Merge commit 'd93f1e3bd407e5d17441565bb7e7cfbc8f90d6e8'

.travis.yml

@@ -1,30 +1,29 @@
-language: python
-python:
-  - '3.6'
-  - '3.7'
-  - '3.8'
+language: shell
+
+env:
+  - PYTHON_VERSION=3.6
+  - PYTHON_VERSION=3.7
+  - PYTHON_VERSION=3.8
+
+os: 
+  - linux
+  - windows
+
+before_install:
+  - source ./preinstall.sh
+
 install:
-  - sudo apt-get update
-  - wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
-  # install in batch mode i.e. no input
-  - bash Miniconda3-latest-Linux-x86_64.sh -b -p $HOME/conda
-  - export PATH="$HOME/conda/bin:$PATH"
-  # clear bash cache table
-  - hash -r
-  - conda config --set always_yes yes
-  - conda config --set changeps1 no
-  - conda update -q conda
-  - conda config --add channels conda-forge
-  - conda config --set channel_priority strict
-  - conda env create -q -f tcrmenv.yml python=$TRAVIS_PYTHON_VERSION 
-  - source activate tcrm
+  - source ./postinstall.sh
+
 branches:
   except:
     - config
     - notebooks
+
 script:
   - python installer/setup.py build_ext -i
   - nosetests -v --with-coverage --cover-package=.
+
 after_success: coveralls
 notifications:
   slack:

DataProcess/DataProcess.py

@@ -465,8 +465,8 @@ def _speed(self, dist, dt, indicator, initIndex):
         """
         Extract speeds for all obs, initial obs and TC origins
         Input: dist - array of distances between consecutive TC
-                      observations
-               dt - array of times between consecutive TC observations
+                      observations (km)
+               dt - array of times between consecutive TC observations (hours)
                indicator - array of ones/zeros representing initial TC
                            observations (including TCs with a single
                            observation)
@@ -499,17 +499,17 @@ def _speed(self, dist, dt, indicator, initIndex):
             speed_no_init = pjoin(self.processPath, 'speed_no_init')
             # Extract all speeds
             self.logger.debug('Outputting data into {0}'.format(all_speed))
-            header = 'all cyclone speed in m/s'
+            header = 'all cyclone speed in km/h'
             flSaveFile(all_speed, speed, header, fmt='%6.2f')
 
             # Extract initial speeds
             self.logger.debug('Outputting data into {0}'.format(init_speed))
-            header = 'initial cyclone speed in m/s'
+            header = 'initial cyclone speed in km/h'
             flSaveFile(init_speed, initSpeed, header, fmt='%f')
 
             # Extract speeds, excluding initial speeds
             self.logger.debug('Outputting data into {0}'.format(speed_no_init))
-            header = 'cyclone speed without initial ones in m/s'
+            header = 'cyclone speed without initial ones in km/h'
             flSaveFile(speed_no_init, speedNoInit, header, fmt='%6.2f')
 
     def _pressure(self, pressure, indicator):

Evaluate/interpolateTracks.py

@@ -114,7 +114,7 @@ def interpolate(track, delta, interpolation_type=None):
         nLon = interp1d(timestep, track.Longitude, kind='linear')(newtime)
         nLat = interp1d(timestep, track.Latitude, kind='linear')(newtime)
 
-        if len(validIdx) == 2:
+        if len(validIdx) >= 2:
             npCentre = interp1d(timestep,
                                 track.CentralPressure,
                                 kind='linear')(newtime)

TrackGenerator/TrackGenerator.py

@@ -1293,7 +1293,7 @@ def dumpAllCellCoefficients(self):
                 'dtype': 'f',
                 'atts': {
                     'long_name': 'Mean forward speed',
-                    'units': 'm/s'
+                    'units': 'km/h'
                 }
             },
             1: {
@@ -1314,7 +1314,7 @@ def dumpAllCellCoefficients(self):
                 'dtype': 'f',
                 'atts': {
                     'long_name': 'Standard deviation forward speed',
-                    'units': 'm/s'
+                    'units': 'km/h'
                 }
             },
             3: {
@@ -1324,7 +1324,7 @@ def dumpAllCellCoefficients(self):
                 'dtype': 'f',
                 'atts': {
                     'long_name': 'Minimum forward speed',
-                    'units': 'm/s'
+                    'units': 'km/h'
                 }
             },
             4: {
@@ -1334,7 +1334,7 @@ def dumpAllCellCoefficients(self):
                 'dtype': 'f',
                 'atts': {
                     'long_name': 'Mean forward speed (over land)',
-                    'units': 'm/s'
+                    'units': 'km/h'
                 }
             },
             5: {
@@ -1356,7 +1356,7 @@ def dumpAllCellCoefficients(self):
                 'atts': {
                     'long_name': 'Standard deviation of forward' +
                                  ' speed (over land)',
-                    'units': 'm/s'
+                    'units': 'km/h'
                 }
             },
             7: {
@@ -1366,7 +1366,7 @@ def dumpAllCellCoefficients(self):
                 'dtype': 'f',
                 'atts': {
                     'long_name': 'Minimum forward speed (over land)',
-                    'units': 'm/s'
+                    'units': 'km/h'
                 }
             },
             8: {

Utilities/track.py

@@ -324,7 +324,7 @@ def ncSaveTracks(trackfile, tracks,
         tvar.lon_units = 'degrees east'
         tvar.lat_units = 'degrees north'
         tvar.pressure_units = 'hPa'
-        tvar.speed_units = 'm/s'
+        tvar.speed_units = 'km/h'
         tvar.length_units = 'km'
         tvar.trackId = repr(t.trackId)
 

docs/install.rst

@@ -19,18 +19,21 @@ For users wanting to only run the code, a zip file or gzipped tar file
 of the latest releases can be downloaded from the `Releases page
 <https://github.com/GeoscienceAustralia/tcrm/releases>`_.
 
+To have access to the latest updates, users should clone the repository, and
+then regularly pull from the repository as updates are made. 
+
 Those wanting to contribute to development can `fork
 <https://github.com/GeoscienceAustralia/tcrm/fork>`_ the
 repository. Submit a pull request to have your changes integrated into
-TCRM.
+TCRM. Read more about contribting_ to the TCRM code.
 
 .. _dependencies:
 
 Dependencies
 ------------
 
 TCRM relies on a number of additional libraries that are not part of
-the standard library. There are several ways to obtain the required
+the standard Pyhton library. There are several ways to obtain the required
 libraries -- using Python's recommended tool `pip
 <https://pip.readthedocs.org/en/latest/>`_, installing a distribution
 such as `Python(x,y) package <http://code.google.com/p/pythonxy/>`_
@@ -59,23 +62,6 @@ please see the documentation for each individual library.
 * Parallel execution in multi-processor environments (with MPI
   installed) requires `mpi4py <https://mpi4py.readthedocs.io/>`_
 
-Using pip
-~~~~~~~~~
-
-If you have `pip <https://pip.readthedocs.org/en/latest/>`_ installed,
-the required modules can be installed using the following command,
-executed in the main TCRM directory
-
-.. code-block:: bash
-
-    pip -v install -r requirements.txt
-
-This will automatically build the required libraries (listed in the
-``requirements.txt`` file) and any dependencies. ``pip`` must be on
-the ``$PATH`` for this to work.
-
-.. _compilation:
-
 
