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Merged
EBjerrum merged 7 commits into from
May 11, 2025
Merged

Fix notebooks generation flow #76

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b468f27
update dependencies
asiomchen May 8, 2025
da0d755
use py files as the source of truth
asiomchen May 8, 2025
3daa515
re-pair notebooks
asiomchen May 8, 2025
8aaaa52
add more info about the sync
asiomchen May 8, 2025
046f22b
run notebooks
asiomchen May 8, 2025
c070f64
sync py files
asiomchen May 8, 2025
f3fd021
update target Python version to 3.9 in ruff.toml
asiomchen May 8, 2025
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3 changes: 1 addition & 2 deletions .gitignore
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Expand Up @@ -130,8 +130,7 @@ dmypy.json

.scikit-mol.code-workspace.swp
scikit-mol.code-workspace
notebooks/25747817
*.ipynb


# test data
tests/data/
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3 changes: 2 additions & 1 deletion .pre-commit-config.yaml
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Expand Up @@ -20,4 +20,5 @@ repos:
args: [ --fix ]
types_or: [ python, pyi ]
# Run the formatter.
- id: ruff-format
- id: ruff-format

11 changes: 2 additions & 9 deletions Makefile
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@@ -1,13 +1,6 @@
sync-notebooks:
uv run jupytext --set-formats docs//notebooks//ipynb,docs//notebooks//scripts//py:percent --sync docs/notebooks/*.ipynb
uv run ruff format "docs/notebooks/"
uv run jupytext --sync "docs/notebooks/*.ipynb"

run-notebooks:
# Execute the notebooks, gives a .nbconvert.ipynb extension
jupyter nbconvert --to notebook --execute *ipynb
# move the .nbconvert.ipynb to the original .ipynb
for file in *.nbconvert.ipynb; do
fname=${file/.nbconvert.ipynb/};
rm $fname.ipynb
mv $file $fname.ipynb
done
uv run jupytext --execute docs/notebooks/*ipynb
7 changes: 5 additions & 2 deletions docs/contributing.md
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Expand Up @@ -94,11 +94,14 @@ Scikit-Learn has a check_estimator that we should strive to get to work, some cl
## Notebooks

Another way of contributing is by providing notebooks with examples on how to use the project to build models together with Scikit-Learn and other tools. There are .ipynb files in the `docs/notebooks` and .py files in the `script` subfolder as the first are useful for online rendering in the documentation, whereas the latter is useful for sub version control.
If you want to create new notebook you can create .ipynb file, and then you run `make sync-notebooks` to create the corresponding .py file for the commit.

If you want to create new notebook you can first create .ipynb file, and then you run `make sync-notebooks` to create the corresponding .py file for the commit.

If you updated any of the existing py/ipynb files, you can run `make sync-notebooks` to update the outdated file in the pair. The .py files are used for nice diffs, and the .ipynb files are used for rendering in the documentation.

`make sync-notebooks` will sync all the notebooks with the .py files in the `scripts` folder.

`make run-notebooks` will sync, run and save the notebooks, expects an ipython kernel with scikit-mol installed called Python3.
`make run-notebooks` will sync, run and save the notebooks, expects an ipython kernel with scikit-mol installed.

