changes to use Cartopy in place of Basemap (#34)

* changes to use Cartopy in place of Basemap
* reverting to coverage run for Travis
* commenting out Matplotlib.use for issue on Travis Linux
* removed all qt5agg usages

.travis.yml

@@ -1,72 +1,52 @@
 language: cpp # Travis-CI does not currently support Python and Mac OS X
 
-matrix:
- include:
- - os: linux
- dist: xenial
- env: PYTHON_VERSION=3.6
- - os: linux
- dist: trusty
- env: PYTHON_VERSION=3.6
- - os: linux
- dist: xenial
- env: PYTHON_VERSION=3.7
- - os: osx
- env: PYTHON_VERSION=3.6
+os:
+ - linux
+ - osx
+
+env:
+ - PYTHON_VERSION=3.8
+ - PYTHON_VERSION=3.6
+ - PYTHON_VERSION=3.7
 
+matrix:
  fast_finish: true
  allow_failures:
- - os: linux
- dist: trusty
- env: PYTHON_VERSION=3.6
- - os: linux
- dist: xenial
- env: PYTHON_VERSION=3.7
- - os: osx
- env: PYTHON_VERSION=3.6
+ - os: osx
+ - env: PYTHON_VERSION=3.7
 
 install:
- - "export DISPLAY=:99.0"
- - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then
- ( sudo Xvfb :99 -ac -screen 0 1024x768x8; echo ok )&
- curl https://repo.continuum.io/miniconda/Miniconda3-latest-MacOSX-x86_64.sh -o miniconda.sh;
- else
- sudo apt-get update;
- sudo apt-get install -y xvfb;
- /sbin/start-stop-daemon --start --quiet --pidfile /tmp/custom_xvfb_99.pid --make-pidfile --background --exec /usr/bin/Xvfb -- :99 -screen 0 1920x1200x24 -ac +extension GLX +render -noreset;
- wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh;
- fi
- - bash miniconda.sh -b -p $HOME/miniconda
- - export PATH="$HOME/miniconda/bin:$PATH"
- - hash -r
- - conda config --set always_yes yes --set changeps1 no
+ - if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then MINICONDA_OS=Linux; else MINICONDA_OS=MacOSX; fi
+ - wget https://repo.anaconda.com/miniconda/Miniconda3-latest-$MINICONDA_OS-x86_64.sh -O miniconda.sh
+ - bash miniconda.sh -b -p "$HOME"/miniconda
+ - source "$HOME"/miniconda/etc/profile.d/conda.sh
+ - conda config --set always_yes yes --set changeps1 no --set auto_update_conda false --set notify_outdated_conda false
  - conda config --add channels conda-forge
  - conda update -q conda
- # Useful for debugging any issues with conda
  - conda info -a
-
  - conda create -q -n test-environment python=$PYTHON_VERSION
- - source activate test-environment
+ - conda activate test-environment
+ - python --version
+
+ - pip install coveralls PyYAML pytest pytest-cov wheel
+ # for hyo2.abc
+ - conda install appdirs bidict cartopy gdal matplotlib-base numpy psutil pyproj
  - pip install PySide2
- - conda install numpy matplotlib-base gdal pyproj scipy basemap netCDF4 pillow gsw
- - if [[ "$TRAVIS_OS_NAME" != "osx" ]]; then
- conda remove --force PyQt Qt sip;
- export LD_LIBRARY_PATH=$HOME/miniconda/envs/test-environment/lib:$LD_LIBRARY_PATH;
- fi
- - pip install cython
- - pip install coveralls
  - pip install https://github.com/hydroffice/hyo2_abc/archive/master.zip
+ # for hyo2.soundspeed
+ - conda install gsw netCDF4 pillow pyserial scipy
+
  - pip install .
- - rm -f $HOME/miniconda/envs/test-environment/qt.conf
- - pip install pytest pytest-cov
  - conda list --show-channel-urls
 
 script:
- - py.test --cov
+ - coverage run --source hyo2 setup.py test
+ - coverage report -m
+ - coveralls
 
