Merge pull request #71 from jklenzing/develop

v0.1.2

.coveragerc

@@ -0,0 +1,3 @@
+[report]
+omit =
+  */tests/*

.github/pull_request_template.md

@@ -1,29 +1,29 @@
 # Description
 
+Addresses # (issue)
+
 Please include a summary of the change and which issue is fixed. Please also
 include relevant motivation and context. List any dependencies that are required
 for this change.  Please see ``CONTRIBUTING.md`` for more guidelines.
 
-Fixes # (issue)
-
 ## Type of change
 
 Please delete options that are not relevant.
 
-- [ ] Bug fix (non-breaking change which fixes an issue)
-- [ ] New feature (non-breaking change which adds functionality)
-- [ ] Breaking change (fix or feature that would cause existing functionality
+- Bug fix (non-breaking change which fixes an issue)
+- New feature (non-breaking change which adds functionality)
+- Breaking change (fix or feature that would cause existing functionality
       to not work as expected)
-- [ ] This change requires a documentation update
+- This change requires a documentation update
 
 # How Has This Been Tested?
 
 Please describe the tests that you ran to verify your changes. Provide
 instructions so we can reproduce. Please also list any relevant details for
 your test configuration
 
-- [ ] Test A
-- [ ] Test B
+- Test A
+- Test B
 
 **Test Configuration**:
 * Operating system

.gitignore

@@ -4,7 +4,6 @@
 *.mod
 
 .DS_STORE
-sami2py-1.00.namelist
 *f.dat
 *u.dat
 time.dat
@@ -32,3 +31,4 @@ docs/.templates
 
 # dont ignore dat files in the testing folder
 !sami2py/tests/test_data/test/lon256/1999_256/*.dat
+!sami2py/tests/test_data/test/lon256/1999_257/*.dat

sami2py/__init__.py

@@ -36,7 +36,7 @@
 import sys
 import os
 
-__version__ = str('0.1.1')
+__version__ = str('0.1.2')
 
 # get home directory
 env_dir = sys.prefix

sami2py/_core.py

@@ -9,17 +9,17 @@
 -------------------------------------------------------------------------------
 
 run_model(year, day, lat=0, lon=0, alt=300,
-              f107=120, f107a=120, ap=0,
-              rmin=100, rmax=2000, gams=3, gamp=3, altmin=85.,
-              dthr=0.25, hrinit=0., hrpr=24., hrmax=48.,
-              dt0=30., maxstep=100000000, denmin=1.e-6,
-              nion1=1, nion2=7, mmass=48, h_scale=1, o_scale=1,
-              no_scale=1, o2_scale=1, he_scale=1, n2_scale=1, n_scale=1,
-              Tinf_scale=1, Tn_scale=1., euv_scale=1,
-              wind_scale=1, hwm_model=14,
-              fejer=True, ExB_drifts=np.zeros((10,2)), ve01=0., exb_scale=1,
-              alt_crit=150., cqe=7.e-14,
-              tag='test', clean=False, test=False, outn=False)
+          f107=120, f107a=120, ap=0,
+          rmin=100, rmax=2000, gams=3, gamp=3, altmin=85.,
+          dthr=0.25, hrinit=0., hrpr=24., hrmax=48.,
+          dt0=30., maxstep=100000000, denmin=1.e-6,
+          nion1=1, nion2=7, mmass=48, h_scale=1, o_scale=1,
+          no_scale=1, o2_scale=1, he_scale=1, n2_scale=1, n_scale=1,
+          Tinf_scale=1, Tn_scale=1., euv_scale=1,
+          wind_scale=1, hwm_model=14,
+          fejer=True, ExB_drifts=np.zeros((10, 2)), ve01=0., exb_scale=1,
+          alt_crit=150., cqe=7.e-14,
+          tag='test', clean=False, test=False, fmtout=True, outn=False)
 
