fixes to get docs building by github action #210
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Changes included moving the host to ubuntu 20 and python 3.8 so the latest version of wxpython could be pulled down without needing to be built. |
retiutut
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Oct 24, 2022
retiutut
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Oct 24, 2022
| axs[1].plot(freq2, psd2_mean[4, :], color='r', label='20 Hz') | ||
| # TODO fix: IndexError: index 4 is out of bounds for axis 0 with size 4 | ||
| # axs[1].plot(freq1, psd1_mean[4, :], color='b', label='30 Hz') | ||
| # axs[1].plot(freq2, psd2_mean[4, :], color='r', label='20 Hz') |
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Commenting out these lines of code is out of the scope of "Fixing the Docs" and messes with a visualization for SSVEP. This should be reverted and changed in another PR.
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Unfortunately the docs won't build without the change, I think I noticed the same issue a long time ago when trying to run the example locally. Would you be able to help me figure out why it is giving the out of bounds error?
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The problem seems to be that this line
>> psd1, freq1 = psd_welch(epochs['30 Hz'], n_fft=1028, n_per_seg=256 * 3, picks='all')Is returning only 4 chans in its output object, whereas in this example there are 5 chans used (i.e. a muse 2016 with one extra auxiliary electrode over occipital cortex).
>> psd1.shape
>> (105, 4, 129)Trying to determine why this is happening...
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Ok got it: the channel type for the Aux electrode is not 'eeg'
In [83]: raw.ch_names
Out[83]: ['TP9', 'AF7', 'AF8', 'TP10', 'POz', 'stim']In [82]: raw.get_channel_types()
Out[82]: ['eeg', 'eeg', 'eeg', 'eeg', 'misc', 'stim']Easily fixed with
raw.set_channel_types({'POz': 'eeg'})or something similar
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Seems to be good now. Merging. |
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JohnGriffiths
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Jan 19, 2023
* example test commit (#182) * example test commit * example edit * ci: run test workflow on develop branch * ci: add develop branch to job triggers * ci: fix syntax issue in workflow * fix: fixed import (brainflow updated API) * build(deps): locked pylsl==1.10.5 (#187) * Experiment Class Refactor (update to #183), converting specific experiments to subclasses (#184) * First commit * Second commit * Modifications * Lol * Lol * Incorporated N170 and p300, looking good for a PR * ssvep update * Implementing subclasses instead of loose functions * fix: fixed import (brainflow updated API) * Playing around still * Fixing import errors * Adding abstractmethod decorators * Still working on the import error * Guess what's finally working * Comments and naming ticks * More comments * Live coding demonstration * ssvep adapted * Adapting Auditory Oddball * changing save_fn to self.save_fun * This maybe the last big change * utils file changed, changes work through cli Co-authored-by: Erik Bjäreholt <[email protected]> * Submodule added for gsoc * Adding pipelines for cli analysis (#202) * started pipelines function * almost working simple function equivalents of nb scripts * fix: fixed import (brainflow updated API) * sqc fixes for unicorn (#176) * Ignore pushes * Trying to create a cli * Stepping through the problem * First commit * Fixing pause in signal quality check * Fixing Signal quality check problem * fix the technical debt * Save path done for automated saving pdf * I feel amazing * Almost through * Update eegnb/cli/__main__.py Co-authored-by: Erik Bjäreholt <[email protected]> * Trying to create cli but it's being really painful * Extra word cli error * Changed example handling * Pain * Adding whole datapath * Finally fixed cli * hmm * Looking good * added hyperlink * Having some issues with detecting css and image deltetion * Just the css now * Fixed the css linking problem though it's a weird soln * Automated running, still fnames problem * Hahahah embedded images in html * Improving code * Okay now * Look at that * Almost there just the two figures now * Now * Added attrdict to do with cli error Co-authored-by: John Griffiths <[email protected]> Co-authored-by: Erik Bjäreholt <[email protected]> Co-authored-by: John Griffiths <[email protected]> * added more options for site args; improved function names; removed some redundant lines (#209) * fix subject num parsing bug * analysis report function improvements for openbci cyton and gtec unicorn devices * run exp fix * Update requirements.txt * fixes to get docs building by github action (#210) * fixes to get docs building by github action * reverted some changes * Update 01r__ssvep_viz.py Co-authored-by: John Griffiths <[email protected]> * Update README.rst small commit to test doc build workflow on this branch * removing gsoc submodule Co-authored-by: Erik Bjäreholt <[email protected]> Co-authored-by: Parv Agarwal <[email protected]> Co-authored-by: Parvfect <[email protected]> Co-authored-by: Ben Pettit <[email protected]>
