improve notebook handling

google · Feb 23, 2023 · d0a50ec · d0a50ec
1 parent 27c37ed
commit d0a50ec
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Showing 35 changed files with 4,394 additions and 7,936 deletions.
diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
@@ -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"

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -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",
+      ]
diff --git a/docs/advanced_topics/contributing.md b/docs/advanced_topics/contributing.md
@@ -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
@@ -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

diff --git a/docs/getting_started.ipynb b/docs/getting_started.ipynb
@@ -66,12 +66,7 @@
     "executionInfo": {
      "elapsed": 54,
      "status": "ok",
-     "timestamp": 1673483483044,
-     "user": {
-      "displayName": "Marcus Chiam",
-      "userId": "17531616275590396120"
-     },
-     "user_tz": 480
+     "timestamp": 1673483483044
     },
     "id": "bRlrHqZVXZvk"
    },
@@ -126,12 +121,7 @@
     "executionInfo": {
      "elapsed": 53,
      "status": "ok",
-     "timestamp": 1673483483208,
-     "user": {
-      "displayName": "Marcus Chiam",
-      "userId": "17531616275590396120"
-     },
-     "user_tz": 480
+     "timestamp": 1673483483208
     },
     "id": "cbc079cd"
    },
@@ -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"
@@ -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"
@@ -289,12 +269,7 @@
     "executionInfo": {
      "elapsed": 1,
      "status": "ok",
-     "timestamp": 1673483483754,
-     "user": {
-      "displayName": "Marcus Chiam",
-      "userId": "17531616275590396120"
-     },
-     "user_tz": 480
+     "timestamp": 1673483483754
     },
     "id": "CJDaJNijyOji"
    },
@@ -324,12 +299,7 @@
     "executionInfo": {
      "elapsed": 55,
      "status": "ok",
-     "timestamp": 1673483483958,
-     "user": {
-      "displayName": "Marcus Chiam",
-      "userId": "17531616275590396120"
-     },
-     "user_tz": 480
+     "timestamp": 1673483483958
     },
     "id": "7W0qf7FC9uG5"
    },
@@ -360,12 +330,7 @@
     "executionInfo": {
      "elapsed": 54,
      "status": "ok",
-     "timestamp": 1673483484125,
-     "user": {
-      "displayName": "Marcus Chiam",
-      "userId": "17531616275590396120"
-     },
-     "user_tz": 480
+     "timestamp": 1673483484125
     },
     "id": "e0102447"
    },
@@ -418,12 +383,7 @@
     "executionInfo": {
      "elapsed": 52,
      "status": "ok",
-     "timestamp": 1673483484293,
-     "user": {
-      "displayName": "Marcus Chiam",
-      "userId": "17531616275590396120"
-     },
-     "user_tz": 480
+     "timestamp": 1673483484293
     },
     "id": "9b0af486"
    },
@@ -463,12 +423,7 @@
     "executionInfo": {
      "elapsed": 53,
      "status": "ok",
-     "timestamp": 1673483484460,
-     "user": {
-      "displayName": "Marcus Chiam",
-      "userId": "17531616275590396120"
-     },
-     "user_tz": 480
+     "timestamp": 1673483484460
     },
     "id": "961bf70b"
    },
@@ -504,12 +459,7 @@
     "executionInfo": {
      "elapsed": 515,
      "status": "ok",
-     "timestamp": 1673483485090,
-     "user": {
-      "displayName": "Marcus Chiam",
-      "userId": "17531616275590396120"
-     },
-     "user_tz": 480
+     "timestamp": 1673483485090
     },
     "id": "bff5393e"
    },
@@ -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"
    },
@@ -569,12 +514,7 @@
     "executionInfo": {
      "elapsed": 52,
      "status": "ok",
-     "timestamp": 1673483485436,
-     "user": {
-      "displayName": "Marcus Chiam",
-      "userId": "17531616275590396120"
-     },
-     "user_tz": 480
+     "timestamp": 1673483485436
     },
     "id": "e4f6f4d3"
    },
@@ -604,12 +544,7 @@
     "executionInfo": {
      "elapsed": 56,
      "status": "ok",
-     "timestamp": 1673483485606,
-     "user": {
-      "displayName": "Marcus Chiam",
-      "userId": "17531616275590396120"
-     },
-     "user_tz": 480
+     "timestamp": 1673483485606
     },
     "id": "445fcab0"
    },
@@ -627,12 +562,7 @@
     "executionInfo": {
      "elapsed": 52,
      "status": "ok",
-     "timestamp": 1673483485777,
-     "user": {
-      "displayName": "Marcus Chiam",
-      "userId": "17531616275590396120"
-     },
-     "user_tz": 480
+     "timestamp": 1673483485777
     },
     "id": "5221eafd"
    },
@@ -674,12 +604,7 @@
     "executionInfo": {
      "elapsed": 55,
      "status": "ok",
-     "timestamp": 1673483485947,
-     "user": {
-      "displayName": "Marcus Chiam",
-      "userId": "17531616275590396120"
-     },
-     "user_tz": 480
+     "timestamp": 1673483485947
     },
     "id": "74295360"
    },
@@ -697,12 +622,7 @@
     "executionInfo": {
      "elapsed": 1,
      "status": "ok",
-     "timestamp": 1673483486076,
-     "user": {
-      "displayName": "Marcus Chiam",
-      "userId": "17531616275590396120"
-     },
-     "user_tz": 480
+     "timestamp": 1673483486076
     },
     "id": "cRtnMZuQFlKl"
    },
@@ -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"
@@ -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"
@@ -876,12 +783,7 @@
     "executionInfo": {
      "elapsed": 580,
      "status": "ok",
-     "timestamp": 1673483505350,
-     "user": {
-      "displayName": "Marcus Chiam",
-      "userId": "17531616275590396120"
-     },
-     "user_tz": 480
+     "timestamp": 1673483505350
     },
     "id": "DFwxgBQf44ks"
    },
@@ -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"
@@ -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,