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Improve notebook handling #2860

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Feb 24, 2023
Merged

Improve notebook handling #2860

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2 changes: 1 addition & 1 deletion .github/workflows/build.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -72,7 +72,7 @@ jobs:
python-version: ${{ matrix.python-version }}
- name: Install standalone dependencies only
run: |
pip install .
pip install -e .
- name: Test importing Flax
run: |
python -c "import flax"
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10 changes: 10 additions & 0 deletions .pre-commit-config.yaml
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Expand Up @@ -18,3 +18,13 @@ repos:
hooks:
- id: trailing-whitespace
exclude: ^docs/.*\.md$
- repo: https://github.com/kynan/nbstripout
rev: 0.6.1
hooks:
- id: nbstripout
args: [
--keep-output,
--keep-count,
--extra-keys,
"metadata.kernelspec metadata.vscode metadata.colab cell.metadata.executionInfo.user cell.metadata.executionInfo.user_tz cell.metadata.colab",
]
9 changes: 8 additions & 1 deletion docs/advanced_topics/contributing.md
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Expand Up @@ -51,9 +51,12 @@ Follow these steps to contribute code:
```bash
git clone https://github.com/YOUR_USERNAME/flax
cd flax
pip install ".[testing]"
pip install -e .
pip install ".[testing]"
pip install -r docs/requirements.txt
# install in editable mode again because docs/requirements.txt
# reinstalls project in non-editable mode
pip install -e .
```

5. Set up pre-commit hooks, this will run some automated checks during each `git` commit and
Expand Down Expand Up @@ -127,6 +130,10 @@ The former can be opened and executed directly in [Google Colab](https://colab.r
Markdown makes it easier to track changes/diffs within version control and, for example, GitHub
web UI, since `.ipynb` files are based on JSON.

**NOTE**: If your notebook contains a cell that uses `pip` to install a package
you must add a `skip-execution` tag to that cell so `myst-nb` will skip the cell
when testing the notebooks.

