analyze_landscape fails

[azazellochg]

cryodrgn 3.1.0 beta from github

analyze_landscape raises an unexpected kwarg ("affinity") exception. The fix below seems to work:

diff --git a/cryodrgn/commands/analyze_landscape.py b/cryodrgn/commands/analyze_landscape.py
index f14cbd5..64ab60b 100644
--- a/cryodrgn/commands/analyze_landscape.py
+++ b/cryodrgn/commands/analyze_landscape.py
@@ -329,7 +329,7 @@ def analyze_volumes(
if not os.path.exists(subdir):
os.makedirs(subdir)
cluster = AgglomerativeClustering(
-        n_clusters=M, affinity="euclidean", linkage=linkage
+        n_clusters=M, linkage=linkage
)
labels = cluster.fit_predict(vols)
utils.save_pkl(labels, f"{subdir}/state_labels.pkl")

[michal-g]

Thanks, we just came across this bug as well and will be addressing it in 3.2.0-beta — d18522c has the same fix as above.