parametrize census config

chanzuckerberg · Jun 3, 2024 · 48670ff · 48670ff
1 parent 5f19a27
commit 48670ff
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Showing 3 changed files with 8 additions and 4 deletions.
diff --git a/tools/models/scvi/scvi-config.yaml b/tools/models/scvi/scvi-config.yaml
@@ -5,6 +5,8 @@ census:
     null
   obs_query_model: # Required when loading data for model training. Do not change.
     'is_primary_data == True and nnz >= 300'
+  version:
+    "2024-05-20"
 hvg:
   top_n_hvg: 
     8000

diff --git a/tools/models/scvi/scvi-create-latent-update.py b/tools/models/scvi/scvi-create-latent-update.py
@@ -14,12 +14,13 @@
     with open(file) as f:
         config = yaml.safe_load(f)
 
-    census = cellxgene_census.open_soma(census_version="2024-05-20")
-
     census_config = config.get("census")
     experiment_name = census_config.get("organism")
     obs_value_filter = census_config.get("obs_query")
 
+    version = census_config.get("version")
+    census = cellxgene_census.open_soma(census_version=version)
+
     hv = pd.read_pickle("hv_genes.pkl")
     hv_idx = hv[hv].index
 

diff --git a/tools/models/scvi/scvi-prepare.py b/tools/models/scvi/scvi-prepare.py
@@ -11,13 +11,14 @@
     with open(file) as f:
         config = yaml.safe_load(f)
 
-    census = cellxgene_census.open_soma(census_version="2023-12-15")
-
     census_config = config.get("census")
     experiment_name = census_config.get("organism")
     obs_query = census_config.get("obs_query")
     obs_query_model = census_config.get("obs_query_model")
 
+    version = census_config.get("version")
+    census = cellxgene_census.open_soma(census_version=version)
+
     if obs_query is None:
         obs_value_filter = obs_query_model
     else: