Merge branch 'master' of https://srccontrol.orr.noaa.gov/gnome/pygnome

.gitignore

@@ -12,6 +12,8 @@ cy_*.c
 empty_BW_image.png
 .DS_Store
 .cache/
+*.swn
+*.swo
 
 *.ipynb_checkpoints/
 
@@ -53,6 +55,98 @@ py_gnome/junk_tiny.txt
 py_gnome/tests/unit_tests/test_utilities/test_file_tools/test.bna
 py_gnome/tests/unit_tests/test_utilities/test_file_tools/test_bad.bna
 
+# ignore gnerated and sample data for tests
+
+py_gnome/tests/junk.txt
+py_gnome/tests/junk_large.txt
+py_gnome/tests/unit_tests/ElementType_6.json
+py_gnome/tests/unit_tests/Emulsification_1.json
+py_gnome/tests/unit_tests/Evaporation_0.json
+py_gnome/tests/unit_tests/LongIslandSoundMap.BNA
+py_gnome/tests/unit_tests/Model.json
+py_gnome/tests/unit_tests/Model.zip
+py_gnome/tests/unit_tests/Skim_2.json
+py_gnome/tests/unit_tests/Spill_0.json
+py_gnome/tests/unit_tests/Water_0.json
+py_gnome/tests/unit_tests/Waves_3.json
+py_gnome/tests/unit_tests/Wind_1.json
+py_gnome/tests/unit_tests/Wind_1_data.WND
+py_gnome/tests/unit_tests/junk.txt
+py_gnome/tests/unit_tests/junk_conda_list.txt
+py_gnome/tests/unit_tests/junk_large.txt
+py_gnome/tests/unit_tests/test_environment/sample_data/3D_circular.nc
+py_gnome/tests/unit_tests/test_environment/sample_data/currents/
+py_gnome/tests/unit_tests/test_environment/sample_data/staggered_sine_channel.nc
+py_gnome/tests/unit_tests/test_environment/sample_data/tri_ring.nc
+py_gnome/tests/unit_tests/test_weatherers/ElementType_6.json
+py_gnome/tests/unit_tests/test_weatherers/Emulsification_1.json
+py_gnome/tests/unit_tests/test_weatherers/Evaporation_0.json
+py_gnome/tests/unit_tests/test_weatherers/LongIslandSoundMap.BNA
+py_gnome/tests/unit_tests/test_weatherers/Model.json
+py_gnome/tests/unit_tests/test_weatherers/Model.zip
+py_gnome/tests/unit_tests/test_weatherers/Skim_2.json
+py_gnome/tests/unit_tests/test_weatherers/Spill_0.json
+py_gnome/tests/unit_tests/test_weatherers/Water_0.json
+py_gnome/tests/unit_tests/test_weatherers/Waves_3.json
+py_gnome/tests/unit_tests/test_weatherers/Wind_1.json
+py_gnome/tests/unit_tests/test_weatherers/Wind_1_data.WND
+
+#ignore generated and downloaded files from scripts
+py_gnome/scripts/arctic_avg2_0001_gnome.nc
+py_gnome/scripts/arctic_avg2_0002_gnome.nc
+py_gnome/scripts/script_animation_demo/images/
+py_gnome/scripts/script_animation_demo/raster.bmp
+py_gnome/scripts/script_boston/EbbTides.cur
+py_gnome/scripts/script_boston/EbbTidesShio.txt
+py_gnome/scripts/script_boston/MassBayMap.bna
