From cc1a3ff625426fb842132a3f7d8e90a9cafc2126 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Al=C3=A1n=20Mu=C3=B1oz?= <alan.munoz@ed.ac.uk> Date: Thu, 2 Mar 2023 00:22:15 +0000 Subject: [PATCH] refactor(pyproject): add optional groups and baby --- poetry.lock | 863 ++++++++++++++++++++++++++++++++++++++++++++----- pyproject.toml | 19 +- 2 files changed, 798 insertions(+), 84 deletions(-) diff --git a/poetry.lock b/poetry.lock index 550465b5..0666a168 100644 --- a/poetry.lock +++ b/poetry.lock @@ -4,7 +4,7 @@ name = "absl-py" version = "1.4.0" description = "Abseil Python Common Libraries, see https://github.com/abseil/abseil-py." -category = "main" +category = "dev" optional = false python-versions = ">=3.6" files = [ @@ -16,7 +16,7 @@ files = [ name = "aiosignal" version = "1.3.1" description = "aiosignal: a list of registered asynchronous callbacks" -category = "main" +category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -43,7 +43,7 @@ files = [ name = "aliby-baby" version = "0.1.15" description = "Birth Annotator for Budding Yeast" -category = "main" +category = "dev" optional = false python-versions = ">=3.7.1,<3.11" files = [ @@ -94,7 +94,7 @@ 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 = true +optional = false python-versions = "*" files = [ {file = "appdirs-1.4.4-py2.py3-none-any.whl", hash = "sha256:a841dacd6b99318a741b166adb07e19ee71a274450e68237b4650ca1055ab128"}, @@ -219,7 +219,7 @@ test = ["astroid", "pytest"] name = "astunparse" version = "1.6.3" description = "An AST unparser for Python" -category = "main" +category = "dev" optional = false python-versions = "*" files = [ @@ -246,7 +246,7 @@ files = [ name = "attrs" version = "22.2.0" description = "Classes Without Boilerplate" -category = "main" +category = "dev" optional = false python-versions = ">=3.6" files = [ @@ -263,18 +263,18 @@ tests-no-zope = ["cloudpickle", "cloudpickle", "hypothesis", "hypothesis", "mypy [[package]] name = "babel" -version = "2.11.0" +version = "2.12.1" description = "Internationalization utilities" category = "dev" optional = false -python-versions = ">=3.6" +python-versions = ">=3.7" files = [ - {file = "Babel-2.11.0-py3-none-any.whl", hash = "sha256:1ad3eca1c885218f6dce2ab67291178944f810a10a9b5f3cb8382a5a232b64fe"}, - {file = "Babel-2.11.0.tar.gz", hash = "sha256:5ef4b3226b0180dedded4229651c8b0e1a3a6a2837d45a073272f313e4cf97f6"}, + {file = "Babel-2.12.1-py3-none-any.whl", hash = "sha256:b4246fb7677d3b98f501a39d43396d3cafdc8eadb045f4a31be01863f655c610"}, + {file = "Babel-2.12.1.tar.gz", hash = "sha256:cc2d99999cd01d44420ae725a21c9e3711b3aadc7976d6147f622d8581963455"}, ] [package.dependencies] -pytz = ">=2015.7" +pytz = {version = ">=2015.7", markers = "python_version < \"3.9\""} [[package]] name = "backcall" @@ -414,11 +414,35 @@ numpy = "*" [package.extras] doc = ["gitpython", "numpydoc", "sphinx"] +[[package]] +name = "build" +version = "0.10.0" +description = "A simple, correct Python build frontend" +category = "dev" +optional = false +python-versions = ">= 3.7" +files = [ + {file = "build-0.10.0-py3-none-any.whl", hash = "sha256:af266720050a66c893a6096a2f410989eeac74ff9a68ba194b3f6473e8e26171"}, + {file = "build-0.10.0.tar.gz", hash = "sha256:d5b71264afdb5951d6704482aac78de887c80691c52b88a9ad195983ca2c9269"}, +] + +[package.dependencies] +colorama = {version = "*", markers = "os_name == \"nt\""} +packaging = ">=19.0" +pyproject_hooks = "*" +tomli = {version = ">=1.1.0", markers = "python_version < \"3.11\""} + +[package.extras] +docs = ["furo (>=2021.08.31)", "sphinx (>=4.0,<5.0)", "sphinx-argparse-cli (>=1.5)", "sphinx-autodoc-typehints (>=1.10)"] +test = ["filelock (>=3)", "pytest (>=6.2.4)", "pytest-cov (>=2.12)", "pytest-mock (>=2)", "pytest-rerunfailures (>=9.1)", "pytest-xdist (>=1.34)", "setuptools (>=42.0.0)", "setuptools (>=56.0.0)", "toml (>=0.10.0)", "wheel (>=0.36.0)"] +typing = ["importlib-metadata (>=5.1)", "mypy (==0.991)", "tomli", "typing-extensions (>=3.7.4.3)"] +virtualenv = ["virtualenv (>=20.0.35)"] + [[package]] name = "cachetools" version = "5.3.0" description = "Extensible memoizing collections and decorators" -category = "main" +category = "dev" optional = false python-versions = "~=3.7" files = [ @@ -426,6 +450,21 @@ files = [ {file = "cachetools-5.3.0.tar.gz", hash = "sha256:13dfddc7b8df938c21a940dfa6557ce6e94a2f1cdfa58eb90c805721d58f2c14"}, ] +[[package]] +name = "cachey" +version = "0.2.1" +description = "Caching mindful of computation/storage costs" +category = "dev" +optional = false +python-versions = ">=3.6" +files = [ + {file = "cachey-0.2.1-py3-none-any.whl", hash = "sha256:49cf8528496ce3f99d47f1bd136b7c88237e55347a15d880f47cefc0615a83c3"}, + {file = "cachey-0.2.1.tar.gz", hash = "sha256:0310ba8afe52729fa7626325c8d8356a8421c434bf887ac851e58dcf7cf056a6"}, +] + +[package.dependencies] +heapdict = "*" + [[package]] name = "certifi" version = "2022.12.7" @@ -629,7 +668,7 @@ files = [ name = "click" version = "8.0.4" description = "Composable command line interface toolkit" -category = "main" +category = "dev" optional = false python-versions = ">=3.6" files = [ @@ -848,6 +887,7 @@ files = [ [package.dependencies] cloudpickle = ">=1.1.1" fsspec = ">=0.6.0" +numpy = {version = ">=1.18", optional = true, markers = "extra == \"array\""} packaging = ">=20.0" partd = ">=0.3.10" pyyaml = "*" @@ -931,7 +971,7 @@ graph = ["objgraph (>=1.7.2)"] name = "distlib" version = "0.3.6" description = "Distribution utilities" -category = "main" +category = "dev" optional = false python-versions = "*" files = [ @@ -939,6 +979,18 @@ files = [ {file = "distlib-0.3.6.tar.gz", hash = "sha256:14bad2d9b04d3a36127ac97f30b12a19268f211063d8f8ee4f47108896e11b46"}, ] +[[package]] +name = "docstring-parser" +version = "0.15" +description = "Parse Python docstrings in reST, Google and Numpydoc format" +category = "dev" +optional = false +python-versions = ">=3.6,<4.0" +files = [ + {file = "docstring_parser-0.15-py3-none-any.whl", hash = "sha256:d1679b86250d269d06a99670924d6bce45adc00b08069dae8c47d98e89b667a9"}, + {file = "docstring_parser-0.15.tar.gz", hash = "sha256:48ddc093e8b1865899956fcc03b03e66bb7240c310fac5af81814580c55bf682"}, +] + [[package]] name = "docutils" version = "0.18.1" @@ -1009,7 +1061,7 @@ devel = ["colorama", "json-spec", "jsonschema", "pylint", "pytest", "pytest-benc name = "filelock" version = "3.9.0" description = "A platform independent file lock." -category = "main" +category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -1042,7 +1094,7 @@ pyflakes = ">=2.4.0,<2.5.0" name = "flatbuffers" version = "1.12" description = "The FlatBuffers serialization format for Python" -category = "main" +category = "dev" optional = false python-versions = "*" files = [ @@ -1103,11 +1155,28 @@ files = [ {file = "fqdn-1.5.1.tar.gz", hash = "sha256:105ed3677e767fb5ca086a0c1f4bb66ebc3c100be518f0e0d755d9eae164d89f"}, ] +[[package]] +name = "freetype-py" +version = "2.3.0" +description = "Freetype python bindings" +category = "dev" +optional = false +python-versions = ">=3.7" +files = [ + {file = "freetype-py-2.3.0.zip", hash = "sha256:f9b64ce3272a5c358dcee824800a32d70997fb872a0965a557adca20fce7a5d0"}, + {file = "freetype_py-2.3.0-py3-none-macosx_10_9_universal2.whl", hash = "sha256:ca7155de937af6f26bfd9f9089a6e9b01fa8f9d3040a3ddc0aeb3a53cf88f428"}, + {file = "freetype_py-2.3.0-py3-none-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:ccdb1616794a8ad48beaa9e29d3494e6643d24d8e925cc39263de21c062ea5a7"}, + {file = "freetype_py-2.3.0-py3-none-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_12_x86_64.manylinux2010_x86_64.whl", hash = "sha256:c8f17c3ac35dc7cc9571ac37a00a6daa428a1a6d0fe6926a77d16066865ed5ef"}, + {file = "freetype_py-2.3.0-py3-none-musllinux_1_1_aarch64.whl", hash = "sha256:89cee8f4e7cf0a37b73a43a08c88703d84e3b9f9243fc665d8dc0b72a5d206a8"}, + {file = "freetype_py-2.3.0-py3-none-musllinux_1_1_x86_64.whl", hash = "sha256:b95ccd52ff7e9bef34505f8af724cee114a3c3cc9cf13e0fd406fa0cc92b988a"}, + {file = "freetype_py-2.3.0-py3-none-win_amd64.whl", hash = "sha256:3a552265b06c2cb3fa54f86ed6fcbf045d8dc8176f9475bedddf9a1b31f5402f"}, +] + [[package]] name = "frozenlist" version = "1.3.3" description = "A list-like structure which implements collections.abc.MutableSequence" -category = "main" +category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -1237,7 +1306,7 @@ files = [ name = "gast" version = "0.4.0" description = "Python AST that abstracts the underlying Python version" -category = "main" +category = "dev" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" files = [ @@ -1296,7 +1365,7 @@ gitdb = ">=4.0.1,<5" name = "google-auth" version = "2.16.1" description = "Google Authentication Library" -category = "main" +category = "dev" optional = false python-versions = ">=2.7,!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*" files = [ @@ -1321,7 +1390,7 @@ requests = ["requests (>=2.20.0,<3.0.0dev)"] name = "google-auth-oauthlib" version = "0.4.6" description = "Google Authentication Library" -category = "main" +category = "dev" optional = false python-versions = ">=3.6" files = [ @@ -1340,7 +1409,7 @@ tool = ["click (>=6.0.0)"] name = "google-pasta" version = "0.2.0" description = "pasta is an AST-based Python refactoring library" -category = "main" +category = "dev" optional = false python-versions = "*" files = [ @@ -1372,7 +1441,7 @@ numpy = "*" name = "grpcio" version = "1.43.0" description = "HTTP/2-based RPC framework" -category = "main" +category = "dev" optional = false python-versions = ">=3.6" files = [ @@ -1471,6 +1540,30 @@ files = [ numpy = ">=1.7" six = "*" +[[package]] +name = "heapdict" +version = "1.0.1" +description = "a heap with decrease-key and increase-key operations" +category = "dev" +optional = false +python-versions = "*" +files = [ + {file = "HeapDict-1.0.1-py3-none-any.whl", hash = "sha256:6065f90933ab1bb7e50db403b90cab653c853690c5992e69294c2de2b253fc92"}, + {file = "HeapDict-1.0.1.tar.gz", hash = "sha256:8495f57b3e03d8e46d5f1b2cc62ca881aca392fd5cc048dc0aa2e1a6d23ecdb6"}, +] + +[[package]] +name = "hsluv" +version = "5.0.3" +description = "Human-friendly HSL" +category = "dev" +optional = false +python-versions = ">=3.6" +files = [ + {file = "hsluv-5.0.3-py2.py3-none-any.whl", hash = "sha256:f4c31f4daeb9b48895abef992b9ed42ae24cd8753eb4f91556b0fa706385c6d1"}, + {file = "hsluv-5.0.3.tar.gz", hash = "sha256:2586bcb61d29d76e89e563a6836df24d86939961c9657f129a59f7617de45377"}, +] + [[package]] name = "identify" version = "2.5.18" @@ -1631,7 +1724,7 @@ files = [ name = "importlib-metadata" version = "6.0.0" description = "Read metadata from Python packages" -category = "main" +category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -1714,14 +1807,14 @@ test = ["flaky", "ipyparallel", "pre-commit", "pytest (>=7.0)", "pytest-asyncio" [[package]] name = "ipython" -version = "8.10.0" +version = "8.11.0" description = "IPython: Productive Interactive Computing" category = "dev" optional = false python-versions = ">=3.8" files = [ - {file = "ipython-8.10.0-py3-none-any.whl", hash = "sha256:b38c31e8fc7eff642fc7c597061fff462537cf2314e3225a19c906b7b0d8a345"}, - {file = "ipython-8.10.0.tar.gz", hash = "sha256:b13a1d6c1f5818bd388db53b7107d17454129a70de2b87481d555daede5eb49e"}, + {file = "ipython-8.11.0-py3-none-any.whl", hash = "sha256:5b54478e459155a326bf5f42ee4f29df76258c0279c36f21d71ddb560f88b156"}, + {file = "ipython-8.11.0.tar.gz", hash = "sha256:735cede4099dbc903ee540307b9171fbfef4aa75cfcacc5a273b2cda2f02be04"}, ] [package.dependencies] @@ -1733,7 +1826,7 @@ jedi = ">=0.16" matplotlib-inline = "*" pexpect = {version = ">4.3", markers = "sys_platform != \"win32\""} pickleshare = "*" -prompt-toolkit = ">=3.0.30,<3.1.0" +prompt-toolkit = ">=3.0.30,<3.0.37 || >3.0.37,<3.1.0" pygments = ">=2.4.0" stack-data = "*" traitlets = ">=5" @@ -1884,7 +1977,7 @@ files = [ name = "jsonschema" version = "4.17.3" description = "An implementation of JSON Schema validation for Python" -category = "main" +category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -1957,14 +2050,14 @@ test = ["codecov", "coverage", "ipykernel (>=6.14)", "mypy", "paramiko", "pre-co [[package]] name = "jupyter-console" -version = "6.6.1" +version = "6.6.2" description = "Jupyter terminal console" category = "dev" optional = false python-versions = ">=3.7" files = [ - {file = "jupyter_console-6.6.1-py3-none-any.whl", hash = "sha256:b32b5cb673a90909911988a2f1906ced005b07e8dadab6c8664d3f5de44a8191"}, - {file = "jupyter_console-6.6.1.tar.gz", hash = "sha256:5931212d5cbc1f956f6fd615755b5e15f389a8eaa697288dbbe4377017615ecc"}, + {file = "jupyter_console-6.6.2-py3-none-any.whl", hash = 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"libclang" version = "15.0.6.1" description = "Clang Python Bindings, mirrored from the official LLVM repo: https://github.com/llvm/llvm-project/tree/main/clang/bindings/python, to make the installation process easier." -category = "main" +category = "dev" optional = false python-versions = "*" files = [ @@ -2332,11 +2425,44 @@ files = [ {file = "locket-1.0.0.tar.gz", hash = "sha256:5c0d4c052a8bbbf750e056a8e65ccd309086f4f0f18a2eac306a8dfa4112a632"}, ] +[[package]] +name = "magicgui" +version = "0.7.0" +description = "build GUIs from python types" +category = "dev" +optional = false +python-versions = ">=3.8" +files = [ + {file = "magicgui-0.7.0-py3-none-any.whl", hash = "sha256:6c590c70b61a15b14e3344085bbd2ead51f782973c866ba3b69052126e65cf15"}, + {file = "magicgui-0.7.0.tar.gz", hash = "sha256:3c430e15828607ec2b9fc1000c4864014e4e72b3f981ded22b9f4ebace20ca08"}, +] + +[package.dependencies] +docstring-parser = ">=0.7" +psygnal = ">=0.5.0" +qtpy = ">=1.7.0" +superqt = ">=0.4.0" +typing-extensions = "*" + +[package.extras] +dev = ["annotated-types", "attrs", "black", "ipython", "ipywidgets", "isort", "matplotlib", "mypy", "numpy", "pandas", "pdbpp", "pillow (>=4.0)", "pint (>=0.13.0)", "pre-commit", "pydantic", "pydocstyle", "pyqt5 (>=5.12.0)", "pytest", "pytest-cov", "pytest-mypy-plugins", "pytest-qt", "rich", "ruff", "toolz", "tqdm (>=4.30.0)"] +docs = ["ipywidgets (>=8.0.0)", "mkdocs", "mkdocs-gen-files", "mkdocs-literate-nav", "mkdocs-material", "mkdocs-spellcheck[all]", "mkdocstrings-python", "pint", "pyside6"] +image = ["pillow (>=4.0)"] +jupyter = ["ipywidgets (>=8.0.0)"] +min-req = ["docstring-parser (==0.7)", "psygnal (==0.5.0)", "qtpy (==1.7.0)", "superqt (==0.4.0)", "typing-extensions"] +pyqt5 = ["pyqt5 (>=5.12.0)"] +pyqt6 = ["pyqt6"] +pyside2 = ["pyside2 (>=5.14)", "pyside2 (>=5.15)"] +pyside6 = ["pyside6"] +quantity = ["pint (>=0.13.0)"] +testing = ["annotated-types", "attrs", "ipywidgets", "matplotlib", "numpy", "pandas", "pillow (>=4.0)", "pint (>=0.13.0)", "pydantic", "pytest", "pytest-cov", "pytest-mypy-plugins", "pytest-qt", "toolz", "tqdm (>=4.30.0)"] +tqdm = ["tqdm (>=4.30.0)"] + [[package]] name = "markdown" version = "3.4.1" description = "Python implementation of Markdown." -category = "main" +category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -2379,7 +2505,7 @@ testing = ["coverage", "pytest", "pytest-cov", "pytest-regressions"] name = "markupsafe" version = "2.1.2" description = "Safely add untrusted strings to HTML/XML markup." -category = "main" +category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -2585,7 +2711,7 @@ files = [ name = "msgpack" version = "1.0.4" description = "MessagePack serializer" -category = "main" +category = "dev" optional = false python-versions = "*" files = [ @@ -2748,6 +2874,129 @@ linkify = ["linkify-it-py (>=1.0,<2.0)"] rtd = ["ipython", "sphinx-book-theme", "sphinx-design", "sphinxcontrib.mermaid (>=0.7.1,<0.8.0)", "sphinxext-opengraph 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python-versions = ">=3.6" files = [ @@ -5506,4 +6209,4 @@ omero = ["omero-py"] [metadata] lock-version = "2.0" python-versions = ">=3.8, <3.11" -content-hash = "c057d7f7f0b6f9d0069a2ed3b558f017b7c37dd58ffb8d16aac50a8f7d8c1e24" +content-hash = "5bb8f639c60a4e6e38354ef79a4fee587fe85b61306fd416b03f4468c0e61ab0" diff --git a/pyproject.toml b/pyproject.toml index 47e43040..11214d5f 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -34,7 +34,6 @@ scikit-learn = ">=1.0.2" # Used for an extraction metric scipy = ">=1.7.3" # Pipeline + I/O -aliby-baby = "^0.1.15" dask = "^2021.12.0" imageio = "2.8.0" # For image-visualisation utilities requests-toolbelt = "^0.9.1" @@ -59,6 +58,12 @@ zarr = "^2.14.0" omero = [ "omero-py" ] network = [ "omero-py", "zeroc-ice" ] +[tool.poetry.group.baby] +optional = true + +[tool.poetry.group.baby.dependencies] +aliby-baby = "^0.1.15" + [tool.poetry.group.dev] optional = true @@ -74,13 +79,17 @@ pre-commit = "^2.20.0" seaborn = "^0.11.2" debugpy = "^1.6.3" coverage = "^7.0.4" - -# [tool.poetry.group.gui.dependencies] -# napari = ">=0.4.16" jupytext = "^1.14.4" grid-strategy = "^0.0.1" readchar = "^4.0.3" + +[tool.poetry.group.napari] +optional = true + +[tool.poetry.group.napari.dependencies] +napari = ">=0.4.16" + [tool.poetry.group.docs] optional = true @@ -96,6 +105,8 @@ optional = true [tool.poetry.group.test.dependencies] pytest = "^6.2.5" +[tool.poetry.group.torch.dependencies] +torch = "^1.13.1" [tool.black] line-length = 79 -- GitLab