ioc: Initial implementation

Fixes oceanmodeling#5
Fixes oceanmodeling#24

examples/IOC_data.ipynb

@@ -0,0 +1,233 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "65e90d8f-6d7d-4fd2-b700-2ab7854ceb55",
+   "metadata": {
+    "tags": []
+   },
+   "outputs": [],
+   "source": [
+    "import logging\n",
+    "\n",
+    "import shapely\n",
+    "import geopandas as gpd\n",
+    "import matplotlib.pyplot as plt\n",
+    "import pandas as pd\n",
+    "import xarray as xr\n",
+    "\n",
+    "from searvey import ioc\n",
+    "\n",
+    "logging.basicConfig(\n",
+    "    level=20,\n",
+    "    style=\"{\",\n",
+    "    format=\"{asctime:s}; {levelname:8s}; {threadName:23s}; {name:<25s} {lineno:5d}; {message:s}\",\n",
+    ")\n",
+    "\n",
+    "logging.getLogger(\"urllib3\").setLevel(30)\n",
+    "logging.getLogger(\"parso\").setLevel(30)\n",
+    "\n",
+    "logger = logging.getLogger(__name__)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "3d77b75b-17db-45e7-933d-ea7f79351f28",
+   "metadata": {
+    "execution": {
+     "iopub.execute_input": "2022-06-08T12:43:45.973799Z",
+     "iopub.status.busy": "2022-06-08T12:43:45.973432Z",
+     "iopub.status.idle": "2022-06-08T12:43:51.596147Z",
+     "shell.execute_reply": "2022-06-08T12:43:51.595523Z",
+     "shell.execute_reply.started": "2022-06-08T12:43:45.973779Z"
+    },
+    "tags": []
+   },
+   "source": [
+    "## Retrieve Station Metadata"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "f0cb443c-b8a9-4abc-9bb1-e0c6e262e48b",
+   "metadata": {
+    "tags": []
+   },
+   "outputs": [],
+   "source": [
+    "ioc_stations = ioc.get_ioc_stations()\n",
+    "ioc_stations"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "1fabbee2-b165-46a6-b69f-c3bb93972e80",
+   "metadata": {
+    "tags": []
+   },
+   "outputs": [],
+   "source": [
+    "figure, axis = plt.subplots(1, 1)\n",
+    "figure.set_size_inches(12, 12 / 1.61803398875)\n",
+    "\n",
+    "countries = gpd.read_file(gpd.datasets.get_path('naturalearth_lowres'))\n",
+    "_ = countries.plot(color='lightgrey', ax=axis, zorder=-1)\n",
+    "_ = ioc_stations.plot(ax=axis)\n",
+    "_ = axis.set_title(f'all IOC stations')"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "10cf3a7b-8b1b-4b4d-a77e-c3d4f21e743e",
+   "metadata": {
+    "tags": []
+   },
+   "outputs": [],
+   "source": [
+    "ioc_stations.columns"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "d34d10c6-8354-451d-8580-169e2cc001cf",
+   "metadata": {
+    "execution": {
+     "iopub.execute_input": "2022-06-08T12:50:03.778509Z",
+     "iopub.status.busy": "2022-06-08T12:50:03.778244Z",
+     "iopub.status.idle": "2022-06-08T12:50:03.811163Z",
+     "shell.execute_reply": "2022-06-08T12:50:03.810727Z",
+     "shell.execute_reply.started": "2022-06-08T12:50:03.778483Z"
+    },
+    "tags": []
+   },
+   "source": [
+    "## Retrieve station metadata from arbitrary polygon"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "85bb38cc-652b-4d7e-9d1a-8fb8edaecc9c",
+   "metadata": {
+    "tags": []
+   },
+   "outputs": [],
+   "source": [
+    "east_coast = shapely.geometry.box(-85, 25, -65, 45)\n",
+    "east_coast\n",
+    "\n",
+    "east_stations = ioc.get_ioc_stations(region=east_coast)\n",
+    "east_stations"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "3e19b4f0-665a-40d7-b070-91be9b359229",
+   "metadata": {
+    "tags": []
+   },
+   "outputs": [],
+   "source": [
+    "east_stations[~east_stations.contacts.str.contains(\"NOAA\")]"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "28065b99-94cd-4182-ba27-95d6cd61b4a3",
+   "metadata": {},
+   "source": [
+    "## Retrieve IOC station data"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "f2499f27-a993-4906-83d5-43374a92bb58",
+   "metadata": {
+    "tags": []
+   },
+   "outputs": [],
+   "source": [
+    "east_data = ioc.get_ioc_data(\n",
+    "    ioc_metadata=east_stations,\n",
+    "    endtime=\"2020-05-30\",\n",
+    "    period=3,\n",
+    ")\n",
+    "east_data"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "5cf3a9bb-af44-4935-9c0d-0abc51dffed3",
+   "metadata": {
+    "tags": []
+   },
+   "outputs": [],
+   "source": [
+    "def drop_all_nan_vars(ds: xr.Dataset) -> xr.Dataset:\n",
+    "    for var in ds.data_vars:\n",
+    "        if ds[var].notnull().sum() == 0:\n",
+    "            ds = ds.drop_vars(var)\n",
+    "    return ds\n",
+    "\n",
+    "ds = drop_all_nan_vars(east_data.sel(ioc_code=\"setp1\"))\n",
+    "ds"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "bcf72745-a293-4850-9a79-0191569bd556",
+   "metadata": {
+    "tags": []
+   },
+   "outputs": [],
+   "source": [
+    "fix, axes = plt.subplots(1, 1)\n",
+    "\n",
+    "_ = ds.prs.plot(ax=axes)\n",
+    "_ = ds.rad.plot(ax=axes)\n",
+    "_ = ds.ra2.plot(ax=axes)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "acaf9a46-e5bf-4b52-a73f-05566219bed1",
+   "metadata": {
+    "tags": []
+   },
+   "outputs": [],
+   "source": [
+    "ds.where(ds.country == \"Bahamas\")"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "searvey",
+   "language": "python",
+   "name": "searvey"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.9.12"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}

pyproject.toml

@@ -43,6 +43,11 @@ geopandas = "^0.10"
 typepigeon = "^1"
 xarray = "^2022.3"
 Shapely = "^1.8"
+limits = "^2.6"
+tqdm = "^4.64"
+html5lib = "^1.1"
+lxml = "^4.9"
+more-itertools = "^8.0"
 
 [tool.poetry.dev-dependencies]
 ipykernel = "*"
@@ -56,6 +61,7 @@ pytest-recording = "^0.12.0"
 types-requests = "^2.26"
 sphinx = '*'
 sphinx-rtd-theme = '*'
+importlib-metadata = "^4.11.4"
 
 [tool.poetry.extras]
 linting = ["mypy", "prospector"]
@@ -70,6 +76,11 @@ target-version = ['py39']
 minversion = "7.0"
 addopts = "-ra --verbose --showlocals --tb=short --cov=searvey --cov-report term-missing"
 testpaths = ["tests"]
+log_cli = true
+filterwarnings = [
+    'ignore:distutils Version classes are deprecated. Use packaging.version instead:DeprecationWarning',
+]
+
 
 [tool.mypy]
 python_version = "3.9"