Merge pull request #13 from HideyoshiNakazone/chore/removes-nptyping

Chore/removes nptyping
chore: removes nptyping and updates dependencies
2025-09-23 05:09:36 -03:00 · 2025-09-23 05:07:39 -03:00 · 2025-09-23 04:23:42 -03:00 · 2025-09-23 04:20:25 -03:00 · 2025-09-23 04:12:10 -03:00 · 2025-09-23 04:10:56 -03:00
7 changed files with 565 additions and 417 deletions
--- a/.github/workflows/python-test-and-build.yml
+++ b/.github/workflows/python-test-and-build.yml
@@ -1,40 +1,20 @@
                                                                                                                                                      # This workflow will install Python dependencies, run tests and lint with a single version of Python
 # For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python

-name: Upload DicePlayer to PyPI
+name: Build and Upload to PyPI

 on:
-    push
+    push:
+        tags:
+            - 'v*'

 permissions:
    contents: read

 jobs:
-
-    test:
-        runs-on: ubuntu-latest
-        steps:
-            -   uses: actions/checkout@v3
-                with:
-                    fetch-depth: 0
-            -   name: Install poetry
-                run: pipx install poetry
-
-            -   name: Set up Python 3.10
-                uses: actions/setup-python@v3
-                with:
-                    python-version: "3.10"
-            -   name: Install dependencies
-                run: |
-                    poetry self add "poetry-dynamic-versioning[plugin]"
-                    if [ -f pyproject.toml ]; then poetry install; fi
-            -   name: Run unittest
-                run: |
-                    poetry run python -m unittest
-
    pypi-upload:
        needs: [test]
-        if: startsWith(github.ref, 'refs/tags/v')
+        if: github.ref == 'refs/heads/main'
        runs-on: ubuntu-latest
        steps:
            -   uses: actions/checkout@v3
@@ -47,19 +27,21 @@ jobs:
                uses: actions/setup-python@v3
                with:
                    python-version: "3.10"
+
            -   name: Install dependencies
-                run: |
-                    poetry self add "poetry-dynamic-versioning[plugin]"
-                    if [ -f pyproject.toml ]; then poetry install; fi
+                run: poetry install
+
            -   name: Build Python Package
                run: |
                    poetry build -f sdist
                    poetry install
                    echo "Builded DicePlayer - $(poetry version)"
+
            -   name: Configure PyPI
                run: |
                    poetry config repositories.pypi https://upload.pypi.org/legacy/
                    poetry config pypi-token.pypi ${{secrets.PYPI_TOKEN}}
+
            -   name: Upload Python Package
                run: |
                    poetry publish --repository pypi
--- a/.github/workflows/run-tests.yml
+++ b/.github/workflows/run-tests.yml
@@ -0,0 +1,36 @@
+# This workflow will install Python dependencies, run tests and lint with a single version of Python
+# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python
+
+name: Run Tests
+
+on:
+  push
+
+permissions:
+  contents: read
+
+jobs:
+
+  test:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python: ["3.10", "3.11", "3.12", "3.13"]
+    steps:
+      -   uses: actions/checkout@v3
+          with:
+            fetch-depth: 0
+      -   name: Install poetry
+          run: pipx install poetry
+
+      -   name: Set up Python 3.10
+          uses: actions/setup-python@v3
+          with:
+            python-version: ${{ matrix.python }}
+      -   name: Install dependencies
+          run: |
+            poetry self add "poetry-dynamic-versioning[plugin]"
+            if [ -f pyproject.toml ]; then poetry install; fi
+      -   name: Run unittest
+          run: |
+            poetry run python -m unittest
--- 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 = []
--- 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:
--- a/poetry.lock
+++ b/poetry.lock
@@ -1,4 +1,4 @@
-# This file is automatically @generated by Poetry 1.8.3 and should not be changed by hand.
+# This file is automatically @generated by Poetry 2.2.1 and should not be changed by hand.

 [[package]]
 name = "argparse"
@@ -6,6 +6,7 @@ version = "1.4.0"
 description = "Python command-line parsing library"
 optional = false
 python-versions = "*"
+groups = ["main"]
 files = [
    {file = "argparse-1.4.0-py2.py3-none-any.whl", hash = "sha256:c31647edb69fd3d465a847ea3157d37bed1f95f19760b11a47aa91c04b666314"},
    {file = "argparse-1.4.0.tar.gz", hash = "sha256:62b089a55be1d8949cd2bc7e0df0bddb9e028faefc8c32038cc84862aefdd6e4"},
@@ -13,33 +14,34 @@ files = [

 [[package]]
 name = "black"
-version = "24.4.2"
+version = "24.10.0"
 description = "The uncompromising code formatter."
 optional = false
-python-versions = ">=3.8"
+python-versions = ">=3.9"
+groups = ["dev"]
 files = [
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 ]

 [package.dependencies]
@@ -53,7 +55,7 @@ typing-extensions = {version = ">=4.0.1", markers = "python_version < \"3.11\""}

