Upgrade Python 3.11

.github/workflows/main-publish.yml

@@ -0,0 +1,38 @@
+# PyPi publish for magma
+
+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-20.04
+
+    # 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: 3.8
+      - name: Install Python dependencies for publish
+        run: python -m pip install dcicutils==7.5.1
+      - name: Publish
+        env:
+          PYPI_USER: ${{ secrets.PYPI_USER }}
+          PYPI_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
+        run: | 
+          make configure
+          make publish-for-ga

CHANGELOG.rst

@@ -3,6 +3,13 @@
 Change Log
 ==========
 
+
+5.0.0
+=====
+
+* Update to Python 3.11.
+
+
 4.0.0
 =====
 

Makefile

@@ -5,6 +5,9 @@ clean:
 lint:
 	flake8 tibanna
 
+build:
+	poetry install
+
 install:
 	poetry install
 
@@ -17,6 +20,17 @@ 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
 

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "tibanna"
-version = "4.0.0"
+version = "4.0.0.1b1"  # TODO: To become 5.0.0
 description = "Tibanna runs portable pipelines (in CWL/WDL) on the AWS Cloud."
 authors = ["4DN-DCIC Team <[email protected]>"]
 license = "MIT"
@@ -28,10 +28,10 @@ classifiers = [
 ]
 
 [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 = "^1.28.51"
+botocore = "^1.31.51"
 Benchmark-4dn = "^0.5.23"
 tomlkit = "^0.11.0"
 
@@ -55,6 +55,7 @@ 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"]