build

feat: bugfix and enhancements in dynamic conda path detection in Cron Jobs and Add Docker volume management #139

	name: build

	on:
	push:
	branches: [ main ]
	pull_request:
	branches: [ main ]

	env:
	# Elasticsearch Configuration
	STACK_VERSION: 8.12.0
	CLUSTER_NAME: docker-cluster
	MEM_LIMIT: 1073741824
	LICENSE: basic
	#
	ES_PORT: 9200
	ES_HOSTNAME: https://localhost:9200
	ES_USERNAME: elastic
	ES_PASSWORD: worksfine
	ES_CERTIF: containers/esconfig/certs/http_ca.crt
	# Host System Configuration
	HOST_UID: 1000
	HOST_GID: 1000
	ELASTIC_VOLUME: ../containers/elasticsearch/data

	jobs:
	build:
	runs-on: ubuntu-latest
	timeout-minutes: 10
	concurrency:
	group: ci-${{ github.ref }}
	cancel-in-progress: true

	defaults:
	run:
	shell: bash -l {0}

	steps:
	- uses: actions/checkout@v3

	- uses: conda-incubator/setup-miniconda@v3
	with:
	miniconda-version: "latest"
	mamba-version: "*"
	environment-file: conda/base.yaml
	channels: conda-forge,nodefaults
	channel-priority: true
	activate-environment: es-journals
	use-mamba: true
	miniforge-variant: Mambaforge

	- name: Set Environment Variable
	run: echo "GITHUB_PAT=${{ secrets.DEVTOOLS_PAT }}" >> $GITHUB_ENV

	- name: Setup development environment for Rxivs
	run: \|
	for rxiv_name in biorxiv medrxiv; do
	makim develop.setup-dev-env --server-name $rxiv_name
	done

	- name: Start Elasticsearch
	run: \|
	sugar ext start --group dev --options -d

	# - name: Copy and test certificates
	# run: bash .github/ci/healthcheck.sh es 80 && makim develop.test-certs

	- name: Fetch and process MedRxiv data
	run: \|
	bash scripts/fetch_rxivx_data.sh medrxiv

	- name: Count documents in MedRxiv index
	run: \|
	makim develop.count-docs-in-index --index-name medrxiv

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