format and last lints

pyhdtoolkit/__init__.py

@@ -7,6 +7,7 @@
 :copyright: (c) 2019-2020 by Felix Soubelet.
 :license: MIT, see LICENSE for more details.
 """
+
 from . import cpymadtools, maths, models, optics, plotting, utils, version  # noqa: F401, TID252
 
 __title__ = "pyhdtoolkit"

pyhdtoolkit/cpymadtools/constants.py

@@ -6,6 +6,7 @@
 
 Specific constants to be used in `~.cpymadtools` functions, to help with consistency.
 """
+
 _MAX_SECTOR_VALUE: int = 8
 
 # fmt: off
@@ -136,16 +137,24 @@
     for sector in [1, 2, 3, 4, 5, 6, 7, 8]
 ]
 LHC_KSS_KNOBS: list[str] = [  # skew sextupole correctors
-    f"kss.a{sector}{sector+1 if sector < _MAX_SECTOR_VALUE else 1}b{beam}" for beam in [1, 2] for sector in [1, 2, 3, 4, 5, 6, 7, 8]
+    f"kss.a{sector}{sector+1 if sector < _MAX_SECTOR_VALUE else 1}b{beam}"
+    for beam in [1, 2]
+    for sector in [1, 2, 3, 4, 5, 6, 7, 8]
 ]
 LHC_KCS_KNOBS: list[str] = [  # spool piece (skew) sextupoles
-    f"kcs.a{sector}{sector+1 if sector < _MAX_SECTOR_VALUE else 1}b{beam}" for beam in [1, 2] for sector in [1, 2, 3, 4, 5, 6, 7, 8]
+    f"kcs.a{sector}{sector+1 if sector < _MAX_SECTOR_VALUE else 1}b{beam}"
+    for beam in [1, 2]
+    for sector in [1, 2, 3, 4, 5, 6, 7, 8]
 ]
 LHC_KCO_KNOBS: list[str] = [  # spool piece (skew) octupoles
-    f"kco.a{sector}{sector+1 if sector < _MAX_SECTOR_VALUE else 1}b{beam}" for beam in [1, 2] for sector in [1, 2, 3, 4, 5, 6, 7, 8]
+    f"kco.a{sector}{sector+1 if sector < _MAX_SECTOR_VALUE else 1}b{beam}"
+    for beam in [1, 2]
+    for sector in [1, 2, 3, 4, 5, 6, 7, 8]
 ]
 LHC_KCD_KNOBS: list[str] = [  # spool piece (skew) decapoles
-    f"kcd.a{sector}{sector+1 if sector < _MAX_SECTOR_VALUE else 1}b{beam}" for beam in [1, 2] for sector in [1, 2, 3, 4, 5, 6, 7, 8]
+    f"kcd.a{sector}{sector+1 if sector < _MAX_SECTOR_VALUE else 1}b{beam}"
+    for beam in [1, 2]
+    for sector in [1, 2, 3, 4, 5, 6, 7, 8]
 ]
 LHC_KO_KNOBS: list[str] = [  # octupoles in arc short straight sections
     f"ko{family}.a{sector}{sector+1 if sector < _MAX_SECTOR_VALUE else 1}b{beam}"

pyhdtoolkit/cpymadtools/coupling.py

@@ -8,6 +8,7 @@
 Module with functions to perform ``MAD-X`` actions through a `~cpymad.madx.Madx` object, that
 retate to betatron coupling in the machine.
 """
+
 from collections.abc import Sequence
 
 import numpy as np
@@ -78,10 +79,10 @@ def get_closest_tune_approach(
             # Say we have set the LHC coupling knobs to 1e-3
             dqmin = get_closest_tune_approach(
                 madx,
-                "lhc",                    # will find the knobs automatically
+                "lhc",  # will find the knobs automatically
                 sequence="lhcb1",
                 telescopic_squeeze=True,  # influences the knobs definition
-                run3=True,                # influences the knobs definition (LHC Run 3)
+                run3=True,  # influences the knobs definition (LHC Run 3)
             )
             # returns 0.001
     """

pyhdtoolkit/cpymadtools/lhc/_coupling.py

@@ -5,6 +5,7 @@
 
 The functions below are betatron coupling utilities for the ``LHC``.
 """
+
 import tfs
 from cpymad.madx import Madx
 from loguru import logger

pyhdtoolkit/cpymadtools/lhc/_elements.py

@@ -5,11 +5,13 @@
 
 The functions below are utilities to install elements or markers in the ``LHC``.
 """
+
 from cpymad.madx import Madx
 from loguru import logger
 
