Merge pull request #80 from jjjermiah/development #247

Workflow file for this run

	name: Unit Tests

	# only run on pushes to main or pull requests
	on:
	push:
	# push to any branch
	branches: [ main ]
	pull_request:
	branches: [ main , development]

	jobs:
	Continuous-Integration:
	runs-on: ${{ matrix.os }}
	strategy:
	matrix:
	os: [ubuntu-latest, macos-latest, macos-14]
	python-version: ["3.12", "3.11"] # "3.10",

	steps:
	- uses: actions/checkout@v3

	- name: Set up Python ${{ matrix.python-version }}
	uses: actions/setup-python@v4
	with:
	python-version: ${{ matrix.python-version }}

	- name: Install poetry
	uses: snok/install-poetry@v1

	- name: Install dependencies
	run: poetry install

	- name: Test with pytest
	run: \|
	poetry run pytest -n 2 --cov --cov-report xml:coverage-report/coverage.xml

	- name: Build documentation
	run: poetry run make html --directory docs/

	- name: Upload coverage report
	uses: actions/upload-artifact@v2
	with:
	name: coverage-report
	path: coverage-report

	Codecov:
	needs: Continuous-Integration
	runs-on: ubuntu-latest
	steps:
	- name: Checkout code
	uses: actions/checkout@v3

	- name: Download coverage.xml artifact
	uses: actions/download-artifact@v2
	with:
	name: coverage-report
	path: coverage-report

	- name: Use Codecov to track coverage
	uses: codecov/codecov-action@v3
	with:
	token: ${{ secrets.CODECOV_TOKEN }}
	files: ./coverage-report/coverage.xml
	fail_ci_if_error: true
	verbose: true
	name: codecov-umbrella



	# Continuous-Deployment:
	# permissions:
	# contents: write
	# packages: write
	# issues: write
	# pull-requests: write

	# # needs: Continuous-Integration

	# # if pulling to main, deploy to PyPI
	# # if: github.ref == 'refs/heads/main'

	# # Set up operating system
	# runs-on: ubuntu-latest

	# # Define job steps
	# steps:
	# - name: Set up Python 3.12
	# uses: actions/setup-python@v2
	# with:
	# python-version: 3.12

	# - name: Check-out repository
	# uses: actions/checkout@v2
	# with:
	# fetch-depth: 0

	# - name: Install poetry
	# uses: snok/install-poetry@v1

	# - name: Install package
	# run: poetry install


	# # Existing jobs...



	# # This action uses Python Semantic Release v8
	# # What this action does:
	# # - Determines the next version number based on the commit history
	# # - Creates a new tag with the new version number
	# # - Pushes the new tag to GitHub
	# # - Creates a GitHub release with the new version number
	# - name: Python Semantic Release
	# id: release
	# uses: python-semantic-release/python-semantic-release@master
	# with:
	# github_token: ${{ secrets.GITHUB_TOKEN }}
	# git_commit_message: 'chore(release): release ${next_version}'

	# - name: Install packaging-related tool
	# run:
	# python3 -m pip install build twine

	# # Build Package step:
	# # After semantic release, we should have a new tag if the commit history
	# # has been updated. If there isnt a new tag, then we dont need to build
	# # a new package. If there is a new tag, then we need to build a new package
	# # and publish it to PyPI
	# - name: Build package
	# if: steps.release.outputs.released == 'true'
	# run: \|
	# poetry version $(git describe --tags --abbrev=0 \| sed 's/^v//')
	# python -m build --sdist --wheel --outdir dist/ .
	# echo "LATEST_TAG=$(poetry version \| sed 's/^nbiatoolkit //')" >> "$GITHUB_ENV"

	# - name: Publish package distributions to PyPI
	# if: steps.release.outputs.released == 'true'
	# uses: pypa/gh-action-pypi-publish@release/v1
	# with:
	# verbose: true
	# user: __token__
	# password: ${{ secrets.PYPI_API_TOKEN }}

	# - name: Print latest tag name
	# run: \|
	# printf "%s\n" "${LATEST_TAG}"

	# - name: Print branch name
	# run: \|
	# printf "LATEST TAG: %s\n" "${LATEST_TAG}"
	# echo "DOCKER_IMAGE_TAG=${LATEST_TAG}" >> "$GITHUB_ENV"
	# printf "DOCKER_IMAGE_TAG: %s\n" "${DOCKER_IMAGE_TAG}"

	# - name: Set up QEMU
	# if: steps.release.outputs.released == 'true'
	# uses: docker/setup-qemu-action@v3

	# - name: Set up Docker Buildx
	# if: steps.release.outputs.released == 'true'
	# uses: docker/setup-buildx-action@v3

	# - name: Login to Docker Hub
	# if: steps.release.outputs.released == 'true'
	# uses: docker/login-action@v3
	# with:
	# username: ${{ secrets.DOCKERHUB_USERNAME }}
	# password: ${{ secrets.DOCKERHUB_TOKEN }}

	# - name: Login to the GitHub Container Registry
	# if: steps.release.outputs.released == 'true'
	# uses: docker/login-action@v3
	# with:
	# registry: ghcr.io
	# username: ${{ github.actor }}
	# password: ${{ secrets.GITHUB_TOKEN }}

	# - name: Extract metadata (tags, labels) for Docker
	# id: meta
	# uses: docker/metadata-action@v3
	# with:
	# images: \|
	# ${{ secrets.DOCKERHUB_USERNAME }}/nbiatoolkit:${{ env.DOCKER_IMAGE_TAG }}
	# ghcr.io/${{ github.repository }}/nbiatoolkit:${{ env.DOCKER_IMAGE_TAG }}

