Merge pull request #285 from noisepy/carlosg/precommit_nb

chore: Precommit check for notebook outputs
noisepy · Jan 31, 2024 · 8185ca6 · 8185ca6
2 parents baae80e + 65ba350
commit 8185ca6
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Showing 11 changed files with 687 additions and 989 deletions.
diff --git a/.github/workflows/precommit.yaml b/.github/workflows/precommit.yaml
@@ -15,7 +15,7 @@ jobs:
       uses: actions/[email protected]
       with:
         python-version: '3.10'
-    - name: Install pre-commit
-      run: pip install pre-commit==3.3.3
+    - name: Install pre-commit and Jupyter
+      run: pip install pre-commit==3.3.3 jupyter==1.0.0
     - name: Run pre-commit checks
       run: pre-commit run --all-files --show-diff-on-failure
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -15,6 +15,17 @@ repos:
         exclude: \.ipy(n|nb)$
         args: ["--autofix", "--indent=2", "--no-sort-keys"]
 
+    # Clear output from jupyter notebooks so that only the input cells are committed.
+  - repo: local
+    hooks:
+      - id: jupyter-nb-clear-output
+        name: Clear output from Jupyter notebooks
+        description: Clear output from Jupyter notebooks.
+        files: \.ipynb$
+        stages: [commit]
+        language: system
+        entry: jupyter nbconvert --clear-output
+
   - repo: https://github.com/PyCQA/isort
     rev: 5.12.0
     hooks:

diff --git a/script/write_speed/plot.ipynb b/script/write_speed/plot.ipynb
diff --git a/tutorials/monitoring/attenuation_singlestation.ipynb b/tutorials/monitoring/attenuation_singlestation.ipynb
@@ -122,9 +122,7 @@
    "cell_type": "code",
    "execution_count": null,
    "id": "1a3ebcc4",
-   "metadata": {
-    "scrolled": true
-   },
+   "metadata": {},
    "outputs": [],
    "source": [
     "# Ready to read in h5 file\n",
@@ -195,9 +193,7 @@
    "cell_type": "code",
    "execution_count": null,
    "id": "50ace094",
-   "metadata": {
-    "scrolled": true
-   },
+   "metadata": {},
    "outputs": [],
    "source": [
     "freq = [0.5, 1, 2,4]  # targeted frequency band for waveform monitoring\n",
@@ -264,9 +260,7 @@
    "cell_type": "code",
    "execution_count": null,
    "id": "d00a24e6",
-   "metadata": {
-    "scrolled": true
-   },
+   "metadata": {},
    "outputs": [],
    "source": [
     "# get the mean-squared value on each componet and also the average waveform\n",
@@ -472,9 +466,7 @@
    "cell_type": "code",
    "execution_count": null,
    "id": "c9d6f840",
-   "metadata": {
-    "scrolled": true
-   },
+   "metadata": {},
    "outputs": [],
    "source": [
     "# getting the sum of squared residuals (SSR) between Eobs and Esyn  \n",
@@ -539,9 +531,7 @@
    "cell_type": "code",
    "execution_count": null,
    "id": "beda26dc",
-   "metadata": {
-    "scrolled": false
-   },
+   "metadata": {},
    "outputs": [],
    "source": [
     "# getting the optimal value from the SSR\n",

diff --git a/tutorials/noisepy_datastore.ipynb b/tutorials/noisepy_datastore.ipynb
diff --git a/tutorials/noisepy_pnwstore_tutorial.ipynb b/tutorials/noisepy_pnwstore_tutorial.ipynb
@@ -279,8 +279,7 @@
    "cell_type": "code",
    "execution_count": null,
    "metadata": {
-    "id": "pWcrfWO8W1tH",
-    "scrolled": true
+    "id": "pWcrfWO8W1tH"
    },
    "outputs": [],
    "source": [