ENH: Consider warnings as errors when running pytest

Consider warnings as errors when running `pytest`:
- Add the `warnings-as-errors` flag to `pytest` to consider warnings as
  errors.
- Use an environment variable `NIFREEZE_WERRORS` in GHA workflow files
  to mark the corresponding workflows as treating warnings as errors.
- Process the `pytest` session end to mark it as failed if warnings were
  present.

Implementation drawn from DIPY.

Filter two warnings that are being raised by the current tests:
- Filter warnings related to GPR parameter optimal values being close to
  the boundary values raised by `scikit-learn`.
- Filter warnings related to the b0 threshold value being updated in
  gradient table slicing raised by DIPY.

.github/workflows/test.yml

@@ -22,6 +22,7 @@ env:
   TEST_DATA_HOME: /home/runner/nifreeze-tests/
   ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS: 4
   ANTSPATH: /usr/share/miniconda/bin/
+  NIFREEZE_WERRORS: 1
 
 concurrency:
   group: ${{ github.workflow }}-${{ github.ref }}

pyproject.toml

@@ -172,7 +172,13 @@ norecursedirs = [".*", "_*"]
 addopts = "-v --doctest-modules"
 doctest_optionflags = "ALLOW_UNICODE NORMALIZE_WHITESPACE ELLIPSIS"
 env = "PYTHONHASHSEED=0"
-filterwarnings = ["ignore::DeprecationWarning"]
+filterwarnings = [
+  "ignore::DeprecationWarning",
+  # DIPY
+  "ignore:Updating b0_threshold to.*:UserWarning",
+  # scikit-learn
+  "ignore:The optimal value found for dimension.*:sklearn.exceptions.ConvergenceWarning",
+]
 
 
 [tool.coverage.run]

test/conftest.py

@@ -70,3 +70,35 @@ def datadir():
 def repodata():
     """Return the path to this repository's test data folder."""
     return _datadir
+
+
+def pytest_addoption(parser):
+    parser.addoption(
+        "--warnings-as-errors",
+        action="store_true",
+        help="Consider all uncaught warnings as errors.",
+    )
+
+
+@pytest.hookimpl(trylast=True)
+def pytest_sessionfinish(session, exitstatus):
+    have_werrors = os.getenv("NIFREEZE_WERRORS", False)
+    have_werrors = session.config.getoption("--warnings-as-errors", False) or have_werrors
+    if have_werrors:
+        # Check if there were any warnings during the test session
+        reporter = session.config.pluginmanager.get_plugin("terminalreporter")
+        if reporter.stats.get("warnings", None):
+            session.exitstatus = 2
+
+
+@pytest.hookimpl
+def pytest_terminal_summary(terminalreporter, exitstatus, config):
+    have_werrors = os.getenv("NIFREEZE_WERRORS", False)
+    have_werrors = config.getoption("--warnings-as-errors", False) or have_werrors
+    have_warnings = terminalreporter.stats.get("warnings", None)
+    if have_warnings and have_werrors:
+        terminalreporter.ensure_newline()
+        terminalreporter.section("Werrors", sep="=", red=True, bold=True)
+        terminalreporter.line(
+            f"Warnings as errors: Activated.\n{len(have_warnings)} warnings were raised and treated as errors.\n"
+        )