	# - name: Build
	# if: steps.release.outputs.released == 'true'
	# uses: docker/build-push-action@v5
	# with:
	# context: .
	# platforms: linux/amd64,linux/arm64
	# file: ./Dockerfile
	# push: true
	# tags: \|
	# ${{ secrets.DOCKERHUB_USERNAME }}/nbiatoolkit:${{ env.DOCKER_IMAGE_TAG }}
	# ${{ secrets.DOCKERHUB_USERNAME }}/nbiatoolkit:latest
	# ghcr.io/${{ github.repository }}/nbiatoolkit:${{ env.DOCKER_IMAGE_TAG }}
	# ghcr.io/${{ github.repository }}/nbiatoolkit:latest
	# labels: ${{ steps.meta.outputs.labels }}

	# test_install_withPyPi:
	# needs: Continuous-Deployment
	# runs-on: ${{ matrix.os }}
	# strategy:
	# matrix:
	# os: [ubuntu-latest, macos-latest, macos-14]
	# python-version: ["3.12", "3.11"]

	# steps:
	# - uses: actions/checkout@v3

	# - name: Set up Python ${{ matrix.python-version }}
	# uses: actions/setup-python@v4
	# with:
	# python-version: ${{ matrix.python-version }}

	# - name: Install using PyPi
	# run: \|
	# pip install nbiatoolkit;
	# NBIAToolkit


	# test_image_with_new_tag:
	# needs: Continuous-Deployment
	# runs-on: ubuntu-latest
	# steps:
	# - name: Checkout code
	# uses: actions/checkout@v3

	# - name: Test Image With new Tag
	# run: \|
	# # get latest tag
	# LATEST_TAG=$(curl -s \
	# "https://api.github.com/repos/${{ github.repository }}/releases/latest" \
	# \| jq -r .tag_name \| sed 's/^v//')
	# echo "LATEST_TAG=${LATEST_TAG}"

	# # test image with latest tag
	# docker run --rm \
	# ${{ secrets.DOCKERHUB_USERNAME }}/nbiatoolkit:${LATEST_TAG} \
	# NBIAToolkit


	# test_image_with_latest_tag:
	# needs: Continuous-Deployment
	# runs-on: ubuntu-latest
	# steps:
	# - name: Checkout code
	# uses: actions/checkout@v2

	# - name: Test Image with "latest" Tag
	# run: \|
	# docker run --rm \
	# ${{ secrets.DOCKERHUB_USERNAME }}/nbiatoolkit:latest \
	# NBIAToolkit

	Update-README:
	# needs: Continuous-Deployment
	runs-on: ubuntu-latest
	# if: github.ref == 'refs/heads/development'
	steps:
	- name: Checkout code
	uses: actions/checkout@v3

	- name: Get Current branch
	run: \|
	echo "Current branch is: ${{ github.ref }}"
	echo "Current branch is: ${{ github.head_ref }}"
	echo "Current branch is: ${{ github.base_ref }}"
	echo "Current branch is: ${{ github.event_name }}"

	# if main, then git pull main
	if [ "${{ github.ref }}" == "refs/heads/main" ]; then
	git pull origin main
	fi

	# fix diverged branch
	git fetch origin ${{ github.head_ref }}
	git checkout ${{ github.head_ref }}

	- name: Set up Python ${{ matrix.python-version }}
	uses: actions/setup-python@v4
	with:
	python-version: ${{ matrix.python-version }}

	- name: Install using PyPi
	run: \|
	# update pip
	pip install .
	NBIAToolkit

	- name: Update README code block
	run: \|
	awk '/``` bash NBIAToolkit-Output/ {
	print "``` bash NBIAToolkit-Output";
	print "> NBIAToolkit --version";
	system("NBIAToolkit --version");
	f=1;
	next
	} f && /```/ {
	print "```";
	f=0;
	next
	} !f' README.md > temp && mv temp README.md

	- name: Commit and push changes
	run: \|
	LATEST_TAG=$(curl -s \
	"https://api.github.com/repos/${{ github.repository }}/releases/latest" \
	\| jq -r .tag_name \| sed 's/^v//')
	echo "LATEST_TAG=${LATEST_TAG}"
	# Check for changes
	if [[ $(git status --porcelain) ]]; then
	# Changes are present
	echo "Changes found. Committing and pushing..."

	git config --global user.name 'jjjermiah'
	git config --global user.email 'jjjermiah@users.noreply.github.com'

	# Add all changes
	git add .

	# Commit with a timestamp
	git commit -m "Update README with latest version: $LATEST_TAG"

	# Push changes to the remote repository
	# if github.head_ref is not null
	# then push to the branch
	# else push to the base branch
	if [ -n "${{ github.head_ref }}" ]; then
	git push origin HEAD:${{ github.head_ref }}
	else
	git push origin HEAD:${{ github.ref }}
	fi


	echo "Changes committed and pushed successfully."
	else
	# No changes
	echo "No changes found. Nothing to commit or push."
	fi



	# git add README.md

	# git commit -m "Update README with latest version"
	# git push


	# #!/bin/bash

	# # Check for changes
	# if [[ $(git status --porcelain) ]]; then
	# # Changes are present
	# echo "Changes found. Committing and pushing..."

	# # Add all changes
	# git add .

	# # Commit with a timestamp
	# git commit -m "Auto commit: $(date)"

	# # Push changes to the remote repository
	# git push origin <your-branch-name>

	# echo "Changes committed and pushed successfully."
	# else
	# # No changes
	# echo "No changes found. Nothing to commit or push."
	# fi

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Merge pull request #80 from jjjermiah/development #247

Workflow file

Merge pull request #80 from jjjermiah/development #247

Jobs

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Workflow file for this run