From 7ef6f8b0b80992bfdfbbb7ea3dbd20da49a40df4 Mon Sep 17 00:00:00 2001 From: Vitor Hideyoshi Date: Tue, 23 Sep 2025 05:07:39 -0300 Subject: [PATCH] chore: removes nptyping and updates dependencies --- diceplayer/shared/environment/molecule.py | 77 +++++------ .../shared/interface/gaussian_interface.py | 4 +- poetry.lock | 126 +++++++++--------- pyproject.toml | 7 +- 4 files changed, 103 insertions(+), 111 deletions(-) diff --git a/diceplayer/shared/environment/molecule.py b/diceplayer/shared/environment/molecule.py index e4003b4..c4ee5f8 100644 --- a/diceplayer/shared/environment/molecule.py +++ b/diceplayer/shared/environment/molecule.py @@ -1,9 +1,6 @@ -from __future__ import annotations +# from __future__ import annotations -from typing import TYPE_CHECKING - -if TYPE_CHECKING: - from nptyping import Float, NDArray, Shape +import numpy.typing as npt from diceplayer import logger from diceplayer.shared.environment.atom import Atom @@ -25,12 +22,12 @@ class Molecule: Atributes: molname (str): The name of the represented molecule atom (List[Atom]): List of atoms of the represented molecule - position (NDArray[Any, Any]): The position relative to the internal atoms of the represented molecule - energy (NDArray[Any, Any]): The energy of the represented molecule - gradient (NDArray[Any, Any]): The first derivative of the energy relative to the position - hessian (NDArray[Any, Any]): The second derivative of the energy relative to the position + position (npt.NDArray[Any, Any]): The position relative to the internal atoms of the represented molecule + energy (npt.NDArray[Any, Any]): The energy of the represented molecule + gradient (npt.NDArray[Any, Any]): The first derivative of the energy relative to the position + hessian (npt.NDArray[Any, Any]): The second derivative of the energy relative to the position total_mass (int): The total mass of the molecule - com (NDArray[Any, Any]): The center of mass of the molecule + com (npt.NDArray[Any, Any]): The center of mass of the molecule """ def __init__(self, molname: str) -> None: @@ -43,16 +40,16 @@ class Molecule: self.molname: str = molname self.atom: List[Atom] = [] - self.position: NDArray[Any, Any] - self.energy: NDArray[Any, Any] - self.gradient: NDArray[Any, Any] - self.hessian: NDArray[Any, Any] + self.position: npt.NDArray[Any, Any] + self.energy: npt.NDArray[Any, Any] + self.gradient: npt.NDArray[Any, Any] + self.hessian: npt.NDArray[Any, Any] self.ghost_atoms: List[Atom] = [] self.lp_atoms: List[Atom] = [] self.total_mass: int = 0 - self.com: Union[None, NDArray[Any, Any]] = None + self.com: Union[None, npt.NDArray[Any, Any]] = None def add_atom(self, a: Atom) -> None: """ @@ -67,7 +64,7 @@ class Molecule: self.center_of_mass() - def center_of_mass(self) -> NDArray[Any, Any]: + def center_of_mass(self) -> npt.NDArray[Any]: """ Calculates the center of mass of the molecule """ @@ -97,7 +94,7 @@ class Molecule: Calculates the charges and dipole of the molecule atoms Returns: - List[float]: Respectivly magnitude of the: charge magnitude, first dipole, + List[npt.Float]: Respectivly magnitude of the: charge magnitude, first dipole, second dipole, third dipole and total dipole. """ @@ -114,12 +111,12 @@ class Molecule: return [charge, dipole[0], dipole[1], dipole[2], total_dipole] - def distances_between_atoms(self) -> NDArray[Shape["Any,Any"], Float]: + def