diff --git a/.github/workflows/static-checks.yml b/.github/workflows/static-checks.yml index 1c70b6ec55..7548bf6e08 100644 --- a/.github/workflows/static-checks.yml +++ b/.github/workflows/static-checks.yml @@ -27,7 +27,7 @@ jobs: - uses: actions/checkout@v2 - uses: actions/setup-python@v2 with: - python-version: 3.8 + python-version: 3.9 - name: Python Package Setup run: | make configure diff --git a/CHANGELOG.rst b/CHANGELOG.rst index 0d659bc575..843509bb7f 100644 --- a/CHANGELOG.rst +++ b/CHANGELOG.rst @@ -6,6 +6,13 @@ cgap-portal Change Log ---------- +15.4.0 +====== + +* Dropped support for Python 3.8. +* Updates related to Python 3.12. + + 15.3.1 ====== `PR 769: Use snovault command to update inserts `_ diff --git a/Makefile b/Makefile index 9b2281ed47..7aefb63b6f 100644 --- a/Makefile +++ b/Makefile @@ -43,59 +43,29 @@ moto-setup: # optional moto setup that must be done separately @# pip install "moto[server]==1.3.7" @echo "'moto[server]' not being installed here. Regular 'moto' will be installed by pyproject.toml." -macpoetry-install: # Same as 'poetry install' except that on OSX Catalina, an environment variable wrapper is needed - bin/macpoetry-install - -configure: # does any pre-requisite installs +configure: pip install --upgrade pip - pip install poetry==1.4.2 + pip install poetry pip install setuptools pip install wheel -ifeq ($(shell uname -s), Darwin) -ifeq ($(shell uname -m), arm64) - pip install pysam=="0.21.0" - pip install matplotlib=="3.3.4" -endif -endif poetry config virtualenvs.create false --local # do not create a virtualenv - the user should have already done this -wrr 20-Sept-2021 build-poetry: make configure poetry install -macbuild-poetry: - make configure - make macpoetry-install - build: # builds -ifeq ($(shell uname -s), Darwin) - @echo "Looks like this is Mac so executing: make macbuild" - make macbuild -else make build-poetry make build-after-poetry -endif - -macbuild: # Builds for MacOS (see: bin/macpoetry-install) - make macbuild-poetry - make build-after-poetry rebuild: make clean # Among other things, this assures 'make npm-setup' will run, but it also does other cleanup. make build -macrebuild: - make clean # Among other things, this assures 'make npm-setup' will run, but it also does other cleanup. - make macbuild - build-full: # rebuilds for Catalina, addressing zlib possibly being in an alternate location. make clean-node-modules # This effectively assures that 'make npm-setup' will need to run. make build -macbuild-full: # rebuilds for Catalina, addressing zlib possibly being in an alternate location. - make clean-node-modules # This effectively assures that 'make npm-setup' will need to run. - make macbuild - build-after-poetry: # continuation of build after poetry install make moto-setup make npm-setup-if-needed @@ -110,10 +80,6 @@ build-dev: # same as build, but sets up locust as well make build make build-locust -macbuild-dev: # same as macbuild, but sets up locust as well - make macbuild - make build-locust - build-locust: # just pip installs locust - may cause instability pip install locust @@ -345,8 +311,8 @@ help: info: @: $(info Here are some 'make' options:) $(info - Use 'make aws-ip-ranges' to download latest ip range information. Invoked automatically when needed.) - $(info - Use 'make build' (or 'make macbuild' on OSX Catalina) to build only application dependencies.) - $(info - Use 'make build-dev' (or 'make macbuild-dev' on OSX Catalina) to build all dependencies, even locust.) + $(info - Use 'make build' to build only application dependencies.) + $(info - Use 'make build-dev' to build all dependencies, even locust.) $(info - Use 'make build-locust' to install locust. Do not do this unless you know what you are doing.) $(info - Use 'make clean' to clear out (non-python) dependencies.) $(info - Use 'make clean-python' to clear python virtualenv for fresh poetry install.) diff --git a/bin/macpoetry-install b/bin/obsolete-macpoetry-install similarity index 100% rename from bin/macpoetry-install rename to bin/obsolete-macpoetry-install diff --git a/poetry.lock b/poetry.lock index be17907483..f5c05f03af 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,10 +1,9 @@ -# This file is automatically @generated by Poetry 1.4.2 and should not be changed by hand. +# This file is automatically @generated by Poetry 1.8.3 and should not be changed by hand. [[package]] name = "apipkg" version = "3.0.2" description = "apipkg: namespace control and lazy-import mechanism" -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -16,7 +15,6 @@ files = [ name = "appdirs" version = "1.4.4" description = "A small Python module for determining appropriate platform-specific dirs, e.g. a \"user data dir\"." -category = "main" optional = false python-versions = "*" files = [ @@ -28,7 +26,6 @@ files = [ name = "arrow" version = "1.3.0" description = "Better dates & times for Python" -category = "main" optional = false python-versions = ">=3.8" files = [ @@ -42,13 +39,12 @@ types-python-dateutil = ">=2.8.10" [package.extras] doc = ["doc8", "sphinx (>=7.0.0)", "sphinx-autobuild", "sphinx-autodoc-typehints", "sphinx_rtd_theme (>=1.3.0)"] -test = ["dateparser (>=1.0.0,<2.0.0)", "pre-commit", "pytest", "pytest-cov", "pytest-mock", "pytz (==2021.1)", "simplejson (>=3.0.0,<4.0.0)"] +test = ["dateparser (==1.*)", "pre-commit", "pytest", "pytest-cov", "pytest-mock", "pytz (==2021.1)", "simplejson (==3.*)"] [[package]] name = "async-timeout" version = "4.0.3" description = "Timeout context manager for asyncio programs" -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -60,7 +56,6 @@ files = [ name = "attrs" version = "23.2.0" description = "Classes Without Boilerplate" -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -80,7 +75,6 @@ tests-no-zope = ["attrs[tests-mypy]", "cloudpickle", "hypothesis", "pympler", "p name = "aws-requests-auth" version = "0.4.3" description = "AWS signature version 4 signing process for the python requests module" -category = "main" optional = false python-versions = "*" files = [ @@ -93,18 +87,17 @@ requests = ">=0.14.0" [[package]] name = "awscli" -version = "1.33.0" +version = "1.33.18" description = "Universal Command Line Environment for AWS." -category = "main" optional = false python-versions = ">=3.8" files = [ - {file = "awscli-1.33.0-py3-none-any.whl", hash = "sha256:19ebb24b093bb621a93457f05ccfbfe61c83e9788130db1a969a665568165394"}, - {file = "awscli-1.33.0.tar.gz", hash = "sha256:602b04c616bc90d894ea4469a2c741282b1ef510f7d6378a46c30c660a9b1a3c"}, + {file = "awscli-1.33.18-py3-none-any.whl", hash = "sha256:4065a0c9ee7bd2281e0b04616242693abbe17cd9d7be966abc7a850d5044226d"}, + {file = "awscli-1.33.18.tar.gz", hash = "sha256:800cae2c020dae7e86877e2b53dee637c19acc62de8084bc67e3434ac174ca35"}, ] [package.dependencies] -botocore = "1.34.118" +botocore = "1.34.136" colorama = ">=0.2.5,<0.4.7" docutils = ">=0.10,<0.17" PyYAML = ">=3.10,<6.1" @@ -115,7 +108,6 @@ s3transfer = ">=0.10.0,<0.11.0" name = "beautifulsoup4" version = "4.12.3" description = "Screen-scraping library" -category = "main" optional = false python-versions = ">=3.6.0" files = [ @@ -137,7 +129,6 @@ lxml = ["lxml"] name = "bitarray" version = "2.9.2" description = "efficient arrays of booleans -- C extension" -category = "main" optional = false python-versions = "*" files = [ @@ -267,18 +258,17 @@ files = [ [[package]] name = "boto3" -version = "1.34.118" +version = "1.34.136" description = "The AWS SDK for Python" -category = "main" optional = false python-versions = ">=3.8" files = [ - {file = "boto3-1.34.118-py3-none-any.whl", hash = "sha256:e9edaf979fbe59737e158f2f0f3f0861ff1d61233f18f6be8ebb483905f24587"}, - {file = "boto3-1.34.118.tar.gz", hash = "sha256:4eb8019421cb664a6fcbbee6152aa95a28ce8bbc1c4ee263871c09cdd58bf8ee"}, + {file = "boto3-1.34.136-py3-none-any.whl", hash = "sha256:d41037e2c680ab8d6c61a0a4ee6bf1fdd9e857f43996672830a95d62d6f6fa79"}, + {file = "boto3-1.34.136.tar.gz", hash = "sha256:0314e6598f59ee0f34eb4e6d1a0f69fa65c146d2b88a6e837a527a9956ec2731"}, ] [package.dependencies] -botocore = ">=1.34.118,<1.35.0" +botocore = ">=1.34.136,<1.35.0" jmespath = ">=0.7.1,<2.0.0" s3transfer = ">=0.10.0,<0.11.0" @@ -287,14 +277,13 @@ crt = ["botocore[crt] (>=1.21.0,<2.0a0)"] [[package]] name = "boto3-stubs" -version = "1.34.118" -description = "Type annotations for boto3 1.34.118 generated with mypy-boto3-builder 7.24.0" -category = "dev" +version = "1.34.136" +description = "Type annotations for boto3 1.34.136 generated with mypy-boto3-builder 7.24.0" optional = false python-versions = ">=3.8" files = [ - {file = "boto3_stubs-1.34.118-py3-none-any.whl", hash = "sha256:4d1dca9593339791ae403eb5a09f6cf43110599fc147f4429eee4d6043ad2257"}, - {file = "boto3_stubs-1.34.118.tar.gz", hash = "sha256:e28837e42b157b5901818b4b49fe68bece26b17957a9ab10cafecc2373e8c8ba"}, + {file = "boto3_stubs-1.34.136-py3-none-any.whl", hash = "sha256:5826c22c10fc9032376bbee436d1b23b111e5fb1f13c75ecde8727151191f057"}, + {file = "boto3_stubs-1.34.136.tar.gz", hash = "sha256:ecbce782ae19037d1f26673cfc30358493c9658ea0af06dd58a999be963ab275"}, ] [package.dependencies] @@ -307,8 +296,7 @@ accessanalyzer = ["mypy-boto3-accessanalyzer (>=1.34.0,<1.35.0)"] account = ["mypy-boto3-account (>=1.34.0,<1.35.0)"] acm = ["mypy-boto3-acm (>=1.34.0,<1.35.0)"] acm-pca = ["mypy-boto3-acm-pca (>=1.34.0,<1.35.0)"] -alexaforbusiness = ["mypy-boto3-alexaforbusiness (>=1.34.0,<1.35.0)"] -all = ["mypy-boto3-accessanalyzer (>=1.34.0,<1.35.0)", "mypy-boto3-account (>=1.34.0,<1.35.0)", "mypy-boto3-acm (>=1.34.0,<1.35.0)", "mypy-boto3-acm-pca (>=1.34.0,<1.35.0)", "mypy-boto3-alexaforbusiness (>=1.34.0,<1.35.0)", "mypy-boto3-amp (>=1.34.0,<1.35.0)", "mypy-boto3-amplify (>=1.34.0,<1.35.0)", "mypy-boto3-amplifybackend (>=1.34.0,<1.35.0)", "mypy-boto3-amplifyuibuilder (>=1.34.0,<1.35.0)", "mypy-boto3-apigateway (>=1.34.0,<1.35.0)", "mypy-boto3-apigatewaymanagementapi (>=1.34.0,<1.35.0)", "mypy-boto3-apigatewayv2 (>=1.34.0,<1.35.0)", "mypy-boto3-appconfig (>=1.34.0,<1.35.0)", "mypy-boto3-appconfigdata (>=1.34.0,<1.35.0)", "mypy-boto3-appfabric (>=1.34.0,<1.35.0)", "mypy-boto3-appflow (>=1.34.0,<1.35.0)", "mypy-boto3-appintegrations (>=1.34.0,<1.35.0)", "mypy-boto3-application-autoscaling (>=1.34.0,<1.35.0)", 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description = "Backport of pathlib-compatible object wrapper for zip files" -category = "main" optional = false python-versions = ">=3.8" files = [ - {file = "zipp-3.19.1-py3-none-any.whl", hash = "sha256:2828e64edb5386ea6a52e7ba7cdb17bb30a73a858f5eb6eb93d8d36f5ea26091"}, - {file = "zipp-3.19.1.tar.gz", hash = "sha256:35427f6d5594f4acf82d25541438348c26736fa9b3afa2754bcd63cdb99d8e8f"}, + {file = "zipp-3.19.2-py3-none-any.whl", hash = "sha256:f091755f667055f2d02b32c53771a7a6c8b47e1fdbc4b72a8b9072b3eef8015c"}, + {file = "zipp-3.19.2.tar.gz", hash = "sha256:bf1dcf6450f873a13e952a29504887c89e6de7506209e5b1bcc3460135d4de19"}, ] [package.extras] doc = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"] -test = ["big-O", "jaraco.functools", "jaraco.itertools", "jaraco.test", "more-itertools", "pytest (>=6,!=8.1.*)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-ignore-flaky", "pytest-mypy", "pytest-ruff (>=0.2.1)"] +test = ["big-O", "importlib-resources", "jaraco.functools", "jaraco.itertools", "jaraco.test", "more-itertools", "pytest (>=6,!=8.1.*)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-ignore-flaky", "pytest-mypy", "pytest-ruff (>=0.2.1)"] [[package]] name = "zope-deprecation" version = "4.4.0" description = "Zope Deprecation Infrastructure" -category = "main" optional = false python-versions = "*" files = [ @@ -4343,7 +4618,6 @@ test = ["zope.testrunner"] name = "zope-interface" version = "5.5.2" description = "Interfaces for Python" -category = "main" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" files = [ @@ -4397,7 +4671,6 @@ testing = ["coverage (>=5.0.3)", "zope.event", "zope.testing"] name = "zope-sqlalchemy" version = "1.6" description = "Minimal Zope/SQLAlchemy transaction integration" -category = "main" optional = false python-versions = "*" files = [ @@ -4416,5 +4689,5 @@ test = ["zope.testing"] [metadata] lock-version = "2.0" -python-versions = ">=3.8.1,<3.12" -content-hash = "c373209fcf1d433f19935bfd7b9ee14c4f2ae2eb708824029f63d8ac5c9bc02e" +python-versions = ">=3.9,<3.13" +content-hash = "5eba6825e92a1f4ba201244f2c43317e06f01bc3ef696c2c763d5e5aca221b94" diff --git a/pyproject.toml b/pyproject.toml index 33b4558462..893e5e747d 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,7 +1,7 @@ [tool.poetry] # Note: Various modules refer to this system as "encoded", not "cgap-portal". name = "encoded" -version = "15.3.1" +version = "15.4.0" description = "Computational Genome Analysis Platform" authors = ["4DN-DCIC Team "] license = "MIT" @@ -35,13 +35,14 @@ classifiers = [ 'Programming Language :: Python :: 3.9', 'Programming Language :: Python :: 3.10', 'Programming Language :: Python :: 3.11', + 'Programming Language :: Python :: 3.12' ] [tool.poetry.dependencies] -python = ">=3.8.1,<3.12" -awscli = ">=1.29.62" -boto3 = "^1.28.62" -botocore = "^1.31.62" +python = ">=3.9,<3.13" +awscli = ">=1.33.17" +boto3 = "^1.34.136" +botocore = "^1.34.136" certifi = ">=2021.5.30" chardet = "^5.2.0" codeguru-profiler-agent = "^1.2.4" @@ -50,22 +51,28 @@ codeguru-profiler-agent = "^1.2.4" # of cryptography.hazmat.bindings._rust in cryptography package. 2023-04-21. cryptography = "39.0.2" colorama = "0.3.3" -dcicpyvcf = "^3.0.0" -dcicsnovault = "^11.14.2" -dcicutils = "^8.8.5" +dcicpyvcf = "^3.1.0" +dcicsnovault = "^11.18.0" +dcicutils = "^8.13.0" elasticsearch = "7.13.4" execnet = "1.4.1" future = ">=0.18.2,<1" -granite-suite = "0.1.11b0" # Needs this exact vesion until Python 3.6 support is dropped. -kmp 10-Feb-2022 +#granite-suite = "0.1.11b0" # Needs this exact vesion until Python 3.6 support is dropped. -kmp 10-Feb-2022 +granite-suite = "0.2.0.1b4" h5py = "^3.8.0" humanfriendly = "^1.44.9" hupper = "1.5" idna = ">=2.10,<3" isodate = ">=0.6.1,<1" jmespath = ">=0.10.0,<1" +# Added because something (maybe granite-suite) is trying to install matplotlib 3.3.4 which does not install/build with Python 3.12. +# Shoot granite-suite 0.2.0 is the latest and it wants matplotlib 3.3.4 which is problematic. +matplotlib = "^3.9.0" netaddr = ">=0.8.0,<1" negspy = "0.2.24" -numpy = "^1.24.2" # negspy needs it +# numpy = "^1.24.2" # negspy needs it +# numpy = "^2.0.0" +numpy = "^1.26.4" openpyxl = "^3.0.7,!=3.0.8" # a version 3.0.8 appeared but then got withdrawn, for now just pin 3.0.7. try again later. passlib = "^1.7.4" PasteDeploy = "1.5.2" @@ -81,7 +88,7 @@ PyBrowserID = "^0.14.0" pycparser = "2.14" PyJWT = "^2.6.0" pyparsing = "^3.0.7" -pyramid = "1.10.4" +pyramid = "1.10.8" pyramid-multiauth = ">=0.9.0,<1" pyramid-retry = "^1.0" pyramid-tm = "^2.4" @@ -116,7 +123,7 @@ transaction = "^3.0.0" translationstring = "1.3" uptime = ">=3.0.1,<4" urllib3 = "^1.26.4" -venusian = "^1.2.0" +venusian = "^3.1.0" waitress = "^2.1.1" WebOb = "^1.8.7" WebTest = "^2.0.35" @@ -127,8 +134,8 @@ WSGIProxy2 = "0.4.2" [tool.poetry.dev-dependencies] # PyCharm says boto3-stubs contains useful type hints -boto3-stubs = "^1.28.62" -botocore-stubs = "^1.31.62" +boto3-stubs = "^1.34.136" +botocore-stubs = "^1.34.136" coverage = ">=6.2" codacy-coverage = ">=1.3.11" coveralls = ">=3.3.1"