 _MAX_TRACKING_TOP_TURNS: int = 6600
 
+
 def install_ac_dipole_as_kicker(
     madx: Madx,
     /,

pyhdtoolkit/cpymadtools/lhc/_errors.py

@@ -5,6 +5,7 @@
 
 The functions below are utilities to implement errors in elements of the ``LHC``.
 """
+
 from collections.abc import Sequence
 
 from cpymad.madx import Madx
@@ -122,7 +123,8 @@ def misalign_lhc_ir_quadrupoles(
         .. code-block:: python
 
             misalign_lhc_ir_quadrupoles(
-                madx, ips=[5],
+                madx,
+                ips=[5],
                 quadrupoles=[7, 8, 9, 10],
                 beam=1,
                 sides="RL",
@@ -140,7 +142,7 @@ def misalign_lhc_ir_quadrupoles(
                 beam=1,
                 sides="RL",
                 dy=1e-5,  # ok too as cpymad converts this to a string first
-                dpsi="1E-3 + 8E-4 * TGAUSS(2.5)"
+                dpsi="1E-3 + 8E-4 * TGAUSS(2.5)",
             )
     """
     if any(ip not in (1, 2, 5, 8) for ip in ips):

pyhdtoolkit/cpymadtools/lhc/_misc.py

@@ -23,6 +23,7 @@
 _BEAM4: int = 4  # LHC beam 4 is special case
 _VRF_THRESHOLD: int = 5000
 
+
 def make_sixtrack_output(madx: Madx, /, energy: int) -> None:
     """
     .. versionadded:: 0.15.0

pyhdtoolkit/cpymadtools/lhc/_powering.py

@@ -5,6 +5,7 @@
 
 The functions below are magnets or knobs powering utilities for the ``LHC``.
 """
+
 from collections.abc import Sequence
 
 from cpymad.madx import Madx
@@ -14,6 +15,7 @@
 _QUAD_CIRCUIT_HAS_B: int = 7  # Q7 has a .b in the circuit name
 _MAX_IR_QUAD_NUMBER: int = 11  # beyond Q11 are MQTs etc
 
+
 def apply_lhc_colinearity_knob(madx: Madx, /, colinearity_knob_value: float = 0, ir: int | None = None) -> None:
     """
     .. versionadded:: 0.15.0

pyhdtoolkit/cpymadtools/lhc/_queries.py

@@ -5,6 +5,7 @@
 
 The functions below are settings query utilities for the ``LHC``.
 """
+
 from collections.abc import Sequence
 
 import tfs

pyhdtoolkit/cpymadtools/lhc/_routines.py

@@ -5,6 +5,7 @@
 
 The functions below are routines mimicking manipulations that would be done in the ``LHC``.
 """
+
 import numpy as np
 import tfs
 from cpymad.madx import Madx
@@ -52,7 +53,9 @@ def do_kmodulation(
 
         .. code-block:: python
 
-            tune_results = do_kmodulation(madx, ir=1, side="right", steps=100, stepsize=3e-8)
+            tune_results = do_kmodulation(
+                madx, ir=1, side="right", steps=100, stepsize=3e-8
+            )
     """
     element = f"MQXA.1R{ir:d}" if side.lower() == "right" else f"MQXA.1L{ir:d}"
     powering_variable = f"KTQX1.R{ir:d}" if side.lower() == "right" else f"KTQX1.L{ir:d}"

pyhdtoolkit/cpymadtools/lhc/_setup.py

@@ -5,6 +5,7 @@
 
 The functions below are setup utilities for the ``LHC``, to easily get simulations ready.
 """
+
 from pathlib import Path
 
 from cpymad.madx import Madx
@@ -59,7 +60,9 @@ def prepare_lhc_run2(
         .. code-block:: python
 
             madx = prepare_lhc_run2(
-                "/afs/cern.ch/eng/lhc/optics/runII/2018/PROTON/opticsfile.22", beam=2, stdout=True
+                "/afs/cern.ch/eng/lhc/optics/runII/2018/PROTON/opticsfile.22",
+                beam=2,
+                stdout=True,
             )
     """
     if use_b4 and beam != _BEAM_FOR_B4:
@@ -221,14 +224,19 @@ class LHCSetup:
         .. code-block:: python
 
             with LHCSetup(run=2, opticsfile="2018/PROTON/opticsfile.22", beam=2) as madx:
-               pass  # do some stuff
+                pass  # do some stuff
 
