FiberFusing 1.0.0.post0__tar.gz

fiberfusing-1.0.0.post0/.github/dependabot.yml

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+# Specify reviewers for pull requests
+
+version: 2
+updates:
+  - package-ecosystem: "pip"
+    directory: "/"
+    target-branch: "master"
+    schedule:
+      interval: "weekly"
+      day: "sunday"
+      time: "09:00"

fiberfusing-1.0.0.post0/.github/workflows/deploy_anaconda.yml

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+name: Deploy Conda Package
+
+on:
+  push:
+    branches: [ "master" ]
+    tags:
+      - '*'
+  pull_request:
+    branches: [ "master" ]
+
+jobs:
+  build_and_publish_conda_package:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout Repository
+        uses: actions/checkout@v4
+
+      - name: Set up Miniconda
+        uses: conda-incubator/setup-miniconda@v2
+        with:
+          channels: conda-forge
+          python-version: '3.11'
+
+      - name: Upload to Anaconda (if tag)
+        if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags/')
+        run: |
+          conda config --set anaconda_upload true
+
+      - name: Create Conda Environment and Install Dependencies
+        env:
+          ANACONDA_API_TOKEN: ${{ secrets.ANACONDA_API_TOKEN }}  # Ensure the Anaconda token is set
+        run: |
+          conda install conda-build anaconda-client conda-verify -y
+          conda build . -c martinpdes

fiberfusing-1.0.0.post0/.github/workflows/deploy_coverage.yml

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+# .github/workflows/deploy_coverage.yml
+name: Coverage
+
+on:
+  push:
+    branches: [ "master" ]
+    tags:
+      - '*'
+  pull_request:
+    branches: [ "master" ]
+
+
+jobs:
+  coverage:
+    name: Run test and generate coverage data
+    runs-on: ubuntu-latest
+    permissions:
+      pull-requests: write
+      contents: write
+
+    steps:
+      - name: "Set-up: Python 3.10"
+        uses: actions/setup-python@v4
+        id: cp310
+        with:
+            python-version: "3.10"
+
+      - name: "Install: Dependencies for headless server"
+        shell: bash
+        run: |
+            sudo apt-get update
+            sudo apt-get install xvfb
+
+      - name: "Checkout requirements and files for testing"
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+          submodules: true
+
+      - name: Install everything, run the tests, produce the .coverage file
+        run: |
+          python -m pip install wheel build
+          python -m build --wheel
+          python -m pip install .[testing]
+          pytest
+
+      - name: Coverage comment
+        if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags/')
+        uses: py-cov-action/python-coverage-comment-action@v3
+        with:
+          GITHUB_PR_RUN_ID: ${{ github.event.workflow_run.id }}
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          MINIMUM_GREEN: 90
+          MINIMUM_ORANGE: 50

fiberfusing-1.0.0.post0/.github/workflows/deploy_documentation.yml

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+# .github/workflows/deploy_documentation.yml
+name: Documentation
+
+on:
+  push:
+    branches: [ "master" ]
+    tags:
+      - '*'
+  pull_request:
+    branches: [ "master" ]
+
+jobs:
+  documentation:
+    name: Run the documentation building tools
+    runs-on: ubuntu-latest
+    permissions:
+      pull-requests: write
+      contents: write
+
+    steps:
+      - name: "Set-up: Python 3.10"
+        uses: actions/setup-python@v4
+        id: cp310
+        with:
+            python-version: "3.10"
+
+      - name: "Install: Dependencies for headless server"
+        shell: bash
+        run: |
+            sudo apt-get update
+            sudo apt-get install xvfb
+
+      - name: "Checkout requirements and files for testing"
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+          submodules: true
+
+      - name: Install everything, run the tests, produce the .coverage file
+        run: |
+          python -m pip install wheel build
+          python -m build --wheel
+          python -m pip install .[documentation]
+
+      - name: Install dependencies
+        run: |
+          pip install sphinx sphinx_rtd_theme myst_parser
+
+      - name: Sphinx build
+        run: |
+          sphinx-build docs/source _build
+
+      - name: Deploy to GitHub Pages
+        uses: peaceiris/actions-gh-pages@v3
+        if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags/')
+        with:
+          publish_branch: gh-pages
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          publish_dir: _build/
+          force_orphan: true

fiberfusing-1.0.0.post0/.github/workflows/deploy_pypi.yml

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+name: Deploy Wheel
+
+on:
+  push:
+    branches: [ "master" ]
+    tags:
+      - '*'
+  pull_request:
+    branches: [ "master" ]
+
+permissions:
+    contents: write
+
+jobs:
+    build_pure_python:
+        runs-on: ubuntu-latest
+        steps:
+          - uses: MartinPdeS/MPSActions/build_pure_python_package@master
+            with:
+                python-version: '3.10'
+
+    publish_wheel:
+        if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags/')
+        needs: [build_pure_python]
+        runs-on: ubuntu-latest
+        steps:
+          - uses: MartinPdeS/MPSActions/publish_pypi@master
+            with:
+                python-version: "3.10"
+                password: ${{ secrets.PYPI_API_TOKEN }}

fiberfusing-1.0.0.post0/.gitignore

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+*.DS_store
+*.ipynb_checkpoints*
+*__pycache__*
+*.so
+*.pytest_cache
+
+dist
+build
+*.egg*
+Perso/
+
+CMakeCache.txt
+CMakeFiles
+install_manifest.txt
+cmake_install.cmake
+htmlcov
+.coverage

fiberfusing-1.0.0.post0/.readthedocs.yml

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+# .readthedocs.yml
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+submodules:
+  include: all
+  recursive: true
+
+build:
+  os: ubuntu-22.04
+
+
+  tools:
+    python: "3.11"
+  jobs:
+    pre_install:
+      - Xvfb :99 &
+      - export DISPLAY=:99
+      - cd docs && rm -rf source/gallery
+      - sleep 3
+
+python:
+  install:
+    - method: pip
+      path: .
+      extra_requirements:
+        - documentation
+
+sphinx:
+  builder: html
+  configuration: docs/source/conf.py
+  fail_on_warning: false

fiberfusing-1.0.0.post0/FiberFusing/__init__.py

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+from .geometry import Geometry  # noqa: F401
+from .components.point import Point  # noqa: F401
+from .components.linestring import LineString  # noqa: F401
+from .components.polygon import Polygon, EmptyPolygon  # noqa: F401
+from .buffer import Circle, Square  # noqa: F401
+from .background import BackGround  # noqa: F401
+from .optical_structure import CircleOpticalStructure  # noqa: F401
+micro = 1e-6
+
+
+try:
+    from ._version import version as __version__  # noqa: F401
+
+except ImportError:
+    __version__ = "0.0.0"

fiberfusing-1.0.0.post0/FiberFusing/_version.py

@@ -0,0 +1,16 @@
+# file generated by setuptools_scm
+# don't change, don't track in version control
+TYPE_CHECKING = False
+if TYPE_CHECKING:
+    from typing import Tuple, Union
+    VERSION_TUPLE = Tuple[Union[int, str], ...]
+else:
+    VERSION_TUPLE = object
+
+version: str
+__version__: str
+__version_tuple__: VERSION_TUPLE
+version_tuple: VERSION_TUPLE
+
+__version__ = version = '1.0.0.post0'
+__version_tuple__ = version_tuple = (1, 0, 0)

fiberfusing-1.0.0.post0/FiberFusing/background.py

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+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+
+from typing import Tuple, Optional
+from pydantic.dataclasses import dataclass
+from pydantic import ConfigDict
+import numpy as np
+
+from FiberFusing.coordinate_system import CoordinateSystem
+from FiberFusing.overlay_structure_on_mesh import OverlayStructureBaseClass
+from FiberFusing import Circle
+
+
+class NameSpace:
+    """
+    A flexible class that allows dynamic addition of attributes via keyword arguments.
+    """
+    def __init__(self, **kwargs):
+        """
+        Initializes an instance with attributes specified by keyword arguments.
+
+        Parameters
+        ----------
+        **kwargs : dict
+            Arbitrary keyword arguments to set as attributes.
+        """
+        self.__dict__.update(kwargs)
+
+
+@dataclass(config=ConfigDict(extra='forbid', kw_only=True))
+class BackGround(OverlayStructureBaseClass):
+    """
+    Represents a background structure overlayed on a mesh, characterized by a circular shape.
+
+    Attributes
+    ----------
+    index : float
+        Refractive index of the background.
+    radius : float, optional
+        Radius of the circular structure, by default 1000.
+    position : Optional[Tuple[float, float]], optional
+        A tuple (x, y) specifying the position of the circle's center, by default (0, 0).
+    """
+
+    index: float
+    radius: float = 1000
+    position: Optional[Tuple[float, float]] = (0, 0)
+
+    def __post_init__(self):
+        """
+        Initializes the background structure by creating a circular polygon.
+        """
+        polygon = Circle(position=self.position, radius=self.radius, index=self.index)
+        self.structure_list = [NameSpace(index=self.index, polygon=polygon, name='background')]
+
+    @property
+    def refractive_index_list(self) -> list:
+        """
+        Returns the list of refractive indices for the structures.
+
+        Returns
+        -------
+        list
+            A list containing the refractive index of the background.
+        """
+        return [self.index]
+
+    def overlay_structures_on_mesh(self, mesh: np.ndarray, coordinate_system: CoordinateSystem) -> np.ndarray:
+        """
+        Overlays all structures onto the given mesh using the specified coordinate system.
+
+        Parameters
+        ----------
+        mesh : np.ndarray
+            The mesh to overlay structures onto.
+        coordinate_system : CoordinateSystem
+            The coordinate system used for overlaying.
+
+        Returns
+        -------
+        np.ndarray
+            A numpy ndarray with the structures overlayed onto the original mesh.
+        """
+        return self._overlay_structure_on_mesh_(
+            structure_list=self.structure_list,
+            mesh=mesh,
+            coordinate_system=coordinate_system
+        )