summaryrefslogtreecommitdiff
path: root/issues
diff options
context:
space:
mode:
authorFrederick Muriuki Muriithi2024-10-15 16:02:15 -0500
committerFrederick Muriuki Muriithi2024-10-15 16:02:15 -0500
commit0b2bb289f5a9b77505b66e41345514e6ee81ba79 (patch)
treedd2d2c7825ab46769d663d27103ab72c8a8520fa /issues
parent1308102cdbb37a6a60023904ec9ad315104b3bd5 (diff)
downloadgn-gemtext-0b2bb289f5a9b77505b66e41345514e6ee81ba79.tar.gz
GN3: New issue: python-plotly dependency not updatable.
Diffstat (limited to 'issues')
-rw-r--r--issues/genenetwork3/generate-heatmaps-failing.gmi30
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.