diff --git a/poetry.lock b/poetry.lock
index 7e28f024495adf4cd9366fe01b5f787d3f2be449..4ca5371c3967a406b60247442c1153c8181ed0a6 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -2,7 +2,7 @@
name = "absl-py"
version = "1.2.0"
description = "Abseil Python Common Libraries, see https://github.com/abseil/abseil-py."
-category = "main"
+category = "dev"
optional = false
python-versions = ">=3.6"
@@ -10,7 +10,7 @@ python-versions = ">=3.6"
name = "aiosignal"
version = "1.2.0"
description = "aiosignal: a list of registered asynchronous callbacks"
-category = "main"
+category = "dev"
optional = false
python-versions = ">=3.6"
@@ -29,7 +29,7 @@ python-versions = "*"
name = "aliby-agora"
version = "0.2.33"
description = "A gathering of shared utilities for the Swain Lab image processing pipeline."
-category = "main"
+category = "dev"
optional = false
python-versions = ">=3.7.1,<3.11"
@@ -46,7 +46,7 @@ scipy = ">=1.7.3"
name = "aliby-baby"
version = "0.1.14"
description = "Birth Annotator for Budding Yeast"
-category = "main"
+category = "dev"
optional = false
python-versions = ">=3.7.1,<3.11"
@@ -71,7 +71,7 @@ xgboost = "1.4.2"
name = "aliby-post"
version = "0.1.36"
description = "Post-processing tools for aliby pipeline."
-category = "main"
+category = "dev"
optional = false
python-versions = ">=3.7.1,<3.11"
@@ -94,7 +94,7 @@ seaborn = ">=0.11.2,<0.12.0"
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"
+category = "dev"
optional = false
python-versions = "*"
@@ -106,48 +106,17 @@ category = "dev"
optional = false
python-versions = "*"
-[[package]]
-name = "argon2-cffi"
-version = "21.3.0"
-description = "The secure Argon2 password hashing algorithm."
-category = "dev"
-optional = false
-python-versions = ">=3.6"
-
-[package.dependencies]
-argon2-cffi-bindings = "*"
-typing-extensions = {version = "*", markers = "python_version < \"3.8\""}
-
-[package.extras]
-dev = ["cogapp", "coverage[toml] (>=5.0.2)", "furo", "hypothesis", "pre-commit", "pytest", "sphinx", "sphinx-notfound-page", "tomli"]
-docs = ["furo", "sphinx", "sphinx-notfound-page"]
-tests = ["coverage[toml] (>=5.0.2)", "hypothesis", "pytest"]
-
-[[package]]
-name = "argon2-cffi-bindings"
-version = "21.2.0"
-description = "Low-level CFFI bindings for Argon2"
-category = "dev"
-optional = false
-python-versions = ">=3.6"
-
-[package.dependencies]
-cffi = ">=1.0.1"
-
-[package.extras]
-dev = ["cogapp", "pre-commit", "pytest", "wheel"]
-tests = ["pytest"]
-
[[package]]
name = "astunparse"
version = "1.6.3"
description = "An AST unparser for Python"
-category = "main"
+category = "dev"
optional = false
python-versions = "*"
[package.dependencies]
six = ">=1.6.1,<2.0"
+wheel = ">=0.23.0,<1.0"
[[package]]
name = "atomicwrites"
@@ -161,7 +130,7 @@ python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
name = "attrs"
version = "22.1.0"
description = "Classes Without Boilerplate"
-category = "main"
+category = "dev"
optional = false
python-versions = ">=3.5"
@@ -191,72 +160,49 @@ optional = false
python-versions = "*"
[[package]]
-name = "beautifulsoup4"
-version = "4.11.1"
-description = "Screen-scraping library"
+name = "build"
+version = "0.8.0"
+description = "A simple, correct PEP 517 build frontend"
category = "dev"
optional = false
-python-versions = ">=3.6.0"
+python-versions = ">=3.6"
[package.dependencies]
-soupsieve = ">1.2"
+colorama = {version = "*", markers = "os_name == \"nt\""}
+packaging = ">=19.0"
+pep517 = ">=0.9.1"
+tomli = {version = ">=1.0.0", markers = "python_version < \"3.11\""}
[package.extras]
-html5lib = ["html5lib"]
-lxml = ["lxml"]
+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 (>=4.6.4)", "mypy (==0.950)", "typing-extensions (>=3.7.4.3)"]
+virtualenv = ["virtualenv (>=20.0.35)"]
[[package]]
-name = "black"
-version = "22.6.0"
-description = "The uncompromising code formatter."
+name = "cachetools"
+version = "5.2.0"
+description = "Extensible memoizing collections and decorators"
category = "dev"
optional = false
-python-versions = ">=3.6.2"
-
-[package.dependencies]
-click = ">=8.0.0"
-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]
-colorama = ["colorama (>=0.4.3)"]
-d = ["aiohttp (>=3.7.4)"]
-jupyter = ["ipython (>=7.8.0)", "tokenize-rt (>=3.2.0)"]
-uvloop = ["uvloop (>=0.15.2)"]
+python-versions = "~=3.7"
[[package]]
-name = "bleach"
-version = "5.0.1"
-description = "An easy safelist-based HTML-sanitizing tool."
+name = "cachey"
+version = "0.2.1"
+description = "Caching mindful of computation/storage costs"
category = "dev"
optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.6"
[package.dependencies]
-six = ">=1.9.0"
-webencodings = "*"
-
-[package.extras]
-css = ["tinycss2 (>=1.1.0,<1.2)"]
-dev = ["Sphinx (==4.3.2)", "black (==22.3.0)", "build (==0.8.0)", "flake8 (==4.0.1)", "hashin (==0.17.0)", "mypy (==0.961)", "pip-tools (==6.6.2)", "pytest (==7.1.2)", "tox (==3.25.0)", "twine (==4.0.1)", "wheel (==0.37.1)"]
-
-[[package]]
-name = "cachetools"
-version = "5.2.0"
-description = "Extensible memoizing collections and decorators"
-category = "main"
-optional = false
-python-versions = "~=3.7"
+heapdict = "*"
[[package]]
name = "certifi"
version = "2022.6.15"
description = "Python package for providing Mozilla's CA Bundle."
-category = "main"
+category = "dev"
optional = false
python-versions = ">=3.6"
@@ -271,19 +217,11 @@ python-versions = "*"
[package.dependencies]
pycparser = "*"
-[[package]]
-name = "cfgv"
-version = "3.3.1"
-description = "Validate configuration and produce human readable error messages."
-category = "dev"
-optional = false
-python-versions = ">=3.6.1"
-
[[package]]
name = "charset-normalizer"
version = "2.1.1"
description = "The Real First Universal Charset Detector. Open, modern and actively maintained alternative to Chardet."
-category = "main"
+category = "dev"
optional = false
python-versions = ">=3.6.0"
@@ -294,19 +232,18 @@ unicode_backport = ["unicodedata2"]
name = "click"
version = "8.0.4"
description = "Composable command line interface toolkit"
-category = "main"
+category = "dev"
optional = false
python-versions = ">=3.6"
[package.dependencies]
colorama = {version = "*", markers = "platform_system == \"Windows\""}
-importlib-metadata = {version = "*", markers = "python_version < \"3.8\""}
[[package]]
name = "cloudpickle"
version = "2.1.0"
description = "Extended pickling support for Python objects"
-category = "main"
+category = "dev"
optional = false
python-versions = ">=3.6"
@@ -314,15 +251,26 @@ python-versions = ">=3.6"
name = "colorama"
version = "0.4.5"
description = "Cross-platform colored terminal text."
-category = "main"
+category = "dev"
optional = false
python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
+[[package]]
+name = "commonmark"
+version = "0.9.1"
+description = "Python parser for the CommonMark Markdown spec"
+category = "dev"
+optional = false
+python-versions = "*"
+
+[package.extras]
+test = ["flake8 (==3.7.8)", "hypothesis (==3.55.3)"]
+
[[package]]
name = "cycler"
version = "0.11.0"
description = "Composable style cycles"
-category = "main"
+category = "dev"
optional = false
python-versions = ">=3.6"
@@ -330,13 +278,14 @@ python-versions = ">=3.6"
name = "dask"
version = "2021.12.0"
description = "Parallel PyData with Task Scheduling"
-category = "main"
+category = "dev"
optional = false
python-versions = ">=3.7"
[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 = "*"
@@ -350,17 +299,6 @@ diagnostics = ["bokeh (>=2.1.1)", "jinja2"]
distributed = ["distributed (==2021.12.0)"]
test = ["pre-commit", "pytest", "pytest-rerunfailures", "pytest-xdist"]
-[[package]]
-name = "data-science-types"
-version = "0.2.23"
-description = "Type stubs for Python machine learning libraries"
-category = "dev"
-optional = false
-python-versions = ">=3.6"
-
-[package.extras]
-dev = ["black", "flake8", "flake8-pyi", "matplotlib", "mypy (==0.770)", "numpy", "pandas", "pytest"]
-
[[package]]
name = "debugpy"
version = "1.6.3"
@@ -377,19 +315,11 @@ category = "dev"
optional = false
python-versions = ">=3.5"
-[[package]]
-name = "defusedxml"
-version = "0.7.1"
-description = "XML bomb protection for Python stdlib modules"
-category = "dev"
-optional = false
-python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
-
[[package]]
name = "dill"
version = "0.3.5.1"
description = "serialize all of python"
-category = "main"
+category = "dev"
optional = false
python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*, !=3.6.*"
@@ -400,10 +330,18 @@ graph = ["objgraph (>=1.7.2)"]
name = "distlib"
version = "0.3.6"
description = "Distribution utilities"
-category = "main"
+category = "dev"
optional = false
python-versions = "*"
+[[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"
+
[[package]]
name = "docutils"
version = "0.17.1"
@@ -420,22 +358,11 @@ category = "dev"
optional = false
python-versions = ">=3.6"
-[[package]]
-name = "fastjsonschema"
-version = "2.16.1"
-description = "Fastest Python implementation of JSON schema"
-category = "dev"
-optional = false
-python-versions = "*"
-
-[package.extras]
-devel = ["colorama", "json-spec", "jsonschema", "pylint", "pytest", "pytest-benchmark", "pytest-cache", "validictory"]
-
[[package]]
name = "filelock"
version = "3.8.0"
description = "A platform independent file lock."
