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MIALSRK v2.0.1 #53

Merged
merged 144 commits into from
Dec 24, 2020
Merged

MIALSRK v2.0.1 #53

merged 144 commits into from
Dec 24, 2020

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sebastientourbier
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@sebastientourbier sebastientourbier commented Dec 4, 2020 •
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PR dedicated to the development of the upcoming v2.0.1 version.

In particular it includes:

Each new PR proposing new features and bug fixes to be integrated should be now made against this branch.

@sebastientourbier sebastientourbier added this to the v2.0.1 milestone Dec 4, 2020
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@pdedumast @hamzake Just created this new PR (branch v2.0.1-dev) as discussed for development of the next release.

sebastientourbier and others added 26 commits December 5, 2020 11:50
@sebastientourbier
Merge branch 'master' into v2.0.1-dev
0f786b7
@sebastientourbier
Merge branch 'master' into v2.0.1-dev
0f21b33
@sebastientourbier
ENH: upload new checkpoint files (size reduced by a factor of 3) for …
41015f2 
…brain extraction model
@sebastientourbier
NOTEBOOK: add notebook that help investigating reduction of checkpoin…
5665eca 
…ts file size
@sebastientourbier
UPD: use new checkpoints files in srr.py
33cf889
@sebastientourbier
MAINT: moved new model checkpoints for better isolation when packaging
c0845af
@sebastientourbier
UPD: update setup.py to install only new checkpoints and updated path…
9552fce 
… in srr.py
@sebastientourbier
FIX: typo for location of checkpoint files in setup.py
d4c56ad
@sebastientourbier
CI: update version in list of outputs
a4b7705
@sebastientourbier
ENH: add class to verify git tag and version are the same in setup.py
08047ea
@pdedumast
Merge branch 'master' into v2.0.1-dev
5f4566e
@sebastientourbier
CI: added new jobs in config of circleci
d2c447c
@sebastientourbier
FIX: add step to build wheel in .circleci/config.yml
0902378
@sebastientourbier
FIX: review step to build wheel in .circleci/config.yml
568e30e
@sebastientourbier
FIX: review step to build wheel in .circleci/config.yml
346ef19
@sebastientourbier
FIX: review step to build wheel in .circleci/config.yml
91e330d
@sebastientourbier
FIX: update to use pip3 an review to build wheel in .circleci/config.yml
f1cafaf
@sebastientourbier
FIX: review step to build wheel in .circleci/config.yml
25c3903
@sebastientourbier
MAINT: named steps in test_python_install job in .circleci/config.yml
4318fcb
@sebastientourbier
CI: add smoke test to use twine in test_python_install
20f3b4d
@sebastientourbier
MAINT: correct code style issue
08b2c06
@sebastientourbier
FIX: rename tensorflow input graph node
01d7db7
@sebastientourbier
CI: update version in list of outputs
2df8a47
@sebastientourbier
Merge branch 'v2.0.1-dev' into 56_pypi_circleci
14e4571
@sebastientourbier
FIX: revert back to original checkpoint files
222243e
@sebastientourbier
Merge branch 'v2.0.1-dev' into 52_tflearn_model_size
a9965fd
sebastientourbier and others added 27 commits December 15, 2020 12:41
@sebastientourbier
DOC: update appropritely module names in api_cli fo docker and singul…
4e1c57d 
…arity wrapper
@sebastientourbier
DOC: add options to automodules and a blank line at the end of file
070efb3
@sebastientourbier
DOC: reviewed docstring for all Nipype interfaces for correct renderi…
b6a6da9 
…ng of doc using the nipype sphinx extensions
@sebastientourbier
DOC: fix last input description for api doc of super-resolution inter…
5870837 
…face
@sebastientourbier
Merge pull request #65 from Medical-Image-Analysis-Laboratory/64_doc_…
a6fbea4 
…singularity_v2.0.1-dev

 [DOC] Update documentation
@pdedumast
Merge branch 'v2.0.1-dev' of github.com:Medical-Image-Analysis-Labora…
b549fd4 
…tory/mialsuperresolutiontoolkit into v2.0.1-dev
@pdedumast
Fix merge conflicts
ecf3502
@pdedumast
ENH: Custom interfaces parameters must be gathered in a unique dictio…
b50060f 
…nary
@pdedumast
DOC: Custom interfaces dictionary documentation
8c082cc
@pdedumast
ENH: Cleaned output filenames generation in nipype nodes.
25a5545
@pdedumast
FIX: Filenames generation in srtkImageReconstruction
d6b9da1
@pdedumast
FIX: Filenames generation in srtkTVSuperResolution
2194bab
@pdedumast
FIX: Filenames generation in srtkTVSuperResolution and srtkImageRecon…
32b43a6 
…struction
@pdedumast
FIX: Output filenames srtkRefineHRmask
af0b894
@pdedumast
ENH: Use MapNode for stack-wise preprocessing
1a4bf31
@pdedumast
Update test01 and test03 outputs
db819ae
@sebastientourbier
Merge pull request #63 from Medical-Image-Analysis-Laboratory/27_cust…
fd93c69 
…om_skipped_interfaces

[ENH] Add possibility for the user to custom the skipped interfaces
@pdedumast
STYLE: Rename brain extraction module
9e27fd1
@pdedumast
Fixed merge conflicts
395bbe8
@pdedumast
TEST: Update test 01 and 03 outputs
d6a020b
@pdedumast
TEST: Update test 02 and 04 outputs
d495bb4
@pdedumast
TEST: Set skip_stacks_ordering to false in the tests
d8e4cba
@pdedumast
TEST: Update test 01 and 03 outputs
8f4962a
@pdedumast
TEST: Update test 02 and 04 outputs
fa83954
@pdedumast
DOC: Update graph image
9fab753
@pdedumast
STYLE: Removed useless return
eb15c2a
@sebastientourbier
Merge pull request #68 from Medical-Image-Analysis-Laboratory/67_map_…
7e3a611 
…node

[ENH] Usage of nipype MapNode
sebastientourbier
sebastientourbier commented Dec 24, 2020
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Ready to merge 🥳

@sebastientourbier sebastientourbier merged commit 6e00883 into master Dec 24, 2020
@sebastientourbier sebastientourbier deleted the v2.0.1-dev branch December 24, 2020 06:59
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@sebastientourbier @pdedumast