From 7a42a18a7da20862ac441aeef2bca3d4e8ad5ab2 Mon Sep 17 00:00:00 2001 From: Nathan Perkins Date: Thu, 24 Aug 2023 18:24:33 +1000 Subject: [PATCH 1/3] python 3.11 support --- poetry.lock | 495 ++++++++++++++++++++++--------------------------- pyproject.toml | 14 +- 2 files changed, 230 insertions(+), 279 deletions(-) diff --git a/poetry.lock b/poetry.lock index dfc941767..cd71e6d5a 100644 --- a/poetry.lock +++ b/poetry.lock @@ -6,9 +6,6 @@ category = "main" optional = false python-versions = ">=3.6" -[package.dependencies] -importlib-metadata = {version = ">=0.23,<6", markers = "python_version == \"3.7\""} - [package.extras] lint = ["flake8", "mypy"] test = ["coverage", "flake8", "mypy", "pexpect", "wheel"] @@ -21,9 +18,6 @@ category = "main" optional = false python-versions = ">=3.7" -[package.dependencies] -importlib-metadata = {version = "*", markers = "python_version < \"3.8\""} - [package.extras] cov = ["attrs[tests]", "coverage[toml] (>=5.3)"] dev = ["attrs[docs,tests]", "pre-commit"] @@ -45,7 +39,6 @@ mypy-extensions = ">=0.4.3" pathspec = ">=0.9.0" platformdirs = ">=2" tomli = {version = ">=1.1.0", markers = "python_full_version < \"3.11.0a7\""} -typed-ast = {version = ">=1.4.2", markers = "python_version < \"3.8\" and implementation_name == \"cpython\""} typing-extensions = {version = ">=3.10.0.0", markers = "python_version < \"3.10\""} [package.extras] @@ -80,7 +73,6 @@ python-versions = ">=3.7" [package.dependencies] colorama = {version = "*", markers = "platform_system == \"Windows\""} -importlib-metadata = {version = "*", markers = "python_version < \"3.8\""} [[package]] name = "colorama" @@ -131,6 +123,18 @@ python-versions = ">=3.7" [package.extras] test = ["pytest (>=6)"] +[[package]] +name = "filelock" +version = "3.12.2" +description = "A platform independent file lock." +category = "main" +optional = true +python-versions = ">=3.7" + +[package.extras] +docs = ["furo (>=2023.5.20)", "sphinx (>=7.0.1)", "sphinx-autodoc-typehints (>=1.23,!=1.23.4)"] +testing = ["covdefaults (>=2.3)", "coverage (>=7.2.7)", "diff-cover (>=7.5)", "pytest (>=7.3.1)", "pytest-cov (>=4.1)", "pytest-mock (>=3.10)", "pytest-timeout (>=2.1)"] + [[package]] name = "flake8" version = "6.1.0" @@ -167,9 +171,6 @@ category = "main" optional = false python-versions = ">=3.7" -[package.dependencies] -importlib-metadata = {version = "*", markers = "python_version < \"3.8\""} - [package.extras] tests = ["freezegun", "pytest", "pytest-cov"] @@ -181,23 +182,6 @@ category = "main" optional = false python-versions = ">=3.5" -[[package]] -name = "importlib-metadata" -version = "5.2.0" -description = "Read metadata from Python packages" -category = "main" -optional = false -python-versions = ">=3.7" - -[package.dependencies] -typing-extensions = {version = ">=3.6.4", markers = "python_version < \"3.8\""} -zipp = ">=0.5" - -[package.extras] -docs = ["furo", "jaraco.packaging (>=9)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"] -perf = ["ipython"] -testing = ["flake8 (<5)", "flufl.flake8", "importlib-resources (>=1.3)", "packaging", "pyfakefs", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=1.3)", "pytest-flake8", "pytest-mypy (>=0.9.1)", "pytest-perf (>=0.9.2)"] - [[package]] name = "importlib-resources" version = "5.12.0" @@ -235,6 +219,20 @@ pipfile-deprecated-finder = ["pip-shims (>=0.5.2)", "pipreqs", "requirementslib" plugins = ["setuptools"] requirements-deprecated-finder = ["pip-api", "pipreqs"] +[[package]] +name = "jinja2" +version = "3.1.2" +description = "A very fast and expressive template engine." +category = "main" +optional = true +python-versions = ">=3.7" + +[package.dependencies] +MarkupSafe = ">=2.0" + +[package.extras] +i18n = ["Babel (>=2.7)"] + [[package]] name = "joblib" version = "1.3.2" @@ -253,11 +251,9 @@ python-versions = ">=3.7" [package.dependencies] attrs = ">=17.4.0" -importlib-metadata = {version = "*", markers = "python_version < \"3.8\""} importlib-resources = {version = ">=1.4.0", markers = "python_version < \"3.9\""} pkgutil-resolve-name = {version = ">=1.3.10", markers = "python_version < \"3.9\""} pyrsistent = ">=0.14.0,<0.17.0 || >0.17.0,<0.17.1 || >0.17.1,<0.17.2 || >0.17.2" -typing-extensions = {version = "*", markers = "python_version < \"3.8\""} [package.extras] format = ["fqdn", "idna", "isoduration", "jsonpointer (>1.13)", "rfc3339-validator", "rfc3987", "uri-template", "webcolors (>=1.11)"] @@ -273,7 +269,6 @@ python-versions = ">=3.7" [package.dependencies] mdurl = ">=0.1,<1.0" -typing_extensions = {version = ">=3.7.4", markers = "python_version < \"3.8\""} [package.extras] benchmarking = ["psutil", "pytest", "pytest-benchmark"] @@ -285,6 +280,14 @@ profiling = ["gprof2dot"] rtd = ["attrs", "myst-parser", "pyyaml", "sphinx", "sphinx-copybutton", "sphinx-design", "sphinx_book_theme"] testing = ["coverage", "pytest", "pytest-cov", "pytest-regressions"] +[[package]] +name = "markupsafe" +version = "2.1.3" +description = "Safely add untrusted strings to HTML/XML markup." +category = "main" +optional = true +python-versions = ">=3.7" + [[package]] name = "mccabe" version = "0.7.0" @@ -320,6 +323,20 @@ dill = ["multiprocess", "multiprocess (>=0.70.15)"] docs = ["docutils (==0.17.1)", "sphinx (==3.2.1)", "sphinx-autodoc-typehints (==1.11.0)", "sphinx-rtd-theme (==0.5.0)", "sphinx-versions (==1.0.1)", "sphinxcontrib-images (==0.9.2)"] testing = ["dataclasses", "multiprocess", "multiprocess (>=0.70.15)", "numpy", "pywin32 (==225)", "pywin32 (>=301)"] +[[package]] +name = "mpmath" +version = "1.3.0" +description = "Python library for arbitrary-precision floating-point arithmetic" +category = "main" +optional = true +python-versions = "*" + +[package.extras] +develop = ["codecov", "pycodestyle", "pytest (>=4.6)", "pytest-cov", "wheel"] +docs = ["sphinx"] +gmpy = ["gmpy2 (>=2.1.0a4)"] +tests = ["pytest (>=4.6)"] + [[package]] name = "mypy" version = "0.991" @@ -331,7 +348,6 @@ python-versions = ">=3.7" [package.dependencies] mypy-extensions = ">=0.4.3" tomli = {version = ">=1.1.0", markers = "python_version < \"3.11\""} -typed-ast = {version = ">=1.4.0,<2", markers = "python_version < \"3.8\""} typing-extensions = ">=3.10" [package.extras] @@ -348,6 +364,21 @@ category = "main" optional = true python-versions = ">=3.5" +[[package]] +name = "networkx" +version = "3.1" +description = "Python package for creating and manipulating graphs and networks" +category = "main" +optional = true +python-versions = ">=3.8" + +[package.extras] +default = ["matplotlib (>=3.4)", "numpy (>=1.20)", "pandas (>=1.3)", "scipy (>=1.8)"] +developer = ["mypy (>=1.1)", "pre-commit (>=3.2)"] +doc = ["nb2plots (>=0.6)", "numpydoc (>=1.5)", "pillow (>=9.4)", "pydata-sphinx-theme (>=0.13)", "sphinx (>=6.1)", "sphinx-gallery (>=0.12)", "texext (>=0.6.7)"] +extra = ["lxml (>=4.6)", "pydot (>=1.4.2)", "pygraphviz (>=1.10)", "sympy (>=1.10)"] +test = ["codecov (>=2.1)", "pytest (>=7.2)", "pytest-cov (>=4.0)"] + [[package]] name = "nibabel" version = "5.1.0" @@ -377,59 +408,11 @@ zstd = ["pyzstd (>=0.14.3)"] [[package]] name = "numpy" -version = "1.21.6" -description = "NumPy is the fundamental package for array computing with Python." +version = "1.24.4" +description = "Fundamental package for array computing in Python" category = "main" optional = false -python-versions = ">=3.7,<3.11" - -[[package]] -name = "nvidia-cublas-cu11" -version = "11.10.3.66" -description = "CUBLAS native runtime libraries" -category = "main" -optional = true -python-versions = ">=3" - -[package.dependencies] -setuptools = "*" -wheel = "*" - -[[package]] -name = "nvidia-cuda-nvrtc-cu11" -version = "11.7.99" -description = "NVRTC native runtime libraries" -category = "main" -optional = true -python-versions = ">=3" - -[package.dependencies] -setuptools = "*" -wheel = "*" - -[[package]] -name = "nvidia-cuda-runtime-cu11" -version = "11.7.99" -description = "CUDA Runtime native Libraries" -category = "main" -optional = true -python-versions = ">=3" - -[package.dependencies] -setuptools = "*" -wheel = "*" - -[[package]] -name = "nvidia-cudnn-cu11" -version = "8.5.0.96" -description = "cuDNN runtime libraries" -category = "main" -optional = true -python-versions = ">=3" - -[package.dependencies] -setuptools = "*" -wheel = "*" +python-versions = ">=3.8" [[package]] name = "opencv-python-headless" @@ -444,6 +427,7 @@ numpy = [ {version = ">=1.21.0", markers = "python_version <= \"3.9\" and platform_system == \"Darwin\" and platform_machine == \"arm64\""}, {version = ">=1.21.2", markers = "python_version >= \"3.10\""}, {version = ">=1.21.4", markers = "python_version >= \"3.10\" and platform_system == \"Darwin\""}, + {version = ">=1.23.5", markers = "python_version >= \"3.11\""}, {version = ">=1.19.3", markers = "python_version >= \"3.6\" and platform_system == \"Linux\" and platform_machine == \"aarch64\" or python_version >= \"3.9\""}, {version = ">=1.17.0", markers = "python_version >= \"3.7\""}, {version = ">=1.17.3", markers = "python_version >= \"3.8\""}, @@ -501,9 +485,6 @@ category = "main" optional = true python-versions = ">=3.7" -[package.dependencies] -typing-extensions = {version = ">=4.7.1", markers = "python_version < \"3.8\""} - [package.extras] docs = ["furo (>=2023.7.26)", "proselint (>=0.13)", "sphinx (>=7.1.1)", "sphinx-autodoc-typehints (>=1.24)"] test = ["appdirs (==1.4.4)", "covdefaults (>=2.3)", "pytest (>=7.4)", "pytest-cov (>=4.1)", "pytest-mock (>=3.11.1)"] @@ -516,9 +497,6 @@ category = "main" optional = true python-versions = ">=3.7" -[package.dependencies] -importlib-metadata = {version = ">=0.12", markers = "python_version < \"3.8\""} - [package.extras] dev = ["pre-commit", "tox"] testing = ["pytest", "pytest-benchmark"] @@ -584,7 +562,6 @@ python-versions = ">=3.7" [package.dependencies] colorama = {version = "*", markers = "sys_platform == \"win32\""} exceptiongroup = {version = ">=1.0.0rc8", markers = "python_version < \"3.11\""} -importlib-metadata = {version = ">=0.12", markers = "python_version < \"3.8\""} iniconfig = "*" packaging = "*" pluggy = ">=0.12,<2.0" @@ -639,7 +616,6 @@ python-versions = ">=3.7" requests = ">=2.22.0,<3.0" toml = "*" types-toml = "*" -typing-extensions = {version = "*", markers = "python_version < \"3.8\""} urllib3 = ">=1.25.10" [package.extras] @@ -698,17 +674,15 @@ doc = ["matplotlib (>2)", "numpydoc", "pydata-sphinx-theme (==0.9.0)", "sphinx ( test = ["asv", "gmpy2", "mpmath", "pooch", "pytest", "pytest-cov", "pytest-timeout", "pytest-xdist", "scikit-umfpack", "threadpoolctl"] [[package]] -name = "setuptools" -version = "68.0.0" -description = "Easily download, build, install, upgrade, and uninstall Python packages" +name = "sympy" +version = "1.12" +description = "Computer algebra system (CAS) in Python" category = "main" optional = true -python-versions = ">=3.7" +python-versions = ">=3.8" -[package.extras] -docs = ["furo", 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hash = "sha256:473219bd4cbedc62cea0cb309089b593e47c15c4a2531015f94e4e3b9a0f6981"}, - {file = "wheel-0.41.1.tar.gz", hash = "sha256:12b911f083e876e10c595779709f8a88a59f45aacc646492a67fe9ef796c1b47"}, -] zipp = [ {file = "zipp-3.15.0-py3-none-any.whl", hash = "sha256:48904fc76a60e542af151aded95726c1a5c34ed43ab4134b597665c86d7ad556"}, {file = "zipp-3.15.0.tar.gz", hash = "sha256:112929ad649da941c23de50f356a2b5570c954b65150642bccdd66bf194d224b"}, diff --git a/pyproject.toml b/pyproject.toml index 8b7540515..c8288a76d 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -60,7 +60,7 @@ max-line-length = 160 ignore = ["E203", "W503", "E402"] [tool.poetry.dependencies] -python = ">=3.7.0,<3.11" +python = ">=3.8.0,<3.12" argcomplete = "^2.0.0" humanize = "^4.4.0" pillow = "^9.4.0" @@ -72,20 +72,20 @@ jsonschema = ">=4.0.0" deprecation = "^2.1.0" pydantic = "^1.10.4" orjson = "^3.8.5" -numpy = "*" +numpy = "^1.24.0" toml = "^0.10.2" nibabel = { version = "^5.0.0", python = ">=3.8.1", optional = true } connected-components-3d = { version = "^3.10.3", optional = true } -scikit-learn = { version = "^1.2.0", python = ">=3.8.1,<3.11", optional = true } -torch = { version = "^1.13.1", optional = true } -torchvision = { version = "^0.14.1", optional = true } +scikit-learn = { version = "^1.2.0", python = ">=3.8.1,<3.12", optional = true } +torch = { version = "^2.0.0", optional = true } +torchvision = { version = "^0.15.0", optional = true } black = { version = "^22.12.0", optional = true } isort = { version = "^5.11.4", optional = true } -flake8 = { version = "^6.0.0", python = ">=3.8.1,<3.11", optional = true } +flake8 = { version = "^6.0.0", python = ">=3.8.1,<3.12", optional = true } mypy = { version = "^0.991", optional = true } responses = { version = "^0.22.0", optional = true } pytest = { version = "^7.2.1", optional = true } -flake8-pyproject = { version = "^1.2.2", python = ">=3.8.1,<3.11", optional = true } +flake8-pyproject = { version = "^1.2.2", python = ">=3.8.1,<3.12", optional = true } debugpy = { version = "^1.6.5", optional = true } types-requests = { version = "^2.28.11.8" } mpire = { version = "^2.7.0" } From 45808ff3412fc69c5487ed82576dbf5ea35a70ca Mon Sep 17 00:00:00 2001 From: Nathan Perkins Date: Thu, 24 Aug 2023 18:31:08 +1000 Subject: [PATCH 2/3] drop github action for 3.7 and add 3.11 testing --- .github/workflows/tests.yml | 28 +--------------------------- 1 file changed, 1 insertion(+), 27 deletions(-) diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml index 8694d7f97..f93d37db6 100644 --- a/.github/workflows/tests.yml +++ b/.github/workflows/tests.yml @@ -11,37 +11,11 @@ concurrency: cancel-in-progress: true jobs: - version_test: - name: "Testing installs on other versions" - strategy: - fail-fast: false - matrix: - python-version: ["3.7"] - poetry-version: ["1.3.1"] - os: [ubuntu-latest, windows-latest] - runs-on: ${{ matrix.os }} - steps: - - uses: actions/checkout@v2 - - uses: actions/setup-python@v2 - with: - python-version: ${{ matrix.python-version }} - - name: Upgrade pip - run: python -m pip install --upgrade pip - - name: Setup Poetry - uses: abatilo/actions-poetry@v2 - with: - poetry-version: ${{ matrix.poetry-version }} - - name: Install dependencies - run: | - poetry install --no-interaction --no-root -vvv - pip install wheel - pip install --upgrade setuptools - pip install --editable "." ci: strategy: fail-fast: false matrix: - python-version: ["3.8", "3.9", "3.10"] + python-version: ["3.8", "3.9", "3.10", "3.11"] poetry-version: ["1.3.1"] os: [ubuntu-latest, windows-latest] runs-on: ${{ matrix.os }} From b044815c1c1591c7ed4844254647f110f3e3a790 Mon Sep 17 00:00:00 2001 From: Nathan Perkins Date: Thu, 24 Aug 2023 19:30:54 +1000 Subject: [PATCH 3/3] drop dataclasses for pre 3.7 --- pyproject.toml | 1 - 1 file changed, 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index f927d3a0b..61f93d4c0 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -66,7 +66,6 @@ humanize = "^4.4.0" pillow = "^9.4.0" requests = "^2.28.1" rich = "^13.0.1" -dataclasses = { markers = "python_version < \"3.7\"", version = "^0.8" } upolygon = "0.1.10" jsonschema = ">=4.0.0" deprecation = "^2.1.0"