adding copyright to every py file

carsen-stringer · carsen-stringer · commit e17845e334ec · 2023-06-13T14:33:22.000-04:00
diff --git a/suite2p/__init__.py b/suite2p/__init__.py
@@ -1,3 +1,6 @@
+"""
+Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu.
+"""
 from .version import version
 from .default_ops import default_ops
 from .run_s2p import run_s2p, run_plane, pipeline
diff --git a/suite2p/__main__.py b/suite2p/__main__.py
@@ -1,3 +1,6 @@
+"""
+Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu.
+"""
 import argparse
 import numpy as np
 from suite2p import default_ops, version
diff --git a/suite2p/classification/__init__.py b/suite2p/classification/__init__.py
@@ -1,2 +1,5 @@
+"""
+Copright © 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
@@ -1,3 +1,6 @@
+"""
+Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu.
+"""
 import numpy as np
 from scipy.ndimage import gaussian_filter
 from sklearn.linear_model import LogisticRegression
diff --git a/suite2p/classification/classify.py b/suite2p/classification/classify.py
@@ -1,3 +1,6 @@
+"""
+Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu.
+"""
 import numpy as np
 from pathlib import Path
 from typing import Union, Sequence
diff --git a/suite2p/default_ops.py b/suite2p/default_ops.py
@@ -1,3 +1,6 @@
+"""
+Copright © 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
@@ -1,2 +1,5 @@
+"""
+Copright © 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
@@ -1,3 +1,6 @@
+"""
+Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu.
+"""
 import numpy as np
 from typing import Any, Dict
 from scipy.ndimage import find_objects, gaussian_filter
diff --git a/suite2p/detection/chan2detect.py b/suite2p/detection/chan2detect.py
@@ -1,3 +1,6 @@
+"""
+Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu.
+"""
 import numpy as np
 from scipy.ndimage import gaussian_filter
 from ..extraction import masks
diff --git a/suite2p/detection/denoise.py b/suite2p/detection/denoise.py
@@ -1,3 +1,6 @@
+"""
+Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu.
+"""
 import numpy as np
 from typing import List
 import time
diff --git a/suite2p/detection/detect.py b/suite2p/detection/detect.py
@@ -1,3 +1,6 @@
+"""
+Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu.
+"""
 import time
 import numpy as np
 from pathlib import Path
diff --git a/suite2p/detection/metrics.py b/suite2p/detection/metrics.py
@@ -1,3 +1,6 @@
+"""
+Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu.
+"""
 import time
 import numpy as np
 import cv2
diff --git a/suite2p/detection/sourcery.py b/suite2p/detection/sourcery.py
@@ -1,3 +1,6 @@
+"""
+Copright © 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
@@ -1,3 +1,6 @@
+"""
+Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu.
+"""
 from typing import Tuple, Dict, List, Any
 from copy import deepcopy
 from enum import Enum
diff --git a/suite2p/detection/stats.py b/suite2p/detection/stats.py
@@ -1,3 +1,6 @@
+"""
+Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu.
+"""
 from __future__ import annotations
 
 from typing import Tuple, Optional, NamedTuple, Sequence, List, Dict, Any
diff --git a/suite2p/detection/utils.py b/suite2p/detection/utils.py
@@ -1,3 +1,6 @@
+"""
+Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu.
+"""
 import numpy as np
 from numba import jit
 from scipy.optimize import linear_sum_assignment
diff --git a/suite2p/extraction/__init__.py b/suite2p/extraction/__init__.py
@@ -1,3 +1,6 @@
+"""
+Copright © 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
 from .masks import create_cell_mask, create_neuropil_masks, create_cell_pix
diff --git a/suite2p/extraction/dcnv.py b/suite2p/extraction/dcnv.py
@@ -1,3 +1,6 @@
+"""
+Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu.
+"""
 import numpy as np
 from numba import njit, prange
 from scipy.ndimage import maximum_filter1d, minimum_filter1d, gaussian_filter
diff --git a/suite2p/extraction/extract.py b/suite2p/extraction/extract.py
@@ -1,3 +1,6 @@
+"""
+Copright © 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
@@ -1,3 +1,6 @@
+"""
+Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu.
+"""
 from typing import List, Tuple, Dict, Any
 from itertools import count
 import numpy as np
diff --git a/suite2p/gui/__init__.py b/suite2p/gui/__init__.py
@@ -1 +1,4 @@
+"""
+Copright © 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
@@ -1,3 +1,6 @@
+"""
+Copright © 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
diff --git a/suite2p/gui/classgui.py b/suite2p/gui/classgui.py
@@ -1,3 +1,6 @@
+"""
+Copright © 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
@@ -1,3 +1,6 @@
+"""
+Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu.
+"""
 import os
 import time
 