+py_gnome/scripts/script_boston/MassBaySewage.cur
+py_gnome/scripts/script_boston/MerrimackMassCoast.cur
+py_gnome/scripts/script_boston/MerrimackMassCoastOSSM.txt
+py_gnome/scripts/script_boston/WAC10msNW.cur
+py_gnome/scripts/script_boston/WAC10msSW.cur
+py_gnome/scripts/script_boston/gnome_profile
+py_gnome/scripts/script_boston/script_boston.kmz
+py_gnome/scripts/script_boston/script_boston.nc
+py_gnome/scripts/script_boston/script_boston_uncertain.nc
+py_gnome/scripts/script_chesapeake_bay/ChesapeakeBay.bna
+py_gnome/scripts/script_chesapeake_bay/ChesapeakeBay.dat
+py_gnome/scripts/script_chesapeake_bay/ChesapeakeBay.nc
+py_gnome/scripts/script_chesapeake_bay/script_chesapeake_bay.nc
+py_gnome/scripts/script_chesapeake_bay/script_chesapeake_bay_uncertain.nc
+py_gnome/scripts/script_columbia_river/COOPSu_CREOFS24.nc
+py_gnome/scripts/script_columbia_river/COOPSu_CREOFS24.nc.dat
+py_gnome/scripts/script_columbia_river/columbia_river.bna
+py_gnome/scripts/script_delaware_bay/DelawareRiverMap.bna
+py_gnome/scripts/script_delaware_bay/FloodTides.cur
+py_gnome/scripts/script_delaware_bay/FloodTidesShio.txt
+py_gnome/scripts/script_delaware_bay/NW30ktwinds.cur
+py_gnome/scripts/script_delaware_bay/Offshore.cur
+py_gnome/scripts/script_delaware_bay/SW30ktwinds.cur
+py_gnome/scripts/script_delaware_bay/script_delaware_bay.nc
+py_gnome/scripts/script_guam/GuamMap.bna
+py_gnome/scripts/script_guam/OutsideWAC.cur
+py_gnome/scripts/script_guam/WACFTideShioHts.txt
+py_gnome/scripts/script_guam/WACFloodTide.cur
+py_gnome/scripts/script_guam/script_guam.nc
+py_gnome/scripts/script_guam_get_data_test/GuamMap.bna
+py_gnome/scripts/script_guam_get_data_test/OutsideWAC.cur
+py_gnome/scripts/script_guam_get_data_test/WACFTideShioHts.txt
+py_gnome/scripts/script_guam_get_data_test/WACFloodTide.cur
+py_gnome/scripts/script_guam_get_data_test/script_guam.nc
+py_gnome/scripts/script_ice/ak_arctic.bna
+py_gnome/scripts/script_ice/script_ice.nc
+py_gnome/scripts/script_plume/images/
+py_gnome/scripts/script_plume/script_plume.nc
+py_gnome/scripts/script_tamoc/HYCOM_3d.nc
+py_gnome/scripts/script_tamoc/HYCOM_3d.nc.dat
+py_gnome/scripts/script_tamoc/Input/case_01
+py_gnome/scripts/script_tamoc/KIKT.osm
+py_gnome/scripts/script_tamoc/cat
+py_gnome/scripts/script_tamoc/diff.txt
+py_gnome/scripts/script_tamoc/gulf_tamoc.nc
+py_gnome/scripts/script_tamoc/images/
+
+
 # ignore generated oildb
 oil_library/oil_library/OilLib.db
 oil_library/temp.txt