         Get a Run 3 setup for beam 1, with a sliced sequence and muted output:
 
         .. code-block:: python
 
-            with LHCSetup(run=3, opticsfile="R2022a_A30cmC30cmA10mL200cm.madx", slicefactor=4, stdout=False) as madx:
-               pass  # do some stuff
+            with LHCSetup(
+                run=3,
+                opticsfile="R2022a_A30cmC30cmA10mL200cm.madx",
+                slicefactor=4,
+                stdout=False,
+            ) as madx:
+                pass  # do some stuff
     """
 
     def __init__(

pyhdtoolkit/cpymadtools/lhc/_twiss.py

@@ -5,6 +5,7 @@
 
 The functions below are twiss utilities for the ``LHC`` insertion regions.
 """
+
 from collections.abc import Sequence
 
 import tfs

pyhdtoolkit/cpymadtools/matching.py

@@ -6,6 +6,7 @@
 
 Module with functions to perform ``MAD-X`` matchings through a `~cpymad.madx.Madx` object.
 """
+
 from collections.abc import Sequence
 
 from cpymad.madx import Madx
@@ -101,7 +102,7 @@ def match_tunes_and_chromaticities(
 
             matching.match_tunes_and_chromaticities(
                 madx,
-                None,              # this is not LHC or HLLHC
+                None,  # this is not LHC or HLLHC
                 sequence="CAS3",
                 q1_target=6.335,
                 q2_target=6.29,
@@ -131,7 +132,7 @@ def match_tunes_and_chromaticities(
 
             matching.match_tunes_and_chromaticities(
                 madx,
-                "lhc",                    # will find the knobs automatically
+                "lhc",  # will find the knobs automatically
                 sequence="lhcb1",
                 q1_target=62.31,
                 q2_target=60.32,
@@ -242,7 +243,7 @@ def match_tunes(
 
             matching.match_tunes(
                 madx,
-                None,              # this is not LHC or HLLHC
+                None,  # this is not LHC or HLLHC
                 sequence="CAS3",
                 q1_target=6.335,
                 q2_target=6.29,
@@ -268,7 +269,7 @@ def match_tunes(
 
             matching.match_tunes(
                 madx,
-                "lhc",                    # will find the knobs automatically
+                "lhc",  # will find the knobs automatically
                 sequence="lhcb1",
                 q1_target=62.31,
                 q2_target=60.32,
@@ -344,7 +345,7 @@ def match_chromaticities(
 
             matching.match_chromaticities(
                 madx,
-                None,              # this is not LHC or HLLHC
+                None,  # this is not LHC or HLLHC
                 sequence="CAS3",
                 dq1_target=100,
                 dq2_target=100,
@@ -370,7 +371,7 @@ def match_chromaticities(
 
             matching.match_chromaticities(
                 madx,
-                "lhc",                    # will find the knobs automatically
+                "lhc",  # will find the knobs automatically
                 sequence="lhcb1",
                 dq1_target=2.0,
                 dq2_target=2.0,

pyhdtoolkit/cpymadtools/ptc.py

@@ -7,6 +7,7 @@
 Module with functions to manipulate ``MAD-X`` ``PTC`` functionality through a
 `~cpymad.madx.Madx` object.
 """
+
 from collections.abc import Sequence
 from pathlib import Path
 
