Merge pull request #55 from ocefpaf/use_pytest

Use pytest

.github/workflows/tests.yml

@@ -32,6 +32,12 @@ jobs:
       run: |
         python -m pip install -e . --no-deps --force-reinstall
 
+    - name: Install unstable dependencies
+      if: ${{ matrix.python-version == 3.9 }}
+      shell: bash -l {0}
+      run: |
+          micromamba install "netcdf4<1.6.5"
+  
     - name: Default Tests
       shell: bash -l {0}
       run: pytest -s -rxs -v cc_plugin_ncei

.gitignore

@@ -8,3 +8,4 @@ dist
 **/.DS_Store
 .tox/
 .cache
+cc_plugin_ncei/_version.py

cc_plugin_ncei/tests/test_base.py

@@ -1,71 +1,74 @@
+"""Tests the base functionality of the checker that should remain the same
+across all of the discrete sampling geometries
+"""
+
 import numpy as np
+import pytest
 from compliance_checker.base import BaseCheck
+from compliance_checker.tests.helpers import MockNetCDF
 
 from cc_plugin_ncei import ncei_base
-from cc_plugin_ncei.tests.helpers import MockNetCDF
-from cc_plugin_ncei.tests.ncei_test_case import NCEITestCase
 
+# TestNCEIBase
+
+
+@pytest.fixture()
+def nc():
+    """Create a simple timeseries like NetCDF object."""
+    nc = MockNetCDF()
+    nc.createDimension("time", None)
+    tvar = nc.createVariable("time", "f8", ("time",))
+    tvar.axis = "T"
+    tvar.standard_name = "time"
+    tvar.units = "seconds since 1970-01-01"
+    tvar.calendar = "gregorian"
+    tvar[:] = np.array([1, 2], dtype="f8")
+    pres = nc.createVariable("pressure", "f8", ("time",))
+    pres.standard_name = "air_pressure"
+    pres.units = "Pa"
+    pres[:] = np.array([101.325, 101.425], dtype=np.float64)
+    yield nc
+    nc.close()
 
-class TestNCEIBase(NCEITestCase):
-    """Tests the base functionality of the checker that should remain the same
-    across all of the discrete sampling geometries
+
+def test_valid_range(nc):
+    """Check for defined valid range with same dtype as source variable with
+    two elements in min to max order.
     """
+    base_check = ncei_base.BaseNCEICheck()
 
-    def setUp(self):
-        """Create a simple timeseries like NetCDF object."""
-        self.ds = MockNetCDF()
-        self.ds.createDimension("time", None)
-        tvar = self.ds.createVariable("time", "f8", ("time",))
-        tvar.axis = "T"
-        tvar.standard_name = "time"
-        tvar.units = "seconds since 1970-01-01"
-        tvar.calendar = "gregorian"
-        tvar[:] = np.array([1, 2], dtype="f8")
-        pres = self.ds.createVariable("pressure", "f8", ("time",))
-        pres.standard_name = "air_pressure"
-        pres.units = "Pa"
-        pres[:] = np.array([101.325, 101.425], dtype=np.float64)
-        self.base_check = ncei_base.BaseNCEICheck()
+    var = nc.variables["pressure"]
+    tc1 = ncei_base.TestCtx(BaseCheck.MEDIUM, "Test context")
+    var.valid_range = np.array([101.325, 101.425], dtype=np.float64)
+    base_check._check_min_max_range(var, tc1)
+    assert len(tc1.messages) == 0
+    # list-like types get automatically converted to numpy arrays if they
+    # aren't a base numpy type
+    var.valid_range = [100, 200, 300]
+    tc2 = ncei_base.TestCtx(BaseCheck.MEDIUM, "Test context")
+    base_check._check_min_max_range(var, tc2)
+    assert (
+        "valid_range must be a two element vector of min followed by max with the same data type as pressure"
+        in tc2.messages
+    )
 
-    def tearDown(self):
-        """Ensure the NetCDF object closes after each test or if an exception is
-        raised.
-        """
-        self.ds.close()
 
-    def test_valid_range(self):
-        """Check for defined valid range with same dtype as source variable with
-        two elements in min to max order.
-        """
-        var = self.ds.variables["pressure"]
-        tc1 = ncei_base.TestCtx(BaseCheck.MEDIUM, "Test context")
-        var.valid_range = np.array([101.325, 101.425], dtype=np.float64)
-        self.base_check._check_min_max_range(var, tc1)
-        self.assertEqual(len(tc1.messages), 0)
-        # list-like types get automatically converted to numpy arrays if they
-        # aren't a base numpy type
-        var.valid_range = [100, 200, 300]
-        tc2 = ncei_base.TestCtx(BaseCheck.MEDIUM, "Test context")
-        self.base_check._check_min_max_range(var, tc2)
-        self.assertTrue(
-            "valid_range must be a two element vector of min followed by max with the same data type as pressure"
-            in tc2.messages,
-        )
+def test_valid_min_max(nc):
+    """When valid_range is not defined, check for the presence of both
+    attributes valid_min and valid_max which are the same data type as the
+    data in the variable.
+    """
+    base_check = ncei_base.BaseNCEICheck()
 
