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Merged
merged 88 commits into from
May 17, 2024
Merged

Workflow converter #18

merged 88 commits into from
May 17, 2024

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@tclose tclose commented Mar 26, 2024

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@tclose tclose marked this pull request as draft March 26, 2024 10:31
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codecov-commenter commented Mar 27, 2024 •
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Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 84.51%. Comparing base (2af28d1) to head (451b545).

Additional details and impacted files 
@@            Coverage Diff             @@
##             main      #18      +/-   ##
==========================================
- Coverage   89.60%   84.51%   -5.09%     
==========================================
  Files          16       33      +17     
  Lines        1943     4443    +2500     
==========================================
+ Hits         1741     3755    +2014     
- Misses        202      688     +486

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tclose added 26 commits March 28, 2024 16:09
@tclose
implementing workflow conversion
b1a2193
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added local classes and functions to converted workflow files
c8b11d9
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added support for tripple quotes in extract_args
f6ff24b
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workflow spec generation
a6637db
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unused import
88efbea
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unused exception
e4e6be7
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implemented workflow converter
508768d
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added example workflow specs
7eb06c5
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debugging workflow converter
4afe3bc
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reorganised workflow converter code
d798530
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sorted out issues with config params
3fa6413
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fixed up node connections in workflow converter
d9601a4
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sorted out intrapackage module writing
6e8fd04
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fixed up locally defined nested workflows
2651209
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fixed up intra_pkg_funcs writing so that only one function is written…
d465d3d 
… per file
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debugged input_spec + lzin issues
b0de34e
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sorted out multiple potential nodes
54048b2
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added external_nested workflows to anat_qc_workflow
f8319da
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task tests pass after import refactor
4941d25
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fixed up a range of bugs with importing interfaces
6a9da03
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split utils into separate modules
28c46aa
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implementing package translations
a9eb426
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added in mriqc interfaces
e6fe44b
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created package-wide converter for workflow packages
fa070f2
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ensured that callables imports are absolute
9d9fd68
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added new pkg-generation spec for mriqc
4ca63e1
tclose added 27 commits April 24, 2024 11:49
@tclose
added conversion from niu.Function to FunctionTask
c79d0a9
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fixed up workflow conversions to take workflow inputs as function args
697a8ee
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write conftest for workflow tests
8af19a1
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debugging workflow converters
5b8a7b4
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implemented NestedWorkflowAssignmentConverter
cda19bd
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moved config defaults into package converter
e56c4d2
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added test_inputs option
af5818d
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started implementing NodeFactoryConverter
50a2bad
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refactored statements into separate sub-package
521aecf
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refactored parse_statements to put match/parse logic in respective cl…
98afe8a 
…asses
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implemented get_imported_object and node factory handling
5d625cf
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fixed up handling of node factory methods
abb024d
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implementing class and function converters
287f4e0
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debugging workflow and helper function/class generation
bfecbc2
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working on assignment statements to get delayed var info
b67b22e
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handled varfield inputs to nested workflows
e5247d3
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reworked nested workflow input/output detection and top-level export …
c32a2b8 
…completes successfully
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fixing up regressions
8446187
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fixed issue with multiple input conns to same node
28d185b
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debugging input/output mapping
9667474
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finally sorted out nested-workflow input/output propagation
2f63f18
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fixed duplicate output issue caused by replacement mapping
28a2828
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check for replaced connections in get_(input|output)_from_conn methods
c7b274b
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implemented trimming of unused inputs
749a805
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fixed unittests
cc7a270
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added in example specs from mriqc and reworked test_package_complete …
284458d 
…test
@tclose
added dep and use '--break-system-packages' in gha
451b545
@tclose tclose marked this pull request as ready for review May 17, 2024 06:19
@tclose tclose merged commit ebc5eec into main May 17, 2024
5 of 6 checks passed
@tclose tclose deleted the workflow-src-conv branch May 17, 2024 06:19
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@tclose @codecov-commenter