8000 Update installation instructions by Czaki · Pull Request #3 · 4DNucleome/PartSeg-smfish · GitHub
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Update installation instructions #3

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Merged
merged 2 commits into from
Aug 8, 2024
Merged

Update installation instructions #3

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88215da
update installation instructions
Czaki Aug 8, 2024
fe5f471
bump python versions
Czaki Aug 8, 2024
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2 changes: 1 addition & 1 deletion .github/workflows/test_and_deploy.yml
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Expand Up @@ -23,7 +23,7 @@ jobs:
strategy:
matrix:
platform: [ubuntu-latest, windows-latest, macos-latest]
python-version: ['3.8', '3.9', '3.10']
python-version: ['3.9', '3.10', '3.12']

steps:
- uses: actions/checkout@v3
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12 changes: 6 additions & 6 deletions .pre-commit-config.yaml
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@@ -1,31 +1,31 @@
repos:
- repo: https://github.com/pre-commit/pre-commit-hooks
rev: v4.3.0
rev: v4.6.0
hooks:
- id: check-docstring-first
- id: end-of-file-fixer
- id: trailing-whitespace
exclude: ^.napari-hub/*
- repo: https://github.com/PyCQA/isort
rev: 5.10.1
rev: 5.13.2
hooks:
- id: isort
- repo: https://github.com/asottile/pyupgrade
rev: v3.1.0
rev: v3.17.0
hooks:
- id: pyupgrade
args: [--py38-plus, --keep-runtime-typing]
- repo: https://github.com/myint/autoflake
rev: v1.7.7
rev: v2.3.1
hooks:
- id: autoflake
args: ["--in-place", "--remove-all-unused-imports"]
- repo: https://github.com/psf/black
rev: 22.10.0
rev: 24.8.0
hooks:
- id: black
- repo: https://github.com/PyCQA/flake8
rev: 5.0.4
rev: 7.1.1
hooks:
- id: flake8
additional_dependencies: [flake8-typing-imports>=1.9.0]
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14 changes: 14 additions & 0 deletions README.md
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Expand Up @@ -33,6 +33,20 @@ To install latest development version :

pip install git+https://github.com/4DNucleome/PartSeg-smfish.git

## Installation in bundled PartSeg

It is possible to ues PartSeg-smfish in bundled PartSeg.
To do this download PartSeg from PartSeg webpage https://partseg.github.io/#download_bundle
or from github release page https://github.com/4DNucleome/PartSeg/releases.

Then download `PartSeg-smfish` from this repository using link
https://github.com/4DNucleome/PartSeg-smfish/archive/refs/heads/main.zip

Unzip the downloaded file and copy `PartSeg_smfish` folder from `src` to `PartSeg`
folder in the downloaded `PartSeg/_internal/plugins`.




## Contributing

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2 changes: 1 addition & 1 deletion src/PartSeg_smfish/segmentation.py
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Expand Up @@ -13,7 +13,6 @@
AlgorithmSelection,
ROIExtractionProfile,
)
from PartSegImage import Channel
from PartSegCore.convex_fill import convex_fill
from PartSegCore.image_operations import gaussian
from PartSegCore.segmentation import ROIExtractionAlgorithm
Expand All @@ -37,6 +36,7 @@
ThresholdSelection,
)
from PartSegCore.utils import BaseModel
from PartSegImage import Channel
from PartSegImage import Image as PSImage
from pydantic import Field

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