Use latest pytest and xdoctest (#1632)

### What kind of change does this PR introduce? * Unpins the `pytest` version now that `xdoctest` supports it. * Pins to the latest `xdoctest` supporting `pytest~=8.0`. ### Does this PR introduce a breaking change? No. ### Other information: FYI @RondeauG The newest `pytest` (v8.0.0) introduced some regressions for Windows users. An issue is already up and a patch should arrive shortly (pytest-dev/pytest#11895). Until then, use `pytest<8.0` on Windows. See also: pytest-dev/pytest#11969
Ouranosinc · Jul 31, 2024 · da4a79a · da4a79a
2 parents 2dfe738 + 9552997
commit da4a79a
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diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
@@ -68,14 +68,14 @@ jobs:
         run: |
           python -m tox -e lint
 
-  test-py39:
+  test-preliminary:
     name: Python${{ matrix.python-version }} (${{ matrix.tox-env }}, ${{ matrix.os }})
     needs: lint
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
         include:
-          - tox-env: "py39"
+          - tox-env: "py39-coverage"
             python-version: "3.9"
             os: ubuntu-latest
     steps:
@@ -123,32 +123,32 @@ jobs:
             markers: -m 'not slow'
             os: windows-latest
           # macOS builds
-          - tox-env: py310-coverage-lmoments-doctest
+          - tox-env: py310-coverage-extras-lmoments
             python-version: "3.10"
             markers: -m 'not slow'
             os: macos-latest
           # Linux builds
-          - tox-env: py39-coverage-sbck-doctest
+          - tox-env: py39-coverage-offline-prefetch
             python-version: "3.9"
-            markers: -m 'not slow'
+            markers: -m 'not slow and not requires_internet'
             os: ubuntu-latest
           - tox-env: py310-coverage-lmoments  # No markers -- includes slow tests
             python-version: "3.10"
             os: ubuntu-latest
-          - tox-env: py311-coverage-sbck-extras
+          - tox-env: py311-coverage-extras-sbck
             python-version: "3.11"
             markers: -m 'not slow'
             os: ubuntu-latest
-          - tox-env: py312-coverage-lmoments-doctest
+          - tox-env: py312-coverage-extras-lmoments
             python-version: "3.12"
             markers: -m 'not slow'
             os: ubuntu-latest
+          # Specialized tests
           - tox-env: notebooks
             python-version: "3.10"
             os: ubuntu-latest
-          - tox-env: offline-prefetch
-            python-version: "3.11"
-            markers: -m 'not slow and not requires_internet'
+          - tox-env: doctests
+            python-version: "3.12"
             os: ubuntu-latest
     steps:
       - name: Harden Runner
@@ -269,6 +269,7 @@ jobs:
 
   finish:
     needs:
+      - test-preliminary
       - test-pypi
       - test-conda
     runs-on: ubuntu-latest

diff --git a/CHANGELOG.rst b/CHANGELOG.rst
@@ -8,8 +8,9 @@ Contributors to this version: David Huard (:user:`huard`), Trevor James Smith (:
 
 New features and enhancements
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-* ``xclim.sdba.nbutils.quantile`` and its child functions are now faster. If the module `fastnanquantile` is installed, it is used as the backend for the computation of quantiles and yields even faster results. (:issue:`1255`, :pull:`1513`).
+* ``xclim.sdba.nbutils.quantile`` and its child functions are now faster. If the module `fastnanquantile` is installed, it is used as the backend for the computation of quantiles and yields even faster results. This dependency is now listed in the `xclim[extras]` recipe. (:issue:`1255`, :pull:`1513`).
 * New multivariate bias adjustment class `MBCn`, giving a faster and more accurate implementation of the 'MBCn' algorithm (:issue:`1551`, :pull:`1580`).
+* `xclim` is now compatible with `pytest` versions `>=8.0.0`. (:pull:`1632`).
 
