diff --git a/CHANGELOG.md b/CHANGELOG.md index 4964f70..14d19d1 100644 --- a/CHANGELOG.md +++ b/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 diff --git a/conda/meta.yaml b/conda/meta.yaml index 4735273..c624893 100644 --- a/conda/meta.yaml +++ b/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 diff --git a/igseq/data/environment.yml b/igseq/data/environment.yml index 65f945f..12626bd 100644 --- a/igseq/data/environment.yml +++ b/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 diff --git a/test_igseq/data/test_trim/TestTrimLive/output-edgecase/sample.R1.fastq.gz b/test_igseq/data/test_trim/TestTrimLive/output-edgecase/sample.R1.fastq.gz index c3a1d27..c31eea4 100644 Binary files a/test_igseq/data/test_trim/TestTrimLive/output-edgecase/sample.R1.fastq.gz and b/test_igseq/data/test_trim/TestTrimLive/output-edgecase/sample.R1.fastq.gz differ diff --git a/test_igseq/util.py b/test_igseq/util.py index c2504a0..a541533 100644 --- a/test_igseq/util.py +++ b/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()