CHANGELOG.md

Punctured FEM: Change Log

[2023 Oct 27] v0.3.8

Features

• add TracePlot class
• add MeshPlot class
• add GlobalFunctionPlot class
• add LocalFunctionPlot class
• add get_quad_dict() function
• make edgespaces an optional parameter in LocalFunctionSpace init method

Examples

• examples/ex1d-hat-tile.ipynb: add example of hat tile local basis functions

Tests

• deprecate unittest in favor of pytest
• add test_edge_space
• add test_solver

Maintenance

• use enumerate to replace range(len(...)) loops
• rectify nested min/max statements
• locfun.locfunsp: make interior value calculation optional
• use functools.partial to pass logarithmic terms to integrators
• locfun.poly.poly: use list of tuples for polynomial initialization
• clean up integration methods
• add safety check to add_edge() method in PlanarMesh
• mesh.edgelib.teardrop: pass alpha as keyword argument
• solver.solver:
  • move color printing to separate module
  • move plotting functions to separate module
• add init file for util subpackage
• rename classes to use CapWords convention
• fix invalid names introduced by class renaming
• fix type hints in tests

Bug fixes

• fix colorbar position in contour plots

[2023 Oct 02] v0.3.7-alpha

• change exceptions to specific error types
• document TODO comments in doc/TODO.md
• modify CHANGELOG.md, TODO.md, WISHLIST.md to reflect semantic versioning
  • future versions will use git branches to isolate development
  • git tags and GitHub releases will be used to track versions
  • small commits get a descriptive message
  • branch merges get a release number

[2023 Sep 30] v0.3.6: Rename id variables

• rename id variables to either idx or key to avoid shadowing built-ins

[2023 Sep 30] v0.3.5: Docstrings

• write docstrings
  • modules
  • classes
  • methods
  • functions
• add __init__.py to solver subpackage

[2023 Sep 20] v0.3.4: Type hints and clean up

• use generators where appropriate
• fix imports
• use f-strings
• fix spelling errors
• use enumerate in loops where appropriate
• fix superfluous return statements
• fix unnecessary else statements
• change underscore methods in edgelib to capitalized
  • update edge class to reflect change
  • update ex0 example to reflect change
• add type hints
  • functions
  • methods
  • classes
• fix other pylint and mypy errors
• update pyproject.toml

[2023 Sep 20] v0.3.3: Flake8 config

• rename setup.cgf to .flake8 (until flake8 supports pyproject.toml)
• update devtools/convert_examples.sh to support being executed from any directory

[2023 Sep 19] v0.3.2: PyTest support

• added support for pytest
• added pytest and dependencies to requirements-dev.txt
• added pytest parameters to pyproject.toml

[2023 Sep 19] v0.3.1: Style

• Reformatted with black and isort
• Linted with flake8 and pylint (ongoing)
• Type-checked with mypy (ongoing)
• Added requirements.txt and requirements-dev.txt
• Added CHECKLIST.md
• Added setup.cnf, pyproject.toml

[2023 Aug 07] v0.3.0: Meshes

Major changes

• Added local function spaces (locfunspace) to locfun/
  • Class containing a basis of the local Poisson space $V_p(K)$
• Added edge spaces (edgespace) to locfun/
  • Added support for high order (including $p > 3$, unstable for some edges)
  • Added barycentric coordinates and Legendre polynomials to poly/
  • High order edge spaces obtained by traces of integrated Legendre polynomials
• Overhaul of locfun traces
  • Local function traces are by default considered a list of polynomials, one for each edge
  • This list of polynomials is stored in trace_polys attribute
  • Trace values are computed only as needed
  • Trace values can be set manually as before
  • The flag has_poly_trace can be set to False if working functions with functions that do not have a trace that is the trace of a polynomial on each edge
  • locfun objects are now initialized with the Laplacian polynomial, the list of polynomial traces, and an option
• Overhaul of Nystrom solver
  • Replaced nystrom module with nystrom_solver class
  • Overhead of constructing the Nystrom matrix is now consolidated into the constructor
  • Harmonic conjugate computations are now handled as method of nystrom_solver
• Added vert class
  • Vertices of a mesh
• Overhaul of edge class
  • Added topological properties needed for mesh construction
  • Parameterization values computed and stored only as needed
  • Removed dependence on copy package
  • Added integrate_over_edge method
  • Added global_orientation attribute
• Overhaul of cell class
  • Added topological properties needed for mesh construction
  • Edge list replaced with closed_contour list
• Added PlanarMesh class
  • Initialized as a collection of edge and vert objects
  • cell objects are constructed in situ using topological information from edge objects
• Added solver class
  • Handles all aspects of solving a PDE on a mesh
  • Initialized with a PlanarMesh object and a bilinear_form object
  • solve method solves the PDE on the mesh
  • plot method plots the solution
• Added bilinear_form class
  • Stores info about the PDE to be solved
  • Also stores the right-hand side of the PDE as a polynomial
• Added global_function_space class to manage global function space
• Added global_key class to manage continuity across cells

