test: Consolidate and update pytest options in pyproject.toml (#1773)

* Remove .coveragerc and consolidate pytest options to pyproject.toml.
* Apply 'configuring pytest' recommendations for pytest from Scikit-HEP
(c.f. https://scikit-hep.org/developer/pytest#configuring-pytest ).
   - '-ra' includes a report after pytest runs with a summary on all tests
     except those that passed. From 'pytest --help':
     > -r chars: show extra test summary info as specified by chars: (f)ailed,
     > (E)rror, (s)kipped, (x)failed, (X)passed, (p)assed, (P)assed with output,
     > (a)ll except passed (p/P), or (A)ll. (w)arnings are enabled by default
     > (see --disable-warnings), 'N' can be used to reset the list. (default: 'fE').
   - '--showlocal' prints locals in tracebacks.
   - '--strict-markers' will complain if you use an unspecified fixture.
   - '--strict-config' will raise an error if there is a mistake in the pytest config.
   - 'log_cli_level = "info"' reports INFO and above log messages on a failure.
   - 'filterwarnings = ["error"]' sets all warnings to be errors and allows for
     some warnings to be ignored with -W warn control syntax.
     (c.f. https://docs.python.org/dev/using/cmdline.html#cmdoption-W )
* Remove `tests/__init__.py` as no reason to make the tests directory importable.
* Remove '-r sx' from pytest calls in CI jobs as pyproject.toml now applies '-ra'.
* Use 'with pytest.warns' to assert expected warnings in tests.
(c.f. https://docs.pytest.org/en/7.0.x/how-to/capture-warnings.html#warns )
* Override error on filterwarnings for the 'minimum supported dependencies' GHA workflow
as it is testing for the oldest releases that work with the latest API, not the oldest
releases that are warning free.
* Remove unused nbQA options for black from pyproject.toml.
   - Amends PR #1598

.github/workflows/ci.yml

@@ -49,7 +49,7 @@ jobs:
 
     - name: Test with pytest
       run: |
-        pytest -r sx --ignore tests/benchmarks/ --ignore tests/contrib --ignore tests/test_notebooks.py
+        pytest --ignore tests/benchmarks/ --ignore tests/contrib --ignore tests/test_notebooks.py
 
     - name: Launch a tmate session if tests fail
       if: failure() && github.event_name == 'workflow_dispatch'
@@ -64,7 +64,7 @@ jobs:
 
     - name: Test Contrib module with pytest
       run: |
-        pytest -r sx tests/contrib --mpl --mpl-baseline-path tests/contrib/baseline
+        pytest tests/contrib --mpl --mpl-baseline-path tests/contrib/baseline
 
     - name: Report contrib coverage with Codecov
       if: github.event_name != 'schedule' && matrix.python-version == '3.9' && matrix.os == 'ubuntu-latest'
@@ -75,7 +75,7 @@ jobs:
 
     - name: Test docstring examples with doctest
       if: matrix.python-version == '3.9'
-      run: pytest -r sx src/ README.rst
+      run: pytest src/ README.rst
 
     - name: Report doctest coverage with Codecov
       if: github.event_name != 'schedule' && matrix.python-version == '3.9' && matrix.os == 'ubuntu-latest'
@@ -87,4 +87,4 @@ jobs:
     - name: Run benchmarks
       if: github.event_name == 'schedule' && matrix.python-version == '3.9'
       run: |
-        pytest -r sx --benchmark-sort=mean tests/benchmarks/test_benchmark.py
+        pytest --benchmark-sort=mean tests/benchmarks/test_benchmark.py

.github/workflows/dependencies-head.yml

@@ -31,7 +31,7 @@ jobs:
 
     - name: Test with pytest
       run: |
-        pytest -r sx --ignore tests/benchmarks/ --ignore tests/contrib --ignore tests/test_notebooks.py
+        pytest --ignore tests/benchmarks/ --ignore tests/contrib --ignore tests/test_notebooks.py
 
   scipy:
 
@@ -61,7 +61,7 @@ jobs:
 
