Merge branch 'master' into performance-improvements

.github/workflows/benchmark.yml

@@ -19,7 +19,7 @@ jobs:
           submodules: recursive
       - uses: actions/setup-python@v5
         with:
-          python-version: "3.12"
+          python-version: "3.13"
       - name: Install deps
         run: |
           curl -LsSf https://astral.sh/uv/install.sh | sh

.github/workflows/linting.yml

@@ -13,10 +13,10 @@ jobs:
       - uses: actions/checkout@v4
       - uses: actions/setup-python@v5
         with:
-          python-version: "3.10"
+          python-version: "3.13"
       - name: Install deps
         run: |
-          pip install sphinx-lint ruff==0.4.8
+          pip install sphinx-lint ruff==0.8.5
       - name: ruff
         run: |
           ruff check src/elli tests

.github/workflows/pytest.yml

@@ -15,7 +15,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python_version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
+        python_version: ["3.9", "3.10", "3.11", "3.12", "3.13"]
 
     steps:
       - uses: actions/checkout@v4

.github/workflows/python-publish.yml

@@ -1,20 +1,10 @@
-# This workflow will upload a Python Package using Twine when a release is created
-# For more information see: https://help.github.com/en/actions/language-and-framework-guides/using-python-with-github-actions#publishing-to-package-registries
+name: Publish 📦
 
-# This workflow uses actions that are not certified by GitHub.
-# They are provided by a third-party and are governed by
-# separate terms of service, privacy policy, and support
-# documentation.
-
-name: Upload Python Package
-
-on:
-  release:
-    types: [published]
+on: push
 
 jobs:
-  deploy:
-
+  build:
+    name: Build distribution 📦
     runs-on: ubuntu-latest
 
     steps:
@@ -24,15 +14,78 @@ jobs:
     - name: Set up Python
       uses: actions/setup-python@v5
       with:
-        python-version: '3.x'
-    - name: Install dependencies
-      run: |
-        python -m pip install --upgrade pip
-        pip install build
-    - name: Build package
-      run: python -m build
-    - name: Publish package
-      uses: pypa/gh-action-pypi-publish@27b31702a0e7fc50959f5ad993c78deac1bdfc29
+        python-version: "3.x"
+    - name: Install pypa/build
+      run: >-
+        python3 -m
+        pip install
+        build
+        --user
+    - name: Build a binary wheel and a source tarball
+      run: python3 -m build
+    - name: Store the distribution packages
+      uses: actions/upload-artifact@v4
+      with:
+        name: python-package-distributions
+        path: dist/
+
+  publish-to-pypi:
+    name: >-
+      Publish to PyPi
+    if: startsWith(github.ref, 'refs/tags/')
+    needs:
+    - build
+    runs-on: ubuntu-latest
+    environment:
+      name: pypi
+      url: https://pypi.org/p/pyElli/
+    permissions:
+      id-token: write
+
+    steps:
+    - name: Download all the dists
+      uses: actions/download-artifact@v4
+      with:
+        name: python-package-distributions
+        path: dist/
+    - name: Publish distribution 📦 to PyPI
+      uses: pypa/gh-action-pypi-publish@release/v1
+
+  github-release:
+    name: >-
+      GitHub Release
+    needs:
+    - publish-to-pypi
+    runs-on: ubuntu-latest
+
+    permissions:
+      contents: write
+      id-token: write
+
+    steps:
+    - name: Download all the dists
+      uses: actions/download-artifact@v4
+      with:
+        name: python-package-distributions
+        path: dist/
+    - name: Sign the dists with Sigstore
+      uses: sigstore/[email protected]
       with:
-        user: __token__
-        password: ${{ secrets.PYPI_API_TOKEN }}
+        inputs: >-
+          ./dist/*.tar.gz
+          ./dist/*.whl
+    - name: Create GitHub Release
+      env:
+        GITHUB_TOKEN: ${{ github.token }}
+      run: >-
+        gh release create
+        '${{ github.ref_name }}'
+        --repo '${{ github.repository }}'
+        --notes ""
+    - name: Upload artifact signatures to GitHub Release
+      env:
+        GITHUB_TOKEN: ${{ github.token }}
+      run: >-
+        gh release upload
+        '${{ github.ref_name }}' dist/**
+        --repo '${{ github.repository }}'

.pre-commit-config.yaml

@@ -1,7 +1,7 @@
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
     # Ruff version.
-    rev: v0.4.8
+    rev: v0.8.5
     hooks:
       # Run the linter.
       - id: ruff

