Tags: Team-RADDISH/ParticleDA.jl
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[Diff since v1.1.0](v1.1.0...v1.2.0) **Merged pull requests:** - CompatHelper: add new compat entry for ChunkSplitters at version 2 for package test, (keep existing compat) (#272) (@github-actions[bot]) - CompatHelper: add new compat entry for Statistics at version 1 for package docs, (keep existing compat) (#278) (@github-actions[bot]) - CompatHelper: add new compat entry for DelimitedFiles at version 1 for package docs, (keep existing compat) (#279) (@github-actions[bot]) - CompatHelper: bump compat for Documenter to 1 for package docs (#280) (@github-actions[bot]) - CompatHelper: add new compat entry for PDMats at version 0.11 for package docs, (keep existing compat) (#281) (@github-actions[bot]) - Bump julia-actions/setup-julia from 1 to 2 (#282) (@dependabot[bot]) - Bump julia-actions/cache from 1 to 2 (#283) (@dependabot[bot]) - Update ChunkSplitters.jl to v3 (#284) (@giordano) - [CI] Fix version of `julia-actions/julia-docdeploy` workflow (#285) (@giordano) - Solve some deprecation warnings (#286) (@giordano) - Register custom MPI operator for aarch64 (#287) (@giordano) - Update benchmarks environment to Julia v1.10 (#288) (@giordano) - [docs] Add `sources` section to `Project.toml` (#289) (@giordano) **Closed issues:** - Add missing docstrings to documentation (#268)
[Diff since v1.0.1](v1.0.1...v1.1.0) **Merged pull requests:** - Update `GaussianRandomFields` version and add additional tests for linear Gaussian models (#244) (@matt-graham) - fix: Replacing Threads.@threads :static (#247) (@DanGiles) - Bump to version 1.1.0 (#254) (@matt-graham) - Remove explicit dependency on `SciMLBase` (#256) (@giordano) - Allow `HDF.jl` v0.17 (#258) (@giordano) - Reduce LLW2d model mesh dimensions + number of samples for test (#259) (@matt-graham) - [CI] Add dependabot, use newer workflows, use concurrency groups (#260) (@giordano) - Bump codecov/codecov-action from 3 to 4 (#261) (@dependabot[bot]) - Bump actions/checkout from 3 to 4 (#262) (@dependabot[bot]) - Ignore result of runs with nightly builds in CI job status (#263) (@matt-graham) - Add extra links to README and improve description (#264) (@matt-graham) - Run different CI jobs only when relevant files are touched (#266) (@giordano) - Add compat bound for `ChunkSplitters` (#267) (@giordano) **Closed issues:** - Update `GaussianRandomFields` version in test dependencies (#243) - Replace the use of `Threads.@threads :static` (#246) - Request for code for Lorenz63 plot in paper (#250) - Adjust number of samples and/or mesh dimension for optimal proposal unit tests with llw2d model (#257) - Rename default branch to `main` (#265)
**Closed issues:** - Implement particle filter (#2) - Parameters shouldn't be hard-coded in the module (#4) - Add noise to the model (#6) - Add distributed parallelism (#7) - Create test/Project.toml (#14) - Initial condition in llw2d is obscure (#15) - Add noise to the observations (#17) - Add some documentation (#18) - Add plotting function(s) (#19) - Rename the package (#23) - Change output format (#26) - Benchmark suite (#34) - Slow performance in Process Noise (#35) - Timeseries outputs, ESS (#36) - Don't get observations when PF is not called (#40) - Redefine time stepping (#44) - Redefine grid parameters (#45) - Add variance to output (#46) - Possible memory allocations improvements (#53) - Represent states with structs (#58) - Add integration test that tests particles (#62) - Names bikeshedding (#64) - New Initial State of Particles (#67) - Error when changing nx, ny (#74) - Simplify station setup (#75) - Observations should be independent (#76) - Plot to show estimated *Standard Deviation* instead of *Variance* (#81) - Extra Plot to check effect of Background Noise (#82) - Parellelisation (#83) - Add station coordinates to output (#84) - Provide station coordinates in an input file (#86) - Consistency at colouring at plots of "true height" and "assimilated height" (#92) - jupyter notebook for plotting (#96) - Parallelise resampling (#97) - Provide plot for initial condition of (the two) true Velocity Fields (not only of initial Height Field) (#101) - add_random_field is not thread-safe after #94 (#105) - Discontinuities in variance and mean (#108) - Parallel performance (#115) - Thread Scaling (#117) - Separate particle filter from the model (#124) - Parametrize initial condition in llw2d properly (#134) - Optimal particle filter (#136) - Different Background Noise Parameters for Each of Three State Variables (#175) - Plotting tool in Julia (#182) - Add SPEEDY climate model (#199) - Precompiling ParticleDA Error (#202) - Role of `weight_std` parameter not clear (#205) - Generalise update_particle_proposal! (#208) - OptimalFilter BoundsError when running with mpiexecjl (#209) - Covariance function assumed in optimal proposal not guaranteed to match that used for process noise (#213) - Fix TODO about covariance in comment (#214) - Generalising the optimal proposal implementation (#215) - Allow returning particles as well summary statistics and at multiple time steps (#220) - Simplify interface for doing reproducible runs when using MPI (#221) - Optimal proposal filter not using correct weights (#223) - Observations currently generated within filtering loop (#224) - Adding test cases for analytically tractable models (#225) - Inconsistent conventions around spatial grid coordinates in LLW2d model (#229) - Optimal proposal particle weights are being computed incorrectly (#230) - Summary statistics computed on every time step when not outputted (#231) **Merged pull requests:** - Particle filter (#1) (@tkoskela) - Add keyword argument to `tdac` to enable/disable verbosity (#3) (@giordano) - Refactor parameters (#5) (@tkoskela) - Add instructions on how to install the package in the README (#8) (@giordano) - Fix copyright of the package in the LICENSE file (#9) (@giordano) - Add GitHub Actions script for CI (#10) (@giordano) - MPI Parallelisation (#11) (@tkoskela) - Bug fix, initheight was called on the wrong state array (#12) (@tkoskela) - First integration test (#13) (@tkoskela) - Remove now unused submodule (#16) (@giordano) - Update README.md (#20) (@tkoskela) - Jupyter notebook for plotting output files (#21) (@tkoskela) - Fix link in README.md (#22) (@tkoskela) - Add gaussian random noise (#25) (@tkoskela) - [skip ci] Do not fail fast in GitHub Actions (#27) (@giordano) - Run tests with 1 and 2 threads (#28) (@giordano) - Update `GaussianRandomFields` and fix lower/upper bounds for deps (#29) (@giordano) - [skip ci] Add CompatHelper (#30) (@giordano) - Clean up function argument lists (#31) (@tkoskela) - Move output into HDF5 file (#32) (@tkoskela) - CompatHelper: bump compat for "Distributions" to "0.23" (#33) (@github-actions[bot]) - Do not run `MPI.Finalize()` (#37) (@giordano) - Add new get_params - function where user can pass dict of parameters (#38) (@tkoskela) - Generate Gaussian random field with `primes=true` (#39) (@giordano) - Do process noise and observations only when DA is done (#41) (@tkoskela) - Read default parameters using multiple dispatch (#42) (@tkoskela) - Define a custom type for the random field (#43) (@giordano) - Update structure of the time stepping loop (#47) (@tkoskela) - Set total domain size and derive cell size from it (#48) (@tkoskela) - Add variance to output, collect arrays in structs (#49) (@tkoskela) - Introduce timers with the `@timeit_debug` macro (#50) (@tkoskela) - Fix timer on first run, add print on screen (#51) (@tkoskela) - Use `params.verbose` to check verbosity setting (#52) (@giordano) - Remove dependency on Distributed (#54) (@tkoskela) - Use multi-dimensional arrays to represent states (#55) (@giordano) - CompatHelper: add new compat entry for "TimerOutputs" at version "0.5" (#56) (@github-actions[bot]) - Preallocate the buffer for tsunami update (#57) (@giordano) - Disable FFTW threads in tests (#59) (@giordano) - Use preallocated buffer in add_random_field (#60) (@tkoskela) - Use a buffer array to generate the