First commit after hyo2

.coveralls.yml

@@ -0,0 +1 @@
+repo_token: KO5kEqusCo0g0QMubi9Bv7V8AUV7NWXtu

.gitignore

@@ -1,3 +1,5 @@
+syntax: glob
+
 # temp files
 *.sh~
 *.*~
@@ -8,11 +10,12 @@ __pycache__/
 *.pyc
 *.pyo
 *.cache/
-*.mypy_cache/
+*.aux.xml
 
 # coverage files
 .coverage
 .coverage.*
+htmlcov/
 
 # google drive settings
 *desktop.ini
@@ -42,24 +45,31 @@ dist/
 downloads/
 eggs/
 .eggs/
-lib/
 lib64/
 parts/
 sdist/
 var/
 *.egg-info/
 .installed.cfg
 *.egg
-docs/_build/*
+_build/
+
+# notebooks checkpoint
+*.ipynb_checkpoints
 
-# Downloaded/Output data
+data/temp/
 data/download/
 data/output/
 
 tests/soundspeed/atlas/outputs
 tests/soundspeed/atlas/projects
 tests/soundspeed/atlas/releases
 tests/rtofs
-/examples/soundspeed/listener/seacat_capture.txt
-hyo/soundspeed/profile/ray_tracing/tracedprofile.cpp
-hyo/soundspeed/profile/ray_tracing/tracedprofile.html
+
+examples/soundspeed/listener/seacat_capture.txt
+
+hyo2/soundspeed/profile/ray_tracing/tracedprofile.cpp
+hyo2/soundspeed/profile/ray_tracing/tracedprofile.html
+
+# resources folder
+resources/~$icons.pptx

.travis.yml

@@ -1,62 +1,52 @@
-# Based on: http:https://conda.pydata.org/docs/travis.html
-
-sudo: false
-
-# Travis-CI does not currently support Python and Mac OS X
-language: c
+language: cpp # Travis-CI does not currently support Python and Mac OS X
 
 os:
  - linux
  - osx
 
 env:
-# - PYTHON_VERSION=3.5
  - PYTHON_VERSION=3.6
+ - PYTHON_VERSION=3.7
 
 matrix:
+ fast_finish: true
  allow_failures:
  - os: osx
-# - env: PYTHON_VERSION=3.5
+ - env: PYTHON_VERSION=3.7
 
-# before_script:
-# - "export DISPLAY=:99.0"
-# - if [[ "$TRAVIS_OS_NAME" != "osx" ]]; then apt-get install xvfb; fi
-# - if [[ "$TRAVIS_OS_NAME" != "osx" ]]; then "sh -e /etc/init.d/xvfb start"; fi
-# - sleep 3 # give xvfb some time to start
-
-before_install:
- # Set the anaconda environment
+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;
+ sh -e /etc/init.d/xvfb start;
  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
+ - conda config --add channels conda-forge
  - conda update -q conda
+ # Useful for debugging any issues with conda
  - conda info -a
 
- # create and activate a test-environment
  - conda create -q -n test-environment python=$PYTHON_VERSION
  - source activate test-environment
-
-install:
- - conda config --set channel_priority true
- - conda config --append channels conda-forge
- - conda install -q cython numpy scipy basemap matplotlib netCDF4 gdal pyproj krb5 pyserial pillow python=3.6
- - conda uninstall -q pyqt sip
- - conda install -q pyside
+ - pip install PySide2
+ - conda install numpy matplotlib-base gdal pyproj scipy basemap netCDF4 pillow
  - pip install gsw==3.0.6
- - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then conda install jpeg; fi
- - pip install --no-deps -e .
+ - pip install coveralls
+ - pip install https://github.com/hydroffice/hyo2_abc/archive/master.zip
+ - pip install .
+ # - conda remove --force PyQt Qt sip
+ # - rm -f $HOME/miniconda/envs/test-environment/qt.conf
+ - conda list --show-channel-urls
 
 script:
- - python -m unittest discover
+ - coverage run --source hyo2 setup.py test
 
-after_script:
- # If tests are successful, create a source distribution.
- # - python setup.py sdist
- - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then python setup.py bdist_wheel; fi
+after_success:
+ - coveralls

HISTORY.rst

@@ -1,13 +1,22 @@
 History
 -------
 
+2019.0.0
+~~~~~~~~
+
+2018-11-30
+
+- Started migration to PySide2 and hyo.abc
+
+
 2018.0.5
 ~~~~~~~~
 
 2018-01-10
 
 - Added automated processing setup and other improvements
 
+
 2017.3.0
 ~~~~~~~~
 

LICENSE

@@ -1,5 +1,5 @@
-Copyright Notice and License Terms for: hyo.soundspeed - Sound Speed package for HydrOffice
-Copyright (c) 2018, University of New Hampshire, Center for Coastal and Ocean Mapping. All rights reserved.
+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.
 

README.rst

@@ -1,31 +1,35 @@
 HydrOffice Sound Speed
 ======================
 
-.. image:: https://img.shields.io/pypi/v/hyo.soundspeed.svg
- :target: https://pypi.python.org/pypi/hyo.soundspeed
- :alt: PyPi version
+..
+ .. image:: https://img.shields.io/pypi/v/hyo2.soundspeed.svg
+ :target: https://pypi.python.org/pypi/hyo2.soundspeed
+ :alt: PyPi version
 
 .. image:: https://img.shields.io/badge/docs-latest-brightgreen.svg
  :target: https://www.hydroffice.org/manuals/soundspeed/index.html
  :alt: Latest Documentation
 
-.. image:: https://ci.appveyor.com/api/projects/status/6krhsxkcqo0jrvu6?svg=true
- :target: https://ci.appveyor.com/project/giumas/hyo-soundspeed
- :alt: AppVeyor Status
+..
+ .. image:: https://ci.appveyor.com/api/projects/status/6krhsxkcqo0jrvu6?svg=true
+ :target: https://ci.appveyor.com/project/hydroffice/hyo2-soundspeed
+ :alt: AppVeyor Status
 
-.. image:: https://travis-ci.org/hydroffice/hyo_soundspeed.svg?branch=master
- :target: https://travis-ci.org/hydroffice/hyo_soundspeed
- :alt: Travis-CI Status
+..
+ .. image:: https://travis-ci.org/hydroffice/hyo_soundspeed.svg?branch=master
+ :target: https://travis-ci.org/hydroffice/hyo_soundspeed
+ :alt: Travis-CI Status
 
-.. image:: https://api.codacy.com/project/badge/Grade/9b1d844ce51846c4b78bb7694096fde7
- :target: https://www.codacy.com/app/hydroffice/hyo_soundspeed?utm_source=github.com&utm_medium=referral&utm_content=hydroffice/hyo_soundspeed&utm_campaign=Badge_Grade
- :alt: Codacy Status
+..
+ .. image:: https://api.codacy.com/project/badge/Grade/9b1d844ce51846c4b78bb7694096fde7
+ :target: https://www.codacy.com/app/hydroffice/hyo2_soundspeed?utm_source=github.com&utm_medium=referral&utm_content=hydroffice/hyo_soundspeed&utm_campaign=Badge_Grade
+ :alt: Codacy badge
 
 .. image:: https://zenodo.org/badge/54854024.svg
  :target: https://zenodo.org/badge/latestdoi/54854024
  :alt: Zenodo DOI
 
-* Code: `GitHub repo <https://github.com/hydroffice/hyo_soundspeed>`_
+* Code: `GitHub repo <https://github.com/hydroffice/hyo2_soundspeed>`_
 * Project page: `url <https://www.hydroffice.org/soundspeed/>`_
 * Download page: `url <https://bitbucket.org/hydroffice/hyo_sound_speed_manager/downloads/>`_
 * License: LGPLv2.1 or IA license (See `Dual license <https://www.hydroffice.org/license_lgpl21/>`_)

appveyor.yml

@@ -1,5 +1,71 @@
 version: 0.1.{build}-{branch}
 
+branches:
+ only:
+ - master
+
+environment:
+
+ matrix:
+
+ - PYTHON_VERSION: 3.6
+ PYTHON_ARCH: x64
+ MINICONDA: C:\Miniconda36-x64
+
+ - PYTHON_VERSION: 3.5
+ PYTHON_ARCH: x64
+ MINICONDA: C:\Miniconda36-x64
+
+matrix:
+
+ allow_failures:
+
+ - PYTHON_VERSION: 3.5
+ PYTHON_ARCH: x64
+ MINICONDA: C:\Miniconda36-x64
+
+install:
+ - set PATH=%MINICONDA%;%MINICONDA%\Scripts;%PATH%
+
+ # Install the build and runtime dependencies of the project.
+ - conda config --set always_yes yes --set changeps1 no
+ - conda update -q conda
+ - conda info -a
+ - 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 coveralls
+ - pip install PySide2
+ - pip install gsw==3.0.6
+ - conda install numpy matplotlib-base gdal pyproj scipy basemap netCDF4 pillow
+ - 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:
+ - coverage run --source hyo2 setup.py test
+ - coverage report -m
+
+after_test:
+ - python setup.py bdist_wheel
+
+artifacts:
+ - path: dist\*
+
+
+version: 0.1.{build}-{branch}
+
 branches:
  only:
  - master