#### Editing Jupyter Notebooks (`.ipynb`)

For making large changes that substantially modify code and outputs, it's recommended to edit
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163 changes: 20 additions & 143 deletions docs/getting_started.ipynb
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Expand Up @@ -66,12 +66,7 @@
"executionInfo": {
"elapsed": 54,
"status": "ok",
"timestamp": 1673483483044,
"user": {
"displayName": "Marcus Chiam",
"userId": "17531616275590396120"
},
"user_tz": 480
"timestamp": 1673483483044
},
"id": "bRlrHqZVXZvk"
},
Expand Down Expand Up @@ -126,12 +121,7 @@
"executionInfo": {
"elapsed": 53,
"status": "ok",
"timestamp": 1673483483208,
"user": {
"displayName": "Marcus Chiam",
"userId": "17531616275590396120"
},
"user_tz": 480
"timestamp": 1673483483208
},
"id": "cbc079cd"
},
Expand Down Expand Up @@ -177,12 +167,7 @@
"executionInfo": {
"elapsed": 103,
"status": "ok",
"timestamp": 1673483483427,
"user": {
"displayName": "Marcus Chiam",
"userId": "17531616275590396120"
},
"user_tz": 480
"timestamp": 1673483483427
},
"id": "lDHfog81zLQa",
"outputId": "2c580f41-bf5d-40ec-f1cf-ab7f319a84da"
Expand Down Expand Up @@ -266,12 +251,7 @@
"executionInfo": {
"elapsed": 52,
"status": "ok",
"timestamp": 1673483483631,
"user": {
"displayName": "Marcus Chiam",
"userId": "17531616275590396120"
},
"user_tz": 480
"timestamp": 1673483483631
},
"id": "qXr7JDpIxGNZ",
"outputId": "1249b7fb-6787-41eb-b34c-61d736300844"
Expand All @@ -289,12 +269,7 @@
"executionInfo": {
"elapsed": 1,
"status": "ok",
"timestamp": 1673483483754,
"user": {
"displayName": "Marcus Chiam",
"userId": "17531616275590396120"
},
"user_tz": 480
"timestamp": 1673483483754
},
"id": "CJDaJNijyOji"
},
Expand Down Expand Up @@ -324,12 +299,7 @@
"executionInfo": {
"elapsed": 55,
"status": "ok",
"timestamp": 1673483483958,
"user": {
"displayName": "Marcus Chiam",
"userId": "17531616275590396120"
},
"user_tz": 480
"timestamp": 1673483483958
},
"id": "7W0qf7FC9uG5"
},
Expand Down Expand Up @@ -360,12 +330,7 @@
"executionInfo": {
"elapsed": 54,
"status": "ok",
"timestamp": 1673483484125,
"user": {
"displayName": "Marcus Chiam",
"userId": "17531616275590396120"
},
"user_tz": 480
"timestamp": 1673483484125
},
"id": "e0102447"
},
Expand Down Expand Up @@ -418,12 +383,7 @@
"executionInfo": {
"elapsed": 52,
"status": "ok",
"timestamp": 1673483484293,
"user": {
"displayName": "Marcus Chiam",
"userId": "17531616275590396120"
},
"user_tz": 480
"timestamp": 1673483484293
},
"id": "9b0af486"
},
Expand Down Expand Up @@ -463,12 +423,7 @@
"executionInfo": {
"elapsed": 53,
"status": "ok",
"timestamp": 1673483484460,
"user": {
"displayName": "Marcus Chiam",
"userId": "17531616275590396120"
},
"user_tz": 480
"timestamp": 1673483484460
},
"id": "961bf70b"
},
Expand Down Expand Up @@ -504,12 +459,7 @@
"executionInfo": {
"elapsed": 515,
"status": "ok",
"timestamp": 1673483485090,
"user": {
"displayName": "Marcus Chiam",
"userId": "17531616275590396120"
},
"user_tz": 480
"timestamp": 1673483485090
},
"id": "bff5393e"
},
Expand Down Expand Up @@ -547,12 +497,7 @@
"executionInfo": {
"elapsed": 59,
"status": "ok",
"timestamp": 1673483485268,
"user": {
"displayName": "Marcus Chiam",
"userId": "17531616275590396120"
},
"user_tz": 480
"timestamp": 1673483485268
},
"id": "xC4MFyBsfT-U"
},
Expand All @@ -569,12 +514,7 @@
"executionInfo": {
"elapsed": 52,
"status": "ok",
"timestamp": 1673483485436,
"user": {
"displayName": "Marcus Chiam",
"userId": "17531616275590396120"
},
"user_tz": 480
"timestamp": 1673483485436
},
"id": "e4f6f4d3"
},
Expand Down Expand Up @@ -604,12 +544,7 @@
"executionInfo": {
"elapsed": 56,
"status": "ok",
"timestamp": 1673483485606,
"user": {
"displayName": "Marcus Chiam",
"userId": "17531616275590396120"
},
"user_tz": 480
"timestamp": 1673483485606
},
"id": "445fcab0"
},
Expand All @@ -627,12 +562,7 @@
"executionInfo": {
"elapsed": 52,
"status": "ok",
"timestamp": 1673483485777,
"user": {
"displayName": "Marcus Chiam",
"userId": "17531616275590396120"
},
"user_tz": 480
"timestamp": 1673483485777
},
"id": "5221eafd"
},
Expand Down Expand Up @@ -674,12 +604,7 @@
"executionInfo": {
"elapsed": 55,
"status": "ok",
"timestamp": 1673483485947,
"user": {
"displayName": "Marcus Chiam",
"userId": "17531616275590396120"
},
"user_tz": 480
"timestamp": 1673483485947
},
"id": "74295360"
},
Expand All @@ -697,12 +622,7 @@
"executionInfo": {
"elapsed": 1,
"status": "ok",
"timestamp": 1673483486076,
"user": {
"displayName": "Marcus Chiam",
"userId": "17531616275590396120"
},
"user_tz": 480
"timestamp": 1673483486076
},
"id": "cRtnMZuQFlKl"
},
Expand All @@ -722,12 +642,7 @@
"executionInfo": {
"elapsed": 17908,
"status": "ok",
"timestamp": 1673483504133,
"user": {
"displayName": "Marcus Chiam",
"userId": "17531616275590396120"
},
"user_tz": 480
"timestamp": 1673483504133
},
"id": "2c40ce90",
"outputId": "258a2c76-2c8f-4a9e-d48b-dde57c342a87"
Expand Down Expand Up @@ -803,18 +718,10 @@
"execution_count": 65,
"id": "Zs5atiqIG9Kz",
"metadata": {
"colab": {
"height": 353
},
"executionInfo": {
"elapsed": 358,
"status": "ok",
"timestamp": 1673483504621,
"user": {
"displayName": "Marcus Chiam",
"userId": "17531616275590396120"
},
"user_tz": 480
"timestamp": 1673483504621
},
"id": "Zs5atiqIG9Kz",
"outputId": "431a2fcd-44fa-4202-f55a-906555f060ac"
Expand Down Expand Up @@ -876,12 +783,7 @@
"executionInfo": {
"elapsed": 580,
"status": "ok",
"timestamp": 1673483505350,
"user": {
"displayName": "Marcus Chiam",
"userId": "17531616275590396120"
},
"user_tz": 480
"timestamp": 1673483505350
},
"id": "DFwxgBQf44ks"
},
Expand All @@ -901,18 +803,10 @@
"execution_count": 67,
"id": "5d5nF3u44JFI",
"metadata": {
"colab": {
"height": 699
},
"executionInfo": {
"elapsed": 1250,
"status": "ok",
"timestamp": 1673483506723,
"user": {
"displayName": "Marcus Chiam",
"userId": "17531616275590396120"
},
"user_tz": 480
"timestamp": 1673483506723
},
"id": "5d5nF3u44JFI",
"outputId": "1db5a01c-9d70-4f7d-8c0d-0a3ad8252d3e"
Expand Down Expand Up @@ -953,29 +847,12 @@
}
],
"metadata": {
"colab": {
"last_runtime": {
"build_target": "//learning/deepmind/public/tools/ml_python:ml_notebook",
"kind": "private"
},
"provenance": []
},
"jupytext": {
"formats": "ipynb,md:myst",
"main_language": "python"
},
"kernelspec": {
"display_name": "Python 3",
"language": "python",
"name": "python3"
},
"language_info": {
"name": "python"
},
"vscode": {
"interpreter": {
"hash": "31f2aee4e71d21fbe5cf8b01ff0e069b9275f58929596ceb00d14d90e3e16cd6"
}
}
},
"nbformat": 4,
Expand Down
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