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CHANGELOG.md

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Unreleased

Added

Changed

Fixed

Removed

0.0.7

Added

  • time_residuals, scaled_toa_uncertainties, and model_dm, from_pint methods in SPNTA
  • NE_SW derivatives in SolarWind
  • Pulsar class
  • pyvela script
  • get_free_param_units function
  • "Known issues" page in documentation
  • DMX: Piecewise-constant model for DM (DispersionPiecewise)
  • CMX: Piecewise-constant model for CM (ChromaticPiecewise)
  • BinaryELL1k model

Changed

  • Reduced the number of pyvela tests

Fixed

  • DMX and CMX cannot be used alongside other stochastic DM variation models

Removed

  • test_alloc and test_likelihood from test_data_files.py
  • Unnecessary test & example data files

0.0.6

Added

  • pyvela.SPNTA class
  • get_unit_conversion_factor function
  • prior_scaling methods and scale_prior_args function

Changed

  • Reorganized pyvela code
  • Rerun failures in pyvela CI tests.
  • Example scripts now use pyvela.SPNTA
  • Updated documentation to use pyvela.SPNTA and installation instructions
  • Made the repository public and deployed the documentation website.
  • Migrated Python package settings from setup.py to pyproject.toml
  • Migrated from Codecov to Coveralls for code coverage
  • Prior JSON files now accept parameters in "normal" units.
  • SPNTA constructor now accepts "raw" prior dictionaries similar to the prior files rather than those containing actual Distribution objects.
  • Renamed parse_custom_prior_file to process_custom_priors
  • Renamed read_model_and_toas to convert_model_and_toas
  • Updated lowest versions for Python dependencies

Fixed

  • Memory allocation in GP components

Removed

  • Some unnecessary test datasets
  • Installation instructions from README file

[0.0.5]

Added

  • Check for ECORR exclusivity
  • Vectorize option in get_lnpost_func
  • GP noise models - PowerlawRedNoiseGP, PowerlawDispersionNoiseGP, PowerlawChromaticNoiseGP
  • Examples - sim3.gp, sim4.gp, sim6.gp
  • Detailed documentation
  • Abstract base classes RedNoiseBase, DispersionNoiseBase, ChromaticNoiseBase, FrequencyDependentBase

Changed

  • Renamed pint2vela -> pyvela
  • Infer is_tzr(toa) from toa.index
  • Infer is_barycentered(toa) from toa.ephem.ssb_obs_pos
  • Renamed CorrectedTOA, CorrectedWidebandTOA, and CorrectedDMInfo respectively to TOACorrection, WidebandTOACorrection, and DMInfoCorrection
  • Removed the TOA from TOACorrection (it's passed separately to functions). This reduces copy overhead.
  • Avoid unnecessary repeated computations in Spindown
  • Specialized methods of taylor_horner and taylor_horner_integral for faster execution
  • Split correct_toa into more specialized methods correct_toa_delay, correct_toa_phase, and correct_toa_error
  • Multiplication instead of power in dispersion delay
  • Subtract PEPOCH from all TOA and MJDParameter values; add epoch attribute to TimingModel
  • Moved basis_dot to jump.jl
  • Better priors for KOM, SINI, KIN, STIGMA, SHAPMAX, EFAC, etc.

Fixed

  • Unnecessary repetition of sin and cos in ecliptic coordinate conversion
  • Bug in _ecorr_lnlike_group

Removed

  • level attribute from TOACorrection
  • obs_earth_pos from SolarSystemEphemeris

[0.0.4]

Added

  • Doppler factor in BinaryELL1
  • BinaryDD, BinaryDDH, BinaryDDS, BinaryELL1H, and BinaryDDK models
  • Doppler factor in BinaryDD
  • get_free_param_labels() function
  • Examples - J0613-0200.sim, J1856-3754.sim, J1802-2124.sim, J0955-6150.sim, J1208-5936.sim, J2302+4442.sim, J1227-6208.sim, sim6, sim_dd, sim_ddk, sim_sw.wb, sim_dmjump, sim_dmwn, sim2, sim_glitch
  • Test Python formatting using black
  • Use BinaryDD for par files with the BT model.
  • Basic wideband timing implementation
    • TOABase as the base type for TOA and WidebandTOA
    • WidebandTOA as the composition of TOA and DMInfo. The latter contains DM measurement and error.
    • CorrectedTOABase as the base type for CorrectedTOA and CorrectedWidebandTOA
    • CorrectedWidebandTOA as the composition of CorrectedTOA and CorrectedDMInfo. The latter contains model DM and DM error.
    • Methods of correct_toa(), form_residual(), calc_chi2(), calc_lnlike(), and calc_lnpost() that act on WidebandTOAs and relatives.
    • load_pulsar_data() and save_pulsar_data() now work with wideband TOAs
    • pint2vela can now read wideband TOAs.
  • degrees_of_freedom() and reduced_chi2() functions
  • Wideband DM offsets (DMJUMPs)
  • DispersionMeasurementNoise component (DMEFACs and DMEQUADs) for wideband data
  • ECORR implementation
    • Kernel as the abstract base class for all likelihood kernels; added the kernel member in TimingModel.
    • WhiteNoiseKernel marks white noise-only likelihood computation.
    • EcorrKernel marks likelihood computation with only white noise and ECORR.
    • Methods of calc_chi2 and calc_lnlike specialized for WhiteNoiseKernel and EcorrKernel
    • ecorr_sort function in pint2vela
    • get_kernel function in pint2vela that constructs Kernels based on the PINT TimingModel object
  • Glitch component
  • FrequencyDependentJump component (FDJUMPs)
  • Documentation - Getting Started and Explanation pages

Changed

  • Exposed cheat_prior_scale and custom_prior_dists options in read_model_and_toas()
  • Made changes according to the GeometricUnits API changes (GQ now represents dimensions as a type parameter)
  • Use the github version of PINT for testing
  • Split test_components.jl into multiple files.
  • Simplify the type hierarchy of Components. Now all Components are TOA-uncorrelated by definition.