-category = "main"
+category = "dev"
optional = false
python-versions = ">=3.7"
@@ -444,32 +371,29 @@ docs = ["furo (>=2022.6.21)", "sphinx (>=5.1.1)", "sphinx-autodoc-typehints (>=1
testing = ["covdefaults (>=2.2)", "coverage (>=6.4.2)", "pytest (>=7.1.2)", "pytest-cov (>=3)", "pytest-timeout (>=2.1)"]
[[package]]
-name = "flake8"
-version = "4.0.1"
-description = "the modular source code checker: pep8 pyflakes and co"
+name = "flatbuffers"
+version = "1.12"
+description = "The FlatBuffers serialization format for Python"
category = "dev"
optional = false
-python-versions = ">=3.6"
-
-[package.dependencies]
-importlib-metadata = {version = "<4.3", markers = "python_version < \"3.8\""}
-mccabe = ">=0.6.0,<0.7.0"
-pycodestyle = ">=2.8.0,<2.9.0"
-pyflakes = ">=2.4.0,<2.5.0"
+python-versions = "*"
[[package]]
-name = "flatbuffers"
-version = "1.12"
-description = "The FlatBuffers serialization format for Python"
+name = "flatten-dict"
+version = "0.4.2"
+description = "A flexible utility for flattening and unflattening dict-like objects in Python."
category = "main"
optional = false
-python-versions = "*"
+python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
+
+[package.dependencies]
+six = ">=1.12,<2.0"
[[package]]
name = "fonttools"
version = "4.37.1"
description = "Tools to manipulate font files"
-category = "main"
+category = "dev"
optional = false
python-versions = ">=3.7"
@@ -487,11 +411,19 @@ ufo = ["fs (>=2.2.0,<3)"]
unicode = ["unicodedata2 (>=14.0.0)"]
woff = ["brotli (>=1.0.1)", "brotlicffi (>=0.8.0)", "zopfli (>=0.1.4)"]
+[[package]]
+name = "freetype-py"
+version = "2.3.0"
+description = "Freetype python bindings"
+category = "dev"
+optional = false
+python-versions = ">=3.7"
+
[[package]]
name = "frozenlist"
version = "1.3.1"
description = "A list-like structure which implements collections.abc.MutableSequence"
-category = "main"
+category = "dev"
optional = false
python-versions = ">=3.7"
@@ -499,7 +431,7 @@ python-versions = ">=3.7"
name = "fsspec"
version = "2022.7.1"
description = "File-system specification"
-category = "main"
+category = "dev"
optional = false
python-versions = ">=3.7"
@@ -530,7 +462,7 @@ tqdm = ["tqdm"]
name = "future"
version = "0.18.2"
description = "Clean single-source support for Python 3 and 2"
-category = "main"
+category = "dev"
optional = false
python-versions = ">=2.6, !=3.0.*, !=3.1.*, !=3.2.*"
@@ -538,7 +470,7 @@ python-versions = ">=2.6, !=3.0.*, !=3.1.*, !=3.2.*"
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.*"
@@ -546,7 +478,7 @@ python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
name = "gaussianprocessderivatives"
version = "0.1.5"
description = "Uses Gaussian processes to smooth data and estimate first- and second-order derivatives"
-category = "main"
+category = "dev"
optional = false
python-versions = ">=3.6.0,<3.11"
@@ -559,7 +491,7 @@ scipy = ">=1.7.3,<2.0.0"
name = "google-auth"
version = "2.11.0"
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.*"
@@ -579,7 +511,7 @@ reauth = ["pyu2f (>=0.1.5)"]
name = "google-auth-oauthlib"
version = "0.4.6"
description = "Google Authentication Library"
-category = "main"
+category = "dev"
optional = false
python-versions = ">=3.6"
@@ -594,7 +526,7 @@ 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 = "*"
@@ -605,7 +537,7 @@ six = "*"
name = "grpcio"
version = "1.43.0"
description = "HTTP/2-based RPC framework"
-category = "main"
+category = "dev"
optional = false
python-versions = ">=3.6"
@@ -619,7 +551,7 @@ protobuf = ["grpcio-tools (>=1.43.0)"]
name = "h5py"
version = "2.10.0"
description = "Read and write HDF5 files from Python"
-category = "main"
+category = "dev"
optional = false
python-versions = "*"
@@ -628,21 +560,26 @@ numpy = ">=1.7"
six = "*"
[[package]]
-name = "identify"
-version = "2.5.3"
-description = "File identification library for Python"
+name = "HeapDict"
+version = "1.0.1"
+description = "a heap with decrease-key and increase-key operations"
category = "dev"
optional = false
-python-versions = ">=3.7"
+python-versions = "*"
-[package.extras]
-license = ["ukkonen"]
+[[package]]
+name = "hsluv"
+version = "5.0.3"
+description = "Human-friendly HSL"
+category = "dev"
+optional = false
+python-versions = ">=3.6"
[[package]]
name = "idna"
version = "3.3"
description = "Internationalized Domain Names in Applications (IDNA)"
-category = "main"
+category = "dev"
optional = false
python-versions = ">=3.5"
@@ -650,7 +587,7 @@ python-versions = ">=3.5"
name = "igraph"
version = "0.9.11"
description = "High performance graph data structures and algorithms"
-category = "main"
+category = "dev"
optional = false
python-versions = ">=3.6"
@@ -667,7 +604,7 @@ test-musl = ["networkx (>=2.5)", "pytest (>=7.0.1)"]
name = "imageio"
version = "2.8.0"
description = "Library for reading and writing a wide range of image, video, scientific, and volumetric data formats."
-category = "main"
+category = "dev"
optional = false
python-versions = ">=3.5"
@@ -690,27 +627,11 @@ category = "dev"
optional = false
python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
-[[package]]
-name = "importlib-metadata"
-version = "4.2.0"
-description = "Read metadata from Python packages"
-category = "main"
-optional = false
-python-versions = ">=3.6"
-
-[package.dependencies]
-typing-extensions = {version = ">=3.6.4", markers = "python_version < \"3.8\""}
-zipp = ">=0.5"
-
-[package.extras]
-docs = ["jaraco.packaging (>=8.2)", "rst.linker (>=1.9)", "sphinx"]
-testing = ["flufl.flake8", "importlib-resources (>=1.3)", "packaging", "pep517", "pyfakefs", "pytest (>=4.6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=1.0.1)", "pytest-flake8", "pytest-mypy"]
-
[[package]]
name = "importlib-resources"
version = "5.9.0"
description = "Read resources from Python packages"
-category = "main"
+category = "dev"
optional = false
python-versions = ">=3.7"
@@ -772,6 +693,7 @@ pexpect = {version = ">4.3", markers = "sys_platform != \"win32\""}
pickleshare = "*"
prompt-toolkit = ">=2.0.0,<3.0.0 || >3.0.0,<3.0.1 || >3.0.1,<3.1.0"
pygments = "*"
+setuptools = ">=18.5"
traitlets = ">=4.2"
[package.extras]
@@ -793,38 +715,6 @@ category = "dev"
optional = false
python-versions = "*"
-[[package]]
-name = "ipywidgets"
-version = "8.0.1"
-description = "Jupyter interactive widgets"
-category = "dev"
-optional = false
-python-versions = ">=3.7"
-
-[package.dependencies]
-ipykernel = ">=4.5.1"
-ipython = ">=6.1.0"
-jupyterlab-widgets = ">=3.0,<4.0"
-traitlets = ">=4.3.1"
-widgetsnbextension = ">=4.0,<5.0"
-
-[package.extras]
-test = ["jsonschema", "pytest (>=3.6.0)", "pytest-cov", "pytz"]
-
-[[package]]
-name = "isort"
-version = "5.10.1"
-description = "A Python utility / library to sort Python imports."
-category = "dev"
-optional = false
-python-versions = ">=3.6.1,<4.0"
-
-[package.extras]
-colors = ["colorama (>=0.4.3,<0.5.0)"]
-pipfile_deprecated_finder = ["pipreqs", "requirementslib"]
-plugins = ["setuptools"]
-requirements_deprecated_finder = ["pip-api", "pipreqs"]
-
[[package]]
name = "jedi"
version = "0.18.1"
@@ -858,7 +748,7 @@ i18n = ["Babel (>=2.7)"]
name = "joblib"
version = "1.1.0"
description = "Lightweight pipelining with Python functions"
-category = "main"
+category = "dev"
optional = false
python-versions = ">=3.6"
@@ -866,38 +756,20 @@ python-versions = ">=3.6"
name = "jsonschema"
version = "4.14.0"
description = "An implementation of JSON Schema validation for Python"
-category = "main"
+category = "dev"
optional = false
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)"]
format-nongpl = ["fqdn", "idna", "isoduration", "jsonpointer (>1.13)", "rfc3339-validator", "rfc3986-validator (>0.1.0)", "uri-template", "webcolors (>=1.11)"]
-[[package]]
-name = "jupyter"
-version = "1.0.0"
-description = "Jupyter metapackage. Install all the Jupyter components in one go."
-category = "dev"
-optional = false
-python-versions = "*"
-
-[package.dependencies]
-ipykernel = "*"
-ipywidgets = "*"
-jupyter-console = "*"
-nbconvert = "*"
-notebook = "*"
-qtconsole = "*"
-
[[package]]
name = "jupyter-client"
version = "7.3.5"
@@ -919,24 +791,6 @@ traitlets = "*"
doc = ["ipykernel", "myst-parser", "sphinx (>=1.3.6)", "sphinx-rtd-theme", "sphinxcontrib-github-alt"]
test = ["codecov", "coverage", "ipykernel (>=6.5)", "ipython", "mypy", "pre-commit", "pytest", "pytest-asyncio (>=0.18)", "pytest-cov", "pytest-timeout"]
-[[package]]
-name = "jupyter-console"
-version = "6.4.4"
-description = "Jupyter terminal console"
-category = "dev"
-optional = false
-python-versions = ">=3.7"
-
-[package.dependencies]
-ipykernel = "*"
-ipython = "*"
-jupyter-client = ">=7.0.0"
-prompt-toolkit = ">=2.0.0,<3.0.0 || >3.0.0,<3.0.1 || >3.0.1,<3.1.0"
-pygments = "*"
-
-[package.extras]
-test = ["pexpect"]
-
[[package]]
name = "jupyter-core"
version = "4.11.1"
@@ -952,46 +806,11 @@ traitlets = "*"
[package.extras]
test = ["ipykernel", "pre-commit", "pytest", "pytest-cov", "pytest-timeout"]
-[[package]]
-name = "jupyterlab-pygments"
-version = "0.2.2"
-description = "Pygments theme using JupyterLab CSS variables"
-category = "dev"
-optional = false
-python-versions = ">=3.7"
-
-[[package]]
-name = "jupyterlab-widgets"
-version = "3.0.2"
-description = "Jupyter interactive widgets for JupyterLab"
-category = "dev"
-optional = false
-python-versions = ">=3.7"
-
-[[package]]
-name = "jupytext"
-version = "1.14.1"
-description = "Jupyter notebooks as Markdown documents, Julia, Python or R scripts"
-category = "dev"
-optional = false
-python-versions = "~=3.6"
-
-[package.dependencies]
-markdown-it-py = ">=1.0.0,<3.0.0"
-mdit-py-plugins = "*"
-nbformat = "*"
-pyyaml = "*"
-toml = "*"
-
-[package.extras]
-rst2md = ["sphinx-gallery (>=0.7.0,<0.8.0)"]
-toml = ["toml"]
-
[[package]]
name = "keras"
version = "2.9.0"
description = "Deep learning for humans."
