Merge pull request #126 from pysat/tst/ga_update

MAINT/BUG: GA updates, pandas 2.0+ compatibility

Author: jklenzing

.github/workflows/pip_rc_install.yml

@@ -0,0 +1,40 @@
+# This workflow will install Python dependencies and the latest RC of pysatNASA from test pypi.
+# This test should be manually run before a pysatModels RC is officially approved and versioned.
+# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
+
+name: Test install of latest RC from pip
+
+on: [workflow_dispatch]
+
+jobs:
+  build:
+    strategy:
+      fail-fast: false
+      matrix:
+        os: ["ubuntu-latest", "macos-latest", "windows-latest"]
+        python-version: ["3.8", "3.9", "3.10"]  # Keep this version at the highest supported Python version
+
+    name: Python ${{ matrix.python-version }} on ${{ matrix.os }}
+    runs-on: ${{ matrix.os }}
+    steps:
+    - uses: actions/checkout@v3
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v4
+      with:
+        python-version: ${{ matrix.python-version }}
+
+    - name: Install standard dependencies
+      run: pip install -r requirements.txt
+
+    - name: Install pysatModels RC
+      run: pip install --no-deps --pre -i https://test.pypi.org/simple/ --extra-index-url https://pypi.org/simple/ pysatModels
+
+    - name: Set up pysat
+      run: |
+        mkdir pysatData
+        python -c "import pysat; pysat.params['data_dirs'] = 'pysatData'"
+
+    - name: Check that install imports correctly
+      run: |
+        cd ..
+        python -c "import pysatModels; print(pysatModels.__version__)"

.github/workflows/pysat_rc.yml

@@ -1,4 +1,4 @@
-# This workflow will install Python dependencies (including the latest RC 
+# This workflow will install Python dependencies (including the latest RC
 # for pysat packages) and run tests for supported operating systems.
 # For more information see:
 # https://help.github.com/actions/language-and-framework-guides/
@@ -27,7 +27,7 @@ jobs:
         python-version: ${{ matrix.python-version }}
 
     - name: Install RC package
-      run: pip install --no-deps -i https://test.pypi.org/simple/ ${{ matrix.rc-package }}
+      run: pip install --no-deps --pre -i https://test.pypi.org/simple/ --extra-index-url https://pypi.org/simple/ ${{ matrix.rc-package }}
 
     - name: Install standard dependencies
       run: |

CHANGELOG.md

@@ -10,6 +10,8 @@ This project adheres to [Semantic Versioning](https://semver.org/).
   * Switched pydineof_dineof load code to use newer `pysat.utils.io.load_netcdf`
   * Updated NEP29 and GitHub actions versions
   * Added manual test for pysat and pysatNASA Release Candidates
+  * Added manual test for pysatModels RC pip install
+  * Updated tests to new pysat and pytest standards
 * Documentation
   * Added badges and instructions for PyPi and Zenodo
 

README.md

@@ -30,7 +30,7 @@ the Space Physics community.  This module officially supports Python 3.6+.
 |   Common modules   | Community modules |
 | ------------------ | ----------------- |
 | numpy              | pyForecastTools   |
-| pandas             | pysat >= 3.0.4    |
+| pandas >= 1.4.0    | pysat >= 3.0.4    |
 | requests           | pysatNASA         |
 | scipy              |                   |
 | xarray             |                   |

pysatModels/tests/test_models.py

@@ -235,7 +235,7 @@ def test_multidayload(self):
         assert meta_two_days == meta_one_days
 
         # Confirm time index information
-        assert data_two_days.indexes['time'].is_monotonic
+        assert data_two_days.indexes['time'].is_monotonic_increasing
         assert data_two_days.indexes['time'][0] >= test_date
         assert data_two_days.indexes['time'][0] < date
         assert data_two_days.indexes['time'][-1] > date

pysatModels/tests/test_utils_compare.py

@@ -11,7 +11,7 @@
 class TestUtilsCompare(object):
     """Unit tests for utils.compare."""
 
-    def setup(self):
+    def setup_method(self):
         """Set up the unit test environment for each method."""
 
         coords = {"lat": np.arange(-90, 90, 10), "alt": np.arange(200, 800, 10)}
@@ -29,7 +29,7 @@ def setup(self):
         self.out_units = dict()
         return
 
-    def teardown(self):
+    def teardown_method(self):
         """Clean up the unit test environment after each method."""
 
         del self.dat_key, self.mod_key, self.units, self.pairs, self.input_args

pysatModels/tests/test_utils_match.py

@@ -13,17 +13,18 @@
 class TestUtilsMatchCollectInstModPairs(object):
     """Unit tests for utils.match.collect_inst_model_pairs."""
 
-    def setup(self):
+    def setup_method(self):
         """Set up the unit test environment for each method."""
 
-        self.inst = pysat.Instrument(platform='pysat', name='testing')
+        self.inst = pysat.Instrument(platform='pysat', name='testing',
+                                     use_header=True)
         self.stime = pysat.instruments.pysat_testing._test_dates['']['']
         self.inst.load(date=self.stime)
         self.input_args = [self.stime, self.stime + dt.timedelta(days=1),
                            dt.timedelta(days=1), self.inst]
         self.ref_col = 'dummy1'
         self.model = pysat.Instrument(platform='pysat', name='testmodel',
-                                      tag='', num_samples=10)
+                                      tag='', num_samples=10, use_header=True)
         self.required_kwargs = {"model_load_kwargs":
                                 {"model_inst": self.model},
                                 "inst_clean_rout": lambda x: True,
@@ -37,7 +38,7 @@ def setup(self):
         self.out = None
         return
 
-    def teardown(self):
+    def teardown_method(self):
         """Clean up the unit test environment after each method."""
 
         del self.input_args, self.required_kwargs, self.inst, self.model

pysatModels/utils/match.py

@@ -163,7 +163,7 @@ def collect_inst_model_pairs(start, stop, tinc, inst, inst_download_kwargs=None,
     if not skip_download and (stop
                               - start).days != len(inst.files[start:stop]):
         missing_times = [tt for tt in pds.date_range(start, stop, freq='1D',
-                                                     closed='left')
+                                                     inclusive='left')
                          if tt not in inst.files[start:stop].index]
         for tt in missing_times:
             inst.download(start=tt, stop=tt + pds.DateOffset(days=1),

requirements.txt

@@ -1,6 +1,6 @@
 numpy
 packaging
-pandas
+pandas >= 1.4.0
 pyForecastTools
 pysat >= 3.0.4
 pysatNASA

test_requirements.txt

@@ -1,10 +1,10 @@
 coveralls
 flake8
 flake8-docstrings
-hacking>=1.0
+hacking>=1.0,<6.0
 m2r2
 numpydoc
 pytest-cov
 pytest-ordering
-sphinx
+sphinx<7.0
 sphinx_rtd_theme