[r] [WIP] Remove tiledb-r as a dependency from tiledbsoma-r #3644
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
mojaveazure
force-pushed
the
paulhoffman/sc-62760/remove-tiledb-r-as-a-dependency-from-tiledbsoma
branch
2 times, most recently
from
6c9ff80 to
7dad1d7
Compare
mojaveazure
force-pushed
the
paulhoffman/sc-62760/remove-tiledb-r-as-a-dependency-from-tiledbsoma
branch
from
35f0038 to
e616a0d
Compare
mojaveazure
force-pushed
the
paulhoffman/sc-62760/remove-tiledb-r-as-a-dependency-from-tiledbsoma
branch
from
e616a0d to
a0c7fc4
Compare
mojaveazure
force-pushed
the
paulhoffman/sc-62760/remove-tiledb-r-as-a-dependency-from-tiledbsoma
branch
from
a0c7fc4 to
a031e2b
Compare
Remove the dependency of tiledb-r from tiledbsoma-r [SC-62760](https://app.shortcut.com/tiledb-inc/story/62760)
* [r] Remove `arrow_*_from_tiledb_*()` Helpers Remove the following arrow <> tiledb-r helpers as they are unused and to start removing tiledb-r from the code/tests - `arrow_field_from_tiledb_dim()` - `arrow_field_from_tiledb_attr()` - `arrow_schema_from_tiledb_schema()` [SC-62761](https://app.shortcut.com/tiledb-inc/story/62761)
Replace calls to `tiledb::tiledb_object_type()` with `get_tiledb_object_type()` [SC-62778](https://app.shortcut.com/tiledb-inc/story/62778)
* [r] Remove calls to `tiledb::tiledb_version()` Replace calls to `tiledb::tiledb_version()` with new helper function `get_tiledb_version()`; `get_tiledb_version()` wraps `tiledb_embedded_version()`, but adds a parameter `compact` to replicate the `compact = TRUE` mode of `tiledb::tiledb_version()` Also add names to `get_tiledb_version(compact = FALSE)` [SC-62779](https://app.shortcut.com/tiledb-inc/story/62779)
Remove an unused custom class as part of replacing `TileDBObject` with a new SOMA base-object class that is not reliant on tiledb-r [SC-63206](https://app.shortcut.com/tiledb-inc/story/63206) continues work for #2406
Replace `tiledb::is.sparse()` and `tiledb::allows_dups()` with new R/Rcpp functions in tiledbsoma-r - `tiledb::is.sparse()` is replaced by `c_is_sparse()` and exposed as `SOMAArrayBase$is_sparse()` - `tiledb::allows_dups()` is replaced with `c_allows_dups()` and exposed as `SOMAArrayBase$allows_duplicates()` [SC-64424](https://app.shortcut.com/tiledb-inc/story/64424) continues work for #2406
…3834) Replace `TileDBArray$attributes()` with new `SOMAArrayBase$attributes()`; this method uses a libtiledbsoma/Rcpp function rather than `tiledb::attrs()` and returns a named list instead of a tiledb-r wrapper around external pointers [SC-64814](https://app.shortcut.com/tiledb-inc/story/64814) continues work for #2406
mojaveazure
force-pushed
the
paulhoffman/sc-62760/remove-tiledb-r-as-a-dependency-from-tiledbsoma
branch
from
d0f0bb0 to
9f03677
Compare
Replace calls to `tiledb::attrs()` with `$attributes()` accessor [SC-64999](https://app.shortcut.com/tiledb-inc/story/64999) continues work for #2406
* [r] Replace calls to tiledb-r schema checkers with libtiledbsoma Replace calls the following tiledb-r schema accessors with new libtiledbsoma functions: - `tiledb::capacity()` replaced with `c_capacity()` - `tiledb::tile_order()` replaced with `c_tile_order()` - `tiledb::cell_order()` replaced with `c_cell_order()` [SC-64997](https://app.shortcut.com/tiledb-inc/story/64997) * Address code review feedback Move internal helper function to `rutilities.[cpp,h]`
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
Remove the dependency of tiledb-r from tiledbsoma-r
SC-62760
resolves #2406