FiberFusing 1.5.0.3__tar.gz → 1.6.0__tar.gz

fiberfusing-1.6.0/.github/workflows/build_documentation.yml

@@ -0,0 +1,60 @@
+# .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 3.11"
+        uses: actions/setup-python@v5
+        id: cp311
+        with:
+            python-version: 3.11
+
+      - name: "Install: Dependencies for headless server"
+        shell: bash
+        run: |
+            sudo apt-get update
+            sudo apt-get install -y xvfb jq
+
+      - name: "Checkout requirements and files for testing"
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+          submodules: true
+          ref: master
+
+      - 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: Get current tag
+        id: get_tag
+        run: |
+          git fetch --tags
+          echo "tag=$(git describe --tags --abbrev=0)" >> $GITHUB_ENV
+
+      - name: "Sphinx build"
+        run: |
+          sphinx-build docs/source documentation_build
+
+      - name: "Upload Documentation Artifact"
+        uses: actions/upload-artifact@v4
+        with:
+          name: documentation_build
+          path: documentation_build

{fiberfusing-1.5.0.3 → fiberfusing-1.6.0}/.github/workflows/deploy_PyPI.yml

@@ -1,4 +1,4 @@
-name: Deploy Wheel
+name: Deploy Wheel to PyPi
 
 on:
   push:

fiberfusing-1.6.0/.github/workflows/deploy_documentation.yml

@@ -0,0 +1,123 @@
+# Simple workflow for deploying static content to GitHub Pages
+name: Deploy static content to Pages
+
+
+on:
+  workflow_run:
+    workflows: ["Documentation"]  # This references the name of the first workflow
+    types:
+      - completed  # Run when the Documentation workflow is completed successfully
+
+
+# Sets permissions of the GITHUB_TOKEN  to allow deployment to GitHub Pages
+permissions:
+  contents: write
+  pages: write
+  id-token: write
+
+jobs:
+  deploy:
+    runs-on: ubuntu-latest
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+          ref: documentation_page
+
+      - name: Set up Git user
+        run: |
+          git config --global user.name  "GitHub Actions"
+          git config --global user.email "actions@github.com"
+
+      - name: Download artifact
+        id: download-artifact
+        uses: dawidd6/action-download-artifact@v6
+        with:
+          workflow: build_documentation.yml
+          name: documentation_build
+          path: ./documentation_build
+
+      - name: Get current tag
+        id: get_tag
+        run: |
+          # Fetch all tags to ensure they are available
+          git fetch --tags
+          git tag -l
+
+          # Get the latest tag by creation date
+          TAG=$(git tag --sort=-creatordate | head -n 1)
+
+          # Fallback to a default tag if no tag is found
+          if [ -z "$TAG" ]; then
+            TAG="0.0.0.0"
+          fi
+
+          echo "tag=$TAG" >> $GITHUB_ENV
+          echo "Tag found or default: $TAG"
+
+      - name: Update new documentation version
+        run: |
+          rm -rf docs/${{ env.tag }}
+          mv documentation_build docs/${{ env.tag }}
+
+      - name: Scan, sort versions, and update version_switcher.json
+        run: |
+          # Define the path to version_switcher.json
+          json_file="version_switcher.json"
+          rm $json_file
+          docs_path="docs"
+          base_url="https://martinpdes.github.io/FiberFusing"
+
+          # Start the JSON array
+          echo "[" > $json_file
+
+          # Get sorted version directories in descending order
+          version_dirs=$(ls -v $docs_path | sort -V -r)
+
+
+          # Loop over sorted versions and add to JSON file
+          first_entry=true
+          for version in $version_dirs; do
+            version_url="${base_url}/${docs_path}/${version}"
+
+            # Add a comma if it's not the first entry
+            if [ "$first_entry" = true ]; then
+              first_entry=false
+            else
+              echo "," >> $json_file
+            fi
+
+            # Append each version as a JSON entry
+            jq -n \
+              --arg name "$version" \
+              --arg version "$version" \
+              --arg url "$version_url" \
+              '{name: $name, version: $version, url: $url}' >> $json_file
+          done
+
+          # End the JSON array
+          echo "]" >> $json_file
+
+          # Add and commit the updated version_switcher.json
+          git add $json_file
+          echo $json_file
+          git add docs/
+          git commit --allow-empty -m "Update version_switcher.json"
+          git push origin HEAD
+
+      - name: Setup Pages
+        uses: actions/configure-pages@v5
+
+      - name: Upload artifact
+        uses: actions/upload-pages-artifact@v3
+        with:
+          path: '.'
+
+      - name: Deploy to GitHub Pages
+        id: deployment
+        uses: actions/deploy-pages@v4

