From 16a2b81698af1a2f28fa95fd430d681c409deffc Mon Sep 17 00:00:00 2001 From: Jesse Connell Date: Thu, 12 Jun 2025 16:34:46 -0400 Subject: [PATCH 1/3] For #97: failing test for cutadapt behavior >=4 Also tweak test helper code to work with newer Python --- .../output-edgecase/sample.R1.fastq.gz | Bin 198 -> 203 bytes test_igseq/util.py | 9 +++++++-- 2 files changed, 7 insertions(+), 2 deletions(-) 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 c3a1d27d6240a5dbc71add406a8f9fe292123cbc..c31eea4ee500250bd7b788dc861e341ec0f24ff7 100644 GIT binary patch literal 203 zcmV;+05ty}iwFP!00000|20fOPQ)+}yZ05Go2=AmNs}GelBtvN1vsGm|1D@L7}>JN ziKl&SIoB#>ud@Bm?epg`vm{ArOOp0`xl79F^(D!-Y%(z?04}6bIpH8VJ)ZPeRVXh@ zDo9l?5XAKx0Mv#2;}s|Yr{Cd(UvsYjeZRVjB`on4V~lU3pob7bZKw6|z<|a0?tt;5 z)bT9kY2Cn4aGuRz7zUaR3k@hRf$`{CyNzftGi&IFtHEOHYg_Yi0PDK$%P$3Z8wM=_ F008fOU~T{a literal 198 zcmV;%06G63iwFR;wp3>T12s&`Zp0uAyyq)=CR7UA5?I{B4Ut_V4&_g~BAcU|le+j{9lPLiJ0B?I= AlmGw# 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() From 6eb3199a41ea5775a7a76a6ff7a854272d600a62 Mon Sep 17 00:00:00 2001 From: Jesse Connell Date: Thu, 12 Jun 2025 16:49:54 -0400 Subject: [PATCH 2/3] For #91: update dependencies python>=3.9.7,<3.13; biopython>=1.82,<1.86; cutadapt>=5.1,<6; igblast=1.22 --- conda/meta.yaml | 8 ++++---- igseq/data/environment.yml | 8 ++++---- 2 files changed, 8 insertions(+), 8 deletions(-) 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 From b3f17229b7b5ec2344a89b0cb09111683c69ba90 Mon Sep 17 00:00:00 2001 From: Jesse Connell Date: Thu, 12 Jun 2025 17:01:41 -0400 Subject: [PATCH 3/3] For #98: changelog [skip ci] --- CHANGELOG.md | 11 +++++++++++ 1 file changed, 11 insertions(+) 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