Upgrade to Python 3.7 (#18)

* Combine the three component multipliers (Ms, Mh and Mt) into a single band, repeated for each wind direction (E, N, NE, NW, S, SE, SW, W). Each band is then stored in a single geotiff file for each tile.
* `mpi_runner.py` creates a Virtual Raster Table (VRT) that allows a virtual GDAL dataset to be composed from other datasets.
* Created dataset dimensions are set by the input dataset dimensions, not fixed
* Handles the case of an empty input file, but not in an ideal way (replace missing file with values of 1)
* PyPar replaced by mpi4py
* TCRM-108: Fixed crash due to fraction indices.
* TCRM-108: Python version change to 3.7
* TCRM-108: Adding test terrain_table data.
* Update for PEP8 conformance test

Co-authored-by: MahmudulHasanGA <[email protected]>

.travis.yml

@@ -3,40 +3,42 @@ branches:
   except:
   - notebooks
 python:
-  - "2.7"
-# install system dependencies 
+  - "3.7"
+# install system dependencies
 before_install: 
   - sudo apt-get update -qq
   - sudo apt-get install build-essential
   - sudo apt-get install libhdf5-serial-dev
   - sudo apt-get install libnetcdf-dev 
-  - sudo apt-get install python-dev
-  - sudo apt-get install libgeos-c1 libgeos-dev
+  - sudo apt-get install python3-dev
+  - sudo apt-get install libgeos-c1v5 libgeos-dev
   - sudo apt-get install libatlas-base-dev gfortran
-  - sudo apt-get install libblas3gf
+  - sudo apt-get install libblas3
   - sudo apt-get install libc6
   - sudo apt-get install libgcc1
   - sudo apt-get install libgfortran3
-  - sudo apt-get install liblapack3gf
+  - sudo apt-get install liblapack3
   - sudo apt-get install libstdc++6 
 
 # install Python dependencies 
 install:
 #  - sudo pip install conda 
 #  - sudo conda init 
-- if [[ "$TRAVIS_PYTHON_VERSION" == "2.7" ]]; then wget https://repo.continuum.io/miniconda/Miniconda-latest-Linux-x86_64.sh
-  -O miniconda.sh; else wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
-  -O miniconda.sh; fi
+- wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh
 - bash miniconda.sh -b -p $HOME/miniconda
 - export PATH="$HOME/miniconda/bin:$PATH"
 - hash -r
 - conda config --set always_yes yes --set changeps1 no
 - conda update -q conda
-- deps='pip numpy scipy matplotlib nose coverage numexpr gdal' 
-- conda create -p $HOME/py --yes $deps "python=$TRAVIS_PYTHON_VERSION" 
+- conda info -a
+- deps='pip numpy scipy nose coverage numexpr gdal mpi4py openssh'
+- conda create -p $HOME/py --yes $deps "python=$TRAVIS_PYTHON_VERSION" -c conda-forge
 - export PATH=$HOME/py/bin:$PATH 
 - pip install pycurl
-- pip -v install -r requirements.txt 
+- pip -v install -r requirements.txt
+- export PYTHONPATH="${PYTHONPATH}:$HOME:${TRAVIS_BUILD_DIR}/utilities:${TRAVIS_BUILD_DIR}/topographic:${TRAVIS_BUILD_DIR}/tests:${TRAVIS_BUILD_DIR}/tests/test_topographic"
+#- echo "${PYTHONPATH}"
+#- echo "${TRAVIS_BUILD_DIR}"
 branches:
   except:
   - notebooks

README.rst

@@ -1,15 +1,15 @@
 The Wind Multiplier Computation Software 
-=============================
+========================================
 
 This package is used to produce wind multipliers including terrain, shielding and topographic multipliers.
 
 Dependencies 
-=========
-* `Python (2.7 preferred) <https://www.python.org/>`_, `Numpy <http://www.numpy.org/>`_, `Scipy <http://www.scipy.org/>`_, `GDAL <http://www.gdal.org/>`_, `netcdf4-python <https://code.google.com/p/netcdf4-python>`_; 
-* For parallel execution, `Pypar <http://github.com/daleroberts/pypar>`_ is required; 
+============
+* `Python (3.7 preferred) <https://www.python.org/>`_, `Numpy <http://www.numpy.org/>`_, `Scipy <http://www.scipy.org/>`_, `GDAL <http://www.gdal.org/>`_, `netcdf4-python <https://code.google.com/p/netcdf4-python>`_;
+* For parallel execution, `mpi4py <https://github.com/mpi4py/mpi4py>`_ is required;
 
 Usage
-==== 
+=====
 
 The script for deriving terrain, shielding and topographic multipliers is
 all_multipliers.py that links four modules: terrain, shielding, topographic and utilities.
@@ -26,7 +26,7 @@ configured. The following options need to be set in the configuration file:
 
 Start to run all_multipliers.py. The results are located under output folder (created automatically during the process) under root directory.
 
-This software implements parallelisation using PyPar for MPI handling. To run it in parallel mode, use  
+This software implements parallelisation using mpi4py for MPI handling. To run it in parallel mode, use
 mpirun -np ncpu python all_mulitpliers.py, while ncpu is the
 number of CPUs adopted.
 
@@ -43,7 +43,7 @@ The csv file requires the following headings:
 Values for these parameters can be found in the following GA Record, `'Local Wind Assessment in Australia: Computation Methodology for Wind Multipliers' <https://ecat.ga.gov.au/geonetwork/srv/eng/search#!d5a59415-611a-4ad5-e044-00144fdd4fa6>`_.
 
 Change log (develop branch)
-==========    
+===========================
     * Terrain classification input dataset configuration is no longer hard-coded. A terrain_table is now used
       to facilitate ingenstion of the terrain dataset. (May 2017)
     * Input file formats no longer fixed. File formats able to be read in with gdal.Open can now be used as the