Update testing environments (#2321)

* test numpy 2.0 release candidate

* Update CHANGELOG.md

* test numpy2 on preview job only

* try testing with nightlies and without optional requirements

* modify importorskip logic

* update importorskip test

* use nightly wheels for all available dependencies

* try force reinstall with nightlies

* fix format_coords_as_labels

* update changelog

.azure-pipelines/azure-pipelines-base.yml

@@ -5,26 +5,33 @@ jobs:
   variables:
     - name: NUMBA_DISABLE_JIT
       value: 1
-    - name: ARVIZ_CI_MACHINE
-      value: 1
   timeoutInMinutes: 360
   strategy:
     matrix:
+      Python_312_optionals:
+        python.version: "3.12"
+        Nightlies: false
+        OptionalRequirements: true
+        name: "Python 3.12"
       Python_312:
         python.version: "3.12"
-        PyPIGithub: false
+        Nightlies: false
+        OptionalRequirements: false
         name: "Python 3.12"
-      Python_311:
+      Python_311_optionals:
         python.version: "3.11"
-        PyPIGithub: false
+        Nightlies: false
+        OptionalRequirements: true
         name: "Python 3.11"
       Python_311_preview:
         python.version: "3.11"
-        PyPIGithub: true
+        Nightlies: true
+        OptionalRequirements: false
         name: "Python 3.11"
-      Python_310:
+      Python_310_optionals:
         python.version: "3.10"
-        PyPIGithub: false
+        Nightlies: false
+        OptionalRequirements: true
         name: "Python 3.10"
 
 
@@ -51,22 +58,20 @@ jobs:
       python -m pip install --upgrade pip
       python -m pip install wheel
       python -m pip install --no-cache-dir -r requirements.txt
-      python -m pip install --no-cache-dir -r requirements-optional.txt
       python -m pip install --no-cache-dir -r requirements-dev.txt
       python -m pip install pytest-azurepipelines
-    condition: and(succeeded(), eq(variables.PyPIGithub, false))
-    displayName: 'Install requirements'
+    displayName: 'Install base requirements'
 
   - script: |
-      python -m pip install --upgrade pip
-      python -m pip install wheel
-      python -m pip install --no-cache-dir --pre -r requirements.txt
       python -m pip install --no-cache-dir --pre -r requirements-optional.txt
-      python -m pip install --no-cache-dir -r requirements-dev.txt
-      python -m pip install --upgrade git+https://github.com/pydata/xarray.git
-      python -m pip install pytest-azurepipelines
-    condition: and(succeeded(), eq(variables.PyPIGithub, true))
-    displayName: 'Install requirements (pypi preview / github)'
+    condition: and(succeeded(), eq(variables.OptionalRequirements, true))
+    displayName: 'Install optional requirements'
+
+  - script: |
+      python -m pip install --no-cache-dir --upgrade --pre -r requirements.txt
+      python -m pip install --no-cache-dir --force-reinstall --no-deps --pre -i https://pypi.anaconda.org/scientific-python-nightly-wheels/simple contourpy h5py matplotlib numpy pandas scipy xarray
+    condition: and(succeeded(), eq(variables.Nightlies, true))
+    displayName: 'Update with nightlies'
 
   - script: |
       python -m pip install .
@@ -76,9 +81,15 @@ jobs:
       python -m pip freeze
     displayName: 'Print packages'
 
+  - script: |
+      ARVIZ_REQUIRE_ALL_DEPS=TRUE python -m pytest arviz/tests/base_tests --cov arviz --cov-report=xml
+    condition: and(succeeded(), eq(variables.OptionalRequirements, true))
+    displayName: 'pytest (require all dependencies)'
+
   - script: |
       python -m pytest arviz/tests/base_tests --cov arviz --cov-report=xml
-    displayName: 'pytest'
+    condition: and(succeeded(), eq(variables.OptionalRequirements, false))
+    displayName: 'pytest (skip if dependency missing)'
 
   - script: |
       ls -ahl

.azure-pipelines/azure-pipelines-external.yml

@@ -5,7 +5,7 @@ jobs:
   variables:
     - name: NUMBA_DISABLE_JIT
       value: 1
-    - name: ARVIZ_CI_MACHINE
+    - name: ARVIZ_REQUIRE_ALL_DEPS
       value: 1
   timeoutInMinutes: 360
   strategy:

CHANGELOG.md

@@ -5,6 +5,9 @@
 ### New features
 
 ### Maintenance and fixes
+- Ensure support with numpy 2.0 ([2321](https://github.com/arviz-devs/arviz/pull/2321))
+- Update testing strategy to include an environment without optional dependencies and
+  an environment with [scientific python nightlies](https://anaconda.org/scientific-python-nightly-wheels) ([2321](https://github.com/arviz-devs/arviz/pull/2321))
 
 - Fix legend overwriting issue in `plot_trace` ([2334](https://github.com/arviz-devs/arviz/pull/2334))
 
@@ -15,7 +18,6 @@
 ## v0.18.0 (2024 Apr 4)
 
