Merge pull request #38 from harmsm/main

updated for pandas 2
harmslab · Apr 4, 2023 · 86913d4 · 86913d4
2 parents f20da7e + 6a899a2
commit 86913d4
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Showing 3 changed files with 11 additions and 8 deletions.
diff --git a/docs/badges/ghwf.svg b/docs/badges/ghwf.svg
diff --git a/topiary/_private/check/topiary_dataframe.py b/topiary/_private/check/topiary_dataframe.py
@@ -165,6 +165,9 @@ def check_topiary_dataframe(df):
         # Validate this as a boolean column
         df.loc[:,"keep"] = column_to_bool(df.loc[:,"keep"],"keep")
 
+        # Force it to really be bool
+        df = df.astype({"keep":bool})
+
     # -------------------------------------------------------------------------
     # Process uid column
 

diff --git a/topiary/ncbi/entrez/proteome.py b/topiary/ncbi/entrez/proteome.py
@@ -186,7 +186,7 @@ def get_proteome(taxid=None,species=None):
     # Now get summary data for these records.
     esummary_query = ",".join(returned_ids)
     esummary_handle = Entrez.esummary(db="assembly",id=esummary_query)
-    esummary_record = Entrez.read(esummary_handle)
+    esummary_record = Entrez.read(esummary_handle,validate=False)
 
     try:
         records = esummary_record["DocumentSummarySet"]["DocumentSummary"]