final linting rules and fixes

fsoubelet · fsoubelet · commit 143224331f9e · 2025-08-14T17:41:17.000+02:00
diff --git a/examples/demo_lhc_setup.py b/examples/demo_lhc_setup.py
@@ -83,13 +83,13 @@
     opticsfile="acc-models-lhc/operation/optics/R2022a_A30cmC30cmA10mL200cm.madx",
     stdout=False,
 )
-df = twiss.get_twiss_tfs(madx)
-ips = get_lhc_ips_positions(df)
+twiss_df = twiss.get_twiss_tfs(madx)
+ips = get_lhc_ips_positions(twiss_df)
 
 with plt.rc_context(_SPHINX_GALLERY_PARAMS):
     fig, ax = plt.subplots(figsize=(18, 10))
-    ax.plot(df.S, df.BETX / 1e3, label=r"$\beta_x$")
-    ax.plot(df.S, df.BETY / 1e3, label=r"$\beta_y$")
+    ax.plot(twiss_df.S, twiss_df.BETX / 1e3, label=r"$\beta_x$")
+    ax.plot(twiss_df.S, twiss_df.BETY / 1e3, label=r"$\beta_y$")
     draw_ip_locations(ips)
     ax.set_xlabel("Longitudinal location [m]")
     ax.set_ylabel(r"$\beta_{x,y}$ [km]")
@@ -111,13 +111,13 @@
 # above becomes:
 
 with lhc.LHCSetup(run=3, opticsfile="R2022a_A30cmC30cmA10mL200cm.madx", stdout=False) as madx:
-    df = twiss.get_twiss_tfs(madx)
-    ips = get_lhc_ips_positions(df)
+    twiss_df = twiss.get_twiss_tfs(madx)
+    ips = get_lhc_ips_positions(twiss_df)
 
     with plt.rc_context(_SPHINX_GALLERY_PARAMS):
         fig, ax = plt.subplots(figsize=(18, 10))
-        ax.plot(df.S, df.BETX / 1e3, label=r"$\beta_x$")
-        ax.plot(df.S, df.BETY / 1e3, label=r"$\beta_y$")
+        ax.plot(twiss_df.S, twiss_df.BETX / 1e3, label=r"$\beta_x$")
+        ax.plot(twiss_df.S, twiss_df.BETY / 1e3, label=r"$\beta_y$")
         draw_ip_locations(ips)
         ax.set_xlabel("Longitudinal location [m]")
         ax.set_ylabel(r"$\beta_{x,y}$ [km]")
@@ -133,8 +133,8 @@
 # IP5 for two different optics. Here below for the 2022 proton injection optics:
 
 with lhc.LHCSetup(run=3, opticsfile="R2022a_A11mC11mA10mL10m.madx", stdout=False) as madx:
-    df = twiss.get_twiss_tfs(madx)
-    ips = get_lhc_ips_positions(df)
+    twiss_df = twiss.get_twiss_tfs(madx)
+    ips = get_lhc_ips_positions(twiss_df)
     limits = (ips["IP5"] - 500, ips["IP5"] + 500)
 
     with plt.rc_context(_SPHINX_GALLERY_PARAMS):
@@ -172,8 +172,8 @@
     madx.call("lhc/aperture.b1.madx")
     madx.call("lhc/aper_tol.b1.madx")
 
-    df = twiss.get_twiss_tfs(madx)
-    ips = get_lhc_ips_positions(df)
+    twiss_df = twiss.get_twiss_tfs(madx)
+    ips = get_lhc_ips_positions(twiss_df)
     limits = (ips["IP5"] - 350, ips["IP5"] + 350)
 
