From 0c61f3fd760c36cc1d96816e0eb5a89a4f955510 Mon Sep 17 00:00:00 2001 From: Richard Lupat Date: Tue, 13 Jun 2023 17:04:22 +1000 Subject: [PATCH 1/5] Update Python versions for github actions --- .github/workflows/unit_tests.yml | 3 +-- janis_bioinformatics/__meta__.py | 2 +- 2 files changed, 2 insertions(+), 3 deletions(-) diff --git a/.github/workflows/unit_tests.yml b/.github/workflows/unit_tests.yml index 4af547ee..2c4e4e8a 100644 --- a/.github/workflows/unit_tests.yml +++ b/.github/workflows/unit_tests.yml @@ -4,11 +4,10 @@ on: [push, pull_request] jobs: build: - runs-on: ubuntu-latest strategy: matrix: - python-version: [3.6, 3.7, 3.8] + python-version: [3.8.17, 3.10.12, 3.11.4] steps: - uses: actions/checkout@v2 diff --git a/janis_bioinformatics/__meta__.py b/janis_bioinformatics/__meta__.py index 12826eda..626494ab 100644 --- a/janis_bioinformatics/__meta__.py +++ b/janis_bioinformatics/__meta__.py @@ -1,2 +1,2 @@ -__version__ = "v0.11.4" +__version__ = "v0.12.1" description = "Bioinformatics tools for Janis; the Pipeline creation helper" From effa1fb8ddfe407093c8b980d75da9e98d4d418f Mon Sep 17 00:00:00 2001 From: Richard Lupat Date: Tue, 13 Jun 2023 17:41:37 +1000 Subject: [PATCH 2/5] Fix bcftoolsview base missing a comma --- janis_bioinformatics/tools/bcftools/view/base.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/janis_bioinformatics/tools/bcftools/view/base.py b/janis_bioinformatics/tools/bcftools/view/base.py index 2804ad4f..d04477dc 100644 --- a/janis_bioinformatics/tools/bcftools/view/base.py +++ b/janis_bioinformatics/tools/bcftools/view/base.py @@ -92,7 +92,7 @@ def memory(self, hints: Dict[str, Any]): def inputs(self) -> List[ToolInput]: return [ ToolInput("file", CompressedVcf(), position=2), - ToolInput("outputFilename", Filename, prefix=">", position=5) + ToolInput("outputFilename", Filename, prefix=">", position=5), * self.additional_inputs, ] From 95ce5c64b786cbf1c740186d6abd4973a2ef1d55 Mon Sep 17 00:00:00 2001 From: Richard Lupat Date: Tue, 13 Jun 2023 17:42:00 +1000 Subject: [PATCH 3/5] Added a temporary workaround to get nosetests to work --- tests/__init__.py | 2 ++ 1 file changed, 2 insertions(+) diff --git a/tests/__init__.py b/tests/__init__.py index e69de29b..c5eaea24 100644 --- a/tests/__init__.py +++ b/tests/__init__.py @@ -0,0 +1,2 @@ +import collections +collections.Callable = collections.abc.Callable From b9024c1d0116349ee3bf0cca03652ecf9caaa596 Mon Sep 17 00:00:00 2001 From: Richard Lupat Date: Tue, 13 Jun 2023 18:02:26 +1000 Subject: [PATCH 4/5] Add skip_test to CircosPlot tool --- janis_bioinformatics/tools/pmac/circosplot/base.py | 3 +++ 1 file changed, 3 insertions(+) diff --git a/janis_bioinformatics/tools/pmac/circosplot/base.py b/janis_bioinformatics/tools/pmac/circosplot/base.py index c9c1a128..0e7a49a3 100644 --- a/janis_bioinformatics/tools/pmac/circosplot/base.py +++ b/janis_bioinformatics/tools/pmac/circosplot/base.py @@ -97,6 +97,9 @@ def cpus(self, hints: Dict[str, Any]): return val return 1 + def skip_test(cls) -> bool: + return True + def bind_metadata(self) -> ToolMetadata: from datetime import datetime From e833098cb006e507fd104b3495ce58f783689821 Mon Sep 17 00:00:00 2001 From: Richard Lupat Date: Tue, 13 Jun 2023 18:13:33 +1000 Subject: [PATCH 5/5] Add skip_test to CircosPlot tool --- janis_bioinformatics/tools/common/indexfasta.py | 3 +++ 1 file changed, 3 insertions(+) diff --git a/janis_bioinformatics/tools/common/indexfasta.py b/janis_bioinformatics/tools/common/indexfasta.py index 0fdc4d72..31f5ff55 100644 --- a/janis_bioinformatics/tools/common/indexfasta.py +++ b/janis_bioinformatics/tools/common/indexfasta.py @@ -114,6 +114,9 @@ def constructor(self): ) self.output("out_dict", source=self.create_dict, output_name="reference") + def skip_test(cls) -> bool: + return True + def bind_metadata(self): return ToolMetadata( contributors=["Michael Franklin"],