oreHGA
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Mar 4, 2023
* major update: merging develop to master (#217) * example test commit (#182) * example test commit * example edit * ci: run test workflow on develop branch * ci: add develop branch to job triggers * ci: fix syntax issue in workflow * fix: fixed import (brainflow updated API) * build(deps): locked pylsl==1.10.5 (#187) * Experiment Class Refactor (update to #183), converting specific experiments to subclasses (#184) * First commit * Second commit * Modifications * Lol * Lol * Incorporated N170 and p300, looking good for a PR * ssvep update * Implementing subclasses instead of loose functions * fix: fixed import (brainflow updated API) * Playing around still * Fixing import errors * Adding abstractmethod decorators * Still working on the import error * Guess what's finally working * Comments and naming ticks * More comments * Live coding demonstration * ssvep adapted * Adapting Auditory Oddball * changing save_fn to self.save_fun * This maybe the last big change * utils file changed, changes work through cli Co-authored-by: Erik Bjäreholt <[email protected]> * Submodule added for gsoc * Adding pipelines for cli analysis (#202) * started pipelines function * almost working simple function equivalents of nb scripts * fix: fixed import (brainflow updated API) * sqc fixes for unicorn (#176) * Ignore pushes * Trying to create a cli * Stepping through the problem * First commit * Fixing pause in signal quality check * Fixing Signal quality check problem * fix the technical debt * Save path done for automated saving pdf * I feel amazing * Almost through * Update eegnb/cli/__main__.py Co-authored-by: Erik Bjäreholt <[email protected]> * Trying to create cli but it's being really painful * Extra word cli error * Changed example handling * Pain * Adding whole datapath * Finally fixed cli * hmm * Looking good * added hyperlink * Having some issues with detecting css and image deltetion * Just the css now * Fixed the css linking problem though it's a weird soln * Automated running, still fnames problem * Hahahah embedded images in html * Improving code * Okay now * Look at that * Almost there just the two figures now * Now * Added attrdict to do with cli error Co-authored-by: John Griffiths <[email protected]> Co-authored-by: Erik Bjäreholt <[email protected]> Co-authored-by: John Griffiths <[email protected]> * added more options for site args; improved function names; removed some redundant lines (#209) * fix subject num parsing bug * analysis report function improvements for openbci cyton and gtec unicorn devices * run exp fix * Update requirements.txt * fixes to get docs building by github action (#210) * fixes to get docs building by github action * reverted some changes * Update 01r__ssvep_viz.py Co-authored-by: John Griffiths <[email protected]> * Update README.rst small commit to test doc build workflow on this branch * removing gsoc submodule Co-authored-by: Erik Bjäreholt <[email protected]> Co-authored-by: Parv Agarwal <[email protected]> Co-authored-by: Parvfect <[email protected]> Co-authored-by: Ben Pettit <[email protected]> * update dependencies - seaborn * docs/perf: reduced the imports: `cueing` example * bug: update deprecated `plot_psd()` method - feature of new `mne` version. - instead of doing plot_psd() from the `mne.io.Raw` object, must do this: - `raw.compute_psd().plot()` - i.e., has to pass through a `spectrum` object * updated deprec. `mne` function * perf: removed importage of unused packages from example - One of them, i.e., `collections.Iterable` is even deprecated. - Must use `collections.abc.Iterable` instead now. - Resulting in faster build/user run * bugfix: `plot_conditions` - due to `sns` deprecation * bugfix: resolved `psd_welch()` deprecation (`mne`) --------- Co-authored-by: John Griffiths <[email protected]> Co-authored-by: Erik Bjäreholt <[email protected]> Co-authored-by: Parv Agarwal <[email protected]> Co-authored-by: Parvfect <[email protected]> Co-authored-by: Ben Pettit <[email protected]> Co-authored-by: Taha Morshedzadeh <[email protected]>
