Update doctest references

nextstrain · Jul 28, 2022 · a3fd02c · a3fd02c
1 parent 4f369b3
commit a3fd02c
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Showing 3 changed files with 8 additions and 2 deletions.
diff --git a/augur/filter/include_exclude_rules.py b/augur/filter/include_exclude_rules.py
@@ -51,6 +51,8 @@ def filter_by_exclude(metadata, exclude_file):
         Strains that pass the filter
 
 
+    >>> import os
+    >>> from tempfile import NamedTemporaryFile
     >>> metadata = pd.DataFrame([{"region": "Africa"}, {"region": "Europe"}], index=["strain1", "strain2"])
     >>> with NamedTemporaryFile(delete=False) as exclude_file:
     ...     characters_written = exclude_file.write(b'strain1')
@@ -409,6 +411,8 @@ def force_include_strains(metadata, include_file):
         Strains that pass the filter
 
 
+    >>> import os
+    >>> from tempfile import NamedTemporaryFile
     >>> metadata = pd.DataFrame([{"region": "Africa"}, {"region": "Europe"}], index=["strain1", "strain2"])
     >>> with NamedTemporaryFile(delete=False) as include_file:
     ...     characters_written = include_file.write(b'strain1')

diff --git a/augur/filter/io.py b/augur/filter/io.py
@@ -42,6 +42,8 @@ def filter_kwargs_to_str(kwargs):
         String representation of the kwargs for reporting.
 
 
+    >>> from augur.dates import numeric_date
+    >>> from augur.filter.include_exclude_rules import filter_by_sequence_length, filter_by_date
     >>> sequence_index = pd.DataFrame([{"strain": "strain1", "ACGT": 28000}, {"strain": "strain2", "ACGT": 26000}, {"strain": "strain3", "ACGT": 5000}]).set_index("strain")
     >>> exclude_by = [(filter_by_sequence_length, {"sequence_index": sequence_index, "min_length": 27000})]
     >>> filter_kwargs_to_str(exclude_by[0][1])

diff --git a/augur/filter/subsample.py b/augur/filter/subsample.py
@@ -58,7 +58,7 @@ def get_groups_for_subsampling(strains, metadata, group_by=None):
     >>> get_groups_for_subsampling(strains, metadata, group_by)
     Traceback (most recent call last):
       ...
-    augur.filter.FilterException: The specified group-by categories (['missing_column']) were not found.
+    augur.filter.errors.FilterException: The specified group-by categories (['missing_column']) were not found.
 
     If we try to group by some columns that exist and some that don't, we allow
     grouping to continue and print a warning message to stderr.
@@ -406,7 +406,7 @@ def _calculate_sequences_per_group(
     >>> _calculate_sequences_per_group(1, [4, 2])
     Traceback (most recent call last):
         ...
-    augur.filter.TooManyGroupsError: Asked to provide at most 1 sequences, but there are 2 groups.
+    augur.filter.subsample.TooManyGroupsError: Asked to provide at most 1 sequences, but there are 2 groups.
     """
 
     if len(sequence_lengths) > target_max_value: