Merge pull request #133 from djhoese/bugfix-doctests

Add doctests to CI and fix existing failures

Author: djhoese

.github/workflows/ci.yaml

@@ -71,7 +71,7 @@ jobs:
       - name: Run unit tests
         shell: bash -l {0}
         run: |
-          pytest --cov=geotiepoints geotiepoints/tests --cov-report=xml --cov-report=
+          pytest --cov=geotiepoints geotiepoints --cov-report=xml --cov-report=
 
       - name: Upload unittest coverage to Codecov
         uses: codecov/codecov-action@v7

AGENTS.md

@@ -125,8 +125,8 @@ graph without computing.
 ```bash
 pip install -e .
 python setup.py build_ext --inplace --cython-coverage --force   # required before running tests
-pytest geotiepoints/tests
-pytest --cov=geotiepoints geotiepoints/tests --cov-report=xml   # what CI runs
+pytest                                                    # whole package, doctests included
+pytest --cov=geotiepoints geotiepoints --cov-report=xml   # what CI runs
 make -C doc doctest
 ```
 
@@ -135,7 +135,21 @@ make -C doc doctest
 
 - Tests load HDF5 fixtures by path relative to the test file (`../../testdata/`), so they only work
   from a source checkout, never from an installed wheel.
-- There is **no `conftest.py` and no pytest configuration at all** — no markers, no ini options.
+- There is **no `conftest.py`**. All pytest configuration lives in `[tool.pytest.ini_options]` in
+  `pyproject.toml` (mirroring trollimage): `--doctest-modules` plus `-ra --showlocals
+  --strict-markers --strict-config`, `xfail_strict`, `filterwarnings = ["error"]`, and
+  `testpaths = ["geotiepoints"]`. So a bare `pytest` runs the unit tests *and* every module
+  docstring. No markers. Two consequences worth knowing:
+  - Passing an explicit path (e.g. `pytest geotiepoints/tests`) overrides `testpaths` and skips the
+    package doctests.
+  - **Warnings are errors**, with one scoped exception: the `invalid value encountered in
+    arcsin/arccos` `RuntimeWarning` from `geotiepoints.geointerpolator`. `xyz2lonlat` is *meant* to
+    return NaN for coordinates that interpolation or extrapolation puts off the sphere -- an invalid
+    pixel should stay visibly invalid rather than be clipped to a plausible-looking lat/lon -- while
+    callers (Satpy readers) keep processing the rest of the swath. Do not "fix" that NaN.
+  - `warnings.catch_warnings(record=True)` inherits the error filter and will raise instead of
+    recording, so it needs an explicit `warnings.simplefilter("always")` inside the context (see
+    `test_modisinterpolator.test_sat_angle_based_interp`).
 - `test_simple_modis_interpolator.py` imports its loaders and `assert_geodetic_distance` from
   `test_modisinterpolator.py`. Preserve that cross-module dependency.
 - `testdata/create_modis_test_data.py` regenerates fixtures but needs `pyhdf` plus a real MOD03 file;
@@ -145,6 +159,8 @@ make -C doc doctest
 - CI: ubuntu/macos/windows × Python 3.11/3.12/3.13, plus an experimental nightly-dependency job.
   `python_requires >= 3.11`.
 - There is no `[project]` table — package metadata still lives in `setup.py`.
+- `doc/source/conf.py` mocks nothing; the docs (and RTD, via `pip install .`) need the real package
+  and its dependencies importable, which is what makes the `index.rst` doctests runnable.
 - `geotiepoints/version.py` is versioneer-generated; never edit it. Release steps are in `RELEASING.md`.
 
 ## Known defects and traps

doc/source/conf.py

@@ -24,30 +24,6 @@
 sys.path.insert(0, os.path.abspath('../../geotiepoints'))
 
 
-class Mock(object):
-    def __init__(self, *args, **kwargs):
-        pass
-
-    def __call__(self, *args, **kwargs):
-        return Mock()
-
-    @classmethod
-    def __getattr__(cls, name):
-        if name in ('__file__', '__path__'):
-            return '/dev/null'
-        if name[0] == name[0].upper():
-            mockType = type(name, (), {})
-            mockType.__module__ = __name__
-            return mockType
-        return Mock()
-
-
-MOCK_MODULES = ['numpy', 'scipy.interpolate', 'scipy',
-                'pyhdf.SD', 'pyhdf.error']
-for mod_name in MOCK_MODULES:
-    sys.modules[mod_name] = Mock()
-
-
 # -- General configuration -----------------------------------------------------
 
 # If your documentation needs a minimal Sphinx version, state it here.

geotiepoints/interpolator.py

@@ -37,11 +37,11 @@ def _linear_extrapolate(pos, data, xev):
     >>> data = np.arange(10).reshape((2, 5), order="F")
     >>> xev = 5
     >>> retv = _linear_extrapolate(pos, data, xev)
-    >>> print([val for val in retv])
+    >>> print([float(val) for val in retv])
     [4.0, 6.0, 8.0, 10.0, 12.0]
     >>> xev = 0
     >>> retv = _linear_extrapolate(pos, data, xev)
-    >>> print([val for val in retv])
+    >>> print([float(val) for val in retv])
     [-1.0, 1.0, 3.0, 5.0, 7.0]
     """
     if len(data) != 2 or len(pos) != 2:

geotiepoints/tests/test_modisinterpolator.py

@@ -126,6 +126,7 @@ def test_sat_angle_based_interp(input_func, exp_func, interp_func, dist_max, exp
 
     # when working with dask arrays, we shouldn't compute anything
     with dask.config.set(scheduler=CustomScheduler(0)), warnings.catch_warnings(record=True) as warns:
+        warnings.simplefilter("always")
         lons, lats = interp_func(lon1, lat1, satz1)
     has_5km_warning = any("may result in poor quality" in str(w.message) for w in warns)
     if exp_5km_warning:

geotiepoints/tests/test_multilinear.py

@@ -60,7 +60,10 @@ def test_multilinear_interp(self):
         ])
 
         interp = MultilinearInterpolator(smin, smax, orders)
-        interp.set_values(f(interp.grid))
+        with np.errstate(invalid="ignore"):
+            # x**3 + y**3 is negative over part of the grid; the resulting NaNs are
+            # baked into the expected RES1 values.
+            interp.set_values(f(interp.grid))
 
         result = interp(ARR1)
         # exact_values = f(ARR1)

pyproject.toml

@@ -2,6 +2,21 @@
 requires = ["setuptools", "wheel", "numpy>=2.0.0,<3", "Cython>=3.1.2", "versioneer[toml]"]
 build-backend = "setuptools.build_meta"
 
+[tool.pytest.ini_options]
+minversion = "6.0"
+addopts = ["-ra", "--showlocals", "--strict-markers", "--strict-config", "--doctest-modules"]
+xfail_strict = true
+filterwarnings = [
+    "error",
+    # xyz2lonlat: coordinates that interpolation/extrapolation puts off the sphere make the
+    # arcsin/arccos argument exceed 1. NaN is the intended result there -- an invalid pixel should
+    # be visible as NaN rather than silently corrected -- and callers (Satpy readers) must keep
+    # processing the rest of the swath, so the accompanying RuntimeWarning is not an error.
+    "ignore:invalid value encountered in arc(sin|cos):RuntimeWarning:geotiepoints.geointerpolator",
+]
+log_cli_level = "info"
+testpaths = ["geotiepoints"]
+
 [tool.coverage.run]
 relative_files = true
 plugins = ["Cython.Coverage"]