Merge pull request #636 from xylar/update-unit-tests

Move unit tests out of `mpas_tools`

Author: xylar

conda_package/docs/api.rst

@@ -392,13 +392,3 @@ Visualization
    :toctree: generated/
 
    register_sci_viz_colormaps
-
-Tests
-=====
-
-.. currentmodule:: mpas_tools.tests.test_cime_constants
-
-.. autosummary::
-   :toctree: generated/
-
-   test_cime_constants

conda_package/docs/cime.rst

@@ -8,8 +8,7 @@ sync with `CIME <https://github.com/ESMCI/cime>`_, which provides infrastructure
 and utilities for Earth System Models such at E3SM.  Currently, we sync only
 those constants given numerical values in CIME, not those that are derivied
 from other constants.  Constants are checked against their values on CIME's
-master branch during tests of the conda build.  See
-:py:func:`mpas_tools.tests.test_cime_constants.test_cime_constants`.
+master branch during tests of the conda build.
 
 Some of the constants most likely to be useful in MPAS-Tools, COMPASS and other
 related projects are:

conda_package/recipe/meta.yaml

@@ -65,7 +65,7 @@ test:
     - mesh_tools/mesh_conversion_tools/test/Arctic_Ocean.geojson
     - mesh_tools/mesh_conversion_tools/test/mesh.QU.1920km.151026.nc
     - mesh_tools/mesh_conversion_tools/test/land_mask_final.nc
-    - conda_package/mpas_tools/tests/*
+    - conda_package/tests/*
   imports:
     - mpas_tools
     - mpas_tools.mesh.conversion
@@ -87,7 +87,7 @@ test:
     - MpasMaskCreator.x mesh.nc arctic_mask.nc -f mesh_tools/mesh_conversion_tools/test/Arctic_Ocean.geojson
     - planar_hex --nx=30 --ny=20 --dc=1000. --npx --npy --outFileName='nonperiodic_mesh_30x20_1km.nc'
     - MpasCellCuller.x nonperiodic_mesh_30x20_1km.nc culled_nonperiodic_mesh_30x20_1km.nc
-    - python -m pytest conda_package/mpas_tools/tests
+    - python -m pytest conda_package/tests
     - mark_horns_for_culling --help
     - set_lat_lon_fields_in_planar_grid --help
     - create_scrip_file_from_mpas_mesh --help

…nda_package/mpas_tools/tests/__init__.py conda_package/tests/__init__.pyconda_package/mpas_tools/tests/__init__.py renamed to conda_package/tests/__init__.py conda_package/mpas_tools/tests/__init__.py renamed to conda_package/tests/__init__.py

@@ -1,6 +1,7 @@
-from mpas_tools.cime.constants import constants
 import requests
 
+from mpas_tools.cime.constants import constants
+
 
 def test_cime_constants(e3sm_tag='master'):
     """
@@ -14,7 +15,8 @@ def test_cime_constants(e3sm_tag='master'):
 
     resp = requests.get(
         f'https://raw.githubusercontent.com/E3SM-Project/E3SM/{e3sm_tag}/'
-        f'share/util/shr_const_mod.F90')
+        f'share/util/shr_const_mod.F90'
+    )
 
     text = resp.text
 
@@ -32,10 +34,10 @@ def test_cime_constants(e3sm_tag='master'):
         print(f'parsed: {constant} = {value}')
         if constant in constants:
             if isinstance(value, float):
-                print('verifying {}'.format(constant))
+                print(f'verifying {constant}')
                 assert value == constants[constant]
             else:
-                print('skipping verification for {}'.format(constant))
+                print(f'skipping verification for {constant}')
 
             found[constant] = True
         else:
@@ -46,7 +48,7 @@ def test_cime_constants(e3sm_tag='master'):
     all_found = True
     for constant in found:
         if not found[constant]:
-            print('{} was not found!'.format(constant))
+            print(f'{constant} was not found!')
             all_found = False
 
     assert all_found
@@ -60,7 +62,7 @@ def _parse_value(line):
     end = line.find('=')
 
     key = line[start:end]
-    line = line[end+1:]
+    line = line[end + 1 :]
 
     if '!' in line:
         line, _ = line.split('!', 1)

