Repository: single-cell-data/TileDB-SOMA (language: python)

Issue:
[python/r/c++] Revisit `shape` for component arrays
## PRs

**Merged PRs:**

<details>

* #2909 `kerl/schevo-timestamp-methodize`
* #2913 `kerl/name-neaten`
* #2908 `kerl/ut-soma-exc-simplify`
* #2910 `kerl/test-common-parameterize`
* #2918 `kerl/cpp-test-deadstrip`
* #2919 `kerl/minor-unit-test-helper-mod`
* #2936 `kerl/cpp-ut-helper-neaten`
* #2938 `kerl/more-cur-dom-parameterize`
* #2915 `kerl/cpp-strict-int64-shape`
* #2911 `kerl/arrow-util-current-domain-optional`
* #2939 `kerl/step-two-temp`
* #2947 `kerl/cpp-ndarray-resize-testing`
* #2945 `kerl/dataframe-test-fixture`
* #2944 `kerl/cpp-variant-indexed-dataframes`
* #2916 `kerl/sdf-shape`
* #2917 `kerl/cpp-resizes`
* #2948 `kerl/upgrade-shape-int64`
* #2951 `kerl/sdf-test-accessors`
* #2953 `kerl/py-r-accessor-plumbing`
* #2957 `kerl/sdf-domain-accessors`
* #2960 `kerl/dense-link`
* #2963 `kerl/nightly-fix`
* #2970 `kerl/dense-writeable-after-create`
* #2968 `kerl/minor-trim`
* #2969 `kerl/more-py-domain-name-neaten`
* #2972 `kerl/libtiledbsoma-env-logging-level`
* #2962 `kerl/py-r-creation-paths`
* #2950 `kerl/py-r-test-2`
* #2994 `kerl/nanoarrow-helpers`
* #3011 `kerl/polydom3`
* #3017 `kerl/polydom5`
* #3018 `kerl/polydom6`
* #2990 `kerl/variant-nnz-bug`
* #3019 `kerl/index-swap`
* #3020 `kerl/ut-max-shape`
* #3012 `kerl/polydom4`
* #3025 `kerl/fix-3020-merge`
* #3026 `kerl/one-more-rename`
* #3028 `kerl/ff-not`
* #3029 `kerl/ut-vg`
* #3030 `kerl/table-utils-memory`
* #3067 `kerl/improve-sdf-test-field-names`
* #3068 `kerl/ut-generate`
* #3069 `kerl/cpp-sdf-domain-at-create`
* #3027 `kerl/hll-domainish`
* #3088 `kerl/max-domain-int64`
* #3090 `kerl/maybe-resize-soma-joinid-cpp-tweak`
* #3032 `kerl/sdf-domain-at-create` -- fixes #2967
* #3091 `kerl/maybe-resize-soma-joinid-py-r`
* #3095 `kerl/cpp-exp-resize-prep`
* #3089 `kerl/r-dataframe-shapeable`
* https://github.com/single-cell-data/SOMA/pull/233
* #3125 `kerl/cpp-ut-name-shortens`
* #3127 `kerl/helper-rename`
* #3130 `kerl/cpp-can-resizers-names`
* #3132 `kerl/cpp-dataframe-sizing-helpers`
* #3139 `kerl/cpp-dataframe-upgrade-test`
* #3140 `kerl/py-resizer-connects`
* #3151 `kerl/py-can-upgrade-shape`
* #3152 `kerl/registration-shape-acceessors`
* #3156 `kerl/py-exp-shaping`
* #3157 `kerl/py-exp-shaping2`
* #3148 `kerl/py-exp-resize`
* #3191 `kerl/py-domain-at-create-ut-1`
* #3190 `kerl/py-domain-at-create-ut-2`
* #3192 `kerl/py-domain-at-create-ut-3`
* #3193 `kerl/py-domain-at-create-ut-4`
* #3194 `kerl/py-domain-at-create-ut-5`
* #3203 `kerl/min-size-2`
* #3208 `kerl/r-min-sizing`
* #3211 `kerl/cpp-ugr-dom`
* #3232 `kerl/ff-interop`
* #3230 `kerl/ffon`
* #3234 `kerl/docstring-prune`
* #3236 `kerl/prefixing`
* #3241 `kerl/fix-bad-merge`
* #3235 `kerl/py-r-ugr-dom`
* #3237 `kerl/py-r-ugr-dom-2`
* #3238 `kerl/py-r-ugr-dom-3`
* #3253 `kerl/set-coords-rename`
* #3261 `kerl/pybind11-nda-sizing`
* #3265 `kerl/dense-227-a`
* #3263 `kerl/dense-range-trim`
* #3268 `kerl/dim-explosion`
* #3269 `kerl/python-227-dense-ned-read`
* #3270 `kerl/r-227-dense-fixes`
* #3280 `kerl/r-dense-227-more`
* #3286 `kerl/more-fn4m`
* #3283 `kerl/readthedocs-pre-1.15`
* #3288 `kerl/dense-ugrsh`
* #3289 `kerl/notebook-shape-upgrade`
* #3285 `kerl/new-shape-doc-updates`
* #3295 `kerl/notebook-data-refresh`
* #3290 `kerl/notebook-new-shape-refresh`
* #3301 `kerl/ffena`
* #3303 `kerl/r-data-refresh`
* #3300 `kerl/sdf-sjid-lower-zero`
* #3296 `kerl/dense-example-data-refresh`
* #3294 `kerl/new-shape-notebook-and-vignette`
* #3308 `kerl/upgrade-experiment-resources`
* #3309 `kerl/fix-notebook-merge`
* #3321 `kerl/more-use-shape`
* #3358 `kerl/revert-3300`
* #3368 `kerl/227a`
* #3369 `kerl/ucd1`
* #3370 `kerl/ucd2`
* #3371 `kerl/ucd3`
* #3372 `kerl/ucd4`
* #3396 `kerl/domain-at-create-docstrings`
* #3302 `kerl/new-shape-vignette`
* https://github.com/single-cell-data/SOMA/pull/250
* #3399 `kerl/new-shape-more-docstrings`
* #3400 `kerl/check-only-r`
* https://github.com/TileDB-Inc/somacore-feedstock/pull/27