-category = "main"
+category = "dev"
optional = false
python-versions = "*"
@@ -999,7 +818,7 @@ python-versions = "*"
name = "keras-preprocessing"
version = "1.1.2"
description = "Easy data preprocessing and data augmentation for deep learning models"
-category = "main"
+category = "dev"
optional = false
python-versions = "*"
@@ -1010,13 +829,13 @@ six = ">=1.9.0"
[package.extras]
image = ["Pillow (>=5.2.0)", "scipy (>=0.14)"]
pep8 = ["flake8"]
-tests = ["keras", "pandas", "pillow", "pytest", "pytest-cov", "pytest-xdist", "tensorflow"]
+tests = ["Pillow", "keras", "pandas", "pytest", "pytest-cov", "pytest-xdist", "tensorflow"]
[[package]]
name = "keras-tuner"
version = "1.0.1"
description = "Hypertuner for Keras"
-category = "main"
+category = "dev"
optional = false
python-versions = "*"
@@ -1038,18 +857,15 @@ tests = ["flake8", "mock", "portpicker", "pytest", "pytest-cov", "pytest-xdist"]
name = "kiwisolver"
version = "1.4.4"
description = "A fast implementation of the Cassowary constraint solver"
-category = "main"
+category = "dev"
optional = false
python-versions = ">=3.7"
-[package.dependencies]
-typing-extensions = {version = "*", markers = "python_version < \"3.8\""}
-
[[package]]
name = "leidenalg"
version = "0.8.10"
description = "Leiden is a general algorithm for methods of community detection in large networks."
-category = "main"
+category = "dev"
optional = false
python-versions = "*"
@@ -1060,7 +876,7 @@ igraph = ">=0.9.0,<0.10"
name = "libclang"
version = "14.0.6"
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 = "*"
@@ -1068,62 +884,48 @@ python-versions = "*"
name = "locket"
version = "1.0.0"
description = "File-based locks for Python on Linux and Windows"
-category = "main"
+category = "dev"
optional = false
python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
[[package]]
-name = "lxml"
-version = "4.9.1"
-description = "Powerful and Pythonic XML processing library combining libxml2/libxslt with the ElementTree API."
+name = "magicgui"
+version = "0.5.1"
+description = "build GUIs from functions, using magic"
category = "dev"
optional = false
-python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, != 3.4.*"
+python-versions = ">=3.7"
+
+[package.dependencies]
+docstring-parser = "*"
+psygnal = ">=0.3.0"
+qtpy = ">=1.7.0"
+typing-extensions = "*"
[package.extras]
-cssselect = ["cssselect (>=0.7)"]
-html5 = ["html5lib"]
-htmlsoup = ["beautifulsoup4"]
-source = ["Cython (>=0.29.7)"]
+dev = ["black", "flake8", "flake8-docstrings", "flake8-typing-imports", "ipython", "isort", "matplotlib", "mypy", "numpy", "pandas", "pillow (>=4.0)", "pre-commit", "pydocstyle", "pyqt5 (>=5.12.0)", "pytest", "pytest-cov", "pytest-mypy-plugins", "pytest-qt", "toolz", "tox", "tox-conda", "tqdm (>=4.30.0)"]
+image = ["pillow (>=4.0)"]
+pyqt5 = ["pyqt5 (>=5.12.0)"]
+pyside2 = ["pyside2 (>=5.13)", "pyside2 (>=5.14)", "pyside2 (>=5.15)"]
+testing = ["matplotlib", "numpy", "pandas", "pillow (>=4.0)", "pytest", "pytest-cov", "pytest-mypy-plugins", "pytest-qt", "toolz", "tox", "tqdm (>=4.30.0)"]
+tqdm = ["tqdm (>=4.30.0)"]
[[package]]
name = "markdown"
version = "3.3.5"
description = "Python implementation of Markdown."
-category = "main"
+category = "dev"
optional = false
python-versions = ">=3.6"
[package.extras]
testing = ["coverage", "pyyaml"]
-[[package]]
-name = "markdown-it-py"
-version = "2.1.0"
-description = "Python port of markdown-it. Markdown parsing, done right!"
-category = "dev"
-optional = false
-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 (>=3.2,<4.0)"]
-code_style = ["pre-commit (==2.6)"]
-compare = ["commonmark (>=0.9.1,<0.10.0)", "markdown (>=3.3.6,<3.4.0)", "mistletoe (>=0.8.1,<0.9.0)", "mistune (>=2.0.2,<2.1.0)", "panflute (>=2.1.3,<2.2.0)"]
-linkify = ["linkify-it-py (>=1.0,<2.0)"]
-plugins = ["mdit-py-plugins"]
-profiling = ["gprof2dot"]
-rtd = ["attrs", "myst-parser", "pyyaml", "sphinx", "sphinx-book-theme", "sphinx-copybutton", "sphinx-design"]
-testing = ["coverage", "pytest", "pytest-cov", "pytest-regressions"]
-
[[package]]
name = "markupsafe"
version = "2.1.1"
description = "Safely add untrusted strings to HTML/XML markup."
-category = "main"
+category = "dev"
optional = false
python-versions = ">=3.7"
@@ -1131,7 +933,7 @@ python-versions = ">=3.7"
name = "matplotlib"
version = "3.5.3"
description = "Python plotting package"
-category = "main"
+category = "dev"
optional = false
python-versions = ">=3.7"
@@ -1157,51 +959,11 @@ python-versions = ">=3.5"
[package.dependencies]
traitlets = "*"
-[[package]]
-name = "mccabe"
-version = "0.6.1"
-description = "McCabe checker, plugin for flake8"
-category = "dev"
-optional = false
-python-versions = "*"
-
-[[package]]
-name = "mdit-py-plugins"
-version = "0.3.0"
-description = "Collection of plugins for markdown-it-py"
-category = "dev"
-optional = false
-python-versions = "~=3.6"
-
-[package.dependencies]
-markdown-it-py = ">=1.0.0,<3.0.0"
-
-[package.extras]
-code_style = ["pre-commit (==2.6)"]
-rtd = ["myst-parser (>=0.14.0,<0.15.0)", "sphinx-book-theme (>=0.1.0,<0.2.0)"]
-testing = ["coverage", "pytest (>=3.6,<4)", "pytest-cov", "pytest-regressions"]
-
-[[package]]
-name = "mdurl"
-version = "0.1.2"
-description = "Markdown URL utilities"
-category = "dev"
-optional = false
-python-versions = ">=3.7"
-
-[[package]]
-name = "mistune"
-version = "2.0.4"
-description = "A sane Markdown parser with useful plugins and renderers"
-category = "dev"
-optional = false
-python-versions = "*"
-
[[package]]
name = "more-itertools"
version = "8.14.0"
description = "More routines for operating on iterables, beyond itertools"
-category = "main"
+category = "dev"
optional = false
python-versions = ">=3.5"
@@ -1209,7 +971,7 @@ python-versions = ">=3.5"
name = "msgpack"
version = "1.0.4"
description = "MessagePack serializer"
-category = "main"
+category = "dev"
optional = false
python-versions = "*"
@@ -1217,7 +979,7 @@ python-versions = "*"
name = "multiprocess"
version = "0.70.13"
description = "better multiprocessing and multithreading in python"
-category = "main"
+category = "dev"
optional = false
python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*, !=3.6.*"
@@ -1225,101 +987,111 @@ python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*,
dill = ">=0.3.5.1"
[[package]]
-name = "mypy"
-version = "0.930"
-description = "Optional static typing for Python"
+name = "napari"
+version = "0.4.16"
+description = "n-dimensional array viewer in Python"
category = "dev"
optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.8"
[package.dependencies]
-mypy-extensions = ">=0.4.3"
-tomli = ">=1.1.0"
-typed-ast = {version = ">=1.4.0,<2", markers = "python_version < \"3.8\""}
-typing-extensions = ">=3.10"
+appdirs = ">=1.4.4"
+cachey = ">=0.2.1"
+certifi = ">=2018.1.18"
+dask = {version = ">=2.15.0,<2.28.0 || >2.28.0", extras = ["array"]}
+imageio = ">=2.5.0,<2.11.0 || >2.11.0"
+jsonschema = ">=3.2.0"
+magicgui = ">=0.3.6"
+napari-console = ">=0.0.4"
+napari-plugin-engine = ">=0.1.9"
+napari-svg = ">=0.1.4"
+npe2 = ">=0.3.0"
+numpy = ">=1.18.5"
+numpydoc = ">=0.9.2"
+pandas = [
+ {version = ">=1.1.0", markers = "python_version < \"3.9\""},
+ {version = ">=1.3.0", markers = "python_version >= \"3.9\""},
+]
+Pillow = "<7.1.0 || >7.1.0,<7.1.1 || >7.1.1"
+pint = ">=0.17"
+psutil = ">=5.0"
+pydantic = ">=1.9.0"
+pygments = ">=2.4.0"
+PyOpenGL = ">=3.1.0"
+PyYAML = ">=5.1"
+qtpy = ">=1.7.0"
+scikit-image = ">=0.19.1"
+scipy = [
+ {version = ">=1.4.1", markers = "python_version < \"3.9\""},
+ {version = ">=1.5.4", markers = "python_version >= \"3.9\""},
+]
+superqt = ">=0.2.5"
+tifffile = ">=2020.2.16"
+toolz = ">=0.10.0"
+tqdm = ">=4.56.0"
+typing-extensions = "*"
+vispy = ">=0.10.0,<0.11"
+wrapt = ">=1.11.1"
[package.extras]
-dmypy = ["psutil (>=4.0)"]
-python2 = ["typed-ast (>=1.4.0,<2)"]
-
-[[package]]
-name = "mypy-extensions"
-version = "0.4.3"
-description = "Experimental type system extensions for programs checked with the mypy typechecker."
