Merge branch 'develop' into clean_warning_update

CHANGELOG.md

@@ -13,6 +13,7 @@ This project adheres to [Semantic Versioning](https://semver.org/).
   * Added manual test for pysatModels RC pip install
   * Updated tests to new pysat and pytest standards
   * Updated model Instruments to include the new `_clean_warn` attribute
+  * Removed backwards-support for pysat pre-3.0.4 functions
 * Documentation
   * Added badges and instructions for PyPi and Zenodo
 

README.md

@@ -13,7 +13,7 @@
 pysatModels handles model-centric data loading through pysat and contains a
 variety of tools to perform model-data analysis, including model validation.
 
-Come join us on Slack! An invitation to the pysat workspace is available 
+Come join us on Slack! An invitation to the pysat workspace is available
 in the 'About' section of the
 [pysat GitHub Repository.](https://github.com/pysat/pysat)
 
@@ -31,7 +31,7 @@ the Space Physics community.  This module officially supports Python 3.6+.
 | ------------------ | ------------------ |
 | numpy              | pyForecastTools    |
 | pandas >= 1.4.0    | pysat >= 3.0.4     |
-| requests           | pysatNASA >= 0.0.5 |
+| requests           | pysatNASA          |
 | scipy              |                    |
 | xarray             |                    |
 

docs/installation.rst

@@ -24,8 +24,8 @@ the Space Physics community.  This module officially supports Python 3.6+.
  Common modules Community modules
  ============== =================
   numpy         pysat
-  pandas        pyForecastTools
-  requests
+  pandas        pysatNASA
+  requests      pyForecastTools
   scipy
   xarray
  ============== =================
@@ -85,7 +85,7 @@ is set up, you may choose to register the the :py:mod:`pysatModel` model
 
 .. code:: python
 
-	  
+
    import pysat
    import pysatModels as pymod
 

pysatModels/models/sami2py_sami2.py

@@ -23,7 +23,6 @@
 
 import datetime as dt
 import functools
-from packaging import version as pack_version
 import warnings
 import xarray as xr
 
@@ -147,26 +146,14 @@ def load(fnames, tag='', inst_id='', **kwargs):
                                 file_info['day']):
         epochs.append(dt.datetime(year, month, day))
 
-    vstr = '3.0.2'  # TODO(#112) Remove support for backwards compatibility
     loaded_data = []
     loaded_meta = []
     for epoch, fname in zip(epochs, fnames):
         # Load data
-        # TODO(#112) Remove backwards compatibility
-        if pack_version.Version(pysat.__version__) < pack_version.Version(vstr):
-            data, meta = pysat.utils.load_netcdf4([fname], pandas_format=False,
-                                                  epoch_name='ut')
-            data = data.rename({"ut": "time"})
-
-            # Create datetimes from 'ut' variable
-            data['time'] = [epoch
-                            + dt.timedelta(seconds=int(val * 3600.0))
-                            for val in data['time'].values]
-        else:
-            data, meta = pysat.utils.load_netcdf4([fname], pandas_format=False,
-                                                  epoch_name='ut',
-                                                  epoch_origin=epoch,
-                                                  epoch_unit='h')
+        data, meta = pysat.utils.io.load_netcdf([fname], pandas_format=False,
+                                                epoch_name='ut',
+                                                epoch_origin=epoch,
+                                                epoch_unit='h')
 
         # Store data/meta for each loop
         loaded_data.append(data)

pysatModels/models/ucar_tiegcm.py

@@ -186,13 +186,9 @@ def load(fnames, tag='', inst_id='', **kwargs):
 
     """
 
-    # TODO(#114): eventually remove support for multiple pysat versions
-    if hasattr(pysat.utils, 'io'):
-        data, meta = pysat.utils.io.load_netcdf(fnames, pandas_format=False,
-                                                epoch_name='time',
-                                                decode_times=True)
-    else:
-        data, meta = pysat.utils.load_netcdf4(fnames, pandas_format=False)
+    data, meta = pysat.utils.io.load_netcdf(fnames, pandas_format=False,
+                                            epoch_name='time',
+                                            decode_times=True)
 
     # Move misc parameters from xarray to the Instrument object via Meta.
     # Doing this after `meta` created ensures all metadata is still kept

pysatModels/tests/test_methods_general.py

@@ -14,15 +14,15 @@
 class TestMethodsGeneralLogging(object):
     """Unit tests for log messages raised by general methods."""
 
-    def setup(self):
+    def setup_method(self):
         """Set up the unit test environment."""
         self.ch = logging.StreamHandler()
         self.ch.setLevel(logging.INFO)
         self.model = pysat.Instrument("pysat", "testmodel")
 
         return
 
-    def teardown(self):
+    def teardown_method(self):
         """Clean up the unit test environment."""
 
         del self.ch, self.model
@@ -50,7 +50,7 @@ def test_general_clean(self, caplog):
 class TestMethodsGeneralDownload(object):
     """Unit tests for general methods handling downloads."""
 
-    def setup(self):
+    def setup_method(self):
         """Set up the unit test environment."""
         # TODO(#100): remove if-statement when it is always triggered
         tkwargs = {}
@@ -65,7 +65,7 @@ def setup(self):
 
         return
 
-    def teardown(self):
+    def teardown_method(self):
         """Clean up the unit test environment."""
 
         if os.path.isfile(self.out_file):

pysatModels/tests/test_models.py

@@ -8,159 +8,31 @@
 
 import datetime as dt
 import os
-from packaging import version as pack_version
-import pytest
 import shutil
 import sys
 import tempfile
 
+# Import the test classes from pysat
 import pysat
-from pysat.tests.instrument_test_class import InstTestClass
+from pysat.tests.classes import cls_instrument_library as clslib
 
 import pysatModels
 
 # Retrieve the lists of Model instruments and testing methods
-instruments = pysat.utils.generate_instrument_list(inst_loc=pysatModels.models)
-method_list = [func for func in dir(InstTestClass)
-               if callable(getattr(InstTestClass, func))]
-
-# Search tests for iteration via pytestmark, update instrument list
-for method in method_list:
-    if hasattr(getattr(InstTestClass, method), 'pytestmark'):
-        # Get list of names of pytestmarks
-        mark_name = [mod_mark.name for mod_mark
-                     in getattr(InstTestClass, method).pytestmark]
-
-        # Add instruments from your library
-        if 'all_inst' in mark_name:
-            mark = pytest.mark.parametrize("inst_name", instruments['names'])
-            getattr(InstTestClass, method).pytestmark.append(mark)
-        elif 'download' in mark_name:
-            mark = pytest.mark.parametrize("inst_dict",
-                                           instruments['download'])
-            getattr(InstTestClass, method).pytestmark.append(mark)
-        elif 'no_download' in mark_name:
-            mark = pytest.mark.parametrize("inst_dict",
-                                           instruments['no_download'])
-            getattr(InstTestClass, method).pytestmark.append(mark)
-
-
-class TestModels(InstTestClass):
+instruments = clslib.InstLibTests.initialize_test_package(
+    clslib.InstLibTests, inst_loc=pysatModels.models)
+
+
+class TestModels(clslib.InstLibTests):
     """Main class for instrument tests.
 
     Note
     ----
-    Uses class level setup and teardown so that all tests use the same
-    temporary directory. We do not want to geneate a new tempdir for each test,
-    as the load tests need to be the same as the download tests.
+    All standard tests, setup, and teardown inherited from the core pysat
+    instrument test class.
 
     """
 
