BUG/MAINT: pyproject, workflow updates, pysatNASA temporary fixes

.github/workflows/docs.yml

@@ -13,7 +13,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: [3.9]
+        python-version: ["3.11"]  # Keep this version at the highest supported Python version
 
     name: Documentation tests
     steps:
@@ -26,8 +26,7 @@ jobs:
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
-        pip install -r test_requirements.txt
-        pip install -r requirements.txt
+        pip install .[doc]
 
     - name: Set up pysat
       run: |

.github/workflows/main.yml

@@ -50,16 +50,11 @@ jobs:
       if: ${{ matrix.test_config == 'NEP29'}}
       run: |
         pip install numpy==${{ matrix.numpy_ver }}
-        pip install --upgrade-strategy only-if-needed -r requirements.txt
-        pip install --upgrade-strategy only-if-needed -r test_requirements.txt
-        pip install .
+        pip install --upgrade-strategy only-if-needed .[test]
 
     - name: Install standard dependencies
       if: ${{ matrix.test_config == 'latest'}}
-      run: |
-        pip install -r test_requirements.txt
-        pip install -r requirements.txt
-        pip install .
+      run: pip install .[test]
 
     - name: Set up pysat
       run: |
@@ -72,18 +67,23 @@ jobs:
     - name: Evaluate complexity
       run: flake8 . --count --exit-zero --max-complexity=10 --statistics
 
-    - name: Install Operational dependencies success
-      if: ${{ matrix.test_config == 'Ops'}}
-      run: |
-          pip install pysatNASA==0.0.5
-          which python
-          python --version
-          python -c "import pysatNASA; print(pysatNASA.__version__)"
-
     - name: Run unit and integration tests
       run: pytest --cov=pysatModels/
 
     - name: Publish results to coveralls
       env:
         GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-      run: coveralls --rcfile=setup.cfg --service=github
+        COVERALLS_PARALLEL: true
+      run: coveralls --rcfile=pyproject.toml --service=github
+
+  finish:
+    name: Finish Coverage Analysis
+    needs: build
+    runs-on: ubuntu-latest
+    steps:
+    - name: Coveralls Finished
+      env:
+        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+      run: |
+        pip install --upgrade coveralls
+        coveralls --service=github --finish

.github/workflows/pysat_rc.yml

@@ -14,7 +14,7 @@ jobs:
       fail-fast: false
       matrix:
         os: ["ubuntu-latest", "macos-latest", "windows-latest"]
-        python-version: ["3.10"]
+        python-version: ["3.11"]  # Keep this version at the highest supported Python version
         rc-package: ["pysat", "pysatNASA"]
 
     name: ${{ matrix.os }} with ${{ matrix.rc-package }} RC
@@ -45,4 +45,17 @@ jobs:
     - name: Publish results to coveralls
       env:
         GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-      run: coveralls --rcfile=setup.cfg --service=github
+        COVERALLS_PARALLEL: true
+      run: coveralls --rcfile=pyproject.toml --service=github
+
+  finish:
+    name: Finish Coverage Analysis
+    needs: build
+    runs-on: ubuntu-latest
+    steps:
+    - name: Coveralls Finished
+      env:
+        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+      run: |
+        pip install --upgrade coveralls
+        coveralls --service=github --finish

docs/conf.py

@@ -16,6 +16,7 @@
 import datetime as dt
 import json
 import os
+import pkg_resources
 import sys
 
 sys.path.insert(0, os.path.abspath('..'))
@@ -72,9 +73,7 @@
 #
 # The short X.Y version.
 module_dir = os.path.split(os.path.abspath(os.path.dirname(__file__)))[0]
-version_file = os.path.join(module_dir, project, 'version.txt')
-with open(version_file, 'r') as fin:
-    version = fin.read().strip()
+version = pkg_resources.get_distribution('pysatModels').version
 
 # The full version, including alpha/beta/rc tags.
 release = '{:s}-alpha'.format(version)
@@ -84,7 +83,7 @@
 #
 # This is also used if you do content translation via gettext catalogs.
 # Usually you set "language" from the command line for these cases.
-language = None
+language = 'en'
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.

