Puncturedfem

Maintenance
- [x] change dependency: Python 3.9 (was 3.11)
- [x] change dependency: `scipy` 1.12 (was 1.11)
- [x] change: use `rtol` keyword argument in `scipy.sparse.linalg.gmres` to `tol`
- [x] fix: missing type annotations for tests
- [x] fix: use `Union` for type hints rather than ` | ` operator (to support Python 3.9)

Documentation
- [x] change: `README.md`
- [x] add: installation instructions with `pip`
- [x] add: usage instructions via `readthedocs` link
- [x] change: consolidate `TODO.md` and `WISHLIST.md` into `ROADMAP.md`
- [x] add: documentation with MkDocs
- [x] add: `.readthedocs.yml` for ReadTheDocs configuration
- [x] add: `mkdocs.yml` for MkDocs configuration
- [x] add: `doc/requirements.txt` for MkDocs dependencies
- [x] add: `doc/index.md` for home page
- [x] add: quickstart guide
- [x] add: installation instructions
- [x] add: user guide
- [x] mesh:
- [x] `Edge` class
- [x] `ClosedContour` class
- [x] `MeshCell` class
- [x] `PlanarMesh` class
- [x] `Quad` class
- [x] `QuadDict` class
- [x] `Vert` class
- [x] `get_quad_dict()` function
- [x] `meshlib` module
- [x] `mesh_builder` function
- [x] `split_edge` function
- [x] local function spaces:
- [x] `Polynomial` class
- [x] `DirichletTrace` class
- [x] `NystromSolver` class
- [x] `LocalFunction` class
- [x] `LocalFunctionSpace` class
- [x] FEM solver:
- [x] `BilinearForm` class
- [x] `GlobalFunctionSpace` class
- [x] `Solver` class
- [x] plotting:
- [x] `GlobalFunctionPlot` class
- [x] `LocalFunctionPlot` class
- [x] `MeshPlot` class
- [x] `TracePlot` class
- [x] add: developer guide
- [x] roadmap
- [x] contributing guide
- [x] changelog
Package Management
- [x] add: `poetry` configuration for package management
- [x] change: `pyproject.toml` to use `poetry`
- [x] add: `poetry.lock`

Examples
- [x] modify: `ex1a` to use `DirichletTrace`
- [x] modify: `ex1e` to use `DirichletTrace`
- [x] rename: `ex0` to `ex0a`
- [x] add: `ex0b` to demonstrate how to construct a `LocalFunction` with a `DirichletTrace`
Features
- [x] add: `DirichletTrace` class for handling the traces of `LocalFunction`s
- construct an arbitrary trace, or a polynomial trace in the style of `LocalFunctionSpace`
- will someday replace the default handling of traces in `LocalFunction` class
- [x] modify: `Polynomial` objects are now callable
- [x] add: splitting an edge into multiple edges without recursive subdivision
- [x] add: optional argument to `TracePlot` initializer to specify the maximum number of ticks on the horizontal axis
Maintenance
- [x] add: debug option to `NystromSolver` to show condition number
- [x] preconditioning for `NystromSolver`
- [x] use `numba` to speed up `NystromSolver` matrix assembly with just-in-time compilation
- [x] pass `DirichletTrace` object to the `TracePlot` constructor
Bug fixes
- [x] fix: too many tick marks on `TracePlot`

Documentation
- [x] add a contributing guide
Features
- [x] make minimum distance to boundary for interior points of a `MeshCell` adjustable with `set_interior_point_tolerance()` method
- [x] make computation of interior gradients optional
- [x] add methods to `MeshCell` to get unit tangent and unit normal vectors, and the derivative norm
Maintenance
- [x] vectorize interior value computation
Tests
- [x] add ghost cell to mesh cell testing library
- [x] add test for interior points
Bug Fixes
- [x] Plots of global solution corrupted: fix by not recording edge flips to transformation diary

Examples
- [x] add cubic spline interpolation example to `ex0`
Maintenance
- [x] remove trigonometric interpolation
- [x] remove trigonometric interpolation tests
- [x] format `edgelib/spline`

Documentation
- [x] update README, extend description, add references
Features
- [x] add ability to define an edge parameterization using a cubic spline to interpolate points (thanks, Zack!)
- [x] add edge splitting
- [x] add transformation diary to `Edge` class
- [x] add global stiffness and mass matrices to `solver` class
- [x] add option to turn off axes in plots
- [x] add colormap option to contour plot methods
- [x] add trigonometric interpolation for cell boundary traces
Examples
- [x] add space-filling curve example (thanks, Zack!)
- [x] add `ex1e` to demonstrate heavy sampling of edges via edge splitting
Maintenance
- [x] make colorbar optional for `GlobalFunctionPlot` draw method
- [x] make coefficients optional in `GlobalFunctionPlot` init method
- [x] add warning for `Quad` class when `n > 128 * interp`
- [x] use kwargs for plotting options
- [x] add `PiecewisePolynomial` class to init file
- [x] create `QuadDict` object to standardize quadrature collections
Tests
- [x] add test for trigonometric interpolation
Bug Fixes
- [x] close figure in `draw` methods for plotting classes
- [x] fix `show_plot=False` option not working in `draw` methods for plotting classes
- [x] make directory to save plots if it doesn't exist
- [x] fix `LocalFunctionPlot` saving blank files
- [x] fix Martensen quadrature for large values of n
- [x] raise exception when Nystrom solver encounters non-numeric values