From 5a9894fe9dbc5a17255b13cb388415d4ac78da71 Mon Sep 17 00:00:00 2001
From: Peter Swain <pswain@Home-iMac.local>
Date: Wed, 1 May 2024 15:12:59 +0100
Subject: [PATCH] refactor(pyproject.toml): simplified with baby-seg

---
 poetry.lock    | 7407 ++++++++++--------------------------------------
 pyproject.toml |  137 +-
 2 files changed, 1524 insertions(+), 6020 deletions(-)

diff --git a/poetry.lock b/poetry.lock
index 52a945c..146dfa7 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -1,131 +1,116 @@
-# This file is automatically @generated by Poetry 1.4.0 and should not be changed by hand.
+# This file is automatically @generated by Poetry 1.8.2 and should not be changed by hand.
 
 [[package]]
 name = "absl-py"
-version = "2.0.0"
+version = "2.1.0"
 description = "Abseil Python Common Libraries, see https://github.com/abseil/abseil-py."
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
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-    {file = "absl_py-2.0.0-py3-none-any.whl", hash = "sha256:9a28abb62774ae4e8edbe2dd4c49ffcd45a6a848952a5eccc6a49f3f0fc1e2f3"},
+    {file = "absl-py-2.1.0.tar.gz", hash = "sha256:7820790efbb316739cde8b4e19357243fc3608a152024288513dd968d7d959ff"},
+    {file = "absl_py-2.1.0-py3-none-any.whl", hash = "sha256:526a04eadab8b4ee719ce68f204172ead1027549089702d99b9059f129ff1308"},
 ]
 
 [[package]]
 name = "aiohttp"
-version = "3.8.6"
+version = "3.9.5"
 description = "Async http client/server framework (asyncio)"
-category = "dev"
-optional = true
-python-versions = ">=3.6"
+optional = false
+python-versions = ">=3.8"
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 ]
 
 [package.dependencies]
 aiosignal = ">=1.1.2"
-async-timeout = ">=4.0.0a3,<5.0"
+async-timeout = {version = ">=4.0,<5.0", markers = "python_version < \"3.11\""}
 attrs = ">=17.3.0"
-charset-normalizer = ">=2.0,<4.0"
 frozenlist = ">=1.1.1"
 multidict = ">=4.5,<7.0"
 yarl = ">=1.0,<2.0"
 
 [package.extras]
-speedups = ["Brotli", "aiodns", "cchardet"]
+speedups = ["Brotli", "aiodns", "brotlicffi"]
 
 [[package]]
 name = "aiosignal"
 version = "1.3.1"
 description = "aiosignal: a list of registered asynchronous callbacks"
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -136,77 +121,10 @@ files = [
 [package.dependencies]
 frozenlist = ">=1.1.0"
 
-[[package]]
-name = "alabaster"
-version = "0.7.13"
-description = "A configurable sidebar-enabled Sphinx theme"
-category = "dev"
-optional = false
-python-versions = ">=3.6"
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-]
-
-[[package]]
-name = "aliby-baby"
-version = "0.1.17"
-description = "Birth Annotator for Budding Yeast"
-category = "main"
-optional = false
-python-versions = ">=3.7.1,<3.11"
-files = [
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-
-[package.dependencies]
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-configspace = ">=0.6.1,<0.7.0"
-hpbandster = ">=0.7.4,<0.8.0"
-imageio = "2.8.0"
-keras-tuner = "1.0.1"
-matplotlib = ">=3.5.1,<4.0.0"
-numpy = "1.21.6"
-pandas = "1.3.3"
-Pillow = ">=9.0.0,<10.0.0"
-protobuf = "<=3.20.1"
-ray = ">=1.13.0,<2.0.0"
-scikit-image = ">=0.19.3,<0.20.0"
-scikit-learn = ">=1.0.2"
-scikit-plot = ">=0.3.7,<0.4.0"
-tensorflow = ">=2.0.0,<2.9.1"
-tqdm = ">=4.62.3,<5.0.0"
-tune-sklearn = ">=0.4.1,<0.5.0"
-xgboost = "1.4.2"
-
-[[package]]
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-
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-description = "An easy safelist-based HTML-sanitizing tool."
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+name = "baby-seg"
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 [package.dependencies]
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 [package.extras]
-css = ["tinycss2 (>=1.1.0,<1.3)"]
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 ]
 
