Release 1.3.1

CITATION.cff

@@ -1,8 +1,8 @@
 cff-version: "1.2.0"
 message: "If you use this software, please cite it using these metadata."
 title: ElasticBLAST
-version: "1.3.0"
-date-released: 2024-07-17
+version: "1.3.1"
+date-released: 2024-07-24
 license: "NCBI Public Domain"
 repository-code: "https://github.com/ncbi/elastic-blast/"
 url: "https://blast.ncbi.nlm.nih.gov/doc/elastic-blast/"

bin/create-blastdb-metadata.py

@@ -88,6 +88,7 @@ class BlastDbMetadata:
 
  def to_json(self, pretty = False):
  """Serialize the object as JSON"""
+ self.files.sort()
  output = json.dumps(self, cls=BlastDbMetadataEncoder, sort_keys=False)
  #rename '_' to '-' in keys
  dict = json.loads(output)

setup.cfg

@@ -1,6 +1,6 @@
 [metadata]
 name = elastic_blast
-description = ElasticBLAST speeds up your work by distributing your BLAST+ searches across multiple cloud instances. The ability to scale resources in this way allows larger numbers of queries to be searched in a shorter time than you could with BLAST+ on a single host.  Use of the cloud also allows you to collaborate with colleagues, allowing the sharing of results, datasets and pipelines on a common platform. The National Center for Biotechnology Information ([NCBI](https://www.ncbi.nlm.nih.gov)), part of the National Library of Medicine at the NIH, developed and maintains ElasticBLAST.
+description = ElasticBLAST runs BLAST searches faster by distributing its work to multiple cloud instances. This allows larger numbers of queries to be searched in less time compared to BLAST+ on a single host. Use of the cloud facilitates collaboration, sharing of results, datasets and pipelines on a common platform. The National Center for Biotechnology Information ([NCBI](https://www.ncbi.nlm.nih.gov)), part of the National Library of Medicine at the NIH, developed and maintains ElasticBLAST.
 long_description = file:README.md
 long_description_content_type = text/markdown
 maintainer = NCBI

src/elastic_blast/gcp.py

@@ -1013,7 +1013,10 @@ def check_prerequisites() -> None:
  version_data = json.loads(p.stdout.decode())
  kubectl_version = version_data["clientVersion"]["major"] + "."
  kubectl_version += version_data["clientVersion"]["minor"]
- if is_newer_version(kubectl_version, "1.25") and shutil.which("gke-gcloud-auth-plugin") is None:
+ is_newer_than_1_25 = True
+ try : is_newer_than_1_25 = is_newer_version(kubectl_version, "1.25")
+ except ValueError: pass # ignore version parsing errors
+ if is_newer_than_1_25 and shutil.which("gke-gcloud-auth-plugin") is None:
  message = f"Missing dependency 'gke-gcloud-auth-plugin', "
  message += "for more information, please see "
  message += "https://cloud.google.com/blog/products/containers-kubernetes/kubectl-auth-changes-in-gke"

src/elastic_blast/util.py

@@ -593,11 +593,15 @@ def is_newer_version(version1: str, version2: str) -> bool:
  
  Returns:
  bool: True if version1 is newer than version2, False otherwise.
+
+ Throws: ValueError if any of the arguments cannot be parsed
  """
+ def parse_and_remove_trailing_plus(version_str: str) -> list[str]:
+ return [part[:-1] if re.search(r'\D$', part) else part for part in version_str.split('.')]
 
  # Split version strings into lists of integers
- v1_parts = [int(part) for part in version1.split('.')]
- v2_parts = [int(part) for part in version2.split('.')]
+ v1_parts = [int(part) for part in parse_and_remove_trailing_plus(version1)]
+ v2_parts = [int(part) for part in parse_and_remove_trailing_plus(version2)]
 
  # Compare each part of the version numbers
  for v1, v2 in zip_longest(v1_parts, v2_parts, fillvalue=0):

tests/util/test_util.py

@@ -53,6 +53,25 @@ def test_is_newer_version():
  assert is_newer_version("0.3", "1.0") is False
  assert is_newer_version("1.5", "1.2.3") is True
  assert is_newer_version("1.5", "1.7.3") is False
+ assert is_newer_version("1.27+", "1.25") is True
+ assert is_newer_version("1.27-", "1.25") is True
+ assert is_newer_version("1.34a", "1.25") is True
+ assert is_newer_version("1a.34B", "1.25") is True
+
+ with pytest.raises(ValueError):
+ is_newer_version("1a.hello", "1.25")
+ with pytest.raises(ValueError):
+ is_newer_version("1a.3hello", "1.25")
+ with pytest.raises(ValueError):
+ is_newer_version("invalid_version_string", "1.25")
+ with pytest.raises(ValueError):
+ is_newer_version("1.1", "invalid_version_string")
+ with pytest.raises(ValueError):
+ is_newer_version("", "1.0")
+ with pytest.raises(ValueError):
+ is_newer_version("0.5", "")
+ with pytest.raises(ValueError):
+ is_newer_version("", "")
 
  assert is_newer_version("1.0", "1.0") is False
  assert is_newer_version("1.0", "1.0.0") is False