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Nipype auto conv #52

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merged 224 commits into from
Mar 25, 2024
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48cd321
setup auto conv
tclose Nov 22, 2023
f7c4f26
cleaned up yaml files
tclose Nov 22, 2023
ce5a3e3
cleaned up fileformats extras
tclose Dec 20, 2023
fe79dd0
updated with latest generation of auto-gen yaml files
tclose Jan 10, 2024
47ff295
updated package with latest auto-generation
tclose Mar 22, 2024
e9fa0f8
started to manual touch up auto-conv yaml specs
tclose Mar 22, 2024
c433bc4
updated apply mask to use NiftiGz[Mask] data type
tclose Mar 22, 2024
7415ede
updated to latest package generation version
tclose Mar 22, 2024
587b782
updated nipype converter specs
tclose Mar 22, 2024
fedc154
updated actions versions
tclose Mar 22, 2024
bd9b5a6
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Mar 22, 2024
69935aa
starting to set up install
tclose Mar 22, 2024
12139f1
imported latest ci-cd workflow
tclose Mar 22, 2024
6f11a23
added conda install to ci-cd
tclose Mar 22, 2024
49e6780
fixed up target branch for ci-cd
tclose Mar 22, 2024
dd23472
added melodicIca back into fileformats
tclose Mar 22, 2024
26a0ce0
removed cuda packages and tirl from ci-cd
tclose Mar 24, 2024
9e57726
getting conda install in ci-cd to work
tclose Mar 24, 2024
d8d8556
removed other troublesome packages in ci-cd install
tclose Mar 24, 2024
5eecf2e
fixed up report progress
tclose Mar 24, 2024
c09bb53
added report progress tool
tclose Mar 25, 2024
643bcb4
disable report progress job
tclose Mar 25, 2024
5b56c6f
MNT: Initial project setup
ghisvail Mar 25, 2024
563ac8b
NEW: Add task definition for FLIRT
ghisvail Mar 25, 2024
d097014
NEW: Add task definition for fslmerge
ghisvail Mar 25, 2024
2abdc69
STY: Fix formatting
ghisvail Mar 25, 2024
cec9d8d
STY: Fix docstrings
ghisvail Mar 25, 2024
e21b4cd
CI: Add workflow to test the codebase
ghisvail Mar 25, 2024
955cd1e
CI: Fix permission -> permissions
ghisvail Mar 25, 2024
fefdcd4
CI: Fix content -> contents
ghisvail Mar 25, 2024
d235fd6
MNT: Fix matrix definition
ghisvail Mar 25, 2024
7e80e2f
STY: Rename input and output transformations to matrix
ghisvail Mar 25, 2024
b898fba
NEW: Add task definition for BET
ghisvail Mar 25, 2024
0ffdd64
DOC: Add module docstring to BET
ghisvail Mar 25, 2024
9afccc7
DOC: Add description to FLIRT docstring
ghisvail Mar 25, 2024
7090bec
NEW: Add task definition for FNIRT
ghisvail Mar 25, 2024
1e557a0
FIX: Add public name declarations for fnirt module
ghisvail Mar 25, 2024
8a7b1b0
FIX: Imports of fnirt module
ghisvail Mar 25, 2024
8357bc3
FIX: Use consistent image parameter naming convention
ghisvail Mar 25, 2024
94f656f
MNT: Restrict coverage version
ghisvail Mar 25, 2024
9d24b13
MNT: Exclude .hatch folder from tracking
ghisvail Mar 25, 2024
4ad2b95
CI: Add concurrency settings
ghisvail Mar 25, 2024
79c9858
CI: Run tests on updates
ghisvail Mar 25, 2024
faec148
NEW: Add interfaces for eddy
ghisvail Mar 25, 2024
2bfb1fb
ENH: Remove deprecated options
ghisvail Mar 25, 2024
816d49d
ENH: Add option to disable peas
ghisvail Mar 25, 2024
363e831
ENH: Add option for random seed
ghisvail Mar 25, 2024
85bea4f
ENH: Add default value to FWHM option
ghisvail Mar 25, 2024
