add napari-psf-analysis to env

README.md

@@ -1,11 +1,6 @@
 # M25-napari
 
-[![License](https://img.shields.io/pypi/l/m25-napari.svg?color=green)](https://github.com/SaraLab-Group/m25-napari/blob/main/LICENSE.md)
-[![PyPI](https://img.shields.io/pypi/v/m25-napari.svg?color=green)](https://pypi.org/project/m25-napari)
-[![Python Version](https://img.shields.io/pypi/pyversions/m25-napari.svg?color=green)](https://python.org)
-[![tests](https://github.com/SaraLab-Group/m25-napari/workflows/tests/badge.svg)](https://github.com/SaraLab-Group/m25-napari/actions)
-[![codecov](https://codecov.io/gh/SaraLab-Group/m25-napari/branch/main/graph/badge.svg)](https://codecov.io/gh/SaraLab-Group/m25-napari)
-[![napari hub](https://img.shields.io/endpoint?url=https://api.napari-hub.org/shields/m25-napari)](https://napari-hub.org/plugins/m25-napari)
+[![License](https://img.shields.io/badge/License-BSD_3--Clause-blue.svg)](https://opensource.org/licenses/BSD-3-Clause)
 [![DOI](https://zenodo.org/badge/443224520.svg)](https://zenodo.org/badge/latestdoi/443224520)
 
 ## 🦠🔬 25 plane-camera array mutlifocus microscopy (M25) Controls and Image Visualization 
@@ -28,12 +23,7 @@ https://napari.org/plugins/stable/index.html
 -->
 
 ## Installation
-This repository was tested with CUDA 11.2 and cuDNN 8.1 pre-installed on Windows 10. 
-You can install `m25-napari` via [pip]:
-
-    pip install m25-napari
-
-To install latest development version :
+This repository was tested with CUDA 11.2 and cuDNN 8.1 pre-installed on Windows 10. For install please use the latest development version :
 
     git clone https://github.com/SaraLab-Group/m25-napari.git
     cd m25-napari
@@ -46,7 +36,8 @@ Launch:
 ```python
 napari -w m25-napari
 ```
-The module can be run by running `napari`in the command line and selecting `m25-napari:M25 Controls` under Plugins. By Default, the demo mode is set which skips the connection to the PSoC Timing controller and the cameras and allows viewing of the GUI through Napari. If the user has setup the controller and cameras, the demo mode can be turned off by setting `demo_mode = False` in the file `src/visualizer/_widgetFunctions.py`. 
+
+The module can be run by running `napari` in the command line and selecting `m25-napari:M25 Controls` under Plugins or running `napari -w m25-napari`. By Default, the demo mode is set which skips the connection to the PSoC Timing controller and the cameras and allows viewing of the GUI through Napari. If the user has setup the controller and cameras, the demo mode can be turned off by setting `demo_mode = False` in the file `src/visualizer/_widgetFunctions.py`. 
 
 ## Contributing
 

environment.yml

@@ -80,7 +80,7 @@ dependencies:
       - magicgui==0.7.2
       - markdown-it-py==2.2.0
       - markupsafe==2.1.2
-      - matplotlib==3.5.2
+      - matplotlib
       - matplotlib-inline==0.1.6
       - mdurl==0.1.2
       - mistune==2.0.5
@@ -89,6 +89,7 @@ dependencies:
       - napari-console==0.0.8
       - napari-plugin-engine==0.2.0
       - napari-svg==0.1.7
+      - napari-psf-analysis
       - nbclassic==1.0.0
       - nbclient==0.8.0
       - nbconvert==7.4.0

setup.cfg

@@ -33,16 +33,6 @@ python_requires = >=3.8
 package_dir =
     =src
 
-# add your package requirements here
-install_requires =
-    numpy <=1.23
-    tifffile
-    zarr
-    napari >=0.4.13
-    matplotib
-    opencv-python-headless
-    cupy
-
 pyqt5 = 
     PyQt5
 [options.packages.find]
@@ -54,4 +44,4 @@ M25_napari =
 
 [options.entry_points] 
 napari.manifest = 
-    M25_napari = visualizer:napari.yml
+    M25_napari = visualizer:napari.yml

setup.py

@@ -1,5 +1,5 @@
-#!/usr/bin/env python
-# -*- coding: utf-8 -*-
-from setuptools import setup
-
-setup()
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+from setuptools import setup
+
+setup()

src/visualizer/_tests/test_widget.py

@@ -1,21 +1,21 @@
-
-import sys
-import os
-import pytest
-import visualizer
-
-# this is your plugin name declared in your napari.plugins entry point
-MY_PLUGIN_NAME = "m25-napari"
-# the name of your widget(s)
-MY_WIDGET_NAMES = ["M25Controls"]
-
-
-@pytest.mark.parametrize("widget_name", MY_WIDGET_NAMES)
-def test_something_with_viewer(widget_name, make_napari_viewer):
-    viewer = make_napari_viewer()
-    num_dw = len(viewer.window._dock_widgets)
-    viewer.window.add_plugin_dock_widget(
-        plugin_name=MY_PLUGIN_NAME, widget_name=widget_name
-    )
-    assert len(viewer.window._dock_widgets) == num_dw + 1
-
+
+import sys
+import os
+import pytest
+import visualizer
+
+# this is your plugin name declared in your napari.plugins entry point
+MY_PLUGIN_NAME = "m25-napari"
+# the name of your widget(s)
+MY_WIDGET_NAMES = ["M25Controls"]
+
+
+@pytest.mark.parametrize("widget_name", MY_WIDGET_NAMES)
+def test_something_with_viewer(widget_name, make_napari_viewer):
+    viewer = make_napari_viewer()
+    num_dw = len(viewer.window._dock_widgets)
+    viewer.window.add_plugin_dock_widget(
+        plugin_name=MY_PLUGIN_NAME, widget_name=widget_name
+    )
+    assert len(viewer.window._dock_widgets) == num_dw + 1
+