-category = "dev"
-optional = false
-python-versions = "*"
-
-[[package]]
-name = "nbclient"
-version = "0.6.7"
-description = "A client library for executing notebooks. Formerly nbconvert's ExecutePreprocessor."
+all = ["PyQt5 (>=5.12.3,!=5.15.0)", "scikit-image[data]"]
+build = ["black", "isort", "pyqt5"]
+bundle_build = ["PySide2 (==5.15.2)", "briefcase (==0.3.1)", "dmgbuild (>=1.4.2)", "markupsafe (<2.1)", "ruamel.yaml", "tomlkit", "wheel"]
+bundle_run = ["PySide2 (==5.15.2)", "imagecodecs", "numpy (==1.19.3)", "pims", "pip", "scikit-image[data]", "wheel", "zarr"]
+dev = ["PyQt5 (>=5.12.3,!=5.15.0)", "babel (>=2.9.0)", "black (==20.8b1)", "check-manifest (>=0.42)", "flake8 (==3.8.4)", "fsspec", "hypothesis (>=6.8.0)", "lxml", "matplotlib", "meshzoo", "pooch (>=1.3.0)", "pre-commit (>=2.9.0)", "pydantic[dotenv]", "pytest (>=7.0.0)", "pytest-order", "pytest-qt", "rich", "scikit-image[data]", "semgrep", "tensorstore (>=0.1.13)", "torch (>=1.7)", "xarray", "zarr"]
+docs = ["Jinja2", "PyQt5 (>=5.12.3,!=5.15.0)", "jupytext", "lxml", "myst-nb", "napari-sphinx-theme", "scikit-image[data]", "sphinx-autodoc-typehints (==1.12.0)", "sphinx-external-toc", "sphinx-panels", "sphinx-tabs"]
+optional = ["triangle"]
+pyqt = ["PyQt5 (>=5.12.3,!=5.15.0)"]
+pyqt5 = ["PyQt5 (>=5.12.3,!=5.15.0)"]
+pyside = ["PySide2 (>=5.13.2,!=5.15.0)", "PySide2 (>=5.14.2,!=5.15.0)"]
+pyside2 = ["PySide2 (>=5.13.2,!=5.15.0)", "PySide2 (>=5.14.2,!=5.15.0)"]
+qt = ["PyQt5 (>=5.12.3,!=5.15.0)"]
+release = ["PyGithub (>=1.44.1)", "pygithub", "twine (>=3.1.1)"]
+testing = ["babel (>=2.9.0)", "fsspec", "hypothesis (>=6.8.0)", "lxml", "matplotlib", "meshzoo", "pooch (>=1.3.0)", "pytest (>=7.0.0)", "pytest-order", "pytest-qt", "semgrep", "tensorstore (>=0.1.13)", "torch (>=1.7)", "xarray", "zarr"]
+
+[[package]]
+name = "napari-console"
+version = "0.0.6"
+description = "A plugin that adds a console to napari"
category = "dev"
optional = false
-python-versions = ">=3.7.0"
+python-versions = ">=3.7"
[package.dependencies]
-jupyter-client = ">=6.1.5"
-nbformat = ">=5.0"
-nest-asyncio = "*"
-traitlets = ">=5.2.2"
-
-[package.extras]
-sphinx = ["Sphinx (>=1.7)", "autodoc-traits", "mock", "moto", "myst-parser", "sphinx-book-theme"]
-test = ["black", "check-manifest", "flake8", "ipykernel", "ipython", "ipywidgets", "mypy", "nbconvert", "pip (>=18.1)", "pre-commit", "pytest (>=4.1)", "pytest-asyncio", "pytest-cov (>=2.6.1)", "setuptools (>=60.0)", "testpath", "twine (>=1.11.0)", "xmltodict"]
+ipykernel = ">=5.2.0"
+IPython = ">=7.7.0"
+napari-plugin-engine = ">=0.1.9"
+qtconsole = ">=4.5.1,<4.7.6 || >4.7.6"
+qtpy = ">=1.7.0"
[[package]]
-name = "nbconvert"
-version = "7.0.0"
-description = "Converting Jupyter Notebooks"
+name = "napari-plugin-engine"
+version = "0.2.0"
+description = "napari plugin engine, fork of pluggy"
category = "dev"
optional = false
-python-versions = ">=3.7"
-
-[package.dependencies]
-beautifulsoup4 = "*"
-bleach = "*"
-defusedxml = "*"
-importlib-metadata = {version = ">=3.6", markers = "python_version < \"3.10\""}
-jinja2 = ">=3.0"
-jupyter-core = ">=4.7"
-jupyterlab-pygments = "*"
-lxml = "*"
-markupsafe = ">=2.0"
-mistune = ">=2.0.3,<3"
-nbclient = ">=0.5.0"
-nbformat = ">=5.1"
-packaging = "*"
-pandocfilters = ">=1.4.1"
-pygments = ">=2.4.1"
-tinycss2 = "*"
-traitlets = ">=5.0"
+python-versions = ">=3.6"
[package.extras]
-all = ["ipykernel", "ipython", "ipywidgets (>=7)", "nbsphinx (>=0.2.12)", "pre-commit", "pyppeteer (>=1,<1.1)", "pyqtwebengine (>=5.15)", "pytest", "pytest-cov", "pytest-dependency", "sphinx (==5.0.2)", "sphinx-rtd-theme", "tornado (>=6.1)"]
-docs = ["ipython", "nbsphinx (>=0.2.12)", "sphinx (==5.0.2)", "sphinx-rtd-theme"]
-qtpdf = ["pyqtwebengine (>=5.15)"]
-qtpng = ["pyqtwebengine (>=5.15)"]
-serve = ["tornado (>=6.1)"]
-test = ["ipykernel", "ipywidgets (>=7)", "pre-commit", "pyppeteer (>=1,<1.1)", "pytest", "pytest-cov", "pytest-dependency"]
-webpdf = ["pyppeteer (>=1,<1.1)"]
+dev = ["pre-commit", "pytest", "pytest-cov", "tox", "tox-conda"]
+test = ["pytest", "pytest-cov"]
[[package]]
-name = "nbformat"
-version = "5.4.0"
-description = "The Jupyter Notebook format"
+name = "napari-svg"
+version = "0.1.6"
+description = "A plugin for reading and writing svg files with napari"
category = "dev"
optional = false
python-versions = ">=3.7"
[package.dependencies]
-fastjsonschema = "*"
-jsonschema = ">=2.6"
-jupyter-core = "*"
-traitlets = ">=5.1"
+imageio = ">=2.5.0"
+napari-plugin-engine = ">=0.1.4"
+numpy = ">=1.16.0"
+vispy = ">=0.6.4"
[package.extras]
-test = ["check-manifest", "pre-commit", "pytest", "testpath"]
+testing = ["napari (>=0.4)", "pyqt5", "pytest", "pytest-cov"]
[[package]]
name = "nest-asyncio"
@@ -1333,7 +1105,7 @@ python-versions = ">=3.5"
name = "networkx"
version = "2.6.3"
description = "Python package for creating and manipulating graphs and networks"
-category = "main"
+category = "dev"
optional = false
python-versions = ">=3.7"
@@ -1345,42 +1117,28 @@ extra = ["lxml (>=4.5)", "pydot (>=1.4.1)", "pygraphviz (>=1.7)"]
test = ["codecov (>=2.1)", "pytest (>=6.2)", "pytest-cov (>=2.12)"]
[[package]]
-name = "nodeenv"
-version = "1.7.0"
-description = "Node.js virtual environment builder"
-category = "dev"
-optional = false
-python-versions = ">=2.7,!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,!=3.6.*"
-
-[[package]]
-name = "notebook"
-version = "6.4.12"
-description = "A web-based notebook environment for interactive computing"
+name = "npe2"
+version = "0.6.1"
+description = "proposal for napari plugin refactor"
category = "dev"
optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
[package.dependencies]
-argon2-cffi = "*"
-ipykernel = "*"
-ipython-genutils = "*"
-jinja2 = "*"
-jupyter-client = ">=5.3.4"
-jupyter-core = ">=4.6.1"
-nbconvert = ">=5"
-nbformat = "*"
-nest-asyncio = ">=1.5"
-prometheus-client = "*"
-pyzmq = ">=17"
-Send2Trash = ">=1.8.0"
-terminado = ">=0.8.3"
-tornado = ">=6.1"
-traitlets = ">=4.2.1"
+appdirs = "*"
+build = "*"
+psygnal = ">=0.3.0"
+pydantic = "*"
+pytomlpp = "*"
+PyYAML = "*"
+rich = "*"
+typer = "*"
[package.extras]
-docs = ["myst-parser", "nbsphinx", "sphinx", "sphinx-rtd-theme", "sphinxcontrib-github-alt"]
-json-logging = ["json-logging"]
-test = ["coverage", "nbval", "pytest", "pytest-cov", "requests", "requests-unixsocket", "selenium", "testpath"]
+dev = ["black", "flake8", "flake8-docstrings", "ipython", "isort", "jedi (<0.18.0)", "magicgui", "mypy", "numpy", "pre-commit", "pydocstyle", "pytest", "pytest-cov", "typer"]
+docs = ["Jinja2", "magicgui (>=0.3.3)"]
+json = ["jsonschema"]
+testing = ["magicgui", "napari-plugin-engine", "napari-svg", "numpy", "pytest", "pytest-cov"]
[[package]]
name = "numpy"
@@ -1409,7 +1167,7 @@ testing = ["matplotlib", "pytest", "pytest-cov"]
name = "oauthlib"
version = "3.2.0"
description = "A generic, spec-compliant, thorough implementation of the OAuth request-signing logic"
-category = "main"
+category = "dev"
optional = false
python-versions = ">=3.6"
@@ -1422,7 +1180,7 @@ signedtoken = ["cryptography (>=3.0.0)", "pyjwt (>=2.0.0,<3)"]
name = "omero-py"
version = "5.11.2"
description = "Python bindings to the OMERO.blitz server"
-category = "main"
+category = "dev"
optional = false
python-versions = ">=3"
@@ -1438,25 +1196,20 @@ zeroc-ice = ">=3.6.4,<3.7"
[[package]]
name = "opencv-python"
-version = "4.6.0.66"
+version = "4.1.2.30"
description = "Wrapper package for OpenCV python bindings."