     with plt.rc_context(_SPHINX_GALLERY_PARAMS):
diff --git a/pyhdtoolkit/cpymadtools/coupling.py b/pyhdtoolkit/cpymadtools/coupling.py
@@ -397,10 +397,10 @@ def _filter_outlier_bpms_from_coupling_rdts(twiss_df: TfsDataFrame, stdev: float
         The `~tfs.TfsDataFrame` with the filtered BPMs.
     """
     logger.debug("Filtering out outlier BPMs based on coupling RDTs")
-    df = twiss_df.copy(deep=True)
-    df = df[np.abs(stats.zscore(df.F1001.abs())) < stdev]
-    df = df[np.abs(stats.zscore(df.F1010.abs())) < stdev]
-    removed = len(twiss_df) - len(df)
+    twiss_df = twiss_df.copy(deep=True)
+    twiss_df = twiss_df[np.abs(stats.zscore(twiss_df.F1001.abs())) < stdev]
+    twiss_df = twiss_df[np.abs(stats.zscore(twiss_df.F1010.abs())) < stdev]
+    removed = len(twiss_df) - len(twiss_df)
     if removed > 0:
         logger.debug(f"{removed} BPMs removed due to outlier coupling RDTs")
-    return df
+    return twiss_df
diff --git a/pyhdtoolkit/cpymadtools/lhc/_routines.py b/pyhdtoolkit/cpymadtools/lhc/_routines.py
@@ -101,8 +101,8 @@ def do_kmodulation(
     for powering in k_powerings:
         logger.trace(f"Modulation of '{element}' - Setting '{powering_variable}' to {powering}")
         madx.globals[powering_variable] = powering
-        df = get_ir_twiss(madx, ir=ir, centre=True, columns=["k1l", "l"], **kwargs)
-        results.loc[powering].K = df.loc[element.lower()].k1l / df.loc[element.lower()].l  # Store K
+        twiss_df = get_ir_twiss(madx, ir=ir, centre=True, columns=["k1l", "l"], **kwargs)
+        results.loc[powering].K = twiss_df.loc[element.lower()].k1l / twiss_df.loc[element.lower()].l  # Store K
         results.loc[powering].TUNEX = madx.table.summ.q1[0]  # Store Qx
         results.loc[powering].TUNEY = madx.table.summ.q2[0]  # Store Qy
 
diff --git a/pyhdtoolkit/cpymadtools/tune.py b/pyhdtoolkit/cpymadtools/tune.py
@@ -358,7 +358,7 @@ def get_v_tune(self, ampl: int, angl: int) -> float:
             return self._tunes[ampl][len(self._tunes[ampl]) - 1]["V"]
         return self._tunes[ampl][angl]["V"]
 
-    def get_plottable(self) -> tuple[list[float], list[float]]:
+    def get_plottable(self) -> tuple[list[float], list[float]]:  # noqa: PLR0912
         qxs, qys = [], []
         for i in np.arange(0, self._nampl - 1, 2):
             for j in np.arange(self._maxnangl):
diff --git a/pyhdtoolkit/plotting/__init__.py b/pyhdtoolkit/plotting/__init__.py
@@ -4,4 +4,4 @@
 
 from . import aperture, crossing, envelope, lattice, phasespace, tune, utils  # noqa: TID252
 
-__all__ = ["aperture", "envelope", "crossing", "lattice", "phasespace", "tune", "utils"]
+__all__ = ["aperture", "crossing", "envelope", "lattice", "phasespace", "tune", "utils"]
diff --git a/pyhdtoolkit/plotting/aperture.py b/pyhdtoolkit/plotting/aperture.py
@@ -377,7 +377,7 @@ def _get_positions_and_real_apertures(
         if twiss_df[apercol].iloc[i] != 0:
             new_aper.insert(i, twiss_df[apercol].iloc[i])
             indices.append(i)
-    indices = list(reversed(indices))
+    indices.reverse()
 
     logger.trace("Extrapolating data at beginning of elements")
     # counter keeps track of exact position in new array with counter
diff --git a/pyhdtoolkit/plotting/layout.py b/pyhdtoolkit/plotting/layout.py
@@ -29,7 +29,7 @@
     from pandas import DataFrame
 
 
-def plot_machine_layout(
+def plot_machine_layout(  # noqa: PLR0912 (function branches justified)
     madx: Madx,
     /,
     title: str | None = None,
@@ -191,7 +191,7 @@ def plot_machine_layout(
     dipole_patches_axis = axis.twinx()
     dipole_patches_axis.set_ylabel("$\\theta=K_{0}L$ $[rad]$", color="royalblue")  # dipoles in blue
     dipole_patches_axis.tick_params(axis="y", labelcolor="royalblue")
-    if np.nan not in k0l_lim:
+    if np.nan not in k0l_lim:  # noqa: PLW0177 (not a comparison to NaN)
         dipole_patches_axis.set_ylim(k0l_lim)
     dipole_patches_axis.grid(visible=False)
 