 [package.extras]
 colorama = ["colorama (>=0.4.3)"]
-d = ["aiohttp (>=3.7.4)", "aiohttp (>=3.7.4,!=3.9.0)"]
+d = ["aiohttp (>=3.10)"]
 jupyter = ["ipython (>=7.8.0)", "tokenize-rt (>=3.2.0)"]
 uvloop = ["uvloop (>=0.15.2)"]

@@ -63,6 +65,7 @@ version = "3.4.0"
 description = "Validate configuration and produce human readable error messages."
 optional = false
 python-versions = ">=3.8"
+groups = ["dev"]
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 description = "Composable command line interface toolkit"
 optional = false
 python-versions = ">=3.7"
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 optional = false
 python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,!=3.6.*,>=2.7"
+groups = ["dev"]
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+version = "7.10.7"
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@@ -204,6 +261,7 @@ version = "5.13.2"
 description = "A Python utility / library to sort Python imports."
 optional = false
 python-versions = ">=3.8.0"
+groups = ["dev"]
 files = [
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+version = "1.1.0"
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 optional = false
 python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,!=3.6.*,>=2.7"
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 description = "Bring colors to your terminal."
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
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 name = "poethepoet"
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 description = "A task runner that works well with poetry."
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 python-versions = ">=3.8"
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 [package.extras]
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+    {file = "tomli-2.2.1-cp313-cp313-musllinux_1_2_i686.whl", hash = "sha256:d920f33822747519673ee656a4b6ac33e382eca9d331c87770faa3eef562aeb2"},
+    {file = "tomli-2.2.1-cp313-cp313-musllinux_1_2_x86_64.whl", hash = "sha256:a198f10c4d1b1375d7687bc25294306e551bf1abfa4eace6650070a5c1ae2744"},
+    {file = "tomli-2.2.1-cp313-cp313-win32.whl", hash = "sha256:d3f5614314d758649ab2ab3a62d4f2004c825922f9e370b29416484086b264ec"},
+    {file = "tomli-2.2.1-cp313-cp313-win_amd64.whl", hash = "sha256:a38aa0308e754b0e3c67e344754dff64999ff9b513e691d0e786265c93583c69"},
+    {file = "tomli-2.2.1-py3-none-any.whl", hash = "sha256:cb55c73c5f4408779d0cf3eef9f762b9c9f147a77de7b258bef0a5628adc85cc"},
+    {file = "tomli-2.2.1.tar.gz", hash = "sha256:cd45e1dc79c835ce60f7404ec8119f2eb06d38b1deba146f07ced3bbc44505ff"},
 ]

 [[package]]
 name = "typing-extensions"
-version = "4.12.2"
-description = "Backported and Experimental Type Hints for Python 3.8+"
+version = "4.15.0"
+description = "Backported and Experimental Type Hints for Python 3.9+"
 optional = false
-python-versions = ">=3.8"
+python-versions = ">=3.9"
+groups = ["dev"]
+markers = "python_version == \"3.10\""
 files = [
-    {file = "typing_extensions-4.12.2-py3-none-any.whl", hash = "sha256:04e5ca0351e0f3f85c6853954072df659d0d13fac324d0072316b67d7794700d"},
-    {file = "typing_extensions-4.12.2.tar.gz", hash = "sha256:1a7ead55c7e559dd4dee8856e3a88b41225abfe1ce8df57b7c13915fe121ffb8"},
+    {file = "typing_extensions-4.15.0-py3-none-any.whl", hash = "sha256:f0fa19c6845758ab08074a0cfa8b7aecb71c999ca73d62883bc25cc018c4e548"},
+    {file = "typing_extensions-4.15.0.tar.gz", hash = "sha256:0cea48d173cc12fa28ecabc3b837ea3cf6f38c6d1136f85cbaaf598984861466"},
 ]

 [[package]]
 name = "virtualenv"
-version = "20.26.3"
+version = "20.34.0"
 description = "Virtual Python Environment builder"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
+groups = ["dev"]
 files = [
-    {file = "virtualenv-20.26.3-py3-none-any.whl", hash = "sha256:8cc4a31139e796e9a7de2cd5cf2489de1217193116a8fd42328f1bd65f434589"},
-    {file = "virtualenv-20.26.3.tar.gz", hash = "sha256:4c43a2a236279d9ea36a0d76f98d84bd6ca94ac4e0f4a3b9d46d05e10fea542a"},
+    {file = "virtualenv-20.34.0-py3-none-any.whl", hash = "sha256:341f5afa7eee943e4984a9207c025feedd768baff6753cd660c857ceb3e36026"},
+    {file = "virtualenv-20.34.0.tar.gz", hash = "sha256:44815b2c9dee7ed86e387b842a84f20b93f7f417f95886ca1996a72a4138eb1a"},
 ]

