Merge pull request #1014 from MouseLand/pyqt6

adding pyqt6 and switching to qtpy
MouseLand · Aug 6, 2023 · 095cb66 · 095cb66
2 parents e1f99be + 8304f59
commit 095cb66
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diff --git a/.github/workflows/test_and_deploy.yml b/.github/workflows/test_and_deploy.yml
@@ -41,7 +41,8 @@ jobs:
           sudo apt-get update
           sudo apt-get install -y libdbus-1-3 libxkbcommon-x11-0 libxcb-icccm4 \
             libxcb-image0 libxcb-keysyms1 libxcb-randr0 libxcb-render-util0 \
-            libxcb-xinerama0 libxcb-xinput0 libxcb-xfixes0 pkg-config libhdf5-103 libhdf5-dev
+            libxcb-xinerama0 libxcb-xinput0 libxcb-xfixes0 pkg-config libhdf5-103 libhdf5-dev \
+            libegl1
       # strategy borrowed from vispy for installing opengl libs on windows
       - name: Install Windows OpenGL
         if: runner.os == 'Windows'

diff --git a/README.md b/README.md
@@ -27,10 +27,9 @@ suite2p includes the following modules:
 
 This code was written by Carsen Stringer and Marius Pachitariu.
 For support, please open an [issue](https://github.com/MouseLand/suite2p/issues).
-The reference paper is [here](https://www.biorxiv.org/content/early/2017/07/20/061507).
-The deconvolution algorithm is based on [this paper](https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1005423), with settings based on [this paper](http://www.jneurosci.org/content/early/2018/08/06/JNEUROSCI.3339-17.2018).
+The reference paper is [here](https://www.biorxiv.org/content/early/2017/07/20/061507). The deconvolution algorithm is based on [this paper](https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1005423), with settings based on [this paper](http://www.jneurosci.org/content/early/2018/08/06/JNEUROSCI.3339-17.2018).
 
-You can now run suite2p in google colab, no need to locally install: [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/MouseLand/suite2p/blob/main/jupyter/run_suite2p_colab_2021.ipynb). Note you do not have access to the GUI via google colab, but you can download the processed files and view them locally in the GUI.
+You can now run suite2p in google colab, no need to locally install (although we recommend doing so eventually): [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/MouseLand/suite2p/blob/main/jupyter/run_suite2p_colab_2021.ipynb). Note you do not have access to the GUI via google colab, but you can download the processed files and view them locally in the GUI.
 
 See this **twitter [thread](https://twitter.com/marius10p/status/1032804776633880583)** for GUI demonstrations.
 
@@ -47,9 +46,8 @@ Pachitariu, M., Stringer, C., Schröder, S., Dipoppa, M., Rossi, L. F., Carandin
 
 ## Read the Documentation at https://suite2p.readthedocs.io/
 
-## Installation
+## Local installation
 
-### <a name="installation_section"></a> Installation for Linux, Windows, and MacOS (intel processors) machines
 1. Install an [Anaconda](https://www.anaconda.com/download/) distribution of Python -- Choose **Python 3.8** and your operating system. Note you might need to use an anaconda prompt if you did not add anaconda to the path.
 2. Open an anaconda prompt / command prompt with `conda` for **python 3** in the path
 3. Create a new environment with `conda create --name suite2p python=3.9`.
@@ -61,8 +59,6 @@ Pachitariu, M., Stringer, C., Schröder, S., Dipoppa, M., Rossi, L. F., Carandin
 
 For additional dependencies, like h5py, NWB, Scanbox, and server job support, use the command `python -m pip install suite2p[io]`.
 
-We recommend installing ScanImage Tiff Reader with `pip install scanimage-tiff-reader`.
-
 If you have an older `suite2p` environment you can remove it with `conda env remove -n suite2p` before creating a new one.
 