pyproject.toml

@@ -0,0 +1,74 @@
+[build-system]
+requires = ["setuptools >= 38.6", "pip >= 10"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "pysatModels"
+version = "0.1.0"
+description = "Supports model analysis and model-data comparisons"
+readme = "README.md"
+requires-python = ">=3.6"
+license = {file = "LICENSE"}
+authors = [
+    {name = "Pysat Development Team", email = "[email protected]"},
+]
+classifiers = [
+    "Development Status :: 3 - Alpha",
+    "Topic :: Scientific/Engineering :: Physics",
+    "Intended Audience :: Science/Research",
+    "License :: Freely Distributable",
+    "Natural Language :: English",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.6",
+    "Programming Language :: Python :: 3.9",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Operating System :: MacOS :: MacOS X",
+    "Operating System :: POSIX :: Linux",
+    "Operating System :: Microsoft :: Windows"
+]
+dependencies = [
+  "numpy",
+  "packaging",
+  "pandas",
+  "pyForecastTools",
+  "pysat >= 3.0.4",
+  "pysatNASA",
+  "requests",
+  "scipy",
+  "xarray"
+]
+
+[project.optional-dependencies]
+test = [
+  "coveralls < 3.3",
+  "flake8",
+  "flake8-docstrings",
+  "hacking >= 1.0",
+  "pytest-cov",
+  "pytest-ordering"
+]
+doc = [
+  "extras_require",
+  "m2r2",
+  "numpydoc",
+  "sphinx",
+  "sphinx_rtd_theme >= 1.2.2, < 2.0.0"
+]
+
+[project.urls]
+Documentation = "https://pysatmodels.readthedocs.io/en/latest/"
+Source = "https://github.com/pysat/pysatModels"
+
+[tool.coverage.report]
+
+[tool.pytest.ini_options]
+addopts = "--cov=pysatModels"
+markers = [
+  "all_inst",
+  "download",
+  "no_download",
+  "load_options",
+  "first",
+  "second"
+]

pysatModels/__init__.py

@@ -10,17 +10,19 @@
 
 """
 
+try:
+    from importlib import metadata
+except ImportError:
+    import importlib_metadata as metadata
+
 import logging
-import os
 
 # Import key modules and skip F401 testing in flake8
 from pysatModels import models  # noqa: F401
 from pysatModels import utils  # noqa: F401
 
 # Set the version
-local_dir = os.path.abspath(os.path.dirname(__file__))
-with open(os.path.join(local_dir, 'version.txt')) as version_file:
-    __version__ = version_file.read().strip()
+__version__ = metadata.version('pysatModels')
 
 # Define a logger object to allow easier log handling
 logging.raiseExceptions = False
@@ -30,4 +32,4 @@
 logger.addHandler(handler)
 
 # Clean up variables
-del handler, local_dir, version_file
+del handler

pysatModels/models/ucar_tiegcm.py

@@ -53,7 +53,8 @@
 
 _test_dates = {'': {'': dt.datetime(2019, 1, 1),
                     'icon': dt.datetime(2020, 1, 10)}}
-_test_download = {'': {'': False, 'icon': True}}
+# TODO(#132): Turn on ICON download tests once pysatNASA 0.0.6 is released.
+_test_download = {'': {'': False, 'icon': False}}
 _clean_warn = {'': {tag: general.clean_warn for tag in tags.keys()}}
 
 # ----------------------------------------------------------------------------
@@ -244,7 +245,10 @@ def download(date_array, tag, inst_id, data_path=None, **kwargs):
 
     if tag == '':
         warnings.warn('Not implemented, currently no support for Globus.')
+    # TODO(#132): Ensure new download routine is used after pysatNASA release.
     elif tag == 'icon':
+        warnings.warn('Not implemented, requires pysatNASA 0.0.6.')
+    elif tag == 'future_icon':
         # Set up temporary directory for zip files
         temp_dir = tempfile.TemporaryDirectory()
 

pysatModels/tests/test_utils_convert.py

@@ -66,10 +66,10 @@ class TestUtilsConvertLoadModelXarray(object):
 
     def setup_method(self):
         """Create a clean testing setup before each method."""
-        self.ftime = pysat.instruments.pysat_testing_xarray._test_dates['']['']
+        self.ftime = pysat.instruments.pysat_ndtesting._test_dates['']['']
         self.filename = "%Y-%m-%d.nofile"
         self.model_kwargs = {'platform': str('pysat'),
-                             'name': str('testing_xarray'),
+                             'name': str('ndtesting'),
                              'num_samples': 12,
                              'clean_level': 'clean'}
         self.model_inst = None

pysatModels/tests/test_utils_extract.py

@@ -341,7 +341,7 @@ class TestUtilsExtractModObsXarray(TestUtilsExtractModObs):
     def setup_method(self):
         """Set up the unit test environment for each method."""
 
