Fix 2 typos

.github/workflows/publishdocs.yml

@@ -1,7 +1,7 @@
 name: Publish gxformat2 Docs
 on:
-  push:	
-    branches:	
+  push:
+    branches:
       - master
 jobs:
   deploy:

.github/workflows/tox.yml

@@ -1,5 +1,8 @@
 name: Python CI
 on: [push, pull_request]
+concurrency:
+  group: tox-${{ github.ref }}
+  cancel-in-progress: true
 jobs:
   build:
     runs-on: ubuntu-latest

docs/conf.py

@@ -1,5 +1,4 @@
 #!/usr/bin/env python
-# -*- coding: utf-8 -*-
 #
 # complexity documentation build configuration file, created by
 # sphinx-quickstart on Tue Jul  9 22:26:36 2013.
@@ -62,8 +61,8 @@
 master_doc = 'index'
 
 # General information about the project.
-project = u'gxformat2'
-copyright = u'2015'
+project = 'gxformat2'
+copyright = '2015'
 
 # The version info for the project you're documenting, acts as replacement
 # for |version| and |release|, also used in various other places throughout
@@ -217,8 +216,8 @@
 # [howto/manual]).
 latex_documents = [
     ('index', 'gxformat2.tex',
-     u'gxformat2 Documentation',
-     u'Galaxy Project and Community', 'manual'),
+     'gxformat2 Documentation',
+     'Galaxy Project and Community', 'manual'),
 ]
 
 # The name of an image file (relative to this directory) to place at
@@ -248,8 +247,8 @@
 # (source start file, name, description, authors, manual section).
 man_pages = [
     ('index', 'galaxy-lib',
-     u'Galaxy-lib Documentation',
-     [u'Galaxy Project and Community'], 1)
+     'Galaxy-lib Documentation',
+     ['Galaxy Project and Community'], 1)
 ]
 
 # If true, show URL addresses after external links.
@@ -263,8 +262,8 @@
 #  dir menu entry, description, category)
 texinfo_documents = [
     ('index', 'galaxy-lib',
-     u'Galaxy-Lib Documentation',
-     u'Galaxy Project and Community',
+     'Galaxy-Lib Documentation',
+     'Galaxy Project and Community',
      'galaxy-lib',
      'One line description of project.',
      'Miscellaneous'),

gxformat2/_labels.py

@@ -1,7 +1,7 @@
 """Utilities for handling unlabelled objects when translating workflow formats."""
 
 
-class Labels(object):
+class Labels:
     """Track labels assigned and generate anonymous ones."""
 
     def __init__(self):
@@ -13,7 +13,7 @@ def ensure_new_output_label(self, label: str):
         """Ensure supplied label has value or generate an anonymous one."""
         if label is None:
             self.anonymous_labels += 1
-            label = "_anonymous_output_%d" % self.anonymous_labels
+            label = f"_anonymous_output_{self.anonymous_labels}"
         assert label not in self.seen_labels
         self.seen_labels.add(label)
         return label

gxformat2/abstract.py

@@ -11,8 +11,8 @@
 CWL_VERSION = "v1.2"
 
 SCRIPT_DESCRIPTION = """
-This script converts the an executable Galaxy workflow (in either format -
-Format 2 or native .ga) into an abstract CWL representation.
+This script converts an executable Galaxy workflow (in either format - Format 2
+or native .ga) into an abstract CWL representation.
 
 In order to represent Galaxy tool executions in the Common Workflow Language
 workflow language, they are serialized as v1.2+ abstract 'Operation' classes.
@@ -73,7 +73,7 @@ def _format2_step_to_abstract(format2_step, requirements):
             step_run = from_dict(format2_run, subworkflow=True)
             abstract_step["run"] = step_run
         else:
-            raise NotImplementedError("Unknown runnabled type encountered [%s]" % format2_run_class)
+            raise NotImplementedError(f"Unknown runnabled type encountered [{format2_run_class}]")
     else:
         step_run = {
             "class": "Operation",
@@ -166,7 +166,7 @@ def main(argv=None):
     if workflow_path == "-":
         workflow_dict = ordered_load(sys.stdin)
     else:
-        with open(workflow_path, "r") as f:
+        with open(workflow_path) as f:
             workflow_dict = ordered_load(f)
 