     - name: Test with pytest
       run: |
-        pytest -r sx --ignore tests/benchmarks/ --ignore tests/contrib --ignore tests/test_notebooks.py
+        pytest --ignore tests/benchmarks/ --ignore tests/contrib --ignore tests/test_notebooks.py
 
   iminuit:
 
@@ -87,7 +87,7 @@ jobs:
         python -m pip list
     - name: Test with pytest
       run: |
-        pytest -r sx --ignore tests/benchmarks/ --ignore tests/contrib --ignore tests/test_notebooks.py
+        pytest --ignore tests/benchmarks/ --ignore tests/contrib --ignore tests/test_notebooks.py
 
   uproot4:
 
@@ -112,7 +112,7 @@ jobs:
         python -m pip list
     - name: Test with pytest
       run: |
-        pytest -r sx --ignore tests/benchmarks/ --ignore tests/contrib --ignore tests/test_notebooks.py
+        pytest --ignore tests/benchmarks/ --ignore tests/contrib --ignore tests/test_notebooks.py
 
   pytest:
 
@@ -137,4 +137,4 @@ jobs:
         python -m pip list
     - name: Test with pytest
       run: |
-        pytest -r sx --ignore tests/benchmarks/ --ignore tests/contrib --ignore tests/test_notebooks.py
+        pytest --ignore tests/benchmarks/ --ignore tests/contrib --ignore tests/test_notebooks.py

.github/workflows/lower-bound-requirements.yml

@@ -34,5 +34,9 @@ jobs:
 
     - name: Test with pytest
       run: |
+        # Override the ini option for filterwarnings with an empty list to disable error on filterwarnings
+        # as testing for oldest releases that work with latest API, not the oldest releases that are warning
+        # free. Though still show warnings by setting warning control to 'default'.
+        export PYTHONWARNINGS='default'
         # Run on tests/ to skip doctests of src given examples are for latest APIs
-        pytest -r sx --ignore tests/benchmarks/ --ignore tests/contrib --ignore tests/test_notebooks.py tests/
+        pytest --override-ini filterwarnings= --ignore tests/benchmarks/ --ignore tests/contrib --ignore tests/test_notebooks.py tests/

.github/workflows/notebooks.yml

@@ -27,4 +27,4 @@ jobs:
         python -m pip list
     - name: Test example notebooks
       run: |
-        pytest -r sx tests/test_notebooks.py
+        pytest tests/test_notebooks.py

.github/workflows/release_tests.yml

@@ -40,7 +40,7 @@ jobs:
 
     - name: Canary test public API
       run: |
-        pytest -r sx tests/test_public_api.py
+        pytest tests/test_public_api.py
 
     - name: Verify requirements in codemeta.json
       run: |

pyproject.toml

@@ -42,18 +42,19 @@ ignore = [
 minversion = "6.0"
 xfail_strict = true
 addopts = [
-    "--ignore=setup.py",
-    "--ignore=validation/",
-    "--ignore=binder/",
-    "--ignore=docs/",
+    "-ra",
     "--cov=pyhf",
-    "--cov-config=.coveragerc",
+    "--cov-branch",
+    "--showlocals",
+    "--strict-markers",
+    "--strict-config",
     "--cov-report=term-missing",
     "--cov-report=xml",
     "--cov-report=html",
     "--doctest-modules",
-    "--doctest-glob='*.rst'"
+    "--doctest-glob='*.rst'",
 ]
+log_cli_level = "info"
 testpaths = "tests"
 markers = [
     "fail_jax",
@@ -75,12 +76,21 @@ markers = [
     "skip_pytorch64",
     "skip_tensorflow",
 ]
-
-[tool.nbqa.config]
-black = "pyproject.toml"
+filterwarnings = [
+    "error",
+    'ignore:the imp module is deprecated:DeprecationWarning',  # tensorflow
+    'ignore:distutils Version classes are deprecated:DeprecationWarning',  # tensorflow-probability
+    'ignore:the `interpolation=` argument to percentile was renamed to `method=`, which has additional options:DeprecationWarning',  # Issue #1772
+    "ignore:The interpolation= argument to 'quantile' is deprecated. Use 'method=' instead:DeprecationWarning",  # Issue #1772
+    'ignore: Exception ignored in:pytest.PytestUnraisableExceptionWarning',  #FIXME: Exception ignored in: <_io.FileIO [closed]>
+    'ignore:invalid value encountered in true_divide:RuntimeWarning',  #FIXME
+    'ignore:invalid value encountered in add:RuntimeWarning',  #FIXME
+    "ignore:In future, it will be an error for 'np.bool_' scalars to be interpreted as an index:DeprecationWarning",  #FIXME: tests/test_tensor.py::test_pdf_eval[pytorch]
+    'ignore:Creating a tensor from a list of numpy.ndarrays is extremely slow. Please consider converting the list to a single numpy.ndarray with:UserWarning',  #FIXME: tests/test_optim.py::test_minimize[no_grad-scipy-pytorch-no_stitch]
+    'ignore:divide by zero encountered in true_divide:RuntimeWarning',  #FIXME: pytest tests/test_tensor.py::test_pdf_calculations[numpy]
+]
 
