Move pip installs from notebooks to Dockerfile and configure sentinelhub auth in .netrc

.dockerignore

@@ -1,4 +1,8 @@
 # don't send downloaded artefacts to the docker build daemon
+*.zip
+*.tiff
+*.jp2
+
 **/input/**/*.zip
 **/input/**/*.SAFE*
 **/input/**/*.jp2

.gitignore

@@ -1,8 +1,15 @@
+# avoid exposing secrets
+.netrc
+
 # ignore any raster files
+*.jp2
 *.tiff
 *.zip
 *.SAFE
 
+.jupyter
+.local
+
 # Created by https://www.toptal.com/developers/gitignore/api/python,jupyternotebooks
 # Edit at https://www.toptal.com/developers/gitignore?templates=python,jupyternotebooks
 

.netrc.example

@@ -0,0 +1,3 @@
+machine scihub.copernicus.eu
+login your_username
+password your_password

Cotbusser Ostsee/00 Download.ipynb

@@ -7,40 +7,6 @@
     "Flutungsbeginn war der 12.4.2019. Wir versuchen mit Daten der Sentinel-1- und -2-Satelliten nachzuvollziehen, wie hoch der Wasserstand zum jeweiligen Zeitpunkt war."
    ]
   },
-  {
-   "cell_type": "code",
-   "execution_count": 1,
-   "metadata": {},
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "Collecting sentinelsat\n",
-      "  Using cached https://files.pythonhosted.org/packages/5c/79/c2ac7b71dd13db95a9b83865bbbc7f1e4359c2b141bedad21b0e181fa06e/sentinelsat-0.13-py2.py3-none-any.whl\n",
-      "Requirement already satisfied: click in /home/rus/.anaconda/lib/python3.7/site-packages (from sentinelsat) (7.0)\n",
-      "Collecting html2text\n",
-      "  Downloading https://files.pythonhosted.org/packages/ae/88/14655f727f66b3e3199f4467bafcc88283e6c31b562686bf606264e09181/html2text-2020.1.16-py3-none-any.whl\n",
-      "Requirement already satisfied: six in /home/rus/.anaconda/lib/python3.7/site-packages (from sentinelsat) (1.14.0)\n",
-      "Collecting geomet\n",
-      "  Downloading https://files.pythonhosted.org/packages/c9/81/156ca48f950f833ddc392f8e3677ca50a18cb9d5db38ccb4ecea55a9303f/geomet-0.2.1.post1-py3-none-any.whl\n",
-      "Collecting geojson>=2\n",
-      "  Using cached https://files.pythonhosted.org/packages/e4/8d/9e28e9af95739e6d2d2f8d4bef0b3432da40b7c3588fbad4298c1be09e48/geojson-2.5.0-py2.py3-none-any.whl\n",
-      "Requirement already satisfied: tqdm in /home/rus/.anaconda/lib/python3.7/site-packages (from sentinelsat) (4.36.1)\n",
-      "Requirement already satisfied: requests in /home/rus/.anaconda/lib/python3.7/site-packages (from sentinelsat) (2.22.0)\n",
-      "Requirement already satisfied: chardet<3.1.0,>=3.0.2 in /home/rus/.anaconda/lib/python3.7/site-packages (from requests->sentinelsat) (3.0.4)\n",
-      "Requirement already satisfied: certifi>=2017.4.17 in /home/rus/.anaconda/lib/python3.7/site-packages (from requests->sentinelsat) (2019.11.28)\n",
-      "Requirement already satisfied: urllib3!=1.25.0,!=1.25.1,<1.26,>=1.21.1 in /home/rus/.anaconda/lib/python3.7/site-packages (from requests->sentinelsat) (1.24.2)\n",
-      "Requirement already satisfied: idna<2.9,>=2.5 in /home/rus/.anaconda/lib/python3.7/site-packages (from requests->sentinelsat) (2.8)\n",
-      "Installing collected packages: html2text, geomet, geojson, sentinelsat\n",
-      "Successfully installed geojson-2.5.0 geomet-0.2.1.post1 html2text-2020.1.16 sentinelsat-0.13\n"
-     ]
-    }
-   ],
-   "source": [
-    "! pip install sentinelsat"
-   ]
-  },
   {
    "cell_type": "code",
    "execution_count": 47,
@@ -50,12 +16,11 @@
     "from sentinelsat import SentinelAPI, read_geojson, geojson_to_wkt\n",
     "from datetime import date\n",
     "\n",
-    "user = 'heyarne'\n",
+    "# set up ~/.netrc using the provided ~/.netrc.example in order to be properly authenticated\n",
-    "password='FhnNfPppxNbBm7wCoCGLnfly'\n",
+    "api = SentinelAPI(None, None)\n",
-    "api = SentinelAPI(user, password)\n",
     "\n",
     "# the \"footprint\" is what we can use to preselect a certain area;\n",
-    "# the lake is at (51.7874, 14.4226)\n",
+    "# the lakesentinelsat/ is at (51.7874, 14.4226)\n",
     "footprint = 'POLYGON((14.359428613281251 51.806620319822734,14.466545312500001 51.806620319822734,14.466545312500001 51.757343872357566,14.359428613281251 51.757343872357566,14.359428613281251 51.806620319822734))'"
    ]
   },
@@ -44091,15 +44056,6 @@
     "    f.write('\\n'.join([p['link'] for _, p in products.items()]))"
    ]
   },
-  {
-   "cell_type": "code",
-   "execution_count": 49,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "# ! aria2c --http-user={user} --http-passwd={password} -i link_list.txt"
-   ]
-  },
   {
    "cell_type": "code",
    "execution_count": null,
@@ -44124,7 +44080,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.7.4"
+   "version": "3.8.5"
   }
  },
  "nbformat": 4,

Cotbusser Ostsee/01 SNAP via Python.ipynb

@@ -78,21 +78,21 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 2",
+   "display_name": "Python 3",
    "language": "python",
-   "name": "python2"
+   "name": "python3"
   },
   "language_info": {
    "codemirror_mode": {
     "name": "ipython",
-    "version": 2
+    "version": 3
    },
    "file_extension": ".py",
    "mimetype": "text/x-python",
    "name": "python",
    "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython2",
+   "pygments_lexer": "ipython3",
-   "version": "2.7.12"
+   "version": "3.8.5"
   }
  },
  "nbformat": 4,

Dockerfile

@@ -3,6 +3,6 @@
 FROM jupyter/scipy-notebook
 ENV JUPYTER_LAB_ENABLE=1
 
-# RUN pip install geopandas sentinelsat==0.14 descartes && \
+RUN pip install geopandas==0.18.1 descartes=1.1.0 sentinelsat==0.14 rasterio==1.1.5 && \
-# 	fix-permissions $CONDA_DIR && \
+	fix-permissions $CONDA_DIR && \
-# 	fix-permissions /home/$NB_USER
+	fix-permissions /home/$NB_USER