 [package.dependencies]
@@ -570,257 +275,147 @@ numpy = "*"
 [package.extras]
 doc = ["gitpython", "numpydoc", "sphinx"]
 
-[[package]]
-name = "build"
-version = "1.0.3"
-description = "A simple, correct Python build frontend"
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 ]
 
 [[package]]
 name = "click"
-version = "8.0.4"
+version = "8.1.7"
 description = "Composable command line interface toolkit"
-category = "main"
 optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.7"
 files = [
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-    {file = "click-8.0.4.tar.gz", hash = "sha256:8458d7b1287c5fb128c90e23381cf99dcde74beaf6c7ff6384ce84d6fe090adb"},
+    {file = "click-8.1.7-py3-none-any.whl", hash = "sha256:ae74fb96c20a0277a1d615f1e4d73c8414f5a98db8b799a7931d1582f3390c28"},
+    {file = "click-8.1.7.tar.gz", hash = "sha256:ca9853ad459e787e2192211578cc907e7594e294c7ccc834310722b41b9ca6de"},
 ]
 
 [package.dependencies]
@@ -828,21 +423,19 @@ colorama = {version = "*", markers = "platform_system == \"Windows\""}
 
 [[package]]
 name = "cloudpickle"
-version = "2.2.1"
-description = "Extended pickling support for Python objects"
-category = "main"
+version = "3.0.0"
+description = "Pickler class to extend the standard pickle.Pickler functionality"
 optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.8"
 files = [
-    {file = "cloudpickle-2.2.1-py3-none-any.whl", hash = "sha256:61f594d1f4c295fa5cd9014ceb3a1fc4a70b0de1164b94fbc2d854ccba056f9f"},
-    {file = "cloudpickle-2.2.1.tar.gz", hash = "sha256:d89684b8de9e34a2a43b3460fbca07d09d6e25ce858df4d5a44240403b6178f5"},
+    {file = "cloudpickle-3.0.0-py3-none-any.whl", hash = "sha256:246ee7d0c295602a036e86369c77fecda4ab17b506496730f2f576d9016fd9c7"},
+    {file = "cloudpickle-3.0.0.tar.gz", hash = "sha256:996d9a482c6fb4f33c1a35335cf8afd065d2a56e973270364840712d9131a882"},
 ]
 
 [[package]]
 name = "colorama"
 version = "0.4.6"
 description = "Cross-platform colored terminal text."
-category = "main"
 optional = false
 python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,!=3.6.*,>=2.7"
 files = [
@@ -850,78 +443,10 @@ files = [
     {file = "colorama-0.4.6.tar.gz", hash = "sha256:08695f5cb7ed6e0531a20572697297273c47b8cae5a63ffc6d6ed5c201be6e44"},
 ]
 
-[[package]]
-name = "comm"
-version = "0.1.4"
-description = "Jupyter Python Comm implementation, for usage in ipykernel, xeus-python etc."
-category = "dev"
-optional = false
-python-versions = ">=3.6"
-files = [
-    {file = "comm-0.1.4-py3-none-any.whl", hash = "sha256:6d52794cba11b36ed9860999cd10fd02d6b2eac177068fdd585e1e2f8a96e67a"},
-    {file = "comm-0.1.4.tar.gz", hash = "sha256:354e40a59c9dd6db50c5cc6b4acc887d82e9603787f83b68c01a80a923984d15"},
-]
-
-[package.dependencies]
-traitlets = ">=4"
-
-[package.extras]
-lint = ["black (>=22.6.0)", "mdformat (>0.7)", "mdformat-gfm (>=0.3.5)", "ruff (>=0.0.156)"]
-test = ["pytest"]
-typing = ["mypy (>=0.990)"]
-
-[[package]]
-name = "configspace"
-version = "0.6.1"
-description = "Creation and manipulation of parameter configuration spaces for automated algorithm configuration and hyperparameter tuning."
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 [[package]]
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 description = "Composable style cycles"
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 optional = false
 python-versions = ">=3.8"
 files = [
@@ -1072,436 +531,246 @@ tests = ["pytest", "pytest-cov", "pytest-xdist"]
 
