Merge pull request #113 from mvdbeek/rebuild_autogenerated_python_Code

Rebuild schema, bump up minimum python version to 3.9

.github/workflows/maven.yml

@@ -9,7 +9,7 @@ jobs:
     - name: Set up Python
       uses: actions/setup-python@v1
       with:
-        python-version: 3.8
+        python-version: 3.9
     - name: Install Python dependencies
       run: |
         python -m pip install --upgrade pip

.github/workflows/tox.yml

@@ -10,7 +10,7 @@ jobs:
     strategy:
       max-parallel: 4
       matrix:
-        python-version: ['3.8', '3.9', '3.10', '3.11', '3.12']
+        python-version: ['3.9', '3.10', '3.11', '3.12', '3.13']
 
     steps:
     - uses: actions/checkout@v2

CONTRIBUTING.rst

@@ -102,8 +102,8 @@ Before you submit a pull request, check that it meets these guidelines:
 
 1. If the pull request adds functionality, the docs should be updated. Put
    your new functionality into a function with a docstring.
-2. The pull request should work for Python >=3.6. Check CI results on pull
-   request and make sure that the tests pass for all supported Python versions.
+2. The pull request should work for all supported Python versions. Check the CI
+   results on the pull request and make sure that the tests pass.
 
 Tox_
 ~~~~~~~~~~~
@@ -112,14 +112,14 @@ Tox_ is a tool to automate testing across different Python versions. The
 ``tox`` executable can be supplied with a ``-e`` argument to specify a
 testing environment. gxformat2 defines the following environments:
 
-``py37-lint``
-    Lint the gxformat2 code using Python 3.7.
+``lint``
+    Lint the gxformat2 code.
 
-``py37-lint_docstrings``
+``lintdocstrings``
     Lint the project Python docstrings.
 
-``py36-unit``
-    Run the unit tests with Python 3.6.
+``unit``
+    Run the unit tests.
 
 .. _Tox: https://tox.readthedocs.org/en/latest/
 

Makefile

@@ -1,7 +1,7 @@
 # Default tests run with make test and make quick-tests
 NOSE_TESTS?=tests gxformat2
 # Default environment for make tox
-ENV?=py36
+ENV?=py39
 # Extra arguments supplied to tox command
 ARGS?=
 # Location of virtualenv used for development.

docs/conf.py

@@ -30,7 +30,7 @@
 # version is used.
 sys.path.insert(0, project_root)
 
-import gxformat2 as project_module
+import gxformat2 as project_module  # noqa: E402
 
 # -- General configuration ---------------------------------------------
 

gxformat2/abstract.py

@@ -1,7 +1,7 @@
 """Module for exporting Galaxy workflows to CWL abstract interface."""
 import argparse
 import sys
-from typing import Any, Dict
+from typing import Any
 
 from gxformat2._scripts import ensure_format2
 from gxformat2.converter import steps_as_list
@@ -32,8 +32,8 @@ def from_dict(workflow_dict: dict, subworkflow=False):
     normalized_workflow = NormalizedWorkflow(workflow_dict)
     workflow_dict = normalized_workflow.normalized_workflow_dict
 
-    requirements: Dict[str, Any] = {}
-    abstract_dict: Dict[str, Any] = {
+    requirements: dict[str, Any] = {}
+    abstract_dict: dict[str, Any] = {
         'class': 'Workflow',
     }
     for attr in ('doc', 'label'):

gxformat2/converter.py

@@ -6,7 +6,7 @@
 import os
 import sys
 import uuid
-from typing import Any, Dict, Optional
+from typing import Any, Optional
 
 from ._labels import Labels
 from .model import (
@@ -142,7 +142,7 @@ def _python_to_workflow(as_python, conversion_context):
 
     if isinstance(steps, list):
         append_step_id_to_step_list_elements(steps)
-        steps_as_dict: Dict[str, Any] = {}
+        steps_as_dict: dict[str, Any] = {}
         for i, step in enumerate(steps):
             steps_as_dict[str(i)] = step
             if "label" in step:
@@ -484,8 +484,8 @@ 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: Dict[str, Any] = {}
-        self.graph_id_subworkflow_conversion_contexts: Dict[str, Any] = {}
+        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
 

gxformat2/markdown_parse.py

@@ -9,8 +9,6 @@
 import re
 from typing import (
     cast,
-    Dict,
-    List,
     Union,
 )
 
@@ -25,8 +23,8 @@ class DynamicArguments:
 
 
 DYNAMIC_ARGUMENTS = DynamicArguments()
