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* Add PACE workshop notebook * Update PACE notebooks * Add hypoxia notebook * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Add openpyxl * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Add fiona and geopandas * Update PACE notebook * Update EARTHDATA secrets * Update NASA EARTHDATA API Key * Check file path * Add earthaccess login test * Use earthaccess.login * Fix os import error * Add earthaccess notebook * Add env variables * Update env variable * Update notebook * Update PACE notebook * Update PACE notebook * Deprecate Python 3.8 --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
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@@ -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: | ||
|
|
||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,120 @@ | ||
| { | ||
| "cells": [ | ||
| { | ||
| "cell_type": "markdown", | ||
| "metadata": {}, | ||
| "source": [ | ||
| "[](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 | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,151 @@ | ||
| { | ||
| "cells": [ | ||
| { | ||
| "cell_type": "markdown", | ||
| "metadata": {}, | ||
| "source": [ | ||
| "[](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": [ | ||
| "" | ||
| ] | ||
| } | ||
| ], | ||
| "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 | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -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 |
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