Build and deploy site #2471

Workflow file for this run

.github/workflows/build-deploy.yml at de96d51

	name: Build and deploy site

	on:
	repository_dispatch:
	schedule:
	- cron: '29 11 * * *'
	pull_request:
	push:
	branches: [main]

	jobs:
	cancel-superseded:
	name: Cancel superseded
	runs-on: ubuntu-20.04
	steps:
	- name: Cancel Previous Runs
	uses: styfle/cancel-workflow-action@0.7.0
	with:
	access_token: ${{ github.token }}

	build-core-site:
	needs: cancel-superseded
	name: Build core site
	runs-on: ubuntu-20.04
	steps:
	- name: Cancel Previous Runs
	uses: styfle/cancel-workflow-action@0.11.0
	with:
	access_token: ${{ github.token }}

	- name: Checkout
	uses: actions/checkout@v3

	- name: Set up Ruby 2.7
	uses: actions/setup-ruby@v1
	with:
	ruby-version: 2.7

	- uses: actions/cache@v3
	with:
	path: /opt/hostedtoolcache/Ruby/2.7.2/x64/lib/ruby/gems
	key: ${{ runner.os }}-gems-v3-${{ hashFiles('**/Gemfile.lock') }}
	restore-keys: \|
	${{ runner.os }}-gems-v3

	- name: Install deps
	run: \|
	gem update --system --no-document
	gem install bundler jekyll
	bundle install

	- uses: actions/setup-node@v3
	with:
	node-version: 14
	cache: 'npm'

	- name: Install deps
	run: npm ci

	- name: Build site
	run: GITHUB_TOKEN=${{ github.token }} grunt build

	- name: Debug
	run: \|
	cat Gemfile.lock
	bundle info jekyll
	bundle info jekyll-theme-cayman
	ls
	cat dist/index.html

	- name: Upload built site
	uses: actions/upload-artifact@v2
	with:
	name: core-site
	path: dist/*

	build-msprime-docs:
	name: Build msprime docs
	needs: cancel-superseded
	runs-on: ubuntu-20.04
	steps:
	- uses: actions/checkout@v2
	name: Checkout msprime
	with:
	ref: main
	repository: tskit-dev/msprime
	submodules: true
	fetch-depth: 0 # Needed for setuptools_scm to work correctly

	- name: Get commit SHA1 for cache
	run: git rev-parse HEAD > SHA1

	- uses: actions/cache@v2
	id: docs-cache
	name: Docs cache
	with:
	path: dist
	key: msprime-docs-v11-${{ hashFiles('SHA1') }}

	- name: Install GSL
	if: steps.docs-cache.outputs.cache-hit != 'true'
	run: sudo apt-get install -y libgsl0-dev

	- uses: actions/setup-python@v2
	if: steps.docs-cache.outputs.cache-hit != 'true'
	name: Setup Python
	with:
	python-version: "3.10"

	- name: Build virtualenv
	if: steps.docs-cache.outputs.cache-hit != 'true'
	run: python -m venv venv-latest

	- name: Install deps
	if: steps.docs-cache.outputs.cache-hit != 'true'
	run: \|
	venv-latest/bin/activate && pip install -r requirements/CI-docs/requirements.txt

	- name: Build C module
	if: steps.docs-cache.outputs.cache-hit != 'true'
	run: venv-latest/bin/activate && make

	- name: Build Docs
	if: steps.docs-cache.outputs.cache-hit != 'true'
	run: \|
	venv-latest/bin/activate
	cd docs
	make dist
	# make dist changes the _conf.yml file to write the version number, so drop the change
	git checkout .

	- name: Copy docs
	if: steps.docs-cache.outputs.cache-hit != 'true'
	run: \|
	mkdir -p dist
	cp -r docs/_build/html dist/latest

	- name: Checkout latest stable tag
	if: steps.docs-cache.outputs.cache-hit != 'true'
	run: \|
	git fetch --tags --recurse-submodules=no
	git checkout `git tag --list --sort=creatordate \| grep -vi "[baC]" \| tail -n1`
	git submodule update --init --recursive
	git status

