Merge pull request #22 from ocefpaf/travis

Many Travis-CI config updates...

Author: ocefpaf

.travis.yml

@@ -7,37 +7,44 @@ matrix:
   include:
   - python: 2.7
     env: TEST_TARGET=default
-  - python: 3.4
-    env: TEST_TARGET=default
   - python: 3.5
     env: TEST_TARGET=default
-  - python: 3.5
-    env: TEST_TARGET=coding_standards
-  allow_failures:
-  - python: 3.5
+  - python: 3.6
+    env: TEST_TARGET=default
+  - python: 2.7
+    env: TEST_TARGET=doctest
+  - python: 3.6
+    env: TEST_TARGET=doctest
+  - python: 3.6
     env: TEST_TARGET=coding_standards
 
 before_install:
-    - wget http://bit.ly/miniconda -O miniconda.sh
-    - bash miniconda.sh -b -p $HOME/miniconda
-    - export PATH="$HOME/miniconda/bin:$PATH"
-    - conda update --all --yes
-    - conda config --add channels conda-forge -f
-    - conda create --yes -n TEST python=$TRAVIS_PYTHON_VERSION --file requirements.txt --file requirements-dev.txt
-    - source activate TEST
-    - travis_retry conda install --yes pytest # GUI
-    - "export DISPLAY=:99.0"
-    - "sh -e /etc/init.d/xvfb start"
+  - wget http://bit.ly/miniconda -O miniconda.sh
+  - bash miniconda.sh -b -p $HOME/miniconda
+  - export PATH="$HOME/miniconda/bin:$PATH"
+  - conda config --set always_yes yes --set changeps1 no --set show_channel_urls true
+  - conda update conda
+  - conda config --add channels conda-forge --force
+  - conda create -n TEST python=$TRAVIS_PYTHON_VERSION --file requirements.txt --file requirements-dev.txt
+  - source activate TEST
+  # GUI
+  - "export DISPLAY=:99.0"
+  - "sh -e /etc/init.d/xvfb start"
 
 # Test source distribution.
 install:
-    - python setup.py sdist && version=$(python setup.py --version) && pushd dist  && pip install ctd-${version}.tar.gz && popd
+  - python setup.py sdist && version=$(python setup.py --version) && pushd dist  && pip install ctd-${version}.tar.gz && popd
 
 script:
-    - if [[ $TEST_TARGET == 'default' ]]; then
-        py.test -vv ;
-      fi
+  - if [[ $TEST_TARGET == 'default' ]]; then
+      py.test -s -rxs -v tests ;
+    fi
+
+  - if [[ $TEST_TARGET == 'doctest' ]]; then
+      py.test -s -rxs --doctest-modules -vv ctd ;
+    fi
 
-    - if [[ $TEST_TARGET == 'coding_standards' ]]; then
-        find . -type f -name "*.py" ! -name 'conf.py' | xargs flake8 --max-line-length=100 ;
-      fi
+  - if [[ $TEST_TARGET == 'coding_standards' ]]; then
+      flake8 --max-line-length=100 ctd ;
+      flake8 --max-line-length=100 tests ;
+    fi

LICENSE.txt

@@ -1,20 +1,11 @@
-The MIT License (MIT)
+Copyright 2017 Filipe Fernandes
 
-Copyright (c) 2013 Filipe
+Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:
 
-Permission is hereby granted, free of charge, to any person obtaining a copy of
-this software and associated documentation files (the "Software"), to deal in
-the Software without restriction, including without limitation the rights to
-use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of
-the Software, and to permit persons to whom the Software is furnished to do so,
-subject to the following conditions:
+1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
 
-The above copyright notice and this permission notice shall be included in all
-copies or substantial portions of the Software.
+2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
 
-THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS
-FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR
-COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER
-IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
-CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+3. Neither the name of the copyright holder nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

MANIFEST.in

@@ -1,3 +1,3 @@
 include README.rst
 include *.txt
-include ctd/*.py
+recursive-include ctd *.py

README.rst

@@ -10,7 +10,7 @@ python-ctd
 .. image:: http://img.shields.io/travis/pyoceans/python-ctd/master.svg?style=flat
    :target: https://travis-ci.org/pyoceans/python-ctd
    :alt: Build_status
-.. image:: http://img.shields.io/badge/license-MIT-blue.svg?style=flat
+.. image:: http://img.shields.io/badge/license-BSD-blue.svg?style=flat
    :target: https://github.com/pyoceans/python-ctd/blob/master/LICENSE.txt
    :alt: license
 

ctd/__init__.py

@@ -1,18 +1,56 @@
-from __future__ import absolute_import, unicode_literals
+from __future__ import (absolute_import, division, print_function)
 
