Rename notebooks for easier navigation from the Hub (#35)

ProjectPythia · Jul 18, 2023 · 52baa7a · 52baa7a
1 parent 8e45d17
commit 52baa7a
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Showing 14 changed files with 34 additions and 648 deletions.
diff --git a/_toc.yml b/_toc.yml
@@ -6,13 +6,13 @@ parts:
       - file: notebooks/how-to-cite
   - caption: Foundations
     chapters:
-      - file: notebooks/foundations/kerchunk_basics
-      - file: notebooks/foundations/kerchunk_multi_file
-      - file: notebooks/foundations/kerchunk_dask
+      - file: notebooks/foundations/01_kerchunk_basics
+      - file: notebooks/foundations/02_kerchunk_multi_file
+      - file: notebooks/foundations/03_kerchunk_dask
 
   - caption: Case Studies
     chapters:
-      - file: notebooks/case_studies/ARG_Weather
-      - file: notebooks/case_studies/HRRR
-      - file: notebooks/case_studies/TIFF
-      - file: notebooks/case_studies/pangeo_forge
+      - file: notebooks/case_studies/NetCDF_SMN_Arg
+      - file: notebooks/case_studies/GRIB2_HRRR
+      - file: notebooks/case_studies/GeoTIFF_FMI
+      - file: notebooks/case_studies/NetCDF_Pangeo_Forge_gridMET
diff --git a/binder/environment.yml b/binder/environment.yml
@@ -1,4 +1,4 @@
-name: dask-tutorial
+name: kerchunk-tutorial
 channels:
   - conda-forge
 dependencies:

diff --git a/notebooks/case_studies/ARG_combined.json b/notebooks/case_studies/ARG_combined.json
diff --git a/notebooks/case_studies/HRRR.ipynb → notebooks/case_studies/GRIB2_HRRR.ipynb b/notebooks/case_studies/HRRR.ipynb → notebooks/case_studies/GRIB2_HRRR.ipynb
@@ -17,7 +17,6 @@
    ]
   },
   {
-   "attachments": {},
    "cell_type": "markdown",
    "id": "9eced552",
    "metadata": {},
@@ -70,7 +69,6 @@
    ]
   },
   {
-   "attachments": {},
    "cell_type": "markdown",
    "id": "0e7ce9e2",
    "metadata": {},
@@ -143,8 +141,8 @@
     "# retrieve list of available days in archive\n",
     "days_available = fs_read.glob(\"s3://noaa-hrrr-bdp-pds/hrrr.*\")\n",
     "\n",
-    "# Read HRRR GRIB2 files from latest day\n",
-    "files = fs_read.glob(f\"s3://{days_available[-1]}/conus/*wrfsfcf01.grib2\")\n",
+    "# Read HRRR GRIB2 files from April 19, 2023\n",
+    "files = fs_read.glob(f\"s3://noaa-hrrr-bdp-pds/hrrr.20230419/conus/*wrfsfcf01.grib2\")\n",
     "\n",
     "# Append s3 prefix for filelist\n",
     "files = sorted([\"s3://\" + f for f in files])\n",
@@ -165,18 +163,6 @@
    ]
   },
   {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "cf13b333",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "\"s3://noaa-hrrr-bdp-pds/hrrr.20230419/conus/hrrr.t00z.wrfsfcf01.grib2\"\n",
-    "\"s3://noaa-hrrr-bdp-pds/hrrr.20230419/conus/hrrr.t00z.wrfsfcf01.grib2\""
-   ]
-  },
-  {
-   "attachments": {},
    "cell_type": "markdown",
    "id": "3bec2881",
    "metadata": {},
@@ -327,7 +313,7 @@
    "outputs": [],
    "source": [
     "# Write Kerchunk .json record\n",
-    "output_fname = \"HRRR_combined.json\"\n",
+    "output_fname = \"references/HRRR_combined.json\"\n",
     "with open(f\"{output_fname}\", \"wb\") as f:\n",
     "    f.write(ujson.dumps(multi_kerchunk).encode())"
    ]
@@ -349,7 +335,10 @@
    "source": [
     "# open dataset as zarr object using fsspec reference file system and Xarray\n",
     "fs = fsspec.filesystem(\n",
-    "    \"reference\", fo=multi_kerchunk, remote_protocol=\"s3\", remote_options={\"anon\": True}\n",
+    "    \"reference\",\n",
+    "    fo=\"references/HRRR_combined.json\",\n",
+    "    remote_protocol=\"s3\",\n",
+    "    remote_options={\"anon\": True},\n",
     ")\n",
     "m = fs.get_mapper(\"\")\n",
     "ds = xr.open_dataset(\n",
@@ -396,14 +385,6 @@
    "source": [
     "ds[\"t2m\"][:, 500, 500].plot()"
    ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "be917a4b",
-   "metadata": {},
-   "outputs": [],
-   "source": []
   }
  ],
  "metadata": {
@@ -422,7 +403,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.11.0"
+   "version": "3.10.11"
   },
   "vscode": {
    "interpreter": {

