Yearly update of test file

pyhdtoolkit/utils/decorators.py

@@ -13,16 +13,19 @@
 import inspect
 import traceback
 import warnings
-from typing import TYPE_CHECKING
+from typing import TYPE_CHECKING, ParamSpec, TypeVar
 
 if TYPE_CHECKING:
     from collections.abc import Callable
 
 
+P = ParamSpec("P")  # for params
+R = TypeVar("R")  # for returns
+
 # ----- Utility deprecation decorator ----- #
 
 
-def deprecated(message: str = "") -> Callable:
+def deprecated(message: str = "") -> Callable[[Callable[P, R]], Callable[P, R]]:
     """
     Decorator to mark a function as deprecated. It will result in an
     informative `DeprecationWarning` being issued with the provided
@@ -49,22 +52,23 @@ def old_function():
                 return "I am old!"
     """
 
-    def decorator_wrapper(func):
+    def decorator_wrapper(func: Callable[P, R]) -> Callable[P, R]:
+        last_call_sources: set[str] = set()
+
         @functools.wraps(func)
-        def function_wrapper(*args, **kwargs):
+        def function_wrapper(*args: P.args, **kwargs: P.kwargs) -> R:
             current_call_source = "|".join(traceback.format_stack(inspect.currentframe()))
-            if current_call_source not in function_wrapper.last_call_source:
+
+            if current_call_source not in last_call_sources:
                 warnings.warn(
-                    f"Function {func.__name__} is now deprecated and will be removed in a future release! {message}",
+                    f"Function {func.__name__} is now deprecated and will be removed in a future release! {message}",  # ty:ignore[unresolved-attribute]
                     category=DeprecationWarning,
                     stacklevel=2,
                 )
-                function_wrapper.last_call_source.add(current_call_source)
+                last_call_sources.add(current_call_source)
 
             return func(*args, **kwargs)
 
-        function_wrapper.last_call_source = set()
-
         return function_wrapper
 
     return decorator_wrapper
@@ -73,7 +77,9 @@ def function_wrapper(*args, **kwargs):
 # ----- Utility JIT Compilation decorator ----- #
 
 
-def maybe_jit(func: Callable, **kwargs) -> Callable:
+# We type hint to specify we return a function with the same
+# signature as the input function.
+def maybe_jit(func: Callable[P, R], **kwargs) -> Callable[P, R]:
     """
     .. versionadded:: 1.7.0
 

pyproject.toml

@@ -58,7 +58,7 @@ dependencies = [
   "numpy >= 2.0",
   "pandas >= 2.0",
   "matplotlib >=3.7",
-  "scipy >= 1.6",
+  "scipy >= 1.10",
   "tfs-pandas >= 3.8",
   "loguru < 1.0",
   "cpymad >= 1.16",
@@ -71,22 +71,22 @@ dependencies = [
 [project.optional-dependencies]
 test = [
   "pytest >= 8.0",
-  "pytest-cov >= 5.0",
+  "pytest-cov >= 6.0",
   "pytest-xdist >= 3.0",
   "numba >= 0.60.0",
   "flaky >= 3.5",
-  "pytest-randomly >= 3.3",
+  "pytest-randomly >= 3.10",
   "coverage[toml] >= 7.0",
   "pytest-mpl >= 0.14",
 ]
 dev = [
-  "ruff >= 0.5",
+  "ruff >= 0.12",
 ]
 docs = [
   "joblib >= 1.0",
-  "Sphinx >= 7.0",
-  "sphinx-rtd-theme >= 2.0",
-  "sphinx-issues >= 4.0",
+  "Sphinx >= 8.0",
+  "sphinx-rtd-theme >= 3.0",
+  "sphinx-issues >= 5.0",
   "sphinx_copybutton < 1.0",
   "sphinxcontrib-bibtex >= 2.4",
   "sphinx-design >= 0.6",

tests/test_cpymadtools/test_lhc.py

@@ -487,7 +487,7 @@ def test_rigidity_knob_fails_on_invalid_ir(_non_matched_lhc_madx, caplog):
 def test_rigidity_knob_fails_on_invalid_side(caplog, _non_matched_lhc_madx):
     madx = _non_matched_lhc_madx
 