{fiberfusing-1.5.0.3 → fiberfusing-1.6.0}/.gitignore

@@ -1,6 +1,4 @@
-
-
-
+# General patterns
 *.DS_store
 *.ipynb_checkpoints*
 *__pycache__*
@@ -19,5 +17,12 @@ install_manifest.txt
 cmake_install.cmake
 wheelhouse
 
+# Docs-specific patterns
 docs/source/gallery/*
 !docs/source/gallery/index.rst
+PyOptik/data/**/test*
+PyOptik/data/**/example*
+
+# Override for documentation_build
+!documentation_build
+!documentation_build/**

{fiberfusing-1.5.0.3 → fiberfusing-1.6.0}/FiberFusing/_version.py

@@ -12,5 +12,5 @@ __version__: str
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
 
-__version__ = version = '1.5.0.3'
-__version_tuple__ = version_tuple = (1, 5, 0, 3)
+__version__ = version = '1.6.0'
+__version_tuple__ = version_tuple = (1, 6, 0)

{fiberfusing-1.5.0.3 → fiberfusing-1.6.0}/FiberFusing.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: FiberFusing
-Version: 1.5.0.3
+Version: 1.6.0
 Summary: A package fiber fusing configuration simulating the transverse fusion of fiber optics.
 Author-email: Martin Poinsinet de Sivry-Houle <martin.poinsinet.de.sivry@gmail.com>
 License: MIT License

{fiberfusing-1.5.0.3 → fiberfusing-1.6.0}/FiberFusing.egg-info/SOURCES.txt

@@ -7,6 +7,7 @@ meta.yaml
 notebook.ipynb
 pyproject.toml
 .github/dependabot.yml
+.github/workflows/build_documentation.yml
 .github/workflows/deploy_PyPI.yml
 .github/workflows/deploy_anaconda.yml
 .github/workflows/deploy_coverage.yml
@@ -120,7 +121,6 @@ docs/source/code/buffer.rst
 docs/source/code/components.rst
 docs/source/code/coordinate_system.rst
 docs/source/code/geometry.rst
-docs/source/code/overlay_structure.rst
 docs/source/code/utils.rst
 docs/source/gallery/index.rst
 tests/__init__.py

{fiberfusing-1.5.0.3 → fiberfusing-1.6.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: FiberFusing
-Version: 1.5.0.3
+Version: 1.6.0
 Summary: A package fiber fusing configuration simulating the transverse fusion of fiber optics.
 Author-email: Martin Poinsinet de Sivry-Houle <martin.poinsinet.de.sivry@gmail.com>
 License: MIT License

fiberfusing-1.5.0.3/docs/source/gallery/index.rst → fiberfusing-1.6.0/docs/examples/README.rst

@@ -5,17 +5,3 @@ Coding examples
 
 Explore our gallery of examples demonstrating the usage of FiberFusing. These examples range from general API usage to specific applications, presented in a tutorial format to guide users through practical implementations.
 