218fd61
FIX: Add missing enum value for FLM
ghisvail Mar 25, 2024
2e25c1f
FIX: Rename mporder option
ghisvail Mar 25, 2024
0f8dcde
ENH: Add write options
ghisvail Mar 25, 2024
ee580e1
ENH: Define output spec for eddy
ghisvail Mar 25, 2024
2c9b429
REF: ol -> outlier
ghisvail Mar 25, 2024
40ebae4
ENH: Add allowed values for slice-to-volume interpolation
ghisvail Mar 25, 2024
f474931
REF: acqp -> acquisition_parameters
ghisvail Mar 25, 2024
953cd07
REF: fmap -> fieldmap
ghisvail Mar 25, 2024
83f167a
REF: std -> stdevs
ghisvail Mar 25, 2024
01e6d4c
NEW: Add task definition for convert_xfm
ghisvail Mar 25, 2024
8a97a4a
NEW: Add task definition for fslroi
ghisvail Mar 25, 2024
a215ea4
MNT: Restrict linting to pydra folder
ghisvail Mar 25, 2024
38d8136
NEW: Add task definition for robustfov
ghisvail Mar 25, 2024
bebe20a
NEW: Add task definition for fslreorient2std
ghisvail Mar 25, 2024
bf7a504
ENH: Add output specifications for BET
ghisvail Mar 25, 2024
e2d5819
DOC: List available interfaces
ghisvail Mar 25, 2024
295afb8
DOC: Add table of contents
ghisvail Mar 25, 2024
ffa1f26
DOC: Adjust license section
ghisvail Mar 25, 2024
179caca
DOC: Add reference to FSL installation and licensing
ghisvail Mar 25, 2024
2963422
ENH: Set default output files for FLIRT
ghisvail Mar 25, 2024
6696a35
FIX: Make dof and 2D registration parameters mutually exclusive
ghisvail Mar 25, 2024
9a589f6
ENH: Add verbose logging for FLIRT
ghisvail Mar 25, 2024
63aac60
ENH: Add output_datatype parameter to FLIRT
ghisvail Mar 25, 2024
e201421
ENH: Add cost function parameter to FLIRT
ghisvail Mar 25, 2024
f4afad7
NEW: Add task definition for FAST
ghisvail Mar 25, 2024
37a8bfc
DOC: Add FAST to available interfaces
ghisvail Mar 25, 2024
fd6b17a
DOC: Add Eddy to available interfaces
ghisvail Mar 25, 2024
58d7dd6
ENH: Add verbose parameter to main interfaces
ghisvail Mar 25, 2024
9b4630e
MNT: Rename project to pydra-fsl
ghisvail Mar 25, 2024
4634ef5
CI: Add publish workflow
ghisvail Mar 25, 2024
98c2e66
DOC: Fix install command
ghisvail Mar 25, 2024
e972ea4
DOC: Fix badge URLs
ghisvail Mar 25, 2024
353c922
DOC: Fix licensing paragraph
ghisvail Mar 25, 2024
505142f
ENH: Add interpolation parameter for FLIRT
ghisvail Mar 25, 2024
d325128
DOC: Add badge for downloads
ghisvail Mar 25, 2024
5eba6a5
FIX: Make BET derive from ShellCommandTask
ghisvail Mar 25, 2024
4639c07
REF: Normalize modules layout
ghisvail Mar 25, 2024
aec9c6d
ENH: Add templated output parameters
ghisvail Mar 25, 2024
d0f3ba7
ENH: Add mask for input and reference spaces
ghisvail Mar 25, 2024
9812a09
FIX: FNIRT doctest
ghisvail Mar 25, 2024
8e2ecd0
FIX: Make BETSpec derive ShellSpec
ghisvail Mar 25, 2024
7c4b045
FIX: Use lists for requires metadata in ShellOutSpec
ghisvail Mar 25, 2024
a23f951
FIX: Move verbose and save flags for Eddy
ghisvail Mar 25, 2024
169ad61
FIX: Use pydra.specs.File in BET output spec
ghisvail Mar 25, 2024
ebe6661
FIX: Add missing attrs.define to FAST output spec
ghisvail Mar 25, 2024
0c2991c
MNT: Run lint:fix
ghisvail Mar 25, 2024
7ae9606
FIX: Move callables out of FAST output spec
ghisvail Mar 25, 2024
8a45ea4
MNT: Bump version to 0.0.6
ghisvail Mar 25, 2024
25fb1e2
NEW: Add task definition for fslmaths' mul
ghisvail Mar 25, 2024
64f17c1
MNT: Bump version to 0.0.7
