## plyxp 1.7.3

* `method(vec_slice, class_DF)` now properly slices the rownames instead of the elementMetadata
* Added Preprint to README
* fixed show_tidy bug with "vec_restore.vec_phantom", now using internal `vec_slice` to extract rows

## plyxp 1.7.2

* `mutate.PlySummarizedExperiment` can now remove assays with `NULL` in the assays context.

## plyxp 1.6.1

* Corrected regression of 1.4.2

## plyxp 1.5.5

* `plyxp::vec_ptype_common` should now be aware of the vctrs_partial class.

## plyxp 1.5.1

### Breaking Changes

* location of group data is no longer stored on the metadata of the `SummarizedExperiment` but instead split between
  the metadata of the `rowData()` and `colData()` respectively for row and column groupings. This is in preparation of
  biocmask integration.

## plyxp 1.4.2

* fixed bug when summarizing a plyxp object by the rows and not columns
  would result in assays not being constructed in the correct order.

## plyxp 1.4.1

* fixed bug with recusion case of `plyxp::list_unchop(list(NULL), ptype = NULL)`

## plyxp 1.4.0

* Biocondcutor 3.22 release

## plyxp 1.3.11

* `summarize.PlySummarizedExperiment` now allows no assay context arguments.
* dynamic dots are now permitted within context functions. Namely doing something like
  `rows("{foo}" := bar)` where `foo` is some character string, will now work properly
* allow scalar values in `arrange()` and ungrouped instances.
* `plyxp` now exports `dplyr::group_split` and a method for `PlySummarizedExperiment` objects
* `slice.PlySummarizedExperiment` will now remove indices that are outside of each group - more inline
  with how `dplyr::slice()` works.

## plyxp 1.3.5

* Corrected issue where using `group_by(xp, rows(foo = some_scalar))` would not create proper groupings
* Corrected issue where scalars would capture an empty evaluation environment, which would cause any context specific transforms to fail.
  This was corrected by checking if the quo also has a transformation set, and if so, changes the environment (if empty) to the calling env.

## plyxp 1.3.2

* `slice()` has been added as a supported function for `PlySummarizedExperiment` objects.
* Various methods that were not yet implement for `PlySummarizedExperiment` are now available:
  * metadata/`metadata<-`
  * rownames/`rownames<-`
  * colnames/`colnames<-`
  * dimnames/`dimnames<-`
  * nrow/ncol
* Corrected issue in which across was not working in the default `assays` context.
* can now use `cols()`, `rows()` or `assays()` as the first argument of `across()` to specify
  which cols from potentially different contexts to pull data from.

## plyxp 1.2.7

* `ungroup()` now properly ungroups the named rows() or cols() columns.
* `ungroup()` now does not drop groupings in other contexts if they exists.

## plyxp 1.2.5

* `pull.PlySummarizedExperiment()` now uses `tidyselect::vars_pull()` under the
  hood, which should have more consistent behavior to the original.

## plyxp 1.2.4

* dplyr functions on plyxp objects now allow for empty arguments, which will be
  ignored.
* `pull.PlySummarizedExperiment()` now allows for pulling the names of the
  rowData or colData by specifying `rows(.features)` and `cols(.samples)`
  respectively.

## plyxp 1.2.0

* Bioconductor 3.21 release

## plyxp 1.1.1

* added `plyxp_on()` as a way to have further interior mutability on the
  SummarizedExperiment class.

## plyxp 1.0.0

* BioConductor 3.20 release

## plyxp 0.99.24

* Since `plyxp` does not have a conflict with `tidySummarizedExperiment` anymore,
  we have removed package startup messages warning of potential conflicts.

## plyxp 0.99.21

* Fixed documentation of `?plyxp::mutate` and other dplyr functions reexported
  by `plyxp`.
* `PlySummarizedExperiment` should be able to hold any `SummarizedExperiment`
  object

## plyxp 0.99.20

* plyxp now wraps `SummarizedExperiment` in a shell class named
  `PlySummarizedExperiment` to avoid conflicts with `tidySummarizedExperiment`.
  * Use `PlySummarizedExperiment()` or `new_plyxp()` to create a new object.
  * Use standard Generics `se()` and `se<-()` to get and set the underlying
    `SummarizedExperiment` object.
  * plyxp `dplyr` verbs are now defined for `PlySummarizedExperiment` objects
    instead of `SummarizedExperiment` objects.
  * `PlySummarizedExperiment` uses enhanced printing methods to display
    `SummarizedExperiment` objects in a tidy format.

## plyxp 0.99.19

* Package renamed to `plyxp` to be more specific about its functionality

## plyxp 0.99.18

* messages checking for conflicts use `cli::` methods for pretty printing
* Vignette typo correction

## plyxp 0.99.13

* `print.SummarizedExperiment` has been renamed to
  `show_tidy.SummarizedExperiment` and `show_tidy` is exported as an S3 generic.
* Adjust show function display original show method by default. using
  `show_tidy()` is now opt-in via options or `use_show_tidy()`.
* Verbose messages checking if `tidySummarizedExperiment` is already attached or
  ever becomes loaded with `plyxp`.
* change README and Vignette explaining this package provides an alternative
  approach to `tidySummarizedExperiment` to manipulating `SummarizedExperiment`
  objects. For now they are exclusive in their functionality, but there may be
  plans to reconsile conflicts in the future!

## plyxp 0.99.12

* developer subscribed to bioc-devel mailing list
* used `<-` assignment instead of `=` in top-level functions

## plyxp 0.99.11

Biocondcutor Submission version!
