Merge pull request #2548 from ASFHyP3/mypy

upgrade to python 3.13, add mypy

.github/workflows/deploy-daac.yml

@@ -78,7 +78,7 @@ jobs:
 
       - uses: actions/setup-python@v5
         with:
-          python-version: 3.9
+          python-version: 3.13
 
       - uses: ./.github/actions/deploy-hyp3
         if: github.ref == matrix.deploy_ref

.github/workflows/deploy-enterprise-test.yml

@@ -113,7 +113,7 @@ jobs:
 
       - uses: actions/setup-python@v5
         with:
-          python-version: 3.9
+          python-version: 3.13
 
       - uses: ./.github/actions/deploy-hyp3
         with:

.github/workflows/deploy-enterprise.yml

@@ -270,7 +270,7 @@ jobs:
 
       - uses: actions/setup-python@v5
         with:
-          python-version: 3.9
+          python-version: 3.13
 
       - uses: ./.github/actions/deploy-hyp3
         with:

.github/workflows/deploy-multi-burst-sandbox.yml

@@ -54,7 +54,7 @@ jobs:
 
       - uses: actions/setup-python@v5
         with:
-          python-version: 3.9
+          python-version: 3.13
 
       - uses: ./.github/actions/deploy-hyp3
         with:

.github/workflows/static-analysis.yml

@@ -1,12 +1,18 @@
 name: Static code analysis
 
+permissions:
+  contents: read
+
 on: push
 
 jobs:
   call-ruff-workflow:
     # Docs: https://github.com/ASFHyP3/actions
     uses: ASFHyP3/actions/.github/workflows/[email protected]
 
+  call-mypy-workflow:
+    uses: ASFHyP3/actions/.github/workflows/[email protected]
+
   cfn-lint:
     runs-on: ubuntu-latest
     strategy:
@@ -17,7 +23,7 @@ jobs:
       - uses: actions/[email protected]
       - uses: actions/setup-python@v5
         with:
-          python-version: 3.9
+          python-version: 3.13
       - run: |
           python -m pip install --upgrade pip
           make install
@@ -31,7 +37,7 @@ jobs:
       - uses: actions/[email protected]
       - uses: actions/setup-python@v5
         with:
-          python-version: 3.9
+          python-version: 3.13
       - run: |
           python -m pip install --upgrade pip
           make install
@@ -48,7 +54,7 @@ jobs:
       - run: gem install statelint
       - uses: actions/setup-python@v5
         with:
-          python-version: 3.9
+          python-version: 3.13
       - run: |
           python -m pip install --upgrade pip
           make install
@@ -65,7 +71,7 @@ jobs:
       - uses: snyk/actions/[email protected]
       - uses: actions/setup-python@v5
         with:
-          python-version: 3.9
+          python-version: 3.13
       - run: |
           python -m pip install --upgrade pip
           make install

.github/workflows/tests.yml

@@ -11,7 +11,7 @@ jobs:
 
       - uses: actions/setup-python@v5
         with:
-          python-version: 3.9
+          python-version: 3.13
 
       - run: |
           python -m pip install --upgrade pip

CHANGELOG.md

@@ -4,13 +4,17 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## [9.1.2]
+## [9.2.0]
 
 ### Added
-- OPERA_DISP_TMS job type is now available in EDC UAT deployment
+- Add `mypy` to [`static-analysis`](.github/workflows/static-analysis.yml) workflow
+- `OPERA_DISP_TMS` job type is now available in EDC UAT deployment
+
+### Changed
+- Upgrade to Python 3.13
 