-.. toctree::
-    :maxdepth: 2
-    :hidden:
-
-    clad/index.rst
-    geometry/index.rst
-
-
-.. include:: clad/index.rst
-    :start-after: .. _clad_index:
-
-.. include:: geometry/index.rst
-    :start-after: .. _geometry_index:
-

{fiberfusing-1.5.0.3 → fiberfusing-1.6.0}/docs/examples/clad/radomize_core.py

@@ -17,11 +17,17 @@ structure = FusedProfile(
     index=material.compute_refractive_index(wavelength),
 )
 
+# %%
+factor = 0
+structure.randomize_core_position(random_factor=factor)
+structure.plot(show_centers=True, show_cores=True)
 
-for factor in [0, 10e-6]:
-    structure.randomize_core_position(random_factor=factor)
-
-    structure.plot(show_centers=True, show_cores=True)
-
+# %%
+factor = 10e-6
+structure.randomize_core_position(random_factor=factor)
+structure.plot(show_centers=True, show_cores=True)
 
-# -
+# %%
+factor = 10e-6
+structure.randomize_core_position(random_factor=factor)
+structure.plot(show_centers=True, show_cores=True)

{fiberfusing-1.5.0.3 → fiberfusing-1.6.0}/docs/examples/clad/structure_shift.py

@@ -1,6 +1,6 @@
 """
-Effect of fusion degree
-=======================
+Effect of translation
+=====================
 """
 
 # %%
@@ -17,10 +17,12 @@ structure = FusedProfile(
     index=material.compute_refractive_index(wavelength),
 )
 
-for shift in [(0, 0), (20e-6, 0)]:
-    structure.translate(shift)
-
-    structure.plot()
-
+# %%
+shift = (0, 0)
+structure.translate(shift)
+structure.plot()
 
-# -
+# %%
+shift = (20e-6, 0)
+structure.translate(shift)
+structure.plot()

{fiberfusing-1.5.0.3 → fiberfusing-1.6.0}/docs/source/code/utils.rst

@@ -3,11 +3,6 @@
 Utilities Module
 ----------------
 
-.. autofunction:: FiberFusing.utils.get_silica_index
-    :noindex:
-
-    The `get_silica_index` function calculates the refractive index of silica based on the wavelength, using established empirical formulas. It is a core utility for determining optical properties within the simulation.
-
 .. autofunction:: FiberFusing.utils.union_geometries
     :noindex:
 

{fiberfusing-1.5.0.3 → fiberfusing-1.6.0}/docs/source/code.rst

@@ -14,5 +14,4 @@ This section provides an overview of the primary classes used in the `FiberFusin
    code/coordinate_system.rst
    code/buffer.rst
    code/components.rst
-   code/overlay_structure.rst
    code/utils.rst

{fiberfusing-1.5.0.3 → fiberfusing-1.6.0}/docs/source/conf.py

@@ -3,28 +3,36 @@
 
 import sys
 import os
+from sphinx_gallery.sorting import FileNameSortKey
 from MPSPlots.styles import use_mpsplots_style
-import FiberFusing
 from pathlib import Path
-from FiberFusing.directories import doc_css_path, examples_path
+import FiberFusing
+from FiberFusing.directories import doc_css_path
+
+
+package_name = "FiberFusing"
+version = FiberFusing.__version__
 
-sys.path.append(str(Path(".").resolve()))
+current_dir = Path(".")
+
+sys.path.append(str(current_dir.resolve()))
 
 
 def setup(app):
     app.add_css_file(str(doc_css_path))
 
 
-autodoc_mock_imports = []
+autodoc_mock_imports = [
+    'numpy',
+    'matplotlib',
+    'numpydoc',
+]
 
 
-project = 'FiberFusing'
+project = package_name
 copyright = '2024, Martin Poinsinet de Sivry-Houle'
 author = 'Martin Poinsinet de Sivry-Houle'
 
-
-version = FiberFusing.__version__
-
 extensions = [
     'sphinx.ext.mathjax',
     'pyvista.ext.plot_directive',
@@ -49,21 +57,15 @@ def reset_mpl(gallery_conf, fname):
 
 
 examples_files = [
-    'clad', 'geometry'
-]
-
-
-examples_dirs = [
-    examples_path.joinpath('clad'),
-    examples_path.joinpath('geometry')
+    'utils', 'sellmeier', 'tabulated'
 ]
 