category = "main"
optional = false
-python-versions = ">=3.6"
+python-versions = "*"
[package.dependencies]
-numpy = [
- {version = ">=1.21.2", markers = "python_version >= \"3.10\" or python_version >= \"3.6\" and platform_system == \"Darwin\" and platform_machine == \"arm64\""},
- {version = ">=1.19.3", markers = "python_version >= \"3.6\" and platform_system == \"Linux\" and platform_machine == \"aarch64\" or python_version >= \"3.9\""},
- {version = ">=1.14.5", markers = "python_version >= \"3.7\""},
- {version = ">=1.17.3", markers = "python_version >= \"3.8\""},
-]
+numpy = ">=1.11.1"
[[package]]
name = "opt-einsum"
version = "3.3.0"
description = "Optimizing numpys einsum function"
-category = "main"
+category = "dev"
optional = false
python-versions = ">=3.5"
@@ -1471,7 +1224,7 @@ tests = ["pytest", "pytest-cov", "pytest-pep8"]
name = "p-tqdm"
version = "1.4.0"
description = "Parallel processing with progress bars"
-category = "main"
+category = "dev"
optional = false
python-versions = "*"
@@ -1484,7 +1237,7 @@ tqdm = ">=4.45.0"
name = "packaging"
version = "21.3"
description = "Core utilities for Python packages"
-category = "main"
+category = "dev"
optional = false
python-versions = ">=3.6"
@@ -1507,14 +1260,6 @@ pytz = ">=2017.3"
[package.extras]
test = ["hypothesis (>=3.58)", "pytest (>=6.0)", "pytest-xdist"]
-[[package]]
-name = "pandocfilters"
-version = "1.5.0"
-description = "Utilities for writing pandoc filters in python"
-category = "dev"
-optional = false
-python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
-
[[package]]
name = "parso"
version = "0.8.3"
@@ -1531,7 +1276,7 @@ testing = ["docopt", "pytest (<6.0.0)"]
name = "partd"
version = "1.3.0"
description = "Appendable key-value storage"
-category = "main"
+category = "dev"
optional = false
python-versions = ">=3.7"
@@ -1546,7 +1291,7 @@ complete = ["blosc", "numpy (>=1.9.0)", "pandas (>=0.19.0)", "pyzmq"]
name = "pathos"
version = "0.2.9"
description = "parallel graph management and execution in heterogeneous computing"
-category = "main"
+category = "dev"
optional = false
python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*, !=3.6.*"
@@ -1557,12 +1302,15 @@ pox = ">=0.3.1"
ppft = ">=1.7.6.5"
[[package]]
-name = "pathspec"
-version = "0.9.0"
-description = "Utility library for gitignore style pattern matching of file paths."
+name = "pep517"
+version = "0.13.0"
+description = "Wrappers to build Python packages using PEP 517 hooks"
category = "dev"
optional = false
-python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,>=2.7"
+python-versions = ">=3.6"
+
+[package.dependencies]
+tomli = {version = ">=1.1.0", markers = "python_version < \"3.11\""}
[[package]]
name = "pexpect"
@@ -1587,7 +1335,7 @@ python-versions = "*"
name = "pillow"
version = "9.2.0"
description = "Python Imaging Library (Fork)"
-category = "main"
+category = "dev"
optional = false
python-versions = ">=3.7"
@@ -1595,11 +1343,24 @@ python-versions = ">=3.7"
docs = ["furo", "olefile", "sphinx (>=2.4)", "sphinx-copybutton", "sphinx-issues (>=3.0.1)", "sphinx-removed-in", "sphinxext-opengraph"]
tests = ["check-manifest", "coverage", "defusedxml", "markdown2", "olefile", "packaging", "pyroma", "pytest", "pytest-cov", "pytest-timeout"]
+[[package]]
+name = "Pint"
+version = "0.19.2"
+description = "Physical quantities module"
+category = "dev"
+optional = false
+python-versions = ">=3.8"
+
+[package.extras]
+numpy = ["numpy (>=1.19.5)"]
+test = ["pytest", "pytest-cov", "pytest-mpl", "pytest-subtests"]
+uncertainties = ["uncertainties (>=3.1.6)"]
+
[[package]]
name = "pkgutil-resolve-name"
version = "1.3.10"
description = "Resolve a name to an object."
-category = "main"
+category = "dev"
optional = false
python-versions = ">=3.6"
@@ -1607,7 +1368,7 @@ python-versions = ">=3.6"
name = "platformdirs"
version = "2.5.2"
description = "A small Python module for determining appropriate platform-specific dirs, e.g. a \"user data dir\"."
-category = "main"
+category = "dev"
optional = false
python-versions = ">=3.7"
@@ -1623,9 +1384,6 @@ category = "dev"
optional = false
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"]
@@ -1634,7 +1392,7 @@ testing = ["pytest", "pytest-benchmark"]
name = "pox"
version = "0.3.1"
description = "utilities for filesystem exploration and automated builds"
-category = "main"
+category = "dev"
optional = false
python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*, !=3.6.*"
@@ -1642,7 +1400,7 @@ python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*,
name = "ppft"
version = "1.7.6.5"
description = "distributed and parallel python"
-category = "main"
+category = "dev"
optional = false
python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*, !=3.6.*"
@@ -1652,34 +1410,6 @@ six = ">=1.7.3"
[package.extras]
dill = ["dill (>=0.3.5)"]
-[[package]]
-name = "pre-commit"
-version = "2.20.0"
-description = "A framework for managing and maintaining multi-language pre-commit hooks."
-category = "dev"
-optional = false
-python-versions = ">=3.7"
-
-[package.dependencies]
-cfgv = ">=2.0.0"
-identify = ">=1.0.0"
-importlib-metadata = {version = "*", markers = "python_version < \"3.8\""}
-nodeenv = ">=0.11.1"
-pyyaml = ">=5.1"
-toml = "*"
-virtualenv = ">=20.0.8"
-
-[[package]]
-name = "prometheus-client"
-version = "0.14.1"
-description = "Python client for the Prometheus monitoring system."
-category = "dev"
-optional = false
-python-versions = ">=3.6"
-
-[package.extras]
-twisted = ["twisted"]
-
[[package]]
name = "prompt-toolkit"
version = "3.0.30"
@@ -1695,7 +1425,7 @@ wcwidth = "*"
name = "protobuf"
version = "3.20.1"
description = "Protocol Buffers"
-category = "main"
+category = "dev"
optional = false
python-versions = ">=3.7"
@@ -1710,6 +1440,26 @@ python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
[package.extras]
test = ["enum34", "ipaddress", "mock", "pywin32", "wmi"]
+[[package]]
+name = "psygnal"
+version = "0.3.5"
+description = "Pure python implementation of Qt Signals"
+category = "dev"
+optional = false
+python-versions = ">=3.7"
+
+[package.dependencies]
+typing-extensions = "*"
+
+[package.extras]
+build = ["Cython (>=3.0a7)"]
+dev = ["PyQt5", "black", "dask", "flake8", "flake8-docstrings", "ipython", "isort", "jedi (<0.18.0)", "mypy", "numpy", "pre-commit", "pydantic", "pydocstyle", "pytest", "pytest-cov", "pytest-mypy-plugins", "pytest-qt", "qtpy", "wrapt"]
+docs = ["mkdocs-material", "mkdocs-minify-plugin", "mkdocstrings"]
+proxy = ["wrapt"]
+pydantic = ["pydantic"]
+testing = ["dask", "numpy", "pydantic", "pytest", "pytest-cov", "pytest-mypy-plugins", "wrapt"]
+testingqt = ["PyQt5", "pytest-qt", "qtpy"]
+
[[package]]
name = "ptyprocess"
version = "0.7.0"
@@ -1741,7 +1491,7 @@ numpy = ">=1.13.0"
name = "pyasn1"
version = "0.4.8"
description = "ASN.1 types and codecs"
-category = "main"
+category = "dev"
optional = false
python-versions = "*"
@@ -1749,7 +1499,7 @@ python-versions = "*"
name = "pyasn1-modules"
version = "0.2.8"
description = "A collection of ASN.1-based protocols modules."