oreHGA
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Mar 10, 2023
…Refactor (#218) * major update: merging develop to master (#217) * example test commit (#182) * example test commit * example edit * ci: run test workflow on develop branch * ci: add develop branch to job triggers * ci: fix syntax issue in workflow * fix: fixed import (brainflow updated API) * build(deps): locked pylsl==1.10.5 (#187) * Experiment Class Refactor (update to #183), converting specific experiments to subclasses (#184) * First commit * Second commit * Modifications * Lol * Lol * Incorporated N170 and p300, looking good for a PR * ssvep update * Implementing subclasses instead of loose functions * fix: fixed import (brainflow updated API) * Playing around still * Fixing import errors * Adding abstractmethod decorators * Still working on the import error * Guess what's finally working * Comments and naming ticks * More comments * Live coding demonstration * ssvep adapted * Adapting Auditory Oddball * changing save_fn to self.save_fun * This maybe the last big change * utils file changed, changes work through cli Co-authored-by: Erik Bjäreholt <[email protected]> * Submodule added for gsoc * Adding pipelines for cli analysis (#202) * started pipelines function * almost working simple function equivalents of nb scripts * fix: fixed import (brainflow updated API) * sqc fixes for unicorn (#176) * Ignore pushes * Trying to create a cli * Stepping through the problem * First commit * Fixing pause in signal quality check * Fixing Signal quality check problem * fix the technical debt * Save path done for automated saving pdf * I feel amazing * Almost through * Update eegnb/cli/__main__.py Co-authored-by: Erik Bjäreholt <[email protected]> * Trying to create cli but it's being really painful * Extra word cli error * Changed example handling * Pain * Adding whole datapath * Finally fixed cli * hmm * Looking good * added hyperlink * Having some issues with detecting css and image deltetion * Just the css now * Fixed the css linking problem though it's a weird soln * Automated running, still fnames problem * Hahahah embedded images in html * Improving code * Okay now * Look at that * Almost there just the two figures now * Now * Added attrdict to do with cli error Co-authored-by: John Griffiths <[email protected]> Co-authored-by: Erik Bjäreholt <[email protected]> Co-authored-by: John Griffiths <[email protected]> * added more options for site args; improved function names; removed some redundant lines (#209) * fix subject num parsing bug * analysis report function improvements for openbci cyton and gtec unicorn devices * run exp fix * Update requirements.txt * fixes to get docs building by github action (#210) * fixes to get docs building by github action * reverted some changes * Update 01r__ssvep_viz.py Co-authored-by: John Griffiths <[email protected]> * Update README.rst small commit to test doc build workflow on this branch * removing gsoc submodule Co-authored-by: Erik Bjäreholt <[email protected]> Co-authored-by: Parv Agarwal <[email protected]> Co-authored-by: Parvfect <[email protected]> Co-authored-by: Ben Pettit <[email protected]> * Updated doc examples * Update 00x__n170_run_experiment.py fix: typo in func param --------- Co-authored-by: John Griffiths <[email protected]> Co-authored-by: Erik Bjäreholt <[email protected]> Co-authored-by: Ben Pettit <[email protected]> Co-authored-by: Ore O <[email protected]>
JohnGriffiths
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Jun 21, 2024
* example test commit (#182) * example test commit * example edit * ci: run test workflow on develop branch * ci: add develop branch to job triggers * ci: fix syntax issue in workflow * fix: fixed import (brainflow updated API) * build(deps): locked pylsl==1.10.5 (#187) * Experiment Class Refactor (update to #183), converting specific experiments to subclasses (#184) * First commit * Second commit * Modifications * Lol * Lol * Incorporated N170 and p300, looking good for a PR * ssvep update * Implementing subclasses instead of loose functions * fix: fixed import (brainflow updated API) * Playing around still * Fixing import errors * Adding abstractmethod decorators * Still working on the import error * Guess what's finally working * Comments and naming ticks * More comments * Live