Merge pull request #88 from mvdbeek/fix_tests

Fix tests

Author: mvdbeek

gxformat2/abstract.py

@@ -32,10 +32,10 @@ def from_dict(workflow_dict: dict, subworkflow=False):
     normalized_workflow = NormalizedWorkflow(workflow_dict)
     workflow_dict = normalized_workflow.normalized_workflow_dict
 
-    requirements = {}  # type: Dict[str, Any]
-    abstract_dict = {
+    requirements: Dict[str, Any] = {}
+    abstract_dict: Dict[str, Any] = {
         'class': 'Workflow',
-    }  # type: Dict[str, Any]
+    }
     for attr in ('doc', 'label'):
         value = workflow_dict.get(attr)
         if value:

gxformat2/converter.py

@@ -7,8 +7,7 @@
 import os
 import sys
 import uuid
-from collections import OrderedDict
-from typing import Dict, Optional
+from typing import Any, Dict, Optional
 
 from ._labels import Labels
 from .model import (
@@ -129,7 +128,7 @@ def python_to_workflow(as_python, galaxy_interface, workflow_directory=None, imp
     if conversion_context.import_options.deduplicate_subworkflows:
         # TODO: import only required workflows...
         # TODO: dag sort these...
-        subworkflows = OrderedDict()
+        subworkflows = {}
         for graph_id, subworkflow_content in conversion_context.graph_ids.items():
             if graph_id == "main":
                 continue
@@ -194,7 +193,7 @@ def _python_to_workflow(as_python, conversion_context):
 
     if isinstance(steps, list):
         _append_step_id_to_step_list_elements(steps)
-        steps_as_dict = OrderedDict()
+        steps_as_dict: Dict[str, Any] = {}
         for i, step in enumerate(steps):
             steps_as_dict[str(i)] = step
             if "label" in step:
@@ -577,8 +576,8 @@ class ConversionContext(BaseConversionContext):
     def __init__(self, galaxy_interface, workflow_directory, import_options: Optional[ImportOptions] = None):
         super().__init__()
         self.import_options = import_options or ImportOptions()
-        self.graph_ids = OrderedDict()  # type: Dict
-        self.graph_id_subworkflow_conversion_contexts = {}  # type: Dict
+        self.graph_ids: Dict[str, Any] = {}
+        self.graph_id_subworkflow_conversion_contexts: Dict[str, Any] = {}
         self.workflow_directory = workflow_directory
         self.galaxy_interface = galaxy_interface
 

tox.ini

@@ -1,15 +1,16 @@
 # TODO: implement doc linting
 [tox]
-envlist = py{36,37,38,39}-lint, py36-lintdocstrings, py36-lintreadme, py{36,37,38,39}-mypy, py{36,37,38,39}-unit
+envlist = py{37,38,39,310,311}-lint, py37-lintdocstrings, py37-lintreadme, py{37,38,39,310,311}-mypy, py{37,38,39,310,311}-unit
 source_dir = gxformat2
 test_dir = tests
 
 [gh-actions]
 python =
-    3.6: py36-unit, py36-mypy, py36-lint, py36-lintdocs, py36-lintdocstrings
-    3.7: py37-unit, py37-mypy
+    3.7: py37-unit, py37-mypy, py37-lint, py37-lintdocs, py37-lintdocstrings
     3.8: py38-unit, py38-mypy
-    3.9: py39-unit, py39-mypy, py39-lint, py39-lintdocs
+    3.9: py39-unit, py39-mypy
+    3.10: py310-unit, py310-mypy
+    3.11: py311-unit, py311-mypy, py311-lint, py311-lintdocs
 
 [testenv]
 commands =