ghisvail Mar 25, 2024
f5e2ecd
FIX: Drop redundant requires in ConvertXFM
ghisvail Mar 25, 2024
1269798
DOC: Add fslmaths to available interfaces
ghisvail Mar 25, 2024
349d20f
DOC: Add status badge for test workflow
ghisvail Mar 25, 2024
6ffc076
NEW: Add ConvertXFM and InvertXFM interfaces
ghisvail Mar 25, 2024
9281a82
NEW: Add interface for ApplyXFM
ghisvail Mar 25, 2024
2aa203c
REF: Move FLIRT interface and utilities to their own subpackage
ghisvail Mar 25, 2024
3d01620
ENH: Remove apply_transformation from FLIRT
ghisvail Mar 25, 2024
01c8d3e
REF: Extract common FLIRT specs out
ghisvail Mar 25, 2024
edf5054
ENH: Add search specifications for FLIRT
ghisvail Mar 25, 2024
140d0a1
ENH: Add weighting image spec for FLIRT
ghisvail Mar 25, 2024
cbed348
REF: Update exported symbols by flirt.specs module
ghisvail Mar 25, 2024
1f4cc7d
REF: Simplify Mul interface from fslmaths
ghisvail Mar 25, 2024
9c4d9b0
MNT: Update test paths
ghisvail Mar 25, 2024
60d24fa
DOC: Update list of available interfaces
ghisvail Mar 25, 2024
8c0fce0
REF: Move BET interfaces and utils to own subpackage
ghisvail Mar 25, 2024
d54e674
ENH: Add specifications for BET variations
ghisvail Mar 25, 2024
e602e06
NEW: Add task definition for SUSAN
ghisvail Mar 25, 2024
b9e7812
DOC: Add susan to available interfaces
ghisvail Mar 25, 2024
cfdf564
MNT: Bump version to 0.0.8
ghisvail Mar 25, 2024
6577fa9
FIX: Reorganize module imports
ghisvail Mar 25, 2024
a542fb1
MNT: Bump version to 0.0.9
ghisvail Mar 25, 2024
2f8263c
NEW: Add task definition for applywarp
ghisvail Mar 25, 2024
3688277
NEW: Add task definition for convertwarp
ghisvail Mar 25, 2024
25326e1
NEW: Add task definition for invwarp
ghisvail Mar 25, 2024
8655e0c
DOC: Update list of available tasks
ghisvail Mar 25, 2024
c220538
REF: Use consistent naming for xfm utils
ghisvail Mar 25, 2024
635f461
DOC: Display available tasks in a table
ghisvail Mar 25, 2024
3ab15b9
DOC: Improve layout of tasks table
ghisvail Mar 25, 2024
f92af40
MNT: Bump version to 0.0.10
ghisvail Mar 25, 2024
ae08ff6
REF: Move FSL utils to own subpackage
ghisvail Mar 25, 2024
a37f1f5
NEW: Add task definition for FSLInfo
ghisvail Mar 25, 2024
79c5c35
NEW: Add task definition for fslsplit
ghisvail Mar 25, 2024
4dcefd6
DOC: Update available tasks
ghisvail Mar 25, 2024
19a84cc
MNT: Bump version to 0.0.11
ghisvail Mar 25, 2024
8515173
MNT: Enable black profile for isort
ghisvail Mar 25, 2024
ac22579
NEW: Add task definition for fslslice
ghisvail Mar 25, 2024
b1147be
NEW: Add task definition for fugue
ghisvail Mar 25, 2024
fd5dcbd
NEW: Add task definition for fnirtfileutils
ghisvail Mar 25, 2024
426c775
NEW: Add tasks for coordinates transformation
ghisvail Mar 25, 2024
56ff4ab
REF: Introduce standalone verbose spec in fnirt
ghisvail Mar 25, 2024
47dbb3f
ENH: Improve naming consistency of warp utils
ghisvail Mar 25, 2024
98dd4e8
ENH: Add extra parameters for FNIRT
ghisvail Mar 25, 2024
318119e
ENH: Improve consistency between FNIRT and fnirtfileutils
ghisvail Mar 25, 2024
15d330d
FIX: Default values and typing of some FNIRT parameters
ghisvail Mar 25, 2024
018995d
MNT: lint fix
ghisvail Mar 25, 2024
a8660e3
DOC: Update list of available interfaces
ghisvail Mar 25, 2024
6893979
MNT: Bump version to 0.0.12
ghisvail Mar 25, 2024
9a4e7d3
