feat/textual enrichment #46

Workflow file for this run

.github/workflows/tests_talk2knowledgegraphs.yml at c4667d8

	# This is a basic workflow to help you get started with GitHub Actions
	name: TESTS Talk2KnowledgeGraphs

	# Controls when the workflow will run
	on:
	# Triggers the workflow on push or pull request events
	pull_request:
	branches: [ main ]
	paths:
	- 'aiagents4pharma/talk2knowledgegraphs/**'

	# Allows you to run this workflow manually from the Actions tab
	workflow_dispatch:

	env:
	OPENAI_API_KEY: ${{ secrets.OPENAI_API_KEY }}

	# This workflow contains jobs covering linting and code coverage (along with testing).
	jobs:
	# pylint job for macos
	pylint-macos:
	# The type of runner that the job will run on
	name: pylint
	runs-on: ${{ matrix.os }}

	strategy:
	matrix:
	os: [macos-13]

	# Steps represent a sequence of tasks that will be executed as part of the job
	steps:
	# Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
	- uses: actions/checkout@v4

	- name: Set up Python
	uses: actions/setup-python@v4
	with:
	python-version: 3.12

	- name: Cache files
	uses: actions/cache@v4
	id: cache
	with:
	path: \|
	${{ github.workspace }}/venv/*
	key: ${{ runner.os }}-venv

	# install requirements
	- name: Install the requirements
	if: steps.cache.outputs.cache-hit != 'true'
	working-directory: ${{ github.workspace }}
	run: \|
	python3 -m venv venv
	source venv/bin/activate
	pip install --upgrade pip
	pip3 install --break-system-packages -r requirements.txt

	# pylint
	- name: Run pylint
	working-directory: ${{ github.workspace }}
	run: \|
	source venv/bin/activate
	pylint --disable=R0801,R0902,W0221,W0122 aiagents4pharma/talk2knowledgegraphs

	# pylint job for ubuntu
	pylint-ubuntu:
	# The type of runner that the job will run on
	name: pylint
	runs-on: ${{ matrix.os }}

	strategy:
	matrix:
	os: [ubuntu-latest]

	# Steps represent a sequence of tasks that will be executed as part of the job
	steps:
	# Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
	- uses: actions/checkout@v4

	- name: Set up Python
	uses: actions/setup-python@v4
	with:
	python-version: 3.12

	- name: Cache files
	uses: actions/cache@v4
	id: cache
	with:
	path: \|
	${{ github.workspace }}/venv/*
	key: ${{ runner.os }}-venv

	# install requirements
	- name: Install the requirements
	if: steps.cache.outputs.cache-hit != 'true'
	working-directory: ${{ github.workspace }}
	run: \|
	python3 -m venv venv
	source venv/bin/activate
	pip install --upgrade pip
	pip3 install --break-system-packages -r requirements.txt

	# pylint
	- name: Run pylint
	working-directory: ${{ github.workspace }}
	run: \|
	source venv/bin/activate
	pylint --disable=R0801,R0902,W0221,W0122 aiagents4pharma/talk2knowledgegraphs

	# pylint job for windows
	pylint-windows:
	# The type of runner that the job will run on
	name: pylint
	runs-on: ${{ matrix.os }}

	strategy:
	matrix:
	os: [windows-latest]

	# Steps represent a sequence of tasks that will be executed as part of the job
	steps:
	# Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
	- uses: actions/checkout@v4

	- name: Set up Python
	uses: actions/setup-python@v4
	with:
	python-version: 3.12

	- name: Cache files
	uses: actions/cache@v4
	id: cache
	with:
	path: \|
	${{ github.workspace }}\venv\*
	key: ${{ runner.os }}-venv

	# install requirements
	- name: Install the requirements
	if: steps.cache.outputs.cache-hit != 'true'
	working-directory: ${{ github.workspace }}
	run: \|
	python3 -m venv venv
	venv\Scripts\activate
	pip install --upgrade pip
	pip3 install --break-system-packages -r requirements.txt