-    with pytest.raises(ValueError, match="Invalid value for parameter 'side'."):
+    with pytest.raises(ValueError, match=r"Invalid value for parameter 'side'."):
         apply_lhc_rigidity_waist_shift_knob(madx, 1, 1, "invalid")
 
     for record in caplog.records:
@@ -712,10 +712,10 @@ def test_get_bpms_coupling_rdts(_non_matched_lhc_madx, _reference_twiss_rdts):
 
     twiss_with_rdts = get_lhc_bpms_twiss_and_rdts(madx)
     # We separate the complex components to compare to the reference
-    twiss_with_rdts["F1001R"] = twiss_with_rdts.F1001.apply(np.real)
-    twiss_with_rdts["F1001I"] = twiss_with_rdts.F1001.apply(np.imag)
-    twiss_with_rdts["F1010R"] = twiss_with_rdts.F1010.apply(np.real)
-    twiss_with_rdts["F1010I"] = twiss_with_rdts.F1010.apply(np.imag)
+    twiss_with_rdts["F1001R"] = twiss_with_rdts.F1001.apply(np.real)  # ty:ignore[unresolved-attribute]
+    twiss_with_rdts["F1001I"] = twiss_with_rdts.F1001.apply(np.imag)  # ty:ignore[unresolved-attribute]
+    twiss_with_rdts["F1010R"] = twiss_with_rdts.F1010.apply(np.real)  # ty:ignore[unresolved-attribute]
+    twiss_with_rdts["F1010I"] = twiss_with_rdts.F1010.apply(np.imag)  # ty:ignore[unresolved-attribute]
     twiss_with_rdts = twiss_with_rdts.drop(columns=["F1001", "F1010"]).set_index("NAME")
     # Only care to compare the coupling RDTs columns
     twiss_with_rdts = twiss_with_rdts.loc[:, ["F1001R", "F1001I", "F1010R", "F1010I"]]
@@ -727,8 +727,8 @@ def test_get_bpms_coupling_rdts(_non_matched_lhc_madx, _reference_twiss_rdts):
 def test_k_modulation(_non_matched_lhc_madx, _reference_kmodulation):
     madx = _non_matched_lhc_madx
     results = do_kmodulation(madx)
-    assert all(var == 0 for var in results.ERRTUNEX)
-    assert all(var == 0 for var in results.ERRTUNEY)
+    assert np.all(results.ERRTUNEX.to_numpy() == 0)  # ty:ignore[unresolved-attribute]
+    assert np.all(results.ERRTUNEY.to_numpy() == 0)  # ty:ignore[unresolved-attribute]
 
     reference = tfs.read(_reference_kmodulation)
     assert_frame_equal(results.convert_dtypes(), reference.convert_dtypes())  # avoid dtype comparison error on 0 cols
@@ -841,7 +841,7 @@ def test_lhc_run3_setup_context_manager_raises_on_wrong_b4_conditions():
 @pytest.mark.skipif(not (TESTS_DIR.parent / "acc-models-lhc").is_dir(), reason="acc-models-lhc not found")
 def test_lhc_run3_setup_context_manager_raises_on_wrong_run_value():
     with pytest.raises(  # noqa: SIM117
-        NotImplementedError, match="This setup is only possible for Run 2 and Run 3 configurations."
+        NotImplementedError, match=r"This setup is only possible for Run 2 and Run 3 configurations."
     ):  # using b4 with beam1 setup crashes
         with LHCSetup(run=1, opticsfile="R2022a_A30cmC30cmA10mL200cm.madx") as madx:  # noqa: F841
             pass

tests/test_plotting/test_aperture.py

@@ -87,5 +87,5 @@ def test_plot_physical_apertures_ir5_collision_vertical(_collision_aperture_tole
 def test_plot_physical_apertures_raises_on_wrong_plane():
     madx = Madx(stdout=False)
 
-    with pytest.raises(ValueError, match="Invalid 'plane' argument."):
+    with pytest.raises(ValueError, match=r"Invalid 'plane' argument."):
         plot_physical_apertures(madx, plane="invalid")

tests/test_plotting/test_envelope.py

@@ -18,7 +18,7 @@
 def test_plot_enveloppe_raises_on_wrong_plane():
     madx = Madx(stdout=False)
 