 [[package]]
 name = "dask"
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 ]
 
 [[package]]
 name = "fsspec"
-version = "2023.9.2"
+version = "2024.3.1"
 description = "File-system specification"
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
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-[package.dependencies]
-aiohttp = {version = "<4.0.0a0 || >4.0.0a0,<4.0.0a1 || >4.0.0a1", optional = true, markers = "extra == \"http\""}
-requests = {version = "*", optional = true, markers = "extra == \"http\""}
-
 [package.extras]
 abfs = ["adlfs"]
 adl = ["adlfs"]
@@ -1517,7 +786,7 @@ github = ["requests"]
 gs = ["gcsfs"]
 gui = ["panel"]
 hdfs = ["pyarrow (>=1)"]
-http = ["aiohttp (!=4.0.0a0,!=4.0.0a1)", "requests"]
+http = ["aiohttp (!=4.0.0a0,!=4.0.0a1)"]
 libarchive = ["libarchive-c"]
 oci = ["ocifs"]
 s3 = ["s3fs"]
@@ -1528,20 +797,19 @@ tqdm = ["tqdm"]
 
 [[package]]
 name = "future"
-version = "0.18.3"
+version = "1.0.0"
 description = "Clean single-source support for Python 3 and 2"
-category = "main"
-optional = false
+optional = true
 python-versions = ">=2.6, !=3.0.*, !=3.1.*, !=3.2.*"
 files = [
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 ]
 
 [[package]]
 name = "gast"
 version = "0.4.0"
 description = "Python AST that abstracts the underlying Python version"
-category = "main"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
 files = [
@@ -1553,7 +821,6 @@ files = [
 name = "gaussianprocessderivatives"
 version = "0.1.65"
 description = "Uses Gaussian processes to smooth data and estimate first- and second-order derivatives"
-category = "main"
 optional = false
 python-versions = ">=3.8,<3.11"
 files = [
@@ -1566,49 +833,15 @@ matplotlib = ">=3.3.0"
 numpy = ">=1.16.0"
 scipy = ">=1.7.3"
 
-[[package]]
-name = "gitdb"
-version = "4.0.10"
-description = "Git Object Database"
-category = "main"
-optional = false
-python-versions = ">=3.7"
-files = [
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-
-[package.dependencies]
-smmap = ">=3.0.1,<6"
-
-[[package]]
-name = "gitpython"
-version = "3.1.37"
-description = "GitPython is a Python library used to interact with Git repositories"
-category = "main"
-optional = false
-python-versions = ">=3.7"
-files = [
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-
-[package.dependencies]
-gitdb = ">=4.0.1,<5"
-
-[package.extras]
-test = ["black", "coverage[toml]", "ddt (>=1.1.1,!=1.4.3)", "mypy", "pre-commit", "pytest", "pytest-cov", "pytest-sugar"]
-
 [[package]]
 name = "google-auth"
-version = "2.23.3"
+version = "2.29.0"
 description = "Google Authentication Library"
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
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 ]
 
 [package.dependencies]
@@ -1625,18 +858,17 @@ requests = ["requests (>=2.20.0,<3.0.0.dev0)"]
 
 [[package]]
 name = "google-auth-oauthlib"
-version = "0.4.6"
+version = "1.0.0"
 description = "Google Authentication Library"
-category = "main"
 optional = false
 python-versions = ">=3.6"
 files = [
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+    {file = "google-auth-oauthlib-1.0.0.tar.gz", hash = "sha256:e375064964820b47221a7e1b7ee1fd77051b6323c3f9e3e19785f78ab67ecfc5"},
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 ]
 
