Merge 8e67d1e into 593c241

.coveragerc

@@ -1,3 +1,5 @@
+[run]
+
 [report]
 omit =
   */tests/*

.gitignore

@@ -26,6 +26,10 @@ time.dat
 /*.egg-info
 /*.egg
 
+# Unit test / coverage reports
+.coverage
+.coverage.*
+
 # Sphinx rendered directories
 docs/.build
 docs/.static

.travis.yml

@@ -3,25 +3,36 @@ dist: xenial
 matrix:
   include:
     - python: 2.7
-    - python: 3.4
     - python: 3.5
     - python: 3.6
     - python: 3.7
 
+services: xvfb
+
 addons:
   apt:
     packages:
     - gfortran
 
 before_install:
+  - pip install pytest-cov
   - pip install coveralls
   - pip install future
   - pip install matplotlib
+
 install:
-  - source activate test-environment
   - python setup.py install
+
+before_script:
+  # set up display screen
+  - export DISPLAY=:99.0
+  - if [[ $TRAVIS_PYTHON_VERSION < "3.0" ]]; then
+      sh -e /etc/init.d/xvfb start;
+      sleep 3;
+    fi
+
 script:
-  - nosetests -vs --with-coverage --cover-package=sami2py
+  - pytest -v --cov=sami2py/
 
 after_success:
   - coveralls

CHANGELOG.md

@@ -12,6 +12,7 @@ This project adheres to [Semantic Versioning](http://semver.org/).
   - Move package metadata to setup.cfg
   - Auto-build fortran executables as part of setup.py
   - Added CHANGELOG.md
+  - Switched to pytest for unit testing
 
 ## [0.1.2] - 2019-07-02
 - Patch to fix loading of unformatted output files.

CONTRIBUTING.md

@@ -55,15 +55,15 @@ To set up `sami2py` for local development:
    Now you can make your changes locally. Tests for new instruments are
    performed automatically.  Tests for custom functions should be added to the
    appropriately named file in ``sami2py/tests``.   If no test file exists, then
-   you should create one.  This testing uses nose, which will run tests on any
+   you should create one.  This testing uses pytest, which will run tests on any
    python file in the test directory that starts with ``test_``.
 
 4. When you're done making changes, run all the checks to ensure that nothing
    is broken on your local system
 
 ::
 
-    nosetests -vs sami2py
+    pytest -vs sami2py
 
 5. Update/add documentation (in ``docs``), if relevant
 

sami2py/__init__.py

@@ -19,7 +19,7 @@
 import logging
 import os
 
-__version__ = str('0.1.2')
+__version__ = str('0.2.0-dev')
 
 # get home directory
 env_dir = os.path.expanduser('~')

sami2py/_core_class.py

@@ -189,8 +189,8 @@ def _load_model(self):
 
             # get neutral values
             if self.outn:
-                denn = np.loadtxt(model_path+'dennf.dat')
-                u = np.loadtxt(model_path+'u4f.dat')
+                denn = np.loadtxt(path.join(model_path, 'dennf.dat'))
+                u4 = np.loadtxt(path.join(model_path, 'u4f.dat'))
         else:
             # Get Location
             glat = get_unformatted_data(model_path, 'glat')
@@ -206,10 +206,17 @@ 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
+            if self.outn:
+                denn = get_unformatted_data(model_path, 'denn',
+                                            dim0=dim0, dim1=dim1, reshape=True)
+
+            # Electron Temperatures and neutral wind have only one species
             dim0 = nz*nf + 2
             te = get_unformatted_data(model_path, 'te',
                                       dim0=dim0, dim1=dim1, reshape=True)
+            if self.outn:
+                u4 = get_unformatted_data(model_path, 'u4',
+                                           dim0=dim0, dim1=dim1, reshape=True)
 
         glat = np.reshape(glat, (nz, nf), order="F")
         glon = np.reshape(glon, (nz, nf), order="F")
@@ -228,10 +235,10 @@ def _load_model(self):
                                        'zalt': (['z', 'f'], zalt),
                                        'ut': self.ut})
         if self.outn:
-            denn = np.reshape(denn, (nz, nf, 7, nt), order="F")
-            self.data['denn'] = denn
-            u = np.reshape(u, (nz, nf, nt), order="F")
-            self.data['u'] = u
+            denn = np.reshape(denn, (nz, nf, ni, nt), order="F")
+            self.data['denn'] = (('z', 'f', 'ion', 'ut'), denn)
+            u4 = np.reshape(u4, (nz, nf, nt), order="F")
+            self.data['u4'] = (('z', 'f', 'ut'), u4)
 
     def _generate_metadata(self, namelist):
         """Reads the namelist and generates MetaData based on Parameters
@@ -352,11 +359,16 @@ def plot_lat_alt(self, time_step=0, species=1):
         species : (int)
             ion species index :
             0: H+, 1: O+, 2: NO+, 3: O2+, 4: He+, 5: N2+, 6: N+
+        test : (bool)
+            Suppresses plt.show() for testing
         """
         import matplotlib.pyplot as plt
 