…/mpas_tools/tests/test_cime_constants.py …nda_package/tests/test_cime_constants.pyconda_package/mpas_tools/tests/test_cime_constants.py renamed to conda_package/tests/test_cime_constants.py conda_package/mpas_tools/tests/test_cime_constants.py renamed to conda_package/tests/test_cime_constants.py

@@ -1,26 +1,31 @@
 #!/usr/bin/env python
 
-from mpas_tools.mesh.conversion import convert, cull, mask
-from mpas_tools.io import write_netcdf
 import matplotlib
+
+from mpas_tools.io import write_netcdf
+from mpas_tools.mesh.conversion import convert, cull, mask
+
+from .util import get_test_data_file
+
 matplotlib.use('Agg')
-from geometric_features import read_feature_collection
 import xarray
+from geometric_features import read_feature_collection
 
 
 def test_conversion():
     dsMesh = xarray.open_dataset(
-        'mesh_tools/mesh_conversion_tools/test/mesh.QU.1920km.151026.nc')
+        get_test_data_file('mesh.QU.1920km.151026.nc')
+    )
     dsMesh = convert(dsIn=dsMesh)
     write_netcdf(dsMesh, 'mesh.nc')
 
-    dsMask = xarray.open_dataset(
-        'mesh_tools/mesh_conversion_tools/test/land_mask_final.nc')
+    dsMask = xarray.open_dataset(get_test_data_file('land_mask_final.nc'))
     dsCulled = cull(dsIn=dsMesh, dsMask=dsMask)
     write_netcdf(dsCulled, 'culled_mesh.nc')
 
     fcMask = read_feature_collection(
-        'mesh_tools/mesh_conversion_tools/test/Arctic_Ocean.geojson')
+        get_test_data_file('Arctic_Ocean.geojson')
+    )
     dsMask = mask(dsMesh=dsMesh, fcMask=fcMask)
     write_netcdf(dsMask, 'antarctic_mask.nc')
 

…kage/mpas_tools/tests/test_conversion.py conda_package/tests/test_conversion.pyconda_package/mpas_tools/tests/test_conversion.py renamed to conda_package/tests/test_conversion.py conda_package/mpas_tools/tests/test_conversion.py renamed to conda_package/tests/test_conversion.py

@@ -1,11 +1,19 @@
 #!/usr/bin/env python
+import os
+
 import numpy
 import xarray
-import os
 
 from mpas_tools.io import write_netcdf
-from mpas_tools.ocean.depth import compute_depth, compute_zmid, add_depth, \
-    add_zmid, write_time_varying_zmid
+from mpas_tools.ocean.depth import (
+    add_depth,
+    add_zmid,
+    compute_depth,
+    compute_zmid,
+    write_time_varying_zmid,
+)
+
+from .util import get_test_data_file
 
