fix: update download_databases script and refactor database reference…

…s in tests
bacpop · Dec 20, 2024 · 2bf8cab · 2bf8cab
1 parent 54aab40
commit 2bf8cab
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Showing 3 changed files with 4 additions and 4 deletions.
diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml
@@ -32,7 +32,7 @@ jobs:
     - name: Download and extract GPS database
       working-directory: ./main
       run: |
-        ./scripts/download_databases
+        ./scripts/download_databases --refs
         
     - name: Set up Python 3.9
       uses: actions/setup-python@v2

diff --git a/tests/setup.py b/tests/setup.py
@@ -71,7 +71,7 @@ def do_network_internal(p_hash: str):
     do_assign_clusters(p_hash)
     visualise.network_internal(p_hash,
                                fs,
-                               full_db_fs,
+                               ref_db_fs,
                                args,
                                name_mapping,
                                species)
diff --git a/tests/test_unit.py b/tests/test_unit.py
@@ -154,7 +154,7 @@ def __init__(self, result):
     visualise.microreact(
         p_hash,
         fs,
-        setup.full_db_fs,
+        setup.ref_db_fs,
         args,
         setup.name_mapping,
         setup.species,
@@ -267,7 +267,7 @@ def __init__(self, result):
 
     setup.do_assign_clusters(p_hash)
     visualise.network(
-        p_hash, fs, setup.full_db_fs, args, setup.name_mapping, setup.species
+        p_hash, fs, setup.ref_db_fs, args, setup.name_mapping, setup.species
     )
 
     for cluster in external_to_poppunk_clusters.keys():