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Surface Diffusion Estimator Example and Associated Improvements #13

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merged 10 commits into from
Mar 21, 2024
Merged

Surface Diffusion Estimator Example and Associated Improvements #13

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0bb439b
ensure depth is defined for the Root node
mjohnson541 Mar 20, 2024
f83a359
add function for dumping simple objects to dictionaries
mjohnson541 Mar 20, 2024
0a3c5d6
add function for constructing simple objects from dictionaries
mjohnson541 Mar 20, 2024
61dea0f
improve write_nodes to handle simple objects
mjohnson541 Mar 20, 2024
d19dda3
improve read_nodes to handle simple objects
mjohnson541 Mar 20, 2024
d99a09d
change environment file to use rmgmolecule
mjohnson541 Mar 20, 2024
00dc251
add matplotlib to environment
mjohnson541 Mar 20, 2024
55ab89b
add notebook for Surface Diffusion single eval SIDT example
mjohnson541 Mar 20, 2024
714bb24
remove source install of rmgmolecule in CI tests
mjohnson541 Mar 20, 2024
40dad62
Formatting
hwpang Mar 21, 2024
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13 changes: 1 addition & 12 deletions .github/workflows/CI.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -17,11 +17,6 @@ jobs:
- name: Checkout PySIDT
uses: actions/checkout@v4

- name: Clone ReactionMechanismGenerator/molecule
run: |
cd ..
git clone -b ts_len_improvements https://github.com/ReactionMechanismGenerator/molecule.git

- name: Create pysidt environment
uses: conda-incubator/setup-miniconda@v3
with:
Expand All @@ -37,13 +32,7 @@ jobs:
python -m pip install pytest nbmake
python -m pip install -e .

- name: Make and install molecule
run: |
cd ../molecule
make clean
make
pip install -e .

- name: Test PySIDT notebooks
run: |
pytest --nbmake IPython/multi_eval_SIDT_example.ipynb
pytest --nbmake IPython/Surface_Diffusion_single_eval_SIDT_example.ipynb
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