chore(deps): allow numpy v2

[corneliusroemer]

Description of proposed changes

Looks like we first need to support pandas v2 before we can move to numpy v2.

Resolves #1504

Related issue(s)

Checklist

• Automated checks pass
• Check if you need to add a changelog message
• Check if you need to add tests
• Check if you need to update docs

[corneliusroemer]

Interesting cram failure, doesn't seem like massive issue but good to have cram :)

--- tests/functional/filter/cram/subsample-weighted.t
+++ tests/functional/filter/cram/subsample-weighted.t.err
@@ -112,7 +112,7 @@
   Sampling with weights defined by weights.tsv.
   WARNING: The input metadata contains these values under the following columns that are not directly covered by 'weights.tsv':
   - 'location': ['B']
-  The default weight of 1 will be used for all groups defined by those values.
+  The default weight of np.int64(1) will be used for all groups defined by those values.
   NOTE: Skipping 4 groups due to lack of entries in metadata.
   NOTE: Weights were not provided for the column 'month'. Using equal weights across values in that column.
   2 strains were dropped during filtering
@@ -[16](https://github.com/nextstrain/augur/actions/runs/11817506335/job/32923053728?pr=1533#step:9:17)2,7 +162,7 @@
   WARNING: The input metadata contains these values under the following columns that are not directly covered by 'weights.tsv':
   - 'location': ['B']
   - 'month': ['2000-01', '2000-03']
-  The default weight of 1 will be used for all groups defined by those values.
+  The default weight of np.int64(1) will be used for all groups defined by those values.
   NOTE: Skipping 1 group due to lack of entries in metadata.
   2 strains were dropped during filtering
   	2 were dropped because of subsampling criteria