NEW: Add task definition for fslswapdim
ghisvail Mar 25, 2024
4539eea
DOC: Update list of available interfaces
ghisvail Mar 25, 2024
6a639ac
REF: Rename axis parameters
ghisvail Mar 25, 2024
be98b4d
NEW: Add task definition for fslchfiletype
ghisvail Mar 25, 2024
7d7892c
DOC: Update list of available interfaces
ghisvail Mar 25, 2024
67b31e8
MNT: Bump version to 0.0.13
ghisvail Mar 25, 2024
599a696
MNT: Move to src layout
ghisvail Mar 25, 2024
e06aa6a
DOC: Fix test command
ghisvail Mar 25, 2024
f180186
NEW: Add task definition for FSLFFT
ghisvail Mar 25, 2024
2363bd8
NEW: Add task definition for fslinterleave
ghisvail Mar 25, 2024
cd00761
FIX: Declare input_image and other_image mandatory
ghisvail Mar 25, 2024
a9013f7
NEW: Add task definition for fslselectvols
ghisvail Mar 25, 2024
19556ff
NEW: Add task definition for fslsmoothfill
ghisvail Mar 25, 2024
0e80f67
MNT: Bump version to 0.0.14
ghisvail Mar 25, 2024
6e8014d
FIX: Correct typos and formatting
ghisvail Mar 25, 2024
29a6449
FIX: Typo in output field name
ghisvail Mar 25, 2024
f8d3dec
MNT: Bump version to 0.0.15
ghisvail Mar 25, 2024
742d060
NEW: Add task definition for sigloss
ghisvail Mar 25, 2024
6d05517
NEW: Add task definition for prelude
ghisvail Mar 25, 2024
4cf612c
REF: Move ApplyXFM to flirt module
ghisvail Mar 25, 2024
844d9b8
REF: Move all convert_xfm based utils to same module
ghisvail Mar 25, 2024
d2e8f5b
NEW: Add task definition for fsl_prepare_fieldmap
ghisvail Mar 25, 2024
5ac08c7
MNT: Bump version to 0.0.16
ghisvail Mar 25, 2024
3244a3e
REF: Move fslmaths module from utils to root
ghisvail Mar 25, 2024
7e67ebf
NEW: Add task definition for fslorient
ghisvail Mar 25, 2024
5c174cc
FIX: Expose FixScaleSkew to root imports
ghisvail Mar 25, 2024
1f5591a
MNT: Bump version to 0.0.17
ghisvail Mar 25, 2024
404e7fb
DOC: Remove fslmaths from utils
ghisvail Mar 25, 2024
e2c4d40
NEW: Add task definition for topup
ghisvail Mar 25, 2024
b914b94
NEW: Add task definition for applytopup
ghisvail Mar 25, 2024
72a1239
DOC: Update available interfaces
ghisvail Mar 25, 2024
7df3fb3
ENH: Add doctest for Topup
ghisvail Mar 25, 2024
7d66b89
ENH: Add doctest for ApplyTopup
ghisvail Mar 25, 2024
fe72fee
REF: Rename output fields from Topup
ghisvail Mar 25, 2024
9f0d7e3
REF: Add doctest to Eddy
ghisvail Mar 25, 2024
a62cb31
MNT: Add config for docs environment
ghisvail Mar 25, 2024
e4db59d
DOC: Initial Sphinx config
ghisvail Mar 25, 2024
c573222
DOC: Add API documentation
ghisvail Mar 25, 2024
70f9f6a
MNT: Upload documentation to GitHub Pages
ghisvail Mar 25, 2024
871d9bb
MNT: Add status badge for docs
ghisvail Mar 25, 2024
1e620d5
MNT: Bump version to 0.0.18
ghisvail Mar 25, 2024
beed08c
ENH: Add input and reference weights for FLIRT
ghisvail Mar 25, 2024
a78490f
REF: Normalize flirt module
ghisvail Mar 25, 2024
f433ccc
MNT: Fix testing setup for src layout
ghisvail Mar 25, 2024
655f13a
FIX: Rename input_matrix to initial_matrix in FLIRT / ApplyXFM
ghisvail Mar 25, 2024
dee9f26
ENH: Major improvement for FSLROI
ghisvail Mar 25, 2024
3cae0c2
ENH: Major improvement to fslmaths
ghisvail Mar 25, 2024
075e34b
MNT: Bump version to 0.0.19
ghisvail Mar 25, 2024
b567f15
REF: Normalize all input and output spec names
ghisvail Mar 25, 2024
c346916
ENH: Drop FSL prefix from utils (#58)
ghisvail Mar 25, 2024