.vscode/ltex.dictionary.en-US.txt

@@ -0,0 +1,3 @@
+dispersions
+dataframes
+ellipsometry

CHANGELOG.md

@@ -1,5 +1,28 @@
 # Changelog
 
+## Version 0.21.2
+
+### Bugfixes
+- Include the RII database submodule in the Pypi package again
+
+## Version 0.21.1
+
+### Bugfixes
+- Fix documentation generation
+
+## Version 0.21.0
+
+### New
+- Reenable pytorch 4x4solver
+- Use OIDC for publishing
+- Add custom fitting example
+- Add chardet encoding detection
+- Add reader for accurion data
+
+### Bugfixes
+- Fix deprecation warnings
+
+
 ## Version 0.20.0
 
 ### New

README.md

@@ -40,7 +40,12 @@ pip install pyElli[fitting]
 ```
 
 This installs pyElli with the additional fitting capabilities and interactive widgets.
-If don't want to have this functionality just drop the `[fitting]` in the end.
+If you don't want to have this functionality just drop the `[fitting]` in the end.
+
+To increase performance of the 4x4 Solver, it is recommended to
+install PyTorch manually, as it is too big to include in the standard installation.
+Installation information can be found at the [PyTorch Website](https://pytorch.org/get-started/locally/).
+The CPU variant is sufficient, if you want to save some space.
 
 A complete environment for pyElli is also available as a [Docker Container](https://hub.docker.com/r/domna/pyelli).
 To pull and run it directly just execute
@@ -68,10 +73,15 @@ cd pyElli
 pip install -e ".[fitting]"
 ```
 
+## How to cite
+
+Until we have published a Paper on pyElli, we have prepared a Zenodo entry with DOIs for every pyElli Version. The can be found [here](https://zenodo.org/records/13903325).
+
+
 ## Acknowledgements
 
 - Based on Olivier Castany's [Berreman4x4](https://github.com/Berreman4x4/Berreman4x4)
 - Solver2x2 based on Steve Byrnes' [tmm](https://github.com/sbyrnes321/tmm)
 - Mikhail Polyanskiy's [refractiveindex.info database](https://github.com/polyanskiy/refractiveindex.info-database) and Pavel Dmitriev's [pyTMM](https://github.com/kitchenknif/PyTMM) for his importer script for the database
 
-[@MarJMue](https://github.com/MarJMue) recieves financial support by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation), grant No. 398143140 (FOR 2824).
+[@MarJMue](https://github.com/MarJMue) receives financial support by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation), grant No. 398143140 (FOR 2824).

docs/conf.py

@@ -80,7 +80,7 @@
     "sphinx.ext.napoleon",
     "sphinx_plotly_directive",
     "sphinx_rtd_theme",
-    "m2r2",
+    "sphinx_mdinclude",
     "sphinx_gallery.gen_gallery",
     "sphinxcontrib.mermaid",
 ]

docs/dispersions.rst

@@ -265,7 +265,7 @@ DispersionSum
 This object can be used to add an arbitrary number of dispersions.
 The overloaded `+` operator of the dispersion base class creates an instance
 of this object with two classes as parameters.
-If you want to chain a lot of dispersions it may be more performant to use
+If you want to chain a lot of dispersions, it may be more performant to use
 this class directly.
 
 .. autoclass:: elli.dispersions.base_dispersion.DispersionSum
@@ -274,6 +274,6 @@ this class directly.
 
 InvalidParameters
 -----------------
-This exception is thrown whenever a dispersions got invalid parameters.
+This exception is thrown whenever a dispersion got invalid parameters.
 
 .. autoexception:: elli.dispersions.base_dispersion.InvalidParameters

docs/index.rst

@@ -14,8 +14,8 @@ However, pyElli comes with batteries included and already offers a wide range
 of :doc:`dispersion models<dispersions>` and the material database of Refractiveindex.info.
 
 Most of the models presented in the
-comprehensive book of Fujiwara and Colllins [1]_ are present and additionally
-a lot of other models used by ellipsometry vendor softwares are included.
+comprehensive book of Fujiwara and Collins [1]_ are present and additionally
+a lot of other models used by ellipsometry vendor software are included.
 
 The material database offers the dispersions seen on the `website <https://refractiveindex.info/>`_
 and can be accessed by using the :class:`elli.db.RII<elli.db.RII>` module.
@@ -54,7 +54,7 @@ but can contain arbitrary more :class:`layers<elli.structure.Layer>` which are o
 The :class:`VaryingMixtureLayer<elli.structure.VaryingMixtureLayer>` class can also account for gradient changes of materials in z-direction
 of a layer, which is useful for gradient layers or roughness modeling.
 As the last step the :class:`Structure<elli.structure.Structure>` is plugged into an :class:`Experiment<elli.experiment.Experiment>`, which contains
-the experimental conditions, such as light polarizations.
+the experimental conditions, such as light polarization.
 By evaluating the experiment a :class:`Result<elli.result.Result>` class containing the calculated data is returned.
 The creation of an experiment can be skipped by calling the :meth:`evaluate<elli.structure.Structure.evaluate>` method directly
 on a :class:`Structure<elli.structure.Structure>` class if you want to use standard experimental settings.

