From defd027b31aed9edc3f237e5206b52bc0c6bbfc7 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Al=C3=A1n=20Mu=C3=B1oz?= <alan.munoz@ed.ac.uk>
Date: Wed, 15 Mar 2023 12:54:59 +0000
Subject: [PATCH] change(pyproject.toml): reorganise dependencies
---
pyproject.toml | 18 +++++++-----------
1 file changed, 7 insertions(+), 11 deletions(-)
diff --git a/pyproject.toml b/pyproject.toml
index 769e1d0a..5a82cebd 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -15,6 +15,7 @@ readme = "README.md"
[tool.poetry.scripts]
aliby-run = "aliby.bin.run:run"
aliby-annotate = "aliby.bin.annotate:annotate_image"
+aliby-visualise = "aliby.bin.visualise:napari_overlay"
[build-system]
requires = ["setuptools", "poetry-core>=1.0.0"]
@@ -26,6 +27,7 @@ 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"
@@ -41,14 +43,12 @@ 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"
# Networking
omero-py = { version = ">=5.6.2", optional = true } # contact omero server
-zeroc-ice = { version="3.6.5", optional = true } # networking interface, slow to build
GitPython = "^3.1.27"
-Bottleneck = "^1.3.5"
-zarr = "^2.14.0"
[tool.poetry.extras]
omero = [ "omero-py" ]
@@ -83,14 +83,8 @@ jupytext = "^1.14.4"
grid-strategy = "^0.0.1"
readchar = "^4.0.3"
ipdb = "^0.13.11"
-trio = "^0.22.0"
-[tool.poetry.group.napari]
-optional = true
-
-[tool.poetry.group.napari.dependencies]
-napari = ">=0.4.16"
[tool.poetry.group.docs]
optional = true
@@ -107,13 +101,15 @@ optional = true
[tool.poetry.group.test.dependencies]
pytest = "^6.2.5"
-[tool.poetry.group.torch]
+[tool.poetry.group.utils]
optional = true
-[tool.poetry.group.torch.dependencies]
+[tool.poetry.group.utils.dependencies]
+napari = ">=0.4.16"
torch = "^1.13.1"
pytorch-lightning = "^1.9.3"
torchvision = "^0.14.1"
+trio = "^0.22.0"
[tool.black]
line-length = 79
--
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