</details>

**Closed/abandoned PRs:**

<details>

* #2785 -- This was only dogfooding for the core 2.25 release -- not to be merged
* #2952 `kerl/feature-flag-temp` -- folded into 2962
* #2995 `kerl/polydom`
* #2964 `kerl/tiledbsoma-io-test`
* #3189 `kerl/min-size`
* #3220 `kerl/cpp-ugr-dom-2`
* #3244 `kerl/dense-227-fixes`
* #3276 `kerl/dataframe-shape`

</details>

**Issues which are related but non-blocking:**

* https://github.com/single-cell-data/SOMA/pull/216
* https://github.com/TileDB-Inc/TileDB/pull/5303
* #2966
* #3081
* Note: R append mode does not exist yet -- see #1630 -- so an experiment-level resizer is not a priority in R
* #3271 
* #3272
* #3273

**See also:** [[sc-51048]](https://app.shortcut.com/tiledb-inc/story/51048).

## Problem to be solved

Users want to know the `shape` of an array, in the SciPy sense:

* Reads and writes are bounds-checked against the shape
* This retains its value regardless of which values of a sparse array are or are not actually occupied
* Users can `resize`.
  * Some users need the ability to grow their datasets later, using either `tiledbsoma.io`'s append mode, or subsequent writes using the `tiledbsoma` API.
  * Note that the cellxgene census doesn't need this: eact week's published census has fixed shape, and any updates will happen in new storage, on a new week.

Using TileDB-SOMA up until the present:

* The TIleDB `domain` is immutable after array creation
  * This does bounds-checking for reads and writes, which is good
  * To leverage this to function as a `shape`, users would need to set the `domain` at array-creation time. However, users lose the ability to grow their datasets later.
* There is a `non_empty_domain` accessor
  * This only indicates min/max coordinates _at which data exists_. Consider an `X` array for 100 cells and 200 genes. If non-zero expression counts exist only for cell join IDs 2-17, then the `non_empty_domain` will indicate `(2,17)` along `soma_dim_0`.
  * Consider an `obms["X_pca"]` within the same experiment. This may be 100 cells by 50 PCA components: we need a placd to store the number 50.
  * Therefore users cannot leverage this to function as a `shape` accessor.
* We have offered a `used_shape` accessor since TileDB-SOMA 1.5.
  * This functions as a `shape` accessor, in the SciPy sense, but it is not multi-writer safe.

New feature for TileDB-SOMA 1.15:

* Arrays will have a  `shape`
* Reads and writes are bounds-checked against the shape
* This retains its value regardless of which values of a sparse array are or are not actually occupied
* Users can `resize`
* The `used_shape` accessor will be deprecated in TileDB-SOMA 1.13, and slated for removal in TileDB-SOMA 1.14.

Compatiblity:

This will now require users to do an explicit `resize` before appending/growing TileDB-SOMA Experiments. Guidance in the form of example notebooks will be provided.

##  Tracking

See also: [[sc-41074]](https://app.shortcut.com/tiledb-inc/story/41074) and [[sc-51048]](https://app.shortcut.com/tiledb-inc/story/51048).