random numbers in gaussian field (#63) (@giordano) - Move initialisation of the field buffer to `init_tdac` (#65) (@giordano) - Fix distribution of random numbers for the Gaussian random field (#66) (@giordano) - Update particle initial state (#68) (@tkoskela) - Add colorbars to contourf plots (#69) (@tkoskela) - Mean and Var need to be calculated for IO after initial state (#70) (@tkoskela) - Add particle weights to output + plotting (#71) (@tkoskela) - Add missing argument from list (#72) (@tkoskela) - Make output of MPI test visible (#73) (@giordano) - Fix issue of non-default parameters not getting passed to init_gaussian_random_field_generator (#77) (@tkoskela) - Add test for different grid and time step size (#78) (@tkoskela) - Update to weight and observation noise calculation (#79) (@tkoskela) - Modify to plot standard deviation instead of variance (#85) (@tkoskela) - Update README.md (#87) (@tkoskela) - Fix x-axis in ESS plot to start from 1 (#88) (@tkoskela) - Upgrades to stations (#89) (@tkoskela) - Update README.md (#90) (@tkoskela) - Add threads to process noise (#91) (@tkoskela) - Enforce same color scale in true and avg height plots. Fix unit of var (#93) (@tkoskela) - Define a thread-safe RNG (#94) (@giordano) - Separate copying of state vectors from resampling. (#95) (@tkoskela) - Use in-place version of `var` (#98) (@giordano) - Get rid of unnecessary flattening and reshaping (#99) (@tkoskela) - Use allocation-free `var` everywhere (#100) (@giordano) - Revert state split (#102) (@tkoskela) - Add options for particle initial state (#103) (@tkoskela) - Add tests for particle state (#104) (@tkoskela) - Write velocity fields to output and plot them (#106) (@tkoskela) - Move IO functions to separate file (#107) (@tkoskela) - CompatHelper: bump compat for "MPI" to "0.15" (#109) (@github-actions[bot]) - Move hard-coded parameters from llw2d.jl to parameters.jl and Fix boundary calculation (#110) (@tkoskela) - Parallel resampling (#111) (@tkoskela) - Pack all model matrices in a single struct (#112) (@giordano) - Implementation of custom MPI reduction for mean and variance (#113) (@tkoskela) - Add scripts to run scaling tests on CSD3 and notebook to plot results (#114) (@tkoskela) - Rename functions for readability (#119) (@tkoskela) - Simplify initheight (#120) (@tkoskela) - Update README.md (#121) (@tkoskela) - Do not force FFTW threads to 1 (#122) (@giordano) - Rename `TDAC.jl` -> `ParticleDA.jl` (#123) (@giordano) - Add disclaimer to README (#125) (@tkoskela) - Run CI on more versions of Julia (#126) (@giordano) - Add benchmarks (#127) (@tkoskela) - Separate model from particle filter (#128) (@giordano) - CompatHelper: bump compat for "Distributions" to "0.24" (#129) (@github-actions[bot]) - Fix settings for deployment of documentation (#130) (@giordano) - CompatHelper: bump compat for "MPI" to "0.16" (#131) (@github-actions[bot]) - CompatHelper: bump compat for "HDF5" to "0.14" (#132) (@github-actions[bot]) - Implement optimal particle filter from Alex (#133) (@tkoskela) - Add SSH key to CompatHelper (#135) (@giordano) - Update README.md (#137) (@tkoskela) - Refactor llw2d.initheight (#138) (@tkoskela) - Remove observation noise from model observations (#139) (@tkoskela) - Add new filter type argument for dispatch (#140) (@giordano) - CompatHelper: bump compat for "HDF5" to "0.15" (#141) (@github-actions[bot]) - Move filter initialisations into a function and group arrays into a struct. (#142) (@tkoskela) - Update documentation to mention new argument to `run_particle_filter` (#143) (@giordano) - Change initial value of bathymetry, pointed out by Devaraj (#144) (@giordano) - Update model interface for optimal filter (#145) (@tkoskela) - Add two new functions to implement in the model (#146) (@giordano) - Slightly simplify test project file (#147) (@giordano) - Fix bug in update_reference_data.jl (#148) (@tkoskela) - Restore compat bounds for test dependencies (#149) (@github-actions[bot]) - Add GitHub Action workflow to run benchmarks on CI for pull requests (#153) (@giordano) - Add more benchmarks (#154) (@giordano) - Pass filter type to run_particle_filter and use it to dispatch (#155) (@tkoskela) - Increase required Julia version to v1.5 (#156) (@giordano) - Split get_grid_size into three functions (#157) (@tkoskela) - More generic initialisation of boostrap filter (#158) (@giordano) - Precompute FFTW plan (#159) (@giordano) - Add integration test with optimal filter (#160) (@tkoskela) - Remove duplicate definition of `nprt_per_rank` (#161) (@giordano) - Reduce allocations in `sample_height_proposal!