Merge pull request #59 from openearth/docker-maintenance

Docker maintenance

Dockerfile

@@ -2,22 +2,17 @@ FROM continuumio/miniconda3
 MAINTAINER Fedor Baart <[email protected]>
 ENV LANG=C.UTF-8 LC_ALL=C.UTF-8
 # update system and install wget
-RUN \
-    apt-get install -y apt-utils && \
-    echo "deb http://httpredir.debian.org/debian jessie-backports main non-free" >> /etc/apt/sources.list && \
-    echo "deb-src http://httpredir.debian.org/debian jessie-backports main non-free" >> /etc/apt/sources.list && \
-    apt-get update --fix-missing && \
-    apt-get install -y ffmpeg wget unzip
+RUN apt-get update --fix-missing && \
+	apt-get install -y ffmpeg wget unzip libglu1-mesa-dev gcc\
+	&& rm -rf /var/lib/apt/lists/*
 
-# install everything from condaforge
-RUN conda create -y -n py35 python=3.5
-RUN conda install -c conda-forge -n py35 mayavi libgdal gdal netcdf4 matplotlib scikit-image tqdm cython pillow click pandas
-# install flowmap in the new environment
+RUN conda install -c conda-forge libgdal gdal
 
+# install flowmap
 COPY ./ app/
-RUN /opt/conda/envs/py35/bin/pip install app/
+RUN pip install pip --upgrade
+RUN pip install -r app/requirements.txt
+RUN cd app/ && \
+	python setup.py install
 
-ENV PATH /opt/conda/bin:$PATH
-# not sure what this is
-ENTRYPOINT [ "/usr/bin/tini", "--" ]
-CMD [ "/opt/conda/envs/py35/bin/matroos_flowmap" ]
+CMD [ "/opt/conda/bin/matroos_flowmap" ]

bin/matroos_flowmap

@@ -26,12 +26,8 @@ shift $((OPTIND-1))
 # Generate a flowmap for matroos
 # expects wget, ffmpeg and the flowmap command to be available.
 
-# Fix a bug in anaconda gdal
-source activate py35
-export GDAL_DATA=$(gdal-config --datadir)
-
 # Mount EFS if set
-if [ -n $EFS ]
+if [ -n "$EFS" ]
 then
     mkdir /tmp/efs
     mount -t nfs4 -o nfsvers=4.1,rsize=1048576,wsize=1048576,hard,timeo=15,retrans=2 ${EFS}:/ /tmp/efs

requirements.txt

@@ -1,19 +1,18 @@
-Click>=6.0
-netCDF4==1.3.1
-scikit-image==0.13.1
-numpy==1.13.3
-scipy==1.0.0
-tqdm==4.19.5
-geojson==2.3.0
+Click==7.0
+mayavi==4.6.2
+netcdf4==1.4.2
+scikit-image==0.14.1
+numpy==1.15.4
+scipy==1.1.0
+tqdm==4.28.1
+geojson==2.4.1
 mako==1.0.7
-matplotlib==2.1.1
-pandas==0.21.1
-mayavi==4.5.0
-rasterio==0.36.0
-Mako==1.0.7
-scikit-image==0.13.1
-geojson==2.3.0
-tables==3.4.2
+matplotlib==3.0.2
+pandas==0.23.4
+rasterio==1.0.12
+geojson==2.4.1
 pyugrid==0.3.1
-Shapely==1.6.3
-simplejson==3.11.1
+Shapely==1.6.4
+simplejson==3.16.0
+cython==0.29.1
+pillow==5.3.0