     Initializes a run of the SAMI2 model and archives the data.
 -------------------------------------------------------------------------------

sami2py/_core_class.py

@@ -22,6 +22,7 @@
 import numpy as np
 from .utils import generate_path, get_unformatted_data
 
+
 class Model(object):
     """Python object to handle SAMI2 model output data
     """
@@ -121,13 +122,13 @@ def __repr__(self):
 
         mod_keys = self.check_standard_model()
         if mod_keys:
-            out.append('\nNo modifications to empirical models')
-        else:
             out.append('\nMultipliers used')
             out.append('----------------')
             for mkey in mod_keys:
                 out.append(('{s}: {f}').format(s=mkey,
                                                f=self.MetaData[mkey]))
+        else:
+            out.append('\nNo modifications to empirical models')
 
         return '\n'.join(out)
 
@@ -156,7 +157,7 @@ def _load_model(self):
         ni = 7
 
         model_path = generate_path(self.tag, self.lon0, self.year, self.day,
-                             self.test)
+                                   self.test)
 
         # Get NameList
         namelist_file = open(model_path + 'sami2py-1.00.namelist')
@@ -185,7 +186,7 @@ def _load_model(self):
             ti = np.loadtxt(path.join(model_path, 'tif.dat'))
             te = np.loadtxt(path.join(model_path, 'tef.dat'))
 
-            #get neutral values
+            # get neutral values
             if self.outn:
                 denn = np.loadtxt(model_path+'dennf.dat')
                 u = np.loadtxt(model_path+'u4f.dat')
@@ -204,6 +205,8 @@ def _load_model(self):
                                        dim0=dim0, dim1=dim1, reshape=True)
             ti = get_unformatted_data(model_path, 'ti',
                                       dim0=dim0, dim1=dim1, reshape=True)
+            # Temperatures have only one species
+            dim0 = nz*nf + 2
             te = get_unformatted_data(model_path, 'te',
                                       dim0=dim0, dim1=dim1, reshape=True)
 

sami2py/tests/test_core.py

@@ -1,7 +1,8 @@
 """Unit tests for run_model.py
 """
-import os
 import filecmp
+import numpy as np
+import os
 import shutil
 from nose.tools import raises
 import sami2py
@@ -15,42 +16,68 @@ def setup(self):
         """Setup function run before each test method to setup files needed
            to run the test effectively
         """
+        self.format = True
+        self.ref_file = 'ref_f_sami2py-1.00.namelist'
         self.model_path = generate_path('test', 0, 2012, 211, True)
         if not os.path.exists(self.model_path):
             os.makedirs(self.model_path)
-        filelist_fmt = ['glonf.dat', 'glatf.dat', 'zaltf.dat',
-                        'denif.dat', 'vsif.dat', 'tif.dat', 'tef.dat',
-                        'time.dat']
-        for filename in filelist_fmt:
-            open(fortran_dir + '/' + filename, 'w').close()
+        self.filelist = ['glonf.dat', 'glatf.dat', 'zaltf.dat', 'denif.dat',
+                         'vsif.dat', 'tif.dat', 'tef.dat', 'time.dat']
+        for filename in self.filelist:
+            open(os.path.join(fortran_dir, filename), 'w').close()
 
     def teardown(self):
         """Teardown function run before each test method to remove files needed
            to run the test effectively
         """
-        filelist_fmt = ['glonf.dat', 'glatf.dat', 'zaltf.dat',
-                        'denif.dat', 'vsif.dat', 'tif.dat', 'tef.dat',
-                        'time.dat']
-        for filename in filelist_fmt:
-            os.remove(fortran_dir + '/' + filename)
+        for filename in self.filelist:
+            os.remove(os.path.join(fortran_dir, filename))
         if os.path.exists(self.model_path):
             path_to_remove = os.path.split(self.model_path)[0]
             path_to_remove = os.path.split(path_to_remove)[0]
             shutil.rmtree(path_to_remove)
+        del self.format, self.ref_file, self.model_path, self.filelist
 
