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V2: Add all notebooks to test #840

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merged 8 commits into from
May 24, 2024
Merged

V2: Add all notebooks to test #840

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b082b98
Add all notebooks to test
hwpang May 23, 2024
f254ccb
Add verbose and no coverage
hwpang May 23, 2024
d85a769
[drop] test that incorrect notebook will fail the CI
hwpang May 23, 2024
b81736c
Fix cannot import name 'MoleculeFeaturizer' error
hwpang May 23, 2024
4b385f3
Remove intentional error
hwpang May 23, 2024
8bac88e
Fix notebook
hwpang May 24, 2024
3eeedd1
Fix notebook and add matplotlib for notebook test
hwpang May 24, 2024
54f348b
Add test back
hwpang May 24, 2024
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19 changes: 8 additions & 11 deletions .github/workflows/ci.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -85,20 +85,17 @@ jobs:
if: ${{ matrix.python-version == '3.11' }}
run: |
python -m pip install ".[hpopt]"
- name: Test with pytest
shell: bash -l {0}
run: |
# specifically disable running on GPU, otherwise Lightning will attempt to use the Apple GPU
# that the GitHub actions runners still have but are not allowed to actually use
pytest -v tests
# - name: Test with pytest
# shell: bash -l {0}
# run: |
# # specifically disable running on GPU, otherwise Lightning will attempt to use the Apple GPU
# # that the GitHub actions runners still have but are not allowed to actually use
# pytest -v tests
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- name: Test notebooks
shell: bash -l {0}
run: |
pytest --nbmake examples/training.ipynb
pytest --nbmake examples/predicting.ipynb
pytest --nbmake examples/convert_v1_to_v2.ipynb
pytest --nbmake examples/training_regression_multicomponent.ipynb
pytest --nbmake examples/predicting_regression_multicomponent.ipynb
python -m pip install matplotlib
pytest --no-cov -v --nbmake examples/*.ipynb

conda-test:
name: Execute Tests with Conda-based Install
Expand Down
17 changes: 8 additions & 9 deletions examples/extra_features_from_featurizer.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -26,7 +26,6 @@
"from rdkit import Chem\n",
"from pathlib import Path\n",
"from chemprop import data, utils\n",
"from chemprop.featurizers import MoleculeFeaturizer\n",
"from rdkit.Chem import rdFingerprintGenerator\n",
"from dataclasses import dataclass"
]
Expand Down Expand Up @@ -182,7 +181,7 @@
"metadata": {},
"source": [
"# Creating custom featurizers\n",
"Custom featurizers can be made by inheriting the ```MoleculeFeaturizer``` class.\n",
"Custom featurizers can be made by inheriting the ```SimpleMoleculeMolGraphFeaturizer``` class.\n",
"These featurizers must override the following methods:\n",
"- ```__len__(self)```\n",
"- ```__call__(self, mol: Chem.mol)```\n",
Expand All @@ -197,7 +196,7 @@
"outputs": [],
"source": [
"@dataclass\n",
"class MorganFingerprintMoleculeFeaturizer(MoleculeFeaturizer):\n",
"class MorganFingerprintMoleculeFeaturizer:\n",
" fp_size: int = 2048\n",
"\n",
" def __post_init__(self):\n",
Expand Down Expand Up @@ -257,11 +256,11 @@
{
"data": {
"text/plain": [
"[MoleculeDatapoint(mol=<rdkit.Chem.rdchem.Mol object at 0x7f0aa8a018c0>, y=array([-0.77]), weight=1, gt_mask=None, lt_mask=None, x_d=array([0, 1, 0, ..., 0, 0, 0], dtype=uint8), x_phase=None, V_f=None, E_f=None, V_d=None),\n",
" MoleculeDatapoint(mol=<rdkit.Chem.rdchem.Mol object at 0x7f0aa8a01850>, y=array([-3.3]), weight=1, gt_mask=None, lt_mask=None, x_d=array([0, 0, 0, ..., 0, 0, 0], dtype=uint8), x_phase=None, V_f=None, E_f=None, V_d=None),\n",
" MoleculeDatapoint(mol=<rdkit.Chem.rdchem.Mol object at 0x7f0aa8a019a0>, y=array([-2.06]), weight=1, gt_mask=None, lt_mask=None, x_d=array([0, 0, 0, ..., 0, 0, 0], dtype=uint8), x_phase=None, V_f=None, E_f=None, V_d=None),\n",
" MoleculeDatapoint(mol=<rdkit.Chem.rdchem.Mol object at 0x7f0aa8a01a80>, y=array([-7.87]), weight=1, gt_mask=None, lt_mask=None, x_d=array([0, 0, 0, ..., 0, 0, 0], dtype=uint8), x_phase=None, V_f=None, E_f=None, V_d=None),\n",
" MoleculeDatapoint(mol=<rdkit.Chem.rdchem.Mol object at 0x7f0aa8a01b60>, y=array([-1.33]), weight=1, gt_mask=None, lt_mask=None, x_d=array([0, 0, 0, ..., 0, 0, 0], dtype=uint8), x_phase=None, V_f=None, E_f=None, V_d=None)]"
"[MoleculeDatapoint(mol=<rdkit.Chem.rdchem.Mol object at 0x7f8f12c369d0>, y=array([-0.77]), weight=1.0, gt_mask=None, lt_mask=None, x_d=array([0, 1, 0, ..., 0, 0, 0], dtype=uint8), x_phase=None, name='OCC3OC(OCC2OC(OC(C#N)c1ccccc1)C(O)C(O)C2O)C(O)C(O)C3O', V_f=None, E_f=None, V_d=None),\n",
" MoleculeDatapoint(mol=<rdkit.Chem.rdchem.Mol object at 0x7f8f12c36810>, y=array([-3.3]), weight=1.0, gt_mask=None, lt_mask=None, x_d=array([0, 0, 0, ..., 0, 0, 0], dtype=uint8), x_phase=None, name='Cc1occc1C(=O)Nc2ccccc2', V_f=None, E_f=None, V_d=None),\n",
" MoleculeDatapoint(mol=<rdkit.Chem.rdchem.Mol object at 0x7f8f12c368f0>, y=array([-2.06]), weight=1.0, gt_mask=None, lt_mask=None, x_d=array([0, 0, 0, ..., 0, 0, 0], dtype=uint8), x_phase=None, name='CC(C)=CCCC(C)=CC(=O)', V_f=None, E_f=None, V_d=None),\n",
" MoleculeDatapoint(mol=<rdkit.Chem.rdchem.Mol object at 0x7f8f12c36ab0>, y=array([-7.87]), weight=1.0, gt_mask=None, lt_mask=None, x_d=array([0, 0, 0, ..., 0, 0, 0], dtype=uint8), x_phase=None, name='c1ccc2c(c1)ccc3c2ccc4c5ccccc5ccc43', V_f=None, E_f=None, V_d=None),\n",
" MoleculeDatapoint(mol=<rdkit.Chem.rdchem.Mol object at 0x7f8f12c36b90>, y=array([-1.33]), weight=1.0, gt_mask=None, lt_mask=None, x_d=array([0, 0, 0, ..., 0, 0, 0], dtype=uint8), x_phase=None, name='c1ccsc1', V_f=None, E_f=None, V_d=None)]"
]
},
"execution_count": 7,
Expand Down Expand Up @@ -299,7 +298,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.11.6"
"version": "3.11.8"
},
"orig_nbformat": 4
},
Expand Down