Vectorized calculations

.github/workflows/lint_and_test.yml

@@ -0,0 +1,55 @@
+name: Lint, then test on all platforms
+
+on:
+  # empty "push:" will trigger CI on push to any branch
+  push:
+  pull_request:
+    branches: [ "develop", "master" ]
+
+jobs:
+  lint:
+    # only need to run on one platform since we're just looking at the code
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        shell: bash -el {0}
+    steps:
+    - uses: actions/checkout@v4
+    - uses: astral-sh/ruff-action@v3
+      with:
+        # check based on rulesets defined in pyproject.toml and fail if errors
+        args: "check"
+      # do another run to produce a linting report for pull requests. exit-zero
+      # treats all errors as warnings. This will flag codestyle problems in the
+      # PR
+    - run: ruff check --exit-zero --output-format=github
+
+  test:
+    # linting must succeed for testing to run; this helps us rapidly flag code
+    # errors before going to testing
+    needs: lint
+    runs-on: ${{ matrix.os }}
+    # conda enviroment activation requires bash
+    defaults:
+      run:
+        shell: bash -el {0}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest, macos-latest, windows-latest]
+        python-version: ["3.13"] # , "3.10", "3.11", "3.12"]
+      max-parallel: 5
+
+    steps:
+    - uses: actions/checkout@v4
+    - name: Set up miniforge with pymie environment
+      uses: conda-incubator/setup-miniconda@v3
+      with:
+        environment-file: environment.yml
+        miniforge-version: latest
+        conda-remove-defaults: "true"
+    - name: Install plugin to annotate test results
+      run: pip install pytest-github-actions-annotate-failures
+    - name: Test with pytest
+      run: |
+        pytest

README.md

@@ -3,9 +3,31 @@ Pure Python package for Mie scattering calculations. This package is used by,
 for example, the [structural-color python
 package](https://github.com/manoharan-lab/structural-color).
 
+To install:
+
+```shell
+git clone https://github.com/manoharan-lab/python-mie.git
+python -m pip install ./python-mie
+```
+
+To remove:
+
+```shell
+python -m pip uninstall pymie
+```
+
+You can then run the tests to make sure the package works properly:
+```shell
+cd python-mie
+pytest -v
+```
+
 The original code was developed by Jerome Fung in the [Manoharan Lab at Harvard
-University](http://manoharan.seas.harvard.edu). This research was supported by
-the National Science Foundation under grant numbers CBET-0747625, DMR-0820484,
-DMR-1306410, and DMR-1420570. The code has since been updated. It now works in
-Python 3, and it can handle quantities with dimensions (using
+University](http://manoharan.seas.harvard.edu). The code has since been updated
+by Victoria Hwang, Anna B. Stephenson, and Vinothan N. Manoharan. It works
+in Python 3, and it can handle quantities with dimensions (using
 [pint](https://github.com/hgrecco/pint)).
+
+The development of this code was made possible with support from the National
+Science Foundation under award numbers CBET-0747625, DMR-0820484, DMR-1306410,
+DMR-1420570, and DMR-2011754.

environment.yml

@@ -1,7 +1,7 @@
-# dependencies for structural color package
+# dependencies for pymie package
 #
 # To use:
-#   conda env create -f .\environment.yml
+#   conda env create -f environment.yml
 # and then
 #   conda activate pymie
 #
@@ -12,7 +12,6 @@
 name: pymie
 channels:
   - conda-forge
-  - defaults
 dependencies:
   - python>=3.11
   - numpy

pymie/__init__.py

@@ -28,8 +28,8 @@
 Github: https://github.com/hgrecco/pint
 Docs: https://pint.readthedocs.io/en/latest/
 
-.. moduleauthor :: Vinothan N. Manoharan <vnm@seas.harvard.edu>
-.. moduleauthor :: Sofia Magkiriadou <sofia@physics.harvard.edu>.
+.. moduleauthor:: Vinothan N. Manoharan <vnm@seas.harvard.edu>
+.. moduleauthor:: Sofia Magkiriadou <sofia@physics.harvard.edu>.
 """
 
 import numpy as np
@@ -68,20 +68,22 @@ def index_ratio(n_particle, n_matrix):
 
     Parameters
     ----------
-    n_particle: structcol.Quantity [dimensionless]
-        refractive index of particle at a particular wavelength
+    n_particle: structcol.Quantity [dimensionless] or ndarray thereof
+        refractive index of particle at particular wavelength(s)
         can be complex
     n_matrix: structcol.Quantity [dimensionless]
         refractive index of matrix at a particular wavelength
 
     Notes
     -----
-    Returns a scalar rather than a Quantity because scipy special functions
-    don't seem to be able to handle pint Quantities
+    Nondimensionalizes from input arguments and strips units, returning a pure
+    ndarray (not a Quantity object)
 
     Returns
     -------
-    float
+    ndarray or scalar (complex or float):
+        Return type depends on type of n_particle and n_matrix, and return
+        shape should be the same as n_particle
     """
     return (n_particle/n_matrix).magnitude
 
@@ -92,26 +94,42 @@ def size_parameter(wavelen, n_matrix, radius):
 
     Parameters
     ----------
-    wavelen: structcol.Quantity [length]
+    wavelen: structcol.Quantity [length], array-like
         wavelength in vacuum
-    n_matrix: structcol.Quantity [dimensionless]
+    n_matrix: structcol.Quantity [dimensionless], array-like
         refractive index of matrix at wavelength=wavelen
-    radius: structcol.Quantity [length]
+    radius: structcol.Quantity [length], array-like
         radius of particle
 
     Notes
     -----
-    Returns a scalar rather than a Quantity because scipy special functions
-    don't seem to be able to handle pint Quantities
+    Nondimensionalizes from input arguments and strips units, returning a pure
+    ndarray (not a Quantity object)
 
     Returns
     -------
-    complex or float
+    ndarray or scalar (complex or float):
+        returns scalar if both wavelen and radius are scalars. If wavelen is an
+        array, returns shape [len(wavelen), 1]. If radius is an array, returns
+        shape [1, len(radius)].  If both are arrays, returns shape
+        [len(wavelen), len(radius)]
+
     """
+    # ensure size parameter calculation broadcasts correctly when both
+    # wavelength and radius are arrays
+    radius = np.broadcast_to(radius, (np.size(wavelen), np.size(radius)))
+    wavelen = np.reshape(wavelen, (np.size(wavelen), 1))
+    # matrix index may be specifed as an array to account for dispersion
+    if isinstance(n_matrix, np.ndarray):
+        n_matrix = np.reshape(n_matrix, (np.size(wavelen), 1))
+    sp = (2 * np.pi * n_matrix / wavelen * radius)
+
     # must use to('dimensionless') in case the wavelength and radius are
     # specified in different units; pint doesn't automatically make
     # ratios such as 'nm'/'um' dimensionless
-    sp = (2 * np.pi * n_matrix / wavelen * radius)
     if isinstance(sp, Quantity):
         sp = sp.to('dimensionless').magnitude
+    if np.size(sp) == 1:
+        sp = sp.item()
+
     return sp