-category = "main"
+category = "dev"
optional = false
python-versions = "*"
@@ -1760,17 +1510,9 @@ pyasn1 = ">=0.4.6,<0.5.0"
name = "pycatch22"
version = "0.4.2"
description = "22 CAnonical Time-series Features"
-category = "main"
-optional = false
-python-versions = "*"
-
-[[package]]
-name = "pycodestyle"
-version = "2.8.0"
-description = "Python style guide checker"
category = "dev"
optional = false
-python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
+python-versions = "*"
[[package]]
name = "pycparser"
@@ -1781,12 +1523,19 @@ optional = false
python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
[[package]]
-name = "pyflakes"
-version = "2.4.0"
-description = "passive checker of Python programs"
+name = "pydantic"
+version = "1.10.2"
+description = "Data validation and settings management using python type hints"
category = "dev"
optional = false
-python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
+python-versions = ">=3.7"
+
+[package.dependencies]
+typing-extensions = ">=4.1.0"
+
+[package.extras]
+dotenv = ["python-dotenv (>=0.10.4)"]
+email = ["email-validator (>=1.0.3)"]
[[package]]
name = "pygments"
@@ -1799,38 +1548,30 @@ python-versions = ">=3.6"
[package.extras]
plugins = ["importlib-metadata"]
+[[package]]
+name = "PyOpenGL"
+version = "3.1.6"
+description = "Standard OpenGL bindings for Python"
+category = "dev"
+optional = false
+python-versions = "*"
+
[[package]]
name = "pyparsing"
version = "3.0.9"
description = "pyparsing module - Classes and methods to define and execute parsing grammars"
-category = "main"
+category = "dev"
optional = false
python-versions = ">=3.6.8"
[package.extras]
diagrams = ["jinja2", "railroad-diagrams"]
-[[package]]
-name = "pyright"
-version = "1.1.268"
-description = "Command line wrapper for pyright"
-category = "dev"
-optional = false
-python-versions = ">=3.7"
-
-[package.dependencies]
-nodeenv = ">=1.6.0"
-typing-extensions = {version = ">=3.7", markers = "python_version < \"3.8\""}
-
-[package.extras]
-all = ["twine (>=3.4.1)"]
-dev = ["twine (>=3.4.1)"]
-
[[package]]
name = "pyrsistent"
version = "0.18.1"
description = "Persistent/Functional/Immutable data structures"
-category = "main"
+category = "dev"
optional = false
python-versions = ">=3.7"
@@ -1846,7 +1587,6 @@ python-versions = ">=3.6"
atomicwrites = {version = ">=1.0", markers = "sys_platform == \"win32\""}
attrs = ">=19.2.0"
colorama = {version = "*", markers = "sys_platform == \"win32\""}
-importlib-metadata = {version = ">=0.12", markers = "python_version < \"3.8\""}
iniconfig = "*"
packaging = "*"
pluggy = ">=0.12,<2.0"
@@ -1868,47 +1608,13 @@ python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,>=2.7"
six = ">=1.5"
[[package]]
-name = "python-lsp-jsonrpc"
-version = "1.0.0"
-description = "JSON RPC 2.0 server library"
+name = "pytomlpp"
+version = "1.0.11"
+description = "A python wrapper for toml++"
category = "dev"
optional = false
python-versions = "*"
-[package.dependencies]
-ujson = ">=3.0.0"
-
-[package.extras]
-test = ["coverage", "pycodestyle", "pyflakes", "pylint", "pytest", "pytest-cov"]
-
-[[package]]
-name = "python-lsp-server"
-version = "1.5.0"
-description = "Python Language Server for the Language Server Protocol"
-category = "dev"
-optional = false
-python-versions = ">=3.7"
-
-[package.dependencies]
-jedi = ">=0.17.2,<0.19.0"
-pluggy = ">=1.0.0"
-python-lsp-jsonrpc = ">=1.0.0"
-ujson = ">=3.0.0"
-
-[package.extras]
-all = ["autopep8 (>=1.6.0,<1.7.0)", "flake8 (>=4.0.0,<4.1.0)", "mccabe (>=0.6.0,<0.7.0)", "pycodestyle (>=2.8.0,<2.9.0)", "pydocstyle (>=2.0.0)", "pyflakes (>=2.4.0,<2.5.0)", "pylint (>=2.5.0)", "rope (>=0.10.5)", "whatthepatch", "yapf"]
-autopep8 = ["autopep8 (>=1.6.0,<1.7.0)"]
-flake8 = ["flake8 (>=4.0.0,<4.1.0)"]
-mccabe = ["mccabe (>=0.6.0,<0.7.0)"]
-pycodestyle = ["pycodestyle (>=2.8.0,<2.9.0)"]
-pydocstyle = ["pydocstyle (>=2.0.0)"]
-pyflakes = ["pyflakes (>=2.4.0,<2.5.0)"]
-pylint = ["pylint (>=2.5.0)"]
-rope = ["rope (>0.10.5)"]
-test = ["coverage", "flaky", "matplotlib", "numpy (<1.23)", "pandas", "pylint (>=2.5.0)", "pyqt5", "pytest", "pytest-cov"]
-websockets = ["websockets (>=10.3)"]
-yapf = ["whatthepatch (>=1.0.2,<2.0.0)", "yapf"]
-
[[package]]
name = "pytz"
version = "2022.2.1"
@@ -1921,7 +1627,7 @@ python-versions = "*"
name = "pywavelets"
version = "1.3.0"
description = "PyWavelets, wavelet transform module"
-category = "main"
+category = "dev"
optional = false
python-versions = ">=3.7"
@@ -1932,17 +1638,9 @@ numpy = ">=1.17.3"
name = "pywin32"
version = "304"
description = "Python for Window Extensions"
-category = "main"
-optional = false
-python-versions = "*"
-
-[[package]]
-name = "pywinpty"
-version = "2.0.7"
-description = "Pseudo terminal support for Windows from Python."
category = "dev"
optional = false
-python-versions = ">=3.7"
+python-versions = "*"
[[package]]
name = "pyyaml"
@@ -2004,7 +1702,7 @@ test = ["pytest (>=6,!=7.0.0,!=7.0.1)", "pytest-cov (>=3.0.0)", "pytest-qt"]
name = "ray"
version = "1.13.0"
description = "Ray provides a simple, universal API for building distributed applications."
-category = "main"
+category = "dev"
optional = false
python-versions = "*"
@@ -2044,7 +1742,7 @@ tune = ["pandas", "requests", "tabulate", "tensorboardX (>=1.9)"]
name = "requests"
version = "2.28.1"
description = "Python HTTP for Humans."
-category = "main"
+category = "dev"
optional = false
python-versions = ">=3.7, <4"
@@ -2062,7 +1760,7 @@ use_chardet_on_py3 = ["chardet (>=3.0.2,<6)"]
name = "requests-oauthlib"
version = "1.3.1"
description = "OAuthlib authentication support for Requests."
-category = "main"
+category = "dev"
optional = false
python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
@@ -2077,18 +1775,34 @@ rsa = ["oauthlib[signedtoken] (>=3.0.0)"]
name = "requests-toolbelt"
version = "0.9.1"
description = "A utility belt for advanced users of python-requests"
-category = "main"
+category = "dev"
optional = false
python-versions = "*"
[package.dependencies]
requests = ">=2.0.1,<3.0.0"
+[[package]]
+name = "rich"
+version = "12.5.1"
+description = "Render rich text, tables, progress bars, syntax highlighting, markdown and more to the terminal"
+category = "dev"
+optional = false
+python-versions = ">=3.6.3,<4.0.0"
+
+[package.dependencies]
+commonmark = ">=0.9.0,<0.10.0"
+pygments = ">=2.6.0,<3.0.0"
+typing-extensions = {version = ">=4.0.0,<5.0", markers = "python_version < \"3.9\""}
+
+[package.extras]
+jupyter = ["ipywidgets (>=7.5.1,<8.0.0)"]
+
[[package]]
name = "rsa"
version = "4.9"
description = "Pure-Python RSA implementation"
-category = "main"
+category = "dev"
optional = false
python-versions = ">=3.6,<4"
@@ -2099,7 +1813,7 @@ pyasn1 = ">=0.1.3"
name = "scikit-image"
version = "0.19.3"
description = "Image processing in Python"
-category = "main"
+category = "dev"
optional = false
python-versions = ">=3.7"
@@ -2116,14 +1830,14 @@ tifffile = ">=2019.7.26"
[package.extras]
data = ["pooch (>=1.3.0)"]
docs = ["cloudpickle (>=0.2.1)", "dask[array] (>=0.15.0,!=2.17.0)", "ipywidgets", "kaleido", "matplotlib (>=3.3)", "myst-parser", "numpydoc (>=1.0)", "pandas (>=0.23.0)", "plotly (>=4.14.0)", "pooch (>=1.3.0)", "pytest-runner", "scikit-learn", "seaborn (>=0.7.1)", "sphinx (>=1.8)", "sphinx-copybutton", "sphinx-gallery (>=0.10.1)", "tifffile (>=2020.5.30)"]
-optional = ["astropy (>=3.1.2)", "cloudpickle (>=0.2.1)", "dask[array] (>=1.0.0,!=2.17.0)", "matplotlib (>=3.0.3)", "pooch (>=1.3.0)", "pyamg", "qtpy", "simpleitk"]
+optional = ["SimpleITK", "astropy (>=3.1.2)", "cloudpickle (>=0.2.1)", "dask[array] (>=1.0.0,!=2.17.0)", "matplotlib (>=3.0.3)", "pooch (>=1.3.0)", "pyamg", "qtpy"]
test = ["asv", "codecov", "flake8", "matplotlib (>=3.0.3)", "pooch (>=1.3.0)", "pytest (>=5.2.0)", "pytest-cov (>=2.7.0)", "pytest-faulthandler", "pytest-localserver"]
[[package]]
name = "scikit-learn"
version = "1.0.2"
description = "A set of python modules for machine learning and data mining"
-category = "main"
+category = "dev"
optional = false
python-versions = ">=3.7"
@@ -2154,7 +1868,7 @@ numpy = ">=1.16.5,<1.23.0"
name = "seaborn"
version = "0.11.2"
description = "seaborn: statistical data visualization"
-category = "main"
+category = "dev"
optional = false
python-versions = ">=3.6"
@@ -2165,28 +1879,29 @@ pandas = ">=0.23"
scipy = ">=1.0"
[[package]]
-name = "send2trash"
-version = "1.8.0"
-description = "Send file to trash natively under Mac OS X, Windows and Linux."
+name = "setuptools"
+version = "65.3.0"
+description = "Easily download, build, install, upgrade, and uninstall Python packages"
category = "dev"
optional = false
-python-versions = "*"
+python-versions = ">=3.7"
[package.extras]
-nativelib = ["pyobjc-framework-cocoa", "pywin32"]
-objc = ["pyobjc-framework-cocoa"]
-win32 = ["pywin32"]
+docs = ["furo", "jaraco.packaging (>=9)", "jaraco.tidelift (>=1.4)", "pygments-github-lexers (==0.0.5)", "rst.linker (>=1.9)", "sphinx", "sphinx-favicon", "sphinx-hoverxref (<2)", "sphinx-inline-tabs", "sphinx-notfound-page (==0.8.3)", "sphinx-reredirects", "sphinxcontrib-towncrier"]
+testing = ["build[virtualenv]", "filelock (>=3.4.0)", "flake8 (<5)", "flake8-2020", "ini2toml[lite] (>=0.9)", "jaraco.envs (>=2.2)", "jaraco.path (>=3.2.0)", "mock", "pip (>=19.1)", "pip-run (>=8.8)", "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", "pytest-xdist", "tomli-w (>=1.0.0)", "virtualenv (>=13.0.0)", "wheel"]
+testing-integration = ["build[virtualenv]", "filelock (>=3.4.0)", "jaraco.envs (>=2.2)", "jaraco.path (>=3.2.0)", "pytest", "pytest-enabler", "pytest-xdist", "tomli", "virtualenv (>=13.0.0)", "wheel"]
[[package]]
name = "setuptools-scm"
version = "6.4.2"
description = "the blessed package to manage your versions by scm tags"
-category = "main"
+category = "dev"
optional = false
python-versions = ">=3.6"
[package.dependencies]
packaging = ">=20.0"
+setuptools = "*"
tomli = ">=1.0.0"
[package.extras]
@@ -2209,14 +1924,6 @@ category = "dev"
optional = false
python-versions = "*"
-[[package]]
-name = "soupsieve"
-version = "2.3.2.post1"
-description = "A modern CSS selector implementation for Beautiful Soup."
