Merge pull request #7 from jsta/ci

Add ghactions ci validation

.github/workflows/validate.yaml

@@ -0,0 +1,58 @@
+name: validate
+on:  
+  push:
+    branches:
+      - master
+    paths:
+      - '**.ipynb'      
+  pull_request:
+    branches:
+      - master
+    paths:
+      - '**.ipynb'      
+
+jobs:
+    build:
+        name: validate notebooks
+        runs-on: ubuntu-latest
+
+        defaults:
+            run:
+              shell: bash -l {0}
+
+        steps:
+            - uses: actions/checkout@v4
+
+            - name: setup env
+              uses: conda-incubator/setup-miniconda@v3
+              with:                
+                activate-environment: cmip6env
+                channels: conda-forge
+                mamba-version: "*"
+                channel-priority: strict
+                auto-update-conda: false
+                environment-file: environment.yml
+                auto-activate-base: false
+
+            - name: verify env
+              run: |
+                conda info
+                conda list
+                python -m ipykernel install --user --name cmip6env
+
+            - name: get changed ipynb files
+              id: changed-ipynb-files
+              uses: tj-actions/changed-files@v44
+              with:          
+                files: |
+                    **.ipynb
+
+            - name: validate all changed ipynb files
+              if: steps.changed-ipynb-files.outputs.any_changed == 'true'
+              env:
+                ALL_CHANGED_FILES: ${{ steps.changed-ipynb-files.outputs.all_changed_files }}
+              run: |                
+                for file in ${ALL_CHANGED_FILES}; do
+                    echo "$file was changed"
+                    papermill -k cmip6env $file -
+                done

basic_search_and_load.ipynb

@@ -16,11 +16,10 @@
    "outputs": [],
    "source": [
     "from matplotlib import pyplot as plt\n",
-    "import numpy as np\n",
     "import pandas as pd\n",
     "import xarray as xr\n",
-    "import zarr\n",
     "import fsspec\n",
+    "import gcsfs\n",
     "\n",
     "%matplotlib inline\n",
     "%config InlineBackend.figure_format = 'retina' \n",
@@ -102,7 +101,8 @@
     "print(zstore)\n",
     "\n",
     "# create a mutable-mapping-style interface to the store\n",
-    "mapper = fsspec.get_mapper(zstore)\n",
+    "fs = gcsfs.GCSFileSystem(token='anon', session_kwargs={'trust_env': True})\n",
+    "mapper = fs.get_mapper(zstore)\n",
     "\n",
     "# open it using xarray and zarr\n",
     "ds = xr.open_zarr(mapper, consolidated=True)\n",
@@ -139,7 +139,7 @@
    "outputs": [],
    "source": [
     "df_area = df.query(\"variable_id == 'areacella' & source_id == 'CESM2'\")\n",
-    "ds_area = xr.open_zarr(fsspec.get_mapper(df_area.zstore.values[0]), consolidated=True)\n",
+    "ds_area = xr.open_zarr(fs.get_mapper(df_area.zstore.values[0]), consolidated=True)\n",
     "ds_area"
    ]
   },
@@ -181,13 +181,6 @@
     "plt.legend()\n",
     "plt.title('Global Mean Surface Air Temperature')"
    ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": []
   }
  ],
  "metadata": {

environment.yml

@@ -0,0 +1,13 @@
+name: cmip6env
+channels:
+  - conda-forge
+dependencies:
+  - zarr
+  - xarray
+  - s3fs
+  - gcsfs
+  - cftime
+  - nc-time-axis
+  - papermill
+  - notebook
+  - matplotlib