@@ -20,6 +21,7 @@
 _MAX_PTC_AMPDET_ORDER: int = 2
 _MIN_PTC_AMPDET_ORDER: int = 1
 
+
 def get_amplitude_detuning(
     madx: Madx, /, order: int = 2, file: Path | str | None = None, fringe: bool = False, **kwargs
 ) -> tfs.TfsDataFrame:
@@ -428,8 +430,13 @@ def ptc_track_particle(
         .. code-block:: python
 
             tracks_dict = ptc_track_particle(
-                madx, nturns=10, initial_coordinates=(2e-4, 0, 1e-4, 0, 0, 0),
-                model=3, method=6, nst=3, exact=True
+                madx,
+                nturns=10,
+                initial_coordinates=(2e-4, 0, 1e-4, 0, 0, 0),
+                model=3,
+                method=6,
+                nst=3,
+                exact=True,
             )
     """
     logger.debug("Performing single particle PTC (thick) tracking")

pyhdtoolkit/cpymadtools/track.py

@@ -7,6 +7,7 @@
 Module with functions to manipulate ``MAD-X`` ``TRACK`` functionality through a
 `~cpymad.madx.Madx` object.
 """
+
 from collections.abc import Sequence
 
 import pandas as pd

pyhdtoolkit/cpymadtools/tune.py

@@ -7,6 +7,7 @@
 Module with functions to manipulate ``MAD-X`` functionality around the tune through
 a `~cpymad.madx.Madx` object.
 """
+
 import math
 import sys
 from pathlib import Path
@@ -250,7 +251,7 @@ def _get_dynap_string_rep(dynap_dframe: tfs.TfsDataFrame) -> str:
     return string_rep
 
 
-def _make_tune_groups(dynap_string_rep: str, dsigma: float = 1.0) -> list[list[dict[str, float]]]:
+def _make_tune_groups(dynap_string_rep: str, dsigma: float = 1.0) -> list[list[dict[str, float]]]:  # noqa: ARG001
     """
     Creates appropriate tune points groups from the arcane string representation returned by
     `~.tune._get_dynap_string_rep` based on starting amplitude and angle for each particle.

pyhdtoolkit/cpymadtools/twiss.py

@@ -7,6 +7,7 @@
 Module with functions to manipulate ``MAD-X`` ``TWISS`` functionality through a
 `~cpymad.madx.Madx` object.
 """
+
 from collections.abc import Sequence
 
 import tfs

pyhdtoolkit/cpymadtools/utils.py

@@ -6,6 +6,7 @@
 
 Module with utility functions to do mundane operations with `~cpymad.madx.Madx` objects.
 """
+
 from pathlib import Path
 
 import pandas as pd

pyhdtoolkit/maths/stats_fitting.py

@@ -6,6 +6,7 @@
 
 Module implementing methods to find the best fit of statistical distributions to data.
 """
+
 import warnings
 
 import matplotlib.pyplot as plt  # noqa: F401 | if omitted, get AttributeError: module 'matplotlib' has no attribute 'axes'
@@ -46,6 +47,7 @@ def set_distributions_dict(dist_dict: dict[st.rv_continuous, str]) -> None:
         .. code-block:: python
 
             import scipy.stats as st
+
             tested_dists = {st.chi: "Chi", st.expon: "Exponential", st.laplace: "Laplace"}
             set_distributions_dict(tested_dists)
     """

pyhdtoolkit/maths/utils.py

@@ -69,7 +69,8 @@ def get_scaled_values_and_magnitude_string(
         .. code-block:: python
 
             import numpy as np
-            q = np.array([-330,  230,  430, -720,  750, -110,  410, -340, -950, -630])
+
+            q = np.array([-330, 230, 430, -720, 750, -110, 410, -340, -950, -630])
             get_scaled_values_and_magnitude_string(q)
             # returns (array([-3.3,  2.3,  4.3, -7.2,  7.5, -1.1,  4.1, -3.4, -9.5, -6.3]), '{-2}')
     """

pyhdtoolkit/models/beam.py

@@ -6,6 +6,7 @@
 
 Module with ``pydantic`` models to validate and store data structures relative to particle beams.
 """
+
 from math import sqrt
 
 from pydantic import BaseModel

pyhdtoolkit/models/htc.py

@@ -46,6 +46,7 @@ class HTCTaskSummary(BaseModel):
 
     Class to encompass and validate a specific job's line in the ``condor_q`` output.
     """
+
     # This is so pydantic accepts pendulum.DateTime as a validated type
     model_config = ConfigDict(arbitrary_types_allowed=True)