-    def test_valid_min_max(self):
-        """When valid_range is not defined, check for the presence of both
-        attributes valid_min and valid_max which are the same data type as the
-        data in the variable.
-        """
-        var = self.ds.variables["pressure"]
-        var.valid_min, var.valid_max = 101.325, 101.425
-        tc1 = ncei_base.TestCtx(BaseCheck.MEDIUM, "Test context")
-        self.base_check._check_min_max_range(var, tc1)
-        var.valid_min, var.valid_max = "101", "102"
-        tc2 = ncei_base.TestCtx(BaseCheck.MEDIUM, "Test context")
-        self.base_check._check_min_max_range(var, tc2)
-        expected = [
-            f"{v} attribute should exist, have the same type as pressure, and not be empty or valid_range should be defined"
-            for v in ["valid_min", "valid_max"]
-        ]
-        self.assertEqual(expected, tc2.messages)
+    var = nc.variables["pressure"]
+    var.valid_min, var.valid_max = 101.325, 101.425
+    tc1 = ncei_base.TestCtx(BaseCheck.MEDIUM, "Test context")
+    base_check._check_min_max_range(var, tc1)
+    var.valid_min, var.valid_max = "101", "102"
+    tc2 = ncei_base.TestCtx(BaseCheck.MEDIUM, "Test context")
+    base_check._check_min_max_range(var, tc2)
+    expected = [
+        f"{v} attribute should exist, have the same type as pressure, and not be empty or valid_range should be defined"
+        for v in ["valid_min", "valid_max"]
+    ]
+    assert expected == tc2.messages

