Add files via upload #30

Workflow file for this run

	# Model workflow code

	name: Model CI # ==============================================================

	on: # controls when the workflow will run

	push: # trigger workflow on push events, but only for the main branch
	branches: [ main ]
	paths:
	- "model-api/**"
	- ".github/actions/build-model/**"
	- ".github/workflows/main.yml"
	- "st-kit/**"
	- "!README.md" # don't rebuild on documentation changes

	pull_request: # triggers workflow on pull request events (main branch only)
	branches: [ main ] # ensures changes are "mergeable"

	workflow_dispatch: # permits manual triggers from the Actions tab
	# inputs:
	# debug_enabled:
	# description: 'Run the build with tmate debugging enabled'
	# required: false
	# default: false

	# workflow_run:
	# workflows: [ "Docker" ]
	# branches: [ main ]
	# types: [ completed ]

	jobs: # =======================================================================

	# ---------------------------------------------------------------------------
	count-vars: # creates template models for count data
	# ---------------------------------------------------------------------------

	strategy:
	matrix:
	likelihood: [ poisson,
	negative-binomial-simple, negative-binomial,
	gen-pois,
	zero-inflated-poisson, zero-inflated-negative-binomial ]
	link: [ linear, exponential ]
	gle: [ b0, b0-b1 ]
	include:
	# Includes a new variable demo with a value of true for the matrix leg
	# matching the following likelihood, link, and gle.
	- likelihood: poisson
	link: exponential
	gle: b0-b1
	demo: true
	exclude:
	# excludes parameterizations
	- likelihood: gen-pois
	link: linear
	runs-on: ubuntu-latest
	# if: ${{ github.event.workflow_run.conclusion == 'success' }}

	steps:
	- uses: actions/checkout@v2
	- name: Pull model API from GitLab
	run: \|
	git submodule update --init --remote model-api

	# Build the JAGS model and save it in tmp
	- name: Build model
	uses: ./.github/actions/build-model # composite action to create model
	with:
	data-type: ${{ github.job }}
	likelihood: ${{ matrix.likelihood }}
	link: ${{ matrix.link }}
	gle: ${{ matrix.gle }}
	demo: ${{ matrix.demo }}

	# Each artifact behaves as a file share. Uploading to the same artifact
	# multiple times in the same workflow can overwrite and append to already
	# uploaded files.
	- name: Upload tmp directory as an artifact
	uses: actions/upload-artifact@v2
	with:
	name: artifact-${{ github.sha }}
	path: tmp
	retention-days: 1

	# ---------------------------------------------------------------------------
	binomial-vars: # creates template models for successes / trials data
	# ---------------------------------------------------------------------------

	strategy:
	matrix:
	likelihood: [ binomial, beta-binomial ] # zero-inflated-binomial, zero-inflated-beta-binomial
	link: [ inverse-logit ]
	gle: [ b0, b0-b1 ]
	include:
	- likelihood: binomial
	link: inverse-logit
	gle: b0
	demo: true

	runs-on: ubuntu-latest

	steps:
	- uses: actions/checkout@v2
	- name: Pull model API from GitLab
	run: \|
	git submodule update --init --remote model-api

	- name: Build model
	uses: ./.github/actions/build-model # composite action to create model
	with:
	data-type: ${{ github.job }}
	likelihood: ${{ matrix.likelihood }}
	link: ${{ matrix.link }}
	gle: ${{ matrix.gle }}
	demo: ${{ matrix.demo }}

	- name: Upload tmp directory as an artifact
	uses: actions/upload-artifact@v2
	with:
	name: artifact-${{ github.sha }}
	path: tmp
	retention-days: 1

	# ---------------------------------------------------------------------------
	nonnegative-continuous-vars: # template models for non-zero continuous data
	# ---------------------------------------------------------------------------

	strategy:
	matrix:
	likelihood: [ lognormal, gamma ] #, beta-binomial
	link: [ linear ] # TODO: is exponential here even an option?
	gle: [ b0, b0-b1 ]
	include:
	- likelihood: gamma
	link: linear
	gle: b0-b1
	demo: true

	runs-on: ubuntu-latest

	steps:
	- uses: actions/checkout@v2
	# with:
	# submodules: true # fetch model and data API submodules
	# fetch-depth: 0 # fetch all history for .GitInfo and .Lastmod
	- name: Pull model API from GitLab
	run: \|
	git submodule update --init --remote model-api

	- name: Build model
	uses: ./.github/actions/build-model # composite action to create model
	with:
	data-type: ${{ github.job }}
	likelihood: ${{ matrix.likelihood }}
	link: ${{ matrix.link }}
	gle: ${{ matrix.gle }}
	demo: ${{ matrix.demo }}

	- name: Upload tmp directory as an artifact
	uses: actions/upload-artifact@v2
	with:
	name: artifact-${{ github.sha }}
	path: tmp
	retention-days: 1

	# ---------------------------------------------------------------------------
	define-jags-model-matrix:
	# ---------------------------------------------------------------------------

	needs: [ count-vars, binomial-vars, nonnegative-continuous-vars ]
	runs-on: ubuntu-latest

	steps:
	- uses: actions/checkout@v2

	- name: Download file share
	uses: actions/download-artifact@v2
	with:
	name: artifact-${{ github.sha }}
	path: tmp

	- name: Create JAGS model file list as a JSON array
	id: set-matrix # we need an "id" so we can use it in "outputs" below
	run: \|
	echo "::set-output name=matrix::$(find tmp -name "model.jags" \| \
	perl -e 'use JSON; @in=grep(s/\n$//, <>); print encode_json(\@in)."\n";')"

