add new parsed params #97

Workflow file for this run

	name: main
	on: [push]

	jobs:
	conda-env:
	runs-on: ubuntu-latest
	steps:
	- uses: actions/checkout@v2


	- name: git setup
	# Set up git and export env vars to be used in later steps.
	# Note the unconventional mechanism for exporting envs by appending to
	# $GITHUB_ENV.
	id: git-setup
	run: \|
	git config --global user.email "action@github.com"
	git config --global user.name "GitHub Action"
	echo "BRANCH=${GITHUB_REF##*/}" >> $GITHUB_ENV
	echo "WORKDIR=$(pwd)" >> $GITHUB_ENV


	- name: load cached conda env
	# Load cached env.
	# This looks for a cache based on the hash of requirements.txt and
	# test-requirements.txt; if it's found the cached directory is
	# restored. There's an extra "v1" on the end so it can be forced to be
	# regenerated when needed.
	id: cache-env
	uses: actions/cache@v2
	with:
	path: /tmp/test-env
	key: ${{ hashFiles('requirements.txt') }}-${{ hashFiles('test-requirements.txt') }}-v1


	- name: build new conda env
	# Build cache if needed.
	# Only runs if there was a cache miss. If this is created. there's
	# a "Post load cached env" job (which is automatically created, it's
	# not defined here) that will load this into the cache for use next
	# time.
	if: steps.cache-env.outputs.cache-hit != 'true'
	run: \|
	eval "$(conda shell.bash hook)"
	conda create -p /tmp/test-env -y --file requirements.txt --file test-requirements.txt --channel conda-forge --channel bioconda


	- name: run pytests and build docs
	# pytests and doctests happen here
	run: \|
	eval "$(conda shell.bash hook)"
	source activate /tmp/test-env
	python setup.py install
	pytest -vv --doctest-modules trackhub

	# To make sure that the links in the built docs refer to the correct
	# branch on the trackhub-demo repo, we replace the branch names in the
	# .rst files. Note if we're on master branch then this is a no-op.
	cd doc
	find . -name "*.rst" \| xargs sed -i "s\|trackhub-demo/master\|trackhub-demo/$BRANCH\|g"
	make doctest html
	conda deactivate

	- name: test command-line script
	# Ensure that the installed command-line script can be run and creates
	# the correct files
	run: \|
	eval "$(conda shell.bash hook)"
	source activate /tmp/test-env
	trackhub_from_excel --template
	trackhub_from_excel --create-example a.xlsx
	trackhub_from_excel --excel-file a.xlsx
	err=0
	for f in template.xlsx a.xlsx staging staging/test_excel_to_trackhub.hub.txt; do
	if [ ! -e $f ]; then
	echo "file $f not present!"
	err=1
	fi
	done
	if [ err == 1 ]; then
	exit 1
	fi


	- name: upload the just-built docs as an artifact
	# The built docs will be uploaded as a zip file (called docs.zip).
	# This file will be available on the Actions page and can be used to
	# inspect the final rendered docs. This is useful when building on
	# a branch and for contributors to make corrections to the docs without
	# needing to set everything up locally.
	uses: actions/upload-artifact@v2
	with:
	name: docs
	path: doc/build/html


	- name: commit built docs to gh-pages branch
	# Commit to the gh-pages branch.
	# Note that this step is not restricted to the master branch, which
	# lets us better test the process. The changes aren't actually pushed
	# though unless we're on the master branch (see next step).
	#
	# Note that cloning just the gh-pages branch to a new directory ended
	# up being easier than staying in this directory and copying stuff
	# around within it.
	run: \|
	git clone \
	--single-branch \
	--branch gh-pages "https://x-access-token:${{ secrets.GITHUB_TOKEN }}@github.com/$GITHUB_REPOSITORY" \
	/tmp/docs

	# recall that this does leave hidden files
	rm -rf /tmp/docs/*
	cp -r doc/build/html/* /tmp/docs
	touch /tmp/docs/.nojekyll
	cd /tmp/docs
	git add .

