Docker, Jp notebook configurations

.gitignore

@@ -1,4 +1,5 @@
 .DS_Store
+.env
 *.pyc
 __pycache__/
 ptenv/

Dockerfile

@@ -0,0 +1,12 @@
+FROM kuanb/peartree
+
+RUN mkdir /code && \
+    pip install numpy==1.14.0 scipy==1.0.0
+
+WORKDIR /code
+
+COPY requirements_dev.txt /code/
+RUN pip install -r requirements_dev.txt
+
+COPY requirements.txt /code/
+RUN pip install -r requirements.txt

Makefile

@@ -2,4 +2,21 @@ test:
 	PYTHONPATH=. MPLBACKEND="agg" coverage run --source peartree -m py.test --verbose
 
 performance:
-	PYTHONPATH=. MPLBACKEND="agg" pytest profiler/test_graph_assembly.py -s	
+	PYTHONPATH=. MPLBACKEND="agg" pytest profiler/test_graph_assembly.py -s
+
+notebook:
+	docker-compose build
+	mkdir -p ./notebooks
+	docker-compose up notebook
+
+docker-clean:
+	docker network prune --force
+	docker volume prune --force
+	docker image prune --force
+
+install-graph-tool:
+	sed -i -e '$$a\
+	deb http://downloads.skewed.de/apt/stretch stretch main\
+	deb-src http://downloads.skewed.de/apt/stretch stretch main' /etc/apt/sources.list && \
+	apt-get update && \
+	apt-get install python3-graph-tool

docker-compose.yml

@@ -0,0 +1,16 @@
+
+version: "3"
+
+services:
+
+  # Jupyter Notebook
+  notebook:
+    build:
+      context: .
+    env_file: .env
+    command: jupyter notebook --config jupyter_notebook_config.py
+    volumes:
+      - .:/code
+      - /tmp:/tmp
+    ports:
+      - "9797:9797"

docker/Dockerfile

@@ -0,0 +1,92 @@
+FROM python:3.6-stretch
+
+RUN mkdir -p /provisioning
+WORKDIR /provisioning
+
+# Install OS dependencies
+RUN apt-get update && apt-get install -y \
+      build-essential \
+      dialog \
+      curl \
+      less \
+      nano \
+      unzip \
+      vim \
+      gcc \
+      libgeos-dev \
+      zlib1g-dev && \
+    rm -rf /var/lib/apt/lists/*
+
+# Get libgeos for Python Shapely package
+# https://trac.osgeo.org/geos/
+ARG GEOS_VERSION=3.6.2
+RUN echo "Installing GEOS libraries..." && \
+    mkdir -p /provisioning/geos && \
+    cd /provisioning/geos && \
+    curl -# -O http://download.osgeo.org/geos/geos-${GEOS_VERSION}.tar.bz2 && \
+    tar -xjf geos-${GEOS_VERSION}.tar.bz2 && \
+    cd geos-${GEOS_VERSION} && \
+    ./configure && \
+    make -j$(python -c 'import multiprocessing; print(multiprocessing.cpu_count())') && \
+    make install && \
+    ldconfig -v && \
+    rm -rf /provisioning/geos*
+
+# Get ESRI FileGDB libraries for Fiona/Geopandas Python packages
+# http://appsforms.esri.com/products/download/
+ARG FILEGDB_VERSION=1_5
+RUN echo "Installing ESRI FileGDB libraries..." && \
+    mkdir -p /provisioning/filegdb && \
+    curl -L -o filegdb_api_${FILEGDB_VERSION}-64.tar.gz https://www.dropbox.com/s/xi11vshwt9uojsy/FileGDB_API_1_5_64gcc51.tar.gz?dl=1 && \
+    tar -zxvf filegdb_api_${FILEGDB_VERSION}-64.tar.gz && \
+    cp -r FileGDB_API-64gcc51/lib/* /usr/local/lib && \
+    cp -r FileGDB_API-64gcc51/include/* /usr/local/include && \
+    ldconfig -v && \
+    rm -rf /provisioning/filegdb* /provisioning/FileGDB*
+
+# Compile GDAL with FileGDB support for Fiona/Geopandas Python packages
+RUN echo "Installing GDAL libraries..." && \
+    mkdir -p /provisioning/gdal && \
+    cd /provisioning/gdal && \
+    curl -# -o gdal-2.2.1.tar.gz http://download.osgeo.org/gdal/2.2.1/gdal-2.2.1.tar.gz && \
+    tar -zxvf gdal-2.2.1.tar.gz && \
+    cd /provisioning/gdal/gdal-2.2.1 && \
+    ./configure --prefix=/usr/ --with-python --with-fgdb && \
+    make -j$(python -c 'import multiprocessing; print(multiprocessing.cpu_count())') && \
+    make install && \
+    rm -rf /provisioning/gdal*
+
+RUN echo "Installing Spatial Index library..." && \
+    mkdir -p /provisioning/spatialindex && \
+    cd /provisioning/spatialindex && \
+    curl -# -O http://download.osgeo.org/libspatialindex/spatialindex-src-1.8.5.tar.gz && \
+    tar -xzf spatialindex-src-1.8.5.tar.gz && \
+    cd spatialindex-src-1.8.5 && \
+    ./configure --prefix=/usr/local && \
+    make -j$(python -c 'import multiprocessing; print(multiprocessing.cpu_count())') && \
+    make install && \
+    ldconfig && \
+    rm -rf /provisioning/spatialindex*
+
+RUN echo "Installing Proj4 library..." && \
+    mkdir -p /provisioning/proj4 && \
+    cd /provisioning/proj4 && \
+    curl -# -O http://download.osgeo.org/proj/proj-4.9.3.tar.gz && \
+    tar -xzf proj-4.9.3.tar.gz && \
+    cd proj-4.9.3 && \
+    ./configure && \
+    make -j$(python -c 'import multiprocessing; print(multiprocessing.cpu_count())') && \
+    make install && \
+    ldconfig -v && \
+    rm -rf /provisioning/proj4
+
+# basemap (incorrectly) requires numpy to be installed *before* installing it
+RUN pip install --upgrade numpy && \
+    echo "Installing Basemap plotting library..." && \
+    mkdir -p /provisioning/matplotlib-basemap && \
+    cd /provisioning/matplotlib-basemap && \
+    curl -# -o basemap-1.0.7rel.tar.gz https://codeload.github.com/matplotlib/basemap/tar.gz/v1.0.7rel && \
+    tar -xzf basemap-1.0.7rel.tar.gz && \
+    cd basemap-1.0.7rel && \
+    python setup.py install && \
+    rm -rf /provisioning/matplotlib-basemap