 after_script:
- - coverage report -m
+ - python setup.py bdist_wheel
 
 after_success:
- - pip install PyYAML
- - coveralls
+ - path: dist\*
+

HISTORY.rst

@@ -1,6 +1,14 @@
 History
 -------
 
+2020.0.0
+~~~~~~~~
+
+2020-04-09
+
+- Started migration from Basemap to Cartopy
+
+
 2019.0.0
 ~~~~~~~~
 

LICENSE

@@ -1,15 +1,3 @@
-Copyright Notice and License Terms for: hyo2.soundspeed - Sound Speed package for HydrOffice
-Copyright (c) 2019, University of New Hampshire, Center for Coastal and Ocean Mapping. All rights reserved.
-Portions of this project were developed under a cooperative agreement with NOAA Coast Survey Development 
-Laboratory, and contain NOAA-developed code in the public domain.
-
-Released under a dual license:
-- Community license (LGPL v2.1)
-- Industrial Associate license
-
-For more info, visit: http:https://www.hydroffice.org/license_lgpl21/
-
------------------------------------------------------------------------------
 
  GNU LESSER GENERAL PUBLIC LICENSE
  Version 2.1, February 1999

appveyor.yml

@@ -1,9 +1,13 @@
-version: 0.1.{build}-{branch}
+version: 2020.0.{build}-{branch}
 
 environment:
 
  matrix:
 
+ - PYTHON_VERSION: 3.8
+ PYTHON_ARCH: x64
+ MINICONDA: C:\Miniconda36-x64
+
  - PYTHON_VERSION: 3.6
  PYTHON_ARCH: x64
  MINICONDA: C:\Miniconda36-x64
@@ -30,33 +34,28 @@ install:
  - conda config --add channels conda-forge
  - conda create -q -n test-environment python=%PYTHON_VERSION%
  - activate test-environment
- - pip install wheel
 
  # Check that we have the expected version of Python
  - python --version
 
- - pip install pytest pytest-cov
- - pip install coveralls
- - pip install PySide2
+ - pip install coveralls PyYAML pytest pytest-cov wheel
  # for hyo2.abc
- - conda install numpy matplotlib-base gdal pyproj appdirs bidict coverage psutil
+ - conda install appdirs bidict cartopy gdal matplotlib-base numpy psutil pyproj
+ - pip install PySide2
  # for hyo2.soundspeed
- - conda install scipy basemap netCDF4 pillow gsw cython pyproj
+ - conda install gsw netCDF4 pillow pyserial scipy
  # --no-deps because of pip not detecting the installed GDAL
  - pip install https://github.com/hydroffice/hyo2_abc/archive/master.zip
 
 build: off
 build_script:
  - pip install .
- # - conda remove --force PyQt Qt sip
- - del /q %MINICONDA%\envs\test-environment\qt.conf
  - conda list --show-channel-urls
 
 test: off
 test_script:
  - py.test --cov
  - coverage report -m
- - pip install PyYAML
  - coveralls
 
 after_test:

examples/soundspeed/ex_plot_export_metadata.py

@@ -2,6 +2,7 @@
 import os
 
 from hyo2.abc.lib.gdal_aux import GdalAux
+# noinspection PyUnresolvedReferences
 from hyo2.soundspeedmanager import app_info
 from hyo2.soundspeed.soundspeed import SoundSpeedLibrary
 
@@ -22,8 +23,8 @@
 logger.info("Profiles: %s" % len(lst))
 
 # plots/maps/exports
-# - map
-lib.map_db_profiles()
+# - mapt
+lib.map_db_profiles(show_plot=False)
 lib.save_map_db_profiles()
 
 # - aggregate plot

hyo2/soundspeed/__init__.py

@@ -12,7 +12,7 @@
 logger.addHandler(logging.NullHandler())
 
 name = "Sound Speed"
-__version__ = '2019.2.6'
+__version__ = '2020.0.0'
 __copyright__ = 'Copyright 2020 University of New Hampshire, Center for Coastal and Ocean Mapping'
 
 lib_info = LibInfo()
@@ -44,6 +44,6 @@
  "numpy": "numpy",
  "pyproj": "pyproj",
  "matplotlib": "matplotlib",
- "basemap": "mpl_toolkits.basemap",
+ "cartopy": "cartopy",
  "PySide2": "PySide2"
 }

hyo2/soundspeed/db/plot.py

@@ -1,15 +1,17 @@
 import os
 import numpy as np
 
+# noinspection PyUnresolvedReferences
 from PySide2 import QtWidgets
 import matplotlib
 from matplotlib import rc_context
 
-from mpl_toolkits.basemap import Basemap
+import cartopy.crs as ccrs
+import cartopy.feature as cfeature
 import matplotlib.pyplot as plt
 import logging
 
-matplotlib.use('qt5agg')
+# matplotlib.use('qt5agg')
 logger = logging.getLogger(__name__)
 
 
@@ -48,7 +50,7 @@ def plots_folder(cls, output_folder):
  os.makedirs(folder)
  return folder
 
- def map_profiles(self, pks=None, output_folder=None, save_fig=False):
+ def map_profiles(self, pks=None, output_folder=None, save_fig=False, show_plot=False):
  """plot all the ssp in the database"""
 
  with rc_context(self.rc_context):
@@ -81,81 +83,60 @@ def map_profiles(self, pks=None, output_folder=None, save_fig=False):
 
  # make the world map
  plt.close("Profiles Map")
- fig = plt.figure("Profiles Map")
