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"sha256:ed5eee1974372595f9e416cc7bbeeb12335201d8081ca8a0743c954d4446e5cb"}, -] +lock-version = "2.0" +python-versions = "^3.9,<4.0" +content-hash = "d4756cd83e85f52435678f3a6b07a4d16cc0b3e423a8b0aa6ed4fefb59327d89" diff --git a/pyaccelerator/__init__.py b/pyaccelerator/__init__.py index 44b9d81..0864340 100644 --- a/pyaccelerator/__init__.py +++ b/pyaccelerator/__init__.py @@ -1,5 +1,5 @@ -"""Python package to build simple toy accelerator. -""" +"""Python package to build simple toy accelerator.""" + import logging from . import elements @@ -11,7 +11,6 @@ TargetTwiss, TargetTwissSolution, ) -from .elements import * from .lattice import Lattice __all__ = [ diff --git a/pyaccelerator/beam.py b/pyaccelerator/beam.py index adef9b7..c1f59e4 100644 --- a/pyaccelerator/beam.py +++ b/pyaccelerator/beam.py @@ -1,4 +1,5 @@ """Accelerator Beam""" + from typing import Optional, Sequence, Tuple, Union import numpy as np @@ -92,7 +93,7 @@ def gamma_relativistic(self): @property def beta_relativistic(self): - return np.sqrt(1 - 1 / self.gamma_relativistic ** 2) + return np.sqrt(1 - 1 / self.gamma_relativistic**2) @property def geo_emittance_h(self): @@ -105,20 +106,20 @@ def geo_emittance_v(self): @property def p(self): # in MeV/c - return np.sqrt(self.energy ** 2 + 2 * self.energy * self.mass) + return np.sqrt(self.energy**2 + 2 * self.energy * self.mass) @property def sigma_p(self): absolute_sigma_e = self.sigma_energy * self.energy # in MeV/c - return np.sqrt(absolute_sigma_e ** 2 + 2 * absolute_sigma_e * self.mass) + return np.sqrt(absolute_sigma_e**2 + 2 * absolute_sigma_e * self.mass) def ellipse( self, - twiss_h: Sequence[float], - twiss_v: Optional[Sequence[float]] = None, + twiss_h: Union[Sequence[float], np.ndarray], + twiss_v: Optional[Union[Sequence[float], np.ndarray]] = None, closure_tol: float = 1e-10, - n_angles: int = 1e3, + n_angles: int = 1000, ) -> PhasespaceDistribution: """Compute the beam's phase space ellipse given the twiss parameters. @@ -137,17 +138,13 @@ def ellipse( Position, angle phase and dp/p space coordrinates of the ellipse. Note, dp/p will be set to 0. """ - twiss_h = to_twiss(twiss_h) - if twiss_v is None: - # if no vertical twiss provided use the same as the horizontal - twiss_v = twiss_h - else: - twiss_v = to_twiss(twiss_v) - beta_h, alpha_h, _ = twiss_h.T[0] # pylint: disable=unsubscriptable-object - beta_v, alpha_v, _ = twiss_v.T[0] # pylint: disable=unsubscriptable-object + twiss_h_ = to_twiss(twiss_h) + twiss_v_ = twiss_h_ if twiss_v is None else to_twiss(twiss_v) + beta_h, alpha_h, _ = twiss_h_.T[0] + beta_v, alpha_v, _ = twiss_v_.T[0] # check the twiss parameters - for twiss in (twiss_h, twiss_v): - closure = compute_twiss_clojure(twiss) + for twiss in (twiss_h_, twiss_v_): + closure = compute_twiss_clojure(twiss) # type: ignore if not -closure_tol <= closure - 1 <= closure_tol: raise ValueError( f"Closure condition not met for {twiss}: beta * gamma - alpha**2 = {closure} != 1" @@ -169,8 +166,8 @@ def ellipse( def match( self, - twiss_h: Sequence[float], - twiss_v: Optional[Sequence[float]] = None, + twiss_h: Union[Sequence[float], np.ndarray], + twiss_v: Optional[Union[Sequence[float], np.ndarray]] = None, closure_tol: float = 1e-10, ) -> PhasespaceDistribution: """Generate a matched beam phase space distribution to the provided @@ -188,17 +185,13 @@ def match( Returns: Position, angle and dp/p phase space coordinates. """ - twiss_h = to_twiss(twiss_h) - if twiss_v is None: - # if no vertical twiss provided use the same as the horizontal - twiss_v = twiss_h - else: - twiss_v = to_twiss(twiss_v) - beta_h, alpha_h, _ = twiss_h.T[0] # pylint: disable=unsubscriptable-object - beta_v, alpha_v, _ = twiss_v.T[0] # pylint: disable=unsubscriptable-object + twiss_h_ = to_twiss(twiss_h) + twiss_v_ = twiss_h_ if twiss_v is None else to_twiss(twiss_v) + beta_h, alpha_h, _ = twiss_h_.T[0] + beta_v, alpha_v, _ = twiss_v_.T[0] # check the twiss parameters - for twiss in (twiss_h, twiss_v): - closure = compute_twiss_clojure(twiss) + for twiss in (twiss_h_, twiss_v_): + closure = compute_twiss_clojure(twiss) # type: ignore if not -closure_tol <= closure - 1 <= closure_tol: raise ValueError( f"Closure condition not met: beta * gamma - alpha**2 = {closure} != 1" diff --git a/pyaccelerator/constraints.py b/pyaccelerator/constraints.py index b7e596d..e6e92c0 100644 --- a/pyaccelerator/constraints.py +++ b/pyaccelerator/constraints.py @@ -4,14 +4,12 @@ from typing import TYPE_CHECKING, Optional, Sequence, Tuple, Union import numpy as np -from scipy.optimize import minimize +from scipy.optimize import OptimizeResult, minimize from .elements.base import BaseElement from .utils import PLANE_INDICES -if TYPE_CHECKING: # pragma: no cover - from scipy.optimize import OptimizeResult - +if TYPE_CHECKING: from .lattice import Lattice @@ -19,7 +17,7 @@ class BaseTarget: """Base target.""" @abstractmethod - def loss(self, lattice: "Lattice"): + def loss(self, lattice: "Lattice") -> float: """Compute the loss for this target.""" @@ -83,8 +81,8 @@ def loss(self, lattice: "Lattice") -> float: transported_rows = [ i for i, value in enumerate(self.value) if value is not None ] - result = transported[transported_rows, transported_columns] - return abs(result - self.value[transported_rows]) + result: float = transported[transported_rows, transported_columns] # type: ignore + return abs(result - self.value[transported_rows]) # type: ignore def __repr__(self) -> str: args = ["element", "value", "initial"] @@ -136,8 +134,8 @@ def loss(self, lattice: "Lattice") -> float: transported_rows = [ i for i, value in enumerate(self.value) if value is not None ] - result = transported[transported_rows, transported_columns] - return abs(result - self.value[transported_rows]) + result: float = transported[transported_rows, transported_columns] # type: ignore + return abs(result - self.value[transported_rows]) # type: ignore def __repr__(self) -> str: args = ["element", "value", "plane"] @@ -185,13 +183,13 @@ def loss(self, lattice: "Lattice") -> float: except ValueError: return np.inf - transported_columns = -1 # Use Twiss values at end of lattice + transported_columns = -1 # Use Twiss values at end of lattice transported_rows = [ i for i, value in enumerate(self.value) if value is not None ] - result = transported[transported_rows, transported_columns] - return abs(result - self.value[transported_rows]) + result: float = transported[transported_rows, transported_columns] # type: ignore + return abs(result - self.value[transported_rows]) # type: ignore def __repr__(self) -> str: args = ["value", "plane"] @@ -440,7 +438,9 @@ def match_function(new_settings): if res.fun > 1e-1: # as this is a minimzation algorithm, it can find a minimum # but the matching could still be off. - self._logger.warning("Loss is high:%f, double check the matching.", res.fun) + self._logger.warning( + "Loss is high:%f, double check the matching.", res.fun + ) return lattice, res def _set_parameters(self, new_settings: Sequence[float], lattice: "Lattice"): diff --git a/pyaccelerator/elements/__init__.py b/pyaccelerator/elements/__init__.py index 04c92cf..b0b6e4b 100644 --- a/pyaccelerator/elements/__init__.py +++ b/pyaccelerator/elements/__init__.py @@ -1,4 +1,5 @@ """Accelerator elements.""" + from .custom import CustomThin from .dipole import Dipole, DipoleThin from .drift import Drift