0b612da
ENH: Drop FSL prefix from prepare_fieldmap (#59)
ghisvail Mar 25, 2024
6ca81ad
FIX: FSLPrepareFieldmap -> PrepareFieldmap in docs
ghisvail Mar 25, 2024
8af8e47
ENH: Drop FSL prefix from maths (#60)
ghisvail Mar 25, 2024
b9ddf08
CI: Drop testing on Python 3.7 (#61)
ghisvail Mar 25, 2024
45177d4
MNT: Bump version to 0.0.20
ghisvail Mar 25, 2024
cb8841c
ENH: Use explicit name for image type argument in FAST (#62)
ghisvail Mar 25, 2024
44e9333
Bump actions/upload-pages-artifact from 1 to 2 (#63)
dependabot[bot] Mar 25, 2024
fc107c8
add missing decorator to Eddy output specs (#64)
NicolasGensollen Mar 25, 2024
09a9d49
make eddy fieldmap optional (#65)
NicolasGensollen Mar 25, 2024
f622806
MNT: Bump version to 0.0.21
ghisvail Mar 25, 2024
9838723
Bump actions/checkout from 3 to 4 (#66)
dependabot[bot] Mar 25, 2024
22ff22b
FIX: Use equal-separated option value pairs in eddy (#67)
NicolasGensollen Mar 25, 2024
0269041
FIX: Use equal-separated option value pairs in applytopup
ghisvail Mar 25, 2024
429e479
FIX: Use equal-separated option value pairs in topup
ghisvail Mar 25, 2024
2e8c3bc
MNT: Bump version to 0.0.22
ghisvail Mar 25, 2024
1fc0c51
NEW: Add Threshold to fsl.maths (#68)
NicolasGensollen Mar 25, 2024
d3f2b73
Bump actions/deploy-pages from 2 to 3
dependabot[bot] Mar 25, 2024
9c31212
Bump actions/setup-python from 4 to 5
dependabot[bot] Mar 25, 2024
e8d0be4
Bump actions/configure-pages from 3 to 4
dependabot[bot] Mar 25, 2024
ef78624
Bump actions/download-artifact from 3 to 4
dependabot[bot] Mar 25, 2024
b16f0e7
Bump actions/upload-artifact from 3 to 4
dependabot[bot] Mar 25, 2024
9d44bdc
Bump actions/deploy-pages from 3 to 4
dependabot[bot] Mar 25, 2024
9985b1a
Bump actions/upload-pages-artifact from 2 to 3
dependabot[bot] Mar 25, 2024
dc54ad7
moved packages out of src and set up auto version
tclose Mar 25, 2024
29e28aa
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Mar 25, 2024
1b20f47
deleted hatch.toml
tclose Mar 25, 2024
f3c24e0
removed duplicate _version.py ignore in gitignore
tclose Mar 25, 2024
3ee2136
updated NOTICE file
tclose Mar 25, 2024
170b92d
updated notice file to include aramis lab
tclose Mar 25, 2024
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20 changes: 20 additions & 0 deletions .editorconfig
Original file line number Diff line number Diff line change
@@ -0,0 +1,20 @@
# EditorConfig <editorconfig.org>

root = true

[*]
indent_style = space
indent_size = 4
end_of_line = lf
charset = utf-8
trim_trailing_whitespace = true
insert_final_newline = true

[*.md]
trim_trailing_whitespace = false

[*.toml]
indent_size = 2

[*.yaml]
indent_size = 2
15 changes: 15 additions & 0 deletions .flake8
Original file line number Diff line number Diff line change
@@ -0,0 +1,15 @@

[flake8]
doctests = True
exclude =
**/__init__.py
*build/
docs/sphinxext/
docs/tools/
docs/conf.py
docs/source/conf.py
max-line-length = 88
select = C,E,F,W,B,B950
extend-ignore = E203,E501,E129,W503
per-file-ignores =
__init__.py:F401,F403
6 changes: 6 additions & 0 deletions .github/dependabot.yaml
Original file line number Diff line number Diff line change
@@ -0,0 +1,6 @@
version: 2
updates:
- package-ecosystem: github-actions
directory: /
schedule:
interval: weekly
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