 Bug fixes
 ^^^^^^^^^
@@ -18,7 +19,8 @@ Bug fixes
 
 Internal changes
 ^^^^^^^^^^^^^^^^
-* Changed french translation of "wet days" from "jours mouillés" to "jours pluvieux". (:issue:`1825`, :pull:`1826`).
+* Changed the French translation of "wet days" from "jours mouillés" to "jours pluvieux". (:issue:`1825`, :pull:`1826`).
+* In order to adapt to changes in `pytest`, the doctest fixtures have been split from the main testing suite and doctests are now run using ``$ python -c 'from xclim.testing.utils import run_doctests; run_doctests()'``. (:pull:`1632`).
 
 CI changes
 ^^^^^^^^^^

diff --git a/environment.yml b/environment.yml
@@ -61,7 +61,7 @@ dependencies:
   - pre-commit >=3.7
   - pybtex >=0.24.0
   - pylint >=3.1
-  - pytest <8.0  # Pinned due to breakage with xdoctest. See: https://github.com/Erotemic/xdoctest/issues/151
+  - pytest >=8.0.0
   - pytest-cov
   - pytest-socket
   - pytest-xdist >=3.2
@@ -77,7 +77,7 @@ dependencies:
   - tox >=4.15.1
 #  - tox-conda  # Will be added when a [email protected]+ compatible plugin is released.
   - vulture # ==2.11  # The conda-forge version is out of date.
-  - xdoctest
+  - xdoctest >=1.1.5
   - yamllint
   - pip
   - pip:

diff --git a/pyproject.toml b/pyproject.toml
@@ -38,9 +38,11 @@ dependencies = [
   "cftime>=1.4.1",
   "click>=8.1",
   "dask[array]>=2.6",
+  "filelock",
   "jsonpickle",
   "numba",
   "numpy>=1.20.0,<2.0.0",
+  "packaging",
   "pandas>=2.2",
   "pint>=0.10,<0.24",
   "platformdirs >=3.2",
@@ -78,7 +80,7 @@ dev = [
   "pooch",
   "pre-commit >=3.7",
   "pylint >=3.2.4",
-  "pytest <8.0", # Pinned due to breakage with xdoctest. See: https://github.com/Erotemic/xdoctest/issues/151
+  "pytest >=8.0.0",
   "pytest-cov",
   "pytest-socket",
   "pytest-xdist[psutil] >=3.2",
@@ -88,7 +90,7 @@ dev = [
   # "tox-conda",  # Will be added when a [email protected]+ compatible plugin is released.
   "tox-gh >=1.3.1",
   "vulture ==2.11",
-  "xdoctest",
+  "xdoctest >=1.1.5",
   "yamllint ==1.35.1"
 ]
 docs = [
@@ -166,7 +168,7 @@ ignore-words-list = "absolue,astroid,bloc,bui,callendar,degreee,environnement,ha
 
 [tool.coverage.run]
 relative_files = true
-omit = ["tests/*.py"]
+omit = ["tests/*.py", "src/xclim/testing/conftest.py"]
 
 [tool.deptry]
 extend_exclude = ["docs"]
@@ -180,7 +182,7 @@ pep621_dev_dependency_groups = ["all", "dev", "docs"]
 [tool.deptry.per_rule_ignores]
 DEP001 = ["SBCK"]
 DEP002 = ["bottleneck", "pyarrow"]
-DEP004 = ["matplotlib", "pytest_socket"]
+DEP004 = ["matplotlib", "pytest", "pytest_socket"]
 
 [tool.flit.sdist]
 include = [
@@ -259,8 +261,9 @@ addopts = [
 ]
 norecursedirs = ["docs/notebooks/*"]
 filterwarnings = ["ignore::UserWarning"]
-testpaths = "tests tests/test_sdba"
-usefixtures = "xdoctest_namespace"
+testpaths = [
+  "tests"
+]
 doctest_optionflags = ["NORMALIZE_WHITESPACE", "IGNORE_EXCEPTION_DETAIL", "NUMBER", "ELLIPSIS"]
 markers = [
   "slow: marks tests as slow (deselect with '-m \"not slow\"')",

diff --git a/tests/conftest.py b/tests/conftest.py
@@ -2,24 +2,14 @@
 from __future__ import annotations
 
 import os
-import re
-import shutil
-import sys
-import time
-import warnings
-from datetime import datetime as dt
 from functools import partial
 from pathlib import Path
 
 import numpy as np
 import pandas as pd
 import pytest
 import xarray as xr
-from filelock import FileLock
-from packaging.version import Version
 
