bye pytz (#4890)

* pytz is not needed in Python 3.9+, or with the zoneinfo backport

* make diff_mypy: quieter and target the correct branch

* Linting.

* Satisfy MyPy more (new MyPy?)

---------

Co-authored-by: Adam Novak <[email protected]>
Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: DailyDreaming <[email protected]>

Makefile

@@ -325,8 +325,8 @@ diff_pydocstyle_report: pydocstyle_report.txt
 	diff-quality --compare-branch=master --violations=pycodestyle --fail-under=100 $^
 
 diff_mypy:
-	mypy --cobertura-xml-report . src/toil || true
-	diff-cover --fail-under=100 cobertura.xml
+	mypy --cobertura-xml-report . src/toil > /dev/null || true
+	diff-cover --fail-under=100 --compare-branch origin/master cobertura.xml
 
 pyupgrade: $(PYSOURCES)
 	pyupgrade --exit-zero-even-if-changed --py37-plus $^

requirements-dev.txt

@@ -11,10 +11,15 @@ sphinx-autodoc-typehints>=1.24.0,<3
 sphinxcontrib-autoprogram==0.1.9
 cwltest>=2.2.20211116163652
 mypy==1.10.0
+types-aws-xray-sdk
+types-boto<2.49.18.20240205
+types-Flask-Cors
 types-requests
+types-psutil
+types-python-dateutil
 types-setuptools
-types-boto<2.49.18.20240205
-types-pytz
+types-xmltodict
+backports.zoneinfo[tzdata];python_version<"3.9"
 flake8>=3.8.4,<8
 flake8-bugbear>=20.11.1,<25
 black

requirements.txt

@@ -7,7 +7,6 @@ python-dateutil
 psutil >= 3.0.1, <6
 PyPubSub >=4.0.3, <5
 addict>=2.2.1, <2.5
-pytz>=2012
 enlighten>=1.5.2, <2
 configargparse>=1.7,<2
 ruamel.yaml>=0.15

src/toil/__init__.py

@@ -22,7 +22,6 @@
 from typing import TYPE_CHECKING, Optional, Tuple
 
 import requests
-from pytz import timezone
 
 from docker.errors import ImageNotFound
 from toil.lib.memoize import memoize
@@ -475,5 +474,6 @@ def str_to_datetime(s):
         datetime.datetime(1970, 1, 1, 0, 0)
         """
         return datetime.strptime(s, datetime_format)
+
 except ImportError:
     pass

src/toil/lib/misc.py

@@ -11,8 +11,6 @@
 from contextlib import closing
 from typing import Iterator, List, Optional
 
-import pytz
-
 logger = logging.getLogger(__name__)
 
 
@@ -56,7 +54,7 @@ def get_user_name() -> str:
 
 def utc_now() -> datetime.datetime:
     """Return a datetime in the UTC timezone corresponding to right now."""
-    return datetime.datetime.utcnow().replace(tzinfo=pytz.UTC)
+    return datetime.datetime.utcnow().replace(tzinfo=datetime.timezone.utc)
 
 def unix_now_ms() -> float:
     """Return the current time in milliseconds since the Unix epoch."""

src/toil/lib/threading.py

@@ -28,7 +28,7 @@
 from contextlib import contextmanager
 from typing import Dict, Iterator, Optional, Union, cast
 
-import psutil  # type: ignore
+import psutil
 
 from toil.lib.exceptions import raise_
 from toil.lib.io import robust_rmtree

src/toil/server/app.py

@@ -87,7 +87,7 @@ def create_app(args: argparse.Namespace) -> "connexion.FlaskApp":
 
     if args.cors:
         # enable cross origin resource sharing
-        from flask_cors import CORS  # type: ignore
+        from flask_cors import CORS
         CORS(flask_app.app, resources={r"/ga4gh/*": {"origins": args.cors_origins}})
 
     # add workflow execution service (WES) API endpoints

src/toil/test/__init__.py

@@ -46,12 +46,13 @@
 from urllib.error import HTTPError, URLError
 from urllib.request import urlopen
 
-import pytz
 
 if sys.version_info >= (3, 8):
     from typing import Literal
+    import zoneinfo
 else:
     from typing_extensions import Literal
+    from backports import zoneinfo
 
 from toil import ApplianceImageNotFound, applianceSelf, toilPackageDirPath
 from toil.lib.accelerators import (have_working_nvidia_docker_runtime,
@@ -85,8 +86,8 @@ class ToilTest(unittest.TestCase):
     _tempDirs: List[str] = []
 
     def setup_method(self, method: Any) -> None:
-        western = pytz.timezone('America/Los_Angeles')
-        california_time = western.localize(datetime.datetime.now())
+        western = zoneinfo.ZoneInfo("America/Los_Angeles")
+        california_time = datetime.datetime.now(tz=western)
         timestamp = california_time.strftime("%b %d %Y %H:%M:%S:%f %Z")
         print(f"\n\n[TEST] {strclass(self.__class__)}:{self._testMethodName} ({timestamp})\n\n")