MIH

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  90. added support for multi-line mif header values

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  91. added manually constructed mrcalc interface

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  92. added alias to Op in mrcalc operators

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  93. imported gzipped image formats into base fileformats package

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  94. converted command names to pascal case

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  95. removed generated pydra files from git

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  96. moved pydra src inside 'interfaces' directory

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  97. added _version.py to gitignore

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  98. removed stray .DS_Store

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  99. replace 'input' and 'output' fields with "in_file" and "out_file" to … 

    …make it more pydronic
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  100. added pytest_cache to gitignore

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Commits on Feb 23, 2024

  1. removed generated pydra files from git repo

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  2. touch up

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  3. updating pydra package github action

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  4. touched up pydra GH action workflow

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  5. debugging pydra GH action

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  6. fix up

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  7. log generation errors instead of raising them to test rest of deploym… 

    …ent pipeline
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  8. touched up logging in generation script

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  9. fix up GH action

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  10. fix up

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Commits on Feb 29, 2024

  1. delete stray generated files

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  2. removed more stray files

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  3. stripped back pydra GH action to be testing only

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  4. deleted pydra package stub in favour of storing it in nipype/pydra-mr… 

    …trix3
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  5. removed flake8 config

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  6. Merge branch 'dev' into pydra-usage

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