Merge pull request #127 from PMCC-BioinformaticsCore/release-v0.12.1

Release v0.12.1

Author: rlupat

.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

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"

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,
         ]
 

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"],

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
 

tests/__init__.py

@@ -0,0 +1,2 @@
+import collections
+collections.Callable = collections.abc.Callable