 ### New features
-
 - Add new example data `rugby_field` and update `rugby` example data ([2322](https://github.com/arviz-devs/arviz/pull/2322))
 - Support for `pytree`s and robust to nested dictionaries. ([2291](https://github.com/arviz-devs/arviz/pull/2291))
 - Add `.close` method to `InferenceData` ([2338](https://github.com/arviz-devs/arviz/pull/2338))

arviz/plots/plot_utils.py

@@ -245,10 +245,8 @@ def format_coords_as_labels(dataarray, skip_dims=None):
     coord_labels = coord_labels.values
     if isinstance(coord_labels[0], tuple):
         fmt = ", ".join(["{}" for _ in coord_labels[0]])
-        coord_labels[:] = [fmt.format(*x) for x in coord_labels]
-    else:
-        coord_labels[:] = [f"{s}" for s in coord_labels]
-    return coord_labels
+        return np.array([fmt.format(*x) for x in coord_labels])
+    return np.array([f"{s}" for s in coord_labels])
 
 
 def set_xticklabels(ax, coord_labels):

arviz/tests/base_tests/test_data.py

@@ -42,7 +42,6 @@
     draws,
     eight_schools_params,
     models,
-    running_on_ci,
 )
 
 
@@ -1469,7 +1468,7 @@ def test_json_converters(self, models):
 
 
 @pytest.mark.skipif(
-    not (importlib.util.find_spec("datatree") or running_on_ci()),
+    not (importlib.util.find_spec("datatree") or "ARVIZ_REQUIRE_ALL_DEPS" in os.environ),
     reason="test requires xarray-datatree library",
 )
 class TestDataTree:

arviz/tests/base_tests/test_data_zarr.py

@@ -16,7 +16,6 @@
     draws,
     eight_schools_params,
     importorskip,
-    running_on_ci,
 )
 
 zarr = importorskip("zarr")  # pylint: disable=invalid-name

arviz/tests/base_tests/test_diagnostics_numba.py

@@ -1,7 +1,5 @@
 """Test Diagnostic methods"""
 
-import importlib
-
 # pylint: disable=redefined-outer-name, no-member, too-many-public-methods
 import numpy as np
 import pytest
@@ -11,13 +9,10 @@
 from ...stats import bfmi, mcse, rhat
 from ...stats.diagnostics import _mc_error, ks_summary
 from ...utils import Numba
-from ..helpers import running_on_ci
+from ..helpers import importorskip
 from .test_diagnostics import data  # pylint: disable=unused-import
 
-pytestmark = pytest.mark.skipif(  # pylint: disable=invalid-name
-    (importlib.util.find_spec("numba") is None) and not running_on_ci(),
-    reason="test requires numba which is not installed",
-)
+importorskip("numba")
 
 rcParams["data.load"] = "eager"
 

arviz/tests/base_tests/test_helpers.py

@@ -6,13 +6,13 @@
 
 def test_importorskip_local(monkeypatch):
     """Test ``importorskip`` run on local machine with non-existent module, which should skip."""
-    monkeypatch.delenv("ARVIZ_CI_MACHINE", raising=False)
+    monkeypatch.delenv("ARVIZ_REQUIRE_ALL_DEPS", raising=False)
     with pytest.raises(Skipped):
         importorskip("non-existent-function")
 
 
 def test_importorskip_ci(monkeypatch):
     """Test ``importorskip`` run on CI machine with non-existent module, which should fail."""
-    monkeypatch.setenv("ARVIZ_CI_MACHINE", 1)
+    monkeypatch.setenv("ARVIZ_REQUIRE_ALL_DEPS", 1)
     with pytest.raises(ModuleNotFoundError):
         importorskip("non-existent-function")

arviz/tests/base_tests/test_plot_utils.py

@@ -1,5 +1,6 @@
 # pylint: disable=redefined-outer-name
 import importlib
+import os
 
 import numpy as np
 import pytest
@@ -20,10 +21,10 @@
 from ...sel_utils import xarray_sel_iter, xarray_to_ndarray
 from ...stats.density_utils import get_bins
 from ...utils import get_coords
-from ..helpers import running_on_ci
 
 # Check if Bokeh is installed
 bokeh_installed = importlib.util.find_spec("bokeh") is not None  # pylint: disable=invalid-name
+skip_tests = (not bokeh_installed) and ("ARVIZ_REQUIRE_ALL_DEPS" not in os.environ)
 
 
 @pytest.mark.parametrize(
@@ -212,10 +213,7 @@ def test_filter_plotter_list_warning():
     assert len(plotters_filtered) == 5
 
 
-@pytest.mark.skipif(
-    not (bokeh_installed or running_on_ci()),
-    reason="test requires bokeh which is not installed",
-)
+@pytest.mark.skipif(skip_tests, reason="test requires bokeh which is not installed")
 def test_bokeh_import():
     """Tests that correct method is returned on bokeh import"""
     plot = get_plotting_function("plot_dist", "distplot", "bokeh")
@@ -290,10 +288,7 @@ def test_mpl_dealiase_sel_kwargs():
     assert res["line_color"] == "red"
 
 
-@pytest.mark.skipif(
-    not (bokeh_installed or running_on_ci()),
-    reason="test requires bokeh which is not installed",
-)
+@pytest.mark.skipif(skip_tests, reason="test requires bokeh which is not installed")
 def test_bokeh_dealiase_sel_kwargs():
     """Check bokeh dealiase_sel_kwargs behaviour.
 