-    def setup_class(self):
-        """Initialize the testing setup once before all tests are run."""
-        # Make sure to use a temporary directory so that the user setup is not
-        # altered
-        # TODO(#100): remove if-statement when it is always triggered
-        tkwargs = {}
-        if sys.version_info.major >= 3 and sys.version_info.minor >= 10:
-            tkwargs = {"ignore_cleanup_errors": True}
-        self.tempdir = tempfile.TemporaryDirectory(**tkwargs)
-        self.saved_path = pysat.params['data_dirs']
-        pysat.params.data['data_dirs'] = [self.tempdir.name]
-
-        # Assign the location of the model Instrument sub-modules
-        self.inst_loc = pysatModels.models
-        return
-
-    def teardown_class(self):
-        """Clean up downloaded files and parameters from tests."""
-
-        pysat.params.data['data_dirs'] = self.saved_path
-
-        # TODO(#100): Remove try/except when Python 3.10 is the lowest version
-        try:
-            self.tempdir.cleanup()
-        except Exception:
-            pass
-
-        del self.inst_loc, self.saved_path, self.tempdir
-        return
-
-
-class TestSAMIPysatVersion(object):
-    """Test SAMI load code for pysat version differences across v3.0.2."""
-
-    def setup_class(self):
-        """Initialize the testing setup once before all tests are run."""
-        # Make sure to use a temporary directory so that the user setup is not
-        # altered
-
-        # TODO(#100): remove if-statement when it is always triggered
-        tkwargs = {}
-        if sys.version_info.major >= 3 and sys.version_info.minor >= 10:
-            tkwargs = {"ignore_cleanup_errors": True}
-        self.tempdir = tempfile.TemporaryDirectory(**tkwargs)
-        self.saved_path = pysat.params['data_dirs']
-        self.saved_ver = pysat.__version__
-        pysat.params.data['data_dirs'] = [self.tempdir.name]
-
-        # Assign the location of the model Instrument sub-modules
-        self.inst_loc = pysatModels.models
-        return
-
-    def teardown_class(self):
-        """Clean up downloaded files and parameters from tests."""
-
-        pysat.params.data['data_dirs'] = self.saved_path
-        pysat.__version__ = self.saved_ver
-
-        # Remove the temporary directory
-        # TODO(#100): Remove try/except when Python 3.10 is the lowest version
-        try:
-            self.tempdir.cleanup()
-        except Exception:
-            pass
-
-        del self.inst_loc, self.saved_path, self.tempdir, self.saved_ver
-        return
-
-    def test_load_failure(self):
-        """Test for SAMI load failure when faking a different pysat version."""
-
-        if (pack_version.Version(pysat.__version__)
-                >= pack_version.Version('3.0.2')):
-            # Define target error variable label
-            label = 'ut'
-
-            # Replace reported version with one before 3.0.2
-            vlabel = '3.0.1'
-
-            # Expected error
-            error = ValueError
-        else:
-            # Define target error variable label
-            label = 'epoch_origin'
-
-            # Expected error
-            error = TypeError
-
-            # Replace reported version with one including 3.0.2
-            vlabel = '3.0.2'
-
-        # Update reported pysat version
-        pysat.__version__ = vlabel
-
-        with pytest.raises(error) as verr:
-            inst = pysat.Instrument(inst_module=self.inst_loc.sami2py_sami2,
-                                    tag='test')
-            inst.download(self.inst_loc.sami2py_sami2._test_dates['']['test'],
-                          self.inst_loc.sami2py_sami2._test_dates['']['test'])
-            inst.load(date=self.inst_loc.sami2py_sami2._test_dates['']['test'])
-
-        assert str(verr).find(label) >= 0
-
-        return
-
 
 class TestSAMILoadMultipleDays(object):
     """Test SAMI load code for multiple days."""

pysatModels/tests/test_utils_convert.py

@@ -64,7 +64,7 @@ def eval_xarray_output(inst, xdata):
 class TestUtilsConvertLoadModelXarray(object):
     """Unit tests for `utils.convert.load_model_xarray`."""
 
-    def setup(self):
+    def setup_method(self):
         """Create a clean testing setup before each method."""
         self.ftime = pysat.instruments.pysat_testing_xarray._test_dates['']['']
         self.filename = "%Y-%m-%d.nofile"
@@ -76,7 +76,7 @@ def setup(self):
         self.xout = None
         self.temp_file = 'None'
 
-    def teardown(self):
+    def teardown_method(self):
         """Clean up test environment after each method."""
         if os.path.isfile(self.temp_file):
             os.remove(self.temp_file)
@@ -130,11 +130,11 @@ def test_load_inst(self, mkey, mval):
 class TestUtilsConvertPysatXarray(object):
     """Unit tests for utils.convert.convert_pysat_to_xarray."""
 
-    def setup(self):
+    def setup_method(self):
         """Create a clean testing setup before each method."""
         self.ref_time = pysat.instruments.pysat_testing._test_dates['']['']
 
-    def teardown(self):
+    def teardown_method(self):
         """Clean up test environment after each method."""
         del self.ref_time