 [tool.nbqa.mutate]
-black = 1
 pyupgrade = 1
 
 [tool.nbqa.addopts]

tests/test_export.py

@@ -352,17 +352,14 @@ def test_export_sample_zerodata(mocker, spec):
     sampledata = [0.0] * len(samplespec['data'])
 
     mocker.patch('pyhf.writexml._ROOT_DATA_FILE')
-    # make sure no RuntimeWarning, https://stackoverflow.com/a/45671804
-    with pytest.warns(None) as record:
-        for modifierspec in samplespec['modifiers']:
-            pyhf.writexml.build_modifier(
-                {'measurements': [{'config': {'parameters': []}}]},
-                modifierspec,
-                channelname,
-                samplename,
-                sampledata,
-            )
-    assert not record.list
+    for modifierspec in samplespec['modifiers']:
+        pyhf.writexml.build_modifier(
+            {'measurements': [{'config': {'parameters': []}}]},
+            modifierspec,
+            channelname,
+            samplename,
+            sampledata,
+        )
 
 
 @pytest.mark.parametrize(
@@ -424,7 +421,8 @@ def test_integer_data(datadir, mocker):
     """
     Test that a spec with only integer data will be written correctly
     """
-    spec = json.load(open(datadir.join("workspace_integer_data.json")))
+    with open(datadir.join("workspace_integer_data.json")) as spec_file:
+        spec = json.load(spec_file)
     channel_spec = spec["channels"][0]
     mocker.patch("pyhf.writexml._ROOT_DATA_FILE")
 

tests/test_optim.py

@@ -4,6 +4,7 @@
 from pyhf.tensor.common import _TensorViewer
 import pytest
 from scipy.optimize import minimize, OptimizeResult
+from scipy.optimize import OptimizeWarning
 import iminuit
 import itertools
 import numpy as np
@@ -563,7 +564,8 @@ def test_solver_options_scipy(mocker):
 
 
 # Note: in this case, scipy won't usually raise errors for arbitrary options
-# so this test exists as a sanity reminder that scipy is not perfect
+# so this test exists as a sanity reminder that scipy is not perfect.
+# It does raise a scipy.optimize.OptimizeWarning though.
 def test_bad_solver_options_scipy(mocker):
     optimizer = pyhf.optimize.scipy_optimizer(
         solver_options={'arbitrary_option': 'foobar'}
@@ -573,7 +575,11 @@ def test_bad_solver_options_scipy(mocker):
 
     model = pyhf.simplemodels.uncorrelated_background([50.0], [100.0], [10.0])
     data = pyhf.tensorlib.astensor([125.0] + model.config.auxdata)
-    assert pyhf.infer.mle.fit(data, model).tolist()
+
+    with pytest.warns(
+        OptimizeWarning, match="Unknown solver options: arbitrary_option"
+    ):
+        assert pyhf.infer.mle.fit(data, model).tolist()
 
 
 def test_minuit_param_names(mocker):