 [package.dependencies]
-google-auth = ">=1.0.0"
+google-auth = ">=2.15.0"
 requests-oauthlib = ">=0.7.0"
 
 [package.extras]
@@ -1646,7 +878,6 @@ tool = ["click (>=6.0.0)"]
 name = "google-pasta"
 version = "0.2.0"
 description = "pasta is an AST-based Python refactoring library"
-category = "main"
 optional = false
 python-versions = "*"
 files = [
@@ -1658,358 +889,168 @@ files = [
 [package.dependencies]
 six = "*"
 
-[[package]]
-name = "grid-strategy"
-version = "0.0.1"
-description = "A package for organizing matplotlib plots."
-category = "dev"
-optional = false
-python-versions = ">=3.6"
-files = [
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-]
-
-[package.dependencies]
-matplotlib = "*"
-numpy = "*"
-
 [[package]]
 name = "grpcio"
-version = "1.43.0"
+version = "1.63.0"
 description = "HTTP/2-based RPC framework"
-category = "main"
 optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.8"
 files = [
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-
 [[package]]
 name = "imageio"
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 description = "Library for reading and writing a wide range of image, video, scientific, and volumetric data formats."
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 optional = false
-python-versions = ">=3.5"
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 files = [
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 [package.dependencies]
 numpy = "*"
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 [package.extras]
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+all-plugins = ["astropy", "av", "imageio-ffmpeg", "pillow-heif", "psutil", "tifffile"]
+all-plugins-pypy = ["av", "imageio-ffmpeg", "pillow-heif", "psutil", "tifffile"]
+build = ["wheel"]
+dev = ["black", "flake8", "fsspec[github]", "pytest", "pytest-cov"]
+docs = ["numpydoc", "pydata-sphinx-theme", "sphinx (<6)"]
+ffmpeg = ["imageio-ffmpeg", "psutil"]
 fits = ["astropy"]
-full = ["astropy", "gdal", "imageio-ffmpeg", "itk"]
+full = ["astropy", "av", "black", "flake8", "fsspec[github]", "gdal", "imageio-ffmpeg", "itk", "numpydoc", "pillow-heif", "psutil", "pydata-sphinx-theme", "pytest", "pytest-cov", "sphinx (<6)", "tifffile", "wheel"]
 gdal = ["gdal"]
 itk = ["itk"]
-
-[[package]]
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+tifffile = ["tifffile"]
 
 [[package]]
 name = "importlib-metadata"
-version = "6.8.0"
+version = "7.1.0"
 description = "Read metadata from Python packages"
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
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 [package.dependencies]
 zipp = ">=0.5"
 
 [package.extras]
-docs = ["furo", "jaraco.packaging (>=9)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"]
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 perf = ["ipython"]
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 [[package]]
 name = "importlib-resources"
-version = "6.1.0"
+version = "6.4.0"
 description = "Read resources from Python packages"
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
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 ]
 
 [package.dependencies]
@@ -2017,663 +1058,34 @@ zipp = {version = ">=3.1.0", markers = "python_version < \"3.10\""}
 
 [package.extras]
 docs = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (<7.2.5)", "sphinx (>=3.5)", "sphinx-lint"]
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-
-[[package]]
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-category = "dev"
-optional = false
-python-versions = ">=3.7"
-files = [
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 [[package]]
-name = "ipdb"
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-description = "IPython-enabled pdb"
-category = "dev"
-optional = false
-python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
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-
-[package.dependencies]
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-tomli = {version = "*", markers = "python_version > \"3.6\" and python_version < \"3.11\""}
-
-[[package]]
-name = "ipykernel"
-version = "6.25.2"
-description = "IPython Kernel for Jupyter"
-category = "dev"
+name = "joblib"
+version = "1.4.0"
+description = "Lightweight pipelining with Python functions"
 optional = false
 python-versions = ">=3.8"
 files = [
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 ]
 
