Addressing JOSS review #15
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* bump up python and numpy versions * Parallelize at leg level * add AI-generated tests * wip - implement parallelization over time * parallelize over time * get parallelization example working and run scaling test on SCITAS * refactor different processing modes into separate methods * fix typos in parallel pipeline * update unit tests for parallelization * fix more typos and inconsistencies in docs * minor doc/assertion updates * Python 3.9 no more - EOL reached. This simplifies typehinting syntax
* Consolidate hard-coded constants into dataclass. Simplify logging convention in the meantime. * introduce new body_config module manage constant deprecation * fix typos and filter out dof type warnings from ikpy
* run black * update contributing.md * fix various doc site formatting issue and fix jupyter-book version to <2. * remove largely duplicated walking tutorial from main menu of the doc site * Add explicit instruction for cloning the directory if the data folder is needed * fix link to nmf zero pose image * update python version in CI to match new python version range * typo/doc improvement
* update paper * (auto) Paper PDF Draft * add background info on kalman filter and DL-based ik approaches. Recompile paper pdf * (auto) Paper PDF Draft * fix typo * keep pdf in repo after all - it's managed by ci * (auto) Paper PDF Draft * add information on optimization of all dofs instead of sequentially * (auto) Paper PDF Draft --------- Co-authored-by: sibocw <[email protected]>
* add new tutorial on parallel processing * fix typos
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Pull request overview
This pull request addresses feedback from the JOSS peer review process, implementing several major improvements to the seqikpy package including parallelization support, refactored body configuration management, updated dependencies, and enhanced documentation.
Key changes:
- Implemented parallel processing for inverse kinematics over legs and time dimensions using joblib
- Consolidated hardcoded body parameters into a new
BodyConfigdataclass with deprecated backward compatibility - Updated Python support to 3.9-3.13, upgraded numpy to >=2.0, and added joblib dependency
Reviewed changes
Copilot reviewed 31 out of 37 changed files in this pull request and generated 2 comments.
Show a summary per file
| File | Description |
|---|---|
| setup.py | Updated Python version constraints, dependencies (numpy 2.0, joblib), and package classifiers |
| seqikpy/body_config.py | New module introducing BodyConfig dataclass for centralized body parameter management |
| seqikpy/data.py | Deprecated module now redirects to body_config with deprecation warnings |
| seqikpy/leg_inverse_kinematics.py | Added parallelization support with n_workers parameter and parallel processing over legs/time |
| seqikpy/utils.py | Added split_arrays_into_chunks and merge_chunks_into_arrays functions for time-series chunking |
| tests/test_parallelization.py | Comprehensive new test suite covering parallelization functionality |
| seqikpy/kinematic_chain.py | Refactored to use body_config and suppress ikpy warnings more cleanly |
| seqikpy/alignment.py | Updated imports to use body_config instead of deprecated data module |
| docs/* | Updated documentation, tutorials, and paper with parallelization info and corrections |
| examples/* | Updated all examples to use new body_config API |
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Hi @sibocw, Thanks again for your help! I’ve incorporated my edits — mostly fixing the aforementioned bugs and adding a new example that demonstrates how to use seqikpy on mouse forelimb kinematics. All tutorials run smoothly on my end. I’m mostly done with the text edits and will move on to reviewing your changes next. |
gizemozd
reviewed
Dec 12, 2025
…ons (offer uv as an alternative to pip, but allow native pip as well)
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Pull request overview
Copilot reviewed 36 out of 49 changed files in this pull request and generated 2 comments.
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Addressing points raised in peer review at JOSS: openjournals/joss-reviews#8557
TODO
@sibocw
Code/tutorial change
Paper/docs only
@gizemozd
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