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refactor(tsp): Elevate APT to generalized transport class #1300

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refactor(tsp): Elevate APT to generalized transport class

refactor(tsp): Elevate APT to generalized transport class #1300

Workflow file for this run

.github/workflows/docs.yml at 47a360b
name: MODFLOW 6 documentation
on:
push:
paths-ignore:
- '.github/workflows/release.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:
GCC_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
- name: Install Conda environment from environment.yml
uses: mamba-org/setup-micromamba@v1
with:
environment-file: modflow6/environment.yml
cache-environment: true
cache-downloads: true
- name: Install additional packages for Sphinx using pip
working-directory: modflow6/.build_rtd_docs
run: pip install -r requirements.rtd.txt
- name: Print python package versions
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: pytest -v build_mfio_tex.py
- name: Setup GNU Fortran ${{ env.GCC_V }}
uses: fortran-lang/setup-fortran@v1
with:
compiler: gcc
version: ${{ env.GCC_V }}
- name: Cache modflow6 examples
id: cache-examples
uses: actions/cache@v3
with:
path: modflow6-examples/examples
key: modflow6-examples-${{ hashFiles('modflow6-examples/scripts/**') }}
- name: Install extra Python packages
if: steps.cache-examples.outputs.cache-hit != 'true'
working-directory: modflow6-examples/etc
run: |
pip install -r requirements.pip.txt
pip install -r requirements.usgs.txt
- name: Update FloPy
if: steps.cache-examples.outputs.cache-hit != 'true'
working-directory: modflow6/autotest
run: python update_flopy.py
- name: Build example models
if: steps.cache-examples.outputs.cache-hit != 'true'
working-directory: modflow6-examples/etc
run: |
python ci_build_files.py
ls -lh ../examples/
- name: Run benchmarks
working-directory: modflow6/distribution
run: python benchmark.py
env:
GITHUB_TOKEN: ${{ github.token }}
- name: Show benchmarks
working-directory: modflow6/distribution
run: cat run-time-comparison.md
- name: Upload benchmarks
uses: actions/upload-artifact@v3
with:
name: run-time-comparison
path: modflow6/distribution/run-time-comparison.md
- name: Collect deprecations
working-directory: modflow6/doc/mf6io/mf6ivar
run: python deprecations.py
- name: Show deprecations
working-directory: modflow6/doc/mf6io/mf6ivar/md
run: cat deprecations.md
- name: Upload deprecations
uses: actions/upload-artifact@v3
with:
name: deprecations
path: modflow6/doc/mf6io/mf6ivar/md/deprecations.md
- name: Run sphinx
working-directory: modflow6/.build_rtd_docs
run: make html
- name: Upload results
uses: actions/upload-artifact@v3
with:
name: rtd-files-for-${{ 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
distribution-directory: distribution
common-directory: .github/common
branch-name: ${GITHUB_REF##*/}
defaults:
run:
shell: bash -l {0}
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
- name: Install Conda environment from environment.yml
uses: mamba-org/setup-micromamba@v1
with:
environment-file: environment.yml
cache-environment: true
cache-downloads: true
- name: Print python package versions
run: pip list
- name: update MODFLOW 6 version
run: python update_version.py
working-directory: ${{env.distribution-directory}}
- name: update MODFLOW 6 version in Doxyfile
run: |
import sys
import os
sys.path.insert(0, os.path.abspath(os.path.join("..", "doc")))
from version import __version__
print("Update the Doxyfile with the latest version number")
with open("Doxyfile", "r") as fp:
lines = fp.readlines()
tag = "PROJECT_NUMBER"
with open("Doxyfile", "w") as fp:
for line in lines:
if tag in line:
line = '{} = "version {}"\n'.format(tag, __version__)
fp.write(line)
shell: python
working-directory: ${{env.working-directory}}
- 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@v2