-[package.dependencies]
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-debugpy = ">=1.6.5"
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-packaging = "*"
-psutil = "*"
-pyzmq = ">=20"
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-traitlets = ">=5.4.0"
-
-[package.extras]
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-
 [[package]]
-name = "ipython"
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-description = "IPython: Productive Interactive Computing"
-category = "dev"
+name = "keras"
+version = "2.13.1"
+description = "Deep learning for humans."
 optional = false
 python-versions = ">=3.8"
 files = [
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-
-[package.dependencies]
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-
-[package.extras]
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-nbconvert = ["nbconvert"]
-nbformat = ["nbformat"]
-notebook = ["ipywidgets", "notebook"]
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-qtconsole = ["qtconsole"]
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-test-extra = ["curio", "matplotlib (!=3.2.0)", "nbformat", "numpy (>=1.21)", "pandas", "pytest (<7.1)", "pytest-asyncio", "testpath", "trio"]
-
-[[package]]
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-description = "Vestigial utilities from IPython"
-category = "dev"
-optional = false
-python-versions = "*"
-files = [
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 ]
 
 [[package]]
-name = "ipywidgets"
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-category = "dev"
-optional = false
-python-versions = ">=3.7"
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-traitlets = ">=4.3.1"
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-
-[package.extras]
-test = ["ipykernel", "jsonschema", "pytest (>=3.6.0)", "pytest-cov", "pytz"]
-
-[[package]]
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-arrow = ">=0.15.0"
-
-[[package]]
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-version = "5.12.0"
-description = "A Python utility / library to sort Python imports."
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@@ -2927,156 +1261,129 @@ importlib-metadata = {version = ">=4.4", markers = "python_version < \"3.10\""}
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 testing = ["coverage", "pyyaml"]
 
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-category = "dev"
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-
-[package.dependencies]
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-
-[package.extras]
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-testing = ["coverage", "pytest", "pytest-cov", "pytest-regressions"]
-
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 wrapt = ">=1.11.0"
 
 [[package]]
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 [[package]]
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 version = "0.34.0"
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 python-versions = ">=3.7, <3.12"
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@@ -6412,82 +2488,50 @@ tensorflow-gpu = ["tensorflow-gpu (>=2.13.0,<2.14.0)"]
 tensorflow-rocm = ["tensorflow-rocm (>=2.13.0,<2.14.0)"]
 
 [[package]]
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-
-[package.extras]
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-
-[[package]]
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-category = "dev"
+name = "tensorflow-metal"
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 [[package]]
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 [[package]]
 name = "threadpoolctl"
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+version = "3.5.0"
 description = "threadpoolctl"
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 python-versions = ">=3.8"
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+version = "4.66.2"
 description = "Fast, Extensible Progress Meter"
-category = "main"
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 python-versions = ">=3.7"
 files = [
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@@ -6720,131 +2576,37 @@ notebook = ["ipywidgets (>=6)"]
 slack = ["slack-sdk"]
 telegram = ["requests"]
 
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-category = "dev"
+name = "tzdata"
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+python-versions = ">=2"
 files = [
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-
 [[package]]
 name = "urllib3"
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 description = "HTTP library with thread-safe connection pooling, file post, and more."
-category = "main"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*"
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@@ -6852,141 +2614,15 @@ brotli = ["brotli (==1.0.9)", "brotli (>=1.0.9)", "brotlicffi (>=0.8.0)", "brotl
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-
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-optional = ["python-socks", "wsaccel"]
-test = ["websockets"]
-
 [[package]]
 name = "werkzeug"
-version = "3.0.0"
+version = "3.0.2"
 description = "The comprehensive WSGI web application library."
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
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 ]
 
 [package.dependencies]
@@ -6997,147 +2633,101 @@ watchdog = ["watchdog (>=2.3)"]
 
 [[package]]
 name = "wheel"
-version = "0.41.2"
+version = "0.43.0"
 description = "A built-package format for Python"
-category = "main"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
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+    {file = "yarl-1.9.4-py3-none-any.whl", hash = "sha256:928cecb0ef9d5a7946eb6ff58417ad2fe9375762382f1bf5c55e61645f2c43ad"},
+    {file = "yarl-1.9.4.tar.gz", hash = "sha256:566db86717cf8080b99b58b083b773a908ae40f06681e87e589a976faf8246bf"},
 ]
 