     abstract_dict = from_dict(workflow_dict)

gxformat2/converter.py

@@ -1,5 +1,4 @@
 """Functionality for converting a Format 2 workflow into a standard Galaxy workflow."""
-from __future__ import print_function
 
 import argparse
 import copy
@@ -94,13 +93,13 @@ def rename_arg(argument):
 def clean_connection(value):
     if value and "#" in value and SUPPORT_LEGACY_CONNECTIONS:
         # Hope these are just used by Galaxy testing workflows and such, and not in production workflows.
-        log.warn("Legacy workflow syntax for connections [%s] will not be supported in the future" % value)
+        log.warn(f"Legacy workflow syntax for connections [{value}] will not be supported in the future")
         value = value.replace("#", "/", 1)
     else:
         return value
 
 
-class ImportOptions(object):
+class ImportOptions:
 
     def __init__(self):
         self.deduplicate_subworkflows = False
@@ -151,7 +150,7 @@ def steps_as_list(format2_workflow: dict, add_ids: bool = False, inputs_offset:
     Add keys as labels instead of IDs. Why am I doing this?
     """
     if "steps" not in format2_workflow:
-        raise Exception("No 'steps' key in dict, keys are %s" % format2_workflow.keys())
+        raise Exception(f"No 'steps' key in dict, keys are {format2_workflow.keys()}")
     steps = format2_workflow["steps"]
     steps = convert_dict_to_id_list_if_needed(steps, add_label=True, mutate=mutate)
     if add_ids:
@@ -229,9 +228,9 @@ def _python_to_workflow(as_python, conversion_context):
         step_type = step.get("type", "tool")
         step_type = STEP_TYPE_ALIASES.get(step_type, step_type)
         if step_type not in STEP_TYPES:
-            raise Exception("Unknown step type encountered %s" % step_type)
+            raise Exception(f"Unknown step type encountered {step_type}")
         step["type"] = step_type
-        eval("transform_%s" % step_type)(conversion_context, step)
+        eval(f"transform_{step_type}")(conversion_context, step)
 
     outputs = as_python.pop("outputs", [])
     outputs = convert_dict_to_id_list_if_needed(outputs)
@@ -512,7 +511,7 @@ def run_tool_to_step(conversion_context, step, run_action):
     step["tool_uuid"] = tool_description.get("uuid")
 
 
-class BaseConversionContext(object):
+class BaseConversionContext:
 
     def __init__(self):
         self.labels = {}
@@ -559,7 +558,7 @@ def get_runnable_description(self, run_action):
 
             run_action_path = run_action["@import"]
             runnable_path = os.path.join(self.workflow_directory, run_action_path)
-            with open(runnable_path, "r") as f:
+            with open(runnable_path) as f:
                 runnable_description = ordered_load(f)
                 run_action = runnable_description
 
@@ -572,7 +571,7 @@ def get_runnable_description(self, run_action):
 class ConversionContext(BaseConversionContext):
 
     def __init__(self, galaxy_interface, workflow_directory, import_options: Optional[ImportOptions] = None):
-        super(ConversionContext, self).__init__()
+        super().__init__()
         self.import_options = import_options or ImportOptions()
         self.graph_ids = OrderedDict()  # type: Dict
         self.graph_id_subworkflow_conversion_contexts = {}  # type: Dict
@@ -595,7 +594,7 @@ def get_subworkflow_conversion_context_graph(self, graph_id):
 class SubworkflowConversionContext(BaseConversionContext):
 
     def __init__(self, parent_context):
-        super(SubworkflowConversionContext, self).__init__()
+        super().__init__()
         self.parent_context = parent_context
 
