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[nicozerep-lab]

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[Copilot]

Pull Request Overview

This PR introduces a new GitHub Actions workflow for building and testing a Python package using Conda. The workflow sets up a CI/CD pipeline that runs on every push to automatically test the codebase.

• Adds automated testing with pytest and code quality checks with flake8
• Configures Python 3.10 environment using Conda for dependency management
• Sets up continuous integration pipeline triggered on push events

---

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[Copilot]

Updating the base conda environment is not recommended as it can cause conflicts. Consider creating a dedicated environment instead using 'conda env create' or 'conda create'.

Suggested change

	- name: Install dependencies
	run: |
	conda env update --file environment.yml --name base
	- name: Lint with flake8
	run: |
	conda install flake8
	# stop the build if there are Python syntax errors or undefined names
	flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
	# exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
	flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
	- name: Test with pytest
	run: |
	- name: Create conda environment
	run: |
	conda env create --file environment.yml
	- name: Activate environment and lint with flake8
	run: |
	source activate $(head -1 environment.yml | cut -d' ' -f2)
	conda install flake8
	# stop the build if there are Python syntax errors or undefined names
	flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
	# exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
	flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
	- name: Activate environment and test with pytest
	run: |
	source activate $(head -1 environment.yml | cut -d' ' -f2)

[Copilot]

Installing packages separately with multiple conda install commands is inefficient. Consider installing all dependencies in a single command: 'conda install flake8 pytest' or include them in the environment.yml file.

Suggested change

	- name: Lint with flake8
	run: |
	conda install flake8
	# stop the build if there are Python syntax errors or undefined names
	flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
	# exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
	flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
	- name: Test with pytest
	run: |
	conda install pytest
	- name: Install flake8 and pytest
	run: |
	conda install flake8 pytest
	- name: Lint with flake8
	run: |
	# stop the build if there are Python syntax errors or undefined names
	flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
	# exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
	flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
	- name: Test with pytest
	run: |

[Copilot]

Installing packages separately with multiple conda install commands is inefficient. Consider installing all dependencies in a single command: 'conda install flake8 pytest' or include them in the environment.yml file.

Suggested change

	conda install flake8
	# stop the build if there are Python syntax errors or undefined names
	flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
	# exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
	flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
	- name: Test with pytest
	run: |
	conda install pytest
	conda install flake8 pytest
	# stop the build if there are Python syntax errors or undefined names
	flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
	# exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
	flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
	- name: Test with pytest
	run: |