diff --git a/suite2p/gui/graphics.py b/suite2p/gui/graphics.py
@@ -1,3 +1,6 @@
+"""
+Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu.
+"""
 import numpy as np
 import pyqtgraph as pg
 from PyQt5 import QtCore
diff --git a/suite2p/gui/gui2p.py b/suite2p/gui/gui2p.py
@@ -1,3 +1,6 @@
+"""
+Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu.
+"""
 import os, pathlib, shutil, sys, warnings
 
 import numpy as np
diff --git a/suite2p/gui/io.py b/suite2p/gui/io.py
@@ -1,3 +1,6 @@
+"""
+Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu.
+"""
 import os, time
 import numpy as np
 import scipy.io
diff --git a/suite2p/gui/masks.py b/suite2p/gui/masks.py
@@ -1,3 +1,6 @@
+"""
+Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu.
+"""
 from pathlib import Path
 import matplotlib.cm
 import numpy as np
diff --git a/suite2p/gui/menus.py b/suite2p/gui/menus.py
@@ -1,3 +1,6 @@
+"""
+Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu.
+"""
 from PyQt5 import QtGui
 from PyQt5.QtWidgets import QAction, QMenu
 from pkg_resources import iter_entry_points
diff --git a/suite2p/gui/merge.py b/suite2p/gui/merge.py
@@ -1,3 +1,6 @@
+"""
+Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu.
+"""
 import os
 import numpy as np
 import pyqtgraph as pg
diff --git a/suite2p/gui/reggui.py b/suite2p/gui/reggui.py
@@ -1,3 +1,6 @@
+"""
+Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu.
+"""
 # heavily modified script from a pyqt4 release
 import os
 import time
diff --git a/suite2p/gui/rungui.py b/suite2p/gui/rungui.py
@@ -1,3 +1,6 @@
+"""
+Copright © 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
@@ -1,3 +1,6 @@
+"""
+Copright © 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 QLabel, QComboBox, QPushButton, QLineEdit, QCheckBox
diff --git a/suite2p/gui/utils.py b/suite2p/gui/utils.py
@@ -1,3 +1,6 @@
+"""
+Copright © 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
@@ -1,3 +1,6 @@
+"""
+Copright © 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, QSlider, QButtonGroup, QLabel, QStyle, QStyleOptionSlider, QApplication
diff --git a/suite2p/gui/visualize.py b/suite2p/gui/visualize.py
@@ -1,3 +1,6 @@
+"""
+Copright © 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
@@ -1,3 +1,6 @@
+"""
+Copright © 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
 from .save import combined, compute_dydx, save_mat
diff --git a/suite2p/io/binary.py b/suite2p/io/binary.py
@@ -1,3 +1,6 @@
+"""
+Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu.
+"""
 from typing import Optional, Tuple, Sequence
 from contextlib import contextmanager
 import os
diff --git a/suite2p/io/h5.py b/suite2p/io/h5.py
@@ -1,3 +1,6 @@
+"""
+Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu.
+"""
 import math
 
