Update software dependencies

CHANGELOG.md

@@ -1,5 +1,16 @@
 # Changelog
 
+## dev
+
+### Changed
+
+ * `igblast` updated to 1.22 ([#98])
+ * Cutadapt (for `trim`) updated to version 5 ([#98]).  **NOTE: this will
+   result in very slightly different output from the trim command for the same
+   input, compared to previous igseq versions using Cutadapt 3.**
+
+[#98]: https://github.com/ShawHahnLab/igseq/pull/98
+
 ## 0.7.0 - 2025-06-12
 
 ### Added

conda/meta.yaml

@@ -42,14 +42,14 @@ requirements:
   # installed automatically whenever the package is installed. Package names
   # should follow the package match specifications."
   run:
-    - python>=3.9.7,<4
-    - biopython>=1.80,<2
+    - python>=3.9.7,<3.13
+    - biopython>=1.82,<1.86
+    - cutadapt>=5.1,<6
+    - igblast=1.22
     - python-newick>=1.9,<2
     - bwa>=0.7.18,<0.8
     - samtools>=1.19,<2
-    - cutadapt>=3.7,<4
     - pear>=0.9.6,<1
-    - igblast>=1.21,<1.22
     - muscle>=5.1,<6
     - fasttree>=2.1,<3
 

igseq/data/environment.yml

@@ -5,13 +5,13 @@ channels:
   - bioconda
   - defaults
 dependencies:
-  - python>=3.9.7,<4
-  - biopython>=1.80,<2
+  - python>=3.9.7,<3.13
+  - biopython>=1.82,<1.86
+  - cutadapt>=5.1,<6
+  - igblast=1.22
   - python-newick>=1.9,<2
   - bwa>=0.7.18,<0.8
   - samtools>=1.19,<2
-  - cutadapt>=3.7,<4
   - pear>=0.9.6,<1
-  - igblast>=1.21,<1.22
   - muscle>=5.1,<6
   - fasttree>=2.1,<3

test_igseq/util.py

@@ -146,8 +146,13 @@ def setUp(self):
 
     def tearDown(self):
         # adapted from https://stackoverflow.com/a/39606065
-        result = self.defaultTestResult()
-        self._feedErrorsToResult(result, self._outcome.errors)
+        if hasattr(self._outcome, "errors"):
+            # Python 3.4 - 3.10
+            result = self.defaultTestResult()
+            self._feedErrorsToResult(result, self._outcome.errors)
+        else:
+            # Python 3.11+
+            result = self._outcome.result
         if result.errors or result.failures:
             shutil.copytree(self.tmp, Path("/tmp/igseq-testdirs")/str(self.tmp).lstrip("/"))
         self.__tmp.cleanup()