	# - name: Build virtualenv
	# if: steps.docs-cache.outputs.cache-hit != 'true'
	# run: python -m venv venv-stable
	#
	# - name: Install deps
	# if: steps.docs-cache.outputs.cache-hit != 'true'
	# run: \|
	# venv-stable/bin/activate
	# [ -f requirements/CI-docs/requirements.txt ] && pip install -r requirements/CI-docs/requirements.txt
	# [ -f requirements/development.txt ] && pip install -r requirements/development.txt
	- name: Build C module
	if: steps.docs-cache.outputs.cache-hit != 'true'
	# run: venv-stable/bin/activate && make
	run: venv-latest/bin/activate && make

	- name: Build Docs
	if: steps.docs-cache.outputs.cache-hit != 'true'
	run: \|
	rm -rf docs/_build
	venv-latest/bin/activate
	cd docs
	make dist
	# make dist changes the _conf.yml file to write the version number, so drop the change
	git checkout .
	# run: \|
	# rm -rf docs/_build
	# venv-stable/bin/activate
	# cd docs
	# ### Temp fix for unpinned dependency change (#156)
	# sed -i 's/sphinxarg.ext/sphinxarg.ext\n - IPython.sphinxext.ipython_console_highlighting/g' _config.yml
	# # Install jsonschema for bugfix
	# pip install jsonschema[format-nongpl]==4.17.3
	# ### Temp changes for theme
	# pip install tskit-book-theme
	# sed -i 's/ config:/ config:\n html_theme: tskit_book_theme\n pygments_style: monokai/g' _config.yml
	# ### Temp changes for theme
	# make dist
	# # make dist changes the _conf.yml file to write the version number, so drop the change
	# git checkout .

	- name: Copy docs
	if: steps.docs-cache.outputs.cache-hit != 'true'
	run:
	cp -r docs/_build/html dist/stable

	- name: Upload msprime docs
	uses: actions/upload-artifact@v2
	with:
	name: msprime-docs
	path: dist/*

	build-tsinfer-docs:
	name: Build tsinfer docs
	needs: cancel-superseded
	runs-on: ubuntu-20.04
	steps:
	- uses: actions/checkout@v2
	name: Checkout tsinfer
	with:
	ref: main
	repository: tskit-dev/tsinfer
	submodules: true
	fetch-depth: 0 # Needed for setuptools_scm to work correctly

	- name: Get commit SHA1 for cache
	run: git rev-parse HEAD > SHA1

	- uses: actions/cache@v2
	id: docs-cache
	name: Docs cache
	with:
	path: dist
	key: tsinfer-docs-v1-${{ hashFiles('SHA1') }}

	- uses: actions/setup-python@v4
	if: steps.docs-cache.outputs.cache-hit != 'true'
	name: Setup Python
	with:
	python-version: "3.10"

	- name: Build virtualenv
	if: steps.docs-cache.outputs.cache-hit != 'true'
	run: python -m venv venv-latest

	- name: Install deps
	if: steps.docs-cache.outputs.cache-hit != 'true'
	run: \|
	venv-latest/bin/activate && pip install -r requirements/CI-docs/requirements.txt

	- name: Build C module
	if: steps.docs-cache.outputs.cache-hit != 'true'
	run: venv-latest/bin/activate && make

	- name: Build Docs
	if: steps.docs-cache.outputs.cache-hit != 'true'
	run: \|
	venv-latest/bin/activate
	cd docs
	make dist
	# make dist changes the _conf.yml file to write the version number, so drop the change
	git checkout .

	- name: Copy docs
	if: steps.docs-cache.outputs.cache-hit != 'true'
	run: \|
	mkdir -p dist
	cp -r docs/_build/html dist/latest

	- name: Checkout latest stable tag
	if: steps.docs-cache.outputs.cache-hit != 'true'
	run: \|
	git fetch --tags --recurse-submodules=no
	git checkout `git tag --list --sort=creatordate \| grep -vi "[baC]" \| tail -n1`
	git submodule update --init --recursive
	git status

	# - uses: actions/setup-python@v4
	# if: steps.docs-cache.outputs.cache-hit != 'true'
	# name: Setup Python
	# with:
	# python-version: "3.8"
	#
	# - name: Build virtualenv
	# if: steps.docs-cache.outputs.cache-hit != 'true'
	# run: python -m venv venv-stable