-import xclim
-from xclim import __version__ as __xclim_version__
 from xclim.core import indicator
 from xclim.core.calendar import max_doy
 from xclim.testing import helpers
@@ -28,37 +18,6 @@
 from xclim.testing.utils import get_file
 from xclim.testing.utils import open_dataset as _open_dataset
 
-if (
-    re.match(r"^\d+\.\d+\.\d+$", __xclim_version__)
-    and helpers.TESTDATA_BRANCH == "main"
-):
-    # This does not need to be emitted on GitHub Workflows and ReadTheDocs
-    if not os.getenv("CI") and not os.getenv("READTHEDOCS"):
-        warnings.warn(
-            f'`xclim` {__xclim_version__} is running tests against the "main" branch of `Ouranosinc/xclim-testdata`. '
-            "It is possible that changes in xclim-testdata may be incompatible with test assertions in this version. "
-            "Please be sure to check https://github.com/Ouranosinc/xclim-testdata for more information.",
-            UserWarning,
-        )
-
-if re.match(r"^v\d+\.\d+\.\d+", helpers.TESTDATA_BRANCH):
-    # Find the date of last modification of xclim source files to generate a calendar version
-    install_date = dt.strptime(
-        time.ctime(os.path.getmtime(xclim.__file__)),
-        "%a %b %d %H:%M:%S %Y",
-    )
-    install_calendar_version = (
-        f"{install_date.year}.{install_date.month}.{install_date.day}"
-    )
-
-    if Version(helpers.TESTDATA_BRANCH) > Version(install_calendar_version):
-        warnings.warn(
-            f"Installation date of `xclim` ({install_date.ctime()}) "
-            f"predates the last release of `xclim-testdata` ({helpers.TESTDATA_BRANCH}). "
-            "It is very likely that the testing data is incompatible with this build of `xclim`.",
-            UserWarning,
-        )
-
 
 @pytest.fixture
 def random() -> np.random.Generator:
@@ -366,42 +325,6 @@ def _open_session_scoped_file(
     return _open_session_scoped_file
 
 
-@pytest.fixture(autouse=True, scope="session")
-def add_imports(xdoctest_namespace, threadsafe_data_dir) -> None:
-    """Add these imports into the doctests scope."""
-    ns = xdoctest_namespace
-    ns["np"] = np
-    ns["xr"] = xclim.testing  # xr.open_dataset(...) -> xclim.testing.open_dataset(...)
-    ns["xclim"] = xclim
-    ns["open_dataset"] = partial(
-        _open_dataset,
-        cache_dir=threadsafe_data_dir,
-        branch=helpers.TESTDATA_BRANCH,
-        engine="h5netcdf",
-    )  # Needed for modules where xarray is imported as `xr`
-
-
-@pytest.fixture(autouse=True, scope="function")
-def add_example_dataarray(xdoctest_namespace, tas_series, pr_series) -> None:
-    ns = xdoctest_namespace
-    ns["tas"] = tas_series(np.random.rand(365) * 20 + 253.15)
-    ns["pr"] = pr_series(np.random.rand(365) * 5)
-
-
-@pytest.fixture(autouse=True, scope="session")
-def is_matplotlib_installed(xdoctest_namespace) -> None:
-    def _is_matplotlib_installed():
-        try:
-            import matplotlib  # noqa
-
-            return
-        except ImportError:
-            return pytest.skip("This doctest requires matplotlib to be installed.")
-
-    ns = xdoctest_namespace
-    ns["is_matplotlib_installed"] = _is_matplotlib_installed
-
-
 @pytest.fixture
 def official_indicators():
     # Remove unofficial indicators (as those created during the tests, and those from YAML-built modules)
@@ -423,7 +346,7 @@ def atmosds(threadsafe_data_dir) -> xr.Dataset:
 
