juaml/junifer
Watch
3
0
Fork
You've already forked junifer
 0
Code Issues 14 Pull requests 2 Packages Activity Actions

[MAINT]: Drop Python 3.9 and add Python 3.14 support #474

Merged
synchon merged 11 commits from chore/maintenance into main 2026-03-12 12:19:51 +00:00
Conversation 7 Commits 11 Files changed 122 +3960 -722
synchon commented 2025-11-07 11:50:57 +00:00 (Migrated from github.com)
Copy link
  • description of feature/fix
  • tests added/passed
  • add an entry for the latest changes

This PR drops Python 3.9 support and adds Python 3.14 support. Upgrades codebase to follow Python >=3.10 syntax changes, bumps dependencies and also adds proper uv support by adding lockfile.

* [x] description of feature/fix * [x] tests added/passed * [x] add an entry for the latest changes This PR drops Python 3.9 support and adds Python 3.14 support. Upgrades codebase to follow Python >=3.10 syntax changes, bumps dependencies and also adds proper `uv` support by adding lockfile.
codecov[bot] commented 2025-11-07 11:51:35 +00:00 (Migrated from github.com)
Copy link

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 91.55%. Comparing base (9d87a01) to head (ee3c4e6).
⚠️ Report is 12 commits behind head on main.

Additional details and impacted files

Impacted file tree graph

@@            Coverage Diff             @@
##             main     #474      +/-   ##
==========================================
- Coverage   91.70%   91.55%   -0.15%     
==========================================
  Files         146      146              
  Lines        5845     5744     -101     
  Branches      931      929       -2     
==========================================
- Hits         5360     5259     -101     
  Misses        313      313              
  Partials      172      172
Flag Coverage Δ
docs 100.00% <ø> (ø)

Flags with carried forward coverage won't be shown. Click here to find out more.

