Run mypy on all packages' files

Also:
- mypy fixes.
- Use `with` statement to open/close files.

lib/galaxy_ext/expressions/handle_job.py

@@ -16,7 +16,7 @@ warnings.filterwarnings("ignore", message=r"[\n.]DEPRECATION: Python 2", module=
 try:
     from cwltool import expression
 except ImportError:
-    expression = None
+    expression = None  # type: ignore[assignment]
 
 from galaxy.tools.expressions import evaluate
 

lib/galaxy_test/base/populators.py

@@ -67,7 +67,7 @@ from typing import (
     Union,
 )
 
-import cwltest
+import cwltest.utils
 import requests
 import yaml
 from bioblend.galaxy import GalaxyClient
@@ -2102,7 +2102,7 @@ class CwlPopulator:
         try:
             for key, value in expected_outputs.items():
                 actual_output = run.get_output_as_object(key)
-                cwltest.compare(value, actual_output)
+                cwltest.utils.compare(value, actual_output)
         except Exception:
             self.dataset_populator._summarize_history(run.history_id)
             raise

packages/app/setup.py

@@ -20,8 +20,9 @@ with open(f"{SOURCE_DIR}/project_galaxy_{project_short_name}.py") as f:
 
 def get_var(var_name):
     pattern = re.compile(rf"{var_name}\s+=\s+(.*)")
-    match = pattern.search(init_contents).group(1)
-    return str(ast.literal_eval(match))
+    match = pattern.search(init_contents)
+    assert match
+    return str(ast.literal_eval(match.group(1)))
 
 
 version = get_var("__version__")

packages/auth/setup.py

@@ -3,6 +3,10 @@
 import ast
 import os
 import re
+from typing import (
+    Dict,
+    List,
+)
 
 try:
     from setuptools import setup
@@ -20,8 +24,9 @@ with open(f"{SOURCE_DIR}/project_galaxy_{project_short_name}.py") as f:
 
 def get_var(var_name):
     pattern = re.compile(rf"{var_name}\s+=\s+(.*)")
-    match = pattern.search(init_contents).group(1)
-    return str(ast.literal_eval(match))
+    match = pattern.search(init_contents)
+    assert match
+    return str(ast.literal_eval(match.group(1)))
 
 
 version = get_var("__version__")
@@ -40,7 +45,7 @@ PACKAGES = [
 ENTRY_POINTS = """
         [console_scripts]
 """
-PACKAGE_DATA = {
+PACKAGE_DATA: Dict[str, List[str]] = {
     # Be sure to update MANIFEST.in for source dist.
     "galaxy": [],
 }

packages/build_scripts/commit_version.py

@@ -6,27 +6,31 @@ import re
 import subprocess
 import sys
 
-DEV_RELEASE = os.environ.get("DEV_RELEASE", None) == "1"
-PROJECT_DIRECTORY = os.getcwd()
-PROJECT_DIRECTORY_NAME = os.path.basename(os.path.abspath(PROJECT_DIRECTORY))
-PROJECT_MODULE_FILENAME = f"project_galaxy_{PROJECT_DIRECTORY_NAME}.py"
-PROJECT_NAME = PROJECT_DIRECTORY_NAME.replace("_", "-")
-
 
 def main(argv):
+    DEV_RELEASE = os.environ.get("DEV_RELEASE", None) == "1"
+    PROJECT_DIRECTORY = os.getcwd()
+    PROJECT_DIRECTORY_NAME = os.path.basename(os.path.abspath(PROJECT_DIRECTORY))
+    PROJECT_MODULE_FILENAME = f"project_galaxy_{PROJECT_DIRECTORY_NAME}.py"
+    PROJECT_NAME = PROJECT_DIRECTORY_NAME.replace("_", "-")
+
     source_dir = argv[1]
     version = argv[2]
     mod_path = os.path.join(PROJECT_DIRECTORY, source_dir, PROJECT_MODULE_FILENAME)
     if not DEV_RELEASE:
         history_path = os.path.join(PROJECT_DIRECTORY, "HISTORY.rst")
-        history = open(history_path).read()
+        with open(history_path) as f:
+            history = f.read()
         today = datetime.datetime.today()
         today_str = today.strftime("%Y-%m-%d")
         history = history.replace(".dev0", f" ({today_str})")
-        open(history_path, "w").write(history)
-        mod = open(mod_path).read()
+        with open(history_path, "w") as f:
+            f.write(history)
+        with open(mod_path) as f:
+            mod = f.read()
         mod = re.sub(r"__version__ = '[\d\.]*\.dev\d+'", f"__version__ = '{version}'", mod)
-        mod = open(mod_path, "w").write(mod)
+        with open(mod_path, "w") as f:
+            f.write(mod)
     tag = f"galaxy-{PROJECT_NAME}-{version}"
     shell(["git", "commit", "-m", f"Version {version} of {PROJECT_NAME} (tag {tag}).", "HISTORY.rst", mod_path])
     shell(["git", "tag", tag])