-__version__ = '0.2.3'
+__version__ = '0.3.0'
 
-from pandas import Index, Series, DataFrame
+from pandas import DataFrame, Index, Series
 
-from .ctd import asof, from_edf, from_cnv, from_fsi, rosette_summary
-from .processing import (data_conversion, align, despike, lp_filter,
-                         cell_thermal_mass, press_check, bindata, split,
-                         movingaverage, pmel_inversion_check, smooth,
-                         mixed_layer_depth, barrier_layer_thickness,
-                         derive_cnv)
-from .plotting import (get_maxdepth, extrap_sec, gen_topomask, plot, plot_vars,
-                       plot_section)
+from .ctd import asof, from_cnv, from_edf, from_fsi, rosette_summary
+from .plotting import (
+    extrap_sec,
+    gen_topomask,
+    get_maxdepth,
+    plot,
+    plot_section,
+    plot_vars,
+)
+from .processing import (
+    barrier_layer_thickness,
+    bindata,
+    cell_thermal_mass,
+    derive_cnv,
+    despike,
+    lp_filter,
+    mixed_layer_depth,
+    movingaverage,
+    press_check,
+    smooth,
+    split,
+)
 
+__all__ = [
+    asof,
+    barrier_layer_thickness,
+    bindata,
+    cell_thermal_mass,
+    derive_cnv,
+    despike,
+    extrap_sec,
+    from_cnv,
+    from_edf,
+    from_fsi,
+    gen_topomask,
+    get_maxdepth,
+    lp_filter,
+    mixed_layer_depth,
+    movingaverage,
+    plot,
+    plot_section,
+    plot_vars,
+    press_check,
+    rosette_summary,
+    smooth,
+    split,
+]
 
 # Attach methods.
 Index.asof = asof

ctd/ctd.py

@@ -1,29 +1,22 @@
-from __future__ import absolute_import, unicode_literals
+from __future__ import (absolute_import, division, print_function)
 
-# Standard library.
 import os
 import warnings
 
-# Scientific stack.
 import numpy as np
+
 from pandas import DataFrame
 from pandas import read_table
 
-from .utilities import read_file, basename, normalize_names
-
-data_path = os.path.join(os.path.dirname(__file__), 'tests', 'data')
+from .utilities import basename, normalize_names, read_file
 
-__all__ = ['CTD',
-           'asof',
-           'from_edf',
-           'from_cnv',
-           'from_fsi',
-           'rosette_summary']
+data_path = os.path.join(
+    os.path.dirname(os.path.dirname(__file__)), 'tests', 'data'
+)
 
 
-# TODO: https://github.com/nilmtk/nilmtk/issues/83
 def asof(self, label):
-    """FIXME: pandas index workaround."""
+    """pandas index workaround."""
     if label not in self:
         loc = self.searchsorted(label, side='left')
         if loc > 0:
@@ -178,7 +171,7 @@ def from_cnv(fname, compression=None, below_water=False, lon=None,
             elif hemisphere == 'N':
                 lat = lat[0] + lat[1] / 60.
             else:
-                raise ValueError("Latitude not recognized.")
+                raise ValueError('Latitude not recognized.')
         if 'NMEA Longitude' in line:
             hemisphere = line[-1]
             lon = line.strip(hemisphere).split('=')[1].strip()
@@ -188,7 +181,7 @@ def from_cnv(fname, compression=None, below_water=False, lon=None,
             elif hemisphere == 'E':
                 lon = lon[0] + lon[1] / 60.
             else:
-                raise ValueError("Latitude not recognized.")
+                raise ValueError('Latitude not recognized.')
         if line == '*END*':  # Get end of header.
             skiprows = k + 1
             break
@@ -280,6 +273,7 @@ def rosette_summary(fname):
     ros.set_index('nbf', drop=True, inplace=True, verify_integrity=False)
     return ros
 
