small-fish-gui 1.0.1__tar.gz → 1.0.3__tar.gz

{small_fish_gui-1.0.1 → small_fish_gui-1.0.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: small_fish_gui
-Version: 1.0.1
+Version: 1.0.3
 Summary: Small Fish is a python application for the analysis of smFish images. It provides a ready to use graphical interface to combine famous python packages for cell analysis without any need for coding.
 Project-URL: Homepage, https://github.com/2Echoes/small_fish
 Project-URL: Issues, https://github.com/2Echoes/small_fish/issues

{small_fish_gui-1.0.1 → small_fish_gui-1.0.3}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "hatchling.build"
 
 [project]
 name = "small_fish_gui"
-version = "1.0.1"
+version = "1.0.3"
 authors = [
   { name="Slimani Floric", email="floric.slimani@live.com" },
 ]

small_fish_gui-1.0.3/src/small_fish_gui/.github/workflows/python-publish.yml

@@ -0,0 +1,39 @@
+# This workflow will upload a Python Package using Twine when a release is created
+# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python#publishing-to-package-registries
+
+# This workflow uses actions that are not certified by GitHub.
+# They are provided by a third-party and are governed by
+# separate terms of service, privacy policy, and support
+# documentation.
+
+name: Upload Python Package
+
+on:
+  release:
+    types: [published]
+
+permissions:
+  contents: read
+
+jobs:
+  deploy:
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v4
+    - name: Set up Python
+      uses: actions/setup-python@v3
+      with:
+        python-version: '3.x'
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install build
+    - name: Build package
+      run: python -m build
+    - name: Publish package
+      uses: pypa/gh-action-pypi-publish@27b31702a0e7fc50959f5ad993c78deac1bdfc29
+      with:
+        user: __token__
+        password: ${{ secrets.PYPI_API_TOKEN }}

small_fish_gui-1.0.3/src/small_fish_gui/LICENSE

@@ -0,0 +1,24 @@
+BSD 2-Clause License
+
+Copyright (c) 2023, Floric Slimani
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice, this
+   list of conditions and the following disclaimer.
+
+2. Redistributions in binary form must reproduce the above copyright notice,
+   this list of conditions and the following disclaimer in the documentation
+   and/or other materials provided with the distribution.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

small_fish_gui-1.0.3/src/small_fish_gui/README.md

@@ -0,0 +1,43 @@
+# Small Fish
+**Small Fish** is a python application for the analysis of smFish images. It provides a ready to use graphical interface to combine famous python packages for cell analysis without any need for coding.
+
+Cell segmentation is peformed using *cellpose* (published work) : https://github.com/MouseLand/cellpose
+
+Spot detection is performed via *big-fish* (published work) : https://github.com/fish-quant/big-fish
+
+Time stacks are not yet supported.
+
+## Installation
+
+It is higly recommanded to create a specific [conda](https://docs.conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html) or [virtual](https://docs.python.org/3.6/library/venv.html) environnement to install small fish.
+
+```bash
+conda create -n small_fish python=3.8
+activate small_fish
+```
+Then download the small_fish package : 
+```bash
+pip install small_fish_gui
+```
+<b> (Recommended) </b> Results visualisation is achieved through *Napari* which you can install with :
+
+```bash
+pip install napari[all]
+```
+
+## Run Small fish
+
+First activate your python environnement : 
+```bash
+activate small_fish
+```
+Then launch Small fish : 
+```bash
+python -m small_fish_gui
+```
+## Developpement
+
+Optional features to include in future versions : 
+- batch processing
+- time stack (which would include cell tracking)
+- 3D segmentation

{small_fish_gui-1.0.1 → small_fish_gui-1.0.3}/src/small_fish_gui/__main__.py

@@ -3,7 +3,7 @@ import os
 import PySimpleGUI as sg
 
 def main():
-    import small_fish.pipeline.main
+    import small_fish_gui.pipeline.main
 
 
 if __name__ == "__main__":

small_fish_gui-1.0.3/src/small_fish_gui/requirements.txt

@@ -0,0 +1,17 @@
+big-fish==0.6.2
+cellpose==3.0.7
+czifile==2019.7.2
+imageio==2.34.0
+napari==0.4.19.post1
+napari-console==0.0.9
+napari-plugin-engine==0.2.0
+napari-plugin-manager==0.1.0a2
+napari-svg==0.1.10
+numpy==1.24.4
+pandas==1.5.3
+PySimpleGUI==4.60.5
+scipy==1.9.1
+scikit-image==0.19.1
+scikit-learn==1.3.2
+openpyxl==3.1.2
+pyarrow==11.0.0