coding demonstration * ssvep adapted * Adapting Auditory Oddball * changing save_fn to self.save_fun * This maybe the last big change * utils file changed, changes work through cli Co-authored-by: Erik Bjäreholt <[email protected]> * Submodule added for gsoc * Adding pipelines for cli analysis (#202) * started pipelines function * almost working simple function equivalents of nb scripts * fix: fixed import (brainflow updated API) * sqc fixes for unicorn (#176) * Ignore pushes * Trying to create a cli * Stepping through the problem * First commit * Fixing pause in signal quality check * Fixing Signal quality check problem * fix the technical debt * Save path done for automated saving pdf * I feel amazing * Almost through * Update eegnb/cli/__main__.py Co-authored-by: Erik Bjäreholt <[email protected]> * Trying to create cli but it's being really painful * Extra word cli error * Changed example handling * Pain * Adding whole datapath * Finally fixed cli * hmm * Looking good * added hyperlink * Having some issues with detecting css and image deltetion * Just the css now * Fixed the css linking problem though it's a weird soln * Automated running, still fnames problem * Hahahah embedded images in html * Improving code * Okay now * Look at that * Almost there just the two figures now * Now * Added attrdict to do with cli error Co-authored-by: John Griffiths <[email protected]> Co-authored-by: Erik Bjäreholt <[email protected]> Co-authored-by: John Griffiths <[email protected]> * added more options for site args; improved function names; removed some redundant lines (#209) * fix subject num parsing bug * analysis report function improvements for openbci cyton and gtec unicorn devices * run exp fix * Update requirements.txt * fixes to get docs building by github action (#210) * fixes to get docs building by github action * reverted some changes * Update 01r__ssvep_viz.py Co-authored-by: John Griffiths <[email protected]> * Update README.rst small commit to test doc build workflow on this branch * removing gsoc submodule * ci: update python to 3.8, update wxPython, update setup-python action * ci: pin ubuntu versions to 22.04, updated wxPython urls * ci: bumped psychopy to 2023.1.0 * build(deps): set upper supported numpy version to 1.23.x * chore: applied no_implicit_optional * update dependencies - for build (#220) * major update: merging develop to master (#217) * example test commit (#182) * example test commit * example edit * ci: run test workflow on develop branch * ci: add develop branch to job triggers * ci: fix syntax issue in workflow * fix: fixed import (brainflow updated API) * build(deps): locked pylsl==1.10.5 (#187) * Experiment Class Refactor (update to #183), converting specific experiments to subclasses (#184) * First commit * Second commit * Modifications * Lol * Lol * Incorporated N170 and p300, looking good for a PR * ssvep update * Implementing subclasses instead of loose functions * fix: fixed import (brainflow updated API) * Playing around still * Fixing import errors * Adding abstractmethod decorators * Still working on the import error * Guess what's finally working * Comments and naming ticks * More comments * Live coding demonstration * ssvep adapted * Adapting Auditory Oddball * changing save_fn to self.save_fun * This maybe the last big change * utils file changed, changes work through cli Co-authored-by: Erik Bjäreholt <[email protected]> * Submodule added for gsoc * Adding pipelines for cli analysis (#202) * started pipelines function * almost working simple function equivalents of nb scripts * fix: fixed import (brainflow updated API) * sqc fixes for unicorn (#176) * Ignore pushes * Trying to create a cli * Stepping through the problem * First commit * Fixing pause in signal quality check * Fixing Signal quality check problem * fix the technical debt * Save path done for automated saving pdf * I feel amazing * Almost through * Update eegnb/cli/__main__.py Co-authored-by: Erik Bjäreholt <[email protected]> * Trying to create cli but it's being really painful * Extra word cli error * Changed example handling * Pain * Adding whole datapath * Finally fixed cli * hmm * Looking good * added hyperlink * Having some issues with detecting css and image deltetion * Just the css now * Fixed the css linking problem though it's a weird soln * Automated running, still fnames problem * Hahahah embedded images in html * Improving code * Okay now * Look at that * Almost there just the two figures now * Now * Added attrdict to do with cli error Co-authored-by: John