-category = "dev"
-optional = false
-python-versions = ">=3.6"
-
[[package]]
name = "sphinx"
version = "4.3.2"
@@ -2235,6 +1942,7 @@ Jinja2 = ">=2.3"
packaging = "*"
Pygments = ">=2.0"
requests = ">=2.5.0"
+setuptools = "*"
snowballstemmer = ">=1.1"
sphinxcontrib-applehelp = "*"
sphinxcontrib-devhelp = "*"
@@ -2319,11 +2027,35 @@ python-versions = ">=3.5"
lint = ["docutils-stubs", "flake8", "mypy"]
test = ["pytest"]
+[[package]]
+name = "superqt"
+version = "0.3.5"
+description = "Missing widgets for PyQt/PySide"
+category = "dev"
+optional = false
+python-versions = ">=3.7"
+
+[package.dependencies]
+packaging = "*"
+pygments = ">=2.4.0"
+qtpy = ">=1.1.0"
+typing-extensions = "*"
+
+[package.extras]
+dev = ["ipython", "isort", "jedi (<0.18.0)", "mypy", "pre-commit", "pyside2", "pytest", "pytest-cov", "pytest-qt", "tox", "tox-conda"]
+font_fa5 = ["fonticon-fontawesome5"]
+font_mi5 = ["fonticon-materialdesignicons5"]
+pyqt5 = ["pyqt5"]
+pyqt6 = ["pyqt6"]
+pyside2 = ["pyside2"]
+pyside6 = ["pyside6"]
+testing = ["pytest", "pytest-cov", "pytest-qt", "tox", "tox-conda"]
+
[[package]]
name = "tabulate"
version = "0.8.10"
description = "Pretty-print tabular data"
-category = "main"
+category = "dev"
optional = false
python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
@@ -2334,7 +2066,7 @@ widechars = ["wcwidth"]
name = "tensorboard"
version = "2.9.0"
description = "TensorBoard lets you watch Tensors Flow"
-category = "main"
+category = "dev"
optional = false
python-versions = ">=3.6"
@@ -2347,15 +2079,17 @@ markdown = ">=2.6.8"
numpy = ">=1.12.0"
protobuf = ">=3.9.2"
requests = ">=2.21.0,<3"
+setuptools = ">=41.0.0"
tensorboard-data-server = ">=0.6.0,<0.7.0"
tensorboard-plugin-wit = ">=1.6.0"
werkzeug = ">=1.0.1"
+wheel = ">=0.26"
[[package]]
name = "tensorboard-data-server"
version = "0.6.1"
description = "Fast data loading for TensorBoard"
-category = "main"
+category = "dev"
optional = false
python-versions = ">=3.6"
@@ -2363,7 +2097,7 @@ python-versions = ">=3.6"
name = "tensorboard-plugin-wit"
version = "1.8.1"
description = "What-If Tool TensorBoard plugin."
-category = "main"
+category = "dev"
optional = false
python-versions = "*"
@@ -2371,7 +2105,7 @@ python-versions = "*"
name = "tensorboardx"
version = "2.5.1"
description = "TensorBoardX lets you watch Tensors Flow without Tensorflow"
-category = "main"
+category = "dev"
optional = false
python-versions = "*"
@@ -2383,7 +2117,7 @@ protobuf = ">=3.8.0,<=3.20.1"
name = "tensorflow"
version = "2.9.0"
description = "TensorFlow is an open source machine learning framework for everyone."
-category = "main"
+category = "dev"
optional = false
python-versions = ">=3.7"
@@ -2402,6 +2136,7 @@ numpy = ">=1.20"
opt-einsum = ">=2.3.2"
packaging = "*"
protobuf = ">=3.9.2"
+setuptools = "*"
six = ">=1.12.0"
tensorboard = ">=2.9,<2.10"
tensorflow-estimator = ">=2.9.0rc0,<2.10.0"
@@ -2414,7 +2149,7 @@ wrapt = ">=1.11.0"
name = "tensorflow-estimator"
version = "2.9.0"
description = "TensorFlow Estimator."
-category = "main"
+category = "dev"
optional = false
python-versions = ">=3.7"
@@ -2422,7 +2157,7 @@ python-versions = ">=3.7"
name = "tensorflow-io-gcs-filesystem"
version = "0.26.0"
description = "TensorFlow IO"
-category = "main"
+category = "dev"
optional = false
python-versions = ">=3.7, <3.11"
@@ -2437,31 +2172,15 @@ tensorflow-rocm = ["tensorflow-rocm (>=2.9.0,<2.10.0)"]
name = "termcolor"
version = "1.1.0"
description = "ANSII Color formatting for output in terminal."
-category = "main"
-optional = false
-python-versions = "*"
-
-[[package]]
-name = "terminado"
-version = "0.15.0"
-description = "Tornado websocket backend for the Xterm.js Javascript terminal emulator library."
category = "dev"
optional = false
-python-versions = ">=3.7"
-
-[package.dependencies]
-ptyprocess = {version = "*", markers = "os_name != \"nt\""}
-pywinpty = {version = ">=1.1.0", markers = "os_name == \"nt\""}
-tornado = ">=6.1.0"
-
-[package.extras]
-test = ["pre-commit", "pytest (>=6.0)", "pytest-timeout"]
+python-versions = "*"
[[package]]
name = "terminaltables"
version = "3.1.10"
description = "Generate simple tables in terminals from a nested list of strings."
-category = "main"
+category = "dev"
optional = false
python-versions = ">=2.6"
@@ -2469,7 +2188,7 @@ python-versions = ">=2.6"
name = "texttable"
version = "1.6.4"
description = "module for creating simple ASCII tables"
-category = "main"
+category = "dev"
optional = false
python-versions = "*"
@@ -2477,7 +2196,7 @@ python-versions = "*"
name = "threadpoolctl"
version = "3.1.0"
description = "threadpoolctl"
-category = "main"
+category = "dev"
optional = false
python-versions = ">=3.6"
@@ -2485,7 +2204,7 @@ python-versions = ">=3.6"
name = "tifffile"
version = "2021.11.2"
description = "Read and write TIFF files"
-category = "main"
+category = "dev"
optional = false
python-versions = ">=3.7"
@@ -2495,21 +2214,6 @@ numpy = ">=1.15.1"
[package.extras]
all = ["imagecodecs (>=2021.7.30)", "lxml", "matplotlib (>=3.2)"]
-[[package]]
-name = "tinycss2"
-version = "1.1.1"
-description = "A tiny CSS parser"
-category = "dev"
-optional = false
-python-versions = ">=3.6"
-
-[package.dependencies]
-webencodings = ">=0.4"
-
-[package.extras]
-doc = ["sphinx", "sphinx-rtd-theme"]
-test = ["coverage", "pytest", "pytest-cov", "pytest-flake8", "pytest-isort"]
-
[[package]]
name = "toml"
version = "0.10.2"
@@ -2522,7 +2226,7 @@ python-versions = ">=2.6, !=3.0.*, !=3.1.*, !=3.2.*"
name = "tomli"
version = "2.0.1"
description = "A lil' TOML parser"
-category = "main"
+category = "dev"
optional = false
python-versions = ">=3.7"
@@ -2530,7 +2234,7 @@ python-versions = ">=3.7"
name = "toolz"
version = "0.12.0"
description = "List processing tools and functional utilities"
-category = "main"
+category = "dev"
optional = false
python-versions = ">=3.5"
@@ -2546,7 +2250,7 @@ python-versions = ">= 3.7"
name = "tqdm"
version = "4.64.0"
description = "Fast, Extensible Progress Meter"
-category = "main"
+category = "dev"
optional = false
python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,>=2.7"
@@ -2574,7 +2278,7 @@ test = ["pre-commit", "pytest"]
name = "tune-sklearn"
version = "0.4.3"
description = "A drop-in replacement for Scikit-Learn's GridSearchCV / RandomizedSearchCV with cutting edge hyperparameter tuning techniques."
-category = "main"
+category = "dev"
optional = false
python-versions = "*"
@@ -2585,25 +2289,26 @@ scikit-learn = "*"
scipy = "*"
[[package]]
-name = "typed-ast"
-version = "1.5.4"
-description = "a fork of Python 2 and 3 ast modules with type comment support"
+name = "typer"
+version = "0.6.1"
+description = "Typer, build great CLIs. Easy to code. Based on Python type hints."
category = "dev"
optional = false
python-versions = ">=3.6"
+[package.dependencies]
+click = ">=7.1.1,<9.0.0"
+
+[package.extras]
+all = ["colorama (>=0.4.3,<0.5.0)", "rich (>=10.11.0,<13.0.0)", "shellingham (>=1.3.0,<2.0.0)"]
+dev = ["autoflake (>=1.3.1,<2.0.0)", "flake8 (>=3.8.3,<4.0.0)", "pre-commit (>=2.17.0,<3.0.0)"]
+doc = ["mdx-include (>=1.4.1,<2.0.0)", "mkdocs (>=1.1.2,<2.0.0)", "mkdocs-material (>=8.1.4,<9.0.0)"]
+test = ["black (>=22.3.0,<23.0.0)", "coverage (>=5.2,<6.0)", "isort (>=5.0.6,<6.0.0)", "mypy (==0.910)", "pytest (>=4.4.0,<5.4.0)", "pytest-cov (>=2.10.0,<3.0.0)", "pytest-sugar (>=0.9.4,<0.10.0)", "pytest-xdist (>=1.32.0,<2.0.0)", "rich (>=10.11.0,<13.0.0)", "shellingham (>=1.3.0,<2.0.0)"]
+
[[package]]
name = "typing-extensions"
version = "4.3.0"
description = "Backported and Experimental Type Hints for Python 3.7+"
-category = "main"
-optional = false
-python-versions = ">=3.7"
-
-[[package]]
-name = "ujson"
-version = "5.4.0"
-description = "Ultra fast JSON encoder and decoder for Python"
category = "dev"
optional = false
python-versions = ">=3.7"
@@ -2612,7 +2317,7 @@ python-versions = ">=3.7"
name = "urllib3"
version = "1.26.12"
description = "HTTP library with thread-safe connection pooling, file post, and more."
-category = "main"
+category = "dev"
optional = false
python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*, <4"
@@ -2625,14 +2330,13 @@ socks = ["PySocks (>=1.5.6,!=1.5.7,<2.0)"]
name = "virtualenv"
version = "20.16.2"
description = "Virtual Python Environment builder"
-category = "main"
+category = "dev"
optional = false
python-versions = ">=3.6"
[package.dependencies]
distlib = ">=0.3.1,<1"
filelock = ">=3.2,<4"
-importlib-metadata = {version = ">=0.12", markers = "python_version < \"3.8\""}
platformdirs = ">=2,<3"
[package.extras]
@@ -2640,17 +2344,37 @@ docs = ["proselint (>=0.10.2)", "sphinx (>=3)", "sphinx-argparse (>=0.2.5)", "sp
testing = ["coverage (>=4)", "coverage-enable-subprocess (>=1)", "flaky (>=3)", "packaging (>=20.0)", "pytest (>=4)", "pytest-env (>=0.6.2)", "pytest-freezegun (>=0.4.1)", "pytest-mock (>=2)", "pytest-randomly (>=1)", "pytest-timeout (>=1)"]
[[package]]
-name = "wcwidth"
-version = "0.2.5"
-description = "Measures the displayed width of unicode strings in a terminal"
+name = "vispy"
+version = "0.10.0"
+description = "Interactive visualization in Python"
category = "dev"
optional = false
-python-versions = "*"
+python-versions = ">=3.6"
+
+[package.dependencies]
+freetype-py = "*"
+hsluv = "*"
+kiwisolver = "*"
+numpy = "*"
+
+[package.extras]
+doc = ["numpydoc", "pydata-sphinx-theme", "sphinx-gallery", "sphinxcontrib-apidoc"]
+io = ["Pillow", "meshio"]
+ipython-static = ["ipython"]
+pyglet = ["pyglet (>=1.2)"]
+pyqt5 = ["pyqt5"]
+pyqt6 = ["pyqt6"]
+pyside = ["PySide"]
+pyside2 = ["PySide2"]
+pyside6 = ["PySide6"]
+sdl2 = ["PySDL2"]
+tk = ["pyopengltk"]
+wx = ["wxPython"]
[[package]]
-name = "webencodings"
-version = "0.5.1"
-description = "Character encoding aliases for legacy web content"
+name = "wcwidth"
+version = "0.2.5"
+description = "Measures the displayed width of unicode strings in a terminal"
category = "dev"
optional = false
python-versions = "*"
@@ -2659,7 +2383,7 @@ python-versions = "*"
name = "werkzeug"
version = "2.2.2"
description = "The comprehensive WSGI web application library."
-category = "main"
+category = "dev"
optional = false
python-versions = ">=3.7"
@@ -2670,18 +2394,21 @@ MarkupSafe = ">=2.1.1"
watchdog = ["watchdog"]
[[package]]
-name = "widgetsnbextension"
-version = "4.0.2"
-description = "Jupyter interactive widgets for Jupyter Notebook"
+name = "wheel"
+version = "0.37.1"
+description = "A built-package format for Python"
category = "dev"
optional = false
-python-versions = ">=3.7"
+python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,>=2.7"
+
+[package.extras]
+test = ["pytest (>=3.0.0)", "pytest-cov"]
[[package]]
name = "wrapt"
version = "1.14.1"
description = "Module for decorators, wrappers and monkey patching."
-category = "main"
+category = "dev"
optional = false
python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,>=2.7"
@@ -2689,7 +2416,7 @@ python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,>=2.7"
name = "xgboost"
version = "1.4.2"
description = "XGBoost Python Package"
-category = "main"
+category = "dev"
optional = false
python-versions = ">=3.6"
@@ -2708,7 +2435,7 @@ scikit-learn = ["scikit-learn"]
name = "xmltodict"
version = "0.13.0"
description = "Makes working with XML feel like you are working with JSON"
-category = "main"
+category = "dev"
optional = false
python-versions = ">=3.4"
@@ -2716,7 +2443,7 @@ python-versions = ">=3.4"
name = "zeroc-ice"
version = "3.6.5"
description = "Ice is a comprehensive RPC framework with support for Python, C++, .NET, Java, JavaScript and more."
-category = "main"
+category = "dev"
optional = false
python-versions = "*"
@@ -2724,7 +2451,7 @@ python-versions = "*"
name = "zipp"
version = "3.8.1"
description = "Backport of pathlib-compatible object wrapper for zip files"
-category = "main"
+category = "dev"
optional = false
python-versions = ">=3.7"
@@ -2734,8 +2461,8 @@ testing = ["func-timeout", "jaraco.itertools", "pytest (>=6)", "pytest-black (>=
[metadata]
lock-version = "1.1"
-python-versions = ">=3.7.1,<3.11"
-content-hash = "0a7fc281e7d5415d548678570c3f74b8721d64bccc7ccf41ceacfd1c160b9ece"
+python-versions = ">=3.8,<3.11"
+content-hash = "b537be9803fe96fcb4f8447618b15e57730f0deedad7c7b046c9753f20dec00b"
[metadata.files]
absl-py = [
@@ -2770,33 +2497,6 @@ appnope = [
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]
-argon2-cffi = [
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@@ -2816,43 +2516,18 @@ backcall = [
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- {file = "widgetsnbextension-4.0.2.tar.gz", hash = "sha256:07f0e8582f920b24316cef16490f1aeb498f2c875d48980540e5c5dbf0ff5e2d"},
+wheel = [
+ {file = "wheel-0.37.1-py2.py3-none-any.whl", hash = "sha256:4bdcd7d840138086126cd09254dc6195fb4fc6f01c050a1d7236f2630db1d22a"},
+ {file = "wheel-0.37.1.tar.gz", hash = "sha256:e9a504e793efbca1b8e0e9cb979a249cf4a0a7b5b8c9e8b65a5e39d49529c1c4"},
]
wrapt = [
{file = "wrapt-1.14.1-cp27-cp27m-macosx_10_9_x86_64.whl", hash = "sha256:1b376b3f4896e7930f1f772ac4b064ac12598d1c38d04907e696cc4d794b43d3"},
diff --git a/pyproject.toml b/pyproject.toml
index b018c7d6bd669f1e9c3abff29bfc94bd760d06b3..44801634e2b1e06e8a459e2a9eb900cff1b0519e 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -6,46 +6,77 @@ authors = ["Alan Munoz <alan.munoz@ed.ac.uk>"]
packages = [
{ include = "aliby" },
{ include = "extraction" },
+ { include = "agora" },
+ { include = "postprocessing" },
]
readme = "README.md"
[tool.poetry.dependencies]
-python = ">=3.7.1,<3.11"
+python = ">=3.8,<3.11"
+PyYAML = "^6.0"
+py-find-1st = "^1.1.5"
+opencv-python = "*"
+scipy = ">=1.7.3"
+flatten-dict = "^0.4.2"
numpy = "1.21.6" # Pinning numpy and pandas makes dep resolution much faster
pandas = "1.3.3"
+
+[tool.poetry.group.pipeline.dependencies]
dask = "^2021.12.0"
-pathos = "^0.2.8" # Lambda-friendly multithreading
tqdm = "^4.62.3" # progress bars
scikit-learn = ">=1.0.2" # Used for an extraction metric
py-find-1st = "^1.1.5" # Fast indexing
scikit-image = ">=0.18.1"
-opencv-python = "*"
requests-toolbelt = "^0.9.1"
h5py = "2.10" # File I/O
imageio = "2.8.0" # For image-visualisation utilities
-omero-py = ">=5.6.2" # contact omero server
aliby-agora = "^0.2.30"
aliby-baby = "^0.1.14"
aliby-post = "^0.1.36"
p-tqdm = "^1.3.3" # Parallel progress bars
xmltodict = "^0.13.0" # read ome-tiff metadata
-zeroc-ice = {version="3.6.5"} # networking interface, slow to build
# zeroc-ice = {version="3.6.5", optional=true} # To be set as optional in the future
-[tool.poetry.dev-dependencies]
-black = "^22.6.0"
+[tool.poetry.group.postprocessor.dependencies]
+numpy = "1.21.6" # Pinning numpy and pandas makes dep resolution much faster
+pandas = "1.3.3"
+scipy = ">=1.4.1"
+PyYAML = "^6.0"
+more-itertools = "^8.12.0"
+leidenalg = "^0.8.8"
+aliby-agora = "^0.2.33"
+seaborn = "^0.11.2"
+scikit-learn = ">=0.22"
+gaussianprocessderivatives = "^0.1.2"
+p-tqdm = "^1.3.3"
+pycatch22 = "^0.4.2"
+pathos = "^0.2.8" # Lambda-friendly multithreading
+
+[tool.poetry.group.network]
+optional = false
+
+[tool.poetry.group.network.dependencies]
+omero-py = ">=5.6.2" # contact omero server
+zeroc-ice = {version="3.6.5"} # networking interface, slow to build
+
+[tool.poetry.group.gui]
+optional = true
+
+[tool.poetry.group.gui.dependencies]
+napari = ">=0.4.16"
+opencv-python = "==4.1.2.30"
+
+[tool.poetry.group.docs]
+optional = true
+
+[tool.poetry.group.docs.dependencies]
Sphinx = "^4.3.2"
+
+[tool.poetry.group.test]
+optional = true
+
+[tool.poetry.group.test.dependencies]
pytest = "^6.2.5"
-mypy = "^0.930"
-numpydoc = "^1.3.1"
-isort = "^5.10.1"
-jupyter = "^1.0.0"
-flake8 = "^4.0.1"
-pyright = "^1.1.258"
-pre-commit = "^2.20.0"
-data-science-types = "^0.2.23"
-jupytext = "^1.14.1"
-python-lsp-server = "^1.5.0"
[build-system]
requires = ["setuptools", "poetry-core>=1.0.0"]