dev: Run flake8 directly as a standalone test instead of using the pytest plugin

The pytest-flake8 plugin is not maintained and has been the source of a
lot of spurious CI failures as pytest's API changes and the plugin isn't
updated along with it.  Rather than continue to play whack-a-mole with
the plugin, just run flake8 ourselves as a single standalone test.  The
plugin broke out flake8 results per Python file in pytest's output, but
that's not really necessary.  This follows a similar move we made with
mypy some time ago.

Author: tsibley

pytest.ini

@@ -1,5 +1,5 @@
 [pytest]
-addopts = --flake8 --doctest-modules
+addopts = --doctest-modules
 testpaths = nextstrain tests
 python_files = *.py
 
@@ -12,7 +12,3 @@ python_functions = pytest_*
 # for them.  Last matching filter wins.
 filterwarnings =
     error
-    ignore:SelectableGroups dict interface:DeprecationWarning:flake8
-    ignore:<class 'pytest_flake8[.]Flake8Item'> is not using a cooperative constructor:pytest.PytestDeprecationWarning
-    ignore:The .+? argument to Flake8Item is deprecated:pytest.PytestDeprecationWarning
-    ignore:Flake8Item is an Item subclass and should not be a collector:pytest.PytestWarning

setup.py

@@ -124,7 +124,6 @@ def find_namespaced_packages(namespace):
             "nextstrain-sphinx-theme",
             "pytest; python_version != '3.9'",
             "pytest !=7.0.0; python_version == '3.9'",
-            "pytest-flake8",
             "recommonmark",
             "sphinx>=3",
             "sphinx-argparse ~=0.3",

tests/flake8.py

@@ -0,0 +1,9 @@
+from pathlib import Path
+from subprocess import run
+
+topdir = Path(__file__).resolve().parent.parent
+
+def pytest_flake8():
+    # Check the exit status ourselves for nicer test output on failure
+    result = run(["flake8"], cwd = topdir)
+    assert result.returncode == 0, "flake8 exited with errors"