Puncturedfem

Examples

- [x] remove import management boilerplate from examples
- [x] change example naming convention
- [x] partition examples into tutorials and examples
- [x] tutorials belong to the user guide in `doc/tutorials/`: describe basic functionality
- [x] examples belong to the `examples/` directory: examples used (or will be used) in papers, advanced functionality, applications
- [x] update examples to use new initialization method for `LocalFunction` objects
- [x] update spacefilling curve example

Documentation

- [x] change: installation instructions for developers to build the package locally with `pip install -e .`
- [x] add: tutorials
- [x] change: update docstrings to use NumPy documentation format
- [x] `locfun`
- [x] `mesh` (except for `edgelib`)
- [x] `plot`
- [x] `solver`
- [x] `util`
- [x] change: MkDocs theme to `material`
- [x] add: site logo
- [x] update `doc/logo/pacman.svg`
- [x] tutorials
- [x] Guide to tutorials
- [x] 1: Meshes
- [x] 1.1: Vertices and edges (taken from Example 0.1)
- [x] 1.2: Mesh cells and planar meshes (taken from Example 0.1)
- [x] 2: Local function spaces
- [x] 2.1: Polynomials (template)
- [x] 2.2: Traces (taken from Example 0.2)
- [x] 2.3: Local Poisson functions (template)
- [x] 2.4: Local Poisson spaces (template)
- [x] 3: Finite elements
- [x] 3.1 Global function spaces (simpler version of Example 2.1)
- [x] 3.2 Global boundary conditions (template)
- [x] 4: Advanced topics
- [x] 4.1 Nystrom solvers (template)
- [x] 4.2 Heavy sampling of edges (taken from Example 1.5)
- [x] run tutorial notebooks when building documentation
- [x] link to notebook source on tutorial pages
- [x] link to tutorial pages from README

Maintenance

- [x] `DirichletTrace` improvements:
- [x] add: weighted normal derivative
- [x] add: weighted tangential derivative
- [x] `LocalFunction` improvements:
- [x] BREAKING CHANGE: replace the handling of traces with `DirichletTrace`
- [x] DEPRECATED: use `LocalPoissonFunction` instead
- [x] add: `LocalPoissonFunction` class, built from `LocalHarmonic` and `LocalPolynomial` objects
- [x] add: arithmetic operations (addition, subtraction, scalar multiplication, scalar division) for `LocalHarmonic`, `LocalPolynomial`, and `LocalPoissonFunction` objects
- [x] `NystromSolver` improvements:
- [x] handle logarithmic functions as instances of `DirichletTrace` class
- [x] `antilap_strategy` option to precompute "normal indicator functions" biharmonic function computation speedup
- [x] compute diagonal of Nystrom matrix directly for preconditioning
- [x] `locfun` module improvements:
- [x] use `DirichletTrace` objects for traces in `antilap` module
- [x] move contents of `antilap` and `d2n` subpackages to `locfun` root
- [x] remove `log_terms` and `log_antilap` modules
- [x] deprecate `PiecewisePolynomial` class
- [x] `Polynomial` improvements:
- [x] deprecate `eval()` method, use `__call__()` method instead
- [x] `LocalFunctionPlot` improvements:
- [x] change: don't store points and values outside of the cell
- [x] interior value interpolation for points close to the boundary
- [x] consolidate the multiple draw methods into one, optional argument to specify what to draw (values, gradient, etc.)
- [x] move generation of interior point triangulation to `MeshCell`
- [x] `GlobalFunctionPlot` improvements:
- [x] stich together `LocalFunctionPlot` objects to plot a global function
- [ ] use computation of H1 error in `Solver` tests

Project Management

- [x] change dev dependency: `black` to `black[jupyter]`
- [x] add dev dependency: `nbconvert``main`

Bug Fixes

- [x] fix: missing logo and favicon in MkDocs build
- [x] fix: broken links in tutorials
- [x] fix: blank images saved by `LocalFunctionPlot` class
- [x] fix: edges on boundary of `MeshCell` being deleted from interior point triangulation

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`