-    with pytest.raises(ValueError, match="Invalid 'plane' argument."):
+    with pytest.raises(ValueError, match=r"Invalid 'plane' argument."):
         plot_beam_envelope(madx, "lhcb1", plane="invalid")
 
 

tests/test_plotting/test_helpers.py

@@ -40,5 +40,5 @@ def test_confidence_ellipse_fails_on_mismatched_dimensions():
 
 
 def test_default_sbs_coupling_label_raises_on_wrong_component():
-    with pytest.raises(ValueError, match="Invalid component for coupling RDT."):
+    with pytest.raises(ValueError, match=r"Invalid component for coupling RDT."):
         _determine_default_sbs_coupling_ylabel(rdt="f1001", component="NONEXISTANT")

tests/test_plotting/test_phasespace.py

@@ -87,7 +87,7 @@ def test_plot_courant_snyder_phase_space_wrong_plane_input():
         match_cas3(madx)
         x_coords_stable, px_coords_stable = np.array([]), np.array([])  # no need for tracking
 
-        with pytest.raises(ValueError, match="Invalid 'plane' argument."):
+        with pytest.raises(ValueError, match=r"Invalid 'plane' argument."):
             plot_courant_snyder_phase_space(madx, x_coords_stable, px_coords_stable, plane="invalid_plane")
 
 
@@ -97,7 +97,7 @@ def test_plot_courant_snyder_phase_space_colored_wrong_plane_input():
         madx.input(BASE_LATTICE)
         match_cas3(madx)
         x_coords_stable, px_coords_stable = np.array([]), np.array([])  # no need for tracking
-        with pytest.raises(ValueError, match="Invalid 'plane' argument."):
+        with pytest.raises(ValueError, match=r"Invalid 'plane' argument."):
             plot_courant_snyder_phase_space_colored(madx, x_coords_stable, px_coords_stable, plane="invalid_plane")
 
 

tests/test_plotting/test_plotting_utils.py

@@ -54,7 +54,7 @@ def test_coupling_ylabel(f1001, f1010, abs_, real, imag):
 
 @pytest.mark.parametrize("rdt", ["invalid", "F1111", "nope"])
 def test_coupling_ylabel_raises_on_invalid_rdt(rdt):
-    with pytest.raises(ValueError, match="Invalid RDT for coupling plot."):
+    with pytest.raises(ValueError, match=r"Invalid RDT for coupling plot."):
         _determine_default_sbs_coupling_ylabel(rdt, "abs")
 
 
@@ -69,7 +69,7 @@ def test_phase_ylabel(plane):
 
 @pytest.mark.parametrize("plane", ["a", "Fb1", "nope", "not a plane"])
 def test_phase_ylabel_raises_on_invalid_plane(plane):
-    with pytest.raises(ValueError, match="Invalid plane for phase plot."):
+    with pytest.raises(ValueError, match=r"Invalid plane for phase plot."):
         _determine_default_sbs_phase_ylabel(plane)
 
 

tests/test_plotting/test_sbs_phase.py

@@ -42,7 +42,7 @@ def test_plot_both_beams(sbs_phasex, sbs_phasey, sbs_model_b2):
 
 @pytest.mark.parametrize("wrongplane", ["not", "accepted", "incorrect", ""])
 def test_plot_phase_segment_raises_on_wrong_plane(wrongplane, sbs_phasex, sbs_model_b2):
-    with pytest.raises(ValueError, match="Invalid 'plane' argument."):
+    with pytest.raises(ValueError, match=r"Invalid 'plane' argument."):
         plot_phase_segment(segment_df=sbs_phasex, model_df=sbs_model_b2, plane=wrongplane)
 
