Update docs action versions, bump main version

Author: johnlees

.github/workflows/docs_pr.yml

@@ -8,7 +8,7 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v1
+    - uses: actions/checkout@v4
 
     - uses: ammaraskar/sphinx-action@master
       with:

.github/workflows/docs_push.yml

@@ -11,13 +11,13 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v1
+    - uses: actions/checkout@v4
 
     - uses: ammaraskar/sphinx-action@master
       with:
         docs-folder: "docs/"
 
-    - uses: actions/upload-pages-artifact@v2
+    - uses: actions/upload-pages-artifact@v3
       with:
         name: github-pages
         path: docs/_build/html/
@@ -39,4 +39,4 @@ jobs:
     steps:
       - name: Deploy to GitHub Pages
         id: deployment
-        uses: actions/deploy-pages@v3
+        uses: actions/deploy-pages@v4

PopPUNK/__init__.py

@@ -3,7 +3,7 @@
 
 '''PopPUNK (POPulation Partitioning Using Nucleotide Kmers)'''
 
-__version__ = '2.7.5'
+__version__ = '2.7.6'
 
 # Minimum sketchlib version
 SKETCHLIB_MAJOR = 2

test/batch12_external_clusters.csv

@@ -38,6 +38,7 @@ def deleteDir(dirname):
     "example_query_stable",
     "example_query_update",
     "example_query_update_2",
+    "example_query_update_fast",
     "example_lineage_query",
     "example_viz",
     "example_viz_subset",