	# pylint
	- name: Run pylint
	working-directory: ${{ github.workspace }}
	run: \|
	venv\Scripts\activate
	pylint --disable=R0801,R0902,W0221,W0122 aiagents4pharma/talk2knowledgegraphs

	# code coverage job for macos
	code-cov-macos:
	name: code-coverage
	needs: pylint-macos
	runs-on: ${{ matrix.os }}

	strategy:
	matrix:
	os: [macos-13]

	steps:
	- name: Checkout code
	uses: actions/checkout@v4

	- name: Set up Python
	uses: actions/setup-python@v4
	with:
	python-version: 3.12

	- name: Cache venv
	uses: actions/cache@v4
	id: cache_venv
	with:
	path: \|
	${{ github.workspace }}/venv/*
	key: ${{ runner.os }}-venv

	- name: Cache Ollama models
	uses: actions/cache@v4
	id: cache_ollama
	with:
	path: \|
	/Users/runner/.ollama/models/*
	key: ${{ runner.os }}-ollama

	- name: Install and Pull Ollama models
	if: steps.cache_ollama.outputs.cache-hit != 'true'
	working-directory: ${{ github.workspace }}
	run: \|
	source venv/bin/activate
	brew install ollama
	ollama serve &
	sleep 10
	ollama pull gemma2:2b
	ollama list

	- name: Reading cached Ollama models
	working-directory: ${{ github.workspace }}
	run: \|
	echo "Cache Hit Status - ${{ steps.cache_ollama.outputs.cache-hit }}"
	source venv/bin/activate
	brew install ollama
	ollama serve &
	sleep 10
	ollama list

	- name: Run tests with coverage
	working-directory: ${{ github.workspace }}
	run: \|
	source venv/bin/activate
	coverage run --include=aiagents4pharma/talk2knowledgegraphs/* -m pytest --cache-clear aiagents4pharma/talk2knowledgegraphs/tests/

	- name: Check coverage
	working-directory: ${{ github.workspace }}
	run: \|
	source venv/bin/activate
	coverage report -m
	TOTAL_COVERAGE=$(coverage report -m \| awk 'END {print int($NF)}')
	if [[ $TOTAL_COVERAGE -ne 100 ]]; then
	echo "Code coverage is not 100%. Please check the coverage report."
	exit 1
	fi
	env:
	COVERAGE_FILE: './.coverage'

	# code coverage job for ubuntu
	code-cov-ubuntu:
	name: code-coverage
	needs: pylint-ubuntu
	runs-on: ${{ matrix.os }}

	strategy:
	matrix:
	os: [ubuntu-latest]

	steps:
	- name: Checkout code
	uses: actions/checkout@v4

	- name: Set up Python
	uses: actions/setup-python@v4
	with:
	python-version: 3.12

	- name: Cache venv
	uses: actions/cache@v4
	id: cache_venv
	with:
	path: \|
	${{ github.workspace }}/venv/*
	key: ${{ runner.os }}-venv

	- name: Cache Ollama models
	uses: actions/cache@v4
	id: cache_ollama
	with:
	path: \|
	${{ github.workspace }}/ollama-models/*
	key: ${{ runner.os }}-ollama

	- name: Install and Pull Ollama models
	if: steps.cache_ollama.outputs.cache-hit != 'true'
	working-directory: ${{ github.workspace }}
	run: \|
	source venv/bin/activate
	curl -fsSL https://ollama.com/install.sh \| sh
	mkdir ollama-models
	export OLLAMA_MODELS=${{ github.workspace }}/ollama-models
	ollama serve &
	sleep 10
	ollama pull gemma2:2b
	ollama list
	ls -l ${{ github.workspace }}/ollama-models/

	- name: Reading cached Ollama models
	working-directory: ${{ github.workspace }}
	run: \|
	echo "Cache Hit Status - ${{ steps.cache_ollama.outputs.cache-hit }}"
	source venv/bin/activate
	curl -fsSL https://ollama.com/install.sh \| sh
	export OLLAMA_MODELS=~/.ollama/models
	ollama serve &
	sleep 10
	ollama list
	ls -l ${{ github.workspace }}/ollama-models

	- name: Run tests with coverage
	working-directory: ${{ github.workspace }}
	run: \|
	source venv/bin/activate
	coverage run --include=aiagents4pharma/talk2knowledgegraphs/* -m pytest --cache-clear aiagents4pharma/talk2knowledgegraphs/tests/

	- name: Check coverage
	working-directory: ${{ github.workspace }}
	run: \|
	source venv/bin/activate
	coverage report -m
	TOTAL_COVERAGE=$(coverage report -m \| awk 'END {print int($NF)}')
	if [[ $TOTAL_COVERAGE -ne 100 ]]; then
	echo "Code coverage is not 100%. Please check the coverage report."
	exit 1
	fi
	env:
	COVERAGE_FILE: './.coverage'

	# code coverage job for windows
	code-cov-windows:
	name: code-coverage
	needs: pylint-windows
	runs-on: ${{ matrix.os }}

	strategy:
	matrix:
	os: [windows-latest]

	steps:
	- name: Checkout code
	uses: actions/checkout@v4

	- name: Set up Python
	uses: actions/setup-python@v4
	with:
	python-version: 3.12

	- name: Cache venv
	uses: actions/cache@v4
	id: cache_venv
	with:
	path: \|
	${{ github.workspace }}\venv\*
	key: ${{ runner.os }}-venv

	- name: Cache Ollama models
	uses: actions/cache@v4
	id: cache_ollama
	with:
	path: \|
	C:\Users\runneradmin\.ollama\models
	key: ${{ runner.os }}-ollama

	- name: Install and Pull Ollama models
	if: steps.cache_ollama.outputs.cache-hit != 'true'
	working-directory: ${{ github.workspace }}
	run: \|
	venv\Scripts\activate
	curl -L https://ollama.com/download/ollama-windows-amd64.zip -o ollama-windows-amd64.zip
	tar -xzf .\ollama-windows-amd64.zip
	start ollama serve
	sleep 10
	cmd /k ollama pull gemma2:2b
	cmd /k ollama list

	- name: Reading cached Ollama models
	working-directory: ${{ github.workspace }}
	run: \|
	echo "Cache Hit Status - ${{ steps.cache_ollama.outputs.cache-hit }}"
	venv\Scripts\activate
	curl -L https://ollama.com/download/ollama-windows-amd64.zip -o ollama-windows-amd64.zip
	tar -xzf .\ollama-windows-amd64.zip
	start ollama serve
	sleep 10
	cmd /k ollama list

	- name: Run tests with coverage
	working-directory: ${{ github.workspace }}
	run: \|
	venv\Scripts\activate
	coverage run --include=aiagents4pharma/talk2knowledgegraphs/* -m pytest --cache-clear aiagents4pharma/talk2knowledgegraphs/tests/

	- name: Check coverage
	working-directory: ${{ github.workspace }}
	run: \|
	venv\Scripts\activate
	coverage report -m
	# $TOTAL_COVERAGE=(& coverage report -m \| Select-Object -Last 1) -replace "[^\d]" # Extract the last line and remove non-numeric characters
	$TOTAL_COVERAGE=(& coverage report -m \| Select-Object -Last 1)
	# split and extract the last element
	$TOTAL_COVERAGE=($TOTAL_COVERAGE -split " ")[-1]
	# remove non-numeric characters
	$TOTAL_COVERAGE=($TOTAL_COVERAGE -replace "[^\d]")
	# convert to int
	$TOTAL_COVERAGE=[int]$TOTAL_COVERAGE
	echo "Total coverage: $TOTAL_COVERAGE"
	if ($TOTAL_COVERAGE -ne 100) {
	Write-Host "Code coverage is not 100%. Please check the coverage report."
	exit 1
	}
	env:
	COVERAGE_FILE: './.coverage'

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feat/textual enrichment #46

Workflow file

feat/textual enrichment #46

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Workflow file for this run