diff --git a/pyhdtoolkit/plotting/utils.py b/pyhdtoolkit/plotting/utils.py
@@ -636,7 +636,7 @@ def _matplotlib_svg_scraper(*args, **kwargs):  # pragma: no cover
     A dummy scraper to import and set for the sphinx-gallery
     configuration, in docs/conf.py.
     """
-    from sphinx_gallery.scrapers import matplotlib_scraper
+    from sphinx_gallery.scrapers import matplotlib_scraper  # noqa: PLC0415
 
     kwargs.pop("format", None)
     return matplotlib_scraper(*args, format="svg", **kwargs)
diff --git a/pyhdtoolkit/utils/__init__.py b/pyhdtoolkit/utils/__init__.py
@@ -1,3 +1,3 @@
 from . import cmdline, contexts, decorators, htc_monitor, logging  # noqa: TID252
 
-__all__ = ["cmdline", "decorators", "contexts", "htc_monitor", "logging"]
+__all__ = ["cmdline", "contexts", "decorators", "htc_monitor", "logging"]
diff --git a/pyhdtoolkit/utils/decorators.py b/pyhdtoolkit/utils/decorators.py
@@ -103,7 +103,7 @@ def calculations(x, y):
                 return (x + y) / (x - y)
     """
     try:
-        from numba import jit
+        from numba import jit  # noqa: PLC0415
 
         return jit(func, **kwargs)
     except ImportError:
diff --git a/pyhdtoolkit/version.py b/pyhdtoolkit/version.py
@@ -1,3 +1,7 @@
+import platform
+import sys
+from pathlib import Path
+
 VERSION = "1.7.0"
 
 
@@ -12,10 +16,6 @@ def version_info() -> str:
         A string with platform and runtime information
         as well as the version of critical dependencies.
     """
-    import platform
-    import sys
-    from pathlib import Path
-
     info = {
         "PyhDToolkit version": VERSION,
         "Install path": Path(__file__).resolve().parent,
diff --git a/pyproject.toml b/pyproject.toml
@@ -181,10 +181,13 @@ exclude = ["pyhdtoolkit/cpymadtools/lhc/__init__.py"]
 # Allow unused variables when underscore-prefixed.
 dummy-variable-rgx = "^(_+|(_+[a-zA-Z0-9_]*[a-zA-Z0-9]+?))$"
 ignore = [
-  "E501",  # line-too-long
-  "FBT001",  # boolean-type-hint-positional-argument
-  "FBT002",  # boolean-default-value-positional-argument
-  "PT019",  # pytest-fixture-param-without-value (but suggested solution fails)
+  "E501",     # line-too-long
+  "FBT001",   # boolean-type-hint-positional-argument
+  "FBT002",   # boolean-default-value-positional-argument
+  "PT019",    # pytest-fixture-param-without-value (but suggested solution fails)
+  "RUF100",   # detects unused noqa but is wrong
+  "PLR0913",  # Expects no more than 5 arguments per function, too low
+  "PLR0915",  # Expects no more than 50 statements per function, too low
 ]
 
 extend-select = [
@@ -194,20 +197,31 @@ extend-select = [
     "I",        # Sort imports properly
     "N",        # enforce naming conventions, e.g. ClassName vs function_name
     "W",        # PyCodeStyle warnings
-    "UP",       # Warn if certain things can changed due to newer Python versions
     "C4",       # Catch incorrect use of comprehensions, dict, list, etc
     "FA",       # Enforce from __future__ import annotations
+    "PD",       # Good pandas practices
+    "PL",       # Pylint rules
+    "PT",       # Enforce pytest conventions
     "TC",       # Enforce importing certain types in a TYPE_CHECKING block
+    "UP",       # Warn if certain things can changed due to newer Python versions
+    "ARG",      # Detect unused arguments
     "BLE",      # disallow catch-all exceptions
     "DTZ",      # Good datetime practices
     "FBT",      # detect boolean traps
+    "FLY",      # Prefer idiomatic expressions over string joins
     "ICN",      # Use common import conventions
     "ISC",      # Good use of string concatenation
+    "LOG",      # Good logging practices
     "NPY",      # Some numpy-specific things
+    "PIE",      # No pointless statements
     "PTH",      # Use pathlib instead of os.path
     "RET",      # Good return practices
+    "RUF",      # Ruff specific rules
     "SIM",      # Common simplification rules
     "TID",      # Some good import practices
+    "TRY",      # Good try/except practices
+    "FURB",     # Refurbishing rules
+    "PERF",     # Good performance practices
 ]
 # Allow fix for all enabled rules (when `--fix`) is provided.
 fixable = ["ALL"]
diff --git a/tests/test_cpymadtools/test_generators.py b/tests/test_cpymadtools/test_generators.py
@@ -8,25 +8,25 @@
 def test_base_cas_lattice_generation():
     base_cas_lattice = LatticeGenerator.generate_base_cas_lattice()
     assert isinstance(base_cas_lattice, str)
-    assert len(base_cas_lattice) == 1493
+    assert len(base_cas_lattice) == 1493  # noqa: PLR2004
 