## Scheduling

Support arrives in TileDB Core 2.25. Deprecations for TileDB-SOMA will be released with 1.13. Full support within TileDB-SOMA will be release in 1.14.

## Details

SOMA API mods as we've discussed in a Google doc are as follows.

### `SOMADataFrame`

* `create`: Retain the `domain` argument
  * Issue:
    * Core has a `(lo, hi)` tuple per dim, e.g. `(0,99)` or `(10,19)`
    * SOMA has count per dim, with 0 implicit: e.g. 100 or 20
    * For `SparseNDArray` and `DenseNDArray` core can have `(lo, hi)` and SOMA can have `count`
    * For `DataFrame` there can be multiple dims --- default is a single `soma_joinid`
    * That could be treated either in `(lo, hi)` fashion or `count` fashion
    * However additional dims (e.g. `cell_type`) can be on any type, including strings, floats, etc. where there is no implicit lo=0
    * Therefore we need to keep the current SOMA API wherein `DataFrame` takes a `domain` argument (in `(lo, hi)` fashion) and not a `shape` argument (in `count` fashion)

### `SparseNDArray and DenseNDArray`

* `create`
  * Have an optional shape argument which is of type `Tuple[Int,...]` where each element is the cell count of the corresponding dimension
    * If unsupplied, or if supplied but None in any slot: use the minimum 0 in each slot – nothing larger makes sense since we will not support downsize
  * User guidance should make clear that it will not be possible to create an ‘old’ style array with the ‘new style’ API. (See also the upgrade logic below.)

### All three of `SOMADataFrame`, `SparseNDArray`, `DenseNDArray`

* `write`
  * For new arrays, created with the new shape feature:
    * Core will bounds-check that coordinates provided at `write` time are within the current shape
    * Core will raise `tiledb.cc.TileDBError` to TileDB-SOMA, which will catch and raise `IndexError`, and R-standard behavior on the R side
  * For old arrays created before this feature:
    * Core will not bounds-check that coordinates provided at write time are within the current shape
* Existing `used_shape` accessor
  * TileDB-SOMA will deprecate this over a release cycle.
  * For new arrays: raise `NotImplementedError`
  * For old arrays: return what’s currently returned, with a deprecation warning.
  * Mechanism for determining old vs. new: `array.schema.version` (the core storage version).
* Existing `shape` accessor
  * For new arrays:
    * Have this return the new shape as proposed by core, no longer returning the TileDB domain.
  * For old arrays created before this feature:
    * Return the TileDB domain as now.
* Existing `non_empty_domain` accessor
  * Same behavior for old and new arrays (unaffected by this proposal).
  * Keep this accessor supported, but, with user notes that it’s generally non-useful
  * This should return None (or R equivalent) when there is a schema but no data have been written.
* New `maxshape` accessor
  * Maps the core-level `(lo, hi)` accessor for domain to count-style accessor hi+1. E.g. if the core domain is either `(0,99)` or `(50,99)` then TileDB-SOMA `maxshape` will say 100.
  * Same behavior for old and new arrays.
  * Let users query for what the TileDB domain is, with user notes that it’s the maximum that users can reshape to.
  * Issac suggests: maybe `domain` or `maxshape` (see h5py).
* New `resize` mutator
  * Note: `reshape` means something else in the community (numpy, zarr, h5py), e.g. a 5x20 (total 100 cells) being reinterpreted as 4x25 (still 100 cells). The standard name for changing cell-count is `resize`.
  * For old arrays created before this feature: raise `NotImplementedError`.
  * For new arrays:
    * Will raise `ValueError` if the new shape is smaller on any dim than currently in storage
    * Regardless of whether any data have been written whatsoever
    * Will raise `ValueError` if the new shape exceeds the TileDB domain from create time, which will serve TileDB-SOMA in a role of “max possible shape the user can reshape to”
    * Otherwise, any calls to write from this point will bounds-check writes within this new shape
    * **We don’t expect resize to be multi-writer safe with regard to write ; user notes must be clear on this point**
* New `tiledbsoma_upgrade_shape` method for SparseNDArray and DenseNDArray
  * This will leverage `array.schema.version` to see if an upgrade is needed
  * Leverage core support for storage-version updates
  * This will take a shape argument as in `create`
  * For arrays created with “just-right” size: this will succeed
  * For arrays created with “room-for-growth” / “two billion-ish” size: this will succeed
  * If the user passes a shape which exceeds the current TileDB domain: this will fail
* New `tiledbsoma_upgrade_domain method` for `DataFrame`
  * Same as for `SparseNDArray`/`DenseNDArray` except it will take a domain at the SOMA-API level just as `DataFrame`'s create method

### `tiledbsoma.io`

* The user-facing API has no shape arguments and thus won’t need changing.
* Internally to `tiledbsoma.io`, we’ll still ask the tiledbsoma API for the “big domain” (2 billionish)
* Append mode:
  * Will need a new `resize` method at the `Experiment` level
  * Users will need to:
    * Register as now
    * Call the experiment-level `resize`
      * Could be `exp.resize(...)`, or (better) this could be `tiledbsoma.io.reshape_experiment`
  * In either case: this method will take the new `obs` and `var` counts as inputs:
    * `exp.obs.reshape` to new `obs` count
    * `exp.ms[name].var.reshape` to new `var` count
    * `exp.ms[name].X[name].reshape` to new `obs` count x `var` count
    * `exp.ms[name].obsm[name].reshape` to new `obs` count x same width
    * `exp.ms[name].obsp[name].reshape` to new `obs` count x `obs` count
    * `exp.ms[name].varm[name].reshape` to new `var` count x same width
    * `exp.ms[name].varp[name].reshape` to new `var` count x `var` count
  * Do the individual append-mode writes as now

[c++] Trivial name-shortens in unit-test code
**Issue and/or context:** In support of issue #2407 / [[sc-51048]](https://app.shortcut.com/tiledb-inc/story/51048).

**Changes:**

1st commit: I prefer longer/clearer names often, but, these are repeated and are causing unnecessary `clang-format` adjustments, particularly in PRs stacked on top of this.

2nd commit: another renaming. Not worth a separate PR IMO.

**Notes for Reviewer:**
[c++] Propagate Python/R function names to C++ for upgrade/resize methods
**Issue and/or context:** As tracked on issue #2407 / [[sc-51048]](https://app.shortcut.com/tiledb-inc/story/51048).

**Changes:**

* This is underpinning for #2964
* As @nguyenv pointed out, it might be nice for the C++ layer to just return enums only ...
* ... but as I pointed out
  * informative messages really require specific context such as the user-provided shape and the limit it ran into
  * I don't want to write those all twice in Python and R
  * So we are making user-presentable strings in the C++ code
* That said, we should not be hard-coding the function names from the caller -- given that C++ is creating user-facing error strings _on behalf of_ Python and R, the C++ code should enable and empower the Python/R code to pass in their function names (whatever those are)

**Notes for Reviewer:**

Despite the line-count this is a trivial PR. I'm splitting out this PR (as well as recents #3125 #3127 #3130) in order to clear the picture for #2964 which is the contentful goal of my recent work this week.
[python] New-shape testing for `tiledbsoma.io` [WIP]
**Issue and/or context:** As tracked on issue #2407 / [[sc-51048]](https://app.shortcut.com/tiledb-inc/story/51048). Atop #2950.

Note that the intended Python and R API changes are all agreed on and finalized as described in #2407.

**Changes:**

Tracks the things needing changed for `tiledbsoma.io` wherein explicit resize will play a key role.

**Notes for Reviewer:**

This PR is a work in progress. It is not ready for review.




Discussion / hints:
#2785 is a quick-and-dirty concept-prover -- its sole function is to flush out any API misunderstandings we might have, in prep for 2.25.0 core release.
## [Codecov](https://app.codecov.io/gh/single-cell-data/TileDB-SOMA/pull/3125?dropdown=coverage&src=pr&el=h1&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=single-cell-data) Report
All modified and coverable lines are covered by tests :white_check_mark:
> Project coverage is 86.61%. Comparing base [(`3bc119e`)](https://app.codecov.io/gh/single-cell-data/TileDB-SOMA/commit/3bc119e91c70ff0fa252a7badb176deaffc29e3e?dropdown=coverage&el=desc&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=single-cell-data) to head [(`c425bfd`)](https://app.codecov.io/gh/single-cell-data/TileDB-SOMA/commit/c425bfd38f949f51293acb725e34fd328304a9b8?dropdown=coverage&el=desc&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=single-cell-data).
> Report is 3 commits behind head on main.

<details><summary>Additional details and impacted files</summary>


```diff
@@            Coverage Diff             @@
##             main    #3125      +/-   ##
==========================================
+ Coverage   86.49%   86.61%   +0.12%     
==========================================
  Files          47       47              
  Lines        4924     4924              
==========================================
+ Hits         4259     4265       +6     
+ Misses        665      659       -6     
```

