diff --git a/.github/workflows/main-deploy-docs.yml b/.github/workflows/main-deploy-docs.yml index f18942cd..72a8fb29 100644 --- a/.github/workflows/main-deploy-docs.yml +++ b/.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: diff --git a/.github/workflows/main-publish.yml b/.github/workflows/main-publish.yml new file mode 100644 index 00000000..3c64dd2f --- /dev/null +++ b/.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 diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index b5e3305d..00a824c4 100644 --- a/.github/workflows/main.yml +++ b/.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: diff --git a/CHANGELOG.rst b/CHANGELOG.rst index 490bbfd5..ef9646fd 100644 --- a/CHANGELOG.rst +++ b/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 ===== diff --git a/Makefile b/Makefile index 7589daa1..ead0fccc 100644 --- a/Makefile +++ b/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 diff --git a/README.md b/README.md index 3896d0b9..fcb8615d 100755 --- a/README.md +++ b/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 ` to `tibanna `! diff --git a/docs/news.rst b/docs/news.rst index 94d26530..e5dda09e 100755 --- a/docs/news.rst +++ b/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. diff --git a/poetry.lock b/poetry.lock index 1a9c2bdd..0e646aa6 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,4 +1,4 @@ -# This file is automatically @generated by Poetry 1.6.1 and should not be changed by hand. +# This file is automatically @generated by Poetry 1.5.1 and should not be changed by hand. 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{file = "urllib3-1.26.16-py2.py3-none-any.whl", hash = "sha256:8d36afa7616d8ab714608411b4a3b13e58f463aee519024578e062e141dce20f"}, - {file = "urllib3-1.26.16.tar.gz", hash = "sha256:8f135f6502756bde6b2a9b28989df5fbe87c9970cecaa69041edcce7f0589b14"}, + {file = "urllib3-1.26.17-py2.py3-none-any.whl", hash = "sha256:94a757d178c9be92ef5539b8840d48dc9cf1b2709c9d6b588232a055c524458b"}, + {file = "urllib3-1.26.17.tar.gz", hash = "sha256:24d6a242c28d29af46c3fae832c36db3bbebcc533dd1bb549172cd739c82df21"}, ] [package.extras] -brotli = ["brotli (>=1.0.9)", "brotlicffi (>=0.8.0)", "brotlipy (>=0.6.0)"] +brotli = ["brotli (==1.0.9)", "brotli (>=1.0.9)", "brotlicffi (>=0.8.0)", "brotlipy (>=0.6.0)"] secure = ["certifi", "cryptography (>=1.3.4)", "idna (>=2.0.0)", "ipaddress", "pyOpenSSL (>=0.14)", "urllib3-secure-extra"] socks = ["PySocks (>=1.5.6,!=1.5.7,<2.0)"] [metadata] lock-version = "2.0" -python-versions = ">=3.8,<3.11" -content-hash = "3a847efe618f437aecd0d77c02a5159dd62af684c91ae1669b8692a84039d6bf" +python-versions = ">=3.8,<3.12" +content-hash = "8235bd334e46563eb60379376681331068d36449a36340ddc285cd732b469067" diff --git a/pyproject.toml b/pyproject.toml index e139e53d..d3ced424 100644 --- a/pyproject.toml +++ b/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 "] 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"] diff --git a/tibanna/lambdas/check_task_awsem.py b/tibanna/lambdas/check_task_awsem.py index a9f574cf..2e9eb90e 100755 --- a/tibanna/lambdas/check_task_awsem.py +++ b/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, diff --git a/tibanna/lambdas/run_task_awsem.py b/tibanna/lambdas/run_task_awsem.py index 4b5eda8a..5ac3c143 100755 --- a/tibanna/lambdas/run_task_awsem.py +++ b/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, diff --git a/tibanna/lambdas/update_cost_awsem.py b/tibanna/lambdas/update_cost_awsem.py index d0c42e10..81ec69cd 100755 --- a/tibanna/lambdas/update_cost_awsem.py +++ b/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,