Remove augur.utils.read strains

CHANGES.md

@@ -6,6 +6,7 @@
 
 * Updated default latitudes and longitudes for geography traits that includes location name changes. See the pull request for more details. [#1744][] (@joverlee521)
 * curate apply-geolocation-rules: Augur's standard geolocation rules are used by default and rules provided via `--geolocation-rules` are considered custom rules that have precedence over the default rules. The `--no-default-rules` flag can be used to ignore the default rules. See the pull request for more details. [#1745][] (@joverlee521)
+* `augur.utils.read_strains` has been removed as it's been deprecated since January 2024. The same function is available through the public API as `augur.io.read_strains`. [#1749][] (@joverlee521)
 
 ### Features
 
@@ -20,8 +21,9 @@ Note that names with spaces in the FASTA header (description line) continue to b
 
 [#1744]: https://github.com/nextstrain/augur/pull/1744
 [#1745]: https://github.com/nextstrain/augur/pull/1745
-[#1755]: https://github.com/nextstrain/augur/pull/1755
+[#1749]: https://github.com/nextstrain/augur/pull/1749
 [#1750]: https://github.com/nextstrain/augur/pull/1750
+[#1755]: https://github.com/nextstrain/augur/pull/1755
 
 ## 28.0.1 (10 February 2025)
 

DEPRECATED.md

@@ -16,7 +16,7 @@ Users who have both 'name' and 'strain' fields in their data, and want to favor
 
 ## `augur.utils.read_strains`
 
-*Deprecated in version 24.0.0 (January 2024). Planned for removal March 2024 or after.*
+*Deprecated in version 24.0.0 (January 2024). Removed in version 29.0.0 (February 2025).*
 
 This is part of a [larger effort](https://github.com/nextstrain/augur/issues/1011)
 to formalize Augur's Python API.

augur/utils.py

@@ -6,13 +6,11 @@
 import pandas as pd
 from collections import defaultdict, OrderedDict
 from io import RawIOBase
-from textwrap import dedent
 from .__version__ import __version__
 
 from augur.data import as_file
 from augur.io.file import PANDAS_READ_CSV_OPTIONS, open_file
 from augur.io.sequences import read_single_sequence
-from augur.io.print import print_err
 
 from augur.types import ValidationMode
 from augur.errors import AugurError
@@ -205,7 +203,7 @@ def _read_nuc_annotation_from_gff(record, reference):
     types. Note that 'source' isn't really a GFF feature type, but is used
     widely in the Nextstrain ecosystem. If there are multiple we check that the
     coordinates agree.
-    
+
     Parameters
     ----------
     record : :py:class:`Bio.SeqRecord.SeqRecord`
@@ -246,7 +244,7 @@ def _read_nuc_annotation_from_gff(record, reference):
     if len(nuc.values())>1:
         coords = [(name, int(feat.location.start), int(feat.location.end)) for name,feat in nuc.items()]
         if not all(el[1]==coords[0][1] and el[2]==coords[0][2] for el in coords):
-            raise AugurError(f"Reference {reference!r} contained contradictory coordinates for the seqid/genome. We parsed the following coordinates: " + 
+            raise AugurError(f"Reference {reference!r} contained contradictory coordinates for the seqid/genome. We parsed the following coordinates: " +
                              ', '.join([f"{el[0]}: [{el[1]+1}, {el[2]}]" for el in coords]) # +1 on the first coord to shift to one-based GFF representation
                              )
 
@@ -358,7 +356,7 @@ def _read_nuc_annotation_from_genbank(record, reference):
     according to <https://www.ncbi.nlm.nih.gov/Sitemap/samplerecord.html>.)
 
     See <https://www.insdc.org/submitting-standards/feature-table/> for more.
-    
+
     Parameters
     ----------
     record : :py:class:`Bio.SeqRecord.SeqRecord` reference: string
@@ -389,7 +387,7 @@ def _read_genbank(reference, feature_names):
     Read a GenBank file. We only read GenBank feature keys 'CDS' or 'source'.
     We create a "feature name" via:
     - for 'source' features use 'nuc'
-    - for 'CDS' features use the locus_tag or the gene. If neither, then silently ignore. 
+    - for 'CDS' features use the locus_tag or the gene. If neither, then silently ignore.
 
     Parameters
     ----------
@@ -766,13 +764,6 @@ def load_mask_sites(mask_file):
 }
 
 
-def read_strains(*files, comment_char="#"):
-    print_err(dedent("""
-        DEPRECATION WARNING: augur.utils.read_strains is no longer maintained and will be removed in the future.
-        Please use augur.io.read_strains instead."""))
-    return set(read_entries(*files, comment_char=comment_char))
-
-
 def read_entries(*files, comment_char="#"):
     """Reads entries (one per line) from one or more plain text files.
 

tests/functional/mask/variants.vcf.gz_maskTemp

@@ -0,0 +1,5 @@
+MTB_anc	1199
+MTB_anc	1200
+MTB_anc	8321
+MTB_anc	8322
+MTB_anc	8323