| [Flag](https://app.codecov.io/gh/single-cell-data/TileDB-SOMA/pull/3125/flags?src=pr&el=flags&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=single-cell-data) | Coverage Δ | |
|---|---|---|
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|---|---|---|
| [python_api](https://app.codecov.io/gh/single-cell-data/TileDB-SOMA/pull/3125/components?src=pr&el=component&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=single-cell-data) | `86.61% <ø> (+0.12%)` | :arrow_up: |
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</details>
## [Codecov](https://app.codecov.io/gh/single-cell-data/TileDB-SOMA/pull/3130?dropdown=coverage&src=pr&el=h1&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=single-cell-data) Report
All modified and coverable lines are covered by tests :white_check_mark:
> Project coverage is 82.60%. Comparing base [(`47f6b73`)](https://app.codecov.io/gh/single-cell-data/TileDB-SOMA/commit/47f6b73005d1483eaa6a96493eb201d2c89b281b?dropdown=coverage&el=desc&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=single-cell-data) to head [(`9b54d0a`)](https://app.codecov.io/gh/single-cell-data/TileDB-SOMA/commit/9b54d0a278dc9c73ace18b55e32dae0d46fe7e4e?dropdown=coverage&el=desc&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=single-cell-data).
> Report is 1 commits behind head on main.

<details><summary>Additional details and impacted files</summary>


```diff
@@            Coverage Diff             @@
##             main    #3130      +/-   ##
==========================================
+ Coverage   82.49%   82.60%   +0.11%     
==========================================
  Files          50       50              
  Lines        5204     5204              
==========================================
+ Hits         4293     4299       +6     
+ Misses        911      905       -6     
```

| [Flag](https://app.codecov.io/gh/single-cell-data/TileDB-SOMA/pull/3130/flags?src=pr&el=flags&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=single-cell-data) | Coverage Δ | |
|---|---|---|
| [python](https://app.codecov.io/gh/single-cell-data/TileDB-SOMA/pull/3130/flags?src=pr&el=flag&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=single-cell-data) | `82.60% <ø> (+0.11%)` | :arrow_up: |

Flags with carried forward coverage won't be shown. [Click here](https://docs.codecov.io/docs/carryforward-flags?utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=single-cell-data#carryforward-flags-in-the-pull-request-comment) to find out more.

| [Components](https://app.codecov.io/gh/single-cell-data/TileDB-SOMA/pull/3130/components?src=pr&el=components&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=single-cell-data) | Coverage Δ | |
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| [python_api](https://app.codecov.io/gh/single-cell-data/TileDB-SOMA/pull/3130/components?src=pr&el=component&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=single-cell-data) | `82.60% <ø> (+0.11%)` | :arrow_up: |
| [libtiledbsoma](https://app.codecov.io/gh/single-cell-data/TileDB-SOMA/pull/3130/components?src=pr&el=component&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=single-cell-data) | `∅ <ø> (∅)` | |

</details>
Thanks @nguyenv !


Fix patch:
diff --git a/libtiledbsoma/src/soma/soma_array.cc b/libtiledbsoma/src/soma/soma_array.cc
index 394427df5a..99138c94d1 100644
--- a/libtiledbsoma/src/soma/soma_array.cc
+++ b/libtiledbsoma/src/soma/soma_array.cc
@@ -1578,17 +1578,30 @@ std::pair<bool, std::string> SOMAArray::_can_set_shape_domainish_subhelper(
     return std::pair(true, "");
 }
 
-std::pair<bool, std::string> SOMAArray::can_resize_soma_joinid_shape(
-    int64_t newshape, std::string function_name_for_messages) {
+std::pair<bool, std::string> SOMAArray::_can_set_soma_joinid_shape_helper(
+    int64_t newshape, bool is_resize, std::string function_name_for_messages) {
     // Fail if the array doesn't already have a shape yet (they should upgrade
     // first).
-    if (!has_current_domain()) {
-        return std::pair(
-            false,
-            fmt::format(
-                "{}: dataframe currently has no domain set: please "
-                "upgrade the array.",
-                function_name_for_messages));
+    if (!is_resize) {
+        // Upgrading an array to give it a current domain
+        if (has_current_domain()) {
+            return std::pair(
+                false,
+                fmt::format(
+                    "{}: dataframe already has its domain set.",
+                    function_name_for_messages));
+        }
+
+    } else {
+        // Resizing an array's existing current domain
+
+        if (!has_current_domain()) {
+            return std::pair(
+                false,
+                fmt::format(
+                    "{}: dataframe currently has no domain set.",
+                    function_name_for_messages));
+        }
     }
 
     // OK if soma_joinid isn't a dim.
@@ -1597,15 +1610,18 @@ std::pair<bool, std::string> SOMAArray::can_resize_soma_joinid_shape(
     }
 