 
 def test_onesext_cas_lattice():
     onesext_cas_lattice = LatticeGenerator.generate_onesext_cas_lattice()
     assert isinstance(onesext_cas_lattice, str)
-    assert len(onesext_cas_lattice) == 2051
+    assert len(onesext_cas_lattice) == 2051  # noqa: PLR2004
 
 
 def test_oneoct_cas_lattice():
     oneoct_cas_lattice = LatticeGenerator.generate_oneoct_cas_lattice()
     assert isinstance(oneoct_cas_lattice, str)
-    assert len(oneoct_cas_lattice) == 2050
+    assert len(oneoct_cas_lattice) == 2050  # noqa: PLR2004
 
 
 def test_tripleterrors_study_reference():
     tripleterrors_study_reference = LatticeGenerator._generate_tripleterrors_study_reference()  # noqa: SLF001
     assert isinstance(tripleterrors_study_reference, str)
-    assert len(tripleterrors_study_reference) == 1617
+    assert len(tripleterrors_study_reference) == 1617  # noqa: PLR2004
 
 
 @pytest.mark.parametrize(
diff --git a/tests/test_cpymadtools/test_lhc.py b/tests/test_cpymadtools/test_lhc.py
@@ -122,7 +122,7 @@ def test_query_undefined_arc_corrector_knobs(_bare_lhc_madx):
     make_lhc_beams(madx)  # parameters don't matter, just need beams and brho defined
     arc_knobs = query_arc_correctors_powering(madx)
     assert all(knob in arc_knobs for knob in ALL_ARC_CORRECTOR_KNOBS)
-    assert all(abs(knob_value) < 115 for knob_value in arc_knobs.values())  # set in opticsfile
+    assert all(abs(knob_value) < 115 for knob_value in arc_knobs.values())  # set in opticsfile  # noqa: PLR2004
 
 
 def test_query_defined_arc_corrector_knobs(_bare_lhc_madx):
@@ -186,7 +186,8 @@ def test_misalign_lhc_ir_quadrupoles_specific_value(_non_matched_lhc_madx):
     madx = _non_matched_lhc_madx
     misalign_lhc_ir_quadrupoles(madx, ips=[1, 5], quadrupoles=list(range(1, 11)), beam=1, sides="RL", dy="0.001")
     error_table = madx.table["ir_quads_errors"].dframe()
-    assert all(error_table["dy"] == 0.001)
+    expected_dy = 0.001
+    assert all(error_table["dy"] == expected_dy)
 
 
 def test_misalign_lhc_ir_quadrupoles_raises_on_wrong_side(_non_matched_lhc_madx, caplog):
@@ -316,7 +317,8 @@ def test_orbit_correction(_bare_lhc_madx):
     madx.select(flag="error", pattern="MQ.13R3.B1")  # arc quad in sector 34
     madx.command.ealign(dx="1E-3")
     madx.twiss()
-    assert madx.table.summ["xcorms"][0] > 1e-3
+    max_orbit_tolerance = 1e-3
+    assert madx.table.summ["xcorms"][0] > max_orbit_tolerance
 
     correct_lhc_orbit(madx, sequence="lhcb1")
     assert math.isclose(madx.table.summ["xcorms"][0], 0, abs_tol=1e-5)
@@ -386,9 +388,12 @@ def test_prepare_sixtrack_output(_non_matched_lhc_madx):
     madx = _non_matched_lhc_madx
     make_sixtrack_output(madx, energy=6500)
 