 [package.dependencies]
@@ -7237,7 +2842,6 @@ multidict = ">=4.0"
 name = "zarr"
 version = "2.16.1"
 description = "An implementation of chunked, compressed, N-dimensional arrays for Python"
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -7259,7 +2863,6 @@ jupyter = ["ipytree (>=0.2.2)", "ipywidgets (>=8.0.0)", "notebook"]
 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"
 optional = true
 python-versions = "*"
 files = [
@@ -7274,24 +2877,20 @@ files = [
 
 [[package]]
 name = "zipp"
-version = "3.17.0"
+version = "3.18.1"
 description = "Backport of pathlib-compatible object wrapper for zip files"
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "zipp-3.17.0-py3-none-any.whl", hash = "sha256:0e923e726174922dce09c53c59ad483ff7bbb8e572e00c7f7c46b88556409f31"},
-    {file = "zipp-3.17.0.tar.gz", hash = "sha256:84e64a1c28cf7e91ed2078bb8cc8c259cb19b76942096c8d7b84947690cabaf0"},
+    {file = "zipp-3.18.1-py3-none-any.whl", hash = "sha256:206f5a15f2af3dbaee80769fb7dc6f249695e940acca08dfb2a4769fe61e538b"},
+    {file = "zipp-3.18.1.tar.gz", hash = "sha256:2884ed22e7d8961de1c9a05142eb69a247f120291bc0206a00a7642f09b5b715"},
 ]
 
 [package.extras]
-docs = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (<7.2.5)", "sphinx (>=3.5)", "sphinx-lint"]
-testing = ["big-O", "jaraco.functools", "jaraco.itertools", "more-itertools", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-ignore-flaky", "pytest-mypy (>=0.9.1)", "pytest-ruff"]
-
-[extras]
-omero = ["omero-py"]
+docs = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"]
+testing = ["big-O", "jaraco.functools", "jaraco.itertools", "more-itertools", "pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-ignore-flaky", "pytest-mypy", "pytest-ruff (>=0.2.1)"]
 
 [metadata]
 lock-version = "2.0"
 python-versions = ">=3.8, <3.11"
-content-hash = "abefc5210bb7995b4c98b2a3cf50bc6a914e9f72a4c2f3cb9488c0f2e4e37fce"
+content-hash = "39094ed93d82943d98be0882b20d6b83511338adc467ab0c4155dab515529ac3"
diff --git a/pyproject.toml b/pyproject.toml
index 219320d..c4a349e 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,8 +1,8 @@
 [tool.poetry]
-name = "aliby"
-version = "0.1.64"
+name = "alibylite"
+version = "0.0.1"
 description = "Process and analyse live-cell imaging data"
-authors = ["Alan Munoz <alan.munoz@ed.ac.uk>"]
+authors = ["Alan Munoz", "Peter Swain <peter.swain@ed.ac.uk>"]
 packages = [
     { include = "aliby", from="src" },
     { include = "extraction", from="src" },
@@ -12,132 +12,37 @@ packages = [
 ]
 readme = "README.md"
 
-[tool.poetry.scripts]
-aliby-run = "aliby.bin.run:run"
-aliby-annotate = "aliby.bin.annotate:annotate"
-aliby-visualise = "aliby.bin.visualise:napari_overlay"
-
 [build-system]
 requires = ["setuptools", "poetry-core>=1.0.0"]
 build-backend = "poetry.core.masonry.api"
 