pyproject.toml

@@ -0,0 +1,106 @@
+[build-system]
+build-backend = "setuptools.build_meta"
+requires = [
+  "setuptools>=42",
+  "setuptools-scm",
+  "wheel",
+]
+
+[project]
+name = "cc-plugin-ncei"
+description = "Compliance Checker NCEI Templates Compliance plugin"
+readme = "README.md"
+license = { text = "Apache-2.0" }
+maintainers = [
+  { name = "Benjamin Adams" },
+  { name = "Bob Fratantonio" },
+  { name = "Filipe Fernandes" },
+  { name = "Luke Campbell" },
+]
+requires-python = ">=3.8"
+classifiers = [
+  "Development Status :: 5 - Production/Stable",
+  "Intended Audience :: Developers",
+  "Intended Audience :: Science/Research",
+  "License :: OSI Approved :: Apache Software License",
+  "Operating System :: MacOS :: MacOS X",
+  "Operating System :: Microsoft :: Windows",
+  "Operating System :: POSIX :: Linux",
+  "Programming Language :: Python",
+  "Programming Language :: Python :: 3 :: Only",
+  "Programming Language :: Python :: 3.8",
+  "Programming Language :: Python :: 3.9",
+  "Programming Language :: Python :: 3.10",
+  "Programming Language :: Python :: 3.11",
+  "Programming Language :: Python :: 3.12",
+  "Topic :: Scientific/Engineering",
+]
+dynamic = [
+  "dependencies",
+  "version",
+]
+
+urls.documentation = "https://ioos.github.io/cc-plugin-ncei"
+urls.homepage = "https://compliance.ioos.us/index.html"
+urls.repository = "https://github.com/ioos/cc-plugin-ncei"
+
+entry-points."compliance_checker.suites"."ncei-grid-1.1" = "cc_plugin_ncei.ncei_grid:NCEIGrid1_1"
+entry-points."compliance_checker.suites"."ncei-grid-2.0" = "cc_plugin_ncei.ncei_grid:NCEIGrid2_0"
+entry-points."compliance_checker.suites"."ncei-point-1.1" = "cc_plugin_ncei.ncei_point:NCEIPoint1_1"
+entry-points."compliance_checker.suites"."ncei-point-2.0" = "cc_plugin_ncei.ncei_point:NCEIPoint2_0"
+entry-points."compliance_checker.suites"."ncei-profile-incomplete-1.1" = "cc_plugin_ncei.ncei_profile:NCEIProfileIncomplete1_1"
+entry-points."compliance_checker.suites"."ncei-profile-incomplete-2.0" = "cc_plugin_ncei.ncei_profile:NCEIProfileIncomplete2_0"
+entry-points."compliance_checker.suites"."ncei-profile-orthogonal-1.1" = "cc_plugin_ncei.ncei_profile:NCEIProfileOrthogonal1_1"
+entry-points."compliance_checker.suites"."ncei-profile-orthogonal-2.0" = "cc_plugin_ncei.ncei_profile:NCEIProfileOrthogonal2_0"
+entry-points."compliance_checker.suites"."ncei-timeseries-incomplete-1.1" = "cc_plugin_ncei.ncei_timeseries:NCEITimeSeriesIncomplete1_1"
+entry-points."compliance_checker.suites"."ncei-timeseries-incomplete-2.0" = "cc_plugin_ncei.ncei_timeseries:NCEITimeSeriesIncomplete2_0"
+entry-points."compliance_checker.suites"."ncei-timeseries-orthogonal-1.1" = "cc_plugin_ncei.ncei_timeseries:NCEITimeSeriesOrthogonal1_1"
+entry-points."compliance_checker.suites"."ncei-timeseries-orthogonal-2.0" = "cc_plugin_ncei.ncei_timeseries:NCEITimeSeriesOrthogonal2_0"
+entry-points."compliance_checker.suites"."ncei-timeseries-profile-incomplete-1.1" = "cc_plugin_ncei.ncei_timeseries_profile:NCEITimeSeriesProfileIncomplete1_1"
+entry-points."compliance_checker.suites"."ncei-timeseries-profile-incomplete-2.0" = "cc_plugin_ncei.ncei_timeseries_profile:NCEITimeSeriesProfileIncomplete2_0"
+entry-points."compliance_checker.suites"."ncei-timeseries-profile-incompletetime-orthdepth-1.1" = "cc_plugin_ncei.ncei_timeseries_profile:NCEITimeSeriesProfileIncompleteTimeOrthDepth1_1"
+entry-points."compliance_checker.suites"."ncei-timeseries-profile-incompletetime-orthdepth-2.0" = "cc_plugin_ncei.ncei_timeseries_profile:NCEITimeSeriesProfileIncompleteTimeOrthDepth2_0"
+entry-points."compliance_checker.suites"."ncei-timeseries-profile-orthogonal-1.1" = "cc_plugin_ncei.ncei_timeseries_profile:NCEITimeSeriesProfileOrthogonal1_1"
+entry-points."compliance_checker.suites"."ncei-timeseries-profile-orthogonal-2.0" = "cc_plugin_ncei.ncei_timeseries_profile:NCEITimeSeriesProfileOrthogonal2_0"
+entry-points."compliance_checker.suites"."ncei-timeseries-profile-orthtime-incompletedepth-1.1" = "cc_plugin_ncei.ncei_timeseries_profile:NCEITimeSeriesProfileOrthTimeIncompleteDepth1_1"
+entry-points."compliance_checker.suites"."ncei-timeseries-profile-orthtime-incompletedepth-2.0" = "cc_plugin_ncei.ncei_timeseries_profile:NCEITimeSeriesProfileOrthTimeIncompleteDepth2_0"
+entry-points."compliance_checker.suites"."ncei-trajectory-1.1" = "cc_plugin_ncei.ncei_trajectory:NCEITrajectory1_1"
+entry-points."compliance_checker.suites"."ncei-trajectory-2.0" = "cc_plugin_ncei.ncei_trajectory:NCEITrajectory2_0"
+entry-points."compliance_checker.suites"."ncei-trajectory-profile-incomplete-1.1" = "cc_plugin_ncei.ncei_trajectory_profile:NCEITrajectoryProfileIncomplete1_1"
+entry-points."compliance_checker.suites"."ncei-trajectory-profile-incomplete-2.0" = "cc_plugin_ncei.ncei_trajectory_profile:NCEITrajectoryProfileIncomplete2_0"
+
+entry-points."compliance_checker.suites"."ncei-trajectory-profile-orthogonal-1.1" = "cc_plugin_ncei.ncei_trajectory_profile:NCEITrajectoryProfileOrthogonal1_1"
+entry-points."compliance_checker.suites"."ncei-trajectory-profile-orthogonal-2.0" = "cc_plugin_ncei.ncei_trajectory_profile:NCEITrajectoryProfileOrthogonal2_0"
+
+[tool.setuptools]
+packages = [
+  "cc_plugin_ncei",
+]
+license-files = [
+  "LICENSE",
+]
+zip-safe = false
+include-package-data = true
+
+[tool.setuptools.package-data]
+cc_plugin_ncei = [
+  "data/*.xml",
+  "data/*.json",
+]
+
+[tool.setuptools.dynamic]
+dependencies = { file = [
+  "requirements.txt",
+] }
+readme = { file = "README.md", content-type = "text/markdown" }
+
+[tool.setuptools_scm]
+write_to = "cc_plugin_ncei/_version.py"
+write_to_template = "__version__ = '{version}'"
+tag_regex = "^(?P<prefix>v)?(?P<version>[^\\+]+)(?P<suffix>.*)?$"
+
+[tool.pytest.ini_options]
+filterwarnings = [
+  # We try to use strings instead od floats in puporse in the tests.
+  "ignore::UserWarning",
+]