 Note you will always have to run **conda activate suite2p** before you run suite2p. Conda ensures mkl_fft and numba run correctly and quickly on your machine. If you want to run jupyter notebooks in this environment, then also `conda install jupyter`.
@@ -72,11 +68,11 @@ To **upgrade** the suite2p (package [here](https://pypi.org/project/suite2p/)),
 pip install --upgrade suite2p
 ~~~~
 
-### Installation for Macs with Apple Silicon chips (e.g., M1)
-1. Follow steps 1 & 2 in the installation section [above](#installation_section) to install anaconda.
-2. Use the following command `CONDA_SUBDIR=osx-64 conda create --name suite2p python=3.9`
-3. Follow steps 4-7 in the installation section [above](#installation_section) to install the `suite2p` package.
+### Dependencies
+
+This package relies on the awesomeness of [pyqtgraph](http://pyqtgraph.org/), [PyQt6](http://pyqt.sourceforge.net/Docs/PyQt6/), [torch](http://pytorch.org), [numpy](http://www.numpy.org/), [numba](http://numba.pydata.org/numba-doc/latest/user/5minguide.html), [scanimage-tiff-reader](https://vidriotech.gitlab.io/scanimagetiffreader-python/), [scipy](https://www.scipy.org/), [scikit-learn](http://scikit-learn.org/stable/), [tifffile](https://pypi.org/project/tifffile/), [natsort](https://natsort.readthedocs.io/en/master/), and our neural visualization tool [rastermap](https://github.com/MouseLand/rastermap). You can pip install or conda install all of these packages. If having issues with PyQt6, then try to install within it conda install pyqt. On Ubuntu you may need to `sudo apt-get install libegl1` to support PyQt6. Alternatively, you can use PyQt5 by running `pip uninstall PyQt6` and `pip install PyQt5`. If you already have a PyQt version installed, suite2p will not install a new one.
 
+The software has been heavily tested on Windows 10 and Ubuntu 18.04, and less well tested on Mac OS. Please post an [issue](https://github.com/MouseLand/suite2p/issues) if you have installation problems. 
 
 ### Installing the latest github version of the code
 
@@ -89,13 +85,8 @@ If you want to download and edit the code, and use that version,
 1. Clone the repository with git and `cd suite2p`
 2. Run `pip install -e .` in that folder
 
-**Common issues**
-
-If you are on Yosemite Mac OS, PyQt doesn't work, and you won't be able to install suite2p. More recent versions of Mac OS are fine.
 
-The software has been heavily tested on Windows 10 and Ubuntu 18.04, and less well tested on Mac OS. Please post an issue if you have installation problems. The registration step runs faster on Ubuntu than Windows, so if you have a choice we recommend using the Ubuntu OS.
-
-## Installation for developers
+### Installation for developers
 
 1. Clone the repository and `cd suite2p` in an anaconda prompt / command prompt with `conda` for **python 3** in the path
 2. Run `conda env create --name suite2p`
@@ -167,7 +158,7 @@ from suite2p.run_s2p import run_s2p
 ops1 = run_s2p(ops, db)
 ~~~~
 
-See our example jupyter notebook [here](jupyter/run_pipeline_tiffs_or_batch.ipynb). It also explains how to batch-run suite2p.
+See our example jupyter notebook [here](https://github.com/MouseLand/suite2p/blob/main/jupyter/run_suite2p_colab_2023.ipynb).
 
 ## Outputs
 
@@ -180,19 +171,11 @@ ops.npy: options and intermediate outputs
 iscell.npy: specifies whether an ROI is a cell, first column is 0/1, and second column is probability that the ROI is a cell based on the default classifier
 ~~~~
 
-## Dependencies
-suite2p relies on the following excellent packages (which are automatically installed with conda/pip if missing):
-- [rastermap](https://github.com/MouseLand/rastermap)
-- [pyqtgraph](http://pyqtgraph.org/)
-- [PyQt5](http://pyqt.sourceforge.net/Docs/PyQt5/)
-- [torch](http://pytorch.org)
-- [numpy](http://www.numpy.org/) (>=1.16.0)
-- [numba](http://numba.pydata.org/numba-doc/latest/user/5minguide.html)
-- [scanimage-tiff-reader](https://vidriotech.gitlab.io/scanimagetiffreader-python/)
-- [scipy](https://www.scipy.org/)
-- [scikit-learn](http://scikit-learn.org/stable/)
-- [tifffile](https://pypi.org/project/tifffile/)
-- [natsort](https://natsort.readthedocs.io/en/master/)
+# License
+
+Copyright (C) 2023 Howard Hughes Medical Institute Janelia Research Campus, the labs of Carsen Stringer and Marius Pachitariu.
+
+**This code is licensed under GPL v3 (no redistribution without credit, and no redistribution in private repos, see the [license](LICENSE) for more details).**
 
 ### Logo
 Logo was designed by Shelby Stringer and [Chris Czaja](http://chrisczaja.com/).
diff --git a/setup.py b/setup.py
@@ -11,17 +11,17 @@
         "scipy>=1.9.0",
         "scikit-learn",
         "cellpose",
+        "scanimage-tiff-reader>=1.4.1"
         ]
 
 gui_deps = [
-        "pyqt5",
-        "pyqt5-tools",
-        "pyqt5.sip",
+        "qtpy",
+        "pyqt6",
+        "pyqt6.sip",
         "pyqtgraph",
       ]
 
 io_deps = [
-    "scanimage-tiff-reader>=1.4.1",
     "paramiko",
     "nd2",
     "sbxreader",

diff --git a/suite2p/__init__.py b/suite2p/__init__.py
@@ -1,5 +1,5 @@
 """
-Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu.
+Copyright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu.
 """
 from .version import version
 from .default_ops import default_ops

diff --git a/suite2p/__main__.py b/suite2p/__main__.py
@@ -1,5 +1,5 @@
 """
-Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu.
+Copyright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu.
 """
 import argparse
 import numpy as np

diff --git a/suite2p/classification/__init__.py b/suite2p/classification/__init__.py
@@ -1,5 +1,5 @@
 """
-Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu.
+Copyright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu.
 """
 from .classifier import Classifier
 from .classify import classify, builtin_classfile, user_classfile
diff --git a/suite2p/classification/classifier.py b/suite2p/classification/classifier.py
@@ -1,5 +1,5 @@
 """
-Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu.
+Copyright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu.
 """
 import numpy as np
 from scipy.ndimage import gaussian_filter

diff --git a/suite2p/classification/classify.py b/suite2p/classification/classify.py
@@ -1,5 +1,5 @@
 """
-Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu.
+Copyright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu.
 """
 import numpy as np
 from pathlib import Path

diff --git a/suite2p/default_ops.py b/suite2p/default_ops.py
@@ -1,5 +1,5 @@
 """
-Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu.
+Copyright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu.
 """
 from .version import version
 

diff --git a/suite2p/detection/__init__.py b/suite2p/detection/__init__.py
@@ -1,5 +1,5 @@
 """
-Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu.
+Copyright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu.
 """
 from .detect import detect, detection_wrapper, bin_movie
 from .stats import roi_stats, ROI
diff --git a/suite2p/detection/anatomical.py b/suite2p/detection/anatomical.py
@@ -1,5 +1,5 @@
 """
-Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu.
+Copyright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu.
 """
 import numpy as np
 from typing import Any, Dict

diff --git a/suite2p/detection/chan2detect.py b/suite2p/detection/chan2detect.py
@@ -1,5 +1,5 @@
 """
-Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu.
+Copyright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu.
 """
 import numpy as np
 from scipy.ndimage import gaussian_filter

diff --git a/suite2p/detection/denoise.py b/suite2p/detection/denoise.py
@@ -1,5 +1,5 @@
 """
-Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu.
+Copyright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu.
 """
 import numpy as np
 from typing import List

diff --git a/suite2p/detection/detect.py b/suite2p/detection/detect.py
@@ -1,5 +1,5 @@
 """
-Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu.
+Copyright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu.
 """
 import time
 import numpy as np

diff --git a/suite2p/detection/metrics.py b/suite2p/detection/metrics.py
@@ -1,5 +1,5 @@
 """
-Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu.
+Copyright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu.
 """
 import time
 import numpy as np

diff --git a/suite2p/detection/sourcery.py b/suite2p/detection/sourcery.py
@@ -1,5 +1,5 @@
 """
-Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu.
+Copyright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu.
 """
 import math
 import time

diff --git a/suite2p/detection/sparsedetect.py b/suite2p/detection/sparsedetect.py
@@ -1,5 +1,5 @@
 """
-Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu.
+Copyright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu.
 """
 from typing import Tuple, Dict, List, Any
 from copy import deepcopy

diff --git a/suite2p/detection/stats.py b/suite2p/detection/stats.py
@@ -1,5 +1,5 @@
 """
-Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu.
+Copyright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu.
 """
 from __future__ import annotations
 

diff --git a/suite2p/detection/utils.py b/suite2p/detection/utils.py
@@ -1,5 +1,5 @@
 """
-Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu.
+Copyright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu.
 """
 import numpy as np
 from numba import jit

diff --git a/suite2p/extraction/__init__.py b/suite2p/extraction/__init__.py
@@ -1,5 +1,5 @@
 """
-Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu.
+Copyright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu.
 """
 from .dcnv import preprocess, oasis
 from .extract import create_masks_and_extract, enhanced_mean_image, extract_traces_from_masks, extraction_wrapper

diff --git a/suite2p/extraction/dcnv.py b/suite2p/extraction/dcnv.py
@@ -1,5 +1,5 @@
 """
-Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu.
+Copyright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu.
 """
 import numpy as np
 from numba import njit, prange

diff --git a/suite2p/extraction/extract.py b/suite2p/extraction/extract.py
@@ -1,5 +1,5 @@
 """
-Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu.
+Copyright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu.
 """
 import os
 import time

diff --git a/suite2p/extraction/masks.py b/suite2p/extraction/masks.py
@@ -1,5 +1,5 @@
 """
-Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu.
+Copyright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu.
 """
 from typing import List, Tuple, Dict, Any
 from itertools import count

diff --git a/suite2p/gui/__init__.py b/suite2p/gui/__init__.py
@@ -1,4 +1,4 @@
 """
-Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu.
+Copyright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu.
 """
 from .gui2p import run
diff --git a/suite2p/gui/buttons.py b/suite2p/gui/buttons.py
@@ -1,9 +1,9 @@
 """
-Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu.
+Copyright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu.
 """
 import numpy as np
-from PyQt5 import QtGui, QtCore
-from PyQt5.QtWidgets import QPushButton, QButtonGroup, QLabel, QLineEdit
+from qtpy import QtGui, QtCore
+from qtpy.QtWidgets import QPushButton, QButtonGroup, QLabel, QLineEdit
 
 
 def make_selection(parent):

diff --git a/suite2p/gui/classgui.py b/suite2p/gui/classgui.py
@@ -1,12 +1,12 @@
 """
-Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu.
+Copyright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu.
 """
 import os
 import shutil
 
 import numpy as np
-from PyQt5 import QtGui
-from PyQt5.QtWidgets import QDialog, QLabel, QPushButton, QMessageBox, QFileDialog, QListWidget, QGridLayout, QWidget, QAbstractItemView
+from qtpy import QtGui
+from qtpy.QtWidgets import QDialog, QLabel, QPushButton, QMessageBox, QFileDialog, QListWidget, QGridLayout, QWidget, QAbstractItemView
 
 from . import masks
 from .. import classification

diff --git a/suite2p/gui/drawroi.py b/suite2p/gui/drawroi.py
@@ -1,13 +1,13 @@
 """
-Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu.
+Copyright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu.
 """
 import os
 import time
 
 import numpy as np
 import pyqtgraph as pg
-from PyQt5 import QtGui, QtCore
-from PyQt5.QtWidgets import QPushButton, QLabel, QLineEdit, QMainWindow, QGridLayout, QButtonGroup, QMessageBox, QWidget
+from qtpy import QtGui, QtCore
+from qtpy.QtWidgets import QPushButton, QLabel, QLineEdit, QMainWindow, QGridLayout, QButtonGroup, QMessageBox, QWidget
 from matplotlib.colors import hsv_to_rgb
 from scipy import stats
 

diff --git a/suite2p/gui/graphics.py b/suite2p/gui/graphics.py
@@ -1,9 +1,9 @@
 """
-Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu.
+Copyright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu.
 """
 import numpy as np
 import pyqtgraph as pg
-from PyQt5 import QtCore
+from qtpy import QtCore
 from pyqtgraph import Point
 from pyqtgraph import functions as fn
 from pyqtgraph.graphicsItems.ViewBox.ViewBoxMenu import ViewBoxMenu

diff --git a/suite2p/gui/gui2p.py b/suite2p/gui/gui2p.py
@@ -1,12 +1,12 @@
 """
-Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu.
+Copyright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu.
 """
 import os, pathlib, shutil, sys, warnings
 
 import numpy as np
 import pyqtgraph as pg
-from PyQt5 import QtGui, QtCore
-from PyQt5.QtWidgets import QMainWindow, QApplication, QWidget, QGridLayout, QCheckBox, QLineEdit, QLabel
+from qtpy import QtGui, QtCore
+from qtpy.QtWidgets import QMainWindow, QApplication, QWidget, QGridLayout, QCheckBox, QLineEdit, QLabel
 
 from . import menus, io, merge, views, buttons, classgui, traces, graphics, masks
 from .. import run_s2p, default_ops

diff --git a/suite2p/gui/io.py b/suite2p/gui/io.py
@@ -1,11 +1,11 @@
 """
-Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu.
+Copyright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu.
 """
 import os, time
 import numpy as np
 import scipy.io
-from PyQt5 import QtGui
-from PyQt5.QtWidgets import QFileDialog, QMessageBox
+from qtpy import QtGui
+from qtpy.QtWidgets import QFileDialog, QMessageBox
 
 from . import utils, masks, views, graphics, traces, classgui
 from .. import io

diff --git a/suite2p/gui/masks.py b/suite2p/gui/masks.py
@@ -1,12 +1,12 @@
 """
-Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu.
+Copyright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu.
 """
 from pathlib import Path
 import matplotlib.cm
 import numpy as np
 import pyqtgraph as pg
-from PyQt5 import QtGui, QtCore
-from PyQt5.QtWidgets import QPushButton, QButtonGroup, QLabel, QComboBox, QLineEdit
+from qtpy import QtGui, QtCore
+from qtpy.QtWidgets import QPushButton, QButtonGroup, QLabel, QComboBox, QLineEdit
 from matplotlib.colors import hsv_to_rgb
 
 import suite2p.gui.merge

diff --git a/suite2p/gui/menus.py b/suite2p/gui/menus.py
@@ -1,8 +1,8 @@
 """
-Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu.
+Copyright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu.
 """
-from PyQt5 import QtGui
-from PyQt5.QtWidgets import QAction, QMenu
+from qtpy import QtGui
+from qtpy.QtWidgets import QAction, QMenu
 from pkg_resources import iter_entry_points
 
 from . import reggui, drawroi, merge, io, rungui, visualize, classgui