	if git diff --cached --quiet; then
	echo "no changes; nothing to commit"
	else
	git commit -m 'update docs'
	fi

	cd $WORKDIR


	- name: push docs to gh-pages branch
	# Push to gh-pages.
	# (but only if we're on the master branch)
	# This is how the docs get hosted on https://github.io/daler/trackhub.
	if: ${{ github.ref == 'refs/heads/master' }}
	run: \|
	cd /tmp/docs
	git push "https://x-access-token:${{ secrets.GITHUB_TOKEN }}@github.com/daler/trackhub" gh-pages
	cd $WORKDIR


	- name: build example hubs
	# Build example hubs into the "example_hubs" directory.
	# See the ci/build_examples.py script for details. Also note that since
	# we were last on the gh-pages branch from the last step, we need to
	# explicitly check out the branch that this PR is for.
	run: \|
	git branch
	git checkout $BRANCH
	eval "$(conda shell.bash hook)"
	source activate /tmp/test-env
	ci/build_examples.py


	- name: start ssh agent
	# Start the SSH agent so that subsequent steps don't need additional SSH
	# setup.
	# The private key has been added as a secret to the trackhub repo (the
	# one running these tests), and the public key has been added as an
	# allowed deploy key for the trackhub-demo repo (the one accepting
	# pushes from this test). Note that this method ensures that the key is
	# never saved to disk, and GitHub Actions automatically protects the
	# secrets from being echoed.
	env:
	SSH_AUTH_SOCK: /tmp/ssh_agent.sock
	run: \|
	mkdir -p ~/.ssh
	ssh-keyscan github.com >> ~/.ssh/known_hosts
	ssh-agent -a $SSH_AUTH_SOCK > /dev/null
	ssh-add - <<< "${{ secrets.SSH_PRIVATE_KEY }}"


	- name: push built hubs to trackhub-demo repo
	# Push to the trackhub-demo repo
	# This creates a matching branch on the trackhub-demo repo, cleans out
	# everything, and copies over the contents of the just-built
	# "example_hubs" directory to that matching branch. This lets us
	# inspect the hubs and correct them if needed on a branch before
	# merging to master.
	env:
	SSH_AUTH_SOCK: /tmp/ssh_agent.sock
	run: \|
	set -x
	here=$(pwd)
	git clone git@github.com:daler/trackhub-demo.git /tmp/trackhub-demo
	cd /tmp/trackhub-demo
	git checkout -B $BRANCH
	git rm -rf ./*

	# Note -L to follow links
	cp -rLv $here/example_hubs/* /tmp/trackhub-demo
	git add -f .
	ls
	git status

	# It's possible that the $BRANCH here in the trackhub repo does not yet
	# exist over in the trackhub-demo repo. In that case, we should be good
	# to push.
	if [[ -z $(git ls-remote --heads origin $BRANCH) ]]; then
	echo "remote branch $BRANCH does not exist"
	git commit -m 'update hub'
	git push origin $BRANCH --force
	exit 0
	fi

	# Otherwise, only push if there are changes.
	if git diff origin/$BRANCH --quiet; then
	echo "no changes to push to branch $BRANCH!";
	else
	echo "Diffs will be pushed to remote branch $BRANCH"
	git commit -m 'update hub'
	git push origin $BRANCH --force
	fi
	set +x

	- name: hubChecks
	# Check hubs
	# Once hubs are uploaded to trackhub-demo repo, we need to check them
	# to make sure they're accessible and have no glaring errors.
	#
	# See ci/check_hubs.py for details.
	run: \|
	git checkout $BRANCH
	eval "$(conda shell.bash hook)"
	source activate /tmp/test-env
	ci/check_hubs.py


	- name: cleanup
	# Remove all the ssh stuff we set up.
	if: always()
	env:
	SSH_AUTH_SOCK: /tmp/ssh_agent.sock
	run: \|
	ssh-add -D
	rm -Rf *


	pip-install:
	# Separate, parallel job for testing pip installation
	runs-on: ubuntu-latest
	steps:
	- uses: actions/checkout@v2
	- run: python setup.py sdist
	- run: pip install dist/*.tar.gz
	- run: python -c 'import trackhub'

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add new parsed params #97

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add new parsed params #97

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