Fixed

  • Tests now handle par files without PHOFF properly.
  • Proper motion computation
  • Default of CorrectedTOA.spin_frequency
  • Shapiro delay expression for BinaryDDBase
  • True anomaly computation in DDState
  • Scale factor computation in get_default_prior()
  • Bug in correct_toa() (ssb_psr_pos was being set incorrectly)
  • black failure now shows up as a CI failure.
  • Handling of prefixParameters with Time quantities
  • Don't apply MeasurementNoise to TZR TOAs

Removed

[0.0.3] - 2024-08-22

Added

  • load_pulsar_data() and save_pulsar_data() functions
  • par_tim_to_jlso() function and par_tim-to-jlso script in pint2vela
  • Prior as the abstract base class for prior distributions
  • SimplePriorBase, SimplePrior and SimplePriorMulti to represent priors that can be factorized parameter-wise.
  • distr(), lnprior() and prior_transform() functions.
  • get_lnprior_func() and get_prior_transform_func() functions.
  • get_default_priors() function in pint2vela
  • More methods for get_free_param_names(), read_param_values_to_vector(), and get_scale_factors() for convenience
  • Added CI tests for pint2vela
  • An alternative implementation of PhaseJump for mutually exclusive JUMPs
  • basis_dot function
  • Simple solar wind model (Edwards+ 2006) (SolarWind)
  • Variable-index chromatic delay as a Taylor expansion (ChromaticTaylor)
  • Auto-generation of HTML documentation using Documenter
  • docs-CI tests
  • Examples - sim1, sim_jump, sim_jump_ex, sim_fdjumpdm, sim_sw, sim_cm, sim_fd, J0613-0200.InPTA.NB, J1857+0943.InPTA.NB
  • Tests corresponding to the example datasets
  • System-dependent DM offsets (DispersionOffset)
  • compare_residuals.py script in examples.
  • Codecov upload for pint2vela
  • Fourier series representation of achromatic red noise (WaveX), DM noise (DMWaveX), and chromatic noise (ChromaticCM)
  • get_lnpost_func function
  • Frequency-dependent profile variability corrections (FrequencyDependent)
  • Memory allocation tests for all components in test_components.jl
  • mean_anomaly and mean_motion functions
  • BinaryELL1 model
  • Memory allocation tests in the pint2vela test suite.

Changed

  • Reorganized source files into subdirectories
  • Replaced par and tim files for testing with JLSO files
  • Moved pint2vela.py to separate repo, added it as a submodule.
  • Rearranged pint2vela code into multiple files.
  • Merged pint2vela into the main repo.
  • Replaced pint2vela test datasets with symlinks.
  • Updated README.md
  • Moved setup.py from Vela.jl/pint2vela to Vela.jl

Fixed

  • show method for MeasurementNoise
  • Copy the toas inside get_lnlike_parallel_func, get_lnlike_serial_func, get_chi2_serial_func, and get_chi2_parallel_func to avoid repeated allocations.

Removed

  • read_model_and_toas() function. Data is now read from JLSO files created using pint2vela
  • plot_summary() function. (This is better done in Python.)
  • Tests using PyArray (This speeds up the test suite)
  • Support for Julia 1.9

[0.0.2] - 2024-07-24

Added

  • CHANGELOG file
  • Environment variables for safe Python interoperability in the README file
  • index field in TOA
  • MeasurementNoise component (EFACs and EQUADs)
  • get_scale_factors() function.
  • Assertion in read_params to make sure that the input has the correct number of values.
  • PhaseJump component (JUMPs)

Changed

  • Split F0 into two Float64 variables (F_ & F0) to preserve precision
  • Use DoubleFloats instead of Quadmath to represent TOA values (it's faster)
  • Rearrange code and tests into multiple files
  • Rearrange test data files
  • Use @spawn and fetch instead of atomic operations for parallel chi2 and likelihood.
  • Move chi2 functions into a separate file chi2.jl
  • Move the higher order functions in pyinter.jl to chi2.jl and likelihood.jl
  • Updated README to use pint2vela

Fixed

Removed

[0.0.1] - 2024-07-10

Added

  • TimingModel to represent the timing & noise model
  • Hierarchy of Component types
  • SolarSystem component (solar system delays)
  • DispersionTaylor component (interstellar dispersion as a Taylor series)
  • Spindown component (pulsar spindown as a Taylor series)
  • PhaseOffset component (overall phase offset between physical TOAs and the TZR TOA)
  • TimingModel to represent the timing & noise model
  • TOA type to represent narrowband TOAs
  • CorrectedTOA type to represent accumulated corrections to a TOA.
  • SolarSystemEphemeris type to store solar system ephemerides
  • ParamHandler class and its friends to convert parameter vectors to named tuples
  • correct_toa() function
  • Parallel and serial versions of the chi2 and lnlike functions
  • read_model_and_toas() to read data from HDF5 files (created using pint2vela.py)
  • pure_rotator and NGC6440E examples
  • GitHub Actions for CI Tests and CodeCov upload
  • Basic README file
  • MIT Licence

Changed

Fixed

Removed