data/input/caris/test.svp

@@ -1,6 +1,6 @@
 [SVP_VERSION_2]
 C:\Users\gmasetti\AppData\Local\HydrOffice\Sound Speed\outputs\caris\test.svp
-Section 2012-126 14:33:12 43:51:34.46 -70:45:16.14 Created by hyo.soundspeed
+Section 2012-126 14:33:12 43:51:34.46 -70:45:16.14 Created by hyo2.soundspeed
 9.773000 1465.337000
 9.795000 1465.361000
 9.798000 1465.401000
@@ -450,7 +450,7 @@ Section 2012-126 14:33:12 43:51:34.46 -70:45:16.14 Created by hyo.soundspeed
 48.910000 1477.834000
 48.913000 1477.571000
 48.914000 1478.043000
-Section 2010-001 15:41:44 14:39:19.80 -144:47:06.00 Created by hyo.soundspeed
+Section 2010-001 15:41:44 14:39:19.80 -144:47:06.00 Created by hyo2.soundspeed
 0.000000 1513.250000
 0.200000 1495.890000
 0.400000 1492.550000
@@ -3144,7 +3144,7 @@ Section 2010-001 15:41:44 14:39:19.80 -144:47:06.00 Created by hyo.soundspeed
 459.800000 1561.340000
 460.000000 1561.340000
 460.100000 1561.350000
-Section 2017-027 19:33:00 01:00:00.00 -162:00:00.00 Created by hyo.soundspeed
+Section 2017-027 19:33:00 01:00:00.00 -162:00:00.00 Created by hyo2.soundspeed
 0.670000 1537.499767
 1.340000 1537.259463
 2.010000 1537.158506
@@ -4620,7 +4620,7 @@ Section 2017-027 19:33:00 01:00:00.00 -162:00:00.00 Created by hyo.soundspeed
 936.770000 1486.428582
 937.370000 1486.438682
 937.970000 1486.935096
-Section 2012-081 22:42:00 22:30:00.00 -156:30:00.00 Created by hyo.soundspeed
+Section 2012-081 22:42:00 22:30:00.00 -156:30:00.00 Created by hyo2.soundspeed
 0.000000 1531.400000
 6.870000 1531.400000
 10.000000 1530.140000
@@ -4656,7 +4656,7 @@ Section 2012-081 22:42:00 22:30:00.00 -156:30:00.00 Created by hyo.soundspeed
 5000.000000 1541.790000
 5500.000000 1550.870000
 12000.000000 1675.820000
-Section 2017-033 00:00:00 37:30:00.00 -42:30:00.00 Created by hyo.soundspeed
+Section 2017-033 00:00:00 37:30:00.00 -42:30:00.00 Created by hyo2.soundspeed
 0.000000 1515.392176
 10.000000 1515.536735
 20.000000 1515.680492
@@ -4689,7 +4689,7 @@ Section 2017-033 00:00:00 37:30:00.00 -42:30:00.00 Created by hyo.soundspeed
 4000.000000 1527.736315
 4500.000000 1536.527663
 5000.000000 1545.680951
-Section 2017-033 00:00:00 37:37:30.00 -42:52:30.00 Created by hyo.soundspeed
+Section 2017-033 00:00:00 37:37:30.00 -42:52:30.00 Created by hyo2.soundspeed
 0.000000 1514.807120
 5.000000 1514.946520
 10.000000 1515.182908
@@ -4788,7 +4788,7 @@ Section 2017-033 00:00:00 37:37:30.00 -42:52:30.00 Created by hyo.soundspeed
 4900.000000 1543.651256
 5000.000000 1545.532823
 5100.000000 1547.474716
-Section 2017-033 00:00:00 37:34:41.63 -42:55:58.98 Created by hyo.soundspeed
+Section 2017-033 00:00:00 37:34:41.63 -42:55:58.98 Created by hyo2.soundspeed
 0.000000 1516.786663
 10.000000 1516.975333
 20.000000 1517.146572
@@ -4820,7 +4820,7 @@ Section 2017-033 00:00:00 37:34:41.63 -42:55:58.98 Created by hyo.soundspeed
 3500.000000 1519.450299
 4000.000000 1527.563232
 4500.000000 1536.715462
-Section 2012-001 03:01:01 22:03:52.35 -157:03:29.94 Created by hyo.soundspeed
+Section 2012-001 03:01:01 22:03:52.35 -157:03:29.94 Created by hyo2.soundspeed
 0.000000 1530.490000
 0.600000 1530.700000
 1.300000 1530.770000

docs/license.rst

@@ -2,7 +2,7 @@
 License
 *******
 
-Copyright Notice and License Terms for: hyo.soundspeed - Sound Speed package for HydrOffice
+Copyright Notice and License Terms for: hyo2.soundspeed - Sound Speed package for HydrOffice
 Copyright (c) 2018, 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.

docs/user_manual_installation_1_requirements.rst

@@ -50,7 +50,7 @@ If you decide to install the package in a Python environment, the dependencies a
 
 If you want to install the last stable version (from PyPI):
 
-* :bash:`pip install hyo.soundspeed`
+* :bash:`pip install hyo2.soundspeed`
 
 Or, if you prefer the last bleeding edge code:
 

examples/sis/ex_sis_process.py

@@ -1,4 +1,4 @@
-from hyo.soundspeed.logging import test_logging
+from hyo2.soundspeed.logging import test_logging
 
 import logging
 import time