 Using Anaconda
 ~~~~~~~~~~~~~~
@@ -98,6 +84,22 @@ The bash promt will look like
 
     (tcrm) user@server:~/tcrm$
 
+Using pip
+~~~~~~~~~
+
+If you have `pip <https://pip.readthedocs.org/en/latest/>`_ installed,
+the required modules can be installed using the following command,
+executed in the main TCRM directory
+
+.. code-block:: bash
+
+    pip -v install -r requirements.txt
+
+This will automatically build the required libraries (listed in the
+``requirements.txt`` file) and any dependencies. ``pip`` must be on
+the ``$PATH`` for this to work.
+
+
 
 .. _environment:
 
@@ -140,79 +142,6 @@ CSH/TCSH shell
     setenv PYTHONPATH $PYTHONPATH:/path/to/tcrm:/path/to/tcrm/Utilities
 
 
-.. _dependencies:
-
-Dependencies
-------------
-
-TCRM relies on a number of additional libraries that are not part of
-the standard library. There are several ways to obtain the required
-libraries -- using Python's recommended tool `pip
-<https://pip.readthedocs.org/en/latest/>`_, installing a distribution
-such as `Python(x,y) package <http://code.google.com/p/pythonxy/>`_
-(for Windows environments) or `Anaconda
-<https://www.anaconda.com/distribution/#download-section>`_ (cross-platform), or
-installing the libraries from source or binary installers
-(pre-compiled binary Windows installer versions for all the libraries
-(both 32-bit and 64-bit) can be obtained `here
-<http://www.lfd.uci.edu/~gohlke/pythonlibs/>`_).
-
-For detailed instructions on installation of these dependencies,
-please see the documentation for each individual library.
-
-* `Python <https://www.python.org/>`_ - v3.5 or later
-* `Numpy <http://www.numpy.org/>`_ - v1.6 or later
-* `Scipy <http://www.scipy.org/>`_ - v0.12 or later
-* `Matplotlib <http://matplotlib.org/>`_ v1.2 or later. 
-* `Basemap <http://matplotlib.org/basemap/index.html>`_
-* `netcdf4-python <https://code.google.com/p/netcdf4-python/>`_ -
-  version 1.0.8 or later
-* `Shapely <http://toblerity.org/shapely/index.html>`_ - v1.2.15 or later
-* `statsmodels <http://statsmodels.sourceforge.net>`_ 
-* `seaborn <http://seaborn.pydata.org>`_
-* `pandas <http://pandas.pydata.org>`_
-* `gitpython <http://gitpython.readthedocs.org>`_
-* Parallel execution in multi-processor environments (with MPI
-  installed) requires `mpi4py <https://mpi4py.readthedocs.io/>`_
-
-Using pip
-~~~~~~~~~
-
-If you have `pip <https://pip.readthedocs.org/en/latest/>`_ installed,
-the required modules can be installed using the following command,
-executed in the main TCRM directory
-
-.. code-block:: bash
-
-    pip -v install -r requirements.txt
-
-This will automatically build the required libraries (listed in the
-``requirements.txt`` file) and any dependencies. ``pip`` must be on
-the ``$PATH`` for this to work.
-
-
-Using Anaconda
-~~~~~~~~~~~~~~
-
-To install ``tcrm``, make a new environment:
-
-.. code-block:: bash
-
-    conda env create -f tcrmenv.yml
-
-After creating the environment the user needs to move to that environment using the command
-
-.. code-block:: bash
-
-     conda activate tcrm
-
-The bash promt will look like
-
-.. code-block::
-
-    (tcrm) user@server:~/tcrm$
-
-
 .. _compilation:
 
 Windows

postinstall.sh

@@ -0,0 +1,46 @@
+# begin installing miniconda
+if [[ "$TRAVIS_OS_NAME" != "windows" ]]; then
+    echo "installing miniconda for posix";
+    bash $HOME/download/miniconda.sh -b -u -p $MINICONDA_PATH;
+elif  [[ "$TRAVIS_OS_NAME" == "windows" ]]; then
+    echo "folder $MINICONDA_SUB_PATH does not exist"
+    echo "installing miniconda for windows";
+    choco install miniconda3 --params="'/JustMe /AddToPath:1 /D:$MINICONDA_PATH_WIN'";
+fi;
+# end installing miniconda
+
+export PATH="$MINICONDA_PATH:$MINICONDA_SUB_PATH:$MINICONDA_LIB_BIN_PATH:$PATH";
+
+# begin checking miniconda existance
+echo "checking if folder $MINICONDA_SUB_PATH exists"
+if [[ -d $MINICONDA_SUB_PATH ]]; then
+    echo "folder $MINICONDA_SUB_PATH exists"
+else
+    echo "folder $MINICONDA_SUB_PATH does not exist"
+fi;
+# end checking miniconda existance
+
+source $MINICONDA_PATH/etc/profile.d/conda.sh;
+hash -r;
+echo $TRAVIS_OS_NAME
+echo $PYTHON_VERSION
+python --version
+
+if [[ "$TRAVIS_OS_NAME" == "windows" ]]; then
+    echo "Removing mpi4py from environment for windows build"
+    echo "Package not available in conda channels"
+    sed -i '/mpi4py/d' ./tcrmenv.yml
+fi
+
+conda config --set always_yes yes --set changeps1 no;
+conda update -q conda;
+conda config --add channels conda-forge;
+conda config --set channel_priority strict;
+# Useful for debugging any issues with conda
+conda info -a
+
+echo "Create TCRM environment"
+conda env create -q -f tcrmenv.yml python=$PYTHON_VERSION;
+conda activate tcrm
+python --version
+conda list

preinstall.sh

@@ -0,0 +1,24 @@
+if [[ "$TRAVIS_OS_NAME" != "windows" ]]; then
+    export MINICONDA_PATH=$HOME/miniconda;
+    export MINICONDA_SUB_PATH=$MINICONDA_PATH/bin;
+elif [[ "$TRAVIS_OS_NAME" == "windows" ]]; then
+    export MINICONDA_PATH=$HOME/miniconda;
+    export MINICONDA_PATH_WIN=`cygpath --windows $MINICONDA_PATH`;
+    export MINICONDA_SUB_PATH=$MINICONDA_PATH/Scripts;
+fi;
+export MINICONDA_LIB_BIN_PATH=$MINICONDA_PATH/Library/bin;
+  # Obtain miniconda installer
+if [[ "$TRAVIS_OS_NAME" != "windows" ]]; then
+    mkdir -p $HOME/download;
+    if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then
+        echo "downloading miniconda.sh for linux";
+        wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O $HOME/download/miniconda.sh;
+    elif  [[ "$TRAVIS_OS_NAME" == "osx" ]]; then
+        echo "downloading miniconda.sh for osx";
+        wget https://repo.continuum.io/miniconda/Miniconda3-latest-MacOSX-x86_64.sh -O $HOME/download/miniconda.sh;
+    fi;
+fi;
+  # Install openssl for Windows
+if [[ "$TRAVIS_OS_NAME" == "windows" ]]; then
+    choco install openssl.light;
+fi;