diff --git a/pyaccelerator/elements/base.py b/pyaccelerator/elements/base.py index 2766202..9a13428 100644 --- a/pyaccelerator/elements/base.py +++ b/pyaccelerator/elements/base.py @@ -1,21 +1,25 @@ from abc import abstractmethod -from typing import Any, Dict +from typing import TYPE_CHECKING, Any, Dict, Optional import numpy as np from matplotlib.patches import Patch from ..transfer_matrix import TransferMatrix +if TYPE_CHECKING: + from ..lattice import Lattice -class BaseElement: - """Base class of a lattice element. - Args: - *instance_args: Arguments required to make the instance of this - class's subclasses. - """ +class BaseElement: + name: str def __init__(self, *instance_args): + """Base class of a lattice element. + + Args: + *instance_args: Arguments required to make the instance of this + class's subclasses. + """ # args of the subclass instance. self._instance_args = instance_args @@ -37,7 +41,7 @@ def _get_length(self) -> float: # pragma: no cover pass @abstractmethod - def _get_patch(self, s: float) -> Patch: + def _get_patch(self, s: float) -> Optional[Patch]: """Generate a ``matplotlib.patches.Patch`` object to represent the element when plotting the lattice. @@ -48,6 +52,15 @@ def _get_patch(self, s: float) -> Patch: ``matplotlib.patches.Patch`` which represents the element. """ + @abstractmethod + def slice(self, n_slices: int) -> "Lattice": + """Slice the element into many smaller elements. + Args: + n_slices: Number of elements to slice the element into. + Returns: + A list of sliced elements. + """ + def _transport(self, phase_coords: np.ndarray) -> np.ndarray: return (self._get_transfer_matrix() @ phase_coords) + self._non_linear_term( phase_coords diff --git a/pyaccelerator/elements/custom.py b/pyaccelerator/elements/custom.py index 12112b0..fee1301 100644 --- a/pyaccelerator/elements/custom.py +++ b/pyaccelerator/elements/custom.py @@ -1,5 +1,5 @@ from itertools import count -from typing import Optional, Tuple, Union +from typing import Optional import numpy as np from matplotlib import patches @@ -8,7 +8,6 @@ class CustomThin(BaseElement): - _instance_count = count(0) def __init__( @@ -44,7 +43,7 @@ def _get_length(self) -> float: def _get_transfer_matrix(self) -> np.ndarray: return self.transfer_matrix - def _get_patch(self, s: float) -> Union[None, patches.Patch]: + def _get_patch(self, s: float) -> patches.Patch: label = self.name colour = "black" @@ -59,6 +58,7 @@ def _get_patch(self, s: float) -> Union[None, patches.Patch]: @staticmethod def _dxztheta_ds( - theta: float, d_s: float # pylint: disable=unused-argument + theta: float, + d_s: float, # pylint: disable=unused-argument ) -> np.ndarray: return np.array([0, 0, 0]) diff --git a/pyaccelerator/elements/dipole.py b/pyaccelerator/elements/dipole.py index f5302df..4ab8498 100644 --- a/pyaccelerator/elements/dipole.py +++ b/pyaccelerator/elements/dipole.py @@ -73,18 +73,18 @@ def _get_transfer_matrix(self) -> np.ndarray: out[4, 4] = 1 return out - def slice(self, n_dipoles: int) -> Lattice: + def slice(self, n_slices: int) -> Lattice: """Slice the element into a many smaller elements. Args: - n_dipoles: Number of :py:class:`Dipole` elements. + n_slices: Number of :py:class:`Dipole` elements. Returns: :py:class:`~accelerator.lattice.Lattice` of sliced :py:class:`Dipole` elements. """ out = [ - Dipole(self.rho, self.theta / n_dipoles, name=f"{self.name}_slice_{i}") - for i in range(n_dipoles) + Dipole(self.rho, self.theta / n_slices, name=f"{self.name}_slice_{i}") + for i in range(n_slices) ] return Lattice(out) @@ -136,7 +136,5 @@ def _get_patch(self, s: float) -> patches.Patch: facecolor="lightcoral", ) - def _dxztheta_ds( - self, theta: float, d_s: float # pylint: disable=unused-argument - ) -> np.ndarray: + def _dxztheta_ds(self, theta: float, d_s: float) -> np.ndarray: return np.array([0, 0, self.theta]) diff --git a/pyaccelerator/elements/drift.py b/pyaccelerator/elements/drift.py index 1324c3a..a540181 100644 --- a/pyaccelerator/elements/drift.py +++ b/pyaccelerator/elements/drift.py @@ -41,19 +41,19 @@ def _get_transfer_matrix(self) -> np.ndarray: out[2, 3] = self.length return out - def slice(self, n_drifts: int) -> Lattice: + def slice(self, n_slices: int) -> Lattice: """Slice the element into a many smaller elements. Args: - n_drifts: Number of :py:class:`Drift` elements. + n_slices: Number of :py:class:`Drift` elements. Returns: :py:class:`~accelerator.lattice.Lattice` of sliced :py:class:`Drift` elements. """ out = [ - Drift(self.length / n_drifts, name=f"{self.name}_slice_{i}") - for i in range(n_drifts) + Drift(self.length / n_slices, name=f"{self.name}_slice_{i}") + for i in range(n_slices) ] return Lattice(out) diff --git a/pyaccelerator/elements/kicker.py b/pyaccelerator/elements/kicker.py index 5680fc6..6c436ab 100644 --- a/pyaccelerator/elements/kicker.py +++ b/pyaccelerator/elements/kicker.py @@ -1,5 +1,5 @@ from itertools import count -from typing import Optional, Union +from typing import Optional import numpy as np from matplotlib import patches @@ -46,7 +46,7 @@ def _transport(self, phase_coords: np.ndarray) -> np.ndarray: out[3] += self.v_kick return out - def _get_patch(self, s: float) -> Union[None, patches.Patch]: + def _get_patch(self, s: float) -> patches.Patch: return patches.FancyArrowPatch( (s, 0.75), (s, -0.75), @@ -57,6 +57,8 @@ def _get_patch(self, s: float) -> Union[None, patches.Patch]: ) def _dxztheta_ds( - self, theta: float, d_s: float # pylint: disable=unused-argument + self, + theta: float, + d_s: float, # pylint: disable=unused-argument ) -> np.ndarray: return np.array([0, 0, self.h_kick]) diff --git a/pyaccelerator/elements/quadrupole.py b/pyaccelerator/elements/quadrupole.py index 502584c..9940c17 100644 --- a/pyaccelerator/elements/quadrupole.py +++ b/pyaccelerator/elements/quadrupole.py @@ -1,5 +1,5 @@ from itertools import count -from typing import Optional, Tuple, Union +from typing import Optional, Union import numpy as np from matplotlib import patches @@ -70,7 +70,7 @@ def _transport(self, phase_coords: np.ndarray) -> np.ndarray: out[4] = phase_coords[4] return out - def _compute_sin_cos(self, k) -> Tuple[Union[float, np.ndarray]]: + def _compute_sin_cos(self, k): # needs to work with arrays in order to track a distribution of particles. if isinstance(k, float): k = np.array(k) @@ -100,11 +100,11 @@ def _compute_sin_cos(self, k) -> Tuple[Union[float, np.ndarray]]: return sin_x, cos_x, sin_y, cos_y - def slice(self, n_quadrupoles: int) -> Lattice: + def slice(self, n_slices: int) -> Lattice: """Slice the element into a many smaller elements. Args: - n_quadrupoles: Number of :py:class:`Quadrupole` elements. + n_slices: Number of :py:class:`Quadrupole` elements. Returns: :py:class:`~accelerator.lattice.Lattice` of sliced :py:class:`Quadrupole` elements. @@ -112,14 +112,14 @@ def slice(self, n_quadrupoles: int) -> Lattice: out = [ Quadrupole( self.k, - self.l / n_quadrupoles, + self.l / n_slices, name=f"{self.name}_slice_{i}", ) - for i in range(n_quadrupoles) + for i in range(n_slices) ] return Lattice(out) - def _get_patch(self, s: float) -> patches.Patch: + def _get_patch(self, s: float) -> Optional[patches.Patch]: if self.k < 0: label = "Defocussing Quad." colour = "tab:red" @@ -164,7 +164,6 @@ def _get_length(self) -> float: return 0 def _get_transfer_matrix(self) -> np.ndarray: - out = np.zeros((5, 5)) out[0, 0] = 1 out[1, 0] = -1 / self.f @@ -217,7 +216,5 @@ def _get_patch(self, s: float) -> Union[None, patches.Patch]: ) @staticmethod - def _dxztheta_ds( - theta: float, d_s: float # pylint: disable=unused-argument - ) -> np.ndarray: + def _dxztheta_ds(theta: float, d_s: float) -> np.ndarray: return np.array([0, 0, 0]) diff --git a/pyaccelerator/elements/sextupole.py b/pyaccelerator/elements/sextupole.py index dc13b9a..d287886 100644 --- a/pyaccelerator/elements/sextupole.py +++ b/pyaccelerator/elements/sextupole.py @@ -55,11 +55,11 @@ def _get_transfer_matrix(self) -> np.ndarray: out[2, 3] = self.l return out - def slice(self, n_sextupoles: int) -> Lattice: + def slice(self, n_slices: int) -> Lattice: """Slice the element into a many smaller elements. Args: - n_sextupoles: Number of :py:class:`Sextupole` elements. + n_slices): Number of :py:class:`Sextupole` elements. Returns: :py:class:`~accelerator.lattice.Lattice` of sliced :py:class:`Sextupole` elements. @@ -67,10 +67,10 @@ def slice(self, n_sextupoles: int) -> Lattice: out = [ Sextupole( self.k, - self.l / n_sextupoles, + self.l / n_slices, name=f"{self.name}_slice_{i}", ) - for i in range(n_sextupoles) + for i in range(n_slices) ] return Lattice(out) @@ -132,7 +132,5 @@ def _get_patch(self, s: float) -> patches.Patch: ) @staticmethod - def _dxztheta_ds( - theta: float, d_s: float # pylint: disable=unused-argument - ) -> np.ndarray: + def _dxztheta_ds(theta: float, d_s: float) -> np.ndarray: return np.array([0, 0, 0]) diff --git a/pyaccelerator/elements/utils.py b/pyaccelerator/elements/utils.py index 84449e6..a598f86 100644 --- a/pyaccelerator/elements/utils.py +++ b/pyaccelerator/elements/utils.py @@ -1,11 +1,9 @@ -from typing import TYPE_CHECKING, Any, Dict +from typing import Any, Dict import numpy as np from .. import elements - -if TYPE_CHECKING: # pragma: no cover - from .base import BaseElement +from .base import BaseElement def straight_element(theta: float, d_s: float) -> np.ndarray: @@ -21,7 +19,7 @@ def bent_element(theta: float, d_s: float, rho: float) -> np.ndarray: return np.array([d_x, d_y, d_theta]) -def deserialize(dic: Dict[str, Any]) -> "BaseElement": +def deserialize(dic: Dict[str, Any]) -> BaseElement: """Deserialize a element dictionary into an element instance. Args: diff --git a/pyaccelerator/lattice.py b/pyaccelerator/lattice.py index d118782..a6baf81 100644 --- a/pyaccelerator/lattice.py +++ b/pyaccelerator/lattice.py @@ -1,4 +1,5 @@ """Accelerator lattice""" + import json import logging import os @@ -7,6 +8,9 @@ import matplotlib.pyplot as plt import numpy as np +from matplotlib.axes import Axes +from matplotlib.figure import Figure +from numpy.typing import ArrayLike from scipy.optimize import root from .constraints import Constraints @@ -201,11 +205,11 @@ def tune( # track for n_turns for _ in range(n_turns - 1): _, *transported = self.transport(out_turns[-1]) - out_turns.append([point[-1] for point in transported]) - out_turns = np.array(out_turns) + out_turns.append([point[-1] for point in transported]) # type: ignore + out_turns_ = np.array(out_turns) # get the frequency with the highest amplitude - position = out_turns[:, PLANE_INDICES[plane][0]] - angle = out_turns[:, PLANE_INDICES[plane][1]] + position = out_turns_[:, PLANE_INDICES[plane][0]] + angle = out_turns_[:, PLANE_INDICES[plane][1]] beta, alpha, _ = self.twiss_solution(plane=plane) sqrt_beta = np.sqrt(beta) @@ -273,7 +277,7 @@ def slice(self, element_type: Type["BaseElement"], n_element: int) -> "Lattice": def transport( self, - initial: Sequence[Union[float, np.ndarray]], + initial: ArrayLike, ) -> TransportedPhasespace: """Transport phase space coordinates or twiss parameters along the lattice. @@ -334,7 +338,7 @@ def transport( def transport_twiss( self, - twiss: Sequence[float], + twiss: Union[Sequence[Union[float, None]], np.ndarray], plane: str = "h", ) -> TransportedTwiss: """Transport the given twiss parameters along the lattice. @@ -348,13 +352,12 @@ def transport_twiss( Named tuple containing the twiss parameters along the lattice the coordinates along the ring. """ - twiss = to_twiss(twiss) - out = [twiss] + out = [to_twiss(twiss)] # type: ignore s_coords = [0] transfer_ms = [element.m.twiss(plane=plane) for element in self] for i, m in enumerate(transfer_ms): out.append(m @ out[i]) - s_coords.append(s_coords[i] + self[i].length) + s_coords.append(s_coords[i] + self[i].length) # type: ignore out = np.hstack(out) return TransportedTwiss(np.array(s_coords), *out) @@ -372,7 +375,7 @@ def search(self, pattern: str, *args, **kwargs) -> List[int]: Return: List of indexes in the lattice where the element's name matches the pattern. """ - pattern = re.compile(pattern) + pattern = re.compile(pattern) # type: ignore out = [ i for i, element in enumerate(self) @@ -426,8 +429,10 @@ def __mul__(self, other): def __getitem__(self, item): result = list.__getitem__(self, item) try: + # if the item is a slice return a lattice return Lattice(result) except TypeError: + # if the item is not a slice return the element return result def save(self, path: os.PathLike): @@ -489,7 +494,7 @@ def __init__(self, lattice: Lattice): def top_down( self, n_s_per_element: int = int(1e3), - ) -> Tuple[plt.Figure, plt.Axes]: + ) -> Tuple[Figure, Axes]: """Plot the s coordinate in the horizontal plane of the lattice. Args: @@ -497,7 +502,7 @@ def top_down( element in the lattice. Returns: - Plotted ``plt.Figure`` and ``plt.Axes``. + Plotted ``Figure`` and ``Axes``. """ xztheta = [np.array([0, 0, np.pi / 2])] s_start = 0 @@ -529,7 +534,7 @@ def top_down( ax.legend() return fig, ax - def layout(self) -> Tuple[plt.Figure, plt.Axes]: + def layout(self) -> Tuple[Figure, Axes]: """Plot the lattice. Returns: diff --git a/pyaccelerator/sampling.py b/pyaccelerator/sampling.py index 5ba96ea..67e04c0 100644 --- a/pyaccelerator/sampling.py +++ b/pyaccelerator/sampling.py @@ -9,7 +9,7 @@ def bigaussian( geometric_emittance_h: float, geometric_emittance_v: float, sigma_p: float, -) -> np.array: +) -> np.ndarray: """Generate a bigaussian distributed distribution. Args: @@ -27,7 +27,7 @@ def bigaussian( geometric_emittance_h, geometric_emittance_v, geometric_emittance_v, - sigma_p ** 2, + sigma_p**2, ) ) return np.random.multivariate_normal(mean, cov, n_particles).T diff --git a/pyaccelerator/utils.py b/pyaccelerator/utils.py index cc513f7..1d54cd4 100644 --- a/pyaccelerator/utils.py +++ b/pyaccelerator/utils.py @@ -1,10 +1,13 @@ from collections import namedtuple from functools import reduce from math import ceil -from typing import Optional, Sequence, Tuple, Union +from typing import Optional, Sequence, Tuple, Union, no_type_check import matplotlib.pyplot as plt import numpy as np +from matplotlib.axes import Axes +from matplotlib.figure import Figure +from numpy.typing import ArrayLike # where the x, x' and y, y' are located in the phase space coord vector PLANE_INDICES = {"h": [0, 1], "v": [2, 3]} @@ -20,7 +23,7 @@ ) -def plot_twiss(self) -> Tuple[plt.Figure, plt.Axes]: +def plot_twiss(self) -> Tuple[Figure, Axes]: """Plot the evolution of twiss parameters through the lattice. Return: @@ -37,7 +40,7 @@ def plot_twiss(self) -> Tuple[plt.Figure, plt.Axes]: def plot_phasespace( self, plane: str = "both", style: str = "auto", add_legend: bool = True -) -> Tuple[plt.Figure, plt.Axes]: +) -> Tuple[Figure, Axes]: """Plot the evolution of phase space coordinates through the lattice. Args: @@ -125,7 +128,7 @@ def