Upgrade Python 3.11

.github/workflows/main-deploy-docs.yml

@@ -12,7 +12,7 @@ jobs:
   # This workflow contains a single job called "build"
   build:
     # The type of runner that the job will run on
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-22.04
 
     # Steps represent a sequence of tasks that will be executed as part of the job
     steps:

.github/workflows/main-publish.yml

@@ -0,0 +1,36 @@
+# PyPi publish for tibanna
+
+name: publish
+
+# Controls when the action will run.
+on:
+
+  # Publish on all tags
+  push:
+    tags:
+    - '*'
+
+  # Allows you to run this workflow manually from the Actions tab
+  workflow_dispatch:
+
+# A workflow run is made up of one or more jobs that can run sequentially or in parallel
+jobs:
+  # This workflow contains a single job called "build"
+  build:
+    # The type of runner that the job will run on
+    runs-on: ubuntu-22.04
+
+    # Steps represent a sequence of tasks that will be executed as part of the job
+    steps:
+      # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
+      - uses: actions/checkout@v2
+      - uses: actions/setup-python@v2
+        with:
+          python-version: 3.11
+      - name: Publish
+        env:
+          PYPI_USER: ${{ secrets.PYPI_USER }}
+          PYPI_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
+        run: | 
+          make configure
+          make publish-for-ga

.github/workflows/main.yml

@@ -18,10 +18,10 @@ jobs:
   # This workflow contains a single job called "build"
   build:
     # The type of runner that the job will run on
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-22.04
     strategy:
       matrix:
-        python_version: ['3.9']
+        python_version: ['3.11']
 
     # Steps represent a sequence of tasks that will be executed as part of the job
     steps:

CHANGELOG.rst

@@ -3,6 +3,15 @@
 Change Log
 ==========
 
+
+5.0.0
+=====
+
+* Update to Python 3.11.
+* Note 3: As of Tibanna version 5.0.0, Python 3.7 (and lower) is no longer supported.
+  Please switch to Python 3.11!
+
+
 4.0.0
 =====
 

Makefile

@@ -2,9 +2,16 @@ clean:
 	rm -rf *.egg-info
 	rm -rf .eggs
 
+configure:
+	pip install poetry==1.4.2
+
 lint:
 	flake8 tibanna
 
+build:
+	make configure
+	poetry install
+
 install:
 	poetry install
 
@@ -17,6 +24,17 @@ retest:  # runs only failed tests from the last test run.
 update:  # updates dependencies
 	poetry update
 
+publish:
+	# New Python based publish script (2023-09-20).
+	poetry run publish-to-pypi
+
+publish-for-ga:
+	# Need this poetry install first for some reason in GitHub Actions, otherwise getting this:
+	# Warning: 'publish-to-pypi' is an entry point defined in pyproject.toml, but it's not installed as a script. You may get improper `sys.argv[0]`.
+	# Only a warning, but then it does not find dcicutils for some reason.
+	poetry install
+	poetry run publish-to-pypi --noconfirm
+
 publish-pypi:
 	scripts/publish-pypi
 

README.md

@@ -43,7 +43,7 @@ API().run_workflow(input_json='myrun.json')
 ---
 Note: Starting `0.8.2`, Tibanna supports local CWL/WDL files as well as shell commands and Snakemake workflows.
 
-Note 2: As of Tibanna version `2.0.0`, Python 3.6 is no longer supported. Please switch to Python 3.8! Python 3.7 is also supported as a fallback, but please prefer 3.8 if you can.
+Note 2: As of Tibanna version `2.0.0`, Python 3.7 (and lower) is no longer supported. Please switch to Python 3.11! Python 3.8 is also supported as a fallback, but please prefer 3.11 if you can.
 
 Note 3: Starting `0.8.0`, one no longer needs to `git clone` the Tibanna repo. 
 * Please switch from `invoke <command>` to `tibanna <command>`! 

docs/news.rst

@@ -22,6 +22,7 @@ Version updates
   **Sep 15, 2023** The latest version is now 4.0.0_.
     - Support for Python 3.7 has been dropped
     - Added support for Python 3.9 and 3.10
+    - Added support for Python 3.11
 
   **Nov 18, 2022** The latest version is now 3.0.0_.
     - Tibanna now supports AWS Graviton-based instances.

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "tibanna"
-version = "4.0.0"
+version = "5.0.0"
 description = "Tibanna runs portable pipelines (in CWL/WDL) on the AWS Cloud."
 authors = ["4DN-DCIC Team <[email protected]>"]
 license = "MIT"
@@ -25,25 +25,30 @@ classifiers = [
   'Programming Language :: Python :: 3.8',
   'Programming Language :: Python :: 3.9',
   'Programming Language :: Python :: 3.10',
+  'Programming Language :: Python :: 3.11',
 ]
 
 [tool.poetry.dependencies]
-python = ">=3.8,<3.11"
+python = ">=3.8,<3.12"
 python-lambda-4dn = "0.12.3"
-boto3 = "^1.9.0"
-botocore = "^1.12.1"
+boto3 = "^1.28.56"
+botocore = "^1.31.56"
 Benchmark-4dn = "^0.5.23"
 tomlkit = "^0.11.0"
 
 [tool.poetry.dev-dependencies]
-invoke = "0.18.1"
+boto3-stubs = "^1.28.56"
+botocore-stubs = "^1.31.56"
+invoke = "^2.2.0"
 flake8 = "^3.9.0"
 
 # PyTest and its auxiliary support files
-pytest = "^6.0"
-pytest-cov = "^3.0.0"
+# Need pytest-redis 3.0.2 or higher for pytest 7.4.2 (or higher).
+pytest = "^7.4.2"
+pytest-redis = "^3.0.2"
+pytest-cov = "^4.1.0"
 pytest-parallel = "^0.1.1"
-pytest-mock = "3.7"
+pytest-mock = "^3.11.1"
 
 coverage = {extras = ["toml"], version = "^6.3.2"}
 
@@ -55,6 +60,7 @@ sphinx-rtd-theme = "0.5.0"  # Do we have a good reason to pin this? -kmp 9-Nov-2
 [tool.poetry.scripts]
 tibanna = "tibanna.__main__:main"
 awsf3 = "awsf3.__main__:main"
+publish-to-pypi = "dcicutils.scripts.publish_to_pypi:main"
 
 [build-system]
 requires = ["poetry-core>=1.0.0"]

tibanna/lambdas/check_task_awsem.py

@@ -7,7 +7,7 @@
     'function_handler': 'handler',
     'handler': 'service.handler',
     'region': AWS_REGION,
-    'runtime': 'python3.9',
+    'runtime': 'python3.11',
     'role': 'tibanna_lambda_init_role',
     'description': 'check status of AWSEM run by interegating appropriate files on S3 ',
     'timeout': 300,

tibanna/lambdas/run_task_awsem.py

@@ -8,7 +8,7 @@
     'function_handler': 'handler',
     'handler': 'service.handler',
     'region': AWS_REGION,
-    'runtime': 'python3.9',
+    'runtime': 'python3.11',
     'role': 'tibanna_lambda_init_role',
     'description': 'launch an ec2 instance',
     'timeout': 300,

tibanna/lambdas/update_cost_awsem.py

@@ -8,7 +8,7 @@
     'function_handler': 'handler',
     'handler': 'service.handler',
     'region': AWS_REGION,
-    'runtime': 'python3.9',
+    'runtime': 'python3.11',
     'role': 'tibanna_lambda_init_role',
     'description': 'update costs of a workflow run',
     'timeout': 300,