Griffiths <[email protected]> Co-authored-by: Erik Bjäreholt <[email protected]> Co-authored-by: John Griffiths <[email protected]> * added more options for site args; improved function names; removed some redundant lines (#209) * fix subject num parsing bug * analysis report function improvements for openbci cyton and gtec unicorn devices * run exp fix * Update requirements.txt * fixes to get docs building by github action (#210) * fixes to get docs building by github action * reverted some changes * Update 01r__ssvep_viz.py Co-authored-by: John Griffiths <[email protected]> * Update README.rst small commit to test doc build workflow on this branch * removing gsoc submodule Co-authored-by: Erik Bjäreholt <[email protected]> Co-authored-by: Parv Agarwal <[email protected]> Co-authored-by: Parvfect <[email protected]> Co-authored-by: Ben Pettit <[email protected]> * update dependencies - seaborn * docs/perf: reduced the imports: `cueing` example * bug: update deprecated `plot_psd()` method - feature of new `mne` version. - instead of doing plot_psd() from the `mne.io.Raw` object, must do this: - `raw.compute_psd().plot()` - i.e., has to pass through a `spectrum` object * updated deprec. `mne` function * perf: removed importage of unused packages from example - One of them, i.e., `collections.Iterable` is even deprecated. - Must use `collections.abc.Iterable` instead now. - Resulting in faster build/user run * bugfix: `plot_conditions` - due to `sns` deprecation * bugfix: resolved `psd_welch()` deprecation (`mne`) --------- Co-authored-by: John Griffiths <[email protected]> Co-authored-by: Erik Bjäreholt <[email protected]> Co-authored-by: Parv Agarwal <[email protected]> Co-authored-by: Parvfect <[email protected]> Co-authored-by: Ben Pettit <[email protected]> Co-authored-by: Taha Morshedzadeh <[email protected]> * Updated psychopy (#215) * update psychopy for psychxr compatibility * updated n170 example to run again. * Updated doc examples for N170, P300 and SSVEP after Experiment Class Refactor (#218) * major update: merging develop to master (#217) * example test commit (#182) * example test commit * example edit * ci: run test workflow on develop branch * ci: add develop branch to job triggers * ci: fix syntax issue in workflow * fix: fixed import (brainflow updated API) * build(deps): locked pylsl==1.10.5 (#187) * Experiment Class Refactor (update to #183), converting specific experiments to subclasses (#184) * First commit * Second commit * Modifications * Lol * Lol * Incorporated N170 and p300, looking good for a PR * ssvep update * Implementing subclasses instead of loose functions * fix: fixed import (brainflow updated API) * Playing around still * Fixing import errors * Adding abstractmethod decorators * Still working on the import error * Guess what's finally working * Comments and naming ticks * More comments * Live coding demonstration * ssvep adapted * Adapting Auditory Oddball * changing save_fn to self.save_fun * This maybe the last big change * utils file changed, changes work through cli Co-authored-by: Erik Bjäreholt <[email protected]> * Submodule added for gsoc * Adding pipelines for cli analysis (#202) * started pipelines function * almost working simple function equivalents of nb scripts * fix: fixed import (brainflow updated API) * sqc fixes for unicorn (#176) * Ignore pushes * Trying to create a cli * Stepping through the problem * First commit * Fixing pause in signal quality check * Fixing Signal quality check problem * fix the technical debt * Save path done for automated saving pdf * I feel amazing * Almost through * Update eegnb/cli/__main__.py Co-authored-by: Erik Bjäreholt <[email protected]> * Trying to create cli but it's being really painful * Extra word cli error * Changed example handling * Pain * Adding whole datapath * Finally fixed cli * hmm * Looking good * added hyperlink * Having some issues with detecting css and image deltetion * Just the css now * Fixed the css linking problem though it's a weird soln * Automated running, still fnames problem * Hahahah embedded images in html * Improving code * Okay now * Look at that * Almost there just the two figures now * Now * Added attrdict to do with cli error Co-authored-by: John Griffiths <[email protected]> Co-authored-by: Erik Bjäreholt <[email protected]> Co-authored-by: John Griffiths <[email protected]> * added more options for site args; improved function names; removed some redundant lines (#209) * fix subject num parsing bug * analysis report function improvements for openbci