Merge dev(version 0.1.0) into main #146

ldr426 · 2023-09-19T01:07:29Z

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* Change importing format to comply with develop mode * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Solve that curtain could not dynamically render * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Select box correctly when not inverting y-axis * local testing * y-axis testing * Y-axis testing * add options for echogram * del testing files * add options * set y-axis inversion * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * 06/06/2023 - testing * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

* Change importing format to comply with develop mode * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Solve that curtain could not dynamically render * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Select box correctly when not inverting y-axis * local testing * y-axis testing * Y-axis testing * add options for echogram * del testing files * add options * set y-axis inversion * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Add testing files * rename testing file * a * a * lasso testing * add for testing * 06/06/2023 - testing * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Add trigram * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Delete echoshader/new_version directory * Add testing files * rename testing file * a * a * lasso testing * add for testing * Add trigram * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * ADD testing file * del old one * add test.ipynb * change "= None" to "is None" * little fix * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Add comments * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Sync * Add docstring and customizing colormap * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Update echoshader/new_version/echogram.py Co-authored-by: Wu-Jung Lee <leewujung@gmail.com> * Update echoshader/new_version/echogram.py Co-authored-by: Wu-Jung Lee <leewujung@gmail.com> * Delete .DS_Store * Delete .DS_Store * Solve Undefined Name * Use Literal to solve undefined issue * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Solve 'line too long' issues * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Solve 'line too long' issue * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Solve "compare False should using is not" * Delete testing files * delete testing toy dataset --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Wu-Jung Lee <leewujung@gmail.com>

* Change importing format to comply with develop mode * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Solve that curtain could not dynamically render * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Select box correctly when not inverting y-axis * local testing * y-axis testing * Y-axis testing * add options for echogram * del testing files * add options * set y-axis inversion * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Add testing files * rename testing file * a * a * lasso testing * add for testing * 06/06/2023 - testing * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Add trigram * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Delete echoshader/new_version directory * Add testing files * rename testing file * a * a * lasso testing * add for testing * Add trigram * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * ADD testing file * del old one * add test.ipynb * change "= None" to "is None" * little fix * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Add comments * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Sync * Add docstring and customizing colormap * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Update echoshader/new_version/echogram.py Co-authored-by: Wu-Jung Lee <leewujung@gmail.com> * Update echoshader/new_version/echogram.py Co-authored-by: Wu-Jung Lee <leewujung@gmail.com> * Delete .DS_Store * Delete .DS_Store * Solve Undefined Name * Use Literal to solve undefined issue * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Solve 'line too long' issues * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Solve 'line too long' issue * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Solve "compare False should using is not" * Delete testing files * delete testing toy dataset * Add selected box plotting and extracting feature * Add python doc for extracting box function * Delete testing files * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Solve line too long issue * Change name from ambiguous `gram` to echogram --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Wu-Jung Lee <leewujung@gmail.com>

* Change importing format to comply with develop mode * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Solve that curtain could not dynamically render * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Select box correctly when not inverting y-axis * local testing * y-axis testing * Y-axis testing * add options for echogram * del testing files * add options * set y-axis inversion * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Add testing files * rename testing file * a * a * lasso testing * add for testing * 06/06/2023 - testing * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Add trigram * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Delete echoshader/new_version directory * Add testing files * rename testing file * a * a * lasso testing * add for testing * Add trigram * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * ADD testing file * del old one * add test.ipynb * change "= None" to "is None" * little fix * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Add comments * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Sync * Add docstring and customizing colormap * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Update echoshader/new_version/echogram.py Co-authored-by: Wu-Jung Lee <leewujung@gmail.com> * Update echoshader/new_version/echogram.py Co-authored-by: Wu-Jung Lee <leewujung@gmail.com> * Delete .DS_Store * Delete .DS_Store * Solve Undefined Name * Use Literal to solve undefined issue * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Solve 'line too long' issues * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Solve 'line too long' issue * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Solve "compare False should using is not" * Delete testing files * delete testing toy dataset * Add selected box plotting and extracting feature * Add python doc for extracting box function * Delete testing files * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Add map plotting * Add features of curtain and some comments * Draft PR for map part * Update track, curtain and linked connection logic * Add colormap type (list) for curtain * Add testing file for demo * Delete .DS_Store * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Solve pre-commit * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Store link state of curtain * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Delete .DS_Store * Add .DS_Store to .gitignore * change name of varaiable "gram_plot" to "echogram" * Update echoshader/new_version/echogram.py Co-authored-by: Wu-Jung Lee <leewujung@gmail.com> * Update variable name "old_vmin" to "data_min" --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Wu-Jung Lee <leewujung@gmail.com>

* Change importing format to comply with develop mode * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Solve that curtain could not dynamically render * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Select box correctly when not inverting y-axis * local testing * y-axis testing * Y-axis testing * add options for echogram * del testing files * add options * set y-axis inversion * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Add testing files * rename testing file * a * a * lasso testing * add for testing * 06/06/2023 - testing * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Add trigram * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Delete echoshader/new_version directory * Add testing files * rename testing file * a * a * lasso testing * add for testing * Add trigram * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * ADD testing file * del old one * add test.ipynb * change "= None" to "is None" * little fix * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Add comments * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Sync * Add docstring and customizing colormap * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Update echoshader/new_version/echogram.py Co-authored-by: Wu-Jung Lee <leewujung@gmail.com> * Update echoshader/new_version/echogram.py Co-authored-by: Wu-Jung Lee <leewujung@gmail.com> * Delete .DS_Store * Delete .DS_Store * Solve Undefined Name * Use Literal to solve undefined issue * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Solve 'line too long' issues * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Solve 'line too long' issue * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Solve "compare False should using is not" * Delete testing files * delete testing toy dataset * Add selected box plotting and extracting feature * Add python doc for extracting box function * Delete testing files * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Add map plotting * Add features of curtain and some comments * [pre-commit.ci] pre-commit autoupdate (#105) updates: - [github.com/igorshubovych/markdownlint-cli: v0.34.0 → v0.35.0](igorshubovych/markdownlint-cli@v0.34.0...v0.35.0) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * Draft PR for map part * Update track, curtain and linked connection logic * Add colormap type (list) for curtain * Add testing file for demo * Delete .DS_Store * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Solve pre-commit * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Store link state of curtain * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * [pre-commit.ci] pre-commit autoupdate (#123) updates: - [github.com/psf/black: 23.3.0 → 23.7.0](psf/black@23.3.0...23.7.0) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * Delete .DS_Store * Add .DS_Store to .gitignore * change name of varaiable "gram_plot" to "echogram" * Update echoshader/new_version/echogram.py Co-authored-by: Wu-Jung Lee <leewujung@gmail.com> * Update variable name "old_vmin" to "data_min" * Add stats part * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Create functions for repetitive code * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * delete useless importing lib * Resolve conflict * Resolve conflicts * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Add python doc * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Add docstring * Solve pre-commit issue * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Solve pre-commit issue * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Wu-Jung Lee <leewujung@gmail.com>

* Create folders for new refactoring * Add core.py, echogram.py, map.py and utils.py * Add files * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Add moored point in map & config in utils * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Add echogram in core.py and docstring * Lined echogram and map for 2nd version * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Solve pre-commit issue * High-order structure building * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Solve pre-commit * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Add underlying code for hist and curtain * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * sovle pre-commit * Add curtain, hist and table * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * fix little bugs ahout curtain and hist * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Add subscriber about echogram * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Add curtain * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Add new requirements * Add bidirectional control logic * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Add reset tool * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Add customized opts * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Update file stucture * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Add __init__.py * Add more docstring * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Add testing demo * erase pre-commit warning * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

* Fix channel select bugs * Add testing files * solve pre-commit warnings * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * extract out testing files * Add pytest and CI config * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Set the testing files as expected for a user * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Make the testing files to pytest format * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Improve testing files * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Add more testing cases * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

