mypy support

Author: jmchilton

.github/workflows/ci.yaml

@@ -17,6 +17,7 @@ jobs:
         tox-action:
           - lint
           - lint_docs
+          - mypy
           - unit-quick
           #- unit-diagnostic-servebasic
           #- unit-diagnostic-servebasic-gx-2005

planemo/cli.py

@@ -94,8 +94,6 @@ def handle_blended_options(*args, **kwds):
             )
             _setup_profile_options(ctx, profile_defaults, kwds)
 
-        _setup_galaxy_source_options(args[0], kwds)
-
         try:
             return f(*args, **kwds)
         except ExitCodeException as e:
@@ -104,38 +102,6 @@ def handle_blended_options(*args, **kwds):
     return pass_context(handle_blended_options)
 
 
-EXCLUSIVE_OPTIONS_LIST = [
-]
-
-
-def _setup_galaxy_source_options(ctx, kwds):
-    for exclusive_options in EXCLUSIVE_OPTIONS_LIST:
-        option_source = {}
-        for option in exclusive_options:
-            if option in kwds:
-                option_source[option] = ctx.get_option_source(option)
-            else:
-                option_source[option] = None
-
-        most_authoratative_source = None
-        most_authoratative_source_options = []
-        for key, value in option_source.items():
-            if value is None:
-                continue
-            if most_authoratative_source is None or value.value < most_authoratative_source.value:
-                most_authoratative_source = value
-                most_authoratative_source_options = [key]
-            elif value == most_authoratative_source:
-                most_authoratative_source_options.append(key)
-
-        if most_authoratative_source != OptionSource.default and len(most_authoratative_source_options) > 1:
-            raise click.UsageError("Cannot specify multiple of %s" % most_authoratative_source_options)
-
-        for option in exclusive_options:
-            if option in kwds and option not in most_authoratative_source_options:
-                del kwds[option]
-
-
 def _setup_profile_options(ctx, profile_defaults, kwds):
     for key, value in profile_defaults.items():
         option_present = key in kwds

planemo/engine/interface.py

@@ -4,6 +4,7 @@
 import json
 import os
 import tempfile
+from typing import List
 
 from six import add_metaclass
 
@@ -12,6 +13,7 @@
 from planemo.runnable import (
     cases,
     for_path,
+    RunnableType,
 )
 from planemo.test.results import StructuredData
 
@@ -37,7 +39,7 @@ def test(self, runnables):
 class BaseEngine(Engine):
     """Base class providing context and keywords for Engine implementations."""
 
-    handled_runnable_types = []
+    handled_runnable_types = []  # type: List[RunnableType]
 
     def __init__(self, ctx, **kwds):
         """Store context and kwds."""

planemo/galaxy/test/structures.py

@@ -202,15 +202,14 @@ def _parse_num(num_str):
     return num
 
 
-TestId = namedtuple("TestId", ["name", "num", "id"])
+_TestId = namedtuple("TestId", ["name", "num", "id"])
 
 
-@property
-def _label(self):
-    if self.num is not None:
-        return "{0}[{1}]".format(self.name, self.num)
-    else:
-        return self.id
-
+class TestId(_TestId):
 
-TestId.label = _label
+    @property
+    def label(self):
+        if self.num is not None:
+            return "{0}[{1}]".format(self.name, self.num)
+        else:
+            return self.id

planemo/network_util.py

@@ -1,8 +1,5 @@
 import socket
-try:
-    from http.client import BadStatusLine
-except ImportError:
-    from httplib import BadStatusLine
+from http.client import BadStatusLine
 from time import time as now
 
 from six.moves.urllib.error import URLError

planemo/runnable.py

@@ -6,7 +6,7 @@
 import collections
 import os
 from distutils.dir_util import copy_tree
-from enum import Enum
+from enum import auto, Enum
 
 import yaml
 from galaxy.tool_util.cwl.parser import workflow_proxy
@@ -39,35 +39,30 @@
                               "defintion must field [%s].")
 
 
-RunnableType = Enum(
-    "RunnableType", 'galaxy_tool galaxy_datamanager galaxy_workflow cwl_tool cwl_workflow directory'
-)
-
-
-@property
-def _runnable_type_has_tools(runnable_type):
-    return runnable_type.name in ["galaxy_tool", "galaxy_datamanager", "cwl_tool", "directory"]
-
-
-@property
-def _runnable_type_is_single_artifact(runnable_type):
-    return runnable_type.name not in ["directory"]
+class RunnableType(Enum):
+    galaxy_tool = auto()
+    galaxy_datamanager = auto()
+    galaxy_workflow = auto()
+    cwl_tool = auto()
+    cwl_workflow = auto()
+    directory = auto()
 
+    @property
+    def has_tools(runnable_type):
+        return runnable_type.name in ["galaxy_tool", "galaxy_datamanager", "cwl_tool", "directory"]
 
-@property
-def _runnable_type_test_data_in_parent_dir(runnable_type):
-    return runnable_type.name in ["galaxy_datamanager"]
-
+    @property
+    def is_single_artifact(runnable_type):
+        return runnable_type.name not in ["directory"]
 