packages/build_scripts/new_version.py

@@ -24,13 +24,16 @@ def main(argv):
         new_version = ".".join(map(str, new_version_tuple))
         new_dev_version = 0
     else:
-        dev_version = re.compile(r"dev([\d]+)").search(version).group(1)
+        dev_match = re.compile(r"dev([\d]+)").search(version)
+        assert dev_match
+        dev_version = dev_match.group(1)
         new_dev_version = int(dev_version) + 1
         new_version = version.replace(f"dev{dev_version}", f"dev{new_dev_version}")
 
     history_path = os.path.join(PROJECT_DIRECTORY, "HISTORY.rst")
     if not DEV_RELEASE:
-        history = open(history_path).read()
+        with open(history_path) as f:
+            history = f.read()
 
         def extend(from_str, line):
             from_str += "\n"
@@ -45,15 +48,18 @@ def main(argv):
 
 """,
         )
-        open(history_path, "w").write(history)
+        with open(history_path, "w") as f:
+            f.write(history)
 
     mod_path = os.path.join(PROJECT_DIRECTORY, source_dir, PROJECT_MODULE_FILENAME)
-    mod = open(mod_path).read()
+    with open(mod_path) as f:
+        mod = f.read()
     if not DEV_RELEASE:
         mod = re.sub(r"__version__ = '[\d\.]+'", f"__version__ = '{new_version}.dev0'", mod, 1)
     else:
         mod = re.sub(f"dev{dev_version}", f"dev{new_dev_version}", mod, 1)
-    mod = open(mod_path, "w").write(mod)
+    with open(mod_path, "w") as f:
+        f.write(mod)
     shell(["git", "commit", "-m", f"Starting work on {PROJECT_NAME} {new_version}", "HISTORY.rst", mod_path])
 
 

packages/build_scripts/print_version_for_release.py

@@ -4,21 +4,30 @@ import re
 import sys
 from distutils.version import LooseVersion
 
-DEV_RELEASE = os.environ.get("DEV_RELEASE", None) == "1"
-PROJECT_DIRECTORY = os.getcwd()
-PROJECT_DIRECTORY_NAME = os.path.basename(os.path.abspath(PROJECT_DIRECTORY))
-PROJECT_MODULE_FILENAME = f"project_galaxy_{PROJECT_DIRECTORY_NAME}.py"
-
-source_dir = sys.argv[1]
-PROJECT_MODULE_PATH = os.path.join(PROJECT_DIRECTORY, source_dir, PROJECT_MODULE_FILENAME)
-
 _version_re = re.compile(r"__version__\s+=\s+(.*)")
-with open(PROJECT_MODULE_PATH, "rb") as f:
-    version = str(ast.literal_eval(_version_re.search(f.read().decode("utf-8")).group(1)))
 
-if not DEV_RELEASE:
-    # Strip .devN
-    version_tuple = LooseVersion(version).version[0:3]
-    print(".".join(map(str, version_tuple)))
-else:
-    print(version)
+
+def main():
+    DEV_RELEASE = os.environ.get("DEV_RELEASE", None) == "1"
+    PROJECT_DIRECTORY = os.getcwd()
+    PROJECT_DIRECTORY_NAME = os.path.basename(os.path.abspath(PROJECT_DIRECTORY))
+    PROJECT_MODULE_FILENAME = f"project_galaxy_{PROJECT_DIRECTORY_NAME}.py"
+
+    source_dir = sys.argv[1]
+    PROJECT_MODULE_PATH = os.path.join(PROJECT_DIRECTORY, source_dir, PROJECT_MODULE_FILENAME)
+
+    with open(PROJECT_MODULE_PATH, "rb") as f:
+        version_match = _version_re.search(f.read().decode("utf-8"))
+    assert version_match
+    version = str(ast.literal_eval(version_match.group(1)))
+
+    if not DEV_RELEASE:
+        # Strip .devN
+        version_tuple = LooseVersion(version).version[0:3]
+        print(".".join(map(str, version_tuple)))
+    else:
+        print(version)
+
+
+if __name__ == "__main__":
+    main()

packages/config/setup.py

@@ -20,8 +20,9 @@ with open(f"{SOURCE_DIR}/project_galaxy_{project_short_name}.py") as f:
 
