From 5019836df5dc2b682722e39d5f9c62799b658929 Mon Sep 17 00:00:00 2001 From: Anton Rau Date: Sun, 12 Sep 2021 22:08:50 +0200 Subject: [PATCH] Updated version and changelog. --- CHANGELOG.md | 3 + imctools/__init__.py | 2 +- poetry.lock | 489 +++++++++++++++++++++++-------------------- pyproject.toml | 2 +- 4 files changed, 268 insertions(+), 228 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 65b5b4e..104099b 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -5,6 +5,9 @@ All notable changes to this project will be documented in this file. The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/), and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). +## [2.1.8] - 2021-09-12 +- Fix: Fix OME-XML element order (#114). + ## [2.1.7] - 2021-05-21 - Fix: broken assertion (#110). - Fix: ome2histocat stripps .tiff file ending from masks (#111). diff --git a/imctools/__init__.py b/imctools/__init__.py index f4e6d2a..ddcb916 100644 --- a/imctools/__init__.py +++ b/imctools/__init__.py @@ -6,4 +6,4 @@ __author__ = """Vito Zanotelli, Anton Rau""" __email__ = "vito.zanotelli@uzh.ch, anton.rau@uzh.ch" -__version__ = "2.1.7" +__version__ = "2.1.8" diff --git a/poetry.lock b/poetry.lock index 029552f..130c65e 100644 --- a/poetry.lock +++ b/poetry.lock @@ -6,17 +6,9 @@ category = "dev" optional = false python-versions = "*" -[[package]] -name = "appdirs" -version = "1.4.4" -description = "A small Python module for determining appropriate platform-specific dirs, e.g. a \"user data dir\"." -category = "dev" -optional = false -python-versions = "*" - [[package]] name = "astroid" -version = "2.5.6" +version = "2.7.3" description = "An abstract syntax tree for Python with inference support." category = "dev" optional = false @@ -25,6 +17,7 @@ python-versions = "~=3.6" [package.dependencies] lazy-object-proxy = ">=1.4.0" typed-ast = {version = ">=1.4.0,<1.5", markers = "implementation_name == \"cpython\" and python_version < \"3.8\""} +typing-extensions = {version = ">=3.7.4", markers = "python_version < \"3.8\""} wrapt = ">=1.11,<1.13" [[package]] @@ -73,42 +66,50 @@ pytz = ">=2015.7" [[package]] name = "black" -version = "21.5b1" +version = "21.8b0" description = "The uncompromising code formatter." category = "dev" optional = false python-versions = ">=3.6.2" [package.dependencies] -appdirs = "*" click = ">=7.1.2" mypy-extensions = ">=0.4.3" -pathspec = ">=0.8.1,<1" +pathspec = ">=0.9.0,<1" +platformdirs = ">=2" regex = ">=2020.1.8" -toml = ">=0.10.1" +tomli = ">=0.2.6,<2.0.0" typed-ast = {version = ">=1.4.2", markers = "python_version < \"3.8\""} -typing-extensions = {version = ">=3.7.4", markers = "python_version < \"3.8\""} +typing-extensions = [ + {version = ">=3.10.0.0", markers = "python_version < \"3.10\""}, + {version = "!=3.10.0.1", markers = "python_version >= \"3.10\""}, +] [package.extras] colorama = ["colorama (>=0.4.3)"] -d = ["aiohttp (>=3.6.0)", "aiohttp-cors"] +d = ["aiohttp (>=3.6.0)", "aiohttp-cors (>=0.4.0)"] +jupyter = ["ipython (>=7.8.0)", "tokenize-rt (>=3.2.0)"] python2 = ["typed-ast (>=1.4.2)"] +uvloop = ["uvloop (>=0.15.2)"] [[package]] name = "certifi" -version = "2020.12.5" +version = "2021.5.30" description = "Python package for providing Mozilla's CA Bundle." category = "dev" optional = false python-versions = "*" [[package]] -name = "chardet" -version = "4.0.0" -description = "Universal encoding detector for Python 2 and 3" +name = "charset-normalizer" +version = "2.0.4" +description = "The Real First Universal Charset Detector. Open, modern and actively maintained alternative to Chardet." category = "dev" optional = false -python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" +python-versions = ">=3.5.0" + +[package.extras] +unicode_backport = ["unicodedata2"] [[package]] name = "click" @@ -138,9 +139,6 @@ category = "dev" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, <4" -[package.dependencies] -toml = {version = "*", optional = true, markers = "extra == \"toml\""} - [package.extras] toml = ["toml"] @@ -168,15 +166,15 @@ pyflakes = ">=2.3.0,<2.4.0" [[package]] name = "idna" -version = "2.10" +version = "3.2" description = "Internationalized Domain Names in Applications (IDNA)" category = "dev" optional = false -python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" +python-versions = ">=3.5" [[package]] name = "imagecodecs" -version = "2021.4.28" +version = "2021.8.26" description = "Image transformation, compression, and decompression codecs" category = "main" optional = false @@ -198,7 +196,7 @@ python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" [[package]] name = "importlib-metadata" -version = "4.0.1" +version = "4.8.1" description = "Read metadata from Python packages" category = "dev" optional = false @@ -210,7 +208,8 @@ zipp = ">=0.5" [package.extras] docs = ["sphinx", "jaraco.packaging (>=8.2)", "rst.linker (>=1.9)"] -testing = ["pytest (>=4.6)", "pytest-checkdocs (>=2.4)", "pytest-flake8", "pytest-cov", "pytest-enabler (>=1.0.1)", "packaging", "pep517", "pyfakefs", "flufl.flake8", "pytest-black (>=0.3.7)", "pytest-mypy", "importlib-resources (>=1.3)"] +perf = ["ipython"] +testing = ["pytest (>=4.6)", "pytest-checkdocs (>=2.4)", "pytest-flake8", "pytest-cov", "pytest-enabler (>=1.0.1)", "packaging", "pep517", "pyfakefs", "flufl.flake8", "pytest-perf (>=0.9.2)", "pytest-black (>=0.3.7)", "pytest-mypy", "importlib-resources (>=1.3)"] [[package]] name = "iniconfig" @@ -222,16 +221,17 @@ python-versions = "*" [[package]] name = "isort" -version = "5.8.0" +version = "5.9.3" description = "A Python utility / library to sort Python imports." category = "dev" optional = false -python-versions = ">=3.6,<4.0" +python-versions = ">=3.6.1,<4.0" [package.extras] pipfile_deprecated_finder = ["pipreqs", "requirementslib"] requirements_deprecated_finder = ["pipreqs", "pip-api"] colors = ["colorama (>=0.4.3,<0.5.0)"] +plugins = ["setuptools"] [[package]] name = "jinja2" @@ -309,7 +309,7 @@ testing = ["coverage", "pytest (>=3.6,<4)", "pytest-cov", "pytest-regressions"] [[package]] name = "mypy" -version = "0.812" +version = "0.910" description = "Optional static typing for Python" category = "dev" optional = false @@ -317,11 +317,13 @@ python-versions = ">=3.5" [package.dependencies] mypy-extensions = ">=0.4.3,<0.5.0" -typed-ast = ">=1.4.0,<1.5.0" +toml = "*" +typed-ast = {version = ">=1.4.0,<1.5.0", markers = "python_version < \"3.8\""} typing-extensions = ">=3.7.4" [package.extras] dmypy = ["psutil (>=4.0)"] +python2 = ["typed-ast (>=1.4.0,<1.5.0)"] [[package]] name = "mypy-extensions" @@ -333,7 +335,7 @@ python-versions = "*" [[package]] name = "myst-parser" -version = "0.14.0" +version = "0.15.2" description = "An extended commonmark compliant parser, with bridges to docutils & sphinx." category = "dev" optional = false @@ -345,17 +347,17 @@ jinja2 = "*" markdown-it-py = ">=1.0.0,<2.0.0" mdit-py-plugins = ">=0.2.8,<0.3.0" pyyaml = "*" -sphinx = ">=2.1,<4" +sphinx = ">=3.1,<5" [package.extras] code_style = ["pre-commit (>=2.12,<3.0)"] linkify = ["linkify-it-py (>=1.0,<2.0)"] -rtd = ["ipython", "sphinx-book-theme (>=0.1.0,<0.2.0)", "sphinx-panels (>=0.5.2,<0.6.0)", "sphinxcontrib-bibtex (>=2.1,<3.0)"] +rtd = ["ipython", "sphinx-book-theme (>=0.1.0,<0.2.0)", "sphinx-panels (>=0.5.2,<0.6.0)", "sphinxcontrib-bibtex (>=2.1,<3.0)", "sphinxext-rediraffe (>=0.2,<1.0)", "sphinxcontrib.mermaid (>=0.6.3,<0.7.0)", "sphinxext-opengraph (>=0.4.2,<0.5.0)"] testing = ["beautifulsoup4", "coverage", "docutils (>=0.17.0,<0.18.0)", "pytest (>=3.6,<4)", "pytest-cov", "pytest-regressions"] [[package]] name = "numpy" -version = "1.20.3" +version = "1.21.1" description = "NumPy is the fundamental package for array computing with Python." category = "main" optional = false @@ -363,11 +365,11 @@ python-versions = ">=3.7" [[package]] name = "packaging" -version = "20.9" +version = "21.0" description = "Core utilities for Python packages" category = "main" optional = false -python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" +python-versions = ">=3.6" [package.dependencies] pyparsing = ">=2.0.2" @@ -390,25 +392,38 @@ test = ["pytest (>=4.0.2)", "pytest-xdist", "hypothesis (>=3.58)"] [[package]] name = "pathspec" -version = "0.8.1" +version = "0.9.0" description = "Utility library for gitignore style pattern matching of file paths." category = "dev" optional = false -python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" +python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,>=2.7" + +[[package]] +name = "platformdirs" +version = "2.3.0" +description = "A small Python module for determining appropriate platform-specific dirs, e.g. a \"user data dir\"." +category = "dev" +optional = false +python-versions = ">=3.6" + +[package.extras] +docs = ["Sphinx (>=4)", "furo (>=2021.7.5b38)", "proselint (>=0.10.2)", "sphinx-autodoc-typehints (>=1.12)"] +test = ["appdirs (==1.4.4)", "pytest (>=6)", "pytest-cov (>=2.7)", "pytest-mock (>=3.6)"] [[package]] name = "pluggy" -version = "0.13.1" +version = "1.0.0" description = "plugin and hook calling mechanisms for python" category = "dev" optional = false -python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" +python-versions = ">=3.6" [package.dependencies] importlib-metadata = {version = ">=0.12", markers = "python_version < \"3.8\""} [package.extras] dev = ["pre-commit", "tox"] +testing = ["pytest", "pytest-benchmark"] [[package]] name = "py" @@ -436,7 +451,7 @@ python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" [[package]] name = "pygments" -version = "2.9.0" +version = "2.10.0" description = "Pygments is a syntax highlighting package written in Python." category = "dev" optional = false @@ -444,17 +459,18 @@ python-versions = ">=3.5" [[package]] name = "pylint" -version = "2.8.2" +version = "2.10.2" description = "python code static checker" category = "dev" optional = false python-versions = "~=3.6" [package.dependencies] -astroid = ">=2.5.6,<2.7" +astroid = ">=2.7.2,<2.8" colorama = {version = "*", markers = "sys_platform == \"win32\""} isort = ">=4.2.5,<6" mccabe = ">=0.6,<0.7" +platformdirs = ">=2.2.0" toml = ">=0.7.1" [[package]] @@ -467,7 +483,7 @@ python-versions = ">=2.6, !=3.0.*, !=3.1.*, !=3.2.*" [[package]] name = "pytest" -version = "6.2.4" +version = "6.2.5" description = "pytest: simple powerful testing with Python" category = "dev" optional = false @@ -480,7 +496,7 @@ colorama = {version = "*", markers = "sys_platform == \"win32\""} importlib-metadata = {version = ">=0.12", markers = "python_version < \"3.8\""} iniconfig = "*" packaging = "*" -pluggy = ">=0.12,<1.0.0a1" +pluggy = ">=0.12,<2.0" py = ">=1.8.2" toml = "*" @@ -489,22 +505,23 @@ testing = ["argcomplete", "hypothesis (>=3.56)", "mock", "nose", "requests", "xm [[package]] name = "pytest-cov" -version = "2.12.0" +version = "2.12.1" description = "Pytest plugin for measuring coverage." category = "dev" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" [package.dependencies] -coverage = {version = ">=5.2.1", extras = ["toml"]} +coverage = ">=5.2.1" pytest = ">=4.6" +toml = "*" [package.extras] -testing = ["fields", "hunter", "process-tests (==2.0.2)", "six", "pytest-xdist", "virtualenv"] +testing = ["fields", "hunter", "process-tests", "six", "pytest-xdist", "virtualenv"] [[package]] name = "python-dateutil" -version = "2.8.1" +version = "2.8.2" description = "Extensions to the standard Python datetime module" category = "main" optional = false @@ -531,7 +548,7 @@ python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*" [[package]] name = "regex" -version = "2021.4.4" +version = "2021.8.28" description = "Alternative regular expression module, to replace re." category = "dev" optional = false @@ -539,21 +556,21 @@ python-versions = "*" [[package]] name = "requests" -version = "2.25.1" +version = "2.26.0" description = "Python HTTP for Humans." category = "dev" optional = false -python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" +python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*" [package.dependencies] certifi = ">=2017.4.17" -chardet = ">=3.0.2,<5" -idna = ">=2.5,<3" +charset-normalizer = {version = ">=2.0.0,<2.1.0", markers = "python_version >= \"3\""} +idna = {version = ">=2.5,<4", markers = "python_version >= \"3\""} urllib3 = ">=1.21.1,<1.27" [package.extras] -security = ["pyOpenSSL (>=0.14)", "cryptography (>=1.3.4)"] socks = ["PySocks (>=1.5.6,!=1.5.7)", "win-inet-pton"] +use_chardet_on_py3 = ["chardet (>=3.0.2,<5)"] [[package]] name = "six" @@ -666,11 +683,11 @@ test = ["pytest"] [[package]] name = "sphinxcontrib-htmlhelp" -version = "1.0.3" +version = "2.0.0" description = "sphinxcontrib-htmlhelp is a sphinx extension which renders HTML help files" category = "dev" optional = false -python-versions = ">=3.5" +python-versions = ">=3.6" [package.extras] lint = ["flake8", "mypy", "docutils-stubs"] @@ -701,7 +718,7 @@ test = ["pytest"] [[package]] name = "sphinxcontrib-serializinghtml" -version = "1.1.4" +version = "1.1.5" description = "sphinxcontrib-serializinghtml is a sphinx extension which outputs \"serialized\" HTML files (json and pickle)." category = "dev" optional = false @@ -713,7 +730,7 @@ test = ["pytest"] [[package]] name = "tifffile" -version = "2021.4.8" +version = "2021.8.30" description = "Read and write TIFF files" category = "main" optional = false @@ -723,7 +740,7 @@ python-versions = ">=3.7" numpy = ">=1.15.1" [package.extras] -all = ["imagecodecs (>=2021.3.31)", "matplotlib (>=3.2)", "lxml"] +all = ["imagecodecs (>=2021.7.30)", "matplotlib (>=3.2)", "lxml"] [[package]] name = "toml" @@ -733,6 +750,14 @@ category = "dev" optional = false python-versions = ">=2.6, !=3.0.*, !=3.1.*, !=3.2.*" +[[package]] +name = "tomli" +version = "1.2.1" +description = "A lil' TOML parser" +category = "dev" +optional = false +python-versions = ">=3.6" + [[package]] name = "typed-ast" version = "1.4.3" @@ -743,7 +768,7 @@ python-versions = "*" [[package]] name = "typing-extensions" -version = "3.10.0.0" +version = "3.10.0.2" description = "Backported and Experimental Type Hints for Python 3.5+" category = "main" optional = false @@ -751,16 +776,16 @@ python-versions = "*" [[package]] name = "urllib3" -version = "1.26.4" +version = "1.26.6" description = "HTTP library with thread-safe connection pooling, file post, and more." category = "dev" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, <4" [package.extras] +brotli = ["brotlipy (>=0.6.0)"] secure = ["pyOpenSSL (>=0.14)", "cryptography (>=1.3.4)", "idna (>=2.0.0)", "certifi", "ipaddress"] socks = ["PySocks (>=1.5.6,!=1.5.7,<2.0)"] -brotli = ["brotlipy (>=0.6.0)"] [[package]] name = "vulture" @@ -791,7 +816,7 @@ python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" [[package]] name = "xtiff" -version = "0.7.4" +version = "0.7.6" description = "A tiny Python library for writing multi-channel TIFF stacks" category = "main" optional = false @@ -803,7 +828,7 @@ tifffile = ">=2020.6.3,<2020.7.17 || >2020.7.17" [[package]] name = "zipp" -version = "3.4.1" +version = "3.5.0" description = "Backport of pathlib-compatible object wrapper for zip files" category = "dev" optional = false @@ -811,7 +836,7 @@ python-versions = ">=3.6" [package.extras] docs = ["sphinx", "jaraco.packaging (>=8.2)", "rst.linker (>=1.9)"] -testing = ["pytest (>=4.6)", "pytest-checkdocs (>=1.2.3)", "pytest-flake8", "pytest-cov", "pytest-enabler", "jaraco.itertools", "func-timeout", "pytest-black (>=0.3.7)", "pytest-mypy"] +testing = ["pytest (>=4.6)", "pytest-checkdocs (>=2.4)", "pytest-flake8", "pytest-cov", "pytest-enabler (>=1.0.1)", "jaraco.itertools", "func-timeout", "pytest-black (>=0.3.7)", "pytest-mypy"] [metadata] lock-version = "1.1" @@ -823,13 +848,9 @@ alabaster = [ {file = "alabaster-0.7.12-py2.py3-none-any.whl", hash = "sha256:446438bdcca0e05bd45ea2de1668c1d9b032e1a9154c2c259092d77031ddd359"}, {file = "alabaster-0.7.12.tar.gz", hash = "sha256:a661d72d58e6ea8a57f7a86e37d86716863ee5e92788398526d58b26a4e4dc02"}, ] -appdirs = [ - {file = "appdirs-1.4.4-py2.py3-none-any.whl", hash = "sha256:a841dacd6b99318a741b166adb07e19ee71a274450e68237b4650ca1055ab128"}, - {file = "appdirs-1.4.4.tar.gz", hash = "sha256:7d5d0167b2b1ba821647616af46a749d1c653740dd0d2415100fe26e27afdf41"}, -] astroid = [ - {file = "astroid-2.5.6-py3-none-any.whl", hash = "sha256:4db03ab5fc3340cf619dbc25e42c2cc3755154ce6009469766d7143d1fc2ee4e"}, - {file = "astroid-2.5.6.tar.gz", hash = "sha256:8a398dfce302c13f14bab13e2b14fe385d32b73f4e4853b9bdfb64598baa1975"}, + {file = "astroid-2.7.3-py3-none-any.whl", hash = "sha256:dc1e8b28427d6bbef6b8842b18765ab58f558c42bb80540bd7648c98412af25e"}, + {file = "astroid-2.7.3.tar.gz", hash = "sha256:3b680ce0419b8a771aba6190139a3998d14b413852506d99aff8dc2bf65ee67c"}, ] atomicwrites = [ {file = "atomicwrites-1.4.0-py2.py3-none-any.whl", hash = "sha256:6d1784dea7c0c8d4a5172b6c620f40b6e4cbfdf96d783691f2e1302a7b88e197"}, @@ -847,16 +868,16 @@ babel = [ {file = "Babel-2.9.1.tar.gz", hash = "sha256:bc0c176f9f6a994582230df350aa6e05ba2ebe4b3ac317eab29d9be5d2768da0"}, ] black = [ - {file = "black-21.5b1-py3-none-any.whl", hash = "sha256:8a60071a0043876a4ae96e6c69bd3a127dad2c1ca7c8083573eb82f92705d008"}, - {file = "black-21.5b1.tar.gz", hash = "sha256:23695358dbcb3deafe7f0a3ad89feee5999a46be5fec21f4f1d108be0bcdb3b1"}, + 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