distances_between_atoms(self) -> npt.NDArray[np.float64]: """ Calculates distances between the atoms of the molecule Returns: - NDArray[Shape["Any,Any"],Float]: distances between the atoms. + npt.NDArray[npt.Shape["Any,Any"],npt.Float]: distances between the atoms. """ distances = [] @@ -134,12 +131,12 @@ class Molecule: return np.array(distances).reshape(dim, dim - 1) - def inertia_tensor(self) -> NDArray[Shape["3, 3"], Float]: + def inertia_tensor(self) -> npt.NDArray[np.float64]: """ Calculates the inertia tensor of the molecule. Returns: - NDArray[Shape["3, 3"], Float]: inertia tensor of the molecule. + npt.NDArray[npt.Shape["3, 3"], npt.Float]: inertia tensor of the molecule. """ self.center_of_mass() @@ -160,12 +157,12 @@ class Molecule: return np.array([[Ixx, Ixy, Ixz], [Ixy, Iyy, Iyz], [Ixz, Iyz, Izz]]) - def principal_axes(self) -> Tuple[np.ndarray, np.ndarray]: + def principal_axes(self) -> Tuple[npt.NDArray, npt.NDArray]: """ Calculates the principal axes of the molecule Returns: - Tuple[np.ndarray, np.ndarray]: Tuple where the first value is the Eigen Values and the second is the Eigen Vectors, + Tuple[npt.NDArray, npt.NDArray]: Tuple where the first value is the Eigen Values and the second is the Eigen Vectors, representing the principal axes of the molecule. """ @@ -178,11 +175,11 @@ class Molecule: return evals, evecs - def read_position(self) -> np.ndarray: + def read_position(self) -> npt.NDArray: """Reads the position of the molecule from the position values of the atoms Returns: - np.ndarray: internal position relative to atoms of the molecule + npt.NDArray: internal position relative to atoms of the molecule """ position_list = [] @@ -193,7 +190,7 @@ class Molecule: return position - def update_charges(self, charges: NDArray) -> int: + def update_charges(self, charges: npt.NDArray) -> int: """ Updates the charges of the atoms of the molecule and returns the max difference between the new and old charges @@ -207,22 +204,22 @@ class Molecule: # @staticmethod # def update_hessian( - # step: np.ndarray, - # cur_gradient: np.ndarray, - # old_gradient: np.ndarray, - # hessian: np.ndarray, - # ) -> np.ndarray: + # step: npt.NDArray, + # cur_gradient: npt.NDArray, + # old_gradient: npt.NDArray, + # hessian: npt.NDArray, + # ) -> npt.NDArray: # """ # Updates the Hessian of the molecule based on the current hessian, the current gradient and the previous gradient # # Args: - # step (np.ndarray): step value of the iteration - # cur_gradient (np.ndarray): current gradient - # old_gradient (np.ndarray): previous gradient - # hessian (np.ndarray): current hessian + # step (npt.NDArray): step value of the iteration + # cur_gradient (npt.NDArray): current gradient + # old_gradient (npt.NDArray): previous gradient + # hessian (npt.NDArray): current hessian # # Returns: - # np.ndarray: updated hessian of the molecule + # npt.NDArray: updated hessian of the molecule # """ # # dif_gradient = cur_gradient - old_gradient @@ -238,7 +235,7 @@ class Molecule: Calculates sides of the smallest box that the molecule could fit Returns: - List[float]: list of the sizes of the molecule + List[npt.Float]: list of the sizes of the molecule """ x_list = [] @@ -289,12 +286,12 @@ class Molecule: atom.ry = new_position[1] atom.rz = new_position[2] - def translate(self, vector: np.ndarray) -> "Molecule": + def translate(self, vector: npt.NDArray) -> "Molecule": """ Creates a new