Merge branch 'master' into add-citation-info-to-dipclust-19-03-25

Author: leehart

docs/source/_static/switcher.json

@@ -2,81 +2,81 @@
     {
         "name": "15.0.1",
         "version": "v15.0.1",
-        "url": "https:///malariagen.github.io/malariagen-data-python/v15.0.1/",
+        "url": "https://malariagen.github.io/malariagen-data-python/v15.0.1/",
         "preferred": true
     },
     {
         "name": "14.0.0",
         "version": "v14.0.0",
-        "url": "https:///malariagen.github.io/malariagen-data-python/v14.0.0/",
+        "url": "https://malariagen.github.io/malariagen-data-python/v14.0.0/"
     },
     {
         "name": "13.5.0",
         "version": "v13.5.0",
-        "url": "https:///malariagen.github.io/malariagen-data-python/v13.5.0/",
+        "url": "https://malariagen.github.io/malariagen-data-python/v13.5.0/"
     },
     {
         "name": "13.4.0",
         "version": "v13.4.0",
-        "url": "https:///malariagen.github.io/malariagen-data-python/v13.4.0/",
+        "url": "https://malariagen.github.io/malariagen-data-python/v13.4.0/"
     },
     {
         "name": "13.3.0",
         "version": "v13.3.0",
-        "url": "https:///malariagen.github.io/malariagen-data-python/v13.3.0/",
+        "url": "https://malariagen.github.io/malariagen-data-python/v13.3.0/"
     },
     {
         "name": "13.2.1",
         "version": "v13.2.1",
-        "url": "https:///malariagen.github.io/malariagen-data-python/v13.2.0/",
+        "url": "https://malariagen.github.io/malariagen-data-python/v13.2.0/"
     },
     {
         "name": "13.1.0",
         "version": "v13.1.0",
-        "url": "https:///malariagen.github.io/malariagen-data-python/v13.1.0/",
+        "url": "https://malariagen.github.io/malariagen-data-python/v13.1.0/"
     },
     {
         "name": "13.0.4",
         "version": "v13.0.4",
-        "url": "https:///malariagen.github.io/malariagen-data-python/v13.0.4/",
+        "url": "https://malariagen.github.io/malariagen-data-python/v13.0.4/"
     },
     {
         "name": "12.0.0",
         "version": "v12.0.0",
-        "url": "https:///malariagen.github.io/malariagen-data-python/v12.0.0/"
+        "url": "https://malariagen.github.io/malariagen-data-python/v12.0.0/"
     },
     {
         "name": "11.0.0",
         "version": "v11.0.0",
-        "url": "https:///malariagen.github.io/malariagen-data-python/v11.0.0/"
+        "url": "https://malariagen.github.io/malariagen-data-python/v11.0.0/"
     },
     {
         "name": "10.0.0",
         "version": "v10.0.0",
-        "url": "https:///malariagen.github.io/malariagen-data-python/v10.0.0/"
+        "url": "https://malariagen.github.io/malariagen-data-python/v10.0.0/"
     },
     {
         "name": "9.0.0",
         "version": "v9.0.0",
-        "url": "https:///malariagen.github.io/malariagen-data-python/v9.0.0/"
+        "url": "https://malariagen.github.io/malariagen-data-python/v9.0.0/"
     },
     {
         "name": "8.0.0",
         "version": "v8.0.0",
-        "url": "https:///malariagen.github.io/malariagen-data-python/v8.0.0/"
+        "url": "https://malariagen.github.io/malariagen-data-python/v8.0.0/"
     },
     {
         "name": "7.15.0",
         "version": "v7.15.0",
-        "url": "https:///malariagen.github.io/malariagen-data-python/v7.15.0/"
+        "url": "https://malariagen.github.io/malariagen-data-python/v7.15.0/"
     },
     {
         "name": "7.14.0",
         "version": "v7.14.0",
-        "url": "https:///malariagen.github.io/malariagen-data-python/v7.14.0/"
+        "url": "https://malariagen.github.io/malariagen-data-python/v7.14.0/"
     },
     {
         "version": "dev",
-        "url": "https:///malariagen.github.io/malariagen-data-python/latest/"
+        "url": "https://malariagen.github.io/malariagen-data-python/latest/"
     }
 ]

poetry.lock

@@ -27,6 +27,9 @@ llvmlite = "*"
 scipy = "*"
 pandas = "*"
 zarr = ">=2.11, <3.0.0"
+# zarr<3.0.0 is not compatible with numcodecs 0.16.0
+# https://github.com/zarr-developers/zarr-python/issues/2963
+numcodecs = "<0.16"
 dask = {version="*", extras=["array"]}
 distributed = "*"
 fsspec = "*"
@@ -37,10 +40,10 @@ BioPython = "*"
 scikit-allel = ">=1.3.13"
 xarray = "*"
 plotly = "*"
-# Bokeh 3.7.0 causes type checking issues.
+# Bokeh 3.7.x causes type checking issues.
 # https://github.com/bokeh/bokeh/issues/14412
 # https://github.com/malariagen/malariagen-data-python/issues/734
-bokeh = "!=3.7.0"
+bokeh = "<3.7.0"
 statsmodels = "*"
 ipyleaflet = ">=0.17.0"
 ipywidgets = "*"
@@ -55,7 +58,7 @@ tqdm = "*"
 # ensure support for dash in jupyter notebooks
 # https://dash.plotly.com/dash-in-jupyter
 # Dash 3.0.0 causes type checking issues.
-# https://github.com/plotly/dash/issues/3226
+# https://github.com/plotly/dash/issues/3226
 dash = "<3.0.0"
 # constrain minimum version to accelerate solve
 dash-cytoscape = ">=1.0.0"