## Documentation

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120 changes: 67 additions & 53 deletions docs/notebooks/01_basic_usage.ipynb
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Expand Up @@ -25,10 +25,10 @@
"id": "2c8cad03",
"metadata": {
"execution": {
"iopub.execute_input": "2024-11-24T09:27:16.292725Z",
"iopub.status.busy": "2024-11-24T09:27:16.292083Z",
"iopub.status.idle": "2024-11-24T09:27:16.306663Z",
"shell.execute_reply": "2024-11-24T09:27:16.304935Z"
"iopub.execute_input": "2025-05-08T16:22:29.627872Z",
"iopub.status.busy": "2025-05-08T16:22:29.627571Z",
"iopub.status.idle": "2025-05-08T16:22:29.632065Z",
"shell.execute_reply": "2025-05-08T16:22:29.631373Z"
}
},
"outputs": [],
Expand All @@ -42,10 +42,10 @@
"id": "8d5b2333",
"metadata": {
"execution": {
"iopub.execute_input": "2024-11-24T09:27:16.313611Z",
"iopub.status.busy": "2024-11-24T09:27:16.313028Z",
"iopub.status.idle": "2024-11-24T09:27:16.510254Z",
"shell.execute_reply": "2024-11-24T09:27:16.509620Z"
"iopub.execute_input": "2025-05-08T16:22:29.634712Z",
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"iopub.status.idle": "2025-05-08T16:22:29.845389Z",
"shell.execute_reply": "2025-05-08T16:22:29.844169Z"
}
},
"outputs": [],
Expand Down Expand Up @@ -78,10 +78,10 @@
"id": "0a625dda",
"metadata": {
"execution": {
"iopub.execute_input": "2024-11-24T09:27:16.513123Z",
"iopub.status.busy": "2024-11-24T09:27:16.512856Z",
"iopub.status.idle": "2024-11-24T09:27:17.089043Z",
"shell.execute_reply": "2024-11-24T09:27:17.088357Z"
"iopub.execute_input": "2025-05-08T16:22:29.850211Z",
"iopub.status.busy": "2025-05-08T16:22:29.848822Z",
"iopub.status.idle": "2025-05-08T16:22:30.986417Z",
"shell.execute_reply": "2025-05-08T16:22:30.984810Z"
}
},
"outputs": [
Expand Down Expand Up @@ -118,10 +118,10 @@
"id": "9a801d0f",
"metadata": {
"execution": {
"iopub.execute_input": "2024-11-24T09:27:17.091942Z",
"iopub.status.busy": "2024-11-24T09:27:17.091571Z",
"iopub.status.idle": "2024-11-24T09:27:17.098501Z",
"shell.execute_reply": "2024-11-24T09:27:17.097922Z"
"iopub.execute_input": "2025-05-08T16:22:30.991850Z",
"iopub.status.busy": "2025-05-08T16:22:30.990911Z",
"iopub.status.idle": "2025-05-08T16:22:31.011512Z",
"shell.execute_reply": "2025-05-08T16:22:31.010309Z"
}
},
"outputs": [
Expand All @@ -130,7 +130,8 @@
"text/html": [
"<style>#sk-container-id-1 {\n",
" /* Definition of color scheme common for light and dark mode */\n",
" --sklearn-color-text: black;\n",
" --sklearn-color-text: #000;\n",
" --sklearn-color-text-muted: #666;\n",
" --sklearn-color-line: gray;\n",
" /* Definition of color scheme for unfitted estimators */\n",
" --sklearn-color-unfitted-level-0: #fff5e6;\n",
Expand Down Expand Up @@ -275,12 +276,21 @@
"/* Toggleable label */\n",
"#sk-container-id-1 label.sk-toggleable__label {\n",
" cursor: pointer;\n",
" display: block;\n",
" display: flex;\n",
" width: 100%;\n",
" margin-bottom: 0;\n",
" padding: 0.5em;\n",
" box-sizing: border-box;\n",
" text-align: center;\n",
" align-items: start;\n",
" justify-content: space-between;\n",
" gap: 0.5em;\n",
"}\n",
"\n",
"#sk-container-id-1 label.sk-toggleable__label .caption {\n",
" font-size: 0.6rem;\n",
" font-weight: lighter;\n",
" color: var(--sklearn-color-text-muted);\n",
"}\n",
"\n",
"#sk-container-id-1 label.sk-toggleable__label-arrow:before {\n",
Expand Down Expand Up @@ -433,7 +443,8 @@
" height: 1em;\n",
" width: 1em;\n",
" text-decoration: none !important;\n",
" margin-left: 1ex;\n",
" margin-left: 0.5em;\n",
" text-align: center;\n",
" /* unfitted */\n",
" border: var(--sklearn-color-unfitted-level-1) 1pt solid;\n",
" color: var(--sklearn-color-unfitted-level-1);\n",
Expand Down Expand Up @@ -532,7 +543,7 @@
" /* fitted */\n",
" background-color: var(--sklearn-color-fitted-level-3);\n",
"}\n",
"</style><div id=\"sk-container-id-1\" class=\"sk-top-container\"><div class=\"sk-text-repr-fallback\"><pre>MorganFingerprintTransformer(radius=3)</pre><b>In a Jupyter environment, please rerun this cell to show the HTML representation or trust the notebook. <br />On GitHub, the HTML representation is unable to render, please try loading this page with nbviewer.org.</b></div><div class=\"sk-container\" hidden><div class=\"sk-item\"><div class=\"sk-estimator sk-toggleable\"><input class=\"sk-toggleable__control sk-hidden--visually\" id=\"sk-estimator-id-1\" type=\"checkbox\" checked><label for=\"sk-estimator-id-1\" class=\"sk-toggleable__label sk-toggleable__label-arrow \">&nbsp;MorganFingerprintTransformer<span class=\"sk-estimator-doc-link \">i<span>Not fitted</span></span></label><div class=\"sk-toggleable__content \"><pre>MorganFingerprintTransformer(radius=3)</pre></div> </div></div></div></div>"
"</style><div id=\"sk-container-id-1\" class=\"sk-top-container\"><div class=\"sk-text-repr-fallback\"><pre>MorganFingerprintTransformer(radius=3)</pre><b>In a Jupyter environment, please rerun this cell to show the HTML representation or trust the notebook. <br />On GitHub, the HTML representation is unable to render, please try loading this page with nbviewer.org.</b></div><div class=\"sk-container\" hidden><div class=\"sk-item\"><div class=\"sk-estimator fitted sk-toggleable\"><input class=\"sk-toggleable__control sk-hidden--visually\" id=\"sk-estimator-id-1\" type=\"checkbox\" checked><label for=\"sk-estimator-id-1\" class=\"sk-toggleable__label fitted sk-toggleable__label-arrow\"><div><div>MorganFingerprintTransformer</div></div><div><a class=\"sk-estimator-doc-link fitted\" rel=\"noreferrer\" target=\"_blank\" href=\"https://scikit-mol.readthedocs.org/en/latest/api/scikit_mol.fingerprints/#scikit_mol.fingerprints.MorganFingerprintTransformer\">?<span>Documentation for MorganFingerprintTransformer</span></a><span class=\"sk-estimator-doc-link fitted\">i<span>Fitted</span></span></div></label><div class=\"sk-toggleable__content fitted\"><pre>MorganFingerprintTransformer(radius=3)</pre></div> </div></div></div></div>"
],
"text/plain": [
"MorganFingerprintTransformer(radius=3)"
Expand Down Expand Up @@ -561,18 +572,18 @@
"id": "500dc6f7",
"metadata": {
"execution": {
"iopub.execute_input": "2024-11-24T09:27:17.101153Z",
"iopub.status.busy": "2024-11-24T09:27:17.100929Z",
"iopub.status.idle": "2024-11-24T09:27:17.105319Z",
"shell.execute_reply": "2024-11-24T09:27:17.104586Z"
"iopub.execute_input": "2025-05-08T16:22:31.015226Z",
"iopub.status.busy": "2025-05-08T16:22:31.014511Z",
"iopub.status.idle": "2025-05-08T16:22:31.022448Z",
"shell.execute_reply": "2025-05-08T16:22:31.021051Z"
}
},
"outputs": [
{
"data": {
"text/plain": [
"{'fpSize': 2048,\n",
" 'parallel': False,\n",
" 'n_jobs': None,\n",
" 'radius': 3,\n",
" 'safe_inference_mode': False,\n",
" 'useBondTypes': True,\n",
Expand Down Expand Up @@ -605,10 +616,10 @@
"id": "3a27b07a",
"metadata": {
"execution": {
"iopub.execute_input": "2024-11-24T09:27:17.107710Z",
"iopub.status.busy": "2024-11-24T09:27:17.107495Z",
"iopub.status.idle": "2024-11-24T09:27:17.111268Z",
"shell.execute_reply": "2024-11-24T09:27:17.110754Z"
"iopub.execute_input": "2025-05-08T16:22:31.026293Z",
"iopub.status.busy": "2025-05-08T16:22:31.025546Z",
"iopub.status.idle": "2025-05-08T16:22:31.032975Z",
"shell.execute_reply": "2025-05-08T16:22:31.031700Z"
}
},
"outputs": [
Expand Down Expand Up @@ -641,10 +652,10 @@
"id": "0f141920",
"metadata": {
"execution": {
"iopub.execute_input": "2024-11-24T09:27:17.113572Z",
"iopub.status.busy": "2024-11-24T09:27:17.113344Z",
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"shell.execute_reply": "2024-11-24T09:27:17.116845Z"
"iopub.execute_input": "2025-05-08T16:22:31.036752Z",
"iopub.status.busy": "2025-05-08T16:22:31.036118Z",
"iopub.status.idle": "2025-05-08T16:22:31.043904Z",
"shell.execute_reply": "2025-05-08T16:22:31.042561Z"
}
},
"outputs": [
Expand Down Expand Up @@ -675,10 +686,10 @@
"id": "481e527f",
"metadata": {
"execution": {
"iopub.execute_input": "2024-11-24T09:27:17.119855Z",
"iopub.status.busy": "2024-11-24T09:27:17.119584Z",
"iopub.status.idle": "2024-11-24T09:27:17.124520Z",
"shell.execute_reply": "2024-11-24T09:27:17.124025Z"
"iopub.execute_input": "2025-05-08T16:22:31.047228Z",
"iopub.status.busy": "2025-05-08T16:22:31.046700Z",
"iopub.status.idle": "2025-05-08T16:22:31.054569Z",
"shell.execute_reply": "2025-05-08T16:22:31.053275Z"
}
},
"outputs": [
Expand All @@ -690,7 +701,7 @@
" [1, 0, 0, ..., 0, 0, 0],\n",
" [0, 0, 0, ..., 0, 0, 1],\n",
" [1, 1, 0, ..., 0, 0, 0],\n",
" [1, 1, 0, ..., 0, 0, 0]], dtype=uint8)"
" [1, 1, 0, ..., 0, 0, 0]], shape=(6, 256), dtype=uint8)"
]
},
"execution_count": 8,
Expand All @@ -717,10 +728,10 @@
"id": "7773a5a0",
"metadata": {
"execution": {
"iopub.execute_input": "2024-11-24T09:27:17.126934Z",
"iopub.status.busy": "2024-11-24T09:27:17.126713Z",
"iopub.status.idle": "2024-11-24T09:27:17.131063Z",
"shell.execute_reply": "2024-11-24T09:27:17.130539Z"
"iopub.execute_input": "2025-05-08T16:22:31.057901Z",
"iopub.status.busy": "2025-05-08T16:22:31.057134Z",
"iopub.status.idle": "2025-05-08T16:22:31.064119Z",
"shell.execute_reply": "2025-05-08T16:22:31.063046Z"
}
},
"outputs": [
Expand All @@ -745,23 +756,23 @@
"id": "fa484453",
"metadata": {
"execution": {
"iopub.execute_input": "2024-11-24T09:27:17.133328Z",
"iopub.status.busy": "2024-11-24T09:27:17.133133Z",
"iopub.status.idle": "2024-11-24T09:27:17.137378Z",
"shell.execute_reply": "2024-11-24T09:27:17.136857Z"
"iopub.execute_input": "2025-05-08T16:22:31.067178Z",
"iopub.status.busy": "2025-05-08T16:22:31.066755Z",
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"shell.execute_reply": "2025-05-08T16:22:31.073587Z"
}
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"[[<rdkit.Chem.rdchem.Mol object at 0x7ec3603d1e00>]\n",
" [<rdkit.Chem.rdchem.Mol object at 0x7ec3603d1e70>]\n",
" [<rdkit.Chem.rdchem.Mol object at 0x7ec3603d1ee0>]\n",
" [<rdkit.Chem.rdchem.Mol object at 0x7ec3603d1f50>]\n",
" [<rdkit.Chem.rdchem.Mol object at 0x7ec3603d1fc0>]\n",
" [<rdkit.Chem.rdchem.Mol object at 0x7ec3603d2030>]]\n"
"[[<rdkit.Chem.rdchem.Mol object at 0x7feda5e663b0>]\n",
" [<rdkit.Chem.rdchem.Mol object at 0x7feda5e66420>]\n",
" [<rdkit.Chem.rdchem.Mol object at 0x7feda5e66490>]\n",
" [<rdkit.Chem.rdchem.Mol object at 0x7feda5e66500>]\n",
" [<rdkit.Chem.rdchem.Mol object at 0x7feda5e66570>]\n",
" [<rdkit.Chem.rdchem.Mol object at 0x7feda5e665e0>]]\n"
]
}
],
Expand All @@ -771,6 +782,9 @@
}
],
"metadata": {
"jupytext": {
"formats": "docs//notebooks//ipynb,docs//notebooks//scripts//py:percent"
},
"kernelspec": {
"display_name": "Python 3.9.4 ('rdkit')",
"language": "python",
Expand All @@ -786,7 +800,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.10.12"
"version": "3.12.6"
}
},
"nbformat": 4,
Expand Down
65 changes: 28 additions & 37 deletions docs/notebooks/02_descriptor_transformer.ipynb
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