 

tests/test_plotting/test_tunediagram.py

@@ -38,7 +38,7 @@ def test_plot_tune_diagram_colored_by_resonance_order():
 @pytest.mark.parametrize("max_order", [2, 3, 4, 5])
 @pytest.mark.parametrize("differentiate", [False, True])
 def test_plot_tune_diagram_arguments(figure_title, legend_title, max_order, differentiate):
-    figure, ax = plt.subplots(figsize=(10, 10))
+    _figure, ax = plt.subplots(figsize=(10, 10))
     plot_tune_diagram(
         title=figure_title,
         legend_title=legend_title,

tests/test_utils.py

@@ -5,6 +5,7 @@
 import subprocess
 import sys
 import time
+from collections.abc import Iterator
 
 import numpy as np
 import pandas as pd
@@ -45,7 +46,7 @@ def test_check_pid(self):
         assert CommandLine.check_pid_exists(0) is True
         assert CommandLine.check_pid_exists(int(1e6)) is False  # default max PID is 32768 on linux, 99999 on macOS
         with pytest.raises(TypeError):
-            CommandLine.check_pid_exists("not_an_integer")
+            CommandLine.check_pid_exists("not_an_integer")  # ty:ignore[invalid-argument-type]
 
     def test_run_cmd(self):
         assert isinstance(CommandLine.run("echo hello"), tuple)
@@ -70,7 +71,10 @@ def test_terminate_nonexistent_pid(self, pid):
     @pytest.mark.parametrize("sleep_time", list(range(10, 60)))  # each one will spawn a different process
     def test_terminate_pid(self, sleep_time):
         sacrificed_process = subprocess.Popen(f"sleep {sleep_time}", shell=True)
-        assert CommandLine.terminate(sacrificed_process.pid) is True
+        try:
+            assert CommandLine.terminate(sacrificed_process.pid) is True
+        finally:  # the process would hang, we make sure to cleanup
+            sacrificed_process.wait()
 
 
 class TestHTCMonitor:
@@ -101,11 +105,11 @@ def test_cluster_table_creation(self, _condor_q_output):
         assert isinstance(cluster_table, Table)
 
     def test_tasks_table_creation(self, _condor_q_output, _taskless_condor_q_output):
-        user_tasks, cluster_info = read_condor_q(_condor_q_output)
+        user_tasks, _ = read_condor_q(_condor_q_output)
         tasks_table = _make_tasks_table(user_tasks)
         assert isinstance(tasks_table, Table)
 
-        user_tasks, cluster_info = read_condor_q(_taskless_condor_q_output)
+        user_tasks, _ = read_condor_q(_taskless_condor_q_output)
         tasks_table = _make_tasks_table(user_tasks)
         assert isinstance(tasks_table, Table)
 
@@ -133,7 +137,7 @@ def test_query_betastar_from_opticsfile(self):
 
     def test_query_betastar_from_opticsfile_raises_on_invalid_symmetry_if_required(self):
         with pytest.raises(
-            AssertionError, match="The betastar values for IP1 and IP5 are not the same in both planes."
+            AssertionError, match=r"The betastar values for IP1 and IP5 are not the same in both planes."
         ):
             _misc.get_betastar_from_opticsfile(INPUTS_DIR / "madx" / "opticsfile.asymmetric", check_symmetry=True)
 
@@ -239,24 +243,24 @@ def _taskless_condor_q_output() -> str:
 
 
 @pytest.fixture
-def _correct_user_tasks() -> list[HTCTaskSummary]:
+def _correct_user_tasks() -> Iterator[list[HTCTaskSummary]]:
     pickle_file_path = INPUTS_DIR / "utils" / "correct_user_tasks.pkl"
     with pickle_file_path.open("rb") as file:
-        return pickle.load(file)
+        yield pickle.load(file)
 
 
 @pytest.fixture
-def _correct_cluster_summary() -> ClusterSummary:
+def _correct_cluster_summary() -> Iterator[ClusterSummary]:
     pickle_file_path = INPUTS_DIR / "utils" / "correct_cluster_summary.pkl"
     with pickle_file_path.open("rb") as file:
-        return pickle.load(file)
+        yield pickle.load(file)
 
 
 @pytest.fixture
 def _complex_columns_df() -> pd.DataFrame:
     rng = np.random.default_rng()
     array = rng.random(size=(50, 5)) + 1j * rng.random(size=(50, 5))
-    return pd.DataFrame(data=array, columns=["A", "B", "C", "D", "E"])
+    return pd.DataFrame(data=array, columns=["A", "B", "C", "D", "E"])  # ty:ignore[invalid-argument-type]
 
 
 @pytest.fixture