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njtierney committed Nov 6, 2024
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Expand Up @@ -28,51 +28,65 @@ The following optimisers are removed, as they are no longer supported by Tensorf

## Installation revamp

This release provides a few improvements to installation in greta. It should now provide more information about installation progress, and be more robust. The intention is, it should _just work_, and if it doesn't fail gracefully with some useful advice on problem solving.
This release provides a few improvements to installation in greta. It should now provide more information about installation progress, and be more robust. The intention is, it should _just work_, and if it doesn't, it should fail gracefully with some useful advice on problem solving.

* Added option to restart R + run `library(greta)` after installation (#523)
* Added installation deps object, `greta_deps_sepc()` to help simplify specifying package versions (#664)
* removed `method` and `conda` arguments from `install_greta_deps()` as they
* Added option to restart R + run `library(greta)` after installation (#523).
* Added installation deps object, `greta_deps_sepc()` to help simplify specifying package versions (#664).
* Removed `method` and `conda` arguments from `install_greta_deps()` as they
were not used.
* removed `manual` argument in `install_greta_deps()`.
* added default 5 minute timer to installation processes
* Added `greta_deps_receipt()` to list the current main python packages installed. (#668)
* Added checking suite to ensure you are using valid versions of TF, TFP, and Python(#666)
* Removed `manual` argument in `install_greta_deps()`.
* Added default 5 minute timer to installation processes.
* Added `greta_deps_receipt()` to list the current main python packages installed (#668).
* Added checking suite to ensure you are using valid versions of TF, TFP, and Python(#666).
* Added data `greta_deps_tf_tfp` (#666), which contains valid versions combinations of TF, TFP, and Python.
* remove `greta_nodes_install/conda_*()` options as #493 makes them defunct.
* Added option to write to a single logfile with `greta_set_install_logfile()`, and `write_greta_install_log()`, and `open_greta_install_log()` (#493)
* Added `destroy_greta_deps()` function to remove miniconda and python conda environment
* Improved `write_greta_install_log()` and `open_greta_install_log()` to use `tools::R_user_dir()` to always write to a file location. `open_greta_install_log()` will open one found from an environment variable or go to the default location. (#703)
* Remove `greta_nodes_install/conda_*()` options as #493 makes them defunct.
* Added option to write to a single logfile with `greta_set_install_logfile()`, and `write_greta_install_log()`, and `open_greta_install_log()` (#493).
* Added `destroy_greta_deps()` function to remove miniconda and python conda environment.
* Improved `write_greta_install_log()` and `open_greta_install_log()` to use `tools::R_user_dir()` to always write to a file location. `open_greta_install_log()` will open one found from an environment variable or go to the default location (#703).

## New Print methods

* New print method for `greta_mcmc_list`. This means MCMC output will be shorter and more informative. (#644)
* greta arrays now have a print method that stops them from printing too many rows into the console. Similar to MCMC print method, you can control the print output with the `n` argument: `print(object, n = <elements to print>)`. (#644)
* New print method for `greta_mcmc_list`. This means MCMC output will be shorter and more informative (#644).
* greta arrays now have a print method that stops them from printing too many rows into the console. Similar to MCMC print method, you can control the print output with the `n` argument: `print(object, n = <elements to print>)` (#644).

## Minor

* `greta_sitrep()` now checks for installations of Python, TF, and TFP
* `greta_sitrep()` now checks for installations of Python, TF, and TFP.
* Slice sampler no longer needs precision = "single" to work.
* greta now depends on R 4.1.0, which was released May 2021, over 3 years ago.
* export `is.greta_array()` and `is.greta_mcmc_list()`
* `restart` argument for `install_greta_deps()` and `reinstall_greta_deps()` to automatically restart R (#523)
* export `is.greta_array()` and `is.greta_mcmc_list()`.
* `restart` argument for `install_greta_deps()` and `reinstall_greta_deps()` to automatically restart R (#523).

## Internals

* Internally we are replacing most of the error handling code as separate
`check_*` functions.
* Implemented `cli::cli_abort/warn/inform()` in place of `cli::format_error/warning/message()` + `stop/warning/message(msg, call. = FALSE)` pattern.
* Uses legacy optimizer internally (Use `tf$keras$optimizers$legacy$METHOD` over `tf$keras$optimizers$METHOD`). No user impact expected.
* Update photo of Grete Hermann (#598)
* Use `%||%` internally to replace the pattern: `if (is.null(x)) x <- thing` with `x <- x %||% thing`. (#630)
* Update photo of Grete Hermann (#598).
* Use `%||%` internally to replace the pattern: `if (is.null(x)) x <- thing` with `x <- x %||% thing` (#630).
* Add more explaining variables - replace `if (thing & thing & what == this)` with `if (explanation_of_thing)`.
* Refactored repeated uses of `vapply` into functions (#377, #658)
* Refactored repeated uses of `vapply` into functions (#377, #658).
* Add internal data files `.deps_tf` and `.deps_tfp` to track dependencies of TF and TFP. Related to #666.

- Posterior density checks (#720):
- Don't run Geweke on CI as it takes 30 minutes to run.
- Add thinning to Geweke tests.
- Fix broken geweke tests from TF1-->TF2 change.
- Increase the number of effective samples for check_samples for lkj distribution
- Add more checks to posterior to run on CI/on each test of greta

## Bug fixes

* Fix bug where matrix multiply had dimension error before coercing to greta array. (#464)
*
- Fixes for Wishart and LKJ Correlation distributions (#729 #733 #734):
- Add bijection density to choleskied distributions.
- Note about some issues with LKJ and our normalisation constant for the density.
- Removed our custom `forward_log_det_jacobian()` function from `tf_correlation_cholesky_bijector()` (used in `lkj_correlation()`). Previously, it did not work with unknown dimensions, but it now works with them.
- Ensure wishart uses sigma_chol in scale_tril
- Wishart uses `tf$matmul(chol_draws, chol_draws, adjoint_b = TRUE)` instead of `tf_chol2symm(chol_draws)`.
- Test log prob function returns valid numeric numbers.
- Addresses issue with log prob returning NaNs--replace `FillTriangular` with `FillScaleTriL` and apply Chaining to first transpose input.

# greta 0.4.5

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