	# Changes have meant that the stable version docs won't build - so use the venv-latest instead for now. #
	# - name: Install deps
	# if: steps.docs-cache.outputs.cache-hit != 'true'
	# run: \|
	# venv-stable/bin/activate
	# [ -f requirements/CI-docs/requirements.txt ] && pip install -r requirements/CI-docs/requirements.txt
	# # Remove this line after 0.4.0
	# pip install jsonschema[format-nongpl]==4.17.3
	- name: Build C module
	if: steps.docs-cache.outputs.cache-hit != 'true'
	# run: venv-stable/bin/activate && make
	run: \|
	venv-latest/bin/activate
	venv-latest/bin/activate && which python
	venv-latest/bin/activate && python -c "import numpy;print(numpy.__file__)"
	venv-latest/bin/activate && make

	- name: Build Docs
	if: steps.docs-cache.outputs.cache-hit != 'true'
	run: \|
	rm -rf docs/_build
	#venv-stable/bin/activate
	venv-latest/bin/activate
	cd docs
	### Temp fix for unpinned dependency change (#156)
	sed -i 's/sphinxarg.ext/sphinxarg.ext\n - IPython.sphinxext.ipython_console_highlighting/g' _config.yml
	make dist
	# make dist changes the _conf.yml file to write the version number, so drop the change
	git checkout .

	- name: Copy docs
	if: steps.docs-cache.outputs.cache-hit != 'true'
	run:
	cp -r docs/_build/html dist/stable

	- name: Upload tsinfer docs
	uses: actions/upload-artifact@v2
	with:
	name: tsinfer-docs
	path: dist/*


	build-tskit-docs:
	name: Build tskit docs
	needs: cancel-superseded
	runs-on: ubuntu-20.04
	steps:
	- uses: actions/checkout@v2
	name: Checkout tskit
	with:
	ref: main
	repository: tskit-dev/tskit
	submodules: true
	fetch-depth: 0 # Needed for setuptools_scm to work correctly

	- name: Get commit SHA1 for cache
	run: git rev-parse HEAD > SHA1

	- uses: actions/cache@v2
	id: docs-cache
	name: Docs cache
	with:
	path: dist
	key: tskit-docs-v7-${{ hashFiles('SHA1') }}

	- uses: actions/setup-python@v4
	if: steps.docs-cache.outputs.cache-hit != 'true'
	name: Setup Python
	with:
	python-version: "3.10"

	- name: Build virtualenv
	if: steps.docs-cache.outputs.cache-hit != 'true'
	run: python -m venv venv-latest

	- name: Install deps
	if: steps.docs-cache.outputs.cache-hit != 'true'
	run: \|
	sudo apt-get install doxygen
	venv-latest/bin/activate && pip install -r python/requirements/CI-docs/requirements.txt

	- name: Build C module
	if: steps.docs-cache.outputs.cache-hit != 'true'
	run: venv-latest/bin/activate && make -C python

	- name: Build Docs
	if: steps.docs-cache.outputs.cache-hit != 'true'
	run: \|
	venv-latest/bin/activate
	cd docs
	make dist

	- name: Copy docs
	if: steps.docs-cache.outputs.cache-hit != 'true'
	run: \|
	mkdir -p dist
	cp -r docs/_build/html dist/latest

	- name: Checkout latest stable tag
	if: steps.docs-cache.outputs.cache-hit != 'true'
	run: \|
	git stash
	git fetch --tags --recurse-submodules=no
	git checkout `git tag --list --sort=creatordate \| grep -vi "[baC]" \| tail -n1`
	git submodule update --init --recursive
	git status

	- uses: actions/setup-python@v4
	if: steps.docs-cache.outputs.cache-hit != 'true'
	name: Setup Python
	with:
	python-version: 3.8

	- name: Build virtualenv
	if: steps.docs-cache.outputs.cache-hit != 'true'
	run: python -m venv venv-stable

	- name: Downgrade pip (for conflicting dependencies)
	if: steps.docs-cache.outputs.cache-hit != 'true'
	run: venv-stable/bin/activate && pip install pip==20.0.2

	- name: Install deps
	if: steps.docs-cache.outputs.cache-hit != 'true'
	# Remove this second line after next release of tskit
	run: \|
	venv-stable/bin/activate && pip install -r python/requirements/CI-docs/requirements.txt
	venv-stable/bin/activate && pip install nbclient==0.5.13

	- name: Build C module
	if: steps.docs-cache.outputs.cache-hit != 'true'
	run: venv-stable/bin/activate && make -C python