Files with missing lines Coverage Δ
junifer/api/functions.py 91.24% <ø> (-0.13%) ⬇️
...er/api/queue_context/gnu_parallel_local_adapter.py 92.78% <ø> (-0.15%) ⬇️
junifer/api/queue_context/htcondor_adapter.py 95.93% <ø> (-0.07%) ⬇️
junifer/cli/cli.py 81.48% <ø> (-0.34%) ⬇️
junifer/cli/parser.py 85.89% <ø> (-0.53%) ⬇️
junifer/data/_dispatch.py 93.50% <ø> (-0.09%) ⬇️
junifer/data/coordinates/_coordinates.py 100.00% <ø> (ø)
junifer/data/maps/_ants_maps_warper.py 100.00% <ø> (ø)
junifer/data/maps/_maps.py 98.88% <ø> (-0.02%) ⬇️
junifer/data/masks/_ants_mask_warper.py 75.00% <ø> (-1.93%) ⬇️
... and 80 more
🚀 New features to boost your workflow:
  • ❄️ Test Analytics: Detect flaky tests, report on failures, and find test suite problems.
## [Codecov](https://app.codecov.io/gh/juaml/junifer/pull/474?dropdown=coverage&src=pr&el=h1&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=juaml) Report :white_check_mark: All modified and coverable lines are covered by tests. :white_check_mark: Project coverage is 91.55%. Comparing base ([`9d87a01`](https://app.codecov.io/gh/juaml/junifer/commit/9d87a015ad680edd8d236165cece8cecdda51ab5?dropdown=coverage&el=desc&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=juaml)) to head ([`ee3c4e6`](https://app.codecov.io/gh/juaml/junifer/commit/ee3c4e6c7aadea6aa05692b7421f83cb76b8c2d0?dropdown=coverage&el=desc&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=juaml)). :warning: Report is 12 commits behind head on main. <details><summary>Additional details and impacted files</summary> [![Impacted file tree graph](https://app.codecov.io/gh/juaml/junifer/pull/474/graphs/tree.svg?width=650&height=150&src=pr&token=5H21JuZXMw&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=juaml)](https://app.codecov.io/gh/juaml/junifer/pull/474?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=juaml) ```diff @@ Coverage Diff @@ ## main #474 +/- ## ========================================== - Coverage 91.70% 91.55% -0.15% ========================================== Files 146 146 Lines 5845 5744 -101 Branches 931 929 -2 ========================================== - Hits 5360 5259 -101 Misses 313 313 Partials 172 172 ``` | [Flag](https://app.codecov.io/gh/juaml/junifer/pull/474/flags?src=pr&el=flags&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=juaml) | Coverage Δ | | |---|---|---| | [docs](https://app.codecov.io/gh/juaml/junifer/pull/474/flags?src=pr&el=flag&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=juaml) | `100.00% <ø> (ø)` | | Flags with carried forward coverage won't be shown. [Click here](https://docs.codecov.io/docs/carryforward-flags?utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=juaml#carryforward-flags-in-the-pull-request-comment) to find out more. | [Files with missing lines](https://app.codecov.io/gh/juaml/junifer/pull/474?dropdown=coverage&src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=juaml) | Coverage Δ | | |---|---|---| | [junifer/api/functions.py](https://app.codecov.io/gh/juaml/junifer/pull/474?src=pr&el=tree&filepath=junifer%2Fapi%2Ffunctions.py&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=juaml#diff-anVuaWZlci9hcGkvZnVuY3Rpb25zLnB5) | `91.24% <ø> (-0.13%)` | :arrow_down: | | [...er/api/queue\_context/gnu\_parallel\_local\_adapter.py](https://app.codecov.io/gh/juaml/junifer/pull/474?src=pr&el=tree&filepath=junifer%2Fapi%2Fqueue_context%2Fgnu_parallel_local_adapter.py&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=juaml#diff-anVuaWZlci9hcGkvcXVldWVfY29udGV4dC9nbnVfcGFyYWxsZWxfbG9jYWxfYWRhcHRlci5weQ==) | `92.78% <ø> (-0.15%)` | :arrow_down: | | [junifer/api/queue\_context/htcondor\_adapter.py](https://app.codecov.io/gh/juaml/junifer/pull/474?src=pr&el=tree&filepath=junifer%2Fapi%2Fqueue_context%2Fhtcondor_adapter.py&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=juaml#diff-anVuaWZlci9hcGkvcXVldWVfY29udGV4dC9odGNvbmRvcl9hZGFwdGVyLnB5) | `95.93% <ø> (-0.07%)` | :arrow_down: | | [junifer/cli/cli.py](https://app.codecov.io/gh/juaml/junifer/pull/474?src=pr&el=tree&filepath=junifer%2Fcli%2Fcli.py&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=juaml#diff-anVuaWZlci9jbGkvY2xpLnB5) | `81.48% <ø> (-0.34%)` | :arrow_down: | | [junifer/cli/parser.py](https://app.codecov.io/gh/juaml/junifer/pull/474?src=pr&el=tree&filepath=junifer%2Fcli%2Fparser.py&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=juaml#diff-anVuaWZlci9jbGkvcGFyc2VyLnB5) | `85.89% <ø> (-0.53%)` | :arrow_down: | | [junifer/data/\_dispatch.py](https://app.codecov.io/gh/juaml/junifer/pull/474?src=pr&el=tree&filepath=junifer%2Fdata%2F_dispatch.py&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=juaml#diff-anVuaWZlci9kYXRhL19kaXNwYXRjaC5weQ==) | `93.50% <ø> (-0.09%)` | :arrow_down: | | [junifer/data/coordinates/\_coordinates.py](https://app.codecov.io/gh/juaml/junifer/pull/474?src=pr&el=tree&filepath=junifer%2Fdata%2Fcoordinates%2F_coordinates.py&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=juaml#diff-anVuaWZlci9kYXRhL2Nvb3JkaW5hdGVzL19jb29yZGluYXRlcy5weQ==) | `100.00% <ø> (ø)` | | | [junifer/data/maps/\_ants\_maps\_warper.py](https://app.codecov.io/gh/juaml/junifer/pull/474?src=pr&el=tree&filepath=junifer%2Fdata%2Fmaps%2F_ants_maps_warper.py&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=juaml#diff-anVuaWZlci9kYXRhL21hcHMvX2FudHNfbWFwc193YXJwZXIucHk=) | `100.00% <ø> (ø)` | | | [junifer/data/maps/\_maps.py](https://app.codecov.io/gh/juaml/junifer/pull/474?src=pr&el=tree&filepath=junifer%2Fdata%2Fmaps%2F_maps.py&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=juaml#diff-anVuaWZlci9kYXRhL21hcHMvX21hcHMucHk=) | `98.88% <ø> (-0.02%)` | :arrow_down: | | [junifer/data/masks/\_ants\_mask\_warper.py](https://app.codecov.io/gh/juaml/junifer/pull/474?src=pr&el=tree&filepath=junifer%2Fdata%2Fmasks%2F_ants_mask_warper.py&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=juaml#diff-anVuaWZlci9kYXRhL21hc2tzL19hbnRzX21hc2tfd2FycGVyLnB5) | `75.00% <ø> (-1.93%)` | :arrow_down: | | ... and [80 more](https://app.codecov.io/gh/juaml/junifer/pull/474?src=pr&el=tree-more&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=juaml) | | </details> <details><summary> :rocket: New features to boost your workflow: </summary> - :snowflake: [Test Analytics](https://docs.codecov.com/docs/test-analytics): Detect flaky tests, report on failures, and find test suite problems. </details>
fraimondo (Migrated from github.com) requested changes 2025-11-07 12:00:32 +00:00
fraimondo (Migrated from github.com) left a comment
Copy link

I think you have some UV stuff filtered. Maybe add them to the .gitignore?

