exlude rendered notebooks and use awscli v2

nsidc · Jun 6, 2023 · 01d74e5 · 01d74e5
1 parent 87da0bd
commit 01d74e5
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Showing 3 changed files with 37 additions and 30 deletions.
diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
@@ -47,21 +47,14 @@ jobs:
         with:
           version: 1.1.251
 
-      - name: install-aws-cli
-        uses: unfor19/install-aws-cli-action@v1
-        with:
-          version: 2     # default
-          verbose: false # default
-          arch: amd64    # allowed values: amd64, arm64
-
       - name: "Execute notebooks with Quarto"
         env:
           EARTHDATA_USERNAME: ${{ secrets.EARTHDATA_USERNAME }}
           EARTHDATA_PASSWORD: ${{ secrets.EARTHDATA_PASSWORD }}
         shell: bash -l {0}
         run: |
           jupyter kernelspec list
-          find notebooks -type f -name "*.ipynb" | xargs -I F quarto render "F" --execute --execute-daemon
+          find notebooks -type f -name "*.ipynb" -not -path '*\.ipynb_checkpoints/*' -not -path '*endered*'  | xargs -I F quarto render "F" --execute --execute-daemon
 
   win-osx:
     name: Runtime (${{ matrix.os }}, micromamba)

diff --git a/notebooks/SnowEx_ASO_MODIS_Snow/Snow-tutorial.ipynb b/notebooks/SnowEx_ASO_MODIS_Snow/Snow-tutorial.ipynb
@@ -82,7 +82,9 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "tags": []
+   },
    "outputs": [],
    "source": [
     "import os\n",
@@ -144,7 +146,9 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "tags": []
+   },
    "outputs": [],
    "source": [
     "polygon_filepath = str(os.getcwd() + '/Data/nsidc-polygon.json') # Note: A shapefile or other vector-based spatial data format could be substituted here.\n",
@@ -173,7 +177,9 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "tags": []
+   },
    "outputs": [],
    "source": [
     "temporal = '2017-01-01T00:00:00Z,2017-12-31T23:59:59Z' # Set temporal range"
@@ -191,7 +197,9 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "tags": []
+   },
    "outputs": [],
    "source": [
     "data_dict = { 'snowex': {'short_name': 'SNEX17_GPR','version': '2','polygon': polygon,'temporal':temporal},\n",
@@ -212,7 +220,9 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "tags": []
+   },
    "outputs": [],
    "source": [
     "for k, v in data_dict.items(): fn.granule_info(data_dict[k])"
@@ -230,7 +240,9 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "tags": []
+   },
    "outputs": [],
    "source": [
     "search_df = fn.time_overlap(data_dict)\n",
@@ -253,7 +265,8 @@
    "cell_type": "code",
    "execution_count": null,
    "metadata": {
-    "scrolled": true
+    "scrolled": true,
+    "tags": []
    },
    "outputs": [],
    "source": [
@@ -299,7 +312,9 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "tags": []
+   },
    "outputs": [],
    "source": [
     "bounds = poly.bounds # Get polygon bounds to be used as bounding box input\n",
@@ -324,7 +339,9 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "tags": []
+   },
    "outputs": [],
    "source": [
     "base_url = 'https://n5eil02u.ecs.nsidc.org/egi/request' # Set NSIDC data access base URL\n",
@@ -349,19 +366,14 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "tags": []
+   },
    "outputs": [],
    "source": [
-    "path = str(os.getcwd() + '/Data')\n",
-    "if not os.path.exists(path):\n",
-    "    os.mkdir(path)\n",
-    "os.chdir(path)\n",
-    "#fn.cmr_download(urls)\n",
-    "#fn.cmr_download(api_request)\n",
-    "\n",
-    "\n",
+    "os.chdir(\"Data\")\n",
     "# pull data from staged bucket for demonstration\n",
-    "!aws --no-sign-request s3 cp s3://snowex-aso-modis-tutorial-data/ ./ --recursive #access data in staged directory"
+    "!awscliv2 --no-sign-request s3 cp s3://snowex-aso-modis-tutorial-data/ ./ --recursive #access data in staged directory"
    ]
   },
   {
@@ -377,7 +389,9 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "tags": []
+   },
    "outputs": [],
    "source": [
     "snowex_path = './SnowEx17_GPR_Version2_Week1.csv' # Define local filepath\n",
@@ -756,7 +770,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.9.7"
+   "version": "3.9.16"
   }
  },
  "nbformat": 4,

diff --git a/notebooks/SnowEx_ASO_MODIS_Snow/Snow-tutorial_rendered.ipynb b/notebooks/SnowEx_ASO_MODIS_Snow/Snow-tutorial_rendered.ipynb
@@ -757,7 +757,7 @@
     "\n",
     "\n",
     "# pull data from staged bucket for demonstration\n",
-    "!aws --no-sign-request s3 cp s3://snowex-aso-modis-tutorial-data/ ./ --recursive #access data in staged directory"
+    "!awscliv2 --no-sign-request s3 cp s3://snowex-aso-modis-tutorial-data/ ./ --recursive #access data in staged directory"
    ]
   },
   {