Mark converter tests obsolete and deactivate flaky CI-blocking tests (including test_input on macOS/Windows) (#2091)

* Initial plan

* fix: 🐛 mark converter tests obsolete and skip on win/macOS

Co-authored-by: Anselmoo <13209783+Anselmoo@users.noreply.github.com>

* test: ✅ deactivate requested flaky CLI and notebook tests

Co-authored-by: Anselmoo <13209783+Anselmoo@users.noreply.github.com>

* test: ✅ clarify skip reasons for deactivated tests

Co-authored-by: Anselmoo <13209783+Anselmoo@users.noreply.github.com>

* test: ✅ format lambda function for clarity and deactivate flaky subprocess version test

* test: ✅ deactivate test_input suite on macOS and Windows

Co-authored-by: Anselmoo <13209783+Anselmoo@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: Anselmoo <13209783+Anselmoo@users.noreply.github.com>
Co-authored-by: Anselm Hahn <Anselm.Hahn@gmail.com>

Author: Copilot

pyproject.toml

@@ -175,7 +175,6 @@ extend-ignore = [
   "UP007",
   "PLR0913",
   "S301",
-  "PD901",
   "COM812",
   "FBT001",  # Boolean type hint positional argument
   "FBT002",  # Boolean default value positional argument
@@ -249,6 +248,7 @@ markers = [
   "models: tests for model implementations",
   "performance: tests that check performance characteristics",
   "integration: tests that check integration between components",
+  "obsolete: obsolete or end-of-life tests",
 ]
 
 [tool.coverage.report]

spectrafit/models/test/test_moessbauer.py

@@ -478,8 +478,9 @@ def patch_dependencies(monkeypatch: pytest.MonkeyPatch) -> None:
     monkeypatch.setattr(
         moessbauer_mod,
         "lorentzian",
-        lambda x, center, fwhml, amplitude: np.ones_like(x, dtype=np.float64)  # noqa: ARG005
-        * amplitude,
+        lambda x, center, fwhml, amplitude: (  # noqa: ARG005
+            np.ones_like(x, dtype=np.float64) * amplitude
+        ),
     )
     # Patch constants
     monkeypatch.setattr(moessbauer_mod, "MIN_EFG_THRESHOLD", 1e-5)

spectrafit/plugins/test/test_converter.py

@@ -6,6 +6,7 @@
 import json
 import pickle
 import shutil
+import sys
 
 from pathlib import Path
 from typing import TYPE_CHECKING
@@ -31,6 +32,15 @@
 from spectrafit.plugins.rixs_converter import RIXSConverter
 
 
+pytestmark = [
+    pytest.mark.obsolete,
+    pytest.mark.skipif(
+        sys.platform in {"win32", "darwin"},
+        reason="obsolete converter plugin tests are skipped on Windows and macOS",
+    ),
+]
+
+
 if TYPE_CHECKING:
     from matplotlib.figure import Figure
     from numpy.typing import NDArray

spectrafit/plugins/test/test_notebook.py

@@ -285,6 +285,7 @@ def test_dataframe_plot_4(self, dataframe_2: pd.DataFrame) -> None:
             )
             mock_show.assert_called_once()
 
+    @pytest.mark.skip(reason="deactivated due to flaky external HTTP dependency")
     def test_dataframe_plot_global(self, dataframe_global: pd.DataFrame) -> None:
         """Test global plot."""
         pp = DataFramePlot()
@@ -586,6 +587,7 @@ def test_plot_fit(
             mock_show.assert_called_once()
 
     @pytest.mark.skipif(sys.platform == "win32", reason="does not run on windows")
+    @pytest.mark.skip(reason="deactivated due to flaky external HTTP dependency")
     @pytest.mark.webtest
     def test_plot_global(
         self,

spectrafit/test/test_input.py

@@ -15,6 +15,11 @@
 
 BUILTINS_INPUT = "builtins.input"
 
+pytestmark = pytest.mark.skipif(
+    sys.platform in {"win32", "darwin"},
+    reason="test_input CLI tests are deactivated on Windows and macOS",
+)
+
 
 def assert_no_critical_stderr(ret: Any) -> None:
     """Allow warnings in stderr while ensuring no fatal errors occurred."""
@@ -25,6 +30,9 @@ def assert_no_critical_stderr(ret: Any) -> None:
 class TestCommandLineRunner:
     """Testing the command line interface."""
 
+    @pytest.mark.skip(
+        reason="deactivated flaky subprocess version test for CI stability"
+    )
     def test_version(self, monkeypatch: Any, script_runner: Any) -> None:
         """Testing the version command."""
         from spectrafit import __version__