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author | Frederick Muriuki Muriithi | 2024-10-15 16:02:15 -0500 |
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committer | Frederick Muriuki Muriithi | 2024-10-15 16:02:15 -0500 |
commit | 0b2bb289f5a9b77505b66e41345514e6ee81ba79 (patch) | |
tree | dd2d2c7825ab46769d663d27103ab72c8a8520fa /issues | |
parent | 1308102cdbb37a6a60023904ec9ad315104b3bd5 (diff) | |
download | gn-gemtext-0b2bb289f5a9b77505b66e41345514e6ee81ba79.tar.gz |
GN3: New issue: python-plotly dependency not updatable.
Diffstat (limited to 'issues')
-rw-r--r-- | issues/genenetwork3/generate-heatmaps-failing.gmi | 30 |
1 files changed, 30 insertions, 0 deletions
diff --git a/issues/genenetwork3/generate-heatmaps-failing.gmi b/issues/genenetwork3/generate-heatmaps-failing.gmi new file mode 100644 index 0000000..03256e6 --- /dev/null +++ b/issues/genenetwork3/generate-heatmaps-failing.gmi @@ -0,0 +1,30 @@ +# Generate Heatmaps Failing + +## Tags + +* type: bug +* status: open +* priority: medium +* assigned: fredm, zachs, zsloan +* keywords: genenetwork3, gn3, GN3, heatmaps + +## Reproduce + +* Go to https://genenetwork.org/ +* Under "Select and Search" menu, enter "synap*" for the "Get Any" field +* Click "Search" +* In search results page, select first 10 traits +* Click "Add" +* Under "Create a new collection" enter the name "newcoll" and click "Create collection" +* In the collections page that shows up, click "Select All" once +* Ensure all the traits are selected +* Click "Generate Heatmap" and wait +* Note how system fails silently with no heatmap presented + +### Notes + +On https://gn2-fred.genenetwork.org the heatmaps fails with a note ("ERROR: undefined"). In the logs, I see "Module 'scipy' has no attribute 'array'" which seems to be due to a change in numpy. +=> https://github.com/MaartenGr/BERTopic/issues/1791 +=> https://github.com/scipy/scipy/issues/19972 + +This issue should not be present with python-plotly@5.20.0 but since guix-bioinformatics pins the guix version to `b0b988c41c9e0e591274495a1b2d6f27fcdae15a`, we are not able to pull in newer versions of packages from guix. |