-SHARED_ARGUMENTS: List[str] = ["collapse"]
-VALID_ARGUMENTS: Dict[str, Union[List[str], DynamicArguments]] = {
+SHARED_ARGUMENTS: list[str] = ["collapse"]
+VALID_ARGUMENTS: dict[str, Union[list[str], DynamicArguments]] = {
     "history_link": ["history_id"],
     "history_dataset_display": ["input", "output", "history_dataset_id"],
     "history_dataset_embedded": ["input", "output", "history_dataset_id"],
@@ -144,7 +142,7 @@ def _validate_arg(arg_str, valid_args, line_no):
                 valid_args_raw = VALID_ARGUMENTS[container]
                 if isinstance(valid_args_raw, DynamicArguments):
                     continue
-                valid_args = cast(List[str], valid_args_raw)
+                valid_args = cast(list[str], valid_args_raw)
 
                 first_arg_call = func_call_match.group("firstargcall")
 

gxformat2/model.py

@@ -4,8 +4,6 @@
 from typing import (
     Any,
     cast,
-    Dict,
-    List,
     Optional,
     Union,
 )
@@ -14,7 +12,7 @@
 
 log = logging.getLogger(__name__)
 
-DictOrList = Union[Dict, List]
+DictOrList = Union[dict, list]
 ConnectDict = dict
 
 
@@ -42,7 +40,7 @@
     "pause",
     "parameter_input",
 ]
-STEP_TYPE_ALIASES: Dict[GxFormat2StepTypeAlias, NativeGalaxyStepType] = {
+STEP_TYPE_ALIASES: dict[GxFormat2StepTypeAlias, NativeGalaxyStepType] = {
     'input': 'data_input',
     'input_collection': 'data_collection_input',
     'parameter': 'parameter_input',
@@ -105,7 +103,7 @@ def pop_connect_from_step_dict(step: dict) -> ConnectDict:
     return connect
 
 
-def setup_connected_values(value, key: str = "", append_to: Optional[Dict[str, list]] = None) -> Any:
+def setup_connected_values(value, key: str = "", append_to: Optional[dict[str, list]] = None) -> Any:
     """Replace links with connected value."""
 
     def append_link(key: str, value: dict):
@@ -129,13 +127,13 @@ def recurse(sub_value, sub_key) -> Any:
         # which should be further validated by Galaxy
         return _connected_value()
     if isinstance(value, dict):
-        new_dict_values: Dict[str, Any] = {}
+        new_dict_values: dict[str, Any] = {}
         for dict_k, dict_v in value.items():
             new_key = _join_prefix(key, dict_k)
             new_dict_values[dict_k] = recurse(dict_v, new_key)
         return new_dict_values
     elif isinstance(value, list):
-        new_list_values: List[Any] = []
+        new_list_values: list[Any] = []
         for i, list_v in enumerate(value):
             # If we are a repeat we need to modify the key
             # but not if values are actually $links.
@@ -235,7 +233,7 @@ def prune_position(step):
     return {k: v for k, v in step.get('position', {}).items() if k in ('left', 'top')}
 
 
-def native_input_to_format2_type(step: dict, tool_state: dict) -> Union[str, List[str]]:
+def native_input_to_format2_type(step: dict, tool_state: dict) -> Union[str, list[str]]:
     """Return a Format2 input type ('type') from a native input step dictionary."""
     module_type = step.get("type")
     if module_type == 'data_collection_input':
@@ -373,7 +371,7 @@ def outputs_as_list(as_python: dict) -> list:
     return outputs
 
 
-def steps_as_list(format2_workflow: dict, add_ids: bool = False, inputs_offset: int = 0, mutate: bool = False) -> List[Dict[str, Any]]:
+def steps_as_list(format2_workflow: dict, add_ids: bool = False, inputs_offset: int = 0, mutate: bool = False) -> list[dict[str, Any]]:
     """Return steps as a list, converting ID map to list representation if needed.
 
     This method does mutate the supplied steps, try to make progress toward not doing this.
@@ -392,7 +390,7 @@ def steps_as_list(format2_workflow: dict, add_ids: bool = False, inputs_offset:
     return steps
 
 
-def append_step_id_to_step_list_elements(steps: List[Dict[str, Any]], inputs_offset: int = 0) -> None:
+def append_step_id_to_step_list_elements(steps: list[dict[str, Any]], inputs_offset: int = 0) -> None:
     """Ensure a list of steps each contains an 'id' element."""
     assert isinstance(steps, list)
     for i, step in enumerate(steps):