plot_plane_s(ax_u, ax_u_prime, u, u_prime, plane): ax_x_prime = ax[0].twinx() ax_y = ax[1] ax_y_prime = ax[1].twinx() - ax_x_prime.get_shared_y_axes().join(ax_x_prime, ax_y_prime) + ax_x_prime.sharey(ax_y_prime) plot_plane_s(ax_x, ax_x_prime, self.x, self.x_prime, "x") plot_plane_s(ax_y, ax_y_prime, self.y, self.y_prime, "y") else: @@ -139,9 +142,7 @@ def plot_plane_s(ax_u, ax_u_prime, u, u_prime, plane): return fig, ax -def plot_phasespace_distribution( - self, plane: str = "both" -) -> Tuple[plt.Figure, plt.Axes]: +def plot_phasespace_distribution(self, plane: str = "both") -> Tuple[Figure, Axes]: """Plot the phase space coordinates distribution. Args: @@ -168,7 +169,7 @@ def plot_plane(ax, u, u_prime, plane, add_cbar=False): scatter = ax.scatter(u, u_prime, c=self.dp, s=4) if add_cbar: fig.subplots_adjust(right=0.8) - cbar_ax = fig.add_axes([0.85, 0.15, 0.05, 0.7]) + cbar_ax = fig.add_axes((0.85, 0.15, 0.05, 0.7)) cbar = fig.colorbar(scatter, cax=cbar_ax) cbar.set_label("dp/p", rotation=90) ax.set_xlabel(f"{plane} [m]") @@ -191,7 +192,7 @@ def plot_plane(ax, u, u_prime, plane, add_cbar=False): TransportedTwiss.plot = plot_twiss -def to_v_vec(vec: Sequence[float]) -> np.ndarray: +def to_v_vec(vec: ArrayLike) -> np.ndarray: """Helper function to create 1D vertical arrays. Args: @@ -200,13 +201,12 @@ def to_v_vec(vec: Sequence[float]) -> np.ndarray: Returns: Vertical 1D ``np.ndarray``. """ - vec = np.array(vec) if np.squeeze(vec).ndim > 1: raise ValueError("'vec' is not 1D.") return np.array(vec).reshape(-1, 1) -def to_twiss(twiss: Sequence[Union[float, None]]) -> np.ndarray: +def to_twiss(twiss: Union[Sequence[Union[float, None]], np.ndarray]) -> np.ndarray: """Helper function to create twiss vectors. Args: @@ -217,8 +217,7 @@ def to_twiss(twiss: Sequence[Union[float, None]]) -> np.ndarray: """ if len(twiss) != 3: raise ValueError("Length of 'twiss' != 3.") - twiss = complete_twiss(*twiss) - return to_v_vec(twiss) + return to_v_vec(complete_twiss(*twiss)) def to_phase_coord(phase_coord: Sequence[float]) -> np.ndarray: @@ -235,6 +234,7 @@ def to_phase_coord(phase_coord: Sequence[float]) -> np.ndarray: return to_v_vec(phase_coord) +@no_type_check def complete_twiss( beta: Optional[float] = None, alpha: Optional[float] = None, @@ -250,22 +250,21 @@ def complete_twiss( Returns: Tuple of completes twiss parameters, (beta, alpha, gamma). """ - number_of_none = sum([param is None for param in (beta, alpha, gamma)]) if number_of_none == 0: return (beta, alpha, gamma) if number_of_none != 1: raise ValueError("Only one twiss parameter can be omitted.") if beta is None: - beta = (1 + alpha ** 2) / gamma + beta = (1 + alpha**2) / gamma elif alpha is None: alpha = np.sqrt(beta * gamma - 1) elif gamma is None: - gamma = (1 + alpha ** 2) / beta + gamma = (1 + alpha**2) / beta return (beta, alpha, gamma) -def compute_one_turn(list_of_m: Sequence[np.array]) -> np.array: +def compute_one_turn(list_of_m: Sequence[np.ndarray]) -> np.ndarray: """Iteratively compute the matrix multiplictions of the arrays in the provided sequence. @@ -293,7 +292,7 @@ def compute_twiss_clojure(twiss: Sequence[float]) -> float: return twiss[0] * twiss[2] - twiss[1] ** 2 -def compute_m_twiss(m: np.array) -> np.array: +def compute_m_twiss(m: np.ndarray) -> np.ndarray: """Compute the twiss transfer matrix from a 2x2 phase space transfer matrix. @@ -340,7 +339,7 @@ def compute_twiss_solution(transfer_m: np.ndarray, tol: float = 1e-10) -> np.nda denom = np.sqrt(denom) beta = 2 * transfer_m[0, 1] / denom alpha = (transfer_m[0, 0] - transfer_m[1, 1]) / denom - gamma = (1 + alpha ** 2) / beta + gamma = (1 + alpha**2) / beta out = to_v_vec((beta, alpha, gamma)) if out[0, 0] < 0: out *= -1 diff --git a/pyproject.toml