 
 def create_3d_mesh():
@@ -14,19 +22,25 @@ def create_3d_mesh():
         dsMesh = xarray.open_dataset(outFileName)
     else:
         dsMesh = xarray.open_dataset(
-            'mesh_tools/mesh_conversion_tools/test/mesh.QU.1920km.151026.nc')
+            get_test_data_file('mesh.QU.1920km.151026.nc')
+        )
         nCells = dsMesh.sizes['nCells']
         nVertLevels = 10
-        zmax = 1000.
-        layerThickness = zmax/nVertLevels
-        dsMesh['refBottomDepth'] = \
-            ('nVertLevels', numpy.linspace(layerThickness, zmax, nVertLevels))
-        dsMesh['maxLevelCell'] = \
-            ('nCells', nVertLevels*numpy.ones(nCells, dtype=int))
-        dsMesh['bottomDepth'] = ('nCells', zmax*numpy.ones(nCells))
-        dsMesh['layerThickness'] = \
-            (('Time', 'nCells', 'nVertLevels'),
-             layerThickness*numpy.ones((1, nCells, nVertLevels)))
+        zmax = 1000.0
+        layerThickness = zmax / nVertLevels
+        dsMesh['refBottomDepth'] = (
+            'nVertLevels',
+            numpy.linspace(layerThickness, zmax, nVertLevels),
+        )
+        dsMesh['maxLevelCell'] = (
+            'nCells',
+            nVertLevels * numpy.ones(nCells, dtype=int),
+        )
+        dsMesh['bottomDepth'] = ('nCells', zmax * numpy.ones(nCells))
+        dsMesh['layerThickness'] = (
+            ('Time', 'nCells', 'nVertLevels'),
+            layerThickness * numpy.ones((1, nCells, nVertLevels)),
+        )
         write_netcdf(dsMesh, 'test_depth_mesh.nc')
 
     return dsMesh
@@ -35,23 +49,30 @@ def create_3d_mesh():
 def test_compute_depth():
     dsMesh = create_3d_mesh()
     depth, depth_bnds = compute_depth(dsMesh.refBottomDepth)
-    assert numpy.all(numpy.isclose(depth, numpy.linspace(50., 950., 10)))
-    assert numpy.all(numpy.isclose(depth_bnds[:, 0],
-                                   numpy.linspace(0., 900., 10)))
-    assert numpy.all(numpy.isclose(depth_bnds[:, 1],
-                                   numpy.linspace(100., 1000., 10)))
+    assert numpy.all(numpy.isclose(depth, numpy.linspace(50.0, 950.0, 10)))
+    assert numpy.all(
+        numpy.isclose(depth_bnds[:, 0], numpy.linspace(0.0, 900.0, 10))
+    )
+    assert numpy.all(
+        numpy.isclose(depth_bnds[:, 1], numpy.linspace(100.0, 1000.0, 10))
+    )
 
 
 def test_compute_zmid():
     dsMesh = create_3d_mesh()
-    zMid = compute_zmid(dsMesh.bottomDepth, dsMesh.maxLevelCell,
-                        dsMesh.layerThickness, depth_dim='nVertLevels')
+    zMid = compute_zmid(
+        dsMesh.bottomDepth,
+        dsMesh.maxLevelCell,
+        dsMesh.layerThickness,
+        depth_dim='nVertLevels',
+    )
 
     assert zMid.dims == ('Time', 'nCells', 'nVertLevels')
 
     depth = zMid.isel(Time=0, nCells=0)
-    assert numpy.all(numpy.isclose(depth.values,
-                                   numpy.linspace(-50., -950., 10)))
+    assert numpy.all(
+        numpy.isclose(depth.values, numpy.linspace(-50.0, -950.0, 10))
+    )
 
 
 def test_add_depth():
@@ -65,15 +86,18 @@ def test_add_depth():
 
     # test adding depth coordinate once to the mesh and once to the input file,
     # with the mesh passed in separately
-    for in_filename, coord_filename in [(mesh_filename, None),
-                                        ('test_depth_in.nc', mesh_filename)]:
+    for in_filename, coord_filename in [
+        (mesh_filename, None),
+        ('test_depth_in.nc', mesh_filename),
+    ]:
         add_depth(in_filename, out_filename, coordFileName=coord_filename)
         dsOut = xarray.open_dataset(out_filename)
         assert 'depth' in dsOut.dims
 
         depth = dsOut.depth
-        assert numpy.all(numpy.isclose(depth.values,
-                                       numpy.linspace(50., 950., 10)))
+        assert numpy.all(
+            numpy.isclose(depth.values, numpy.linspace(50.0, 950.0, 10))
+        )
 
 
 def test_add_zmid():
@@ -87,8 +111,10 @@ def test_add_zmid():
 