-    assert madx.globals["VRF400"] == 16
-    assert madx.globals["LAGRF400.B1"] == 0.5
-    assert madx.globals["LAGRF400.B2"] == 0.0
+    expected_voltage = 16  # hard-coded in the function
+    expected_phase_b1 = 0.5  # hard-coded in the function
+    expected_phase_b2 = 0.0  # hard-coded in the function
+    assert madx.globals["VRF400"] == expected_voltage
+    assert madx.globals["LAGRF400.B1"] == expected_phase_b1
+    assert madx.globals["LAGRF400.B2"] == expected_phase_b2
 
 
 def test_get_lhc_bpms_list(_non_matched_lhc_madx, _correct_bpms_list):
@@ -517,13 +522,15 @@ def test_install_ac_dipole_as_kicker(top_turns, _matched_lhc_madx):
     madx = _matched_lhc_madx
     make_lhc_thin(madx, sequence="lhcb1", slicefactor=4)
     install_ac_dipole_as_kicker(madx, deltaqx=-0.01, deltaqy=0.012, sigma_x=1, sigma_y=1, top_turns=top_turns)
-    ramp3 = 2100 + top_turns
+    ramp1 = 100  # default for AC Dipole kicker
+    ramp2 = 2100  # default for AC Dipole kicker
+    ramp3 = ramp2 + top_turns
     ramp4 = ramp3 + 2000
 
     assert "MKACH.6L4.B1" in madx.elements
     assert madx.elements["MKACH.6L4.B1"].l == 0
-    assert madx.elements["MKACH.6L4.B1"].ramp1 == 100
-    assert madx.elements["MKACH.6L4.B1"].ramp2 == 2100
+    assert madx.elements["MKACH.6L4.B1"].ramp1 == ramp1
+    assert madx.elements["MKACH.6L4.B1"].ramp2 == ramp2
     assert madx.elements["MKACH.6L4.B1"].ramp3 == ramp3
     assert madx.elements["MKACH.6L4.B1"].ramp4 == ramp4
     assert math.isclose(madx.elements["MKACH.6L4.B1"].at, 9846.0765, rel_tol=1e-2)
@@ -558,7 +565,8 @@ def test_makethin_lhc(_matched_lhc_madx):
     tracks_dict = track_single_particle(madx, initial_coordinates=(1e-4, 0, 1e-4, 0, 0, 0), nturns=10, sequence="lhcb1")
     assert isinstance(tracks_dict, dict)
     tracks = tracks_dict["observation_point_1"]
-    assert len(tracks) == 11  # nturns + 1 because $start coordinates also given by MAD-X
+    expected_n_tracks = 11  # nturns + 1 because $start coordinates also given by MAD-X
+    assert len(tracks) == expected_n_tracks
     assert all(coordinate in tracks.columns for coordinate in ("x", "px", "y", "py", "t", "pt", "s", "e"))
 
 
@@ -647,7 +655,7 @@ def test_vary_independent_ir_quads_raises_on_wrong_quads(_non_matched_lhc_madx,
 @pytest.mark.parametrize("telescopic_squeeze", [False, True])
 @pytest.mark.parametrize("run3", [False, True])
 def test_lhc_tune_and_chroma_knobs(beam, telescopic_squeeze, run3):
-    expected_beam = 2 if beam == 4 else beam
+    expected_beam = 2 if beam == 4 else beam  # noqa: PLR2004
     if run3:
         expected_suffix = "_op"
     elif telescopic_squeeze:
@@ -665,7 +673,7 @@ def test_lhc_tune_and_chroma_knobs(beam, telescopic_squeeze, run3):
 @pytest.mark.parametrize("beam", [1, 2, 3, 4])
 @pytest.mark.parametrize("telescopic_squeeze", [False, True])
 def test_hllhc_tune_and_chroma_knobs(beam, telescopic_squeeze):
-    expected_beam = 2 if beam == 4 else beam
+    expected_beam = 2 if beam == 4 else beam  # noqa: PLR2004
     expected_suffix = "_sq" if telescopic_squeeze else ""
     assert get_lhc_tune_and_chroma_knobs("HLLHC", beam, telescopic_squeeze) == (
         f"kqtf.b{expected_beam}{expected_suffix}",
@@ -734,7 +742,8 @@ def test_carry_colinearity_knob_over(_non_matched_lhc_madx, ir):
 
