# repo 2.1.7 (2026-02-20)

* Fixed NEWS.md formatting to comply with CRAN standards.

# repo 2.1.6 (2021-05-16)

* fixed dependency issues as requested by CRAN
* fixed reference DOI in description

# repo 2.1.5 (2020-02-05)

* fixed minor documentation bug as asked by CRAN

# repo 2.1.5 (2019-12-22)

* Now `repo_info` shows full paths.
* Updated Readme

# repo 2.1.4 (2019-12-18)

* Completely renewed naming convention for the stored files. This
  change is transparent to the user and will not affect previous
  code. Also existing repositories can be used with this new version
  (previous files will be left untouched, new ones will follow the new
  convention). But now the directory tree of the repository has been
  greatly simplified and is human readable. Each item is stored 1
  level (as opposed to 3) under the repo root and using a sanitized
  version of the item name (as opposed to a random string). Possible
  name collisions are avoided by appending a progressive number. Item
  name is still stored as is in the repository (and will still collide
  with previously stored items by the same name as expected).
* fix in the vignette to pass CRAN checks on some platforms

# repo 2.1.3.1 (2018-12-03)

* `repo_get` now allows to suppress name suggestions for faster search
  in large repositories.

# repo 2.1.3 (2018-05-04)

* Significant speedup of all operations involving a search through the
  items, including `find` and `print`. These are now usable with large
  repositories (tested with tens of thousands items).

# repo 2.1.2.2 (2017-12-06)

* Changed error and warning calls with `call.=F`

# repo 2.1.2.1 (2017-11-27)

* `stash` is not deprecated anymore, as it is useful to lazydo
* fixed some `stash` behaviour, like when `put`-ing an item with the
  same name of `stash`-ed item, which now does not throw an error.
* `lazydo` with `force=T` will not throw an error for existing item,
  which is now a `stash`-ed item
* `laxydo` now does not take an object of type `expression`, but an
  expression directly.

# repo 2.1.2 (2017-11-18)

* Fixed broken link to remote sample
* Changed the outputs of `repo_check`, which can now be
  `suppressedMessages`-ed.

# repo 2.1.1 (2017-08-03)

Major release submitted to CRAN.

# repo 2.1.1.0 (2017-08-01)

CRAN candidate release.

* Fixed bug in `repo_build`
* Deprecated `stash`: now that `put` parameters are mostly optional,
  it is not necessary anymore.

# repo 2.1.0.9001 (2017-07-25)

* Correcting vignette for next release
* fixed version numbering (there is no v2.2)

# repo 2.1.0.9000 (2017-04-15)

* Also the item name in `put` is now optional. If not provided, the
  name of the `obj` variable will be used.
* The chunk format has been simplified, the close tag is now just `}`,
  as follows:
  ```
  ## chunk "ChunkName" {
      ## ...
  ## }
  ```
* Some documentation updates.

# repo 2.1.0 (2017-04-11)

New features:

* Descriptions and tags are no more mandatory
* Alternative versions of the same chunk can now be defined like this:
  ```
  ## chunk "ChunkName#fork1"{
      ## ...
  ## chunk "ChunkName#fork1"}
  ## chunk "ChunkName#fork2"{
      ## ...
  ## chunk "ChunkName#fork2"}
  ## the following sets the active chunk:
  rp$options(chunk="fork")
  ```
  Outputs from different forks will be stored together in the repo
  but all operations will refer to the output of the active
  chunk. This is to be better documented.

Change log:

* descriptions and tags are no more mandatory also in `attach`
* fixed regression in `dependencies` (wrong plot edges)
* fixed bug in `set`, was not working when setting `src` parameter

# repo 2.0.5.13 (2017-03-05)

* Added forking

# repo 2.0.5.12 (2017-03-04)

* Added `depends` function
* Added `load` function
* Added `force` parameter to `build`
* More documentation updates

# repo 2.0.5.11 (2017-02-24)

* Runs all checks
* Documentation updated
* `dependencies` now accepts overriding of default visual igraph
  parameters

# repo 2.0.5.10 (2017-02-22)

* A [paper about Repo](https://doi.org/10.1186/s12859-017-1510-6) has been published in BMC
  Bioinformatics.
* Added some testing code.