docs/installation.rst

@@ -10,7 +10,15 @@ To install the package in your current virtual environment execute
 
     .. code-block:: shell
 
-        pip install pyElli
+        pip install pyElli[fitting]
+
+This installs pyElli with the additional fitting capabilities and interactive widgets.
+If you don't want to have this functionality just drop the `[fitting]` in the end.
+
+To increase performance of the 4x4 Solver, it is recommended to
+install PyTorch manually, as it is too big to include in the standard installation.
+Installation information can be found at the `PyTorch Website <https://pytorch.org/get-started/locally/>`_.
+The CPU variant is sufficient, if you want to save some space.
 
 A complete environment for pyElli is also available as a
 `Docker Container <https://hub.docker.com/r/domna/pyelli>`_.

docs/plot.rst

@@ -7,7 +7,7 @@ Interactive fitting
 PyElli offers several classes and decorators to make fitting easy.
 The central idea is to construct a class containing the measurement data and an optical model
 which is fitted to the data with `lmfit <https://lmfit.github.io/lmfit-py/index.html>`_.
-Since pyElli uses lmfit under the hood you may take advantage of it's vast capabilities.
+Since pyElli uses lmfit under the hood you may take advantage of its vast capabilities.
 
 To make creation of the fitting classes as easy as possible pyElli contains decorators to
 automatically instantiate the class by providing a function containing the optical model.
@@ -56,7 +56,7 @@ be inherited from in additional fitting classes.
 
 Parameter class
 ---------------
-The parameter class extending lmfits Parameter class by a history
+The parameter class extending lmfit's Parameter class by a history
 of parameter changes.
 
 .. automodule:: elli.fitting.params_hist

docs/requirements.txt

@@ -3,7 +3,7 @@
 # under `install_requires` in `setup.cfg` is also listed here!
 sphinx!=5.1.0
 sphinx_rtd_theme
-m2r2
+sphinx-mdinclude
 myst_parser
 scipy
 numpy>=1.20
@@ -14,13 +14,12 @@ ipython
 ipywidgets
 sphinx-gallery
 sphinx-plotly-directive
-sphinxcontrib-mermaid 
+sphinxcontrib-mermaid
 matplotlib
 h5py
-importlib-resources
-h5py
 pyyaml
 importlib-resources
 rapidfuzz
 lark>=1.1.5
-pint
+pint
+chardet

docs/solvers.rst

@@ -16,6 +16,7 @@ pyElli provides different implementations to be used in the calculation of the t
 The :class:`PropagatorEig<elli.solver4x4.PropagatorEig>` is based on solving the eigenvalues of the first order approximation of the matrix exponential.
 Although, it is very fast it is not very accurate.
 The :class:`PropagatorExpm<elli.solver4x4.PropagatorExpm>` is solving the matrix exponential by the Pade approximation.
+It can use SciPy as backend, but for performance-critical tasks, it is recommended to install PyTorch.
 
 .. rubric:: References
 

examples/Basic Usage/Basic Usage.ipynb

@@ -185,7 +185,7 @@
     "## Building the model\n",
     "\n",
     "For simple parameter estimation,\n",
-    "the fit decorator (**@fit**) in conjuction with the model definition is used.\n",
+    "the fit decorator (**@fit**) in conjunction with the model definition is used.\n",
     "The fitting decorator takes a pandas dataframe containing\n",
     "the psi/delta measurement data (**psi_delta**) and the model parameters (**params**) as an input.\n",
     "It then passes the wavelength from measurement dataframe (**lbda**)\n",
@@ -204,7 +204,7 @@
     "This is done by calling the :code:`elli.IsotropicMaterial(...)` function\n",
     "with a dispersion model as a parameter\n",
     "or simply calling :code:`.get_mat()` on a dispersion model.\n",
-    "These two approaches are equivalent.From these materials the layer is build,\n",
+    "These two approaches are equivalent. From these materials the layer is build,\n",
     "which only consists of the SiO2 layer in this example.\n",
     "The final structure consists of an incoming half-space,\n",
     "the layers and an outgoing half space. Specifically,\n",
@@ -223,7 +223,7 @@
     "Executing the cell below in a jupyter notebook displays a comparison of the simulated Ψ / Δ values\n",
     "at the current parameter values with their measured counterparts.\n",
     "Additionally, input fields for each model parameter are shown.\n",
-    "You may change the parameters and the calcualted data will change accordingly.\n",
+    "You may change the parameters and the calculated data will change accordingly.\n",
     "For clarification the modeled data is shown with `_calc` postfix in the legend.\n",
     "\n"
    ]