+        fig = plt.gcf()
+
         plt.pcolor(self.data['glat'], self.data['zalt'],
                    self.data['deni'][:, :, species, time_step])
         plt.xlabel('Geo Lat (deg)')
         plt.ylabel('Altitude (km)')
-        plt.show()
+
+        return fig

sami2py/fortran/sami2py-1.00.f

@@ -3053,11 +3053,13 @@ subroutine output ( hrut,ntm,istep )
 !         write(84) u1
 !         write(85) u2
 !         write(86) u3
-!         write(87) u4
+         if (outn) then
+           write(87) u4
 !         write(88) u5
 !         write(90) vot
 !         write(91) vor
-!         write(92) denn
+           write(92) denn
+         endif
 !         write(93) vexbp
        endif
 

sami2py/tests/test_core.py

@@ -4,7 +4,8 @@
 import numpy as np
 import os
 import shutil
-from nose.tools import raises
+import pytest
+
 import sami2py
 from sami2py import fortran_dir, test_data_dir
 from sami2py.utils import generate_path
@@ -77,22 +78,23 @@ def test_run_model_ExB_files(self):
                           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)))
+        with pytest.raises(Exception):
+            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):
         """Test for error output upon incorrect input format
            file.write should throw the error when using string formatting to
            create the file name. Will happen for any variable in the namelist
            set with the wrong type
         """
-        sami2py.run_model(tag='test', year='2012', day='211', test=True,
-                          fmtout=self.format)
+        with pytest.raises(ValueError):
+            sami2py.run_model(tag='test', year='2012', day='211', test=True,
+                              fmtout=self.format)
 
     def test_fortran_executable(self):
         """Short run of fortran executable to ensure the code compiles

sami2py/tests/test_core_class.py

@@ -2,7 +2,7 @@
 """
 import os
 import sami2py
-from nose.tools import raises
+import pytest
 
 
 class TestModelObject():
@@ -14,6 +14,9 @@ def setup(self):
         """
         self.tmp_archive_dir = sami2py.archive_dir
         sami2py.utils.set_archive_dir(path=sami2py.test_data_dir)
+        self.lon = 256
+        self.year = 1999
+        self.day = 256
 
     def teardown(self):
         """Undo any changes made to the archive directory
@@ -26,55 +29,80 @@ def teardown(self):
                 archive_file.write('')
                 sami2py.archive_dir = ''
 
-    @raises(IOError)
     def test_model_input_exception(self):
         """File not found error should be produced if the file does not exist
         """
-        sami2py.Model(tag='none', lon=428, day=428, year=1969)
+        with pytest.raises(IOError):
+            sami2py.Model(tag='none', lon=428, day=428, year=1969)
 
     def test_model_instantiation(self):
         """Test that model object is instantiated as a sami2py_model
         """
-        model = sami2py.Model(tag='test', lon=256, year=1999, day=256,
-                              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)
+        model = sami2py.Model(tag='test', lon=self.lon, year=self.year,
+                              day=self.day, test=True, outn=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
         """
         import matplotlib
-        matplotlib.use('Agg')
-        import matplotlib.pyplot as plt
-        model = sami2py.Model(tag='test', lon=256, year=1999, day=256,
-                              test=True)
-        model.plot_lat_alt()
-        fig = plt.gcf()
+
+        model = sami2py.Model(tag='test', lon=self.lon, year=self.year,
+                              day=self.day, test=True)
+        fig = model.plot_lat_alt()
+        assert isinstance(fig, matplotlib.figure.Figure)
+
+        tol = 1.e-4
         xlims = fig.axes[0].get_xlim()
         ylims = fig.axes[0].get_ylim()
-        assert xlims == (-36.3329, 19.37387)
-        assert ylims == (84.98926, 1999.998)
-        plt.close()
+        assert abs(xlims[0] + 36.3329) < tol
+        assert abs(xlims[1] - 19.37387) < tol
+        assert abs(ylims[0] - 84.98926) < tol
+        assert abs(ylims[1] - 1999.998) < tol
+        matplotlib.pyplot.close(fig)
 
     def test_check_standard_model(self):
         """Test that standard model outputs nothing if there are no changes to
-           the standard model
+           the standard model / changes to EUV in unformatted version
         """
-        model = sami2py.Model(tag='test', lon=256, year=1999, day=256,
-                              test=True)
+        model = sami2py.Model(tag='test', lon=self.lon, year=self.year,
+                              day=self.day, test=True)
         keys = model.check_standard_model()
-        assert keys == list()
+
+        if self.day == 256:
+            assert keys == list()
+        else:
+            assert 'EUV Multiplier' in keys
 
     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)
+        model = sami2py.Model(tag='test', lon=self.lon, year=self.year,
+                              day=self.day, test=True)
         repr_str = model.__repr__()
         assert type(repr_str) is str
+
+
+class TestModelObjectUnformatted(TestModelObject):
+    """Test basic model object functionality
+    """
+    def setup(self):
+        """Set up .dat files in properly named director
+           for model object to load model
+        """
+        self.tmp_archive_dir = sami2py.archive_dir
+        sami2py.utils.set_archive_dir(path=sami2py.test_data_dir)
+        self.lon = 256
+        self.year = 1999
+        self.day = 257
+
+    def teardown(self):
+        """Undo any changes made to the archive directory
+        """
+        if os.path.isdir(self.tmp_archive_dir):
+            sami2py.utils.set_archive_dir(path=self.tmp_archive_dir)
+        else:
+            archive_path = os.path.join(sami2py.sami2py_dir, 'archive_path.txt')
+            with open(archive_path, 'w') as archive_file:
+                archive_file.write('')
+                sami2py.archive_dir = ''