Remove column validations from summarize_clades

Summarize_clades was doing a collect_schema operation to ensure
that items in the group_by paramater exist as colums in the
sequence metadata. However, testing on a lower-memory laptop
revealed that collect_schema was too memory intensive to
introduce in the middle of LazyFrame handling, so we'll
take it out.

src/cladetime/sequence.py

@@ -3,7 +3,6 @@
 import lzma
 import os
 import re
-import warnings
 from datetime import datetime
 from pathlib import Path
 from urllib.parse import urlparse
@@ -15,7 +14,6 @@
 from Bio.SeqIO import FastaIO
 from requests import Session
 
-from cladetime.exceptions import CladeTimeSequenceWarning
 from cladetime.types import StateFormat
 from cladetime.util.reference import _get_date
 from cladetime.util.session import _get_session
@@ -298,32 +296,17 @@ def summarize_clades(sequence_metadata: pl.LazyFrame, group_by: list | None = No
         A Frame that summarizes clade counts by the specified columns. If sequence_metadata
         is a LazyFrame, returns a LazyFrame. Otherwise, returns a DataFrame.
 
-    Raises
-    ------
-    CladeTimeSequenceWarning
-        If group_by contains a column name that is not in sequence_metadata or
-        if group_by contains a column named 'count'
+    Notes
+    -----
+    This function does not validate the group_by columns because doing so on a
+    large LazyFrame would involve a memory-intensive collect_schema operation.
+    If the group_by columns are not in the sequence metadata, this function
+    will succeed, but a subsequent collect() on the returned LazyFrame will
+    result in an error.
     """
     if group_by is None:
         group_by = ["clade_nextstrain", "country", "date", "location", "host"]
 
-    # Validate group_by columns
-    metadata_cols = sequence_metadata.collect_schema().names()
-    warning_msg = ""
-    if not all(col in metadata_cols for col in group_by):
-        warning_msg = warning_msg + f"Invalid group_by columns: {group_by} \n"
-    if "count" in group_by:
-        warning_msg = warning_msg + "Group_by cannot contain 'count' column \n"
-    if len(warning_msg) > 0:
-        warnings.warn(
-            warning_msg[0],
-            category=CladeTimeSequenceWarning,
-        )
-        if isinstance(sequence_metadata, pl.LazyFrame):
-            return pl.LazyFrame()
-        else:
-            return pl.DataFrame()
-
     counts = (
         sequence_metadata.select(group_by).group_by(group_by).agg(pl.len().alias("count")).cast({"count": pl.UInt32})
     )

tests/unit/test_sequence.py

@@ -9,7 +9,6 @@
 from polars.testing import assert_frame_equal
 
 from cladetime import sequence
-from cladetime.exceptions import CladeTimeSequenceWarning
 from cladetime.types import StateFormat
 
 
@@ -320,26 +319,3 @@ def test_summarize_clades_custom_group():
 
     summarized = sequence.summarize_clades(test_metadata, group_by=["clade_nextstrain"])
     assert_frame_equal(expected_summary, summarized, check_column_order=False, check_row_order=False)
-
-
-def test_summarize_clades_invalid_cols():
-    test_metadata = pl.DataFrame(
-        {
-            "clade_nextstrain": ["11C", "11C", "11C"],
-            "country": ["Canada", "USA", "USA"],
-            "date": ["2022-01-01", "2022-01-01", "2023-12-27"],
-        }
-    )
-    with pytest.warns(CladeTimeSequenceWarning):
-        summarized = sequence.summarize_clades(test_metadata, group_by=["country", "wombat_count"])
-        assert len(summarized) == 0
-
-    test_metadata = pl.DataFrame(
-        {
-            "clade_nextstrain": ["11C", "11C", "11C"],
-            "count": [1, 2, 3],
-        }
-    )
-    with pytest.warns(CladeTimeSequenceWarning):
-        summarized = sequence.summarize_clades(test_metadata, group_by=["clade_nextstrain", "count"])
-        assert len(summarized) == 0