I7 parameters

.github/workflows/python-ci.yml

@@ -23,13 +23,5 @@ jobs:
         pip install -U pip pytest
         pip install -r requirements.txt
         pip install -e .[dev]
-    - name: Test with pytest (full)
-      if: github.ref == 'refs/heads/master'
-      run: |
-        py.test -v
-    - name: Test with pytest (fast)
-      if: github.ref != 'refs/heads/master'
-      run: |
-        py.test -m "not slow" -v
     - name: Code Quality
       run: black . --check

notebooks/demo_individual/demo_convolution.ipynb

@@ -0,0 +1,229 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from birdy import WPSClient\n",
+    "from pkg_resources import resource_filename\n",
+    "\n",
+    "import requests"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import os \n",
+    "while os.path.basename(os.getcwd()) != \"osprey\": # Ensure current directory is always 'osprey'\n",
+    "    os.chdir('../')"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Set up wps application\n",
+    "url = 'http://localhost:5002/wps'\n",
+    "osprey = WPSClient(url=url)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "\u001b[0;31mType:\u001b[0m            WPSClient\n",
+       "\u001b[0;31mString form:\u001b[0m     <birdy.client.base.WPSClient object at 0x7f83da86d390>\n",
+       "\u001b[0;31mFile:\u001b[0m            ~/Desktop/osprey/venv/lib/python3.7/site-packages/birdy/client/base.py\n",
+       "\u001b[0;31mDocstring:\u001b[0m      \n",
+       "A Web Processing Service for Climate Data Analysis.\n",
+       "\n",
+       "Processes\n",
+       "---------\n",
+       "\n",
+       "convolution\n",
+       "    Aggregates the flow contribution from all upstream grid cellsat every timestep lagged according the Impuls Response Functions.\n",
+       "\u001b[0;31mClass docstring:\u001b[0m\n",
+       "Returns a class where every public method is a WPS process available at\n",
+       "the given url.\n",
+       "\n",
+       "Example:\n",
+       "    >>> emu = WPSClient(url='<server url>')\n",
+       "    >>> emu.hello('stranger')\n",
+       "    'Hello stranger'\n",
+       "\u001b[0;31mInit docstring:\u001b[0m \n",
+       "Args:\n",
+       "    url (str): Link to WPS provider. config (Config): an instance\n",
+       "    processes: Specify a subset of processes to bind. Defaults to all\n",
+       "        processes.\n",
+       "    converters (dict): Correspondence of {mimetype: class} to convert\n",
+       "        this mimetype to a python object.\n",
+       "    username (str): passed to :class:`owslib.wps.WebProcessingService`\n",
+       "    password (str): passed to :class:`owslib.wps.WebProcessingService`\n",
+       "    headers (str): passed to :class:`owslib.wps.WebProcessingService`\n",
+       "    auth (requests.auth.AuthBase): requests-style auth class to authenticate,\n",
+       "        see https://2.python-requests.org/en/master/user/authentication/\n",
+       "    verify (bool): passed to :class:`owslib.wps.WebProcessingService`\n",
+       "    cert (str): passed to :class:`owslib.wps.WebProcessingService`\n",
+       "    verbose (str): passed to :class:`owslib.wps.WebProcessingService`\n",
+       "    progress (bool): If True, enable interactive user mode.\n",
+       "    version (str): WPS version to use.\n"
+      ]
+     },
+     "metadata": {},
+     "output_type": "display_data"
+    }
+   ],
+   "source": [
+    "# Check wps info\n",
+    "osprey?"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "\u001b[0;31mSignature:\u001b[0m \u001b[0mosprey\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mconvolution\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mconfig\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mloglevel\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;34m'INFO'\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
+       "\u001b[0;31mDocstring:\u001b[0m\n",
+       "Aggregates the flow contribution from all upstream grid cellsat every timestep lagged according the Impuls Response Functions.\n",
+       "\n",
+       "Parameters\n",
+       "----------\n",
+       "config : string\n",
+       "    Path to input configuration file or input dictionary\n",
+       "loglevel : {'CRITICAL', 'ERROR', 'WARNING', 'INFO', 'DEBUG', 'NOTSET'}string\n",
+       "    Logging level\n",
+       "\n",
+       "Returns\n",
+       "-------\n",
+       "output : ComplexData:mimetype:`application/x-netcdf`\n",
+       "    Output Netcdf File\n",
+       "\u001b[0;31mFile:\u001b[0m      ~/Desktop/osprey/</home/sangwonl/Desktop/osprey/venv/lib/python3.7/site-packages/birdy/client/base.py-1>\n",
+       "\u001b[0;31mType:\u001b[0m      method\n"
+      ]
+     },
+     "metadata": {},
+     "output_type": "display_data"
+    }
+   ],
+   "source": [
+    "# Check info on `convolution` process\n",
+    "osprey.convolution?"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "/home/sangwonl/Desktop/osprey/tests/configs/convolve_opendap.cfg\n"
+     ]
+    }
+   ],
+   "source": [
+    "cfg_file = resource_filename(\"tests\", \"configs/convolve_opendap.cfg\")\n",
+    "print(cfg_file)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [
+    {
+     "ename": "HTTPError",
+     "evalue": "500 Server Error: INTERNAL SERVER ERROR for url: http://localhost:5002/wps",
+     "output_type": "error",
+     "traceback": [
+      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
+      "\u001b[0;31mHTTPError\u001b[0m                                 Traceback (most recent call last)",
+      "\u001b[0;32m<ipython-input-18-0e0dd8b97e55>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m\u001b[0m\n\u001b[1;32m      1\u001b[0m \u001b[0;31m# generate convolution\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m      2\u001b[0m output = osprey.convolution(\n\u001b[0;32m----> 3\u001b[0;31m     \u001b[0mconfig\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mcfg_file\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m      4\u001b[0m )\n",
+      "\u001b[0;32m</home/sangwonl/Desktop/osprey/venv/lib/python3.7/site-packages/birdy/client/base.py-1>\u001b[0m in \u001b[0;36mconvolution\u001b[0;34m(self, config, loglevel)\u001b[0m\n",
+      "\u001b[0;32m~/Desktop/osprey/venv/lib/python3.7/site-packages/birdy/client/base.py\u001b[0m in \u001b[0;36m_execute\u001b[0;34m(self, pid, **kwargs)\u001b[0m\n\u001b[1;32m    291\u001b[0m         \u001b[0;32mtry\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    292\u001b[0m             wps_response = self._wps.execute(\n\u001b[0;32m--> 293\u001b[0;31m                 \u001b[0mpid\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0minputs\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mwps_inputs\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0moutput\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mwps_outputs\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mmode\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mmode\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m    294\u001b[0m             )\n\u001b[1;32m    295\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n",
+      "\u001b[0;32m~/Desktop/osprey/venv/lib/python3.7/site-packages/owslib/wps.py\u001b[0m in \u001b[0;36mexecute\u001b[0;34m(self, identifier, inputs, output, mode, lineage, request, response)\u001b[0m\n\u001b[1;32m    357\u001b[0m         \u001b[0;31m# submit the request to the live server\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    358\u001b[0m         \u001b[0;32mif\u001b[0m \u001b[0mresponse\u001b[0m \u001b[0;32mis\u001b[0m \u001b[0;32mNone\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 359\u001b[0;31m             \u001b[0mresponse\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mexecution\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msubmitRequest\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mrequest\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m    360\u001b[0m         \u001b[0;32melse\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    361\u001b[0m             \u001b[0mresponse\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0metree\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mfromstring\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mresponse\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
+      "\u001b[0;32m~/Desktop/osprey/venv/lib/python3.7/site-packages/owslib/wps.py\u001b[0m in \u001b[0;36msubmitRequest\u001b[0;34m(self, request)\u001b[0m\n\u001b[1;32m    910\u001b[0m         \u001b[0mreader\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mWPSExecuteReader\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mverbose\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mverbose\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mtimeout\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mtimeout\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mauth\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mauth\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    911\u001b[0m         response = reader.readFromUrl(\n\u001b[0;32m--> 912\u001b[0;31m             self.url, request, method='Post', headers=self.headers)\n\u001b[0m\u001b[1;32m    913\u001b[0m         \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mresponse\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mresponse\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    914\u001b[0m         \u001b[0;32mreturn\u001b[0m \u001b[0mresponse\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