` (#162) (@giordano) - Dump particle states to file upon request (#163) (@tkoskela) - Include docstring of `Model.ModelParameters` in documentation (#164) (@giordano) - Fix `s in docstring (#166) (@tkoskela) - Add metadata to StateVectors with FieldMetadata.jl. (#167) (@tkoskela) - CompatHelper: bump compat for "MPI" to "0.17" (#168) (@github-actions[bot]) - CompatHelper: bump compat for "MPI" to "0.17" for package test (#169) (@github-actions[bot]) - CompatHelper: bump compat for "MPI" to "0.17" for package benchmark (#170) (@github-actions[bot]) - CompatHelper: add new compat entry for "Distributions" at version "0.24" for package benchmark (#171) (@github-actions[bot]) - CompatHelper: bump compat for "BenchmarkTools" to "0.7" for package benchmark (#172) (@github-actions[bot]) - CompatHelper: add new compat entry for "HDF5" at version "0.15" for package benchmark (#173) (@github-actions[bot]) - CompatHelper: bump compat for "MPI" to "0.17" for package docs (#174) (@github-actions[bot]) - Support different noise parameters for each state variable (#176) (@tkoskela) - Remove `ParticleDA` from test project (#177) (@giordano) - CompatHelper: bump compat for "Distributions" to "0.25" (#178) (@github-actions[bot]) - CompatHelper: bump compat for "Distributions" to "0.25" for package test (#179) (@github-actions[bot]) - CompatHelper: bump compat for "Distributions" to "0.25" for package benchmark (#180) (@github-actions[bot]) - CompatHelper: bump compat for "Distributions" to "0.25" for package docs (#181) (@github-actions[bot]) - Add Julia plotting notebook (#183) (@giordano) - Fix docstring of `get_model_noise_params` (#184) (@giordano) - CompatHelper: bump compat for "BenchmarkTools" to "1.0" for package benchmark (#185) (@github-actions[bot]) - Remove redundant call to `get_particles` (#186) (@giordano) - Update uninformative parameter description and add two missing ones (#187) (@tkoskela) - Add Pluto notebook to explore the output data (#189) (@giordano) - Pad time stamps in output file with up to 3 zeros (#190) (@tkoskela) - Pad times also when writing the weights (#191) (@giordano) - CompatHelper: bump compat for "Documenter" to "0.27" for package docs (#196) (@github-actions[bot]) - Update to `MPI.jl` v0.19 (#197) (@giordano) - Reorganise how timer strings to be saved in HDF5 are created (#200) (@giordano) - Generalise some dimensions in bootstrap filter (#201) (@giordano) - Add input files to repository (#206) (@tkoskela) - Use correct number of particles in Optimal Filter and add MPI test (#210) (@tkoskela) - Propagate number of threads when running MPI tests (#211) (@giordano) - Move threads flags to `flags` variable in MPI tests (#212) (@giordano) - Use `GaussianRandomFields` to calculate optimal proposal covariance (#216) (@matt-graham) - Update to `HDF5.jl` v0.16 (#217) (@giordano) - Generalising the optimal proposal implementation (#218) (@DanGiles) - Require Julia v1.7 and use new task-local RNG (#219) (@giordano) - Collect code coverage and add badges to README file (#222) (@giordano) - Refactor: using flat vector states and decoupling states from model (#232) (@matt-graham) - Run MPI tests with `Base.julia_cmd` instead of `Base.julia_exename` (#234) (@giordano) - Upgrade to `MPI.jl` 0.20 (#235) (@giordano) - Remove useless dependency on `DifferentialEquations` (#236) (@giordano) - Add linear Gaussian model type + validation notebook (#237) (@matt-graham) - Bump version number to v1.0.0 (#238) (@giordano)