add normalisation initial support and begin setting up tests #2

	name: check-cmdstan

	concurrency:
	group: ${{ github.workflow }}-${{ github.head_ref }}
	cancel-in-progress: true

	on:
	push:
	paths:
	- '**.stan'
	branches:
	- main
	- develop
	schedule:
	- cron: '5 4 * * 1'
	pull_request:
	paths:
	- '**.stan'
	branches:
	- main
	- develop
	merge_group:
	workflow_dispatch:

	jobs:
	check-cmdstan:
	if: "! contains(github.event.head_commit.message, '[ci skip]')"
	runs-on: ubuntu-latest

	env:
	GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}

	steps:
	- name: cmdstan env vars
	run: \|
	echo "CMDSTAN_PATH=${HOME}/.cmdstan" >> $GITHUB_ENV
	shell: bash

	- uses: actions/checkout@v4

	- uses: r-lib/actions/setup-r@v2

	- uses: r-lib/actions/setup-r-dependencies@v2
	with:
	extra-packages: local::.

	- name: Install cmdstan
	uses: epinowcast/actions/install-cmdstan@v1
	with:
	cmdstan-version: 'latest'
	num-cores: 2

	- name: Compile model and check syntax
	run: \|
	model <- epinowcast::enw_model()
	# If the model is not syntactically correct above will fail
	# however it may be correct enougth to compile but still contain
	# soft depreciated syntax and so we check the syntax again below
	# and test the output.
	message <- capture.output(
	model$check_syntax(pedantic = FALSE),
	type = "message"
	)
	# We can't use TRUE here as pendatic check return lots of false
	# positives related to our use of functions.
	stopifnot(
	length(message) != 0 &&
	all(message == "Stan program is syntactically correct")
	)
	shell: Rscript {0}

	- name: Compile and expose stan functions
	run: \|
	model <- epinowcast::enw_stan_to_r()
	shell: Rscript {0}

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