	- name: Copy model files into model zoo in assets
	run: \|
	find tmp -type f -name '*.jags'
	find tmp -type f -name '*.jags' \
	-exec bash -c '
	ZOO=$(sed "s/tmp/assets\/model-zoo/g" <<< $(dirname $0))
	mkdir -p $(dirname $ZOO) && cp $0 $ZOO-model.jags' {} \;

	# Push changes made to the repo during a workflow run
	- name: Commit changes
	uses: EndBug/add-and-commit@v7
	with:
	default_author: github_actions
	branch: main
	add: "assets/*/-model.jags" # --force
	message: Automatic update of model files in model zoo

	outputs:
	matrix: ${{ steps.set-matrix.outputs.matrix }}

	# ---------------------------------------------------------------------------
	use-jags-models-to-sim-data: # create dynamic matrix from json, simulate data
	# ---------------------------------------------------------------------------

	needs: [ define-jags-model-matrix ]
	runs-on: ubuntu-latest

	strategy:
	matrix:
	jags-model: ${{ fromJson(needs.define-jags-model-matrix.outputs.matrix) }}
	options: [ --seed=123 ]

	steps:
	- uses: actions/checkout@v2
	- name: Pull model API from GitLab
	run: \|
	git submodule update --init --remote model-api

	- name: Download file share
	uses: actions/download-artifact@v2
	with:
	name: artifact-${{ github.sha }}
	path: tmp

	- name: Use cached results (simulate data and fit model)
	id: verify
	uses: ./.github/actions/call-r
	with:
	rfile: model-api/demo/sim.R
	args: ${{ matrix.jags-model }}
	opts: ${{ matrix.options }}

	- name: Check status of model verification
	run: echo "The exit status was ${{ steps.verify.outputs.code }}"

	- name: Upload tmp directory as an artifact
	uses: actions/upload-artifact@v2
	with:
	name: artifact-${{ github.sha }}
	path: tmp
	retention-days: 1

	# ---------------------------------------------------------------------------
	cleanup: # summarize sim fits, and write demo data to assets/_data
	# ---------------------------------------------------------------------------

	needs: [ use-jags-models-to-sim-data ]
	runs-on: ubuntu-latest

	steps:
	- uses: actions/checkout@v2
	- name: Pull model API from GitLab
	run: \|
	git submodule update --init --remote model-api

	- name: Download file share
	uses: actions/download-artifact@v2
	with:
	name: artifact-${{ github.sha }}
	path: tmp

	- name: Move datasets flagged for demo to assets/_data
	run: \|
	mkdir -p assets/_data
	HINT_FILE=assets/_data/.generating-models.csv
	rm -f $HINT_FILE && touch $HINT_FILE
	echo file, generating_model >> $HINT_FILE
	find tmp -type f -name 'demo' \
	-exec bash -c '
	DD_DIR=$(dirname $0)
	DD_LAB=$(echo $0 \| grep -oP "(?<=tmp/).*(?=-vars)")
	DD_CSV=assets/_data/$DD_LAB-data.csv
	echo $DD_CSV, $(basename $DD_DIR) >> assets/_data/.generating-models.csv
	cp $DD_DIR/samples.csv $DD_CSV
	cp $DD_DIR/sample-*.csv assets/_data' {} \;
	ls assets/_data

	# Push changes made to the repo during a workflow run
	- name: Commit changes
	uses: EndBug/add-and-commit@v7
	with:
	default_author: github_actions
	branch: main
	add: "assets/_data/**"
	message: Automatic update of demo data

	- name: Create model config file list as a JSON array
	id: config-file-list # we need an "id" so we can use it in "outputs" below
	run: \|
	echo "::set-output name=matrix::$(find assets -name "[a-z]*.yml" \| \
	perl -e 'use JSON; @in=grep(s/\n$//, <>); print encode_json(\@in)."\n";')"

	outputs:
	configs: ${{ steps.config-file-list.outputs.matrix }}

	# ---------------------------------------------------------------------------
	test: # use simulated data in the analysis pipeline
	# ---------------------------------------------------------------------------

	needs: [ cleanup ]
	runs-on: ubuntu-latest

	strategy:
	matrix:
	config-file: ${{ fromJson(needs.cleanup.outputs.configs) }}
	# options: [ --n-adapt=1000 --n-update=5000 --n-iter=2500 --n-cores=1 --rm-dqs ]

	steps:
	- uses: actions/checkout@v2
	- name: Pull model API from GitLab
	run: \|
	git submodule update --init --remote model-api

	- name: Download file share
	uses: actions/download-artifact@v2
	with:
	name: artifact-${{ github.sha }}
	path: tmp

	- name: Test model API using data simulated in prior job
	uses: ./.github/actions/call-r
	with:
	rfile: model-api/analysis-pipeline.R
	args: ${{ matrix.config-file }}
	opts: '--n-adapt=2000 --n-update=6000 --n-iter=3000 --n-cores=1 --rm-dqs' # ${{ matrix.options }}

	# # Enable tmate debugging of manually-triggered workflows if the input
	# # option was provided (i.e., debug_enabled=true)
	# - name: Setup tmate session
	# uses: mxschmitt/action-tmate@v3
	# # if: ${{ github.event_name == 'workflow_dispatch' && github.event.inputs.debug_enabled }}

	- run: sudo mv assets/_output tmp/test-fits
	- name: Upload tmp directory as an artifact
	uses: actions/upload-artifact@v2
	with:
	name: artifact-${{ github.sha }}
	path: tmp
	retention-days: 1

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Add files via upload #30

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Add files via upload #30

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