 
 @pytest.fixture(scope="function")
-def ensemble_dataset_objects() -> dict:
+def ensemble_dataset_objects() -> dict[str, str]:
     edo = dict()
     edo["nc_files_simple"] = [
         "EnsembleStats/BCCAQv2+ANUSPLIN300_ACCESS1-0_historical+rcp45_r1i1p1_1950-2100_tg_mean_YS.nc",
@@ -463,43 +386,18 @@ def lafferty_sriver_ds() -> xr.Dataset:
 
 
 @pytest.fixture(scope="session", autouse=True)
-def gather_session_data(threadsafe_data_dir, worker_id, xdoctest_namespace):
+def gather_session_data(threadsafe_data_dir, worker_id):
     """Gather testing data on pytest run.
 
     When running pytest with multiple workers, one worker will copy data remotely to _default_cache_dir while
     other workers wait using lockfile. Once the lock is released, all workers will then copy data to their local
     threadsafe_data_dir.As this fixture is scoped to the session, it will only run once per pytest run.
 
-    Additionally, this fixture is also used to generate the `atmosds` synthetic testing dataset as well as add the
-    example file paths to the xdoctest_namespace, used when running doctests.
+    Additionally, this fixture is also used to generate the `atmosds` synthetic testing dataset.
     """
-    if (
-        not _default_cache_dir.joinpath(helpers.TESTDATA_BRANCH).exists()
-        or helpers.PREFETCH_TESTING_DATA
-    ):
-        if helpers.PREFETCH_TESTING_DATA:
-            print("`XCLIM_PREFETCH_TESTING_DATA` set. Prefetching testing data...")
-        if sys.platform == "win32":
-            raise OSError(
-                "UNIX-style file-locking is not supported on Windows. "
-                "Consider running `$ xclim prefetch_testing_data` to download testing data."
-            )
-        elif worker_id in ["master"]:
-            helpers.populate_testing_data(branch=helpers.TESTDATA_BRANCH)
-        else:
-            _default_cache_dir.mkdir(exist_ok=True, parents=True)
-            lockfile = _default_cache_dir.joinpath(".lock")
-            test_data_being_written = FileLock(lockfile)
-            with test_data_being_written:
-                # This flag prevents multiple calls from re-attempting to download testing data in the same pytest run
-                helpers.populate_testing_data(branch=helpers.TESTDATA_BRANCH)
-                _default_cache_dir.joinpath(".data_written").touch()
-            with test_data_being_written.acquire():
-                if lockfile.exists():
-                    lockfile.unlink()
-    shutil.copytree(_default_cache_dir, threadsafe_data_dir)
+    helpers.testing_setup_warnings()
+    helpers.gather_testing_data(threadsafe_data_dir, worker_id)
     helpers.generate_atmos(threadsafe_data_dir)
-    xdoctest_namespace.update(helpers.add_example_file_paths(threadsafe_data_dir))
 
 
 @pytest.fixture(scope="session", autouse=True)

diff --git a/tests/test_temperature.py b/tests/test_temperature.py
@@ -1,6 +1,7 @@
 from __future__ import annotations
 
 import os
+import warnings
 
 import numpy as np
 import pytest
@@ -826,7 +827,8 @@ def test_convert_units(self, open_dataset):
         # put a nan somewhere
         tasmin.values[180, 1, 0] = np.nan
 
-        with pytest.warns(None) as record:
+        with warnings.catch_warnings():
+            warnings.simplefilter("error")
             frzthw = atmos.daily_freezethaw_cycles(
                 tasmin,
                 tasmax,
@@ -840,15 +842,8 @@ def test_convert_units(self, open_dataset):
 
         frzthw1 = (((min1 < 0) & (max1 > 0)) * 1.0).sum()
 
-        assert (
-            "This index calculation will soon require user-specified thresholds."
-            not in [str(q.message) for q in record]
-        )
-
         np.testing.assert_allclose(frzthw1, frzthw.values[0, 0, 0])
-
         assert np.isnan(frzthw.values[0, 1, 0])
-
         assert np.isnan(frzthw.values[0, -1, -1])