     # test adding zMid once to the mesh and once to the input file, with the
     # mesh passed in separately
-    for in_filename, coord_filename in [(mesh_filename, None),
-                                        ('test_depth_in.nc', mesh_filename)]:
+    for in_filename, coord_filename in [
+        (mesh_filename, None),
+        ('test_depth_in.nc', mesh_filename),
+    ]:
         add_zmid(in_filename, out_filename, coordFileName=coord_filename)
         dsOut = xarray.open_dataset(out_filename)
         assert 'depth' in dsOut.dims
@@ -97,54 +123,63 @@ def test_add_zmid():
         assert zMid.dims == ('nCells', 'depth')
 
         depth = zMid.isel(nCells=0)
-        assert numpy.all(numpy.isclose(depth.values,
-                                       numpy.linspace(-50., -950., 10)))
+        assert numpy.all(
+            numpy.isclose(depth.values, numpy.linspace(-50.0, -950.0, 10))
+        )
 
 
 def test_write_time_varying_zmid():
-
     dsMesh = create_3d_mesh()
     nCells = dsMesh.sizes['nCells']
     nVertLevels = dsMesh.sizes['nVertLevels']
     mesh_filename = 'test_depth_mesh.nc'
     in_filename = 'test_depth_in.nc'
     out_filename = 'test_depth_out.nc'
 
-    layerThickness = 100.
+    layerThickness = 100.0
 
     # test adding zMid once to the mesh and once to the input file, with the
     # mesh passed in separately, each one without and once with a prefix
-    for coord_filename, prefix in [(None, ''),
-                                   (mesh_filename, ''),
-                                   (None, 'timeMonthly_avg_'),
-                                   (mesh_filename, 'timeMonthly_avg_')]:
+    for coord_filename, prefix in [
+        (None, ''),
+        (mesh_filename, ''),
+        (None, 'timeMonthly_avg_'),
+        (mesh_filename, 'timeMonthly_avg_'),
+    ]:
         print(coord_filename, prefix)
 
         if coord_filename is None:
             dsIn = dsMesh.drop_vars('layerThickness')
         else:
             dsIn = xarray.Dataset()
-        layerThicknessVar = '{}layerThickness'.format(prefix)
-        dsIn[layerThicknessVar] = \
-            (('Time', 'nCells', 'nVertLevels'),
-             layerThickness*numpy.ones((2, nCells, nVertLevels)))
-        dsIn['{}temperature'.format(prefix)] = \
-            xarray.ones_like(dsIn[layerThicknessVar])
+        layerThicknessVar = f'{prefix}layerThickness'
+        dsIn[layerThicknessVar] = (
+            ('Time', 'nCells', 'nVertLevels'),
+            layerThickness * numpy.ones((2, nCells, nVertLevels)),
+        )
+        dsIn[f'{prefix}temperature'] = xarray.ones_like(
+            dsIn[layerThicknessVar]
+        )
         write_netcdf(dsIn, in_filename)
         dsIn.close()
 
-        write_time_varying_zmid(in_filename, out_filename,
-                                coordFileName=coord_filename, prefix=prefix)
+        write_time_varying_zmid(
+            in_filename,
+            out_filename,
+            coordFileName=coord_filename,
+            prefix=prefix,
+        )
 
         dsOut = xarray.open_dataset(out_filename)
         assert 'depth' in dsOut.dims
 
-        zMid = dsOut['{}zMid'.format(prefix)]
+        zMid = dsOut[f'{prefix}zMid']
         assert zMid.dims == ('Time', 'nCells', 'depth')
 
         depth = zMid.isel(Time=0, nCells=0)
-        assert numpy.all(numpy.isclose(depth.values,
-                                       numpy.linspace(-50., -950., 10)))
+        assert numpy.all(
+            numpy.isclose(depth.values, numpy.linspace(-50.0, -950.0, 10))
+        )
         dsOut.close()