I think you have some UV stuff filtered. Maybe add them to the `.gitignore`?
.python-version
@ -0,0 +1 @@
3.12
fraimondo (Migrated from github.com) commented 2025-11-07 11:59:57 +00:00
Copy link

why do we need this?

why do we need this?
github-actions[bot] commented 2025-11-07 12:40:09 +00:00 (Migrated from github.com)
Copy link
PR Preview Action v1.6.2

🚀 View preview at
https://juaml.github.io/junifer/pr-preview/pr-474/

Built to branch gh-pages at 2025-11-07 13:25 UTC.
Preview will be ready when the GitHub Pages deployment is complete.

[PR Preview Action](https://github.com/rossjrw/pr-preview-action) v1.6.2 :---: | <p></p> :rocket: View preview at <br> https://juaml.github.io/junifer/pr-preview/pr-474/ <br><br> | <h6>Built to branch [`gh-pages`](https://github.com/juaml/junifer/tree/gh-pages) at 2025-11-07 13:25 UTC. <br> Preview will be ready when the [GitHub Pages deployment](https://github.com/juaml/junifer/deployments) is complete. <br><br> </h6> <!-- Sticky Pull Request Commentpr-preview -->
synchon (Migrated from github.com) reviewed 2025-11-07 13:30:29 +00:00
.python-version
@ -0,0 +1 @@
3.12
synchon (Migrated from github.com) commented 2025-11-07 13:30:29 +00:00
Copy link

It's for uv to use that version when one does uv sync or any uv stuff. 3.13 or 3.14 does not work due to a versioning issue in scikit-learn.

It's for ``uv`` to use that version when one does ``uv sync`` or any ``uv`` stuff. 3.13 or 3.14 does not work due to a versioning issue in ``scikit-learn``.
fraimondo (Migrated from github.com) reviewed 2025-11-07 17:05:18 +00:00
.python-version
@ -0,0 +1 @@
3.12
fraimondo (Migrated from github.com) commented 2025-11-07 17:05:18 +00:00
Copy link

the uv.lock file is needed too?

the `uv.lock` file is needed too?
synchon (Migrated from github.com) reviewed 2025-11-07 17:08:59 +00:00
.python-version
@ -0,0 +1 @@
3.12
synchon (Migrated from github.com) commented 2025-11-07 17:08:59 +00:00
Copy link

Yes, for reproducible installs using uv.

Yes, for reproducible installs using uv.
synchon commented 2026-03-12 12:19:20 +00:00 (Migrated from github.com)
Copy link

CI passes on juseless.

CI passes on juseless.
Sign in to join this conversation.
Reviewers
No reviewers
fraimondo
Labels
Clear labels   
CRITICAL
High Priority Issue

  
Stale

   
WIP
Work in progress

  
bug
Something isn't working

  
concept
Design/Implementation concepts

  
coordinate
Issues or pull requests related to coordinates (ROIs)

  
dataset
Issues or pull requests related to datagrabbers or datasets

  
dependencies
Pull requests that update a dependency file

  
documentation
Improvements or additions to documentation

  
duplicate
This issue or pull request already exists

  
enhancement
New feature or request

  
github_actions
Pull requests that update GitHub Actions code

  
good first issue
Good for newcomers

  
help wanted
Extra attention is needed

  
invalid
This doesn't seem right

  
maintenance
Issues or pull requests related to maintenance

  
maps
Issues or pull requests related to maps (probabilistic atlases)

  
marker
Issues or pull requests related to markers

  
mask
Issues or pull requests related to masks

  
on hold
Issue waiting on other issue(s)

  
parcellation
Issues or pull requests related to parcellations (deterministic atlases)

  
preprocess
Issues or pull requests related to preprocessors

  
question
Further information is requested

  
ready
Pull request is ready for review and merge

  
storage
Issues or pull requests related to marker storage or retrieval

  
template-space
Issues or pull requests related to template spaces

  
triage
New issues waiting to be reviewed

  
wontfix
This will not be worked on

No labels
CRITICAL
Stale
WIP
bug
concept
coordinate
dataset
dependencies
documentation
duplicate
enhancement
github_actions
good first issue
help wanted
invalid
maintenance
maps
marker
mask
on hold
parcellation
preprocess
question
ready
storage
template-space
triage
wontfix
Milestone
Clear milestone
No items
No milestone
0.0.8
Assignees
Clear assignees
No assignees
1 participant
Notifications
Due date
The due date is invalid or out of range. Please use the format "yyyy-mm-dd".

No due date set.

Dependencies

No dependencies set

Reference
juaml/junifer!474
No description provided.