     @property
@@ -632,7 +631,7 @@ def _is_link(value):
 
 def _join_prefix(prefix, key):
     if prefix:
-        new_key = "%s|%s" % (prefix, key)
+        new_key = f"{prefix}|{key}"
     else:
         new_key = key
     return new_key
@@ -657,7 +656,7 @@ def _init_connect_dict(step):
             elif isinstance(value, dict) and 'default' in value:
                 continue
             elif isinstance(value, dict):
-                raise KeyError('step input must define either source or default %s' % value)
+                raise KeyError(f'step input must define either source or default {value}')
             connect[key] = [value]
             connection_keys.add(key)
 
@@ -731,7 +730,7 @@ def main(argv=None):
     workflow_directory = os.path.abspath(format2_path)
     galaxy_interface = None
 
-    with open(format2_path, "r") as f:
+    with open(format2_path) as f:
         has_workflow = ordered_load(f)
 
     output = python_to_workflow(has_workflow, galaxy_interface=galaxy_interface, workflow_directory=workflow_directory)

gxformat2/cytoscape.py

@@ -5,16 +5,14 @@
 import string
 import sys
 
-import pkg_resources
-
 from gxformat2.model import ensure_step_position
 from gxformat2.normalize import steps_normalized
 
-CYTOSCAPE_JS_TEMPLATE = pkg_resources.resource_filename(__name__, 'cytoscape.html')
+CYTOSCAPE_JS_TEMPLATE = os.path.join(os.path.dirname(__file__), 'cytoscape.html')
 MAIN_TS_PREFIX = "toolshed.g2.bx.psu.edu/repos/"
 SCRIPT_DESCRIPTION = """
-This script converts the an executable Galaxy workflow (in either format -
-Format 2 or native .ga) into a format for visualization with Cytoscape
+This script converts an executable Galaxy workflow (in either format - Format 2
+or native .ga) into a format for visualization with Cytoscape
 (https://cytoscape.org/).
 
 If the target output path ends with .html this script will output a HTML
@@ -35,7 +33,7 @@ def to_cytoscape(workflow_path: str, output_path=None):
     for i, step in enumerate(steps):
         step_id = step.get("id") or step.get("label") or str(i)
         step_type = step.get("type") or 'tool'
-        classes = ["type_%s" % step_type]
+        classes = [f"type_{step_type}"]
         if step_type in ['tool', 'subworkflow']:
             classes.append("runnable")
         else:
@@ -44,7 +42,7 @@ def to_cytoscape(workflow_path: str, output_path=None):
         tool_id = step.get("tool_id")
         if tool_id and tool_id.startswith(MAIN_TS_PREFIX):
             tool_id = tool_id[len(MAIN_TS_PREFIX):]
-        label = step.get("id") or step.get("label") or ("tool:%s" % tool_id) or str(i)
+        label = step.get("id") or step.get("label") or (f"tool:{tool_id}" if tool_id else str(i))
         ensure_step_position(step, i)
         node_position = dict(x=int(step["position"]["left"]), y=int(step["position"]["top"]))
         repo_link = None
@@ -70,12 +68,12 @@ def to_cytoscape(workflow_path: str, output_path=None):
                 from_step, output = value.split("/", 1)
             else:
                 from_step, output = value, None
-            edge_id = "%s__to__%s" % (step_id, from_step)
+            edge_id = f"{step_id}__to__{from_step}"
             edge_data = {"id": edge_id, "source": from_step, "target": step_id, "input": key, "output": output}
             elements.append({"group": "edges", "data": edge_data})
 
     if output_path.endswith(".html"):
-        with open(CYTOSCAPE_JS_TEMPLATE, "r") as f:
+        with open(CYTOSCAPE_JS_TEMPLATE) as f:
             template = f.read()
         viz = string.Template(template).safe_substitute(elements=json.dumps(elements))
         with open(output_path, "w") as f:

gxformat2/export.py

@@ -239,7 +239,7 @@ def _to_source(has_output_name, label_map, output_id=None):
     if output_name == "output":
         source = output_label
     else:
-        source = "%s/%s" % (output_label, output_name)
+        source = f"{output_label}/{output_name}"
     return source
 
 
@@ -252,7 +252,7 @@ def main(argv=None):
 
     format2_path = args.input_path
     output_path = args.output_path or (format2_path + ".gxwf.yml")
-    with open(format2_path, "r") as f:
+    with open(format2_path) as f:
         native_workflow_dict = json.load(f)
 
     as_dict = from_galaxy_native(native_workflow_dict)

gxformat2/interface.py

@@ -7,11 +7,9 @@
 import abc
 
 import bioblend  # type: ignore
-import six
 
 
-@six.add_metaclass(abc.ABCMeta)
-class ImporterGalaxyInterface(object):
+class ImporterGalaxyInterface(metaclass=abc.ABCMeta):
     """An abstract interface describing Galaxy operations used by gxformat2.
 
