Fix for dependencies

.gitignore

@@ -1,4 +1,5 @@
 *egg-info
 .DS_Store
 *.toml
-*__pycache__*
+*__pycache__*
+build/

MANIFEST.in

@@ -0,0 +1 @@
+include eats_worm/napari.yaml

README.md

@@ -3,7 +3,7 @@
 
 
 ### Installation Instructions
-1. Setup your development environment. If you need help with this, there are many resources on Google. Most people in the lab use Conda as a package manager and develop in Conda virtual environments as well. 
+1. Setup your development environment. If you need help with this, there are many resources on Google. Most people in the lab use Conda as a package manager and develop in Conda virtual environments as well. Python versions 3.10-3.13 are recommended. 3.8-3.9 seem to work with minor graphical bugs in Napari but we cannot guarantee consistent results for these versions.
 
 2. Start your virtual environment, and run the command
 ```bash

eats_worm/Curator.py

@@ -155,8 +155,13 @@ def restart(self):
             edge_width_is_relative=False
             point_symbol = 'disc'
             face_color = np.array([0,0,0,0])
-            self.viewer.add_points(np.empty((0, 3)), symbol=point_symbol, face_color=face_color, edge_color='red', name='roi', size=point_size+1, scale=self.scale, edge_width=edge_width*1.25, edge_width_is_relative=edge_width_is_relative)
-            self.other_rois = self.viewer.add_points(np.empty((0, 3)), symbol=point_symbol, face_color=face_color, edge_color='green', name='other rois', size=point_size, scale=self.scale, edge_width=edge_width, edge_width_is_relative=edge_width_is_relative)
+            try:
+                self.viewer.add_points(np.empty((0, 3)), symbol=point_symbol, face_color=face_color, border_color='red', name='roi', size=point_size+1, scale=self.scale, border_width=edge_width*1.25, border_width_is_relative=edge_width_is_relative)
+                self.other_rois = self.viewer.add_points(np.empty((0, 3)), symbol=point_symbol, face_color=face_color, border_color='green', name='other rois', size=point_size, scale=self.scale, border_width=edge_width, border_width_is_relative=edge_width_is_relative)
+
+            except:
+                self.viewer.add_points(np.empty((0, 3)), symbol=point_symbol, face_color=face_color, edge_color='red', name='roi', size=point_size+1, scale=self.scale, edge_width=edge_width*1.25, edge_width_is_relative=edge_width_is_relative)
+                self.other_rois = self.viewer.add_points(np.empty((0, 3)), symbol=point_symbol, face_color=face_color, edge_color='green', name='other rois', size=point_size, scale=self.scale, edge_width=edge_width, edge_width_is_relative=edge_width_is_relative)
 
             if self.curator_layers:
                 for layer in self.curator_layers.keys():
@@ -741,7 +746,7 @@ def add_roi(self, position, t):
             self.num_neurons += 1
             print('Saving blob timeseries as numpy object...')
             self.e.timeseries = np.hstack((self.e.timeseries, np.empty((self.e.timeseries.shape[0], 1))))
-            self.e.timeseries[:,-1] = np.NaN
+            self.e.timeseries[:,-1] = np.nan
             self.e.spool.export(f=os.path.join(self.e.output_dir, 'threads.obj'))
             self.e.save_timeseries()
             self.e.save_dataframe()

eats_worm/Extractor.py

@@ -67,7 +67,7 @@ def background_subtraction_quant_function(im, spool, t, frames, quant_radius=3,
     activity: list
         list of quantifications corresponding to the positions specified
     """
-    intensities = [np.NaN] * len(spool.threads)
+    intensities = [np.nan] * len(spool.threads)
     positions = spool.get_positions_t(t, indices=threads_to_quantify)
     positions = np.rint(np.copy(positions)).astype(int)
     max_z = len(frames) # in case of max_x, max_y, max_z, we're using these as indices so don't subtract 1 because slicing is exclusive 
@@ -234,13 +234,13 @@ def quantify(mft=None, extractor=None, quant_function=background_subtraction_qua
             print(e)
 
     timeseries = np.empty((num_t,num_threads))
-    timeseries[:] = np.NaN
+    timeseries[:] = np.nan
     quantified_voxels = {i: {} for i in range(num_threads)}
     quant_lock = Lock()
     processed_counter = [0]
     def quantify_in_parallel_thread(start, stop):
         thread_timeseries = np.empty((stop - start, num_threads))
-        thread_timeseries[:] = np.NaN
+        thread_timeseries[:] = np.nan
         thread_quantified_voxels = None
         if save_quantification_voxels:
             thread_quantified_voxels = {i: {} for i in range(num_threads)}

eats_worm/Threads.py

@@ -438,7 +438,7 @@ def __init__(self, position = [], t = 0, **kwargs):
         self.found = np.zeros((maxt))
         #self.positions = []
         self.t = []
-        if position != []:
+        if list(position) != []:
             self.positions[t] = np.array(position)
             #self.t = t + 1
             #self.positions.append(np.array(position))

pyproject.toml

@@ -1,5 +1,55 @@
 [build-system]
-build-backend = 'setuptools.build_meta'
-requires = [
-    'setuptools',
-]
+requires = ["setuptools>=61.0"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "eats-worm"
+version = "0.0.3"
+requires-python = "<3.14"
+description = "Method for extracting GCaMP signal from volumetric imaging recordings"
+readme = "README.md"
+authors = [
+  {name = "UCSF FOCO Lab", email = "focolabdev@gmail.com"}
+]
+license = {text = "MIT License"}
+classifiers = [
+    "Programming Language :: Python :: 3",
+    "Framework :: napari",
+    "License :: OSI Approved :: MIT License",
+    "Operating System :: OS Independent",
+]
+dependencies = [
+    "numpy",
+    "scipy",
+    "tifffile",
+    "opencv-python-headless",
+    "matplotlib",
+    "foco-improc",
+    "npex @ git+https://github.com/focolab/npex",
+    "ndx-multichannel-volume @ git+https://github.com/focolab/ndx-multichannel-volume",
+    "imreg_dft",
+    "fastcluster==1.3.0; python_version >= '3.9'",
+    "fastcluster==1.2.6; python_version < '3.9'",
+    "pyqtgraph",
+    "magicgui",
+    "pandas",
+    "scikit-image",
+    "xmltodict",
+    "pynwb",
+    "nwbinspector",
+    "dandi",
+    "remfile",
+    # MacOS (Darwin) specific dependencies
+    "pyqt6; sys_platform == 'darwin'",
+    "napari[pyqt6_experimental]; sys_platform == 'darwin'",
+    # Linux/Windows specific dependencies
+    "napari[all]; sys_platform != 'darwin' and python_version >= '3.8'",
+    "napari; python_version < '3.8'"
+]
+
+[project.entry-points."napari.manifest"]
+eats-worm = "eats_worm:napari.yaml"
+
+[tool.setuptools]
+packages = ["eats_worm"] 
+include-package-data = true