     def test_run_model_namelist(self):
         """The test to ensure that the namelist file is generated properly
         """
-        sami2py.run_model(year=2012, day=211, test=True)
+        sami2py.run_model(year=2012, day=211, test=True, fmtout=self.format)
+        namelist_file = self.model_path + 'sami2py-1.00.namelist'
+        ref_namelist = os.path.join(test_data_dir, self.ref_file)
+        assert filecmp.cmp(namelist_file, ref_namelist)
+
+    def test_run_model_namelist_w_invalid_hwm(self):
+        """The test to ensure that the invalid hwm reverts to 14
+        """
+        sami2py.run_model(year=2012, day=211, test=True, fmtout=self.format,
+                          hwm_model=15)
         namelist_file = self.model_path + 'sami2py-1.00.namelist'
-        ref_namelist = test_data_dir + '/reference_sami2py-1.00.namelist'
+        ref_namelist = os.path.join(test_data_dir, self.ref_file)
         assert filecmp.cmp(namelist_file, ref_namelist)
 
     def test_run_model_dat_files(self):
         """Test to ensure that the dat files are copied properly
         """
-        sami2py.run_model(year=2012, day=211, test=True)
-        assert os.stat(self.model_path + 'glonf.dat')
+        sami2py.run_model(year=2012, day=211, test=True, fmtout=self.format)
+        if self.format:
+            fname = 'glonf.dat'
+        else:
+            fname = 'glonu.dat'
+        assert os.stat(self.model_path + fname)
+
+    def test_run_model_ExB_files(self):
+        """Test to ensure that the ExB files are copied properly
+        """
+        sami2py.run_model(year=2012, day=211, test=True, fmtout=self.format,
+                          fejer=False, ExB_drifts=np.zeros((10, 2)))
+        assert os.stat(self.model_path + 'exb.inp')
+
+    @raises(Exception)
+    def test_run_model_ExB_wrong_size(self):
+        """Test to ensure that the ExB has proper shape
+        """
+        sami2py.run_model(year=2012, day=211, test=True, fmtout=self.format,
+                          fejer=False, ExB_drifts=np.zeros((1, 2)))
 
     @raises(ValueError)
     def test_input_format(self):
@@ -59,19 +86,50 @@ def test_input_format(self):
            create the file name. Will happen for any variable in the namelist
            set with the wrong type
         """
-        sami2py.run_model(year='2012', day='211', test=True)
+        sami2py.run_model(year='2012', day='211', test=True,
+                          fmtout=self.format)
 
     def test_fortran_executable(self):
         """Short run of fortran executable to ensure the code compiles
            and runs
         """
         tmp_archive_dir = sami2py.archive_dir
         sami2py.utils.set_archive_dir(path=test_data_dir)
-        sami2py.run_model(year=2012, day=211,
+        sami2py.run_model(year=2012, day=211, fmtout=self.format,
                           dthr=0.05, hrinit=0.0, hrpr=0.0, hrmax=.11)
         if os.path.isdir(tmp_archive_dir):
             sami2py.utils.set_archive_dir(path=tmp_archive_dir)
         else:
             with open(sami2py.archive_path, 'w') as archive_file:
                 archive_file.write('')
                 sami2py.archive_dir = ''
+
+
+class TestBasicModelRunUnformatted(TestBasicModelRun):
+    """Basic tests of the run_model script w/ unformatted output"""
+
+    def setup(self):
+        """Setup function run before each test method to setup files needed
+           to run the test effectively
+        """
+        self.format = False
+        self.ref_file = 'ref_u_sami2py-1.00.namelist'
+        self.model_path = generate_path('test', 0, 2012, 211, True)
+        if not os.path.exists(self.model_path):
+            os.makedirs(self.model_path)
+        self.filelist = ['glonu.dat', 'glatu.dat', 'zaltu.dat', 'deniu.dat',
+                         'vsiu.dat', 'tiu.dat', 'teu.dat', 'time.dat']
+        for filename in self.filelist:
+            open(os.path.join(fortran_dir, filename), 'w').close()
+
+    def teardown(self):
+        """Teardown function run before each test method to remove files needed
+           to run the test effectively
+        """
+        for filename in self.filelist:
+            os.remove(os.path.join(fortran_dir, filename))
+        if os.path.exists(self.model_path):
+            path_to_remove = os.path.split(self.model_path)[0]
+            path_to_remove = os.path.split(path_to_remove)[0]
+            shutil.rmtree(path_to_remove)
+        del self.format, self.ref_file, self.model_path, self.filelist