- # fig.patch.set_facecolor('#1464F4')
- ax = plt.subplot(111, aspect='equal')
+ _ = plt.figure("Profiles Map")
+ ax = plt.subplot(111, projection=ccrs.PlateCarree())
  plt.subplots_adjust(left=0, bottom=0, right=1, top=1, wspace=0, hspace=0)
- # plt.title("SSP Map (%s profiles)" % len(view_rows))
  plt.ioff()
-
- if rows:
- wm = self._world_draw_polygons()
- else:
- wm = self._world_draw_map()
- x, y = wm(ssp_x, ssp_y)
- wm.scatter(x, y, marker='o', s=16, color='r')
- wm.scatter(x, y, marker='.', s=1, color='k')
+ # noinspection PyUnresolvedReferences
+ ax.coastlines(resolution='50m')
+ # noinspection PyUnresolvedReferences
+ ax.add_feature(cfeature.OCEAN.with_scale('50m'))
+ # noinspection PyUnresolvedReferences
+ ax.add_feature(cfeature.LAND.with_scale('50m'), color='lightgray')
+ # noinspection PyUnresolvedReferences
+ ax.gridlines(color='#cccccc', linestyle='--')
+
+ # noinspection PyUnresolvedReferences
+ ax.scatter(ssp_x, ssp_y, marker='o', s=14, color='r')
+ # noinspection PyUnresolvedReferences
+ ax.scatter(ssp_x, ssp_y, marker='.', s=1, color='k')
  if pks is not None:
  delta = 5.0
- y_min = min(y)
+ y_min = min(ssp_y)
  if (y_min - delta) < -90.0:
  y_min = -90.0
  else:
  y_min -= delta
- y_max = max(y)
+ y_max = max(ssp_y)
  if (y_max + delta) > 90.0:
  y_max = 90.0
  else:
  y_max += delta
 
- x_min = min(x)
+ x_min = min(ssp_x)
  if (x_min - delta) < -180.0:
  x_min = -180.0
  else:
  x_min = x_min - delta
- x_max = max(x)
+ x_max = max(ssp_x)
  if (x_max + delta) > 180.0:
  x_max = 180.0
  else:
  x_max += delta
  # logger.debug("%s %s, %s %s" % (y_min, y_max, x_min, x_max))
+ # noinspection PyUnresolvedReferences
  ax.set_ylim(y_min, y_max)
+ # noinspection PyUnresolvedReferences
  ax.set_xlim(x_min, x_max)
 
  if save_fig and (output_folder is not None):
  plt.savefig(os.path.join(self.plots_folder(output_folder), 'ssp_map.png'),
  bbox_inches='tight')
- # else:
- #  plt.show()
+ elif show_plot:
+ plt.show()
 
  return True
 
- @staticmethod
- def _world_draw_map():
- logger.debug("drawing blue marble")
- m = Basemap(resolution=None)
- # resolution c, l, i, h, f in that order
- img = m.bluemarble(zorder=0)
- img.set_alpha(0.8)
- return m
-
- @staticmethod
- def _world_draw_polygons():
- logger.debug("drawing polygons")
- m = None
- try:
- m = Basemap(resolution='i')
- except OSError:
- logger.debug("using low resolution for basemap")
- m = Basemap(resolution='l')
-
- m.drawcoastlines(zorder=1)
- m.fillcontinents(color='lightgray', zorder=1)
- m.drawparallels(np.arange(-90., 120., 10.), color="#cccccc", labels=[False, True, True, False])
- m.drawmeridians(np.arange(0., 360., 20.), color="#cccccc", labels=[True, False, False, True])
-
- return m
-
  @staticmethod
  def _set_inset_color(x, color):
  for m in x:

hyo2/soundspeed/profile/ray_tracing/plot_tracedprofiles.py

@@ -11,7 +11,7 @@
 
 from hyo2.soundspeed.profile.ray_tracing.diff_tracedprofiles import DiffTracedProfiles
 
-matplotlib.use('qt5agg')
+# matplotlib.use('qt5agg')
 logger = logging.getLogger(__name__)
 
 

hyo2/soundspeed/soundspeed.py

@@ -1504,10 +1504,10 @@ def raise_plot_window(self) -> None:
  _ = db.plot.raise_window()
  db.disconnect()
 
- def map_db_profiles(self, pks: Optional[list] = None) -> bool:
+ def map_db_profiles(self, pks: Optional[list] = None, show_plot: Optional[bool] = False) -> bool:
  """List the profile on the db"""
  db = ProjectDb(projects_folder=self.projects_folder, project_name=self.current_project)
- ret = db.plot.map_profiles(pks=pks)
+ ret = db.plot.map_profiles(pks=pks, show_plot=show_plot)
  db.disconnect()
  return ret
 

hyo2/soundspeed/temp/regex_helpers.py

@@ -354,7 +354,7 @@ def ConvertFromSoundSpeedProfile(p):
  p.data.num_samples = len(self)
  col_types = []
  prof_data = []
- for data, name in ((p.data.pressure, 'pressure'), (p.data.depth, 'depth')
+ for data, name in ((p.data.pressure, 'pressure'), (p.data.depth, 'depth'),
  (p.data.speed, 'soundspeed'), (p.data.temp, 'temperature'),
  (p.data.sal, 'salinity'), (p.data.conductivity, 'conductivity')):
  if data is not None:

hyo2/soundspeedmanager/__init__.py

@@ -11,7 +11,7 @@
 logger.addHandler(logging.NullHandler())
 
 name = "Sound Speed Manager"
-__version__ = "2019.2.6"
+__version__ = "2020.0.0"
 __copyright__ = "Copyright 2020 University of New Hampshire, Center for Coastal and Ocean Mapping"
 
 app_info = AppInfo()