	- name: Build Docs
	if: steps.docs-cache.outputs.cache-hit != 'true'
	run: \|
	rm -rf docs/_build
	venv-stable/bin/activate
	# Install jsonschema for bugfix
	pip install jsonschema[format-nongpl]==4.17.3
	cd docs
	### Temp changes for theme
	pip install tskit-book-theme
	sed -i 's/ config:/ config:\n html_theme: tskit_book_theme\n pygments_style: monokai/g' _config.yml
	### Temp changes for theme
	make dist \|\| make

	- name: Copy docs
	if: steps.docs-cache.outputs.cache-hit != 'true'
	run: \|
	cp -r docs/_build/html dist/stable

	- name: Upload tskit docs
	uses: actions/upload-artifact@v2
	with:
	name: tskit-docs
	path: dist/*


	build-pyslim-docs:
	name: Build pyslim docs
	needs: cancel-superseded
	runs-on: ubuntu-20.04
	steps:
	- uses: actions/checkout@v2
	name: Checkout pyslim
	with:
	ref: main
	repository: tskit-dev/pyslim
	submodules: true
	fetch-depth: 0 # Needed for setuptools_scm to work correctly

	- name: Get commit SHA1 for cache
	run: git rev-parse HEAD > SHA1

	- uses: actions/cache@v2
	id: docs-cache
	name: Docs cache
	with:
	path: dist
	key: pyslim-docs-v6-${{ hashFiles('SHA1') }}

	- uses: actions/setup-python@v2
	if: steps.docs-cache.outputs.cache-hit != 'true'
	name: Setup Python
	with:
	python-version: 3.8

	- name: Build latest SLiM
	if: steps.docs-cache.outputs.cache-hit != 'true'
	run: \|
	git clone https://github.com/messerlab/SLiM.git
	mkdir -p SLiM/Release
	cd SLiM/Release
	cmake -D CMAKE_BUILD_TYPE=Release ..
	make -j 2

	- name: Build virtualenv
	if: steps.docs-cache.outputs.cache-hit != 'true'
	run: python -m venv venv-latest

	- name: Install deps
	if: steps.docs-cache.outputs.cache-hit != 'true'
	run: \|
	venv-latest/bin/activate
	pip install -r requirements/CI-docs/requirements.txt

	- name: Build Docs
	if: steps.docs-cache.outputs.cache-hit != 'true'
	run: \|
	venv-latest/bin/activate
	export PATH=$PATH:$PWD/SLiM/Release
	cd docs
	# don't re-generate these which require tricky prerequisites (inkscape, xmlstarlet)
	touch _static/{pedigree0.svg,pedigree1.svg,pedigree2.svg,pedigree_recapitate.svg,pedigree_simplify.svg,pedigree_mutate.svg}
	touch _static/{pedigree01.png,pedigree0.png,pedigree1.png,pedigree2.png,pedigree_recapitate.png,pedigree_simplify.png,pedigree_mutate.png}
	make dist
	# make dist changes the _conf.yml file to write the version number, so drop the change
	git checkout .

	- name: Copy docs
	if: steps.docs-cache.outputs.cache-hit != 'true'
	run: \|
	mkdir -p dist
	cp -r docs/_build/html dist/latest

	- name: Build stable SLiM
	if: steps.docs-cache.outputs.cache-hit != 'true'
	run: \|
	mkdir -p SLiM/Stable
	cd SLiM/Stable
	git fetch --tags --recurse-submodules=no
	git checkout `git tag --list --sort=creatordate \| grep -vi "[baC]" \| tail -n1`
	git status
	cmake -D CMAKE_BUILD_TYPE=Release ..
	make -j 2

	- name: Checkout latest stable tag
	if: steps.docs-cache.outputs.cache-hit != 'true'
	run: \|
	git fetch --tags --recurse-submodules=no
	git checkout `git tag --list --sort=creatordate \| grep -vi "[baC]" \| tail -n1`
	git submodule update --init --recursive
	git status

	# As docs build has had issues with dependancies, just use venv-latest for now
	# - name: Build virtualenv
	# if: steps.docs-cache.outputs.cache-hit != 'true'
	# run: python -m venv venv-stable
	#
	# - name: Install deps
	# if: steps.docs-cache.outputs.cache-hit != 'true'
	# run: \|
	# venv-stable/bin/activate
	# pip install -r requirements/CI-docs/requirements.txt

