Fix #4

Workflow file for this run

	name: MODFLOW 6 documentation
	on:
	push:
	paths-ignore:
	- '.github/workflows/release.yml'
	- '.github/workflows/ci.yml'
	- '.hpc/**'
	pull_request:
	branches:
	- master
	- develop
	paths-ignore:
	- '.github/workflows/release.yml'
	- '.hpc/**'
	jobs:
	rtd_build:
	name: Build ReadTheDocs
	runs-on: ubuntu-22.04
	defaults:
	run:
	shell: bash -l {0}
	env:
	FC: gfortran
	FC_V: 12
	steps:
	- name: Checkout modflow6
	uses: actions/checkout@v4
	with:
	path: modflow6

	- name: Checkout modflow6-examples
	uses: actions/checkout@v4
	with:
	repository: MODFLOW-USGS/modflow6-examples
	path: modflow6-examples

	- name: Checkout usgslatex
	uses: actions/checkout@v4
	with:
	repository: MODFLOW-USGS/usgslatex
	path: usgslatex

	- uses: prefix-dev/setup-pixi@v0.5.1
	with:
	pixi-version: "latest"
	manifest-path: "modflow6/pixi.toml"

	- name: Setup pixi
	working-directory: modflow6
	run: pixi run install
	- name: Install additional packages for Sphinx using pip
	working-directory: modflow6/.build_rtd_docs
	run: pixi run pip install -r requirements.rtd.txt

	- name: Print python package versions
	run: pixi run pip list

	- name: Install TeX Live
	run: \|
	sudo apt-get update
	sudo apt install texlive-latex-extra texlive-science texlive-font-utils

	- name: Install USGS LaTeX style files and Univers font
	working-directory: usgslatex/usgsLaTeX
	run: sudo ./install.sh --all-users

	- name: Test building files from dfn's for LaTeX
	working-directory: modflow6/autotest
	run: pixi run pytest -v build_mfio_tex.py

	- name: Setup ${{ env.FC }} ${{ env.FC_V }}
	uses: fortran-lang/setup-fortran@v1
	with:
	compiler: gcc
	version: ${{ env.FC_V }}

	- name: Cache modflow6 examples
	id: cache-examples
	uses: actions/cache@v4
	with:
	path: modflow6-examples/examples
	key: modflow6-examples-${{ hashFiles('modflow6-examples/scripts/**') }}

	- name: Install extra Python packages
	if: steps.cache-examples.outputs.cache-hit != 'true'
	working-directory: modflow6-examples/etc
	run: \|
	pixi run pip install -r requirements.pip.txt
	pixi run pip install -r requirements.usgs.txt

	- name: Update FloPy
	if: steps.cache-examples.outputs.cache-hit != 'true'
	working-directory: modflow6/autotest
	run: pixi run update-flopy

	- name: Build example models
	if: steps.cache-examples.outputs.cache-hit != 'true'
	working-directory: modflow6-examples/autotest
	run: \|
	pixi run pytest -v -n auto test_scripts.py --init
	ls -lh ../examples/

	- name: Run benchmarks
	working-directory: modflow6/distribution
	run: python benchmark.py
	env:
	GITHUB_TOKEN: ${{ github.token }}

	- name: Show benchmarks
	working-directory: modflow6/distribution
	run: cat run-time-comparison.md

	- name: Upload benchmarks
	uses: actions/upload-artifact@v3
	with:
	name: run-time-comparison
	path: modflow6/distribution/run-time-comparison.md

	- name: Collect deprecations
	working-directory: modflow6/doc/mf6io/mf6ivar
	run: pixi run deprecations

	- name: Show deprecations
	working-directory: modflow6/doc/mf6io/mf6ivar/md
	run: cat deprecations.md

	- name: Upload deprecations
	uses: actions/upload-artifact@v3
	with:
	name: deprecations
	path: modflow6/doc/mf6io/mf6ivar/md/deprecations.md

	- name: Run sphinx
	working-directory: modflow6/.build_rtd_docs
	run: make html

	- name: Upload results
	uses: actions/upload-artifact@v3
	with:
	name: rtd-files-for-${{ github.sha }}
	path: \|
	modflow6/.build_rtd_docs/index.rst
	modflow6/.build_rtd_docs/mf6io.rst
	# run-time-comparison is moved to _mf6run by conf.py
	modflow6/.build_rtd_docs/_mf6run/
	modflow6/.build_rtd_docs/_mf6io/
	modflow6/.build_rtd_docs/_static/

	rtd_trigger:
	name: rtd-trigger
	needs: rtd_build
	runs-on: ubuntu-22.04
	if: github.repository_owner == 'MODFLOW-USGS' && github.event_name == 'push'
	steps:
	- name: Checkout repo
	uses: actions/checkout@v4

	- name: Trigger RTDs build on push to repo branches
	uses: dfm/rtds-action@v1
	with:
	webhook_url: ${{ secrets.MF6_RTDS_WEBHOOK_URL }}
	webhook_token: ${{ secrets.MF6_RTDS_WEBHOOK_TOKEN }}
	commit_ref: ${{ github.ref }}

	doxygen_build:
	runs-on: ubuntu-22.04
	env:
	working-directory: .build_rtd_docs
	common-directory: .github/common
	branch-name: ${GITHUB_REF##*/}
	defaults:
	run:
	shell: bash

	steps:
	- uses: actions/checkout@v4

	- name: Print branch name
	run: echo ${{env.branch-name}}

	- name: Install doxygen and graphviz
	run: \|
	sudo apt-get update
	sudo apt-get install doxygen graphviz

	- uses: prefix-dev/setup-pixi@v0.5.1
	with:
	pixi-version: "latest"

	- name: Setup pixi
	run: pixi run install

	- name: Print python package versions
	run: pixi run pip list

	- name: update MODFLOW 6 version
	run: pixi run update-version

	- name: update MODFLOW 6 version in Doxyfile
	run: pixi run update-doxyfile-version

	- name: run doxygen
	run: doxygen
	working-directory: ${{env.working-directory}}

	- name: upload pages artifact
	uses: actions/upload-pages-artifact@v2
	with:
	path: ${{env.working-directory}}/html

	pages_deploy:
	if: github.ref == 'refs/heads/develop' && github.event_name == 'push'
	needs: doxygen_build
	permissions:
	pages: write
	id-token: write
	environment:
	name: github-pages
	url: ${{ steps.deployment.outputs.page_url }}
	runs-on: ubuntu-latest
	steps:
	- name: Deploy to GitHub Pages
	id: deployment
	uses: actions/deploy-pages@v3

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Fix #4

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Fix #4

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