Merge pull request #1335: Bump supported pyfastx versions

nextstrain · Nov 7, 2023 · e1b414a · e1b414a
2 parents 378353e + 8b3ecff
commit e1b414a
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diff --git a/CHANGES.md b/CHANGES.md
@@ -2,6 +2,13 @@
 
 ## __NEXT__
 
+### Bug Fixes
+
+* Fix Python 3.11 installation for Conda environments. [#1334][] (@victorlin)
+* Bump `pyfastx` dependency to major versions 1 and 2. [#1335][] (@victorlin)
+
+[#1334]: https://github.com/nextstrain/augur/issues/1334
+[#1335]: https://github.com/nextstrain/augur/pull/1335
 
 ## 23.1.0 (22 September 2023)
 

diff --git a/augur/io/metadata.py b/augur/io/metadata.py
@@ -336,10 +336,11 @@ def read_metadata_with_sequences(metadata, metadata_delimiters, fasta, seq_id_co
         else:
             processed_metadata_ids.add(seq_id)
 
-        # Skip records that do not have a matching sequence
-        # TODO: change this to try/except to fetch sequences and catch
-        # KeyError for non-existing sequences when https://github.com/lmdu/pyfastx/issues/50 is resolved
-        if seq_id not in sequence_ids:
+        try:
+            sequence_record = sequences[seq_id]
+        except KeyError:
+            # Skip records that do not have a matching sequence
+
             # Immediately raise an error if requested to error on the first unmatched record
             if unmatched_reporting is DataErrorMethod.ERROR_FIRST:
                 raise AugurError(f"Encountered metadata record {seq_id!r} without a matching sequence.")

diff --git a/setup.py b/setup.py
@@ -62,7 +62,7 @@
         "packaging >=19.2",
         "pandas >=1.0.0, ==1.*",
         "phylo-treetime >=0.10.0, <0.12",
-        "pyfastx >=0.8.4, ==0.8.*",
+        "pyfastx >=1.0.0, <3.0",
         "scipy ==1.*",
         "xopen[zstd] >=1.7.0, ==1.*"
     ],