Release 0.2.6: support pandas 3.0

eido/_version.py

@@ -1 +1 @@
-__version__ = "0.2.5"
+__version__ = "0.2.6"

eido/output_formatters.py

@@ -112,6 +112,11 @@ def _convert_sample_to_row(
             else:
                 value = sample.get(attribute)
 
+            if isinstance(value, float) and value != value:
+                # pandas (>=3.0) yields float('nan') instead of None for missing
+                # values when a Sample's attributes originate from a DataFrame
+                value = None
+
             sample_row.append(value or "")
 
         return ",".join(sample_row)

requirements/requirements-all.txt

@@ -1,6 +1,6 @@
 importlib-metadata; python_version < '3.10'
 jsonschema>=3.0.1
 logmuse>=0.2.5
-pandas<3.0.0
+pandas
 peppy>=0.40.7
 ubiquerg>=0.5.2

tests/test_conversions.py

@@ -4,6 +4,7 @@
     pep_conversion_plugins,
     convert_project,
 )
+from eido.output_formatters import MultilineOutputFormatter
 import peppy
 
 
@@ -104,3 +105,30 @@ def test_multiple_subsamples(self, test_multiple_subs):
             "yaml-samples",
         )
         assert isinstance(conversion["samples"], str)
+
+
+class TestMultilineOutputFormatterMissingValues:
+    """
+    Under pandas >=3.0 a missing attribute reaches the formatter as float('nan')
+    rather than as an empty string, which used to raise TypeError from the join.
+    """
+
+    def test_missing_attribute_becomes_empty_field(self):
+        sample = peppy.Sample({"sample": "frog_1", "fasta": float("nan")})
+
+        assert MultilineOutputFormatter.format([sample]) == "sample,fasta\nfrog_1,\n"
+
+    def test_missing_subsample_attribute_becomes_empty_field(self):
+        # Merging a subsample table that lacks a column produces a list of nan
+        sample = peppy.Sample(
+            {
+                "sample": "frog_1",
+                "fasta": [float("nan"), float("nan")],
+                "subsample_name": ["0", "1"],
+            }
+        )
+
+        assert (
+            MultilineOutputFormatter.format([sample])
+            == "sample,fasta\nfrog_1,\nfrog_1,\n"
+        )