+
 if __name__ == '__main__':
     import doctest
     doctest.testmod()

ctd/plotting.py

@@ -1,24 +1,20 @@
 # -*- coding: utf-8 -*-
 
-from __future__ import absolute_import, unicode_literals
 
-# Scientific stack.
-import numpy as np
-import numpy.ma as ma
+from __future__ import (absolute_import, division, print_function)
+
 import matplotlib.pyplot as plt
+
 import mpl_toolkits.axisartist as AA
 
-from pandas import Series
 from mpl_toolkits.axes_grid1 import host_subplot
 
-from .utilities import extrap1d
+import numpy as np
+import numpy.ma as ma
 
-__all__ = ['get_maxdepth',
-           'extrap_sec',
-           'gen_topomask',
-           'plot',
-           'plot_vars',
-           'plot_section']
+from pandas import Series
+
+from .utilities import extrap1d
 
 
 def get_maxdepth(self):
@@ -159,20 +155,20 @@ def plot_vars(self, variables=None, **kwds):
 
     # Axis location.
     host_new_axis = ax0.get_grid_helper().new_fixed_axis
-    ax0.axis["bottom"] = host_new_axis(loc="top", axes=ax0, offset=(0, 0))
+    ax0.axis['bottom'] = host_new_axis(loc='top', axes=ax0, offset=(0, 0))
     par_new_axis = ax1.get_grid_helper().new_fixed_axis
-    ax1.axis["top"] = par_new_axis(loc="bottom", axes=ax1, offset=(0, 0))
+    ax1.axis['top'] = par_new_axis(loc='bottom', axes=ax1, offset=(0, 0))
 
     ax0.plot(self[variables[0]], self.index, 'r.', label='Temperature')
     ax1.plot(self[variables[1]], self.index, 'b.', label='Salinity')
 
-    ax0.set_ylabel("Pressure [dbar]")
-    ax0.set_xlabel("Temperature [\u00b0C]")
-    ax1.set_xlabel("Salinity [kg g$^{-1}$]")
+    ax0.set_ylabel('Pressure [dbar]')
+    ax0.set_xlabel('Temperature [\u00b0C]')
+    ax1.set_xlabel('Salinity [kg g$^{-1}$]')
     ax1.invert_yaxis()
 
-    try:  # FIXME with metadata.
-        fig.suptitle(r"Station %s profile" % self.name)
+    try:
+        fig.suptitle(r'Station %s profile' % self.name)
     except AttributeError:
         pass
 
@@ -202,10 +198,11 @@ def plot_section(self, reverse=False, filled=False, **kw):
         lat = lat[::-1]
         data = data.T[::-1].T
         h = h[::-1]
+    lon, lat = map(np.atleast_2d, (lon, lat))
     x = np.append(0, np.cumsum(gsw.distance(lon, lat)[0] / 1e3))
     z = self.index.values.astype(float)
 
-    if filled:  # FIXME: Cause discontinuities.
+    if filled:  # CAVEAT: this method cause discontinuities.
         data = data.filled(fill_value=np.nan)
         data = extrap_sec(data, x, z, w1=0.97, w2=0.03)
 
@@ -257,18 +254,13 @@ def plot_section(self, reverse=False, filled=False, **kw):
     ax.xaxis.set_tick_params(tickdir='out', labelsize=labelsize, pad=1)
     ax.yaxis.set_tick_params(tickdir='out', labelsize=labelsize, pad=1)
 
-    if False:  # TODO: +/- Black-and-White version.
-        cs = ax.contour(x, z, data, colors='grey', levels=levels,
-                        extend=extend, linewidths=1., alpha=1., zorder=2)
-        ax.clabel(cs, fontsize=8, colors='grey', fmt=fmt, zorder=1)
-        cb = None
-    if True:  # Color version.
-        cs = ax.contourf(x, z, data, cmap=cmap, levels=levels, alpha=1.,
-                         extend=extend, zorder=2)  # manual=True
-        # Colorbar.
-        cb = fig.colorbar(mappable=cs, ax=ax, orientation='vertical',
-                          aspect=aspect, shrink=shrink, fraction=fraction,
-                          pad=pad)
+    # Color version.
+    cs = ax.contourf(x, z, data, cmap=cmap, levels=levels, alpha=1.,
+                     extend=extend, zorder=2)  # manual=True
+    # Colorbar.
+    cb = fig.colorbar(mappable=cs, ax=ax, orientation='vertical',
+                      aspect=aspect, shrink=shrink, fraction=fraction,
+                      pad=pad)
     return fig, ax, cb