Merge branch 'master' into fix/mjn-duplicate-nodes

Author: 31puneet

malariagen_data/anoph/dipclust.py

@@ -542,10 +542,10 @@ def _dipclust_concat_subplots(
             if isinstance(figure, go.Figure):
                 # This is a figure, access the traces within it.
                 for trace in range(len(figure["data"])):
-                    fig.append_trace(figure["data"][trace], row=i + 1, col=1)
+                    fig.add_trace(figure["data"][trace], row=i + 1, col=1)
             else:
                 # Assume this is a trace, add directly.
-                fig.append_trace(figure, row=i + 1, col=1)
+                fig.add_trace(figure, row=i + 1, col=1)
 
         fig.update_xaxes(visible=False)
         fig.update_layout(

malariagen_data/anoph/frq_base.py

@@ -276,7 +276,7 @@ def plot_frequencies_heatmap(
         heatmap_df.set_index(index_col, inplace=True)
 
         # Clean column names.
-        heatmap_df.columns = heatmap_df.columns.str.lstrip("frq_")
+        heatmap_df.columns = heatmap_df.columns.str.removeprefix("frq_")
 
         # Deal with width and height.
         if width is None:

malariagen_data/anoph/sample_metadata.py

@@ -1569,11 +1569,11 @@ def plot_sample_location_mapbox(
         # Sort by `color` column by default, which can be overridden via category_orders.
         df_locations = df_samples[location_columns].drop_duplicates().sort_values(color)
 
-        fig = px.scatter_mapbox(
+        fig = px.scatter_map(
             df_locations,
             lat="latitude",
             lon="longitude",
-            mapbox_style="open-street-map",
+            map_style="open-street-map",
             zoom=zoom,
             color=color,
             category_orders=category_orders,

malariagen_data/plasmodium.py

@@ -1,5 +1,6 @@
 import json
 
+import os
 import dask.array as da
 import pandas as pd
 import xarray
@@ -59,7 +60,7 @@ def sample_metadata(self):
             One row per sample.
         """
         if self._cache_sample_metadata is None:
-            path = f"{self._path}/{self.CONF['metadata_path']}"
+            path = os.path.join(self._path, self.CONF["metadata_path"])
             with self._fs.open(path) as f:
                 self._cache_sample_metadata = pd.read_csv(f, sep="\t", na_values="")
         return self._cache_sample_metadata
@@ -74,7 +75,7 @@ def _open_variant_calls_zarr(self):
 
         """
         if self._cache_variant_calls_zarr is None:
-            path = f"{self._path}/{self.CONF['variant_calls_zarr_path']}"
+            path = os.path.join(self._path, self.CONF["variant_calls_zarr_path"])
             store = _init_zarr_store(fs=self._fs, path=path)
             self._cache_variant_calls_zarr = zarr.open_consolidated(store=store)
         return self._cache_variant_calls_zarr
@@ -204,7 +205,7 @@ def open_genome(self):
 
         """
         if self._cache_genome is None:
-            path = f"{self._path}/{self.CONF['reference_path']}"
+            path = os.path.join(self._path, self.CONF["reference_path"])
             store = _init_zarr_store(fs=self._fs, path=path)
             self._cache_genome = zarr.open_consolidated(store=store)
         return self._cache_genome
@@ -316,7 +317,7 @@ def genome_features(self, attributes=("ID", "Parent", "Name")):
         try:
             df = self._cache_genome_features[attributes]
         except KeyError:
-            path = f"{self._path}/{self.CONF['annotations_path']}"
+            path = os.path.join(self._path, self.CONF["annotations_path"])
             with self._fs.open(path, mode="rb") as f:
                 df = _read_gff3(f, compression="gzip")
             if attributes is not None:

pyproject.toml

@@ -6,15 +6,10 @@ readme = "README.md"
 documentation = "https://malariagen.github.io/malariagen-data-python/latest/"
 repository = "https://github.com/malariagen/malariagen-data-python"
 authors = [
-    "Alistair Miles <alistair.miles@sanger.ac.uk>",
-    "Chris Clarkson <chris.clarkson@sanger.ac.uk>",
-    "Anastasia Hernandez-Koutoucheva <ah32@sanger.ac.uk>",
-    "Lee Hart <lee.hart@sanger.ac.uk>",
-    "Kathryn Murie <km22@sanger.ac.uk>",
-    "Nace Kranjc <n.kranjc@imperial.ac.uk>",
-    "Kelly Bennett <kb25@sanger.ac.uk>",
-    "Jon Brenas <jb52@sanger.ac.uk>",
-    "Sanjay Nagi <sanjay.nagi@lstmed.ac.uk>",
+    "Chris Clarkson <Chris.Clarkson@lstmed.ac.uk>",
+    "Anastasia Hernandez-Koutoucheva <Anastasia.Hernandez-Koutoucheva@lstmed.ac.uk>",
+    "Kelly Bennett <Kelly.Bennett@lstmed.ac.uk>",
+    "Jon Brenas <Jon.Brenas@lstmed.ac.uk>",
     "Tristan Dennis <Tristan.Dennis@lstmed.ac.uk>",
 ]
 license = "MIT"