@@ -315,10 +310,7 @@ def test_bokeh_dealiase_sel_kwargs():
     assert res["line_color"] == "red"
 
 
-@pytest.mark.skipif(
-    not (bokeh_installed or running_on_ci()),
-    reason="test requires bokeh which is not installed",
-)
+@pytest.mark.skipif(skip_tests, reason="test requires bokeh which is not installed")
 def test_set_bokeh_circular_ticks_labels():
     """Assert the axes returned after placing ticks and tick labels for circular plots."""
     import bokeh.plotting as bkp

arviz/tests/base_tests/test_stats_numba.py

@@ -1,6 +1,4 @@
 # pylint: disable=redefined-outer-name, no-member
-import importlib
-
 import numpy as np
 import pytest
 
@@ -9,15 +7,12 @@
 from ...utils import Numba
 from ..helpers import (  # pylint: disable=unused-import
     check_multiple_attrs,
+    importorskip,
     multidim_models,
-    running_on_ci,
 )
 from .test_stats import centered_eight, non_centered_eight  # pylint: disable=unused-import
 
-pytestmark = pytest.mark.skipif(  # pylint: disable=invalid-name
-    (importlib.util.find_spec("numba") is None) and not running_on_ci(),
-    reason="test requires numba which is not installed",
-)
+numba = importorskip("numba")
 
 rcParams["data.load"] = "eager"
 

arviz/tests/base_tests/test_utils_numba.py

@@ -8,13 +8,10 @@
 
 from ...stats.stats_utils import stats_variance_2d as svar
 from ...utils import Numba, _numba_var, numba_check
-from ..helpers import running_on_ci
+from ..helpers import importorskip
 from .test_utils import utils_with_numba_import_fail  # pylint: disable=unused-import
 
-pytestmark = pytest.mark.skipif(  # pylint: disable=invalid-name
-    (importlib.util.find_spec("numba") is None) and not running_on_ci(),
-    reason="test requires numba which is not installed",
-)
+importorskip("numba")
 
 
 def test_utils_fixture(utils_with_numba_import_fail):

arviz/tests/external_tests/test_data_pystan.py

@@ -1,6 +1,7 @@
 # pylint: disable=no-member, invalid-name, redefined-outer-name, too-many-function-args
 import importlib
 from collections import OrderedDict
+import os
 
 import numpy as np
 import pytest
@@ -16,19 +17,18 @@
     importorskip,
     load_cached_models,
     pystan_version,
-    running_on_ci,
 )
 
 # Check if either pystan or pystan3 is installed
 pystan_installed = (importlib.util.find_spec("pystan") is not None) or (
     importlib.util.find_spec("stan") is not None
 )
-pytestmark = pytest.mark.skipif(
-    not (pystan_installed | running_on_ci()),
-    reason="test requires pystan/pystan3 which is not installed",
-)
 
 
+@pytest.mark.skipif(
+    not (pystan_installed or "ARVIZ_REQUIRE_ALL_DEPS" in os.environ),
+    reason="test requires pystan/pystan3 which is not installed",
+)
 class TestDataPyStan:
     @pytest.fixture(scope="class")
     def data(self, eight_schools_params, draws, chains):

arviz/tests/helpers.py

@@ -620,11 +620,6 @@ def test_precompile_models(eight_schools_params, draws, chains):
     load_cached_models(eight_schools_params, draws, chains)
 
 
-def running_on_ci() -> bool:
-    """Return True if running on CI machine."""
-    return os.environ.get("ARVIZ_CI_MACHINE") is not None
-
-
 def importorskip(
     modname: str, minversion: Optional[str] = None, reason: Optional[str] = None
 ) -> Any:
@@ -643,9 +638,9 @@ def importorskip(
     Example::
         docutils = pytest.importorskip("docutils")
     """
-    # ARVIZ_CI_MACHINE is True if tests run on CI, where ARVIZ_CI_MACHINE env variable exists
-    ARVIZ_CI_MACHINE = running_on_ci()
-    if not ARVIZ_CI_MACHINE:
+    # Unless ARVIZ_REQUIRE_ALL_DEPS is defined, tests that require a missing dependency are skipped
+    # if set, missing optional dependencies trigger failed tests.
+    if "ARVIZ_REQUIRE_ALL_DEPS" not in os.environ:
         return pytest.importorskip(modname=modname, minversion=minversion, reason=reason)
     import warnings
 

requirements.txt

@@ -1,6 +1,6 @@
 setuptools>=60.0.0
 matplotlib>=3.5
-numpy>=1.23.0,<2.0
+numpy>=1.23.0
 scipy>=1.9.0
 packaging
 pandas>=1.5.0