[r] Use the new tiledb-r release in CI #1663
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This pull request has been linked to Shortcut Story #33875: [r] Temporary switch to rc builds in CI. |
johnkerl
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Sep 11, 2023
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@eddelbuettel we can close this now I believe |
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@johnkerl I fear not as eg r-ci.yml goes to r-universe because what it needs is not available elsewhere and may not be for a day. |
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@eddelbuettel OK. We can't tag 1.5.0 until all 2.17.0-rc0 dependencies are gone, but, if this PR helps soothe concerns until then, all for the good. |
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Sep 14, 2023
* [c++] Support `Enumeration` in C++ Codebase * Addition of `SOMAArray::get_enum` and `SOMAArray::get_enum_label_on_attr` * Attach an enumeration/dictionary to the `ColumnBuffer` if applicable; this is used when converting from `ArrayBuffers` to Arrow Tables in the Python and R APIs * Add `get_attr_to_enum_mapping` Function * WIP fix bug where attr name was passed instead of enum name * Add Unit Tests for Enumeration in C++ * `to_varlen_buffers` Returns `std::string` * Prior to TileDB-Inc/TileDB#4272, the SOMA unit tests were erroneously writing a byte vector for string dimensions which maps to `TILEDB_BLOB` rather than `TILEDB_STRING_ASCII` * Update SOMA Array get_metadata Signatures * Depend on 2.17.0-rc0 * resolve an incomplete merge with #1559 * [r] Update tiledb-r to RC (borrowed from #1663, #1665) * [r] Undo brown-bag typo in helper script * 2.17.0 --------- Co-authored-by: John Kerl <[email protected]> Co-authored-by: Dirk Eddelbuettel <[email protected]>
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@eddelbuettel I did |
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ihnorton
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Sep 15, 2023
As described in #1558 and #866, adding enumeration support is desirable once we have TileDB Embedded 2.17 available **Changes:** This PR supports reading of columns with enumerations (aka dictionaries aka factor variable) directly via Arrow. Preliminary write support is also available (but still goes through the `tiledb` R package for writes). **Notes for Reviewer:** ~This PR is now work-in-progress and not ready for a merge while we await TileDB 2.17.~ The branch and PR are ready but should only be merged once prequisites are been merged. It likely needs #1519 (C++ side) and #1663 (CI support). CI is turned off as the TileDB default build is still without support for enumerations.
johnkerl
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Sep 15, 2023
* **Issue and/or context:** As described in #1558 and #866, adding enumeration support is desirable once we have TileDB Embedded 2.17 available **Changes:** This PR supports reading of columns with enumerations (aka dictionaries aka factor variable) directly via Arrow. Preliminary write support is also available (but still goes through the `tiledb` R package for writes). **Notes for Reviewer:** ~This PR is now work-in-progress and not ready for a merge while we await TileDB 2.17.~ The branch and PR are ready but should only be merged once prequisites are been merged. It likely needs #1519 (C++ side) and #1663 (CI support). CI is turned off as the TileDB default build is still without support for enumerations. * **Issue and/or context:** This PR adds support for return Arrow tables with dictionaries that can include `ordered` enumerations. **Changes:** Given #1559 which it depends upon, a very small change to just three files in `libtiledbsoma`. This should become clearer once the dependent PR is merged and can be rebased. **Notes for Reviewer:** [SC 34073](https://app.shortcut.com/tiledb-inc/story/34073/c-add-ordered-support-to-arrow-export) * **Issue and/or context:** This PR extends the `schema()` function to return an Arrow schema with enumerations including `ordered`. **Changes:** Given #1559 which it depends upon, a very small change to just one file. This should become clearer once the dependent PR is merged and can be rebased. **Notes for Reviewer:** [SC 34074](https://app.shortcut.com/tiledb-inc/story/34074/c-add-ordered-support-to-arrow-export) * [c++] Test fixes for #1559 (#1684) * ihn/bugfix * unit-test update * lint --------- Co-authored-by: John Kerl <[email protected]>
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Issue and/or context:
We need the Enumerations-aware tiledb-r in CI. This adds it.
Changes:
(Temporarily) adds two new segments for macOS and linux to r-ci.yaml
Notes for Reviewer:
SC 33875
#866