* Adding branches for testing * renaming workflow to workflows * addign extra empty line to trigger the workflow * Put the branches into bullet points * remove test coverage * Rename test.py to test_plots.py Adding underscrore for discoverability * fixing get_data call * limit to python 3.10 * pin pandas * test with unpinned Python

* Fix channel select bugs * Add testing files * solve pre-commit warnings * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * extract out testing files * Add pytest and CI config * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Set the testing files as expected for a user * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Make the testing files to pytest format * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Improve testing files * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Add more testing cases * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Add docs for generating data * Add index and design intro page * Add index and structure intro pages * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * code blocks should have a language specified * Add data generation docs * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Add echogram showcases * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Add track and hist exampls * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Add panel server setup * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Solve pre-commit * Improve based on feedback * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * del deprecated testing files * Add Configuration file v2 (.readthedocs.yaml) * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Solve conflicts * Solve doc conflicts --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

review-notebook-app · 2023-09-19T01:07:36Z

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valentina-s

Thanks @ldr426 I made a small PR Dev patch #147 with a few changes. Please check them and merge to dev, before merging to main.
I also noticed that the pictures in the echogram notebook of the box selection do not render in the read the docs version. Could you see if they will be ok?

The curtain plot does not show in the static notebook. Is there a way to make it display so people get an idea of how the plot looks like if they have not heard of "curtain".

* Update setup_server.md removing repeating sentence from panel * splitting user and development installation instructions * removing intro.md * Update index.md adding a more general description and a note that folks can skip to the examples as this will be what most users need. Later we may reorganize the order of the sections. * language * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Update _toc.yml * Update index.md Fix typo --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Dingrui Lei <56751303+ldr426@users.noreply.github.com>

* improve dev based on feedback * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

ldr426 · 2023-10-03T00:35:51Z

Thanks @ldr426 I made a small PR Dev patch #147 with a few changes. Please check them and merge to dev, before merging to main.

I also noticed that the pictures in the echogram notebook of the box selection do not render in the read the docs version. Could you see if they will be ok?

* The curtain plot does not show in the static notebook. Is there a way to make it display so people get an idea of how the plot looks like if they have not heard of "curtain".

@valentina-s Thanks for PR with the changes!

For the second point, I can view it rendered on my device. Let's consider saving pictures in a dedicated folder instead of solely within the IPython Notebook file.
For the third point, I've made a few attempts to save the rendered curtain in the static file, but unfortunately, I've encountered some failures. As a workaround, I suggest showing users an example picture for now.

valentina-s · 2023-10-10T23:32:45Z

@ldr426 could you resolve the conflicts and we can merge into main. Then I will add a patch to reverse the axes so the echograms are plotted in the right orientation #108 .

valentina-s · 2023-10-13T20:32:00Z

This PR closes #144, #135, #120, #126, #106, #80.

ldr426 and others added 10 commits June 6, 2023 17:49

Merge branch 'main' into dev

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ldr426 requested a review from valentina-s September 19, 2023 01:07

ldr426 marked this pull request as ready for review September 19, 2023 01:09

Update README.md

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valentina-s reviewed Sep 22, 2023

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valentina-s and others added 2 commits September 25, 2023 17:01

Fix-dev (#149)

23e7eb9

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ldr426 requested a review from valentina-s October 3, 2023 00:30

Merge branch 'main' into dev

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valentina-s approved these changes Oct 13, 2023

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valentina-s merged commit d43c60d into main Oct 13, 2023
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valentina-s mentioned this pull request Oct 13, 2023

Refactor Histograms; Histograms for Non-Rectangular Region #94

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valentina-s deleted the dev branch October 13, 2023 23:29

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Merge dev(version 0.1.0) into main #146

Merge dev(version 0.1.0) into main #146

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Merge dev(version 0.1.0) into main #146

Merge dev(version 0.1.0) into main #146

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