tests/test_tensor.py

@@ -274,37 +274,39 @@ def test_shape(backend):
 @pytest.mark.fail_pytorch64
 def test_pdf_calculations(backend):
     tb = pyhf.tensorlib
-    assert tb.tolist(tb.normal_cdf(tb.astensor([0.8]))) == pytest.approx(
-        [0.7881446014166034], 1e-07
-    )
-    assert tb.tolist(
-        tb.normal_logpdf(
-            tb.astensor([0, 0, 1, 1, 0, 0, 1, 1]),
-            tb.astensor([0, 1, 0, 1, 0, 1, 0, 1]),
-            tb.astensor([0, 0, 0, 0, 1, 1, 1, 1]),
+    # FIXME
+    with pytest.warns(RuntimeWarning, match="divide by zero encountered in log"):
+        assert tb.tolist(tb.normal_cdf(tb.astensor([0.8]))) == pytest.approx(
+            [0.7881446014166034], 1e-07
+        )
+        assert tb.tolist(
+            tb.normal_logpdf(
+                tb.astensor([0, 0, 1, 1, 0, 0, 1, 1]),
+                tb.astensor([0, 1, 0, 1, 0, 1, 0, 1]),
+                tb.astensor([0, 0, 0, 0, 1, 1, 1, 1]),
+            )
+        ) == pytest.approx(
+            [
+                np.nan,
+                np.nan,
+                np.nan,
+                np.nan,
+                -0.91893853,
+                -1.41893853,
+                -1.41893853,
+                -0.91893853,
+            ],
+            nan_ok=True,
+        )
+        # Allow poisson(lambda=0) under limit Poisson(n = 0 | lambda -> 0) = 1
+        assert tb.tolist(
+            tb.poisson(tb.astensor([0, 0, 1, 1]), tb.astensor([0, 1, 0, 1]))
+        ) == pytest.approx([1.0, 0.3678794503211975, 0.0, 0.3678794503211975])
+        assert tb.tolist(
+            tb.poisson_logpdf(tb.astensor([0, 0, 1, 1]), tb.astensor([0, 1, 0, 1]))
+        ) == pytest.approx(
+            np.log([1.0, 0.3678794503211975, 0.0, 0.3678794503211975]).tolist()
         )
-    ) == pytest.approx(
-        [
-            np.nan,
-            np.nan,
-            np.nan,
-            np.nan,
-            -0.91893853,
-            -1.41893853,
-            -1.41893853,
-            -0.91893853,
-        ],
-        nan_ok=True,
-    )
-    # Allow poisson(lambda=0) under limit Poisson(n = 0 | lambda -> 0) = 1
-    assert tb.tolist(
-        tb.poisson(tb.astensor([0, 0, 1, 1]), tb.astensor([0, 1, 0, 1]))
-    ) == pytest.approx([1.0, 0.3678794503211975, 0.0, 0.3678794503211975])
-    assert tb.tolist(
-        tb.poisson_logpdf(tb.astensor([0, 0, 1, 1]), tb.astensor([0, 1, 0, 1]))
-    ) == pytest.approx(
-        np.log([1.0, 0.3678794503211975, 0.0, 0.3678794503211975]).tolist()
-    )
 
     # Ensure continuous approximation is valid
     assert tb.tolist(
@@ -343,11 +345,12 @@ def test_pdf_calculations_pytorch(backend):
     assert tb.tolist(
         tb.poisson(tb.astensor([0, 0, 1, 1]), tb.astensor([0, 1, 0, 1]))
     ) == pytest.approx([1.0, 0.3678794503211975, 0.0, 0.3678794503211975])
-    assert tb.tolist(
-        tb.poisson_logpdf(tb.astensor([0, 0, 1, 1]), tb.astensor([0, 1, 0, 1]))
-    ) == pytest.approx(
-        np.log([1.0, 0.3678794503211975, 0.0, 0.3678794503211975]).tolist()
-    )
+    with pytest.warns(RuntimeWarning, match="divide by zero encountered in log"):
+        assert tb.tolist(
+            tb.poisson_logpdf(tb.astensor([0, 0, 1, 1]), tb.astensor([0, 1, 0, 1]))
+        ) == pytest.approx(
+            np.log([1.0, 0.3678794503211975, 0.0, 0.3678794503211975]).tolist()
+        )
 
     # Ensure continuous approximation is valid
     assert tb.tolist(