     // Fail if the newshape isn't within the array's core current domain.
-    std::pair cur_dom_lo_hi = _core_current_domain_slot<int64_t>("soma_joinid");
-    if (newshape < cur_dom_lo_hi.second) {
-        return std::pair(
-            false,
-            fmt::format(
-                "{}: new soma_joinid shape {} < existing shape {}",
-                function_name_for_messages,
-                newshape,
-                cur_dom_lo_hi.second));
+    if (is_resize) {
+        std::pair cur_dom_lo_hi = _core_current_domain_slot<int64_t>(
+            "soma_joinid");
+        if (newshape < cur_dom_lo_hi.second) {
+            return std::pair(
+                false,
+                fmt::format(
+                    "{}: new soma_joinid shape {} < existing shape {}",
+                    function_name_for_messages,
+                    newshape,
+                    cur_dom_lo_hi.second + 1));
+        }
     }
 
     // Fail if the newshape isn't within the array's core (max) domain.
@@ -1617,36 +1633,16 @@ std::pair<bool, std::string> SOMAArray::can_resize_soma_joinid_shape(
                 "{}: new soma_joinid shape {} > maxshape {}",
                 function_name_for_messages,
                 newshape,
-                dom_lo_hi.second));
+                dom_lo_hi.second + 1));
     }
 
     // Sucess otherwise.
     return std::pair(true, "");
 }
 
-void SOMAArray::resize(
-    const std::vector<int64_t>& newshape,
-    std::string function_name_for_messages) {
-    if (_get_current_domain().is_empty()) {
-        throw TileDBSOMAError(fmt::format(
-            "{} array must already have a shape", function_name_for_messages));
-    }
-    _set_current_domain_from_shape(newshape, function_name_for_messages);
-}
-
-void SOMAArray::upgrade_shape(
-    const std::vector<int64_t>& newshape,
-    std::string function_name_for_messages) {
-    if (!_get_current_domain().is_empty()) {
-        throw TileDBSOMAError(fmt::format(
-            "{}: array must not already have a shape",
-            function_name_for_messages));
-    }
-    _set_current_domain_from_shape(newshape, function_name_for_messages);
-}
-
-void SOMAArray::_set_current_domain_from_shape(
+void SOMAArray::_set_shape_helper(
     const std::vector<int64_t>& newshape,
+    bool is_resize,
     std::string function_name_for_messages) {
     if (mq_->query_type() != TILEDB_WRITE) {
         throw TileDBSOMAError(fmt::format(
@@ -1654,6 +1650,22 @@ void SOMAArray::_set_current_domain_from_shape(
             function_name_for_messages));
     }
 
+    if (!is_resize) {
+        // Upgrading an array to install a current domain
+        if (!_get_current_domain().is_empty()) {
+            throw TileDBSOMAError(fmt::format(
+                "{}: array must not already have a shape",
+                function_name_for_messages));
+        }
+    } else {
+        // Expanding an array's current domain
+        if (_get_current_domain().is_empty()) {
+            throw TileDBSOMAError(fmt::format(
+                "{} array must already have a shape",
+                function_name_for_messages));
+        }
+    }
+
     // Variant-indexed dataframes must use a separate path
     _check_dims_are_int64();
 
@@ -1684,14 +1696,30 @@ void SOMAArray::_set_current_domain_from_shape(
     schema_evolution.array_evolve(uri_);
 }
 
-void SOMAArray::resize_soma_joinid_shape(
-    int64_t newshape, std::string function_name_for_messages) {
+void SOMAArray::_set_soma_joinid_shape_helper(
+    int64_t newshape, bool is_resize, std::string function_name_for_messages) {
     if (mq_->query_type() != TILEDB_WRITE) {
         throw TileDBSOMAError(fmt::format(
             "{}: array must be opened in write mode",
             function_name_for_messages));
     }
 
+    if (!is_resize) {
+        // Upgrading an array to install a current domain
+        if (!_get_current_domain().is_empty()) {
+            throw TileDBSOMAError(fmt::format(
+                "{}: array must not already have a shape",
+                function_name_for_messages));
+        }
+    } else {
+        // Expanding an array's current domain
+        if (_get_current_domain().is_empty()) {
+            throw TileDBSOMAError(fmt::format(
+                "{} array must already have a shape",
+                function_name_for_messages));
+        }
+    }
+
     ArraySchema schema = arr_->schema();
     Domain domain = schema.domain();
     unsigned ndim = domain.ndim();
diff --git a/libtiledbsoma/src/soma/soma_array.h b/libtiledbsoma/src/soma/soma_array.h
index d6a8508a82..67833277cf 100644
--- a/libtiledbsoma/src/soma/soma_array.h
+++ b/libtiledbsoma/src/soma/soma_array.h
@@ -1092,10 +1092,23 @@ class SOMAArray : public SOMAObject {
 