.gitlab-ci.yml

@@ -1,22 +1,27 @@
-before_script: 
+before_script:
   - yum update -y
   - yum install gcc gcc-c++ -y
   - yum install netcdf-devel -y # needed by the C++ code -- it can't find the conda versions
+  - yum install libXext libSM libXrender -y  # needed by matplotlib on CentOS
+
   # make sure the conda channels are set up right
   # the last channel you add will be first on the list
-  - conda config --add channels NOAA-ORR-ERD
   - conda config --add channels defaults
+  - conda config --add channels NOAA-ORR-ERD
   - conda config --add channels conda-forge
+
+  # install the requirements
   - conda install --file conda_requirements.txt
+
   # get the oil libary package from gitlab
   - pip install -U git+https://srccontrol.orr.noaa.gov/gnome/[email protected]#egg=oil_library
   - cd ./py_gnome
   - python ./setup.py develop
 
-master: 
+master:
   script:
     - py.test -runslow
-  only: 
+  only:
     - master
 
 develop:

InstallingWithAnaconda.rst

@@ -58,7 +58,7 @@ manager that Anaconda is built on. So when working with Anaconda, you
 use the conda package manager for installing conda packages. ``pip``
 can also be used with conda, but it's best to use use conda if you can.
 
-We have made sure that every pacakge you need is available for conda.
+We have made sure that every package you need is available for conda.
 
 Setting up
 ..........
@@ -122,13 +122,21 @@ install a package, conda will first look in conda-forge, then NOAA-ORR-ERD, and
 then in the default channel. This order should work well for PyGNOME. Be sure to add the channels in the order we specify. You can see what channels you have with::
 
     > conda config --get channels
+<<<<<<< HEAD
+=======
 
 It should return something like this::
 
     --add channels 'defaults'   # lowest priority
     --add channels 'NOAA-ORR-ERD'
     --add channels 'conda-forge'   # highest priority
+>>>>>>> develop
 
+It should return something like this::
+
+    --add channels 'defaults'   # lowest priority
+    --add channels 'conda-forge'
+    --add channels 'NOAA-ORR-ERD'   # highest priority
 
 conda environments
 ------------------
@@ -170,7 +178,11 @@ and kept separate from your main Anaconda install.
 You will need to activate the environment any time you want to work with
 ``py_gnome`` in the future
 
+<<<<<<< HEAD
 **NOTE:** Again, if you are only using Python / Anaconda for GNOME, there is not reason to deal with the complications of environments.
+=======
+**NOTE:** Again, if you are only using Python / Anaconda for GNOME, it is not necessary to deal with the complications of environments.
+>>>>>>> develop
 
 Download GNOME
 --------------
@@ -185,9 +197,19 @@ you can "clone" the git repository. If you clone the repository, you will
 be able to update the code with the latest version with a simple command,
 rather than having to re-download the whole package.
 
+Downloading a single release
+----------------------------
+
+zip and tar archives of the PyGnome source code can be found here:
+
+https://github.com/NOAA-ORR-ERD/PyGnome/releases
+
+This will get you the entire source archive of a given release, which is a fine way to work with PyGnome. However, if you want to be able to quickly include changes as we update the code, you may want to work with a git "clone" of the source code instead.
+
 Cloning the PyGNOME git repository
 ----------------------------------
 
+
 git
 ...
 
@@ -266,7 +288,7 @@ If you want to use py_gnome with "real oil", rather than inert particles, you wi
 
 https://github.com/NOAA-ORR-ERD/OilLibrary
 
-This is under active development along with ``py_gnome``, so you are best off downloading the sources from gitHub and installing it from source -- similar to ``py_gnome``.
+This is under active development along with ``py_gnome``, so you are best off downloading the sources from gitHub and installing it from source -- similar to ``py_gnome``. Though the lated releases of each should be compatible.
 
 cloning the repository ::
 
@@ -308,10 +330,13 @@ Store.
 [you may be able to install only the command line tools -- Apple keeps changing its mind]
 
 After installing XCode, you still need to install the "Command Line
-Tools". XCode includes a new "Downloads" preference pane to install
+Tools".  XCode includes a new "Downloads" preference pane to install
 optional components such as command line tools, and previous iOS
 Simulators.
 
+**NOTE:** This may be slightly different on different versions of OS-X
+and XCode -- google is your friend.
+
 To install the XCode command line tools: - Start XCode from the
 launchpad - Click the "XCode" dropdown menu button in the top left of
 the screen near the Apple logo - Click "Preferences", then click
@@ -398,7 +423,7 @@ cleans files generated by the build as well as files auto-generated by
 cython. It is a good idea to run ``cleanall`` after updating from the
 gitHub repo -- particularly if strange errors are occurring.
 