Molecule object where its' atoms has been translated by a vector Args: - vector (np.ndarray): translation vector + vector (npt.NDArray): translation vector Returns: Molecule: new Molecule object translated by a vector @@ -368,7 +365,7 @@ class Molecule: molec (Molecule): Molecule object to be compared Returns: - float: minimum distance between the two molecules + npt.Float: minimum distance between the two molecules """ distances = [] diff --git a/diceplayer/shared/interface/gaussian_interface.py b/diceplayer/shared/interface/gaussian_interface.py index 1dd69bb..ad18154 100644 --- a/diceplayer/shared/interface/gaussian_interface.py +++ b/diceplayer/shared/interface/gaussian_interface.py @@ -10,7 +10,7 @@ from diceplayer.shared.utils.misc import date_time from diceplayer.shared.utils.ptable import atomsymb import numpy as np -from nptyping import NDArray +import numpy.typing as npt import os import shutil @@ -25,7 +25,7 @@ class GaussianInterface(Interface): self.system = system self.step = step_dto - def start(self, cycle: int) -> Dict[str, NDArray]: + def start(self, cycle: int) -> Dict[str, npt.NDArray]: self._make_qm_dir(cycle) if cycle > 1: diff --git a/poetry.lock b/poetry.lock index 44187aa..f292727 100644 --- a/poetry.lock +++ b/poetry.lock @@ -294,73 +294,69 @@ files = [ {file = "nodeenv-1.9.1.tar.gz", hash = "sha256:6ec12890a2dab7946721edbfbcd91f3319c6ccc9aec47be7c7e6b7011ee6645f"}, ] -[[package]] -name = "nptyping" -version = "2.5.0" -description = "Type hints for NumPy." -optional = false -python-versions = ">=3.7" -groups = ["main"] -files = [ - {file = "nptyping-2.5.0-py3-none-any.whl", hash = "sha256:764e51836faae33a7ae2e928af574cfb701355647accadcc89f2ad793630b7c8"}, - {file = "nptyping-2.5.0.tar.gz", hash = "sha256:e3d35b53af967e6fb407c3016ff9abae954d3a0568f7cc13a461084224e8e20a"}, -] - -[package.dependencies] -numpy = 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description = "Backported and Experimental Type Hints for Python 3.9+" optional = false python-versions = ">=3.9" -groups = ["main", "dev"] +groups = ["dev"] +markers = "python_version == \"3.10\"" files = [ {file = "typing_extensions-4.15.0-py3-none-any.whl", hash = "sha256:f0fa19c6845758ab08074a0cfa8b7aecb71c999ca73d62883bc25cc018c4e548"}, {file = "typing_extensions-4.15.0.tar.gz", hash = "sha256:0cea48d173cc12fa28ecabc3b837ea3cf6f38c6d1136f85cbaaf598984861466"}, ] -markers = {main = "python_version == \"3.9\"", dev = "python_version < \"3.11\""} [[package]] name = "virtualenv" @@ -706,5 +702,5 @@ test = ["covdefaults (>=2.3)", "coverage (>=7.2.7)", "coverage-enable-subprocess [metadata] lock-version = "2.1" -python-versions = ">=3.9,<4.0" -content-hash = "80ecbda1b826475e5eef19c940136c907a9687c7f4a6a0577a65ddd9b8a3343b" +python-versions = ">=3.10,<4.0" +content-hash = "f90241137e4e1197ca6a78485387f4227bbcb8ab61f83955c23cb2479ad3c8c4" diff --git a/pyproject.toml b/pyproject.toml index 9533f73..76f40fe 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -19,18 +19,17 @@ diceplayer = "diceplayer.__main__:main" # POETRY [tool.poetry] -version = "0.0.0" packages = [ { include = "diceplayer" } ] +version = "0.0.0" [tool.poetry.dependencies] -python = ">=3.9,<4.0" -numpy = "^1.26.4" +python = ">=3.10,<4.0" +numpy = "^2.2.6" argparse = "^1.4.0" setproctitle = "^1.3.2" pyyaml = "^6.0" -nptyping = "^2.5.0" [tool.poetry.group.dev.dependencies] coverage = "^7.2.7"