diff --git a/notebooks/case_studies/TIFF.ipynb → notebooks/case_studies/GeoTIFF_FMI.ipynb b/notebooks/case_studies/TIFF.ipynb → notebooks/case_studies/GeoTIFF_FMI.ipynb
@@ -1,23 +1,20 @@
 {
  "cells": [
   {
-   "attachments": {},
    "cell_type": "markdown",
    "metadata": {},
    "source": [
     "# Kerchunk, GeoTIFF and Generating Coordinates with `xrefcoord`\n"
    ]
   },
   {
-   "attachments": {},
    "cell_type": "markdown",
    "metadata": {},
    "source": [
     "<img src=\"../images/radar.png\" width=400 alt=\"ARG\"></img>"
    ]
   },
   {
-   "attachments": {},
    "cell_type": "markdown",
    "metadata": {},
    "source": [
@@ -42,7 +39,6 @@
    ]
   },
   {
-   "attachments": {},
    "cell_type": "markdown",
    "metadata": {},
    "source": [
@@ -81,7 +77,6 @@
    ]
   },
   {
-   "attachments": {},
    "cell_type": "markdown",
    "metadata": {},
    "source": [
@@ -124,7 +119,6 @@
    ]
   },
   {
-   "attachments": {},
    "cell_type": "markdown",
    "metadata": {},
    "source": [
@@ -166,7 +160,6 @@
    ]
   },
   {
-   "attachments": {},
    "cell_type": "markdown",
    "metadata": {},
    "source": [
@@ -221,7 +214,6 @@
    ]
   },
   {
-   "attachments": {},
    "cell_type": "markdown",
    "metadata": {},
    "source": [
@@ -264,13 +256,12 @@
     "multi_kerchunk = mzz.translate()\n",
     "\n",
     "# Write kerchunk .json record\n",
-    "output_fname = \"RADAR.json\"\n",
+    "output_fname = \"references/RADAR.json\"\n",
     "with open(f\"{output_fname}\", \"wb\") as f:\n",
     "    f.write(ujson.dumps(multi_kerchunk).encode())"
    ]
   },
   {
-   "attachments": {},
    "cell_type": "markdown",
    "metadata": {},
    "source": [
@@ -285,7 +276,7 @@
    "source": [
     "fs = fsspec.filesystem(\n",
     "    \"reference\",\n",
-    "    fo=\"RADAR.json\",\n",
+    "    fo=\"references/RADAR.json\",\n",
     "    remote_protocol=\"s3\",\n",
     "    remote_options={\"anon\": True},\n",
     "    skip_instance_cache=True,\n",
@@ -304,7 +295,6 @@
    ]
   },
   {
-   "attachments": {},
    "cell_type": "markdown",
    "metadata": {},
    "source": [
@@ -327,7 +317,6 @@
    ]
   },
   {
-   "attachments": {},
    "cell_type": "markdown",
    "metadata": {},
    "source": [
@@ -346,7 +335,6 @@
    ]
   },
   {
-   "attachments": {},
    "cell_type": "markdown",
    "metadata": {},
    "source": [
@@ -367,7 +355,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "kerchunk-cookbook-dev",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -381,9 +369,9 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.10.12"
+   "version": "3.10.11"
   }
  },
  "nbformat": 4,
- "nbformat_minor": 2
+ "nbformat_minor": 4
 }
diff --git a/notebooks/case_studies/pangeo_forge.ipynb → ...studies/NetCDF_Pangeo_Forge_gridMET.ipynb b/notebooks/case_studies/pangeo_forge.ipynb → ...studies/NetCDF_Pangeo_Forge_gridMET.ipynb
@@ -9,7 +9,6 @@
    ]
   },
   {
-   "attachments": {},
    "cell_type": "markdown",
    "metadata": {},
    "source": [
@@ -37,7 +36,6 @@
    ]
   },
   {
-   "attachments": {},
    "cell_type": "markdown",
    "metadata": {},
    "source": [
@@ -135,7 +133,6 @@
    ]
   },
   {
-   "attachments": {},
    "cell_type": "markdown",
    "metadata": {},
    "source": [
@@ -179,7 +176,7 @@
    "metadata": {},
    "source": [
     "## Create a Location For Output\n",
-    "For this example, we are creating a temporary directory to write the data to. If we wanted to persist this Kerchunk reference, we could write to local disc or cloud storage. "
+    "We write to local storage for this example, but the reference file could also be shared via cloud storage. "
    ]
   },
   {
@@ -190,14 +187,8 @@
    },
    "outputs": [],
    "source": [
-    "import os\n",
-    "from tempfile import TemporaryDirectory\n",
-    "\n",
-    "td = TemporaryDirectory()\n",
-    "target_root = td.name\n",
-    "target_root = \"esip\"\n",
-    "store_name = \"PF_kerchunk\"\n",
-    "target_store = os.path.join(target_root, store_name)"
+    "target_root = \"references\"\n",
+    "store_name = \"Pangeo_Forge\""
    ]
   },
   {
@@ -426,8 +417,6 @@
    "outputs": [],
    "source": [
     "# prepare urls\n",
-    "\n",
-    "\n",
     "def url_gen(year):\n",
     "    return (\n",
     "        f\"http://thredds.northwestknowledge.net:8080/thredds/dodsC/MET/bi/bi_{year}.nc\"\n",
@@ -516,7 +505,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "kerchunk-cookbook-dev",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -530,7 +519,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.10.12"
+   "version": "3.10.11"
   }
  },
  "nbformat": 4,

