[UPCOMING] Release preparation for 1.9.0

[skoudoro]

Preparation for 1.9.0 release, targeting March 5-6, 2024.

Desired PR / issues (need review / feedback / update)

PR

• NF: Adding N4 bias correction deep learning model #3081(Submitter: @praitayini)
• return S0 from dki fit #3078 (Submitter: @samcoveney)
• [NF] Add DSI workflow #3073 (Submitter: @skoudoro)
• [NF] Add workflow to convert tensors in different formats #3053 (Submitter: @skoudoro)
• [TEST] Adds support of cython for pytest #3048 (Submitter: @skoudoro)
• [RF] fix dki mask for nlls #3033 (Submitter: @skoudoro)
• Tab names for slice tabs as file names. #2973 (Submitter: @maharshi-gor)
• [ENH] Compute fiber density and fiber spread from ODF using Bingham distributions #2826 (Submitter: @CHrlS98)

Issues / Feature without PR yet

• SH basis legacy option not available for few methods #3079
• I do not see a way to change step as used by reconst.dti.TensorModel.fit() #3030
• Migrating to Keyword Only arguments (PEP 3102) #3029
• DKI masking #2994

Most of them can be done on time, I think 😄

Please comment to flag any other issues or PR that should be addressed for this release

Release checklist

• add release_notes 1.9.0
• Update changelog and api_changes
• Update .mailmap
• Set release number in info.py
• Check the copyright years in doc/conf.py and LICENSE
• Check documentation
• Check Tutorial
• Check unit test and USE-PRE
• Update index.rst
• Update Highligth.rst, old_news.rst, stateofheart.rst
• Update developers.rst list
• Update website
• Update deprecation cycle remove long deprecation

[skoudoro]

Ok, This PR is ready,

Can you have a look @arokem or @Garyfallidis? Everyone else is also welcome? Then, I can start the release process.

Thank you

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 81.76%. Comparing base (ecae56b) to head (e050b8a).
Report is 12 commits behind head on master.

Additional details and impacted files

@@            Coverage Diff             @@
##           master    #3095      +/-   ##
==========================================
- Coverage   81.77%   81.76%   -0.02%     
==========================================
  Files         150      150              
  Lines       21255    21238      -17     
  Branches     3412     3412              
==========================================
- Hits        17382    17365      -17     
  Misses       3034     3034              
  Partials      839      839              

Files	Coverage Δ
dipy/align/imaffine.py	95.91% <ø> (-0.05%)	⬇️
dipy/denoise/gibbs.py	100.00% <ø> (ø)
dipy/direction/peaks.py	83.83% <ø> (-0.25%)	⬇️
dipy/reconst/csdeconv.py	87.22% <100.00%> (-0.04%)	⬇️
dipy/segment/bundles.py	89.01% <ø> (-0.08%)	⬇️
dipy/workflows/denoise.py	81.81% <ø> (-0.37%)	⬇️
dipy/workflows/reconst.py	76.40% <ø> (-0.19%)	⬇️

... and 2 files with indirect coverage changes

[arokem]

I'd say that out of the issues without a PR, #3079 seems the most important to address before a release. I think we can punt the other ones to the next cycle. Or do you think we should punt that one too?

Also, I'd love to understand #3108 better before we make a release, because I am not at all sure that's not a regression. @maharshi-gor or @Garyfallidis : could you tell me a bit more about that PR?

[skoudoro]

Thank you for the feedback @arokem,

• SH basis legacy option not available for few methods #3079 has been fixed by Adding SH basis legacy option support to peaks_from_model #3080. I just forgot to close this issue
• Concerning enabled trx support with correct header #3108, I will let them answer

[maharshi-gor]

Hello @arokem, this is simply enabling the .trx file format in the horizon CLI. CLI was accepting all the types of tractorgrams except the '.trx' extension. Although the method load_tractogram already had the handling of '.trx' files. I just verified if it is a '.trx' file and passed it to the same method to process.

It is tested with a few examples. Let me know if you would like to know more.

Thank you for the feedback.

[maharshi-gor]

@arokem the interactions were not working due to the initial setting. The clusters tab had some bugs and we thought it had something to do with how the reference is passed. It was merged because it worked. It was last minute change for the CLI to support .trx.

Before #3108, there was #3107, where we added the .trx support. The interactions on the horizon tab didn't work. But by introducing #3108 change the interaction started working for .trx files.

[arokem]

Got it! Just to confirm: since this change is local to viz, this presumably wouldn't affect other parts of the code?

[skoudoro]

this presumably wouldn't affect other parts of the code?

I do not think so, this is very local to viz module