b/pyproject.toml index 8695eed..86cd255 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -8,25 +8,25 @@ readme = "README.md" repository = "https://github.com/loiccoyle/pyaccelerator" [tool.poetry.dependencies] -python = "^3.6" -numpy = "^1.19.0" +python = "^3.9,<4.0" +numpy = "^2.0.0" matplotlib = "^3.1.0" scipy = "^1.5.2" -sphinx = {version="<3.3.0", optional = true} -sphinx-autoapi = {version="^1.5.0", optional = true} -sphinx-rtd-theme = {version="^0.5.0", optional = true} -m2r2 = {version="^0.2.5", optional = true} - -[tool.poetry.dev-dependencies] -pytest = "^6.0.1" -pytest-cov = "^2.10.1" -isort = "^5.6.4" -black = "^20.8b1" - [tool.poetry.extras] docs = ["sphinx", "sphinx-autoapi", "sphinx-rtd-theme", "m2r2"] +[tool.poetry.group.docs.dependencies] +sphinx = "^7.3.7" +sphinx-autoapi = "^3.1.2" +sphinx-rtd-theme = "^2.0.0" +m2r2 = "^0.3.3.post2" + + +[tool.poetry.group.dev.dependencies] +pytest = "^8.2.2" +pytest-cov = "^5.0.0" + [build-system] requires = ["poetry>=0.12"] build-backend = "poetry.masonry.api" diff --git a/tests/test_constraints.py b/tests/test_constraints.py index eaf08c9..4961eb2 100644 --- a/tests/test_constraints.py +++ b/tests/test_constraints.py @@ -2,13 +2,9 @@ import numpy as np -from pyaccelerator.constraints import ( - Constraints, - FreeParameter, - TargetDispersion, - TargetPhasespace, - TargetTwiss, -) +from pyaccelerator.constraints import (Constraints, FreeParameter, + TargetDispersion, TargetPhasespace, + TargetTwiss) from pyaccelerator.elements.drift import Drift from pyaccelerator.elements.quadrupole import QuadrupoleThin from pyaccelerator.lattice import Lattice @@ -218,7 +214,3 @@ def test_match(self): s, beta, *_ = matched.twiss() self.assertAlmostEqual(min(beta), 0.5) assert matched[0].f == -2 * matched[2].f - - def test_repr(self): - lat = Lattice([Drift(1)]) - repr(lat.constraints) diff --git a/tests/test_lattice.py b/tests/test_lattice.py index 007b90c..f70ecba 100644 --- a/tests/test_lattice.py +++ b/tests/test_lattice.py @@ -2,8 +2,9 @@ from shutil import rmtree from unittest import TestCase -import matplotlib.pyplot as plt import numpy as np +from matplotlib.axes import Axes +from matplotlib.figure import Figure from pyaccelerator.beam import Beam from pyaccelerator.elements.custom import CustomThin @@ -343,14 +344,14 @@ def test_plotter(self): plotter = Plotter(lat) fig, axes = plotter.top_down() - assert isinstance(fig, plt.Figure) - assert isinstance(axes, plt.Axes) + assert isinstance(fig, Figure) + assert isinstance(axes, Axes) fig, axes = plotter.layout() - assert isinstance(fig, plt.Figure) - assert isinstance(axes, plt.Axes) + assert isinstance(fig, Figure) + assert isinstance(axes, Axes) fig, axes = plotter() - assert isinstance(fig, plt.Figure) - assert isinstance(axes, plt.Axes) + assert isinstance(fig, Figure) + assert isinstance(axes, Axes) # testing the margins lat = Lattice( @@ -360,8 +361,8 @@ def test_plotter(self): ) plotter = Plotter(lat) fig, axes = plotter.top_down() - assert isinstance(fig, plt.Figure) - assert isinstance(axes, plt.Axes) + assert isinstance(fig, Figure) + assert isinstance(axes, Axes) def test_repr(self): lat = Lattice([Drift(1)]) diff --git a/tests/test_utils.py b/tests/test_utils.py index 1a8aec0..79f5431 100644 --- a/tests/test_utils.py +++ b/tests/test_utils.py @@ -40,7 +40,7 @@ def test_complete_twiss(self): assert utils.complete_twiss(beta=1, alpha=None, gamma=1) == (1, 0, 1) assert utils.complete_twiss(beta=None, alpha=0, gamma=1) == (1, 0, 1) with self.assertRaises(ValueError): - assert utils.complete_twiss(beta=1, alpha=None, gamma=None) + utils.complete_twiss(beta=1, alpha=None, gamma=None) def test_compute_one_turn(self): list_of_m = [np.diag([1, 1])] * 2