virtool-workflow 5.5.0a1__tar.gz → 5.5.0a3__tar.gz

{virtool_workflow-5.5.0a1 → virtool_workflow-5.5.0a3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: virtool-workflow
-Version: 5.5.0a1
+Version: 5.5.0a3
 Summary: A framework for developing bioinformatics workflows for Virtool.
 Home-page: https://github.com/virtool/virtool-workflow
 License: MIT

{virtool_workflow-5.5.0a1 → virtool_workflow-5.5.0a3}/pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "virtool-workflow"
-version = "5.5.0-alpha.1"
+version = "5.5.0-alpha.3"
 description = "A framework for developing bioinformatics workflows for Virtool."
 authors = ["Ian Boyes", "Blake Smith", "Ryan Fang"]
 license = "MIT"

virtool_workflow-5.5.0a3/virtool_workflow/analysis/__init__.py

@@ -0,0 +1 @@
+"""Tools for workflows relating to sequence analysis."""

{virtool_workflow-5.5.0a1 → virtool_workflow-5.5.0a3}/virtool_workflow/api/client.py

@@ -8,7 +8,7 @@ from virtool_workflow.api.utils import (
     raise_exception_by_status_code,
     decode_json_response,
 )
-from virtool_workflow.data.files import VirtoolFileFormat
+from virtool_workflow.files import VirtoolFileFormat
 from virtool_workflow.errors import JobsAPIError
 
 CHUNK_SIZE = 1024 * 1024 * 2

{virtool_workflow-5.5.0a1 → virtool_workflow-5.5.0a3}/virtool_workflow/data/analyses.py

@@ -11,7 +11,7 @@ from virtool_core.models.reference import ReferenceNested
 from virtool_core.models.subtraction import SubtractionNested
 
 from virtool_workflow.api.client import APIClient
-from virtool_workflow.data.files import VirtoolFileFormat
+from virtool_workflow.files import VirtoolFileFormat
 
 
 class WFAnalysis:

{virtool_workflow-5.5.0a1 → virtool_workflow-5.5.0a3}/virtool_workflow/data/indexes.py

@@ -12,7 +12,7 @@ from virtool_core.models.reference import ReferenceNested
 from virtool_core.utils import decompress_file
 
 from virtool_workflow.api.client import APIClient
-from virtool_workflow.data.files import VirtoolFileFormat
+from virtool_workflow.files import VirtoolFileFormat
 from virtool_workflow.errors import MissingJobArgument
 
 

{virtool_workflow-5.5.0a1 → virtool_workflow-5.5.0a3}/virtool_workflow/data/samples.py

@@ -11,7 +11,7 @@ from virtool_core.models.samples import Sample, Quality
 
 from virtool_workflow.analysis.utils import ReadPaths
 from virtool_workflow.api.client import APIClient
-from virtool_workflow.data.files import VirtoolFileFormat
+from virtool_workflow.files import VirtoolFileFormat
 from virtool_workflow.data.uploads import WFUploads
 from virtool_workflow.errors import JobsAPINotFound
 

{virtool_workflow-5.5.0a1 → virtool_workflow-5.5.0a3}/virtool_workflow/runtime/discover.py

@@ -41,6 +41,9 @@ def load_builtin_fixtures():
 
     """
     import_module("virtool_workflow.data")
+    import_module("virtool_workflow.analysis.fastqc")
+    import_module("virtool_workflow.analysis.skewer")
+    import_module("virtool_workflow.runtime.run_subprocess")
 
 
 def load_custom_fixtures():

virtool_workflow-5.5.0a1/virtool_workflow/analysis/__init__.py

@@ -1,5 +0,0 @@
-"""Tools for workflows relating to sequence analysis."""
-
-__fixtures__ = [
-    "virtool_workflow.analysis.trim_parameters",
-]