     /**
      * This is similar to can_upgrade_shape, but it's a can-we call
-     * for maybe_resize_soma_joinid.
+     * for resize_soma_joinid_shape.
      */
     std::pair<bool, std::string> can_resize_soma_joinid_shape(
-        int64_t newshape, std::string function_name_for_messages);
+        int64_t newshape, std::string function_name_for_messages) {
+        return _can_set_soma_joinid_shape_helper(
+            newshape, true, function_name_for_messages);
+    }
+
+    /**
+     * This is similar to can_upgrade_shape, but it's a can-we call
+     * for upgrade_soma_joinid_shape.
+     */
+    std::pair<bool, std::string> can_upgrade_soma_joinid_shape(
+        int64_t newshape, std::string function_name_for_messages) {
+        return _can_set_soma_joinid_shape_helper(
+            newshape, false, function_name_for_messages);
+    }
 
     /**
      * @brief Resize the shape (what core calls "current domain") up to the
@@ -1110,7 +1123,9 @@ class SOMAArray : public SOMAObject {
      */
     void resize(
         const std::vector<int64_t>& newshape,
-        std::string function_name_for_messages);
+        std::string function_name_for_messages) {
+        _set_shape_helper(newshape, true, function_name_for_messages);
+    }
 
     /**
      * @brief Given an old-style array without current domain, sets its
@@ -1120,7 +1135,9 @@ class SOMAArray : public SOMAObject {
      */
     void upgrade_shape(
         const std::vector<int64_t>& newshape,
-        std::string function_name_for_messages);
+        std::string function_name_for_messages) {
+        _set_shape_helper(newshape, false, function_name_for_messages);
+    }
 
     /**
      * @brief Increases the tiledbsoma shape up to at most the maxshape,
@@ -1137,7 +1154,30 @@ class SOMAArray : public SOMAObject {
      * maxshape. Throws if the array does not have current-domain support.
      */
     void resize_soma_joinid_shape(
-        int64_t newshape, std::string function_name_for_messages);
+        int64_t newshape, std::string function_name_for_messages) {
+        return _set_soma_joinid_shape_helper(
+            newshape, true, function_name_for_messages);
+    }
+
+    /**
+     * @brief Increases the tiledbsoma shape up to at most the maxshape,
+     * resizing the soma_joinid dimension if it is a dimension.
+     *
+     * While SOMA SparseNDArray and DenseNDArray, along with default-indexed
+     * DataFrame, have int64_t dims, non-default-indexed DataFrame objects need
+     * not: it is only required that they have a dim _or_ an attr called
+     * soma_joinid. If soma_joinid is one of the dims, it will be resized while
+     * the others will be preserved. If soma_joinid is not one of the dims,
+     * nothing will be changed, as nothing _needs_ to be changed.
+     *
+     * @return Throws if the requested shape exceeds the array's create-time
+     * maxshape. Throws if the array does not have current-domain support.
+     */
+    void upgrade_soma_joinid_shape(
+        int64_t newshape, std::string function_name_for_messages) {
+        return _set_soma_joinid_shape_helper(
+            newshape, false, function_name_for_messages);
+    }
 
    protected:
     // These two are for use nominally by SOMADataFrame. This could be moved in
@@ -1211,11 +1251,30 @@ class SOMAArray : public SOMAObject {
         bool check_current_domain,
         std::string function_name_for_messages);
 
+    /**
+     * This is a code-dedupe helper for can_resize_soma_joinid_shape and
+     * can_upgrade_domain_soma_joinid_shape.
+     */
+    std::pair<bool, std::string> _can_set_soma_joinid_shape_helper(
+        int64_t newshape,
+        bool is_resize,
+        std::string function_name_for_messages);
+
     /**
      * This is a code-dedupe helper method for resize and upgrade_shape.
      */
-    void _set_current_domain_from_shape(
+    void _set_shape_helper(
         const std::vector<int64_t>& newshape,
+        bool is_resize,
+        std::string function_name_for_messages);
+
+    /**
+     * This is a code-dedupe helper method for resize_soma_joinid_shape and
+     * upgrade_soma_joinid_shape.
+     */
+    void _set_soma_joinid_shape_helper(
+        int64_t newshape,
+        bool is_resize,
         std::string function_name_for_messages);
 
     /**


Test patch:
diff --git a/libtiledbsoma/test/unit_soma_dataframe.cc b/libtiledbsoma/test/unit_soma_dataframe.cc
index 4a7f114fe7..942e0f8f28 100644
--- a/libtiledbsoma/test/unit_soma_dataframe.cc
+++ b/libtiledbsoma/test/unit_soma_dataframe.cc
@@ -572,13 +572,30 @@ TEST_CASE_METHOD(
         } else {
             REQUIRE(maxdom_sjid[1] > 2000000000);
         }
-
         sdf->close();
 
         REQUIRE(sdf->nnz() == 2);
         write_sjid_u32_str_data_from(8);
         REQUIRE(sdf->nnz() == 4);
 