Minor changes:

• Moved quad module to mesh/ from mesh/quad/
• Added polynomial functionality
  • Added division of a polynomial by a scalar
  • Added powers of polynomials
  • Added polynomial composition
• Changed directory management in Jupyter notebook examples
• Added devtools/ directory
• Added doc/ directory
• Added .py versions of examples
  • Thanks to nbconvert for making this easy!
• Added ex2-pacman-fem example
• Updated tests and examples

[2023 May 01] v0.2.5: API & polynomial overhaul

• Moved examples to a dedicated examples directory
  • Added "Examples used in publications" to README
• Introduced API for more convenient user experience
  • Users call pf.thing rather than pf.foo.bar.baz.thing
  • Updated all examples to reflect API change
  • Restructured puncturedfem directory
• Polynomial overhaul
  • Changed initialization method to something sensible
  • set() method behaves as a re-initializer
  • Added support for polynomial-scalar addition for +,+=,-,-= operators
  • Added support for *= operator
  • Moved integrate_over_cell() method to locfun.int_poly
• Unit tests
  • Relocated test to parent directory
  • Polynomials: test_poly.py
  • Local functions: test_locfun.py

[2023 Apr 17] v0.2.4: Interior values

• Added intval module to locfun for computing interior values
• Added get_conjugable_part() method to locfun that returns the trace of $\psi$
• Renamed is_in_interior() method for contour to is_in_interior_contour()
• Added is_in_interior_cell() method to cell
• Added interior value demo to Punctured Square, Pac-Man, and Ghost examples

[2023 Mar 06] v0.2.3: Pac-Man & Ghost

• Added ex1b-pacman.ipynb
• Added ex1c-ghost.ipynb
• Updated ex1a-square-hole.ipynb with more accurate reference values

[2023 Mar 01] v0.2.2: Anti-Laplacians

• Added compute_h1() and compute_l2() methods to locfun
• Added integrate_over_cell() method to polynomial
• Added methods to contour and cell to integrate over the boundary without multiplying by the norm of the derivative (i.e. 'preweighted' integrands)
• Monomials now default to zero monomial
• Fixed evaluation of zero monomial and zero polynomial to return same size as input
• Removed ext_pt field from cell
• Added id field to contour
• Added get_integrator() method to contour (cell inherits)
• Added neumann module to nystrom for solving Neumann problem
  • Modified harmconj module accordingly
• Completely overhauled anti-Laplacian calculation for punctured cells
• ex1: "Square with circular hole" updated

[2023 Feb 25] v0.2.1: Local functions

• Added /poly subpackage
  • monomial and polynomial objects
• Added locfun/ subpackage
  • locfun object holds all data for local function $v\in V_p(K)$
• Added ext_pt field to cell object, which is an exterior point such that centering the origin at ext_pt placing the cell strictly in the first quadrant

[2023 Feb 16] v0.2.0: Python overhaul

• MATLAB code rewritten in Python to increase accessibility
• Examples presented with Jupyter Notebook
  • ex0-mesh-building: defining edges, cells, and meshes
  • ex1-inner-prod: compute $H^1$ and $L^2$ (semi-)inner products on punctured cell
• New subpackages/modules
  • quad: trapezoid, Kress, and Martensen quadrature objects
  • mesh: mesh construction tools
    • edge: parameterization of an edge
    • contour: collection of edges forming a simple closed contour
    • cell: mesh cell (subclass of contour)
  • plot: functions for
    • plot edges, contours, cell boundaries
    • trace of a function along a collection of edges
  • nystrom: Nystr$\text{"o}$m method for solving integral equations
    • includes single and double layer operators
    • block system support
  • d2n: Dirichlet-to-Neumann map for harmonic functions
    • computation of harmonic conjugate
    • FFT (anti-)derivatives
  • antilap: tools to compute anti-Laplacians of harmonic functions
• Added unit tests to puncturedfem/test/
  • test_harmconj for harmonic conjugates
  • test_fft_deriv for FFT differentiation

[2022 Aug 02] v0.1.0: Initial commit

Only a simple diffusion operator (the Laplacian) is currently supported. Dirichlet and mixed Dirichlet-Neumann boundary conditions are available, but are assumed to be homogeneous. Used to run a simple "pegboard" example.