     # Carry to left
     carry_colinearity_knob_over(madx, ir=ir, to_left=True)
-    assert madx.globals[f"kqsx3.l{ir:d}"] == 0.002
+    expected_left = 0.002  # full load to left MQSX
+    assert madx.globals[f"kqsx3.l{ir:d}"] == expected_left
     assert madx.globals[f"kqsx3.r{ir:d}"] == 0
 
     # Reset
@@ -743,8 +752,9 @@ def test_carry_colinearity_knob_over(_non_matched_lhc_madx, ir):
 
     # Carry to right
     carry_colinearity_knob_over(madx, ir=ir, to_left=False)
+    expected_right = 0.002  # full load to right MQSX
     assert madx.globals[f"kqsx3.l{ir:d}"] == 0
-    assert madx.globals[f"kqsx3.r{ir:d}"] == 0.002
+    assert madx.globals[f"kqsx3.r{ir:d}"] == expected_right
 
 
 @pytest.mark.parametrize("telesqueeze", [True, False])
diff --git a/tests/test_cpymadtools/test_tune.py b/tests/test_cpymadtools/test_tune.py
@@ -47,7 +47,8 @@ def test_make_footprint_table(_non_matched_lhc_madx, tmp_path, sigma, dense):
     foot = make_footprint_table(madx, sigma=sigma, file=str(export_file))
     assert isinstance(foot, tfs.TfsDataFrame)
     assert all(header in foot.headers for header in expected_headers)
-    assert foot.headers["ANGLE"] == 7  # hard-coded in the function
+    expected_angle = 7  # hard-coded in the function
+    assert foot.headers["ANGLE"] == expected_angle
     assert foot.headers["AMPLITUDE"] == sigma
     assert foot.headers["DSIGMA"] == 1 if not dense else 0.5
     assert export_file.exists()
diff --git a/tests/test_optics.py b/tests/test_optics.py
@@ -118,15 +118,15 @@ def test_courant_snyder_transform():
 def test_add_beam_size_to_df(_non_matched_lhc_madx):
     madx = _non_matched_lhc_madx
     madx.command.twiss(ripken=True)
-    df = madx.table.twiss.dframe()
-    df["BETA11"] = df.beta11
-    df["BETA12"] = df.beta12
-    df["BETA21"] = df.beta21
-    df["BETA22"] = df.beta22
-
-    df = ripken._add_beam_size_to_df(df, 1e-6, 1e-6)  # noqa: SLF001
-    assert "SIZE_X" in df.columns
-    assert "SIZE_Y" in df.columns
+    twiss_df = madx.table.twiss.dframe()
+    twiss_df["BETA11"] = twiss_df.beta11
+    twiss_df["BETA12"] = twiss_df.beta12
+    twiss_df["BETA21"] = twiss_df.beta21
+    twiss_df["BETA22"] = twiss_df.beta22
+
+    twiss_df = ripken._add_beam_size_to_df(twiss_df, 1e-6, 1e-6)  # noqa: SLF001
+    assert "SIZE_X" in twiss_df.columns
+    assert "SIZE_Y" in twiss_df.columns
 
 
 def test_rdt_order_and_type():
diff --git a/tests/test_utils.py b/tests/test_utils.py

Original file line number	Diff line number	Diff line change
`@@ -4,4 +4,4 @@`
`4`	`4`
`5`	`5`	`from . import aperture, crossing, envelope, lattice, phasespace, tune, utils # noqa: TID252`
`6`	`6`
`7`		`-__all__ = ["aperture", "envelope", "crossing", "lattice", "phasespace", "tune", "utils"]`
	`7`	`+__all__ = ["aperture", "crossing", "envelope", "lattice", "phasespace", "tune", "utils"]`
Original file line number	Diff line number	Diff line change
`@@ -1,3 +1,3 @@`
`1`	`1`	`from . import cmdline, contexts, decorators, htc_monitor, logging # noqa: TID252`
`2`	`2`
`3`		`-__all__ = ["cmdline", "decorators", "contexts", "htc_monitor", "logging"]`
	`3`	`+__all__ = ["cmdline", "contexts", "decorators", "htc_monitor", "logging"]`