fix: implemented temporary workaround suggested by TileDB. (#2251) #58
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@@ Coverage Diff @@
## main #58 +/- ##
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+ Coverage 70.04% 70.05% +0.01%
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Files 138 138
Lines 10922 10926 +4
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+ Hits 7650 7654 +4
Misses 3272 3272
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server/compute/diffexp_cxg.py
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| futures.append( | ||
| executor.submit( | ||
| _mean_var_sparse_ab, | ||
| adaptor.open_array("X"), row_selector_A, nA, row_selector_B, nB, cols)) |
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adaptor.open_array("X") is the actual workaround the rest is reformatting to placate flake8.
server/compute/diffexp_cxg.py
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| executor.submit(_mean_var_ab, matrix, row_selector_AB, row_selector_A_in_AB, row_selector_B_in_AB, cols) | ||
| executor.submit( | ||
| _mean_var_ab, | ||
| adaptor.open_array("X"), row_selector_AB, row_selector_A_in_AB, row_selector_B_in_AB, cols) |
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adaptor.open_array("X") is the actual workaround the rest is reformatting to placate flake8.
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Note, as discussed at the war room meeting, holding off on merging this workaround until 15:00 PT today til we hear back from TileDB regarding an ETA for a fix. |
| @@ -19,6 +19,6 @@ pandas>=1.0,!=1.1 # pandas 1.1 breaks tests, https://github.com/pandas-dev/pand | |||
| PyYAML>=5.4 # CVE-2020-14343 | |||
| scipy>=1.4 | |||
| requests>=2.22.0 | |||
| tiledb>=0.9 | |||
| tiledb==0.10.0 | |||
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Pinned at 0.10.0 (current version) instead of specifying >=0.10.0 since, under the covers in TileDB-Py, the embedded TileDB versions can also get incremented.
This seems safer to me, but if I'm wrong, please let me know!
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this seems fine to me. I'm unclear why all versions are not pinned. For our internal repo (ie, single-cell-explorer), we have no need to support multiple versions, and can safely pin.
This is not true for the cellxgene repo, which needs to allow users some flexibility.
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I was wondering about that too. 😄
Reviewers
Functional:
@bkmartinjr, @MDunitz
Readability:
@ebezzi
Changes
Reviewer Notes
XandX_col_shiftarrays.