-@property
-def _runnable_type_is_galaxy_artifact(runnable_type):
-    return "galaxy" in runnable_type.name
+    @property
+    def test_data_in_parent_dir(runnable_type):
+        return runnable_type.name in ["galaxy_datamanager"]
 
+    @property
+    def is_galaxy_artifact(runnable_type):
+        return "galaxy" in runnable_type.name
 
-RunnableType.has_tools = _runnable_type_has_tools
-RunnableType.is_single_artifact = _runnable_type_is_single_artifact
-RunnableType.test_data_in_parent_dir = _runnable_type_test_data_in_parent_dir
-RunnableType.is_galaxy_artifact = _runnable_type_is_galaxy_artifact
 
 _Runnable = collections.namedtuple("Runnable", ["path", "type"])
 

planemo/shed/__init__.py

@@ -175,27 +175,24 @@ def construct_yaml_str(self, node):
 yaml.SafeLoader.add_constructor(u'tag:yaml.org,2002:str', construct_yaml_str)
 
 
-ShedContext = namedtuple("ShedContext", ["tsi", "shed_config", "config_owner"])
+_ShedContext = namedtuple("ShedContext", ["tsi", "shed_config", "config_owner"])
 
 
-def _shed_context_owner(self):
-    owner = self.config_owner
-    if owner is None:
-        owner = username(self.tsi)
-    return owner
-
-
-@property
-def _shed_context_label(self):
-    return self.shed_config.get("label") or "tool shed"
+class ShedContext(_ShedContext):
 
+    def owner(self):
+        owner = self.config_owner
+        if owner is None:
+            owner = username(self.tsi)
+        return owner
 
-ShedContext.owner = _shed_context_owner
-ShedContext.label = _shed_context_label
+    @property
+    def label(self):
+        return self.shed_config.get("label") or "tool shed"
 
 
 def shed_init(ctx, path, **kwds):
-    """Intialize a new shed repository."""
+    """Initialize a new shed repository."""
     if not os.path.exists(path):
         os.makedirs(path)
     shed_config_path = os.path.join(path, SHED_CONFIG_NAME)

planemo/shed2tap/base.py

@@ -6,6 +6,7 @@
 import tarfile
 import zipfile
 from ftplib import all_errors as FTPErrors  # tuple of exceptions
+from typing import List
 from xml.etree import ElementTree
 
 from galaxy.util import unicodify
@@ -329,6 +330,8 @@ def __init__(self, name, version, repo):
 
 
 class BaseAction(object):
+    _keys = []  # type: List[str]
+    action_type = None  # type: str
 
     def __repr__(self):
         return "Action[type=%s]" % self.action_type
@@ -686,7 +689,7 @@ def to_bash(self):
 
 class MakeInstallAction(BaseAction):
     action_type = "make_install"
-    _keys = []
+    _keys = []  # type: List[str]
 
     def __init__(self, elem):
         pass

planemo/templates.py

@@ -2,13 +2,13 @@
 try:
     from jinja2 import Template
 except ImportError:
-    Template = None
+    Template = None  # type: ignore
 
 NO_JINJA2_MESSAGE = ("This functionality requires Jinja2 but this library is "
                      "unavailable. Install with `pip install jinja2`.")
 
 
-def render(template_str, **kwds):
+def render(template_str: str, **kwds):
     """Use jinja2 to render specified template."""
     if Template is None:
         raise Exception(NO_JINJA2_MESSAGE)

setup.cfg

@@ -9,10 +9,12 @@ with-coverage=1
 logging-filter=planemo,galaxy
 logging-level=INFO
 
-
 [flake8]
 max-line-length = 150
 max-complexity = 14
 exclude=.eggs,.git,.tox,.venv,.venv3,build,docs/conf.py,docs/standards,project_templates/cwl_draft3_spec/
 import-order-style = smarkets
 application-import-names = planemo,test
+
+[mypy]
+ignore_missing_imports = True

tox.ini

@@ -9,6 +9,7 @@ commands =
     lint_docs: make lint-docs
     lint_docstrings: flake8 --ignore='D107,D401,D105' {[tox]source_dir}
     unit: pytest {env:PYTEST_FAIL_FAIL:} {env:PYTEST_CAPTURE:} -m {env:PYTEST_MARK:""} {env:PYTEST_TARGET:{[tox]test_dir}} {posargs}
+    mypy: mypy {[tox]source_dir} {posargs}
 
 passenv = 
     PLANEMO_*
@@ -25,6 +26,7 @@ deps =
     # unit: pytest-timeout
     unit: coverage
     unit: flask
+    mypy: mypy
 setenv =
     gx: PYTEST_MARK="tests_galaxy_branch"
     diagnostic: PLANEMO_TEST_VERBOSE=1
@@ -52,7 +54,7 @@ setenv =
     2005: PLANEMO_TEST_GALAXY_BRANCH=release_20.05
     2001: PLANEMO_TEST_GALAXY_BRANCH=release_20.01
 skip_install =
-    doc_test,lint,lint_docs,lint_docstrings: True
+    doc_test,lint,lint_docs,lint_docstrings,mypy: True
 whitelist_externals =
     lint_docs: make