Merge pull request #22 from jdavid/master

Plotting and docs

.gitignore

@@ -13,3 +13,6 @@ doc/build/*
 f2py_build/f90/*
 FortFlex.so
 .idea/*
+
+/.cache/
+.*.swp

.travis.yml

@@ -27,9 +27,8 @@ install:
   # Install dependencies in conda
   - conda create -n reflex_env python=$TRAVIS_PYTHON_VERSION libgfortran
   - source activate reflex_env
-  - conda install pyqt   # seems required when running matplotlib
   # Install the remaining requeriments
-  - cat requirements.txt | xargs conda install
+  - conda install --file requirements.txt -c conda-forge
 
   # Install dependencies in PyPI
   - pip install pytest-cov coveralls

README.md

@@ -26,10 +26,9 @@ will have the option to save this converted output for later use.
 
 Initially we aim to provide:
 
-  a. an interface to read model output and provide general information about the simulation
-  b. tools for simple access to the data
-  c. simple visualization tools
-
+- an interface to read model output and provide general information about the simulation
+- tools for simple access to the data
+- simple visualization tools
 
 Some routines were initially created to work with FLEXPART model
 ouput. [FLEXPART](http://transport.nilu.no/flexpart) is a Lagrangian particle
@@ -49,25 +48,37 @@ As for Issues, please use the
 [tool](https://github.com/spectraphilic/reflexible/issues) at
 github.
 
-Direct inquiries may be sent to::
+Direct inquiries may be sent to:
 
 	John F Burkhart, University of Oslo
 	[john.burkhart](mailto://john.burkhart@geo.uio.no)
 
-## Web Resources ##
+## Sphinx Documentation
 
-### GitHub ###
+The documentation is hosted at
+[readthedocs](http://reflexible.readthedocs.org/en/latest/index.html).
 
-Clone the github repository into a folder in your PYTHONPATH::
+## Working with reflexible
 
-  $ git clone https://github.com/spectraphilic/reflexible.git
+Clone the github repository into a folder in your PYTHONPATH:
 
-### Sphinx Documentation ###
+    $ git clone https://github.com/spectraphilic/reflexible.git
 
-The documentation is hosted at
-[readthedocs](http://reflexible.readthedocs.org/en/latest/index.html).
+Install the requirements:
 
-## Working with reflexible
+    $ conda install --file requirements.txt -c conda-forge
+
+Now compile the library:
+
+    $ python setup.py build_ext --inplace
+
+This will compile the pflexcy.pyx file into a pflexcy.so module that
+can be imported and used by the pf.readgrid function. A series of
+tests are run to try and determine the best module to use -- somewhat
+transparently to the user. See the reflexible.readgridV8 function for
+more information.
+
+### Possible issues
 
 There are a few 'gotchas' when using the module. First, you will
 likely have to recompile (f2py) the FortFlex.f file and create a
@@ -78,15 +89,7 @@ an issue.
 An alternative 'BinaryFile' class has been created so one can work
 with pure Python. Alone, it is significantly slower than the FortFlex
 module, however, if you use the dumpgrid module, significant speedups
-can be achieved. For this run::
-
-  $ python setup.py build_ext --inplace
-
-This will compile the pflexcy.pyx file into a pflexcy.so module that
-can be imported and used by the pf.readgrid function. A series of
-tests are run to try and determine the best module to use -- somewhat
-transparently to the user. See the reflexible.readgridV8 function for
-more information.
+can be achieved.
 
 Primary functionality comes from the readheaderV8 function and the
 readgridV8 function. I have created a "Header" class that can be used
@@ -99,24 +102,24 @@ documentation.
 
 reflexible comes with a suite of test units that you can run in a
 series of ways after you compiled the extensions and before you
-install it::
+install it:
 
-  $ PYTHONPATH=. python -c "import reflexible; reflexible.test()"
+    $ PYTHONPATH=. python -c "import reflexible; reflexible.test()"
 
-or::
+or:
 
-  $ PYTHONPATH=. python reflexible/tests/all.py
+    $ PYTHONPATH=. python reflexible/tests/all.py
 
-or using the excellent py.test (recommended for developers)::
+or using the excellent py.test (recommended for developers):
 
-  $ PYTHONPATH=. py.test
+    $ py.test
 
 ## Installation
 
 If all is working correctly, then you can install it (you might need
-to be superuser here)::
+to be superuser here):
 
-  $ python setup.py install
+    $ python setup.py install
 
 And *hopefully* everything works!.
 
@@ -125,17 +128,18 @@ And *hopefully* everything works!.
 When you run into problems it is always nice that when you are filing
 a ticket you would add the information about the versions you are
 using.  You can do that via the `pf.print_versions()`.  Here it is an
-output example::
-
-  $ python -c "import reflexible; reflexible.print_versions()"
-  -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
-  reflexible version: 0.10.0
-  NumPy version:     1.9.0
-  Python version:    2.7.8 |Anaconda 2.1.0 (64-bit)| (default, Aug 21 2014, 18:22:21)
-  [GCC 4.4.7 20120313 (Red Hat 4.4.7-1)]
-  Platform:          linux2-x86_64
-  Byte-ordering:     little
-  -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
+output example:
+
+    $ python -c "import reflexible; reflexible.print_versions()"
+    -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
+    reflexible version: 0.5.0
+    NumPy version:     1.12.0
+    Python version:    3.5.3 | packaged by conda-forge | (default, Feb  9 2017, 14:37:12)
+    [GCC 4.8.2 20140120 (Red Hat 4.8.2-15)]
+    Platform:          linux-x86_64
+    Byte-ordering:     little
+    -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
+
 
 ## Key Tools
 

doc/source/getting_started.rst

@@ -529,7 +529,7 @@ the 0th element is the Total Column.
 
 Using the plotting tools of reflexible we can plot the total column easily::
 
-    In [61]: rf.plot_totalcolumn(H, myc.total_column, map_region='NorthAtlantic')
+    In [61]: rf.plot_totalcolumn(H, myc, map_region='NorthAtlantic')
 
 .. TODO: The above line does not work yet for the stads2 dataset.  Why?
 

doc/source/introduction.rst

@@ -53,6 +53,10 @@ the git repository::
 
     $ git clone https://github.com/spectraphilic/reflexible.git
 
+Install the requirements:
+
+    $ conda install --file requirements.txt -c conda-forge
+
 Build and test
 ==============