 [package.dependencies]
 distlib = ">=0.3.7,<1"
 filelock = ">=3.12.2,<4"
 platformdirs = ">=3.9.1,<5"
+typing-extensions = {version = ">=4.13.2", markers = "python_version < \"3.11\""}

 [package.extras]
 docs = ["furo (>=2023.7.26)", "proselint (>=0.13)", "sphinx (>=7.1.2,!=7.3)", "sphinx-argparse (>=0.4)", "sphinxcontrib-towncrier (>=0.2.1a0)", "towncrier (>=23.6)"]
-test = ["covdefaults (>=2.3)", "coverage (>=7.2.7)", "coverage-enable-subprocess (>=1)", "flaky (>=3.7)", "packaging (>=23.1)", "pytest (>=7.4)", "pytest-env (>=0.8.2)", "pytest-freezer (>=0.4.8)", "pytest-mock (>=3.11.1)", "pytest-randomly (>=3.12)", "pytest-timeout (>=2.1)", "setuptools (>=68)", "time-machine (>=2.10)"]
+test = ["covdefaults (>=2.3)", "coverage (>=7.2.7)", "coverage-enable-subprocess (>=1)", "flaky (>=3.7)", "packaging (>=23.1)", "pytest (>=7.4)", "pytest-env (>=0.8.2)", "pytest-freezer (>=0.4.8) ; platform_python_implementation == \"PyPy\" or platform_python_implementation == \"GraalVM\" or platform_python_implementation == \"CPython\" and sys_platform == \"win32\" and python_version >= \"3.13\"", "pytest-mock (>=3.11.1)", "pytest-randomly (>=3.12)", "pytest-timeout (>=2.1)", "setuptools (>=68)", "time-machine (>=2.10) ; platform_python_implementation == \"CPython\""]

 [metadata]
-lock-version = "2.0"
-python-versions = ">=3.9,<4.0"
-content-hash = "80ecbda1b826475e5eef19c940136c907a9687c7f4a6a0577a65ddd9b8a3343b"
+lock-version = "2.1"
+python-versions = ">=3.10,<4.0"
+content-hash = "f90241137e4e1197ca6a78485387f4227bbcb8ab61f83955c23cb2479ad3c8c4"
--- a/poetry.toml
+++ b/poetry.toml
@@ -0,0 +1,2 @@
+[virtualenvs]
+in-project = true
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,21 +1,35 @@
-[tool.poetry]
+[project]
 name = "diceplayer"
-version = "0.0.0"
 description = ""
-authors = ["Vitor Hideyoshi <vitor.h.n.batista@gmail.com>", "Herbert Georg <hcgeorg@ufg.br>"]
+authors = [
+    {name="Vitor Hideyoshi", email="vitor.h.n.batista@gmail.com"},
+    {name="Herbert Georg", email="hcgeorg@ufg.br"}
+]
 license = "GPL-2.0-only"
 readme = "README.md"
+dynamic = [
+    "version",
+    "dependencies",
+    "requires-python"
+]
+
+[project.scripts]
+diceplayer = "diceplayer.__main__:main"
+
+
+# POETRY
+[tool.poetry]
+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.scripts]
-diceplayer = "diceplayer.__main__:main"

 [tool.poetry.group.dev.dependencies]
 coverage = "^7.2.7"
@@ -24,14 +38,19 @@ black = "^24.4.2"
 pre-commit = "^3.7.1"
 poethepoet = "^0.27.0"

+[tool.poetry.requires-plugins]
+poetry-dynamic-versioning = { version = ">=1.0.0,<2.0.0", extras = ["plugin"] }
+
 [tool.poetry-dynamic-versioning]
 enable = true
 vcs = "git"

 [build-system]
-requires = ["poetry-core"]
+requires = ["poetry-core", "poetry-dynamic-versioning>=1.0.0,<2.0.0"]
 build-backend = "poetry_dynamic_versioning.backend"

+
+# UTILS
 [tool.poe.tasks]
 hooks = "pre-commit install --config .pre-commit-config.yaml"
Author	SHA1	Message	Date
Vitor Hideyoshi	8713a07c7d	Merge pull request #13 from HideyoshiNakazone/chore/removes-nptyping Chore/removes nptyping	2025-09-23 05:09:36 -03:00
Vitor Hideyoshi	7ef6f8b0b8	chore: removes nptyping and updates dependencies	2025-09-23 05:07:39 -03:00
Vitor Hideyoshi	57be666129	Merge pull request #12 from HideyoshiNakazone/updates-project-config chore: updates project config	2025-09-23 04:23:42 -03:00
Vitor Hideyoshi	cc13a7535c	chore: updates build process	2025-09-23 04:20:25 -03:00
Vitor Hideyoshi	8ce407bd8b	chore: adds python3.13 to testing matrix	2025-09-23 04:12:10 -03:00
Vitor Hideyoshi	be29e47070	chore: updates dependencies	2025-09-23 04:10:56 -03:00
Vitor Hideyoshi	a9e11ecf9d	chore: updates project config	2025-09-23 04:00:46 -03:00