Merge pull request #669 from British-Oceanographic-Data-Centre/bug/za…

…rr-notebooks correct zarr installation on workflows
British-Oceanographic-Data-Centre · Dec 11, 2023 · 4998416 · 4998416
2 parents f4bf9d4 + 8d84563
commit 4998416
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Showing 4 changed files with 33 additions and 8 deletions.
diff --git a/.github/workflows/markdown-general.yml b/.github/workflows/markdown-general.yml
@@ -18,7 +18,7 @@ jobs:
         uses: actions/checkout@v4
         with:
           repository: British-Oceanographic-Data-Centre/COAsT
-          ref: develop
+          ref: bug/zarr-notebooks
           path: external
 
       - name: Prepare environment
@@ -42,5 +42,7 @@ jobs:
           sudo apt-get install -y libgeos-dev
           pip install cartopy==0.21.0
           pip install zarr
+          pip install xarray[complete]
+          pip install aiohttp requests
           mv config ./example_scripts/notebook_tutorials/runnable_notebooks/general/config
           bash notebook_to_md.sh general
diff --git a/.github/workflows/unit_test_contents.yml b/.github/workflows/unit_test_contents.yml
@@ -22,6 +22,7 @@ jobs:
           sudo apt-get update
           sudo apt-get install -y libgeos-dev
           pip install cartopy==0.21.0
+          pip install zarr
           python unit_testing/generate_unit_test_contents.py
       - name: Commit changes
         run: |

diff --git a/.github/workflows/verify_package.yml b/.github/workflows/verify_package.yml
@@ -34,4 +34,5 @@ jobs:
           sudo apt-get update
           sudo apt-get install -y libgeos-dev
           pip install cartopy==0.21.0
+          pip install zarr
           pytest tests
diff --git a/example_scripts/notebook_tutorials/runnable_notebooks/general/zarr_files.ipynb b/example_scripts/notebook_tutorials/runnable_notebooks/general/zarr_files.ipynb
@@ -44,7 +44,7 @@
    "id": "761fde27-8ef4-4805-887c-d795da34902e",
    "metadata": {},
    "source": [
-    "`pip install zarr`"
+    "`pip install zarr xarray[complete] aiohttp requests`"
    ]
   },
   {
@@ -73,16 +73,26 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 16,
+   "execution_count": 1,
    "id": "582e5ae5-e61d-409d-aa33-206f6ff3c0bd",
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "/mnt/code/.pyenv/versions/3.10.12/envs/coast-10/lib/python3.10/site-packages/utide/harmonics.py:16: RuntimeWarning: invalid value encountered in cast\n",
+      "/mnt/code/.pyenv/versions/3.10.12/envs/coast-10/lib/python3.10/site-packages/utide/harmonics.py:17: RuntimeWarning: invalid value encountered in cast\n"
+     ]
+    }
+   ],
    "source": [
     "import coast\n",
     "import matplotlib.pyplot as plt\n",
     "import datetime\n",
     "import numpy as np\n",
     "import xarray as xr\n",
+    "import zarr\n",
     "\n",
     "root = \"./\"\n",
     "fn_config_t_grid = root + \"./config/example_nemo_monthly_climate.json\"\n",
@@ -114,10 +124,21 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 43,
+   "execution_count": 2,
    "id": "289bbdfd-991c-41ed-9acd-7e9bb35f157c",
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "/tmp/ipykernel_221474/396929176.py:1: RuntimeWarning: Failed to open Zarr store with consolidated metadata, but successfully read with non-consolidated metadata. This is typically much slower for opening a dataset. To silence this warning, consider:\n",
+      "1. Consolidating metadata in this existing store with zarr.consolidate_metadata().\n",
+      "2. Explicitly setting consolidated=False, to avoid trying to read consolidate metadata, or\n",
+      "3. Explicitly setting consolidated=True, to raise an error in this case instead of falling back to try reading non-consolidated metadata.\n"
+     ]
+    }
+   ],
    "source": [
     "dom = xr.open_zarr(fn_nemo_dom_mask)\n",
     "mesh_zgr = xr.open_zarr(fn_nemo_dom_mesh_zgr)\n",
@@ -126,7 +147,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 44,
+   "execution_count": 3,
    "id": "e1f12c20-4076-4ae0-9135-c95218347805",
    "metadata": {},
    "outputs": [],
@@ -139,7 +160,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 45,
+   "execution_count": 4,
    "id": "50b2cbb7-a1ad-4ebc-aebb-42a1b8286e58",
    "metadata": {},
    "outputs": [],