 def get_var(var_name):
     pattern = re.compile(rf"{var_name}\s+=\s+(.*)")
-    match = pattern.search(init_contents).group(1)
-    return str(ast.literal_eval(match))
+    match = pattern.search(init_contents)
+    assert match
+    return str(ast.literal_eval(match.group(1)))
 
 
 version = get_var("__version__")

packages/data/setup.py

@@ -20,8 +20,9 @@ with open(f"{SOURCE_DIR}/project_galaxy_{project_short_name}.py") as f:
 
 def get_var(var_name):
     pattern = re.compile(rf"{var_name}\s+=\s+(.*)")
-    match = pattern.search(init_contents).group(1)
-    return str(ast.literal_eval(match))
+    match = pattern.search(init_contents)
+    assert match
+    return str(ast.literal_eval(match.group(1)))
 
 
 version = get_var("__version__")

packages/files/setup.py

@@ -3,6 +3,10 @@
 import ast
 import os
 import re
+from typing import (
+    Dict,
+    List,
+)
 
 try:
     from setuptools import setup
@@ -20,8 +24,9 @@ with open(f"{SOURCE_DIR}/project_galaxy_{project_short_name}.py") as f:
 
 def get_var(var_name):
     pattern = re.compile(rf"{var_name}\s+=\s+(.*)")
-    match = pattern.search(init_contents).group(1)
-    return str(ast.literal_eval(match))
+    match = pattern.search(init_contents)
+    assert match
+    return str(ast.literal_eval(match.group(1)))
 
 
 version = get_var("__version__")
@@ -41,7 +46,7 @@ PACKAGES = [
 ENTRY_POINTS = """
         [console_scripts]
 """
-PACKAGE_DATA = {
+PACKAGE_DATA: Dict[str, List[str]] = {
     # Be sure to update MANIFEST.in for source dist.
     "galaxy": [],
 }

packages/job_execution/setup.py

@@ -3,6 +3,10 @@
 import ast
 import os
 import re
+from typing import (
+    Dict,
+    List,
+)
 
 try:
     from setuptools import setup
@@ -20,8 +24,9 @@ with open(f"{SOURCE_DIR}/project_galaxy_{project_short_name}.py") as f:
 
 def get_var(var_name):
     pattern = re.compile(rf"{var_name}\s+=\s+(.*)")
-    match = pattern.search(init_contents).group(1)
-    return str(ast.literal_eval(match))
+    match = pattern.search(init_contents)
+    assert match
+    return str(ast.literal_eval(match.group(1)))
 
 
 version = get_var("__version__")
@@ -43,7 +48,7 @@ ENTRY_POINTS = """
         [console_scripts]
         galaxy-set-metadata=galaxy.metadata.set_metadata:set_metadata
 """
-PACKAGE_DATA = {
+PACKAGE_DATA: Dict[str, List[str]] = {
     # Be sure to update MANIFEST.in for source dist.
     "galaxy": [],
 }

packages/job_metrics/setup.py

@@ -3,6 +3,10 @@
 import ast
 import os
 import re
+from typing import (
+    Dict,
+    List,
+)
 
 try:
     from setuptools import setup
@@ -20,8 +24,9 @@ with open(f"{SOURCE_DIR}/project_galaxy_{project_short_name}.py") as f:
 
 def get_var(var_name):
     pattern = re.compile(rf"{var_name}\s+=\s+(.*)")
-    match = pattern.search(init_contents).group(1)
-    return str(ast.literal_eval(match))
+    match = pattern.search(init_contents)
+    assert match
+    return str(ast.literal_eval(match.group(1)))
 
 
 version = get_var("__version__")
@@ -40,7 +45,7 @@ PACKAGES = [
 ENTRY_POINTS = """
         [console_scripts]
 """
-PACKAGE_DATA = {
+PACKAGE_DATA: Dict[str, List[str]] = {
     # Be sure to update MANIFEST.in for source dist.
     "galaxy": [],
 }

packages/meta/setup.py

@@ -3,6 +3,10 @@
 import ast
 import os
 import re
+from typing import (
+    Dict,
+    List,
+)
 
 try:
     from setuptools import setup
@@ -20,8 +24,9 @@ with open(f"{SOURCE_DIR}/project_galaxy_{project_short_name}.py") as f:
 
 def get_var(var_name):
     pattern = re.compile(rf"{var_name}\s+=\s+(.*)")
-    match = pattern.search(init_contents).group(1)
-    return str(ast.literal_eval(match))
+    match = pattern.search(init_contents)
+    assert match
+    return str(ast.literal_eval(match.group(1)))
 
 
 version = get_var("__version__")
@@ -32,11 +37,11 @@ PROJECT_EMAIL = get_var("PROJECT_EMAIL")
 PROJECT_DESCRIPTION = get_var("PROJECT_DESCRIPTION")
 