 [tool.poetry.dependencies]
 python = ">=3.8, <3.11"
-PyYAML = "^6.0"
-flatten-dict = "^0.4.2"
-gaussianprocessderivatives = "^0.1.5"
 numpy = ">=1.21.6"
-Bottleneck = "^1.3.5"
-opencv-python = "^4.7.0.72"
-pathos = "^0.2.8" # Lambda-friendly multithreading
-p-tqdm = "^1.3.3"
-pandas = ">=1.3.3"
-py-find-1st = "^1.1.5" # Fast indexing
-scikit-learn = ">=1.0.2, <1.3" # Used for an extraction metric
+pandas = ">=2.0.3"
+scikit-learn = ">=1.0.2, <1.3"
 scipy = ">=1.7.3"
-
-# Pipeline + I/O
-dask = "^2021.12.0"
-imageio = "2.8.0" # For image-visualisation utilities
-requests-toolbelt = "^0.9.1"
 scikit-image = ">=0.18.1"
-tqdm = "^4.62.3" # progress bars
-xmltodict = "^0.13.0" # read ome-tiff metadata
-zarr = "^2.14.0"
-GitPython = "^3.1.27"
-h5py = "2.10" # File I/O
-aliby-baby = "^0.1.17"
-
-# Networking
-omero-py = { version = ">=5.6.2", optional = true } # contact omero server
-
-# Postprocessing
-[tool.poetry.group.pp.dependencies]
-leidenalg = "^0.8.8"
-more-itertools = "^8.12.0"
-pycatch22 = "^0.4.2"
-
-[tool.poetry.group.pp]
-optional = true
-
-
-[tool.poetry.group.dev]
-optional = true
 
-[tool.poetry.group.dev.dependencies]
-black = "^22.6.0"
-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"
-seaborn = "^0.11.2"
-debugpy = "^1.6.3"
-coverage = "^7.0.4"
-jupytext = "^1.14.4"
-grid-strategy = "^0.0.1"
-readchar = "^4.0.3"
-ipdb = "^0.13.11"
+bottleneck = ">=1.3.5"
+dask = ">=2021.12.0"
+flatten-dict = ">=0.4.2"
+h5py = ">=3.8.0"
+more-itertools = ">=10.2.0"
+pathos = ">=0.2.8"
+pyyaml = ">=6.0.1"
+py-find-1st = ">=1.1.6"
+tqdm = ">=4.62.3"
+xmltodict = ">=0.13.0"
+zarr = ">=2.14.0"
 
-[tool.poetry.group.docs]
-optional = true
+tensorflow-io-gcs-filesystem = "0.34.0"
+chardet = "^5.2.0"
+tensorflow = "2.13.1"
 
-[tool.poetry.group.docs.dependencies]
-Sphinx = "^5.2.0"
-sphinx-rtd-theme = "^1.0.0"
-sphinx-autodoc-typehints = "^1.19.2"
-myst-parser = "^0.18.0"
+baby-seg = ">=0.30.4"
+omero-py = { version = ">=5.6.2", optional = true }
 
-[tool.poetry.group.test]
-optional = true
-
-[tool.poetry.group.test.dependencies]
-pytest = "^6.2.5"
-
-[tool.poetry.group.utils]
-optional = true
-
-# Dependency groups can only be used by a poetry installation, not pip
-[tool.poetry.group.utils.dependencies]
-napari = {version = ">=0.4.16", optional=true}
-Torch = {version = "^1.13.1", optional=true}
-pytorch-lightning = {version = "^1.9.3", optional=true}
-torchvision = {version = "^0.14.1", optional=true}
-trio = {version = "^0.22.0", optional=true}
-grid-strategy = {version = "^0.0.1", optional=true}
-
-[tool.poetry.extras]
-omero = ["omero-py"]
 
 [tool.black]
 line-length = 79
-target-version = ['py38']
-include = '\.pyi?$'
-extend-exclude = '''
-/(
-    \.git
-  | \.hg
-  | \.mypy_cache
-  | \.tox
-  | \.venv
-  | _build
-  | buck-out
-  | build
-  | dist
-)/
-'''
-
-[tool.isort]
-profile = "black"
-multi_line_output = 3
-line_length = 79
-include_trailing_comma = true
-
-[tool.pytest.ini_options]
-minversion = "6.0"
-addopts = "-ra -q"
-testpaths = [
-    "tests",
-]
-- 
GitLab