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Copy file name to clipboardexpand all lines: NEWS.md
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# greta 0.4.5.9000 (development version)
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# greta (development version)
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## Features
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## Changes
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-`log.greta_array()` function warns if user uses the `base` arg, as it was unused, (#597).
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- Add warmup information to MCMC print method (#652, resolved by #755).
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# greta 0.5.0
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*This version of greta uses Tensorflow 2.0.0, which comes with it a host of new very exciting features!
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This version of greta uses Tensorflow 2.0.0, which comes with it a host of new very exciting features!
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###Optimizers
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## Optimizers
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The latest interface to optimizers in tensorflow are now used, these changes are described.
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## Installation revamp
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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.
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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.
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* Added option to restart R + run `library(greta)` after installation (#523)
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* Added installation deps object, `greta_python_deps()` to help simplify specifying package versions (#664)
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*removed`method` and `conda` arguments from `install_greta_deps()` as they
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* Added option to restart R + run `library(greta)` after installation (#523).
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* Added installation deps object, `greta_deps_sepc()` to help simplify specifying package versions (#664).
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*Removed`method` and `conda` arguments from `install_greta_deps()` as they
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were not used.
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*removed`manual` argument in `install_greta_deps()`.
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*added default 5 minute timer to installation processes
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* Added `greta_deps_receipt()` to list the current main python packages installed. (#668)
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* Added checking suite to ensure you are using valid versions of TF, TFP, and Python(#666)
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*Removed`manual` argument in `install_greta_deps()`.
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*Added default 5 minute timer to installation processes.
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* Added `greta_deps_receipt()` to list the current main python packages installed (#668).
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* Added checking suite to ensure you are using valid versions of TF, TFP, and Python(#666).
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* Added data `greta_deps_tf_tfp` (#666), which contains valid versions combinations of TF, TFP, and Python.
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* Remove `greta_nodes_install/conda_*()` options as #493 makes them defunct.
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* Added option to write to a single logfile with `greta_set_install_logfile()`, and `write_greta_install_log()`, and `open_greta_install_log()` (#493).
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* Added `destroy_greta_deps()` function to remove miniconda and python conda environment.
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* 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).
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## New Print methods
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* New print method for `greta_mcmc_list`. This means MCMC output will be shorter and more informative (#644).
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* 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).
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## Minor
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*`greta_sitrep()` now checks for minimum versions of software, instead of exact versions. It requires at least Python version 3.8, TensorFlow 2.8.0, and Tensorflow Probability 0.14.0.
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*slice sampler no longer needs precision = "single" to work.
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*`greta_sitrep()` now checks for installations of Python, TF, and TFP.
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*Slice sampler no longer needs precision = "single" to work.
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* greta now depends on R 4.1.0, which was released May 2021, over 3 years ago.
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* export `is.greta_array()` and `is.greta_mcmc_list()`
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* 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)
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* New print method for `greta_mcmc_list`. This means MCMC output will be shorter and more informative. (#644)
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*`restart` argument for `install_greta_deps()` and `reinstall_greta_deps()` to automatically restart R (#523)
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* export `is.greta_array()` and `is.greta_mcmc_list()`.
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*`restart` argument for `install_greta_deps()` and `reinstall_greta_deps()` to automatically restart R (#523).
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## Internals
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* Internally we are replacing most of the error handling code as separate
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`check_*` functions.
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* Implemented `cli::cli_abort/warn/inform()` in place of `cli::format_error/warning/message()` + `stop/warning/message(msg, call. = FALSE)` pattern.
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* Uses legacy optimizer internally (Use `tf$keras$optimizers$legacy$METHOD` over `tf$keras$optimizers$METHOD`). No user impact expected.
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* Update photo of Grete Hermann (#598)
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* Use `%||%` internally to replace the pattern: `if (is.null(x)) x <- thing` with `x <- x %||% thing`. (#630)
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* Update photo of Grete Hermann (#598).
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* Use `%||%` internally to replace the pattern: `if (is.null(x)) x <- thing` with `x <- x %||% thing` (#630).
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* Add more explaining variables - replace `if (thing & thing & what == this)` with `if (explanation_of_thing)`.
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* Refactored repeated uses of `vapply` into functions (#377, #658)
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* Refactored repeated uses of `vapply` into functions (#377, #658).
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* Add internal data files `.deps_tf` and `.deps_tfp` to track dependencies of TF and TFP. Related to #666.
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- Posterior density checks (#720):
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- Don't run Geweke on CI as it takes 30 minutes to run.
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- Add thinning to Geweke tests.
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- Fix broken geweke tests from TF1-->TF2 change.
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- Increase the number of effective samples for check_samples for lkj distribution
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- Add more checks to posterior to run on CI/on each test of greta
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## Bug fixes
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* Fix bug where matrix multiply had dimension error before coercing to greta array. (#464)
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*
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- Fixes for Wishart and LKJ Correlation distributions (#729#733#734):
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- Add bijection density to choleskied distributions.
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- Note about some issues with LKJ and our normalisation constant for the density.
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- 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.
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