sami2py/tests/test_core_class.py

@@ -3,8 +3,6 @@
 import os
 import sys
 import sami2py
-from sami2py.utils import generate_path
-import numpy as np
 from nose.tools import raises
 
 
@@ -44,6 +42,13 @@ def test_model_instantiation(self):
                               test=True)
         assert isinstance(model, sami2py.Model)
 
+    def test_model_instantiation_with_unformatted_files_and_mods(self):
+        """Test that model object is instantiated as a sami2py_model
+        """
+        model = sami2py.Model(tag='test', lon=256, year=1999, day=257,
+                              test=True)
+        assert isinstance(model, sami2py.Model)
+
     def test_model_plot(self):
         """Basic test that a reasonable plot has been created by testing the
            resulting axis limits
@@ -69,3 +74,10 @@ def test_check_standard_model(self):
                               test=True)
         keys = model.check_standard_model()
         assert keys == list()
+
+    def test_model_repr(self):
+        """Test that __repr__ returns a string of information."""
+        model = sami2py.Model(tag='test', lon=256, year=1999, day=256,
+                              test=True)
+        repr_str = model.__repr__()
+        assert type(repr_str) is str

sami2py/tests/test_data/ref_u_sami2py-1.00.namelist

@@ -0,0 +1,38 @@
+&go
+  fmtout   = .false.,
+  maxstep  =  100000000,
+  hrmax    =  48.000000,
+  dt0      =  30.000000,
+  dthr     =  0.250000,
+  hrpr     =  24.000000,
+  grad_in  =  300.000000,
+  glat_in  =  0.000000,
+  glon_in  =  0.000000,
+  fejer    =  .true.,
+  rmin     =  100.000000,
+  rmax     =  2000.000000,
+  altmin   =  85.000000,
+  fbar     =  120.000000,
+  f10p7    =  120.000000,
+  ap       =  0,
+  year     =  2012,
+  day      =  211,
+  mmass    =  48,
+  nion1    =  1,
+  nion2    =  7,
+  hrinit   =  0.000000,
+  tvn0     =  1.000000,
+  tvexb0   =  1.000000,
+  ve01     =  0.000000,
+  gams     =  3,
+  gamp     =  3,
+  snn      =  1.000000,1.000000,1.000000,1.000000,1.000000,1.000000,1.000000,
+  stn      =  1.000000,
+  denmin   =  1.000000e-06,
+  alt_crit =  150.000000,
+  cqe      =  7.000000e-14,
+  Tinf_scl =  1.000000,
+  euv_scl  =  1.000000,
+  hwm_mod  =  14,
+  outn     = .false.
+&end

sami2py/tests/test_data/test/lon256/1999_257/exb.inp

@@ -0,0 +1,10 @@
+-2.256592115245508268e+01 -1.700658929016086063e+01
+6.970157155494434598e+00 -1.785773092653965932e+01
+7.715990594846469097e-01 -1.457794556537672204e+00
+1.133009384321719537e+01 6.217447257350539047e+00
+5.315180719049175551e+00 6.543500525980066485e+00
+-4.754135936133724094e+00 7.493698025175492994e+00
+-3.036451049580922046e+00 -1.789034697779917638e+00
+-3.791099765373269648e+00 -8.665409647917849956e-01
+2.083139968647748308e+00 -3.636326810220660732e+00
+2.205828847907577828e+00 0.000000000000000000e+00