Merge pull request #144 from punch-mission/use-units

Use units everywhere!

.github/workflows/CI.yml

@@ -20,7 +20,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.10", "3.11", "3.12"]
+        python-version: ["3.11", "3.12"]
 
     steps:
     - uses: actions/checkout@v3

.github/workflows/docs.yml

@@ -20,12 +20,11 @@ jobs:
     - name: Set up Python 3.10
       uses: actions/setup-python@v2
       with:
-        python-version: "3.10"
+        python-version: "3.11"
 
     - name: Install dependencies
       run: |
-        pip install -r ./docs/requirements.txt
-        pip install ".[test]"
+        pip install ".[docs, test]"
 
     # Build the book
     - name: Sphinx build

README.md

@@ -26,10 +26,11 @@ Please open a discussion or issue for help.
 ## Features Coming Soon
 - [x] core transformation capability
 - [x] clearer examples in the documentation
+- [x] more comprehensive support for 4-polarizer systems
+- [x] functions to deal with the IMAX effect in wide-field imagers
 - [ ] quantification and propagation of error
 - [ ] additional plotting utilities
-- [ ] more comprehensive support for 4-polarizer systems
-- [x] functions to deal with the IMAX effect in wide-field imagers
+
 
 ## Contributing
 We encourage all contributions.

docs/source/conf.py

@@ -18,9 +18,9 @@
 # -- Project information -----------------------------------------------------
 from solpolpy import __version__
 
-project = 'solpolpy'
-copyright = '2023, PUNCH Science Operations Center'
-author = 'PUNCH Science Operations Center'
+project = "solpolpy"
+copyright = "2023, PUNCH Science Operations Center"
+author = "PUNCH Science Operations Center"
 
 # The full version, including alpha/beta/rc tags
 release = __version__
@@ -32,14 +32,14 @@
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
 
-extensions = ['autoapi.extension',
-              'sphinx.ext.autodoc',
-              'sphinx.ext.napoleon',
-              'nbsphinx',
-              'IPython.sphinxext.ipython_console_highlighting']
+extensions = ["autoapi.extension",
+              "sphinx.ext.autodoc",
+              "sphinx.ext.napoleon",
+              "nbsphinx",
+              "IPython.sphinxext.ipython_console_highlighting"]
 
 # Add any paths that contain templates here, relative to this directory.
-templates_path = ['_templates']
+templates_path = ["_templates"]
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
@@ -54,7 +54,7 @@
 #
 html_theme = "pydata_sphinx_theme"
 html_show_sourcelink = False
-html_static_path = ['_static']
+html_static_path = ["_static"]
 html_theme_options = {
     "use_edit_page_button": True,
     "icon_links": [
@@ -63,10 +63,10 @@
             "url": "https://github.com/punch-mission/solpolpy",
             "icon": "fa-brands fa-github",
             "type": "fontawesome",
-        }
+        },
     ],
     "show_nav_level": 1,
-    "show_toc_level": 3
+    "show_toc_level": 3,
 }
 html_context = {
     # "github_url": "https://github.com", # or your GitHub Enterprise site
@@ -77,4 +77,4 @@
 }
 
 
-autoapi_dirs = ['../../solpolpy']
+autoapi_dirs = ["../../solpolpy"]

docs/source/development.rst

@@ -6,23 +6,21 @@ If you're contributing code, we recommend reading `our project-wide evelopment g
 
 We recommend working in a virtual environment.
 This can be created by running ``python -m venv venv``. Then, activate the environment with ``source venv/bin/activate``.
-You can then install the required packages with ``pip install -r requirements_dev.txt``.
+You can then install the required packages with ``pip install -e ".[dev]``.
 
 If at any time you run into issues, please contact us by :doc:`following the guidelines here <help>`.
 
 Setting up pre-commit
 ----------------------
 
 The first time you develop code, you'll need to install the pre-commit. This checks that our style is consistent.
-It gets installed when you do ``pip install -r requirements_dev.txt`` but then requires you to activate them by
+It gets installed when you do ``pip install -e ".[dev]"`` but then requires you to activate them by
 running ``pre-commit install``. Now everytime you commit, our checks will run first.
 
 Building the docs
 ------------------
-The docs are built using ``sphinx``. First, you must install it and the other documentation requirements with ::
-
-    pip install -r ./docs/requirements.txt
-    pip install -r requirements.txt
+The docs are built using ``sphinx``. First, you must install it and the other documentation requirements with
+``pip install -e ".[dev]"``.
 
