Bugfix greatcircle

.gitignore

@@ -1,4 +1,5 @@
 build
+html
 *.so
 *.o
 *.pyc
@@ -7,6 +8,8 @@ build
 *.a
 *.log
 *.status
+*.dSYM
+*.nc
 bathy_smoother/Python/
 examples/Yellow_Sea/Inputs/Initial/compute_remap_weights_in
 examples/Yellow_Sea/YELLOW_grd_v1.nc
@@ -36,3 +39,4 @@ pyroms/external/scrip/source/makefile2
 pyroms/external/scrip/source/scrip
 pyroms/external/scrip/source/scrip_test
 pyroms_toolbox/Python/
+mask_change.txt

README

@@ -10,16 +10,11 @@ rough around the edges.
 Prerequisites
 -------------
 
-Meanwhile, you can prepare by installing Enthought Python
-(http://www.enthought.com/) or by this collection of packages:
+Now using Anaconda python to download python 3.x and a bunch of other stuff:
 
-   * Python itself. You will need a version that's at least 2.4 and
-     less than 3.0.
+   * Python itself. You will need a version that's at least 3.4.
 
-   * numpy. Get a version that's reasonably new, don't count on the
-     version 1.0.1 that you found already on the system. How do you
-     tell the version? At the interactive prompt from python, type
-     "import numpy" then "numpy.__version__".
+   * numpy.
 
    * scipy.
 
@@ -39,10 +34,15 @@ Meanwhile, you can prepare by installing Enthought Python
      interactive fun. It preloads both numpy and the matplotlib
      pylab package.
 
-We may also add pyngl and pynio from NCAR to this list. Or ESMPy.
-Or Python 3...
+   * natgrid from http://github.com/matplotlib/natgrid for at least
+     one of the examples.
 
-If you want a package manager for these bits, check out Anaconda.
+Planning to move to ESMF. Download it with:
+
+     conda install --channel https://conda.anaconda.org/conda-forge esmf
+
+We may also add pyngl and pynio from NCAR to this list.
+Or jupyter.
 
 Installing
 ----------
@@ -53,31 +53,40 @@ setup.py scripts for each, plus an examples directory.
 
 For now,
 
-  cd pyroms_toolbox; python setup.py build --fcompiler=gnu95;
+  cd pyroms_toolbox; python setup.py build
                      python setup.py install --prefix=xxx;
                      cd ..
 
-The above may or may not need something along these lines:
-setenv LDFLAGS '-L/usr/local/pkg/python/python-2.7.2/lib -shared'
-
   cd bathy_smoother; python setup.py build;
                      python setup.py install --prefix=xxx;
                      cd ..
   cd pyroms; check the paths in the install script and see if it runs...
+             Maybe cut and paste from it into a bash shell.
+
+I had to hack the scrip makefile for the fortran90 netcdf stuff. The
+anaconda netcdf-fortran reports:
+    nf-config not yet implemented for cmake builds
+
+A note on the .so files from fortran: They might now end up with names like:
 
-If you needed the LDFLAGS above, you'll need to add it to the
-install script too, at least for the build of scrip.
+    scrip.cpython-35m-x86_64-linux-gnu.so
 
-I'm getting inconsistent results with where the .so files need to be. Best
-results for me are if I go to the site-packages directory where pycnal
-got installed and copy all the .so files:
+It's OK - they'll load as long as they are in your PYTHONPATH. You might
+also need libgu.so to be in your LD_LIBRARY_PATH. I'm getting inconsistent
+results with where the .so files need to be. Best results for me are if I go
+to the site-packages directory where pyroms got installed and copy all the
+.so files:
 
-    cp pycnal/*.so .
-    cp pycnal_toolbox/*.so .
+    cp pyroms/*.so .
+    cp pyroms_toolbox/*.so .
     cp bathy_smoother/*.so .
 
-Make sure this site-packages directory is in your PYTHONPATH.
+Make sure this site-packages directory is in your PYTHONPATH. As for
+libgu.so, it went into $DESTDIR/lib, for me $HOME/python/lib - that's
+what needs to be in the LD_LIBRARY_PATH.
 
+Also, f2py may or may not be called f2py3, depending. It's listed explicitly
+in the scrip makefile and under pyroms_toolbox/pyroms_toolbox/src/makefile.
 
 Running
 -------
@@ -86,3 +95,11 @@ We have a gridid.txt file that's pointed to by the PYROMS_GRIDID_FILE
 environment variable. If you are operating on files containing
 sufficient grid information already, you won't need to use this.
 An example is provided in the examples directory.
+
+
+Doxygen
+-------
+
+Running "doxygen .doxygen" in any of pyroms, pyroms_toolbox or
+bathy_smoother will generate doxygen files. Edit the .doxygen files to
+specify html vs. some other output format.