# repo 2.0.5.8 (2016-10-18)

* Major code refactoring. Direct call of `repo_*` function now
  deprecated.

# repo 2.0.5.7 (2016-10-14)

* added `chunk` and `build` functions and `chunk` parameter to
  `put`. Repo can now associate a specific chunk of code with a
  resources and rebuild it upon request.
* added support for special `project` items and corresponding
  `project` function and `prj` parameter in `put`. `project` items
  store session information automatically when `put` is called. The
  `info` command works differently on `project` items.
* Improved aesthetics for the dependency graph through default visual
  parameters.
* added `testthat` support for internal tests
* added `options` function to set `put` default parameters.

# repo 2.0.5.6 (2016-10-08)

* added `buildURL` parameter to `set`. It will add an URL to all
  items, such that it can be used is the repository is uploaded to a
  website.
* `get` can now be used on attachments, returns file path
* Fixed bugs in `attach` not working with attachments
* Fixed a few bugs with `copy` when copying multiple items. Now also
  accepts `confirm` and `replace`
* Added `related` function to extract items directly or indirectly
  related to an input item.
* added internal `testthat` unit testing
* A few changes to `pies` and `dependencies`. They now support
  additional parameters (...) to pass to `graphics:pie` and
  `igraph:plot` respectively. `pies` now merges together all items with
  size < 5% of the total. `dependencies` now supports tags to filter
  nodes to be showed. Also missing documentation for `pies` has been
  added.

# repo 2.0.2 (2016-05-03)

* new `attr` function in
* `attach` now accepts `URL` parameter
* 2.0.2 is now the latest stable on CRAN

# repo 2.0.1.3 (2016-05-02)

* 2.0.2 contains a fix to repo$pull for OS X
* Documentation updated
* NOTE: previous change implies that not all items have a "source"
  field. This does not seem to be a problem. However, older items
  storing current working directory as source could be affected.

# repo 2.0.1.2 (2016-04-28)

* now src must be an item (meant to be an attachment containing source
  code). Documentation updated accordingly.
* minor updates to vignette

# repo 2.0.1.1 (2016-04-27)

* Bug fixes in lazydo and parameter check

# repo 2.0.1.0 (2016-04-24)

* passes `devtools::check()`
* stash simplified (now `stash(x)` instead of `stash("x")`)
* Fixed bug when replacing entries due to new scheme for naming files.

# repo 2.0.0 (2016-04-01)

* Bug fixes in lazydo
* Minor additions to docs

# repo 1.9.5 (2016-03-20)

* Fixed warnings in cpanel
* All `check()` now passed
* Merged latest fix from the dev branch
* The NEWS file now used for main news

# repo 1.9.4 (2016-03-19)

* Further testing
* vignette updated
* News moved to NEWS file
* Minor release

# repo 1.9.3 (2016-03-18)

* New pull feature now working
* added lazydo (run expression and cache results)
* Sources auto-attach suspended (had problems)

# repo 1.9.0 (2015-12-07)

* Initial Shiny interface

# repo 1.8.0 (2015-11-19)

* Sources are now auto-attached
* Added safe-remove of data
* Added auto-attach of sources
* Added notes field

# repo 1.7.2 (2015-10-21)

* Fixed regression in `check` after moving to relative paths
* Added check points for reserved tags and warnings for existing tags
* Improved print reaction when all matching results are hidden

# repo 1.7.1 (2015-10-19)

* Added Bulk-edit feature.

# repo 1.7.0 (2015-10-17)

* Added "Maybe-you-were-looking-for" feature to `get`.
* Fixed bug with managing new relative paths.

# repo 1.6.0 (2015-10-12)

* Absolute to relative paths for stored objects. This allows to easily
  rebase a repository, for example to a remote machine, without affecting
  the index.
* Automatic update of old repository entries upon resource loading.

# repo 1.5.0 (2015-10-08)

* Atomization of item replacement to avoid the possibility of data
  loss.

# repo 1.0.0 (2015-01-01)

* Added search field in print to match anything in items and the
  corresponding "find" shortcut method.
* When using multiple tags now by default they match when at least one
  matches (OR).
* Now tags can be matched using OR, AND, NOT or any external logical
  function.
* Fixed a bug in print when showing one item.