 Then, navigate to the ``docs`` directory and run ``make html`` to build the docs.
 

docs/source/quickstart.rst

@@ -27,7 +27,8 @@ The easiest way to interact with solpolpy is through the ``resolve`` method:
     # to access the data, just access the appropriate cube
     print(output_collection['B'].data)
 
-``resolve`` takes two parameters: 1. the input data and 2. the desired output polarization system.
+``resolve`` takes two (or more depending on the polarization systems) parameters:
+1. the input data and 2. the desired output polarization system.
 Valid polarization systems are described in the documentation.
 
 .. autofunction:: solpolpy.resolve

pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "solpolpy"
-version = "0.2.0"
+version = "0.3.0"
 authors = [
     { name="J. Marcus Hughes", email="mhughes@boulder.swri.edu"},
     { name="Matthew J. West", email="mwest@boulder.swri.edu"},
@@ -11,7 +11,7 @@ authors = [
 description = "Solar polarization resolver for any instrument"
 readme = "README.md"
 license = { file="LICENSE" }
-requires-python = ">=3.10"
+requires-python = ">=3.11"
 classifiers = [
     "Programming Language :: Python :: 3",
     "License :: OSI Approved :: MIT License",
@@ -33,6 +33,16 @@ test = [
     'pytest-cov',
     'ruff'
 ]
+docs = [
+    "sphinx",
+    "pydata-sphinx-theme",
+    "sphinx-autoapi",
+    "nbsphinx",
+    "ipython",
+    "pandoc"
+]
+
+dev = ["solpolpy[test, docs]", "pre-commit"]
 
 [build-system]
 requires = ["setuptools>=61.0"]
@@ -44,6 +54,12 @@ packages = ['solpolpy']
 [tool.ruff]
 line-length = 120
 ignore-init-module-imports = true
+#lint.select = ["ALL"]
+lint.ignore = ["F403"]
+
+[tool.ruff.lint.per-file-ignores]
+"__init__.py" = ["E402"]
+"tests/*.py" = ['S101']
 
 [tool.isort]
 balanced_wrapping = true

solpolpy/__init__.py

@@ -3,6 +3,7 @@
 from solpolpy.core import resolve
 from solpolpy.instruments import load_data
 from solpolpy.plotting import get_colormap_str, plot_collection
+from solpolpy.transforms import System
 
 __version__ = importlib.metadata.version("solpolpy")
-__all__ = [resolve, load_data, get_colormap_str, plot_collection]
+__all__ = [resolve, load_data, get_colormap_str, plot_collection, System]

solpolpy/alpha.py

@@ -1,11 +1,11 @@
-""" Functions related to constructing an alpha array for transformation"""
+"""Functions related to constructing an alpha array for transformation."""
 
 import astropy.units as u
 import numpy as np
 
 
 def radial_north(shape):
-    """An alpha array oriented west
+    """An alpha array oriented west.
 
     Parameters
     ----------
@@ -18,11 +18,12 @@ def radial_north(shape):
         alpha array used in calculations
 
     Notes
-    ------
+    -----
     - assumes solar north is up
     - assumes polarizer 0 is along solar north axis
     - creates radial polarization map
     - angles increase in counterclockwise direction
+
     """
     x_size, y_size = shape
     x = np.arange(-x_size // 2, x_size // 2)
@@ -31,5 +32,5 @@ def radial_north(shape):
     return np.rot90(np.fliplr(np.arctan2(yy, xx)+np.pi), k=1)*u.radian
 
 
-ALPHA_FUNCTIONS = {'radial_north': radial_north,
-                   'zeros': np.zeros}
+ALPHA_FUNCTIONS = {"radial_north": radial_north,
+                   "zeros": np.zeros}

solpolpy/constants.py

@@ -1,16 +1,6 @@
-"""Constants used in code"""
+"""Constants used in code."""
 import astropy.units as u
 
-VALID_KINDS = {"mzp": [["Bm", "Bz", "Bp", "alpha"], ["Bm", "Bz", "Bp"]],
-               "bpb": [["B", "pB", "alpha"], ["B", "pB"]],
-               "btbr": [["Bt", "Br", "alpha"], ["Bt", "Br"]],
-               "stokes": [["Bi", "Bq", "Bu"], ["Bi", "Bq", "Bu", "alpha"]],
-               "bp3": [["B", "pB", "pBp", "alpha"], ["B", "pB", "pBp"]],
-               "bthp": [["B", "theta", "p"]],
-               "fourpol": [["B0", "B90", "B45", "B135"]],  # fourpol comes before npol to force it instead of npol
-               "npol": [["B*"]],  # star indicates angle in degrees, as many as desired are supported
-               }
-
 # offset angles come from https://www.sciencedirect.com/science/article/pii/S0019103515003620?via%3Dihub
 STEREOA_OFFSET_ANGLE = 45.8 * u.degree
 STEREOB_OFFSET_ANGLE = -18 * u.degree