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fix(mem): address memory leaks #3074

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fix(mem): address memory leaks

fix(mem): address memory leaks #3074

Workflow file for this run

.github/workflows/docs.yml at 6022b00
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/**'
env:
PIXI_BETA_WARNING_OFF: true
concurrency:
group: ${{ github.workflow }}-${{ github.ref }}
cancel-in-progress: true
jobs:
lint:
name: Check format
runs-on: ubuntu-latest
steps:
- name: Checkout modflow6
uses: actions/checkout@v4
- uses: prefix-dev/[email protected]
with:
pixi-version: v0.24.2
- name: Check spelling
run: pixi run check-spelling
rtd_build:
name: Build ReadTheDocs
needs:
- lint
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
- name: Setup pixi
uses: prefix-dev/[email protected]
with:
pixi-version: v0.24.2
manifest-path: "modflow6/pixi.toml"
- name: Custom pixi install
working-directory: modflow6
run: pixi run install
- name: Print python package versions
working-directory: modflow6
run: pixi run pip list
- name: Install TeX Live
run: |
sudo apt-get update
sudo apt install texlive-science \
texlive-latex-extra \
texlive-font-utils \
texlive-fonts-recommended \
texlive-fonts-extra
- name: Install USGS LaTeX style files and Univers font
working-directory: usgslatex/usgsLaTeX
run: sudo ./install.sh --all-users
- name: Test building MF6IO LaTeX from DFNs
working-directory: modflow6/distribution
run: pixi run pytest -v build_docs.py::test_build_mf6io_tex_from_dfn
- name: Test building PDFs from LaTeX
working-directory: modflow6/distribution
run: pixi run pytest -v build_docs.py::test_build_pdfs_from_tex
- 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
run: |
pixi run pip install -r ../modflow6-examples/etc/requirements.pip.txt
pixi run pip install -r ../modflow6-examples/etc/requirements.usgs.txt
- name: Update FloPy
if: steps.cache-examples.outputs.cache-hit != 'true'
working-directory: modflow6/autotest
run: pixi run update-flopy
# the example models also need mf2005, triangle and gridgen
- name: Install extra executables
if: steps.cache-examples.outputs.cache-hit != 'true'
uses: modflowpy/install-modflow-action@v1
with:
subset: mf2005,triangle,gridgen
- name: Build example models
if: steps.cache-examples.outputs.cache-hit != 'true'
working-directory: modflow6
shell: pixi run bash -e {0}
run: |
cd ../modflow6-examples/autotest
pytest -v -n auto test_scripts.py --init
ls -lh ../examples/
- name: Run benchmarks
working-directory: modflow6
run: pixi run benchmark
env:
GITHUB_TOKEN: ${{ github.token }}
- name: Show benchmarks
working-directory: modflow6/distribution
run: cat run-time-comparison.md
- name: Upload benchmarks
uses: actions/upload-artifact@v3
with:
name: run-time-comparison
path: modflow6/distribution/run-time-comparison.md
- name: Collect deprecations
working-directory: modflow6
run: pixi run deprecations
- name: Show deprecations
working-directory: modflow6/doc/mf6io/mf6ivar/md
run: cat deprecations.md
- name: Upload deprecations
uses: actions/upload-artifact@v3
with:
name: deprecations
path: modflow6/doc/mf6io/mf6ivar/md/deprecations.md
- name: Run sphinx
working-directory: modflow6
run: pixi run sphinx
- name: Upload results
uses: actions/upload-artifact@v3
with:
name: rtd-files-for-${{ github.sha }}
path: |
modflow6/.build_rtd_docs/dev.rst
modflow6/.build_rtd_docs/index.rst
modflow6/.build_rtd_docs/mf6io.rst
modflow6/.build_rtd_docs/_dev/
modflow6/.build_rtd_docs/_mf6io/
modflow6/.build_rtd_docs/_mf6run/
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
- name: Setup pixi
uses: prefix-dev/[email protected]
with:
pixi-version: v0.24.2
- name: Custom pixi install
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: 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