MouseLand · yarikoptic · Jul 28, 2023 · Jul 28, 2023 · Jul 28, 2023 · Jul 28, 2023
diff --git a/.codespellrc b/.codespellrc
@@ -0,0 +1,4 @@
+[codespell]
+skip = .git,*.pdf,*.svg
+ignore-regex = ("image/png": *".*|hSI)
+ignore-words-list = iterm,bloaded
diff --git a/.github/workflows/codespell.yml b/.github/workflows/codespell.yml
@@ -0,0 +1,22 @@
+---
+name: Codespell
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+
+permissions:
+  contents: read
+
+jobs:
+  codespell:
+    name: Check for spelling errors
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v3
+      - name: Codespell
+        uses: codespell-project/actions-codespell@v2
diff --git a/conftest.py b/conftest.py
@@ -37,7 +37,7 @@ def download_cached_inputs(data_path):
         extract_zip(data_path.joinpath('test_inputs.zip'), cached_inputs_url, data_path)
 
 def initialize_ops(tmpdir, data_dir):
-    """Initializes ops. Used for both the test_ops function above and for generate_test_data script. This function was made to accomodate creation of ops for both pytest and non-pytest settings."""
+    """Initializes ops. Used for both the test_ops function above and for generate_test_data script. This function was made to accommodate creation of ops for both pytest and non-pytest settings."""
     ops = suite2p.default_ops()
     ops.update(
         {

diff --git a/docs/settings.rst b/docs/settings.rst
@@ -54,7 +54,7 @@ These are the essential settings that are dataset-specific.
 File input/output settings
 ~~~~~~~~~~~~~~~~~~~~~~~~~~
 
-Suite2p can accomodate many different file formats. Refer to this
+Suite2p can accommodate many different file formats. Refer to this
 :ref:`page <inputs-diff-file-types>` for a detailed list of formats suite2p can work with. 
 
 - **fast_disk**: (*list[str], default: empty list*) specifies location where temporary binary file will be stored. Defaults to ``save_path0`` if no directory is provided by user. 

diff --git a/helpers/loadFramesBuff.m b/helpers/loadFramesBuff.m
@@ -2,7 +2,7 @@
 %loadFrames Loads the frames of a Tiff file into an array (Y,X,T)
 %   MOVIE = loadFrames(TIFF, [FIRST], [LAST], [STRIDE], []) loads
 %   frames from the Tiff file specified by TIFF, which should be a filename
-%   or an already open Tiff object. Optionallly FIRST, LAST and STRIDE
+%   or an already open Tiff object. Optionally FIRST, LAST and STRIDE
 %   specify the range of frame indices to load.
 
 if nargin>4 && ~isempty(temp_file)

diff --git a/helpers/make_json_config.m b/helpers/make_json_config.m
@@ -19,7 +19,7 @@ function make_json_config(root)
 % fs = hSI.hRoiManager.scanVolumeRate;
 %     fs = 5;
 
-% get relevant infomation for TIFF header
+% get relevant information for TIFF header
 artist_info     = header(1).Artist;
 
 % retrieve ScanImage ROIs information from json-encoded string

diff --git a/helpers/mesoscope_json_from_scanimage.m b/helpers/mesoscope_json_from_scanimage.m
@@ -20,7 +20,7 @@
     fs = 4;
 end
 
-% get relevant infomation for TIFF header
+% get relevant information for TIFF header
 artist_info     = header(1).Artist;
 
 % retrieve ScanImage ROIs information from json-encoded string 

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
@@ -241,7 +241,7 @@ def two_comps(mpix0, lam, Th2):
 
 
 def extend_mask(ypix, xpix, lam, Ly, Lx):
-    """ extend mask into 8 surrrounding pixels """
+    """ extend mask into 8 surrounding pixels """
     nel = len(xpix)
     yx = ((ypix, ypix, ypix, ypix - 1, ypix - 1, ypix - 1, ypix + 1, ypix + 1,
            ypix + 1), (xpix, xpix + 1, xpix - 1, xpix, xpix + 1, xpix - 1, xpix,

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
 
@@ -87,7 +87,7 @@ def stats_dicts_to_3d_array(cls, stats: Sequence[Dict[str, Any]], Ly: int, Lx: i
         stats : List of dictionary "ypix", "xpix", "lam"
         Ly : y size of frame
         Lx : x size of frame
-        label_id : whether array should be an integer value indicating ROI id or just 1 (indicating precence of ROI).
+        label_id : whether array should be an integer value indicating ROI id or just 1 (indicating presence of ROI).
         """
         arrays = []
         for i, stat in enumerate(stats):

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
@@ -1,5 +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 PyQt5 import QtGui, QtCore

diff --git a/suite2p/gui/classgui.py b/suite2p/gui/classgui.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 shutil

diff --git a/suite2p/gui/drawroi.py b/suite2p/gui/drawroi.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
@@ -233,7 +233,7 @@ def closeEvent(self, event):
     def check_proc(self, event):
         cproc = QMessageBox.question(
             self, "PROC",
-            "Would you like to save traces before closing? (if you havent extracted the traces, click Cancel and extract!)",
+            "Would you like to save traces before closing? (if you haven't extracted the traces, click Cancel and extract!)",
             QMessageBox.Yes | QMessageBox.No | QMessageBox.Cancel)
         if cproc == QMessageBox.Yes:
             self.close_GUI()

diff --git a/suite2p/gui/graphics.py b/suite2p/gui/graphics.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
 import pyqtgraph as pg

diff --git a/suite2p/gui/gui2p.py b/suite2p/gui/gui2p.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, pathlib, shutil, sys, warnings
 

diff --git a/suite2p/gui/io.py b/suite2p/gui/io.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, time
 import numpy as np

diff --git a/suite2p/gui/masks.py b/suite2p/gui/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 pathlib import Path
 import matplotlib.cm

diff --git a/suite2p/gui/menus.py b/suite2p/gui/menus.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 PyQt5 import QtGui
 from PyQt5.QtWidgets import QAction, QMenu

diff --git a/suite2p/gui/merge.py b/suite2p/gui/merge.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 numpy as np

diff --git a/suite2p/gui/reggui.py b/suite2p/gui/reggui.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.
 """
 # heavily modified script from a pyqt4 release
 import os

diff --git a/suite2p/gui/rungui.py b/suite2p/gui/rungui.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 glob, json, os, shutil, pathlib
 from datetime import datetime

diff --git a/suite2p/gui/traces.py b/suite2p/gui/traces.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 PyQt5 import QtGui, QtCore

diff --git a/suite2p/gui/utils.py b/suite2p/gui/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 scipy.ndimage.morphology import binary_dilation, binary_fill_holes

diff --git a/suite2p/gui/views.py b/suite2p/gui/views.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 PyQt5 import QtGui, QtCore

diff --git a/suite2p/gui/visualize.py b/suite2p/gui/visualize.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 sys
 import time

diff --git a/suite2p/io/__init__.py b/suite2p/io/__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 .h5 import h5py_to_binary
 from .nwb import save_nwb, read_nwb, nwb_to_binary

diff --git a/suite2p/io/binary.py b/suite2p/io/binary.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 Optional, Tuple, Sequence
 from contextlib import contextmanager

diff --git a/suite2p/io/h5.py b/suite2p/io/h5.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
 

diff --git a/suite2p/io/nd2.py b/suite2p/io/nd2.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 gc

diff --git a/suite2p/io/nwb.py b/suite2p/io/nwb.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 datetime
 import gc

diff --git a/suite2p/io/save.py b/suite2p/io/save.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
 from natsort import natsorted