-You will need to re-run "develop" or "install" after running "cleanall"
+You will need to re-run ``develop`` or ``install`` after running ``cleanall``
 
 Testing ``py_gnome``
 --------------------

NormalInstall.rst

@@ -1,5 +1,5 @@
-Installation in Development Mode
-================================
+Installation without conda / Anaconda
+=====================================
 
 Since this is development work, it might be good to create and run this
 in a virtual environment. `Virtualenv <http://www.virtualenv.org/en/latest/>`__ and `Virtual envwrapper <http://virtualenvwrapper.readthedocs.org/en/latest/>`__ eases
@@ -12,42 +12,38 @@ may require a virtualenv in order to freely install python packages in
 python's site-packages area. (site-packages is the standard place where
 python installers will put packages after building them)
 
-You may also want to consider using conda environments.
+You may also want to consider using conda environments -- see above.
 
-There is C++/Cython code that must be built - you will need the corect C compiler and recent setuptools, etc.
+There is C++/Cython code that must be built - you will need the correct C compiler and recent setuptools, etc. See "Installing With Anaconda" for more detail.
 
 python.org
 ==========
 
 The following has been tested against `Python
 2.7 <https://www.python.org/downloads/>`__
 
-Linux (Tested in 32-bit, Ubuntu raring 13.04)
----------------------------------------------
+Linux (Tested in 64-bit, CentOS)
+--------------------------------
 
-For Linux use appropriate package manager (apt-get on ubuntu) to
+For Linux use appropriate package manager (yum on CentOS, apt-get on Ubuntu) to
 download/install binary dependencies.
 
+
 Binary Dependencies
 ...................
 
 1. setuptools is required.
     ``> sudo apt-get install python-setuptools``
     \` \`
-2. `Pillow <http://pillow.readthedocs.org/en/latest/installation.html>`__
-   has binary dependencies. Visit the docs to get list of dependencies
-   for your system. Pillow requires Python's development libraries::
+
+2. To compile Python extensions, you need the development libs for Python:
 
     > sudo apt-get install python-dev
 
-This did not build symlinks to libraries for me in /usr/lib, so had to manually create them::
+3. netCDF4 python module requires NetCDF libraries:
 
-    > sudo ln -s /usr/lib/``\ uname
-   -i``-linux-gnu/libfreetype.so /usr/lib/``      ``> sudo ln -s /usr/lib/``\ uname
-   -i``-linux-gnu/libjpeg.so /usr/lib/``      ``> sudo ln -s /usr/lib/``\ uname
-   -i``-linux-gnu/libz.so /usr/lib/```` \`
+   libhdf5-serial-dev
 
-3. netCDF4 python module requires NetCDF libraries: libhdf5-serial-dev,
    libnetcdf-dev
 
 4. The following python packages, documented in PyGnome's
@@ -56,6 +52,7 @@ This did not build symlinks to libraries for me in /usr/lib, so had to manually
 Binaries for
 
 `Numpy <http://packages.ubuntu.com/raring/python/python-numpy>`__ and
+
 `Cython <http://packages.ubuntu.com/raring/python/cython>`__
 can be installed using apt-get.
 
@@ -71,7 +68,6 @@ latest packages in your virtualenv once the above dependencies are met::
     > pip install numpy
     > pip install cython
     > pip install netCDF4
-    > pip install Pillow
 
 The remaining dependencies are python packages and can be installed using::
 
@@ -129,7 +125,7 @@ installed packages::
 
     >  pip
 
-    Usage:   
+    Usage:
       pip <command> [options]
 
     Commands:
@@ -185,7 +181,7 @@ Build PyGnome
 
 4. build the ``py_gnome`` module in develop mode first as install mode may
    still need some testing/work.
-    
+
    The other option you may need is ``cleanall``, which should clean the development environment -- good to do after puling new code from git.
 
 5. If this successfully completes, then run the unit tests::

conda_requirements.txt

@@ -23,8 +23,14 @@ colander>=1.2
 sqlalchemy>=0.7.6
 zope.interface>=4.1
 zope.sqlalchemy>=0.7.6
+<<<<<<< HEAD
 gdal>=2.1.1
 netCDF4=1.2.7
+=======
+hdf5=1.8.*
+netCDF4=1.2.7
+gdal>=2.1.1
+>>>>>>> develop
 awesome-slugify>=1.6
 regex>=2014.12
 unidecode>=0.04.19