 import h5py
diff --git a/suite2p/io/nd2.py b/suite2p/io/nd2.py
@@ -1,3 +1,6 @@
+"""
+Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu.
+"""
 import os
 import gc
 import math
diff --git a/suite2p/io/nwb.py b/suite2p/io/nwb.py
@@ -1,3 +1,6 @@
+"""
+Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu.
+"""
 import datetime
 import gc
 import os
diff --git a/suite2p/io/save.py b/suite2p/io/save.py
@@ -1,3 +1,6 @@
+"""
+Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu.
+"""
 import os
 from natsort import natsorted
 import numpy as np
diff --git a/suite2p/io/sbx.py b/suite2p/io/sbx.py
@@ -1,3 +1,6 @@
+"""
+Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu.
+"""
 import os
 
 import numpy as np
diff --git a/suite2p/io/server.py b/suite2p/io/server.py
@@ -1,3 +1,6 @@
+"""
+Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu.
+"""
 import sys, os, time, glob
 from pathlib import Path
 from natsort import natsorted
diff --git a/suite2p/io/tiff.py b/suite2p/io/tiff.py
@@ -1,3 +1,6 @@
+"""
+Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu.
+"""
 import gc
 import glob
 import json
diff --git a/suite2p/io/utils.py b/suite2p/io/utils.py
@@ -1,3 +1,6 @@
+"""
+Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu.
+"""
 import glob
 import os
 from pathlib import Path
diff --git a/suite2p/ops/clean.py b/suite2p/ops/clean.py
@@ -1,3 +1,6 @@
+"""
+Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu.
+"""
 import argparse
 
 import numpy as np
diff --git a/suite2p/registration/__init__.py b/suite2p/registration/__init__.py
@@ -1,3 +1,6 @@
+"""
+Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu.
+"""
 from .register import (registration_wrapper, save_registration_outputs_to_ops,
                        compute_enhanced_mean_image)
 from .metrics import get_pc_metrics
diff --git a/suite2p/registration/bidiphase.py b/suite2p/registration/bidiphase.py
@@ -1,3 +1,6 @@
+"""
+Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu.
+"""
 import numpy as np
 from numpy import fft
 
diff --git a/suite2p/registration/metrics.py b/suite2p/registration/metrics.py
@@ -1,3 +1,6 @@
+"""
+Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu.
+"""
 from multiprocessing import Pool
 
 import numpy as np
diff --git a/suite2p/registration/nonrigid.py b/suite2p/registration/nonrigid.py
@@ -1,3 +1,6 @@
+"""
+Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu.
+"""
 import warnings
 from typing import Tuple
 
diff --git a/suite2p/registration/register.py b/suite2p/registration/register.py
@@ -1,3 +1,6 @@
+"""
+Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu.
+"""
 import time
 from os import path
 from typing import Dict, Any
diff --git a/suite2p/registration/rigid.py b/suite2p/registration/rigid.py
@@ -1,3 +1,6 @@
+"""
+Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu.
+"""
 from typing import Tuple
 
 import numpy as np
diff --git a/suite2p/registration/utils.py b/suite2p/registration/utils.py
@@ -1,3 +1,6 @@
+"""
+Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu.
+"""
 import warnings
 from functools import lru_cache
 from typing import Tuple
diff --git a/suite2p/registration/zalign.py b/suite2p/registration/zalign.py
@@ -1,3 +1,6 @@
+"""
+Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu.
+"""
 import os
 import time
 
diff --git a/suite2p/run_s2p.py b/suite2p/run_s2p.py
@@ -1,3 +1,6 @@
+"""
+Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu.
+"""
 import os
 import shutil
 import time
diff --git a/suite2p/version.py b/suite2p/version.py
@@ -1,3 +1,6 @@
+"""
+Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu.
+"""
 from importlib_metadata import metadata as _metadata
 
 version = _metadata("suite2p")["version"]

-Original file line number
+Diff line change
@@ @@ -1,3 +1,6 @@ @@
 +"""
 +Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu.
 +"""
 from .version import version