Repository reorganization - #72

Merged

bergsalex merged 122 commits into

mainfrom

repository-reorganization

Aug 26, 2025

Commits on May 30, 2025

Adding pyproject.toml and src structure outline
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7b5c26b
applying ruff formatting
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a850417
Adding tests for new CLI interface
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f5144b1
Cleanup of cli implementation from testing
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17ca46a
Adding pytest and uv lock
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46131a4
Removing tests directory from gitignore
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679a316

Commits on Jun 2, 2025

Commits on Jul 1, 2025

Merge pull request #41 from KumarLabJax/shorten-package-name
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f05887c
Refactoring pose utilities and adding tests
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e00152b
Adding two missed test files
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aa5fa6d
Moving all non top-level code files into the src directory and fixing imports
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50b331c
Adding typing to array utils
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be32b3f
Merge pull request #42 from KumarLabJax/refactor-pose-utils
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39318e6
Merge pull request #43 from KumarLabJax/move-non-top-level-files
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182b331
Adding tests for pose inspect, and adding to CLI
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3d9090d
Fixing imports for CLI modules
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3f32045

Commits on Jul 2, 2025

Adding inspect functions to pose.inspect module
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b020b86

Commits on Jul 7, 2025

Commits on Jul 8, 2025

Adding tests for the utils.writers module
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b216cc1
Migrate fecal_boli CLI definition
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912f4ca
Finishing up initial utils CLI comands
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37b4e63

Commits on Jul 10, 2025

Commits on Jul 11, 2025

First pass at segmentation utils unit tests
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07075db
Better docstrings in new segmentation utils tests
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b34757c
Update CLI tests for Utils commands
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e5ceb4f
Adding additional tests for merge_multiple_seg_instances when no data is available to stack
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d31f0dd
Merge remote-tracking branch 'origin/main' into migrate-inference-commands
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127a247
Fill out implementation of inference cli commands
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e510c76
Updating tests for inference CLI
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5553b8d
Fix pytorch_inference models import
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158ce02
Merge remote-tracking branch 'origin/main' into repository-reorganization
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e82b2db
Updating nextflow command calls to use new Typer CLI
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91a3b60

Commits on Jul 15, 2025

Commits on Jul 16, 2025

Early implementation of vectorized calculate_costs
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8863a01

Commits on Jul 17, 2025

Commits on Jul 23, 2025

Merge pull request #53 from KumarLabJax/migrate-nextflow-command-calls
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68246c4
Vectorizing greedy matching and adding associated tests
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f02a41c
Update comments
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65312e5

Commits on Jul 24, 2025

Cleanup of test organization and removing old utils.matching file
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581b68b

Commits on Aug 4, 2025

Merge pull request #55 from KumarLabJax/improve-generate-tracklets-performance
bergsalex
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bc3ec73

Commits on Aug 5, 2025

Commits on Aug 7, 2025

Merge pull request #57 from KumarLabJax/improve-generate-tracklets-performance
bergsalex
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3283eeb

Commits on Aug 14, 2025

Merge remote-tracking branch 'origin/main' into repository-reorganization
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c99ccd8
Adding PR verification action
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988f9eb
Testing docker image build
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d4ba198
Testing node cleanup
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15f78a8
Debug image size
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34aaff3
Testing GCP Cloud Build
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11ae9b6

Commits on Aug 15, 2025

Commits on Aug 19, 2025

Commits on Aug 20, 2025

Commits on Aug 21, 2025