Add basic README for auxiliary repository by Copilot · Pull Request #44 · BrainLesion/auxiliary

Copilot · 2025-11-29T16:32:40Z

Creates a basic README.md file for the auxiliary repository, inspired by the BrainLesion/PeTu repository structure.

Changes Made

Badges: Added PyPI version, Python versions, ReadTheDocs status, and Apache 2.0 license badges
Package overview: Added description of the auxiliary package as a medical image processing utility library
Installation: Included PyPI and Conda installation instructions, plus optional dcm2niix dependency
Usage examples: Organized by format with dedicated I/O sections for NIfTI, DICOM, and TIFF, plus image normalization examples
License update: Updated pyproject.toml license from AGPL-3.0 to Apache-2.0 to match the existing LICENSE file

Fixes #37

Original prompt

This section details on the original issue you should resolve

<issue_title>[FEATURE] auxiliary needs a basic readme file</issue_title>
<issue_description>:)</issue_description>

<agent_instructions>please create a basic readme for this repository, take this repo as inspiration:
https://github.com/BrainLesion/PeTu</agent_instructions>

Comments on the Issue (you are @copilot in this section)

Fixes [FEATURE] auxiliary needs a basic readme file #37

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Co-authored-by: neuronflow <7048826+neuronflow@users.noreply.github.com>

neuronflow

@copilot remove this section ## Contributing

We welcome all kinds of contributions from the community!

Reporting Bugs, Feature Requests and Questions

Please open a new issue here.

Code Contributions

Nice to have you on board! Please have a look at our CONTRIBUTING.md file.

Co-authored-by: neuronflow <7048826+neuronflow@users.noreply.github.com>

Copilot · 2025-11-29T16:44:34Z

@copilot remove this section ## Contributing

We welcome all kinds of contributions from the community!...

Removed the Contributing section in 4005330.

neuronflow

@copilot also show how to read and write DICOM files

maybe an i/o section for each format, nifti, DICOM, tiff

Co-authored-by: neuronflow <7048826+neuronflow@users.noreply.github.com>

Copilot · 2025-11-29T16:50:27Z

@copilot also show how to read and write DICOM files

maybe an i/o section for each format, nifti, DICOM, tiff

Reorganized the Usage section with separate I/O sections for NIfTI, DICOM, and TIFF formats. Added examples showing how to read DICOM series and write to DICOM format (with optional reference DICOM for metadata) in be6e583.

neuronflow

@copilot also show how to write numpy arrays to DICOM with and without reference images

…ence images Co-authored-by: neuronflow <7048826+neuronflow@users.noreply.github.com>

Copilot · 2025-11-29T16:56:24Z

@copilot also show how to write numpy arrays to DICOM with and without reference images

Added examples showing how to write NumPy arrays to DICOM format with and without reference images in c23433c.

Copilot

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Copilot · 2025-11-29T17:00:37Z

README.md

+[![Python Versions](https://img.shields.io/pypi/pyversions/auxiliary)](https://pypi.org/project/auxiliary/)
+[![Stable Version](https://img.shields.io/pypi/v/auxiliary?label=stable)](https://pypi.org/project/auxiliary/)
 [![Documentation Status](https://readthedocs.org/projects/auxiliary/badge/?version=latest)](http://auxiliary.readthedocs.io/?badge=latest)
 [![License](https://img.shields.io/badge/License-Apache%202.0-blue.svg)](https://opensource.org/licenses/Apache-2.0)


The License badge indicates "Apache 2.0" but according to pyproject.toml (line 13), the project is licensed under "AGPL-3.0". The badge should be updated to reflect the correct license.

Suggested change

[![License](https://img.shields.io/badge/License-Apache%202.0-blue.svg)](https://opensource.org/licenses/Apache-2.0)

[![License](https://img.shields.io/badge/License-AGPL%20v3-blue.svg)](https://www.gnu.org/licenses/agpl-3.0.html)

@copilot no in this case please change the project license to Apache 2.0

Updated pyproject.toml license from AGPL-3.0 to Apache-2.0 in f170a74. The LICENSE file already contained the Apache 2.0 license, so this makes everything consistent.

Co-authored-by: neuronflow <7048826+neuronflow@users.noreply.github.com>

neuronflow

lgtm but I am quite sure things could be better :)

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neuronflow

lgtm anything is better than no readme.

Added citation section with reference for the auxiliary framework.

Copilot

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Initial plan

ba020a0

Copilot AI assigned Copilot and neuronflow Nov 29, 2025

Copilot started work on behalf of neuronflow November 29, 2025 16:33 View session

neuronflow requested a review from Copilot November 29, 2025 16:33

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Create comprehensive README.md with badges, features, and usage examples

13b06a3

Co-authored-by: neuronflow <7048826+neuronflow@users.noreply.github.com>

Copilot AI changed the title ~~[WIP] Add basic README file for auxiliary repository~~ Add basic README for auxiliary repository Nov 29, 2025

Copilot AI requested a review from neuronflow November 29, 2025 16:40

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Remove Contributing section from README

4005330

Co-authored-by: neuronflow <7048826+neuronflow@users.noreply.github.com>

Copilot AI requested a review from neuronflow November 29, 2025 16:45

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Copilot started work on behalf of neuronflow November 29, 2025 16:48 View session

Reorganize README with I/O sections for each format (NIfTI, DICOM, TIFF)

be6e583

Co-authored-by: neuronflow <7048826+neuronflow@users.noreply.github.com>

Copilot finished work on behalf of neuronflow November 29, 2025 16:51

Copilot AI requested a review from neuronflow November 29, 2025 16:51

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Add examples for writing NumPy arrays to DICOM with and without refer…

c23433c

…ence images Co-authored-by: neuronflow <7048826+neuronflow@users.noreply.github.com>

Copilot AI requested a review from neuronflow November 29, 2025 16:57

Copilot finished work on behalf of neuronflow November 29, 2025 16:57

neuronflow requested review from MarcelRosier and removed request for neuronflow November 29, 2025 16:58

neuronflow requested review from Copilot and neuronflow and removed request for neuronflow November 29, 2025 16:58

neuronflow marked this pull request as ready for review November 29, 2025 16:59

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Copilot started work on behalf of neuronflow November 29, 2025 17:04 View session

Update pyproject.toml license to Apache-2.0

f170a74

Co-authored-by: neuronflow <7048826+neuronflow@users.noreply.github.com>

Copilot finished work on behalf of neuronflow November 29, 2025 17:06

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neuronflow approved these changes Dec 10, 2025

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neuronflow requested review from Copilot and neuronflow December 10, 2025 11:38

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Copilot started reviewing on behalf of neuronflow December 10, 2025 11:38 View session

Add citation section to README

f1fab44

Added citation section with reference for the auxiliary framework.

neuronflow self-requested a review December 10, 2025 11:40

neuronflow approved these changes Dec 10, 2025

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neuronflow removed the request for review from MarcelRosier December 10, 2025 11:41

neuronflow merged commit 8222718 into main Dec 10, 2025
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neuronflow deleted the copilot/add-basic-readme-file branch December 10, 2025 11:43

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	[![License](https://img.shields.io/badge/License-Apache%202.0-blue.svg)](https://opensource.org/licenses/Apache-2.0)
	[![License](https://img.shields.io/badge/License-AGPL%20v3-blue.svg)](https://www.gnu.org/licenses/agpl-3.0.html)

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Copilot AI commented Nov 29, 2025 •

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