	- name: Build Docs
	if: steps.docs-cache.outputs.cache-hit != 'true'
	run: \|
	rm -rf docs/_build
	venv-latest/bin/activate
	export PATH=$PWD/SLiM/Stable:$PATH
	cd docs
	# don't re-generate these which require tricky prerequisites (inkscape, xmlstarlet)
	touch _static/{pedigree0.svg,pedigree1.svg,pedigree2.svg,pedigree_recapitate.svg,pedigree_simplify.svg,pedigree_mutate.svg}
	touch _static/{pedigree01.png,pedigree0.png,pedigree1.png,pedigree2.png,pedigree_recapitate.png,pedigree_simplify.png,pedigree_mutate.png}
	make dist
	# make dist changes the _conf.yml file to write the version number, so drop the change
	git checkout .

	- name: Copy docs
	if: steps.docs-cache.outputs.cache-hit != 'true'
	run:
	cp -r docs/_build/html dist/stable

	- name: Upload pyslim docs
	uses: actions/upload-artifact@v2
	with:
	name: pyslim-docs
	path: dist/*


	import-tutorials:
	name: Import tutorials
	needs: cancel-superseded
	runs-on: ubuntu-20.04
	steps:
	- uses: actions/checkout@v2
	name: Checkout tutorials
	with:
	ref: gh-pages
	repository: tskit-dev/tutorials

	- name: Upload tutorials
	uses: actions/upload-artifact@v2
	with:
	name: tutorials
	path: .

	import-rust-tutorial:
	name: Import rust tutorials
	needs: cancel-superseded
	runs-on: ubuntu-20.04
	steps:
	- uses: actions/checkout@v2
	name: Checkout tutorials
	with:
	ref: gh-pages
	repository: tskit-dev/tskit-rust

	- name: Upload tutorials
	uses: actions/upload-artifact@v2
	with:
	name: rust-tutorials
	path: .


	deploy:
	name: Deploy 🚀 (if on main branch)
	needs:
	- build-core-site
	- build-msprime-docs
	- build-tsinfer-docs
	- build-tskit-docs
	- build-pyslim-docs
	- import-tutorials
	- import-rust-tutorial
	runs-on: ubuntu-20.04
	steps:
	- name: Download core site
	uses: actions/download-artifact@v2
	with:
	name: core-site
	path: site

	- name: Download msprime-docs
	uses: actions/download-artifact@v2
	with:
	name: msprime-docs
	path: site/msprime/docs

	- name: Download tsinfer-docs
	uses: actions/download-artifact@v2
	with:
	name: tsinfer-docs
	path: site/tsinfer/docs

	- name: Download tskit-docs
	uses: actions/download-artifact@v2
	with:
	name: tskit-docs
	path: site/tskit/docs

	- name: Download pyslim-docs
	uses: actions/download-artifact@v2
	with:
	name: pyslim-docs
	path: site/pyslim/docs

	- name: Download tutorials
	uses: actions/download-artifact@v2
	with:
	name: tutorials
	path: site/tutorials

	- name: Download rust tutorial
	uses: actions/download-artifact@v2
	with:
	name: rust-tutorials
	path: site/tutorials/rust

	- name: Pages config and tweaks
	run: \|
	touch site/.nojekyll
	echo "tskit.dev" > site/CNAME
	echo "<meta http-equiv=\"Refresh\" content=\"0; url=/msprime/docs/stable\" />" > site/msprime/docs/index.html
	echo "<meta http-equiv=\"Refresh\" content=\"0; url=/tsinfer/docs/stable\" />" > site/tsinfer/docs/index.html
	echo "<meta http-equiv=\"Refresh\" content=\"0; url=/tskit/docs/stable\" />" > site/tskit/docs/index.html
	echo "<meta http-equiv=\"Refresh\" content=\"0; url=/pyslim/docs/stable\" />" > site/pyslim/docs/index.html

	- name: List site contents
	run: \|
	ls -R

	- name: Upload site (for PR inspection)
	uses: actions/upload-artifact@v2
	with:
	name: site
	path: .

	- name: Deploy
	if: github.ref == 'refs/heads/main'
	uses: JamesIves/github-pages-deploy-action@3.7.1
	with:
	GITHUB_TOKEN: ${{ secrets.ADMINBOT_TOKEN }}
	BRANCH: gh-pages
	FOLDER: site
	SINGLE_COMMIT: true

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Build and deploy site #2471

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Build and deploy site #2471

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Workflow file for this run