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Merge pull request #192 from jotelha/joss-review-issue-184-4-issue-18…
…5-1-issue-186-2 Joss review issue 184, 185, issue 186
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name: Test electrochemistry examples including fenics functionality | ||
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on: | ||
push: | ||
branches: | ||
- '**' | ||
tags: | ||
- '**' | ||
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jobs: | ||
tests: | ||
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runs-on: ubuntu-latest | ||
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steps: | ||
- uses: actions/checkout@v3 | ||
with: | ||
fetch-depth: 0 | ||
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- name: install_python | ||
run: | | ||
sudo apt-get update -qy | ||
sudo apt-get install -y python3-dev python3-pip python3-venv libxml2-dev libxslt-dev zlib1g-dev | ||
# Upgrade to latest meson and ninja | ||
sudo pip install --upgrade meson ninja | ||
sudo pip install --upgrade jupyter jupytext pandas | ||
- name: install_fenics | ||
run: | | ||
sudo apt-get install -y --no-install-recommends software-properties-common | ||
sudo add-apt-repository -y ppa:fenics-packages/fenics | ||
sudo apt-get update -qy | ||
sudo apt-get install -y fenics python3-dolfin python3-mshr | ||
- name: install matscipy | ||
run: | | ||
sudo pip install . | ||
- name: build sample ipynb and html | ||
run: | | ||
cd examples/electrochemistry | ||
# check that all sample html files are produced successfully | ||
html_files=(./*.html) | ||
rm *.html | ||
ls -1 *.py | grep -v to_html.py | bash to_html.sh | ||
for f in "${html_files[@]}"; do | ||
if ! test -f "$f"; then | ||
echo "Sample $f creation failed." | ||
exit 1 | ||
fi | ||
done | ||
# use tar here, see https://github.com/actions/upload-artifact/issues/38 | ||
- name: Pack build assets | ||
run: | | ||
bash -c "tar -cvf electrochemistry-sample-ipynb.tar examples/electrochemistry/*.ipynb examples/electrochemistry/*.html" | ||
- name: Upload sample ipynb artifact | ||
uses: actions/upload-artifact@v3 | ||
with: | ||
name: electrochemistry-sample-ipynb | ||
path: electrochemistry-sample-ipynb.tar | ||
if-no-files-found: error |
2 changes: 1 addition & 1 deletion
2
examples/electrochemistry/c2d_batch/cell_1d/concentration_sweep/run.sh
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#!/bin/bash | ||
./run_std.sh | tee run_std.log | ||
bash ./run_std.sh | tee run_std.log |
4 changes: 2 additions & 2 deletions
4
examples/electrochemistry/c2d_batch/cell_1d/potential_sweep/run.sh
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@@ -1,3 +1,3 @@ | ||
#!/bin/bash | ||
./run_std.sh | tee run_std.log | ||
./run_robin.sh | tee run_robin.log | ||
bash ./run_std.sh | tee run_std.log | ||
bash ./run_robin.sh | tee run_robin.log |
4 changes: 2 additions & 2 deletions
4
examples/electrochemistry/pnp_batch/cell_1d/concentration_sweep/run.sh
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@@ -1,3 +1,3 @@ | ||
#!/bin/bash | ||
./run_std.sh | tee run_std.log | ||
./eval.sh | tee eval.log | ||
bash ./run_std.sh | tee run_std.log | ||
bash ./eval.sh | tee eval.log |
6 changes: 3 additions & 3 deletions
6
examples/electrochemistry/pnp_batch/cell_1d/potential_sweep/run.sh
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@@ -1,4 +1,4 @@ | ||
#!/bin/bash | ||
./run_std.sh | tee run_std.log | ||
./run_robin.sh | tee run_robin.log | ||
./eval.sh | tee eval.log | ||
bash ./run_std.sh | tee run_std.log | ||
bash ./run_robin.sh | tee run_robin.log | ||
bash ./eval.sh | tee eval.log |
4 changes: 2 additions & 2 deletions
4
examples/electrochemistry/pnp_batch/cell_1d/stern_layer_sweep/run.sh
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@@ -1,3 +1,3 @@ | ||
#!/bin/bash | ||
./run_robin.sh | tee run_robin.log | ||
./eval.sh | tee eval.log | ||
bash ./run_robin.sh | tee run_robin.log | ||
bash ./eval.sh | tee eval.log |
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