Merge pull request #18 from eWaterCycle/grpc4bmi-refactor

Update notebooks to use grpc4bmi==0.2.12 api
eWaterCycle · Apr 2, 2021 · c0e56bd · c0e56bd
2 parents 339de56 + 49be0a7
commit c0e56bd
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Showing 6 changed files with 103 additions and 71 deletions.
diff --git a/pcrglob/pcrg-bmi-docker-psfetch.ipynb b/pcrglob/pcrg-bmi-docker-psfetch.ipynb
@@ -15,7 +15,9 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from ewatercycle.parametersetdb import build_from_urls"
+    "from ewatercycle.parametersetdb import build_from_urls\n",
+    "from os.path import abspath\n",
+    "from os import mkdir"
    ]
   },
   {
@@ -35,29 +37,57 @@
    "cell_type": "code",
    "execution_count": 3,
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "ename": "Exception",
+     "evalue": "Target directory already exists, will not overwrite",
+     "output_type": "error",
+     "traceback": [
+      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
+      "\u001b[0;31mException\u001b[0m                                 Traceback (most recent call last)",
+      "\u001b[0;32m<ipython-input-3-af844e59bad5>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m\u001b[0m\n\u001b[1;32m      1\u001b[0m \u001b[0minput_dir\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mabspath\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m'./input'\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 \u001b[0;31m# Write data files required by model to './input'\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m----> 3\u001b[0;31m \u001b[0mparameter_set\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msave_datafiles\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0minput_dir\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m",
+      "\u001b[0;32m~/git/eWaterCycle/grpc4bmi-examples/env/lib/python3.8/site-packages/ewatercycle/parametersetdb/__init__.py\u001b[0m in \u001b[0;36msave_datafiles\u001b[0;34m(self, target)\u001b[0m\n\u001b[1;32m     22\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m     23\u001b[0m         \"\"\"\n\u001b[0;32m---> 24\u001b[0;31m         \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mdf\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msave\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mtarget\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     25\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m     26\u001b[0m     \u001b[0;32mdef\u001b[0m \u001b[0msave_config\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mtarget\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;32m~/git/eWaterCycle/grpc4bmi-examples/env/lib/python3.8/site-packages/ewatercycle/parametersetdb/datafiles.py\u001b[0m in \u001b[0;36msave\u001b[0;34m(self, target)\u001b[0m\n\u001b[1;32m     32\u001b[0m     \u001b[0;32mdef\u001b[0m \u001b[0msave\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mtarget\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     33\u001b[0m         \u001b[0;32mif\u001b[0m \u001b[0mos\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mpath\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mexists\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mtarget\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;32m---> 34\u001b[0;31m             \u001b[0;32mraise\u001b[0m \u001b[0mException\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m'Target directory already exists, will not overwrite'\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     35\u001b[0m         \u001b[0msubprocess\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mcheck_call\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;34m'svn'\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m'export'\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msource\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mtarget\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     36\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n",
+      "\u001b[0;31mException\u001b[0m: Target directory already exists, will not overwrite"
+     ]
+    }
+   ],
    "source": [
+    "input_dir = abspath('./input')\n",
     "# Write data files required by model to './input'\n",
-    "parameter_set.save_datafiles('./input')"
+    "parameter_set.save_datafiles(input_dir)"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 3,
+   "execution_count": 4,
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "ename": "FileExistsError",
+     "evalue": "[Errno 17] File exists: './output'",
+     "output_type": "error",
+     "traceback": [
+      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
+      "\u001b[0;31mFileExistsError\u001b[0m                           Traceback (most recent call last)",
+      "\u001b[0;32m<ipython-input-4-8b84d990e09f>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m\u001b[0m\n\u001b[1;32m      5\u001b[0m \u001b[0mparameter_set\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mconfig\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;34m'globalOptions'\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;34m'outputDir'\u001b[0m\u001b[0;34m]\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mabspath\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m'./output'\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m      6\u001b[0m \u001b[0mparameter_set\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msave_config\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m'pcrg_rhinemeuse_ps.ini'\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m----> 7\u001b[0;31m \u001b[0mmkdir\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m'./output'\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m",
+      "\u001b[0;31mFileExistsError\u001b[0m: [Errno 17] File exists: './output'"
+     ]
+    }
+   ],
    "source": [
     "# Overwrite items in config file\n",
     "# parameter_set.config for this model is a configparser.ConfigParser object\n",
     "# inputDir and outputDir must be inside /data because grpc4bmi will mount input_dir output_dir as such inside container\n",
-    "parameter_set.config['globalOptions']['inputDir'] = '/data/input'\n",
-    "parameter_set.config['globalOptions']['outputDir'] = '/data/output'\n",
-    "parameter_set.save_config('pcrg_rhinemeuse_ps.ini')"
+    "parameter_set.config['globalOptions']['inputDir'] = input_dir\n",
+    "parameter_set.config['globalOptions']['outputDir'] = abspath('./output')\n",
+    "parameter_set.save_config('pcrg_rhinemeuse_ps.ini')\n",
+    "mkdir('./output')"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 1,
+   "execution_count": 5,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -66,18 +96,19 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 2,
+   "execution_count": 6,
    "metadata": {},
    "outputs": [],
    "source": [
     "pcrg = BmiClientDocker(image='ewatercycle/pcrg-grpc4bmi:latest', image_port=55555, \n",
-    "                       input_dir=\"./input\", \n",
-    "                       output_dir=\"./output\")"
+    "                       input_dirs=(input_dir,),\n",
+    "                       remove=True,\n",
+    "                       work_dir=\".\")"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 3,
+   "execution_count": 7,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -307,13 +338,13 @@
     {
      "ename": "NameError",
      "evalue": "name 'variable_overtime' is not defined",
+     "output_type": "error",
      "traceback": [
       "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
       "\u001b[0;31mNameError\u001b[0m                                 Traceback (most recent call last)",
       "\u001b[0;32m<ipython-input-30-9cd201c1607b>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m()\u001b[0m\n\u001b[1;32m      7\u001b[0m \u001b[0mp\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mfigure\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mplot_width\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;36m800\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mplot_height\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;36m400\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mx_axis_type\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;34m\"datetime\"\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m      8\u001b[0m \u001b[0mp\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mxaxis\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0maxis_label\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mvariable\u001b[0m \u001b[0;34m+\u001b[0m \u001b[0;34m'['\u001b[0m \u001b[0;34m+\u001b[0m \u001b[0munit\u001b[0m \u001b[0;34m+\u001b[0m \u001b[0;34m']'\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m----> 9\u001b[0;31m \u001b[0mp\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mline\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0mcftime\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mnum2date\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0md\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;36m0\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mtime_unit\u001b[0m\u001b[0;34m)\u001b[0m \u001b[0;32mfor\u001b[0m \u001b[0md\u001b[0m \u001b[0;32min\u001b[0m \u001b[0mvariable_overtime\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m[\u001b[0m\u001b[0md\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;36m1\u001b[0m\u001b[0;34m]\u001b[0m \u001b[0;32mfor\u001b[0m \u001b[0md\u001b[0m \u001b[0;32min\u001b[0m \u001b[0mvariable_overtime\u001b[0m\u001b[0;34m]\u001b[0m \u001b[0;34m,\u001b[0m \u001b[0mline_width\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;36m2\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m     10\u001b[0m \u001b[0mshow\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mp\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
       "\u001b[0;31mNameError\u001b[0m: name 'variable_overtime' is not defined"
-     ],
-     "output_type": "error"
+     ]
     }
    ],
    "source": [
@@ -576,6 +607,15 @@
     "Z"
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": 11,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "del pcrg"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,
@@ -600,9 +640,9 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.6.5"
+   "version": "3.8.5"
   }
  },
  "nbformat": 4,
- "nbformat_minor": 2
+ "nbformat_minor": 4
 }
diff --git a/requirements.txt b/requirements.txt
@@ -1,6 +1,5 @@
-#grpc4bmi
-git+https://github.com/eWaterCycle/grpc4bmi#egg=grpc4bmi
-git+https://github.com/eWaterCycle/parametersetdb#egg=ewatercylce.parametersetdb
+grpc4bmi==0.2.12
+git+https://github.com/eWaterCycle/ewatercycle
 jupyterlab
 matplotlib
 docker

diff --git a/toymodel/toymodel-bmi-docker.ipynb b/toymodel/toymodel-bmi-docker.ipynb
@@ -48,7 +48,7 @@
    "outputs": [],
    "source": [
     "model = BmiClientDocker(image=\"ewatercycle/toymodel:latest\", image_port=55555, \n",
-    "                        input_dir=\"./data\")"
+    "                        work_dir=\"./data\")"
    ]
   },
   {
@@ -188,4 +188,4 @@
  },
  "nbformat": 4,
  "nbformat_minor": 2
-}
+}