Bump bcbio-gff to 0.7.1

.github/workflows/ci.yaml

@@ -27,17 +27,8 @@ jobs:
         biopython-version:
           # list of Biopython versions with support for a new Python version
           # from https://github.com/biopython/biopython/blob/master/NEWS.rst
-          - '1.76' # first to support Python 3.8
-          - '1.79' # first to support Python 3.9
           - '1.80' # first to support Python 3.10 and 3.11
           - ''     # latest
-        exclude:
-          # some older Biopython versions are incompatible with later Python versions
-          - { biopython-version: '1.76', python-version: '3.9' }
-          - { biopython-version: '1.76', python-version: '3.10' }
-          - { biopython-version: '1.76', python-version: '3.11' }
-          - { biopython-version: '1.79', python-version: '3.10' }
-          - { biopython-version: '1.79', python-version: '3.11' }
     defaults:
       run:
         shell: bash -l {0}

CHANGES.md

@@ -11,8 +11,10 @@
 
 * filter, frequencies, refine: Speed up reading of the metadata file. [#1252][] (@victorlin)
 * traits: Previously, columns with only numeric values were treated as numerical data. These are now treated as categorical data for discrete trait analysis. [#1252][] (@victorlin)
+* Support Biopython ≥1.82 by requiring bcbio-gff ≥0.71. [#1400][] (@victorlin)
 
 [#1252]: https://github.com/nextstrain/augur/pull/1252
+[#1400]: https://github.com/nextstrain/augur/pull/1400
 
 ## 24.0.0 (22 January 2024)
 

augur/translate.py

@@ -185,7 +185,7 @@ def str_reverse_comp(str_seq):
 
         #Translate just the codon this nuc diff is in, and find out which AA loc
         #But need numbering to be w/in protin, not whole genome
-        if feature.strand == -1:
+        if feature.location.strand == -1:
             aaRepLocs = {(end-start-i-1)//3:safe_translate( str_reverse_comp( "".join([sequences[seqk][key+start]
                                     if key+start in sequences[seqk].keys() else ref[key+start]
                                 for key in range(i-i%3,i+3-i%3)]) ))

augur/utils.py

@@ -296,12 +296,12 @@ def _read_gff(reference, feature_names):
         # Note that `GFF.parse` doesn't always yield GFF records in the order
         # one may expect, but since we raise AugurError if there are multiple
         # this doesn't matter.
-        gff_entries = list(GFF.parse(in_handle, limit_info={'gff_type': valid_types}))
-
-        # TODO: Remove warning filter reversal after it's addressed upstream:
-        # <https://github.com/chapmanb/bcbb/issues/140>
+        # TODO: Remove warning suppression after it's addressed upstream:
+        # <https://github.com/chapmanb/bcbb/issues/143>
         import warnings
         from Bio import BiopythonDeprecationWarning
+        warnings.simplefilter("ignore", BiopythonDeprecationWarning)
+        gff_entries = list(GFF.parse(in_handle, limit_info={'gff_type': valid_types}))
         warnings.simplefilter("default", BiopythonDeprecationWarning)
 
         if len(gff_entries) == 0:

setup.py

@@ -51,9 +51,9 @@
     package_data = {'augur': ['data/*']},
     python_requires = '>={}'.format('.'.join(str(n) for n in py_min_version)),
     install_requires = [
-        "bcbio-gff >=0.7.0, ==0.7.*",
-        # Skip Biopython >=1.82: https://github.com/nextstrain/augur/issues/1373
-        "biopython >=1.67, !=1.77, !=1.78, <1.82",
+        "bcbio-gff >=0.7.1, ==0.7.*",
+        # TODO: Remove biopython >= 1.80 pin if it is added to bcbio-gff: https://github.com/chapmanb/bcbb/issues/142
+        "biopython >=1.80, ==1.*",
         "cvxopt >=1.1.9, ==1.*",
         "importlib_resources >=5.3.0; python_version < '3.11'",
         "isodate ==0.6.*",