Add PACE workshop notebook

.github/workflows/docs-build.yml

@@ -15,10 +15,6 @@ jobs:
             - uses: actions/setup-python@v5
               with:
                   python-version: "3.11"
-              env:
-                  EARTHDATA_USERNAME: ${{ secrets.EARTHDATA_USERNAME }}
-                  EARTHDATA_PASSWORD: ${{ secrets.EARTHDATA_PASSWORD }}
-
             - name: Install GDAL
               run: |
                   python -m pip install --upgrade pip
@@ -38,6 +34,9 @@ jobs:
             - name: Build docs
               run: |
                   mkdocs build
+              env:
+                  EARTHDATA_USERNAME: ${{ secrets.EARTHDATA_USERNAME }}
+                  EARTHDATA_PASSWORD: ${{ secrets.EARTHDATA_PASSWORD }}
             - name: Deploy to Netlify
               uses: nwtgck/[email protected]
               with:

.github/workflows/docs.yml

@@ -14,7 +14,6 @@ jobs:
             - uses: actions/setup-python@v5
               with:
                   python-version: "3.11"
-
             - name: Install dependencies
               run: |
                   python -m pip install --upgrade pip
@@ -24,4 +23,8 @@ jobs:
             - name: PKG-TEST
               run: |
                   python -m unittest discover tests/
-            - run: mkdocs gh-deploy --force
+            - name: Build docs
+              run: mkdocs gh-deploy --force
+              env:
+                  EARTHDATA_USERNAME: ${{ secrets.EARTHDATA_USERNAME }}
+                  EARTHDATA_PASSWORD: ${{ secrets.EARTHDATA_PASSWORD }}

.github/workflows/ubuntu.yml

@@ -17,7 +17,6 @@ jobs:
             fail-fast: false
             matrix:
                 config:
-                    - { os: ubuntu-latest, py: "3.8" }
                     - { os: ubuntu-latest, py: "3.9" }
                     - { os: ubuntu-latest, py: "3.10" }
                     - { os: ubuntu-latest, py: "3.11" }

docs/examples/_earthaccess.ipynb

@@ -0,0 +1,120 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "[![image](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/opengeos/HyperCoast/blob/main/docs/examples/_earthaccess.ipynb)\n",
+    "\n",
+    "# Testing earthaccess login"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# %pip install \"hypercoast[extra]\""
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import os\n",
+    "import earthaccess\n",
+    "import hypercoast"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# os.environ[\"EARTHDATA_USERNAME\"] = \"your_username\"\n",
+    "# os.environ[\"EARTHDATA_PASSWORD\"] = \"your_password\""
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "if os.environ.get(\"EARTHDATA_USERNAME\") is None:\n",
+    "    raise ValueError(\"Please set the EARTHDATA_USERNAME environment variable\")\n",
+    "if os.environ.get(\"EARTHDATA_PASSWORD\") is None:\n",
+    "    raise ValueError(\"Please set the EARTHDATA_PASSWORD environment variable\")"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "earthaccess.login(persist=True)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "results, gdf = hypercoast.search_pace(\n",
+    "    bounding_box=(-83, 25, -81, 28),\n",
+    "    temporal=(\"2024-07-30\", \"2024-08-15\"),\n",
+    "    short_name=\"PACE_OCI_L2_AOP_NRT\",\n",
+    "    count=10,\n",
+    "    return_gdf=True,\n",
+    ")"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "hypercoast.download_pace(results[:1], out_dir=\"data\")"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "filepath = \"data/PACE_OCI.20240730T181157.L2.OC_AOP.V2_0.NRT.nc\"\n",
+    "if not os.path.exists(filepath):\n",
+    "    raise FileNotFoundError(filepath)"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "hyper",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.10.14"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}

docs/examples/field_data.ipynb

@@ -34,7 +34,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "Download a sample filed dataset."
+    "Download a sample dataset."
    ]
   },
   {

docs/examples/hypoxia.ipynb

@@ -0,0 +1,151 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "[![image](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/opengeos/HyperCoast/blob/main/docs/examples/hypoxia.ipynb)\n",
+    "\n",
+    "# Visualizing Hypoxia Cruise Sampling Locations in the Gulf of Mexico"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# %pip install -U openpyxl hypercoast"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import pandas as pd\n",
+    "import hypercoast"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "url = \"https://github.com/opengeos/datasets/releases/download/hypercoast/Hypoxia_Data_Sheet.xlsx\"\n",
+    "xls_path = \"data/Hypoxia_Data_Sheet.xlsx\"\n",
+    "hypercoast.download_file(url, xls_path, overwrite=True)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "df = pd.read_excel(xls_path)\n",
+    "df.head()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "df_filtered = df.dropna(subset=[\"Lon\", \"Lat\"]).reset_index(drop=True)\n",
+    "df_filtered.head()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "url = (\n",
+    "    \"https://github.com/opengeos/datasets/releases/download/hypercoast/Hypoxia_Path.kml\"\n",
+    ")\n",
+    "kml_path = \"data/Hypoxia_Path.kml\"\n",
+    "hypercoast.download_file(url, kml_path)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "url = \"https://github.com/opengeos/datasets/releases/download/hypercoast/PACE_OCI.20240730T181157.L2.OC_AOP.V2_0.NRT.nc\"\n",
+    "filepath = \"data/PACE_OCI.20240730T181157.L2.OC_AOP.V2_0.NRT.nc\"\n",
+    "hypercoast.download_file(url, filepath)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "dataset = hypercoast.read_pace(filepath)\n",
+    "# dataset"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "m = hypercoast.Map()\n",
+    "m.add_basemap(\"Hybrid\")\n",
+    "wavelengths = [450, 550, 650]\n",
+    "m.add_pace(\n",
+    "    dataset, wavelengths, indexes=[3, 2, 1], vmin=0, vmax=0.02, layer_name=\"PACE\"\n",
+    ")\n",
+    "m.add(\"spectral\")\n",
+    "style = {\"weight\": 2, \"color\": \"red\"}\n",
+    "m.add_kml(kml_path, style=style, layer_name=\"Hypoxia Path\", info_mode=None)\n",
+    "m.add_points_from_xy(\n",
+    "    df_filtered,\n",
+    "    x=\"Lon\",\n",
+    "    y=\"Lat\",\n",
+    "    max_cluster_radius=50,\n",
+    "    layer_name=\"Hypoxia Data Points\",\n",
+    ")\n",
+    "m.set_center(-91.46118, 28.89758, zoom=8)\n",
+    "m"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "![image](https://github.com/user-attachments/assets/9a4bc3b7-2a69-4a94-a4f8-297103cb80d3)"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "hyper",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.10.14"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}

docs/examples/jupytext.toml

@@ -0,0 +1,9 @@
+# Install jupytext using: conda install jupytext -c conda-forge
+# Always pair ipynb notebooks to md files.
+# formats = "ipynb,md"
+formats = "ipynb,myst"
+
+# jupytext --to ipynb *.md                        # convert all .md files to notebooks with no outputs
+# jupytext --to ipynb --execute *.md              # convert all .md files to notebooks and execute them
+# jupytext --set-formats ipynb,md --execute *.md  # convert all .md files to paired notebooks and execute them
+# jupytext --to md *.ipynb                        # convert all .ipynb files to .md files

docs/examples/pace.ipynb

@@ -42,7 +42,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "url = \"https://github.com/opengeos/datasets/releases/download/netcdf/PACE_OCI.20240423T184658.L2.OC_AOP.V1_0_0.NRT.nc\""
+    "url = \"https://github.com/opengeos/datasets/releases/download/hypercoast/PACE_OCI.20240730T181157.L2.OC_AOP.V2_0.NRT.nc\""
    ]
   },
   {
@@ -51,8 +51,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "# filepath = \"data/PACE_OCI.20240423T184658.L2.OC_AOP.V1_0_0.NRT.nc\"\n",
-    "filepath = \"data/PACE_OCI.20240423T184658.L2.OC_AOP.V1_0_0.NRT.nc\"\n",
+    "filepath = \"data/PACE_OCI.20240730T181157.L2.OC_AOP.V2_0.NRT.nc\"\n",
     "hypercoast.download_file(url, filepath)"
    ]
   },
@@ -133,9 +132,9 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "latitude = 25.493961\n",
-    "longitude = -91.25617\n",
-    "hypercoast.filter_pace(dataset, latitude, longitude, return_plot=True)"
+    "latitude = 29.9307\n",
+    "longitude = -87.9106\n",
+    "hypercoast.extract_pace(dataset, latitude, longitude, return_plot=True)"
    ]
   },
   {
@@ -151,8 +150,8 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "latitude = (25.49, 25.50)\n",
-    "longitude = (-92, -91.055)\n",
+    "latitude = (29.49, 29.50)\n",
+    "longitude = (-88.10, -88.00)\n",
     "hypercoast.filter_pace(dataset, latitude, longitude, return_plot=True)"
    ]
   },
@@ -232,7 +231,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.11.9"
+   "version": "3.10.14"
   }
  },
  "nbformat": 4,