     Specifically containing definitions of operations required to load
@@ -30,7 +28,7 @@ def import_tool(self, tool):
         raise NotImplementedError()
 
 
-class BioBlendImporterGalaxyInterface(object):
+class BioBlendImporterGalaxyInterface:
     """Implementation of :class:`ImporterGalaxyInterface` using bioblend."""
 
     def __init__(self, **kwds):

gxformat2/lint.py

@@ -46,7 +46,7 @@ def ensure_key_has_value(lint_context, has_keys, key, value, has_class=None, has
 def _lint_step_errors(lint_context, step):
     step_errors = step.get("errors")
     if step_errors is not None:
-        lint_context.warn("tool step contains error indicated during Galaxy export - %s" % step_errors)
+        lint_context.warn(f"tool step contains error indicated during Galaxy export - {step_errors}")
 
 
 def lint_ga_path(lint_context, path):
@@ -147,7 +147,7 @@ def _validate_report(lint_context, workflow_dict):
             try:
                 validate_galaxy_markdown(markdown)
             except ValueError as e:
-                lint_context.error("Report markdown validation failed [%s]" % e)
+                lint_context.error(f"Report markdown validation failed [{e}]")
 
 
 def _lint_training(lint_context, workflow_dict):
@@ -159,7 +159,7 @@ def _lint_training(lint_context, workflow_dict):
     else:
         tags = workflow_dict["tags"]
         if lint_context.training_topic not in tags:
-            lint_context.warn("Missing expected training topic (%s) as workflow tag." % lint_context.training_topic)
+            lint_context.warn(f"Missing expected training topic ({lint_context.training_topic}) as workflow tag.")
     # Move up into individual lints - all workflows should have docs.
     format2_dict = ensure_format2(workflow_dict)
     if "doc" not in format2_dict:
@@ -174,7 +174,7 @@ def main(argv=None):
         argv = sys.argv
     args = _parser().parse_args(argv[1:])
     path = args.path
-    with open(path, "r") as f:
+    with open(path) as f:
         try:
             workflow_dict = ordered_load(f)
         except Exception:

gxformat2/linting.py

@@ -8,7 +8,7 @@
 DEFAULT_TRAINING_LINT = None
 
 
-class LintContext(object):
+class LintContext:
     """Track running status (state) of linting."""
 
     def __init__(self, level=LEVEL_WARN, training_topic=DEFAULT_TRAINING_LINT):
@@ -46,15 +46,15 @@ def print_messages(self):
         """Print error messages and update state at the end of linting."""
         for message in self.error_messages:
             self.found_errors = True
-            print(".. ERROR: %s" % message)
+            print(f".. ERROR: {message}")
 
         if self.level != LEVEL_ERROR:
             for message in self.warn_messages:
                 self.found_warns = True
-                print(".. WARNING: %s" % message)
+                print(f".. WARNING: {message}")
 
         if self.level == LEVEL_ALL:
             for message in self.info_messages:
-                print(".. INFO: %s" % message)
+                print(f".. INFO: {message}")
             for message in self.valid_messages:
-                print(".. CHECK: %s" % message)
+                print(f".. CHECK: {message}")

gxformat2/main.py

@@ -18,7 +18,7 @@ def convert_and_import_workflow(has_workflow, **kwds):
         workflow_path = has_workflow
         if workflow_directory is None:
             workflow_directory = os.path.dirname(has_workflow)
-        with open(workflow_path, "r") as f:
+        with open(workflow_path) as f:
             has_workflow = ordered_load(f)
 
     if workflow_directory is not None: