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Merged
merged 122 commits into from
Aug 26, 2025
Merged

Repository reorganization #72

merged 122 commits into from
Aug 26, 2025

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bergsalex
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This Pull Request merges all changes from the repository-reorganization branch into main.

This does a few things:

  1. Changes the location of the Python code.
  2. Applies ruff formatting and linting rules to all Python code.
  3. Adds pyproject.toml and related python packaging files.
  4. Adds a command line interface for the python code, available at mtr, mouse-tracking, or mouse-tracking-runtime.
    • Run mtr --help for more information.
  5. Updates nextflow code to call the the new command line interface.
  6. Adds new docker image definitions to remove the Google CoLab dependency.
  7. Adds units tests.
  8. Adds GitHub Actions for running format/lint, unit tests, and image builds.

bergsalex added 30 commits May 30, 2025 14:52
@bergsalex
Adding pyproject.toml and src structure outline
7b5c26b
@bergsalex
applying ruff formatting
a850417
@bergsalex
Adding tests for new CLI interface
f5144b1
@bergsalex
Cleanup of cli implementation from testing
17ca46a
@bergsalex
Adding pytest and uv lock
46131a4
@bergsalex
Removing tests directory from gitignore
679a316
@bergsalex
Adding new CLI definitions for all inference commands
04ebb2f
@bergsalex
Merge pull request #36 from KumarLabJax/YODA-128-build-new-cli-module…
4a9472c 
…-for-mouse-tracking-runtime

Yoda 128 build new cli module for mouse tracking runtime
@bergsalex
Automatic formatting
b9cb119
@bergsalex
Code comment cleanup
1e7de81
@bergsalex
Cleanup tests
77f7da3
@bergsalex
Merge pull request #37 from KumarLabJax/YODA-128-build-new-cli-module…
9e204f8 
…-for-mouse-tracking-runtime

Implement the CLI interfaces for infer CLI commands.
@bergsalex
Merge remote-tracking branch 'origin' into repository-reorganization
1272649
@bergsalex
Renaming root package to
99a1cb4
@bergsalex
Updating root __version__ and pyproject.toml package references
45bcfd3
@bergsalex
Merge pull request #41 from KumarLabJax/shorten-package-name
f05887c 
Shorten package name
@bergsalex
Refactoring pose utilities and adding tests
e00152b
@bergsalex
Adding two missed test files
aa5fa6d
@bergsalex
Moving all non top-level code files into the src directory and fixing…
50b331c 
… imports
@bergsalex
Adding typing to array utils
be32b3f
@bergsalex
Merge pull request #42 from KumarLabJax/refactor-pose-utils
39318e6 
Refactoring pose utilities and adding tests
@bergsalex
Merge pull request #43 from KumarLabJax/move-non-top-level-files
182b331 
Move all code files that aren't top level files
@bergsalex
Adding tests for pose inspect, and adding to CLI
3d9090d
@bergsalex
Fixing imports for CLI modules
3f32045
@bergsalex
Adding inspect functions to pose.inspect module
b020b86
@bergsalex
Switch pose inspect functions to use dict literal syntax
b34500c
@bergsalex
Specifying tf torch and jax related dependencies and updating lock file
26e1217
@bergsalex
Merge remote-tracking branch 'origin/fix-tf-pytorch-jax-dependencies'…
a524c07 
… into migrate-remaining-commands
@bergsalex
Merge pull request #44 from KumarLabJax/implement-single-pose-qa
9d178de 
Implement single pose qa
@bergsalex
Adding pose converter functions with tests
2fff3f5
bergsalex added 15 commits August 19, 2025 19:38
@bergsalex
Fix locally failing tests
cea427e
@bergsalex
Testing if NO_COLOR=1 env fixes formatting issue in Github Actions Tests
19f2a07
@bergsalex
Fixing auto formatting
a90b3a7
@bergsalex
Testing TTY_COMPATIBLE and TERM env vars to get CLI tests to pass in …
f4ccf11 
…GitHub Actions
@bergsalex
Fixing terminal issues in GitHub Actions unit tests, and mocking csv …
6b0952f 
…creation in single_pose command test
@bergsalex
Fix additional terminal errors in GitHub Actions tests
dd6e544
@bergsalex
Fix CUDA version in readme and fix --extra install instructions
837535b
@bergsalex
Merge pull request #65 from KumarLabJax/YODA-217-update-mouse-trackin…
e53b312 
…g-runtime-singularity-image

Update singularity and docker images to remove Google Colab dependency
@bergsalex
Merge remote-tracking branch 'origin/repository-reorganization' into …
4bc4843 
…task/add-github-actions
@bergsalex
Switch from GitHub Artifacts to Docker Hub
87a151c
@bergsalex
Address PR comments
f8860dd
@bergsalex
Deleting mouse-tracking-runtime directory, moving some old files to l…
538ddaf 
…egacy docs directory
@bergsalex
Merge pull request #68 from KumarLabJax/YODA-219-update-the-model-loc…
ef081b6 
…ation-definition-in-mouse-tracking-runtime-to-be-configurable

Yoda 219 Make Model Directory Location Configurable with Environment Variable
@bergsalex
Merge pull request #70 from KumarLabJax/cleanup-before-reorganization…
462366a 
…-merge

Cleanup Before Reorganization PR
@bergsalex
Merge pull request #69 from KumarLabJax/task/add-github-actions
65f3cfa 
Task/add GitHub actions
@bergsalex bergsalex self-assigned this Aug 21, 2025
@bergsalex bergsalex marked this pull request as ready for review August 21, 2025 19:08
SkepticRaven
SkepticRaven approved these changes Aug 26, 2025
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I think I'm ready to pull off this bandaid and get this merged in.
Just for posterity's sake: we're relying on the reviews that were merged into this branch as the primary source of reviews.

@bergsalex bergsalex merged commit 192740d into main Aug 26, 2025
5 of 6 checks passed
@bergsalex bergsalex deleted the repository-reorganization branch September 5, 2025 18:41
@SkepticRaven SkepticRaven mentioned this pull request Oct 2, 2025
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@gbeane gbeane gbeane approved these changes

@SkepticRaven SkepticRaven SkepticRaven approved these changes

@keithshep keithshep Awaiting requested review from keithshep

@vivekJax vivekJax Awaiting requested review from vivekJax

@dahhei dahhei Awaiting requested review from dahhei

@C-1337ka C-1337ka Awaiting requested review from C-1337ka

@pavan-el pavan-el Awaiting requested review from pavan-el

+1 more reviewer

@gerring gerring gerring approved these changes

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@bergsalex @gbeane @gerring @SkepticRaven