-
 sphinx_gallery_conf = {
-    "examples_dirs": ['../examples/' + f for f in examples_files],
-    "gallery_dirs": ['gallery/' + f for f in examples_files],
+    'examples_dirs': ['../examples'],
+    'gallery_dirs': ['gallery'],
     'image_scrapers': ('matplotlib'),
     'ignore_pattern': '/__',
+    'filename_pattern': r'.*\.py',
     'plot_gallery': True,
     'thumbnail_size': [600, 600],
     'download_all_examples': False,
@@ -72,6 +74,7 @@ sphinx_gallery_conf = {
     'remove_config_comments': True,
     'capture_repr': ('_repr_html_', '__repr__'),
     'nested_sections': True,
+    'within_subsection_order': FileNameSortKey,
 }
 
 
@@ -92,7 +95,6 @@ language = 'en'
 highlight_language = 'python3'
 html_theme = "pydata_sphinx_theme"
 
-
 # -- Options for HTML output -------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
 
@@ -101,31 +103,29 @@ exclude_trees = []
 pygments_style = "sphinx"
 
 # -- Sphinx-gallery configuration --------------------------------------------
-binder_branch = "main"
-
 major, minor = version[:2]
 binder_branch = f"v{major}.{minor}.x"
 
 html_theme_options = dict()
 
-html_theme_options['logo'] = dict(text='FiberFusing', image="_static/thumbnail.png")
+html_theme_options['logo'] = dict(text=package_name, image="_static/thumbnail.png")
 html_theme_options["show_nav_level"] = 0
 
 html_theme_options.update({
     "icon_links": [
         {
             "name": "GitHub",
-            "url": "https://github.com/MartinPdeS/FiberFusing",
+            "url": f"https://github.com/MartinPdeS/{package_name}",
             "icon": "fa-brands fa-github",
         },
         {
             "name": "PyPI",
-            "url": "https://pypi.org/project/fiberfusing/",
+            "url": f"https://pypi.org/project/{package_name}/",
             "icon": "fa-solid fa-box",
         },
         {
             "name": "Anaconda",
-            "url": "https://anaconda.org/MartinPdeS/fiberfusing",
+            "url": f"https://anaconda.org/MartinPdeS/{package_name}",
             "icon": "fa-brands fa-python",
         },
     ],
@@ -145,27 +145,28 @@ html_theme_options.update({
 current_version = os.getenv("tag", "latest")
 
 html_theme_options["switcher"] = dict(
-    json_url="https://raw.githubusercontent.com/MartinPdeS/FiberFusing/documentation_page/version_switcher.json",
+    json_url=f"https://raw.githubusercontent.com/MartinPdeS/{package_name}/documentation_page/version_switcher.json",
     version_match=current_version,
 )
 
-htmlhelp_basename = 'FiberFusingdoc'
+htmlhelp_basename = f'{package_name}doc'
 
 latex_elements = {}
 
+
 latex_documents = [
-    (master_doc, 'FiberFusing.tex', 'FiberFusing Documentation',
+    (master_doc, f'{package_name}.tex', f'{package_name} Documentation',
      'Martin Poinsinet de Sivry-Houle', 'manual'),
 ]
 
 man_pages = [
-    (master_doc, 'fiberfusing', 'FiberFusing Documentation',
+    (master_doc, 'supymode', f'{package_name} Documentation',
      [author], 1)
 ]
 
 texinfo_documents = [
-    (master_doc, 'FiberFusing', 'FiberFusing Documentation',
-     author, 'FiberFusing', 'One line description of project.',
+    (master_doc, package_name, f'{package_name} Documentation',
+     author, package_name, 'One line description of project.',
      'Miscellaneous'),
 ]