+      "\u001b[0;32m~/Desktop/osprey/venv/lib/python3.7/site-packages/owslib/wps.py\u001b[0m in \u001b[0;36mreadFromUrl\u001b[0;34m(self, url, data, method, username, password, headers, verify, cert)\u001b[0m\n\u001b[1;32m    601\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    602\u001b[0m         return self._readFromUrl(url, data, self.timeout, method, username=username, password=password,\n\u001b[0;32m--> 603\u001b[0;31m                                  headers=headers, verify=verify, cert=cert)\n\u001b[0m\u001b[1;32m    604\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    605\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n",
+      "\u001b[0;32m~/Desktop/osprey/venv/lib/python3.7/site-packages/owslib/wps.py\u001b[0m in \u001b[0;36m_readFromUrl\u001b[0;34m(self, url, data, timeout, method, username, password, headers, verify, cert)\u001b[0m\n\u001b[1;32m    513\u001b[0m             u = openURL(url, data, method='Post',\n\u001b[1;32m    514\u001b[0m                         \u001b[0musername\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mauth\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0musername\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mpassword\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mauth\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mpassword\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 515\u001b[0;31m                         headers=headers, verify=self.auth.verify, cert=self.auth.cert, timeout=timeout)\n\u001b[0m\u001b[1;32m    516\u001b[0m             \u001b[0;32mreturn\u001b[0m \u001b[0metree\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mfromstring\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mu\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mread\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    517\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n",
+      "\u001b[0;32m~/Desktop/osprey/venv/lib/python3.7/site-packages/owslib/util.py\u001b[0m in \u001b[0;36mopenURL\u001b[0;34m(url_base, data, method, cookies, username, password, timeout, headers, verify, cert, auth)\u001b[0m\n\u001b[1;32m    207\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    208\u001b[0m     \u001b[0;32mif\u001b[0m \u001b[0mreq\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mstatus_code\u001b[0m \u001b[0;32min\u001b[0m \u001b[0;34m[\u001b[0m\u001b[0;36m404\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;36m500\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;36m502\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;36m503\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;36m504\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m:\u001b[0m    \u001b[0;31m# add more if needed\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 209\u001b[0;31m         \u001b[0mreq\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mraise_for_status\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m    210\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    211\u001b[0m     \u001b[0;31m# check for service exceptions without the http header set\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
+      "\u001b[0;32m~/Desktop/osprey/venv/lib/python3.7/site-packages/requests/models.py\u001b[0m in \u001b[0;36mraise_for_status\u001b[0;34m(self)\u001b[0m\n\u001b[1;32m    939\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    940\u001b[0m         \u001b[0;32mif\u001b[0m \u001b[0mhttp_error_msg\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 941\u001b[0;31m             \u001b[0;32mraise\u001b[0m \u001b[0mHTTPError\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mhttp_error_msg\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mresponse\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m    942\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    943\u001b[0m     \u001b[0;32mdef\u001b[0m \u001b[0mclose\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
+      "\u001b[0;31mHTTPError\u001b[0m: 500 Server Error: INTERNAL SERVER ERROR for url: http://localhost:5002/wps"
+     ]
+    }
+   ],
+   "source": [
+    "# generate convolution\n",
+    "output = osprey.convolution(\n",
+    "    config = cfg_file\n",
+    ")"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "convolutionResponse(\n",
+       "    output='http://localhost:5002/outputs/005d478c-cc6b-11ea-abd3-503eaa25cee0/sample.rvic.h0a.2013-01-01.nc'\n",
+       ")"
+      ]
+     },
+     "execution_count": null,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "output.get()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
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+   "mimetype": "text/x-python",
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+   "pygments_lexer": "ipython3",
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+ },
+ "nbformat": 4,
+ "nbformat_minor": 4
+}