+        // Check can_upgrade_soma_joinid_shape
+        sdf->open(OpenMode::read);
+        if (!use_current_domain) {
+            std::pair<bool, std::string>
+                check = sdf->can_upgrade_soma_joinid_shape(1, "testing");
+            REQUIRE(check.first == true);
+            REQUIRE(check.second == "");
+        } else {
+            std::pair<bool, std::string>
+                check = sdf->can_upgrade_soma_joinid_shape(1, "testing");
+            // Must fail since this is too small.
+            REQUIRE(check.first == false);
+            REQUIRE(
+                check.second ==
+                "testing: dataframe already has its domain set.");
+        }
+        sdf->close();
+
         // Resize
         auto new_shape = int64_t{SOMA_JOINID_RESIZE_DIM_MAX + 1};
 
@@ -662,14 +679,13 @@ TEST_CASE_METHOD(
             REQUIRE(check.first == false);
             REQUIRE(
                 check.second ==
-                "testing: dataframe currently has no domain set: please "
-                "upgrade the array.");
+                "testing: dataframe currently has no domain set.");
         } else {
             // Must fail since this is too small.
             REQUIRE(check.first == false);
             REQUIRE(
                 check.second ==
-                "testing: new soma_joinid shape 1 < existing shape 199");
+                "testing: new soma_joinid shape 1 < existing shape 200");
             check = sdf->can_resize_soma_joinid_shape(
                 SOMA_JOINID_RESIZE_DIM_MAX + 1, "testing");
             REQUIRE(check.first == true);
@@ -894,14 +910,13 @@ TEST_CASE_METHOD(
             REQUIRE(check.first == false);
             REQUIRE(
                 check.second ==
-                "testing: dataframe currently has no domain set: please "
-                "upgrade the array.");
+                "testing: dataframe currently has no domain set.");
         } else {
             // Must fail since this is too small.
             REQUIRE(check.first == false);
             REQUIRE(
                 check.second ==
-                "testing: new soma_joinid shape 1 < existing shape 199");
+                "testing: new soma_joinid shape 1 < existing shape 200");
             check = sdf->can_resize_soma_joinid_shape(
                 SOMA_JOINID_RESIZE_DIM_MAX + 1, "testing");
             REQUIRE(check.first == true);
@@ -1142,14 +1157,13 @@ TEST_CASE_METHOD(
             REQUIRE(check.first == false);
             REQUIRE(
                 check.second ==
-                "testing: dataframe currently has no domain set: please "
-                "upgrade the array.");
+                "testing: dataframe currently has no domain set.");
         } else {
             // Must fail since this is too small.
             REQUIRE(check.first == false);
             REQUIRE(
                 check.second ==
-                "testing: new soma_joinid shape 1 < existing shape 99");
+                "testing: new soma_joinid shape 1 < existing shape 100");
             check = sdf->can_resize_soma_joinid_shape(
                 SOMA_JOINID_RESIZE_DIM_MAX + 1, "testing");
             REQUIRE(check.first == true);
@@ -1351,8 +1365,7 @@ TEST_CASE_METHOD(
             REQUIRE(check.first == false);
             REQUIRE(
                 check.second ==
-                "testing: dataframe currently has no domain set: please "
-                "upgrade the array.");
+                "testing: dataframe currently has no domain set.");
         } else {
             // Must pass since soma_joinid isn't a dim in this case.
             REQUIRE(check.first == true);
diff --git a/libtiledbsoma/test/unit_soma_sparse_ndarray.cc b/libtiledbsoma/test/unit_soma_sparse_ndarray.cc
index 4d455cedbe..e21edde284 100644
--- a/libtiledbsoma/test/unit_soma_sparse_ndarray.cc
+++ b/libtiledbsoma/test/unit_soma_sparse_ndarray.cc
@@ -161,7 +161,7 @@ TEST_CASE("SOMASparseNDArray: basic", "[SOMASparseNDArray]") {
             snda->resize(new_shape, "testing");
             snda->close();
 
-            snda = SOMASparseNDArray::open(uri, OpenMode::read, ctx);
+            snda->open(OpenMode::read);
             REQUIRE(snda->shape() == new_shape);
             snda->close();
 
@@ -176,7 +176,7 @@ TEST_CASE("SOMASparseNDArray: basic", "[SOMASparseNDArray]") {
             snda->close();
 
             // Try out-of-bounds write after resize.
-            snda = SOMASparseNDArray::open(uri, OpenMode::write, ctx);
+            snda->open(OpenMode::write);
             snda->set_column_data(dim_name, d0b.size(), d0b.data());
             snda->set_column_data(attr_name, a0b.size(), a0b.data());
             // Implicitly checking for no throw