diff --git a/notebooks/case_studies/ARG_Weather.ipynb → notebooks/case_studies/NetCDF_SMN_Arg.ipynb b/notebooks/case_studies/ARG_Weather.ipynb → notebooks/case_studies/NetCDF_SMN_Arg.ipynb
@@ -15,7 +15,6 @@
    ]
   },
   {
-   "attachments": {},
    "cell_type": "markdown",
    "metadata": {},
    "source": [
@@ -66,7 +65,6 @@
    ]
   },
   {
-   "attachments": {},
    "cell_type": "markdown",
    "metadata": {},
    "source": [
@@ -200,7 +198,6 @@
    ]
   },
   {
-   "attachments": {},
    "cell_type": "markdown",
    "metadata": {},
    "source": [
@@ -254,7 +251,6 @@
    ]
   },
   {
-   "attachments": {},
    "cell_type": "markdown",
    "metadata": {},
    "source": [
@@ -282,7 +278,7 @@
     "multi_kerchunk = mzz.translate()\n",
     "\n",
     "# Write kerchunk .json record\n",
-    "output_fname = \"ARG_combined.json\"\n",
+    "output_fname = \"references/ARG_combined.json\"\n",
     "with open(f\"{output_fname}\", \"wb\") as f:\n",
     "    f.write(ujson.dumps(multi_kerchunk).encode())"
    ]
@@ -307,7 +303,7 @@
     "\n",
     "fs = fsspec.filesystem(\n",
     "    \"reference\",\n",
-    "    fo=\"ARG_combined.json\",\n",
+    "    fo=\"references/ARG_combined.json\",\n",
     "    remote_protocol=\"s3\",\n",
     "    remote_options={\"anon\": True},\n",
     "    skip_instance_cache=True,\n",
@@ -369,7 +365,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.11.0"
+   "version": "3.10.11"
   },
   "vscode": {
    "interpreter": {
@@ -378,5 +374,5 @@
   }
  },
  "nbformat": 4,
- "nbformat_minor": 2
+ "nbformat_minor": 4
 }
diff --git a/notebooks/case_studies/references/ARG_combined.json b/notebooks/case_studies/references/ARG_combined.json