-        self.inst = pysat.Instrument(platform='pysat', name='testing_xarray')
+        self.inst = pysat.Instrument(platform='pysat', name='ndtesting')
         self.model = pysat.Instrument(inst_module=pysat_testmodel, tag='')
 
         # Load the data in the instruments
@@ -377,7 +377,7 @@ class TestUtilsExtractModObsXarray2D(TestUtilsExtractModObs):
     def setup_method(self):
         """Set up the unit test environment for each method."""
 
-        self.inst = pysat.Instrument(platform='pysat', name='testing2d_xarray')
+        self.inst = pysat.Instrument(platform='pysat', name='ndtesting')
         self.model = pysat.Instrument(inst_module=pysat_testmodel, tag='')
 
         # Load the data in the instruments
@@ -413,7 +413,7 @@ class TestUtilsExtractInstModViewXarray(TestUtilsExtractInstThroughMod):
     def setup_method(self):
         """Run before every method to create a clean testing setup."""
 
-        self.inst = pysat.Instrument(platform='pysat', name='testing2d_xarray')
+        self.inst = pysat.Instrument(platform='pysat', name='ndtesting')
         self.model = pysat.Instrument(inst_module=pysat_testmodel)
 
         # Load the data in the instruments
@@ -588,7 +588,7 @@ class TestUtilsAltitudePressureXarray(TestUtilsAltitudePressure):
     def setup_method(self):
         """Set up the unit test environment for each method."""
 
-        self.inst = pysat.Instrument(platform='pysat', name='testing2d_xarray')
+        self.inst = pysat.Instrument(platform='pysat', name='ndtesting')
         self.model = pysat.Instrument(inst_module=pysat_testmodel,
                                       tag='pressure_levels')
 
@@ -731,7 +731,7 @@ class TestUtilsExtractInstModIrregViewXarray(TestUtilsExtractInstModIrregView):
     def setup_method(self):
         """Run before every method to create a clean testing setup."""
 
-        self.inst = pysat.Instrument(platform='pysat', name='testing2d_xarray',
+        self.inst = pysat.Instrument(platform='pysat', name='ndtesting',
                                      num_samples=3, max_latitude=45.)
         self.model = pysat.Instrument(inst_module=pysat_testmodel,
                                       tag='pressure_levels',

pysatModels/tests/test_utils_testing.py

@@ -6,7 +6,6 @@
 """Unit tests for `pysatModels.utils.testing`."""
 
 import numpy as np
-from packaging import version as pack_version
 import pytest
 
 import pysat
@@ -25,9 +24,7 @@ def setup_method(self):
 
         # Load the data in the instruments
         load_kwargs = {'date': pysat_testmodel._test_dates['']['']}
-        if(pack_version.Version(pysat.__version__)
-           > pack_version.Version('3.0.1')):
-            load_kwargs['use_header'] = True
+        load_kwargs['use_header'] = True
 
         self.model.load(**load_kwargs)
 
@@ -92,10 +89,6 @@ def test_compare_model_name_coordinates_failure(self, var, coords, msg,
         return
 
 
-@pytest.mark.skipif(pack_version.Version(pysat.__version__)
-                    <= pack_version.Version('3.0.1'),
-                    reason=''.join(('Requires test model in pysat ',
-                                    ' v3.0.2 or later.')))
 class TestUtilsCompareModNamePressure(TestUtilsCompareModName):
     """Unit tests for `compare_mod_name_coordinates`."""
 
@@ -107,9 +100,7 @@ def setup_method(self):
 
         # Load the data in the instruments
         load_kwargs = {'date': pysat_testmodel._test_dates['']['']}
-        if(pack_version.Version(pysat.__version__)
-           > pack_version.Version('3.0.1')):
-            load_kwargs['use_header'] = True
+        load_kwargs['use_header'] = True
 
         self.model.load(**load_kwargs)
 

pysatModels/utils/extract.py

@@ -859,8 +859,8 @@ def extract_modelled_observations(inst, model, inst_name, mod_name,
             if mod_ind in mind and pair_method == 'closest':
                 # Test to see if this model observation has multiple pairings
                 old_ind = mind.index(mod_ind)
-                if(del_sec[inst_ind, mod_ind]
-                   < del_sec[iind[old_ind], mind[old_ind]]):
+                if (del_sec[inst_ind, mod_ind] < del_sec[iind[old_ind],
+                                                         mind[old_ind]]):
                     # If this one is closer, keep it
                     iind[old_ind] = inst_ind
                     mind[old_ind] = mod_ind