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Release: Connectome Mapper v3.0.0-RC4 #74
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…as mat and graphml files
…ctome files and curvature
… files in test-07
… cmtklib/config.py
…th datalad is enabled
…osx.yml of the GUI [skip ci]
…atlas and scale Merge pull request #79 from connectomicslab/ref/bids-naming
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About ready to merge!
Waiting for new tests with the GUI and on CircleCI to pass.
Merge remote-tracking branch 'origin/master' where commit was made by mistake into release/v3.0.0-RC4
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PR dedicated to the developement of v3.0.0-RC4.
Update
Update version of datalad and dependencies (PR ENH: Update data provenance tracking functionality with Datalad #77):
datalad[full]==0.13.0
todatalad[full]==0.14.0
datalad-container==0.3.1
todatalad-container==1.1.2
datalad_neuroimaging==0.2.0
todatalad-neuroimaging==0.3.1
git-annex=8.20200617
togit-annex=8.20210127
datalad-revolution
was removedMajor changes
Configuration files adopt now the
JSON
format. This have involved a major refactoringof the
cmtklib.config
module with the addition and replacement of a number of new methods(See full diff on GitHub).
Configuration files in the old
INI
format can be converted automatically with the help of the two new methodscheck_configuration_format()
andconvert_config_ini_2_json
to detect if configuration files are in theINI
format and to make the conversion. (PR ENH: Use json format for pipeline configuration files #76 )Update and review code in
cmp/bidsappmanager/gui.py
for data versioning and provenance tracking with Datalad (PR ENH: Update data provenance tracking functionality with Datalad #77)Review the
setup.py
andsetup_gui.py
scripts to be compatible withpip install ...
(PR ENH: Review installation to be compatible with PyPI #78)Rename
setup.py
tosetup_cmp.py
andsetup_gui.py
tosetup.py
(pip
is able to process onlysetup.py
files) (PR ENH: Review installation to be compatible with PyPI #78)cmp.cli
module and migration of scriptsconnectomemapper3
,showmatrix_gpickle
, andcmpbidsappmanager
tocmp.cli
module (PR ENH: Review installation to be compatible with PyPI #78)Documentation
Review usage and add a note regarding the adoption of the new
JSON
format for configuration files (PR ENH: Use json format for pipeline configuration files #76)Update tutorial on using CMP3 and Datalad for collaboration (PR ENH: Update data provenance tracking functionality with Datalad #77)
Update installation command of
cmpbidsappmanager
withpip install .
(PR ENH: Review installation to be compatible with PyPI #78)Bug fixes
Correct attributes related to the diffusion imaging model type
multishell
.Review code in
cmtklib/connectome.py
for saving functional connectome files in GRAPHML format.Fix the dialogs that select files in the BIDS App GUI to be in "open" mode instead of "save as" mode (PR ENH: Update data provenance tracking functionality with Datalad #77)
Software development life cycle
Code coverage improvement by calling the methods
check_stages_execution()
andfill_stages_outputs()
on each pipeline when executed with coverage (PR INFRA: Improve function testing coverage #75)
Code coverage improvement by saving in test-01 structural connectome files in MAT and GRAPHML format (PR Release: Connectome Mapper v3.0.0-RC4 #74)
Code coverage improvement by saving in test-07 functional connectome files in GRAPHML format (PR Release: Connectome Mapper v3.0.0-RC4 #74)
Update the list of outputs for all tests (PR Release: Connectome Mapper v3.0.0-RC4 #74)
Add new
test-python-install
job in CircleCI to test installing and building the distribution wheel (PR ENH: Review installation to be compatible with PyPI #78)