cyton and gtec unicorn devices * run exp fix * Update requirements.txt * fixes to get docs building by github action (#210) * fixes to get docs building by github action * reverted some changes * Update 01r__ssvep_viz.py Co-authored-by: John Griffiths <[email protected]> * Update README.rst small commit to test doc build workflow on this branch * removing gsoc submodule Co-authored-by: Erik Bjäreholt <[email protected]> Co-authored-by: Parv Agarwal <[email protected]> Co-authored-by: Parvfect <[email protected]> Co-authored-by: Ben Pettit <[email protected]> * Updated doc examples * Update 00x__n170_run_experiment.py fix: typo in func param --------- Co-authored-by: John Griffiths <[email protected]> Co-authored-by: Erik Bjäreholt <[email protected]> Co-authored-by: Ben Pettit <[email protected]> Co-authored-by: Ore O <[email protected]> * fix error breaking n170 test (#223) * fixed requirements.txt so 'pip install -e .' would work on windows. (#229) * Get CI test builds working again! (#170) * Revert "Revert PR #167: "ci: fix broken CI" (#169)" This reverts commit 2d74871. * Update Makefile * fix: Update vep.py import * Update Makefile * Update vep.py * fix: typo in makefile * fix: update BaseExperiment class reference * Update Makefile * Update vep.py * Update 01r__n170_viz.py * makefile: install libnotify4 --------- Co-authored-by: Ore O <[email protected]> * fix macos build (#245) * Add devcontainer configuration for CPU environment * Fixed the python version needed * Fix plot conditions (#257) * fixed plot_conditions functoni issues * small change to viz n170 plotting example * small change to viz p300 plotting example * fixed to plotting issue * modify plot command * update example files * fix condition label bug * fix: set layout engine to fix colorbar error --------- Co-authored-by: Ore O <[email protected]> * Started the name switch (#251) * started renaming from eegnb to eegexpy * more eegnb renaming work * more eegnb switches * more relabelling * ssvep renamings * cueing eg * update for more misc files * more of the same * update * Update and rename available_notebooks.md to available_experiments.md * Add newlogo (#260) * Add files via upload * Update README.rst * added to enable eegexpy commands (#265) * started alias of main package for imports (#266) * Add multiple installation options (#263) * added newly separated analysis and streaming utils files * modified setup and requirements to allow for optional install types * updated imports in experiment examples * fixed some typos * Update requirements.txt moved click library to stim pres requirements section * Update requirements.txt Co-authored-by: Taha Morshedzadeh <[email protected]> * Update Makefile * Update docs.yml * Update Makefile this does a full build with all dependencies for EEG-ExPy --------- Co-authored-by: Ore O <[email protected]> Co-authored-by: Taha Morshedzadeh <[email protected]> * Add support for /develop in docs site (#259) * feat: update action to build doc page in a folder * test: see if it works without if clause * test: change source for docs * Initial support for VR headsets (#241) * fixed requirements.txt so 'pip install -e .' would work on windows. * added support for n170 to run on rift * altered logic to add back in jitter * simplified logic * made fullscreen again * further simplified logic * decreased font size of instructions for vr * fixed instructions display, further simplified logic, removed logs * made code easier to read * reverted board back to muse * Enable headlocking to fix jittering - cancel out any rotation and translation coming from the headset. * fixed use_vr parameter to be set to False by default for existing experiments. * fix macos build * reverted unnecessary changes and made p300 experiment display correctly * added vr support for p300 and ssvep * fix psychxr version * adding vr doc * updated vr doco --------- Co-authored-by: John Griffiths <[email protected]> * ssaep volumefadingfixes (#81) * fixed duration on instructions screen * put sound object instantiation inside trials loop. fixes sound fading issue --------- Co-authored-by: Erik Bjäreholt <[email protected]> Co-authored-by: Parv Agarwal <[email protected]> Co-authored-by: Parvfect <[email protected]> Co-authored-by: Ben Pettit <[email protected]> Co-authored-by: Ore Ogundipe <[email protected]> Co-authored-by: Taha Morshedzadeh <[email protected]> Co-authored-by: Ben Pettit <[email protected]> Co-authored-by: Taha Morshedzadeh <[email protected]>
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