 TEST_DIR = "tests"
-PACKAGES = []
+PACKAGES: List[str] = []
 ENTRY_POINTS = """
         [console_scripts]
 """
-PACKAGE_DATA = {
+PACKAGE_DATA: Dict[str, List[str]] = {
     # Be sure to update MANIFEST.in for source dist.
 }
 PACKAGE_DIR = {

packages/objectstore/setup.py

@@ -3,6 +3,10 @@
 import ast
 import os
 import re
+from typing import (
+    Dict,
+    List,
+)
 
 try:
     from setuptools import setup
@@ -20,8 +24,9 @@ with open(f"{SOURCE_DIR}/project_galaxy_{project_short_name}.py") as f:
 
 def get_var(var_name):
     pattern = re.compile(rf"{var_name}\s+=\s+(.*)")
-    match = pattern.search(init_contents).group(1)
-    return str(ast.literal_eval(match))
+    match = pattern.search(init_contents)
+    assert match
+    return str(ast.literal_eval(match.group(1)))
 
 
 version = get_var("__version__")
@@ -40,7 +45,7 @@ PACKAGES = [
 ENTRY_POINTS = """
         [console_scripts]
 """
-PACKAGE_DATA = {
+PACKAGE_DATA: Dict[str, List[str]] = {
     # Be sure to update MANIFEST.in for source dist.
     "galaxy": [],
 }

packages/package.Makefile

@@ -93,5 +93,4 @@ push-release:
 release: release-local push-release
 
 mypy:
-	test -f $(TEST_DIR) && mypy $(SOURCE_DIR) $(TEST_DIR)
-	test -f $(TEST_DIR) || mypy $(SOURCE_DIR)
+	mypy .

packages/selenium/setup.py

@@ -20,8 +20,9 @@ with open(f"{SOURCE_DIR}/project_galaxy_{project_short_name}.py") as f:
 
 def get_var(var_name):
     pattern = re.compile(rf"{var_name}\s+=\s+(.*)")
-    match = pattern.search(init_contents).group(1)
-    return str(ast.literal_eval(match))
+    match = pattern.search(init_contents)
+    assert match
+    return str(ast.literal_eval(match.group(1)))
 
 
 version = get_var("__version__")

packages/test_api/setup.py

@@ -3,6 +3,10 @@
 import ast
 import os
 import re
+from typing import (
+    Dict,
+    List,
+)
 
 try:
     from setuptools import setup
@@ -20,8 +24,9 @@ with open(f"{SOURCE_DIR}/project_galaxy_{project_short_name}.py") as f:
 
 def get_var(var_name):
     pattern = re.compile(rf"{var_name}\s+=\s+(.*)")
-    match = pattern.search(init_contents).group(1)
-    return str(ast.literal_eval(match))
+    match = pattern.search(init_contents)
+    assert match
+    return str(ast.literal_eval(match.group(1)))
 
 
 version = get_var("__version__")
@@ -39,7 +44,7 @@ PACKAGES = [
 ENTRY_POINTS = """
         [console_scripts]
 """
-PACKAGE_DATA = {
+PACKAGE_DATA: Dict[str, List[str]] = {
     # Be sure to update MANIFEST.in for source dist.
     "galaxy": [],
 }

packages/test_base/setup.py

@@ -20,8 +20,9 @@ with open(f"{SOURCE_DIR}/project_galaxy_{project_short_name}.py") as f:
 
 def get_var(var_name):
     pattern = re.compile(rf"{var_name}\s+=\s+(.*)")
-    match = pattern.search(init_contents).group(1)
-    return str(ast.literal_eval(match))
+    match = pattern.search(init_contents)
+    assert match
+    return str(ast.literal_eval(match.group(1)))
 
 
 version = get_var("__version__")

packages/test_selenium/setup.py

@@ -3,6 +3,10 @@
 import ast
 import os
 import re
+from typing import (
+    Dict,
+    List,
+)
 
 try:
     from setuptools import setup
@@ -20,8 +24,9 @@ with open(f"{SOURCE_DIR}/project_galaxy_{project_short_name}.py") as f:
 
 def get_var(var_name):
     pattern = re.compile(rf"{var_name}\s+=\s+(.*)")
-    match = pattern.search(init_contents).group(1)
-    return str(ast.literal_eval(match))
+    match = pattern.search(init_contents)
+    assert match
+    return str(ast.literal_eval(match.group(1)))
 
 
 version = get_var("__version__")
@@ -40,7 +45,7 @@ PACKAGES = [
 ENTRY_POINTS = """
         [console_scripts]
 """
-PACKAGE_DATA = {
+PACKAGE_DATA: Dict[str, List[str]] = {
     # Be sure to update MANIFEST.in for source dist.
     "galaxy": [],
 }

packages/tool_util/setup.py

@@ -20,8 +20,9 @@ with open(f"{SOURCE_DIR}/project_galaxy_{project_short_name}.py") as f:
 
 def get_var(var_name):
     pattern = re.compile(rf"{var_name}\s+=\s+(.*)")
-    match = pattern.search(init_contents).group(1)
-    return str(ast.literal_eval(match))
+    match = pattern.search(init_contents)
+    assert match
+    return str(ast.literal_eval(match.group(1)))
 
 
 version = get_var("__version__")

packages/util/setup.py

@@ -20,8 +20,9 @@ with open(f"{SOURCE_DIR}/project_galaxy_{project_short_name}.py") as f:
 
 def get_var(var_name):
     pattern = re.compile(rf"{var_name}\s+=\s+(.*)")
-    match = pattern.search(init_contents).group(1)
-    return str(ast.literal_eval(match))
+    match = pattern.search(init_contents)
+    assert match
+    return str(ast.literal_eval(match.group(1)))
 
 
 version = get_var("__version__")

packages/web_framework/setup.py

@@ -3,6 +3,10 @@
 import ast
 import os
 import re
+from typing import (
+    Dict,
+    List,
+)
 
 try:
     from setuptools import setup
@@ -20,8 +24,9 @@ with open(f"{SOURCE_DIR}/project_galaxy_{project_short_name}.py") as f:
 
 def get_var(var_name):
     pattern = re.compile(rf"{var_name}\s+=\s+(.*)")
-    match = pattern.search(init_contents).group(1)
-    return str(ast.literal_eval(match))
+    match = pattern.search(init_contents)
+    assert match
+    return str(ast.literal_eval(match.group(1)))
 
 
 version = get_var("__version__")
@@ -45,7 +50,7 @@ PACKAGES = [
 ENTRY_POINTS = """
         [console_scripts]
 """
-PACKAGE_DATA = {
+PACKAGE_DATA: Dict[str, List[str]] = {
     # Be sure to update MANIFEST.in for source dist.
     "galaxy": [],
 }

packages/web_stack/setup.py

@@ -3,6 +3,10 @@
 import ast
 import os
 import re
+from typing import (
+    Dict,
+    List,
+)
 
 try:
     from setuptools import setup
@@ -20,8 +24,9 @@ with open(f"{SOURCE_DIR}/project_galaxy_{project_short_name}.py") as f:
 
 def get_var(var_name):
     pattern = re.compile(rf"{var_name}\s+=\s+(.*)")
-    match = pattern.search(init_contents).group(1)
-    return str(ast.literal_eval(match))
+    match = pattern.search(init_contents)
+    assert match
+    return str(ast.literal_eval(match.group(1)))
 
 
 version = get_var("__version__")
@@ -39,7 +44,7 @@ PACKAGES = [
 ENTRY_POINTS = """
         [console_scripts]
 """
-PACKAGE_DATA = {
+PACKAGE_DATA: Dict[str, List[str]] = {
     # Be sure to update MANIFEST.in for source dist.
     "galaxy": [],
 }

packages/webapps/setup.py

@@ -3,6 +3,10 @@
 import ast
 import os
 import re
+from typing import (
+    Dict,
+    List,
+)
 
 try:
     from setuptools import setup
@@ -20,8 +24,9 @@ with open(f"{SOURCE_DIR}/project_galaxy_{project_short_name}.py") as f:
 
 def get_var(var_name):
     pattern = re.compile(rf"{var_name}\s+=\s+(.*)")
-    match = pattern.search(init_contents).group(1)
-    return str(ast.literal_eval(match))
+    match = pattern.search(init_contents)
+    assert match
+    return str(ast.literal_eval(match.group(1)))
 
 
 version = get_var("__version__")
@@ -67,7 +72,7 @@ PACKAGES = [
 ENTRY_POINTS = """
         [console_scripts]
 """
-PACKAGE_DATA = {
+PACKAGE_DATA: Dict[str, List[str]] = {
     # Be sure to update MANIFEST.in for source dist.
     "galaxy": [],
 }