 ### Removed
-- hyp3-opera-disp-sandbox deployment
+- Remove `hyp3-opera-disp-sandbox` deployment
 
 ## [9.1.1]
 

README.md

@@ -71,7 +71,7 @@ From the repository root,
 make install
 ```
 
-- Install Python dependencies for AWS Lambda functions (requires pip for python 3.9)
+- Install Python dependencies for AWS Lambda functions (requires pip for python 3.13)
 ```sh
 make build
 ```

apps/api/api-cf.yml.j2

@@ -196,7 +196,7 @@ Resources:
       Handler: hyp3_api.lambda_handler.handler
       MemorySize: 3008
       Role: !GetAtt LambdaRole.Arn
-      Runtime: python3.9
+      Runtime: python3.13
       Timeout: 30
       {% if security_environment == 'EDC' %}
       VpcConfig:

apps/api/src/hyp3_api/auth.py

@@ -1,11 +1,10 @@
 import time
 from os import environ
-from typing import Optional
 
 import jwt
 
 
-def decode_token(token) -> Optional[dict]:
+def decode_token(token) -> dict | None:
     try:
         return jwt.decode(token, environ['AUTH_PUBLIC_KEY'], algorithms=environ['AUTH_ALGORITHM'])
     except (jwt.ExpiredSignatureError, jwt.DecodeError):

apps/api/src/hyp3_api/routes.py

@@ -3,6 +3,7 @@
 from decimal import Decimal
 from os import environ
 from pathlib import Path
+from typing import Any
 
 import yaml
 from flask import abort, g, jsonify, make_response, redirect, render_template, request
@@ -98,10 +99,10 @@ def default(self, o):
 
 
 class CustomJSONProvider(JSONProvider):
-    def dumps(self, o):
-        return json.dumps(o, cls=CustomEncoder)
+    def dumps(self, obj: Any, **kwargs) -> str:
+        return json.dumps(obj, cls=CustomEncoder)
 
-    def loads(self, s):
+    def loads(self, s: str | bytes, **kwargs) -> Any:
         return json.loads(s)
 
 
@@ -111,15 +112,15 @@ def __init__(self):
 
     def __call__(self, errors):
         response = super().__call__(errors)
-        error = response.json['errors'][0]
+        error = response.json['errors'][0]  # type: ignore[index]
         return handlers.problem_format(error['status'], error['title'])
 
 
 app.json = CustomJSONProvider(app)
 
 openapi = FlaskOpenAPIViewDecorator(
     api_spec,
-    response_cls=None,
+    response_cls=None,  # type: ignore[arg-type]
     errors_handler_cls=ErrorHandler,
 )
 
@@ -138,7 +139,7 @@ def jobs_post():
 @app.route('/jobs', methods=['GET'])
 @openapi
 def jobs_get():
-    parameters = request.openapi.parameters.query
+    parameters = request.openapi.parameters.query  # type: ignore[attr-defined]
     start = parameters.get('start')
     end = parameters.get('end')
     return jsonify(

apps/check-processing-time/check-processing-time-cf.yml.j2

@@ -66,7 +66,7 @@ Resources:
       Handler: check_processing_time.lambda_handler
       MemorySize: 128
       Role: !GetAtt Role.Arn
-      Runtime: python3.9
+      Runtime: python3.13
       Timeout: 30
       {% if security_environment == 'EDC' %}
       VpcConfig:

apps/check-processing-time/src/check_processing_time.py

@@ -1,14 +1,11 @@
-from typing import Union
-
-
-def get_time_from_result(result: Union[list, dict]) -> Union[list, float]:
+def get_time_from_result(result: list | dict) -> list | float:
     if isinstance(result, list):
         return [get_time_from_result(item) for item in result]
 
     return (result['StoppedAt'] - result['StartedAt']) / 1000
 
 
-def lambda_handler(event, _) -> list[Union[list, float]]:
+def lambda_handler(event, _) -> list | float:
     processing_results = event['processing_results']
     result_list = [processing_results[key] for key in sorted(processing_results.keys())]
     return get_time_from_result(result_list)

apps/disable-private-dns/disable-private-dns-cf.yml.j2

@@ -56,7 +56,7 @@ Resources:
       Handler: disable_private_dns.lambda_handler
       MemorySize: 128
       Role: !GetAtt Role.Arn
-      Runtime: python3.9
+      Runtime: python3.13
       Timeout: 5
       Environment:
         Variables:

apps/get-files/get-files-cf.yml.j2

@@ -86,7 +86,7 @@ Resources:
       Handler: get_files.lambda_handler
       MemorySize: 128
       Role: !GetAtt Role.Arn
-      Runtime: python3.9
+      Runtime: python3.13
       Timeout: 30
       {% if security_environment == 'EDC' %}
       VpcConfig:

apps/get-files/src/get_files.py

@@ -4,7 +4,6 @@
 from os import environ
 from os.path import basename
 from pathlib import Path
-from typing import Union
 
 import boto3
 
@@ -36,7 +35,7 @@ def get_object_file_type(bucket, key):
     return None
 
 
-def visible_product(product_path: Union[str, Path]) -> bool:
+def visible_product(product_path: str | Path) -> bool:
     return Path(product_path).suffix in ('.zip', '.nc', '.geojson')
 
 

apps/handle-batch-event/handle-batch-event-cf.yml.j2

@@ -80,7 +80,7 @@ Resources:
       Handler: handle_batch_event.lambda_handler
       MemorySize: 128
       Role: !GetAtt Role.Arn
-      Runtime: python3.9
+      Runtime: python3.13
       Timeout: 30
       {% if security_environment == 'EDC' %}
       VpcConfig:

apps/render_cf.py

@@ -77,7 +77,7 @@ def get_map_state(job_spec: dict, step: dict) -> dict:
 
 def get_batch_submit_job_state(job_spec: dict, step: dict, filter_batch_params=False) -> dict:
     if filter_batch_params:
-        batch_job_parameters = get_batch_job_parameters(job_spec, step)
+        batch_job_parameters: dict | str = get_batch_job_parameters(job_spec, step)
         parameters_key = 'Parameters'
     else:
         batch_job_parameters = '$.batch_job_parameters'
@@ -120,7 +120,7 @@ def parse_map_statement(map_statement: str) -> tuple[str, str]:
     return tokens[1], tokens[3]
 
 
-def get_batch_job_parameters(job_spec: dict, step: dict, map_item: str = None) -> dict:
+def get_batch_job_parameters(job_spec: dict, step: dict, map_item: str | None = None) -> dict:
     job_params = {'bucket_prefix', *job_spec['parameters'].keys()}
     step_params = get_batch_param_names_for_job_step(step)
     batch_params = {}

apps/scale-cluster/scale-cluster-cf.yml.j2

@@ -104,7 +104,7 @@ Resources:
       Handler: scale_cluster.lambda_handler
       MemorySize: 128
       Role: !GetAtt Role.Arn
-      Runtime: python3.9
+      Runtime: python3.13
       Timeout: 30
       {% if security_environment == 'EDC' %}
       VpcConfig:
@@ -161,7 +161,7 @@ Resources:
       Handler: scale_cluster.lambda_handler
       MemorySize: 128
       Role: !GetAtt Role.Arn
-      Runtime: python3.9
+      Runtime: python3.13
       Timeout: 30
       {% if security_environment == 'EDC' %}
       VpcConfig:

apps/set-batch-overrides/set-batch-overrides-cf.yml.j2

@@ -66,7 +66,7 @@ Resources:
       Handler: set_batch_overrides.lambda_handler
       MemorySize: 128
       Role: !GetAtt Role.Arn
-      Runtime: python3.9
+      Runtime: python3.13
       Timeout: 30
       {% if security_environment == 'EDC' %}
       VpcConfig:

apps/set-batch-overrides/src/set_batch_overrides.py

@@ -19,7 +19,7 @@
 }
 
 
-def get_container_overrides(memory: str, omp_num_threads: str = None) -> dict:
+def get_container_overrides(memory: str, omp_num_threads: str | None = None) -> dict:
     container_overrides = {
         'ResourceRequirements': [
             {

apps/start-execution-manager/start-execution-manager-cf.yml.j2

@@ -78,7 +78,7 @@ Resources:
       Handler: start_execution_manager.lambda_handler
       MemorySize: 128
       Role: !GetAtt Role.Arn
-      Runtime: python3.9
+      Runtime: python3.13
       Timeout: 10
       {% if security_environment == 'EDC' %}
       VpcConfig:

apps/start-execution-worker/start-execution-worker-cf.yml.j2

@@ -75,7 +75,7 @@ Resources:
       Handler: start_execution_worker.lambda_handler
       MemorySize: 128
       Role: !GetAtt Role.Arn
-      Runtime: python3.9
+      Runtime: python3.13
       Timeout: 45
       {% if security_environment == 'EDC' %}
       VpcConfig:

apps/update-db/update-db-cf.yml.j2

@@ -75,7 +75,7 @@ Resources:
       Handler: main.lambda_handler
       MemorySize: 128
       Role: !GetAtt Role.Arn
-      Runtime: python3.9
+      Runtime: python3.13
       Timeout: 30
       {% if security_environment == 'EDC' %}
       VpcConfig:

apps/upload-log/src/upload_log.py

@@ -1,6 +1,5 @@
 import json
 from os import environ
-from typing import Optional
 
 import boto3
 from botocore.config import Config
@@ -11,7 +10,7 @@
 S3 = boto3.client('s3')
 
 
-def get_log_stream(result: dict) -> Optional[str]:
+def get_log_stream(result: dict) -> str | None:
     if 'Error' in result:
         result = json.loads(result['Cause'])
     return result['Container'].get('LogStreamName')

apps/upload-log/upload-log-cf.yml.j2

@@ -80,7 +80,7 @@ Resources:
       Handler: upload_log.lambda_handler
       MemorySize: 128
       Role: !GetAtt Role.Arn
-      Runtime: python3.9
+      Runtime: python3.13
       Timeout: 30
       {% if security_environment == 'EDC' %}
       VpcConfig:

environment.yml

@@ -3,7 +3,7 @@ channels:
   - conda-forge
   - nodefaults
 dependencies:
-  - python=3.9
+  - python=3.13
   - pip
   - pip:
       - -r requirements-all.txt