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Amy/package v2 #326

Merged
merged 65 commits into from
Dec 3, 2024
Merged

Amy/package v2 #326

merged 65 commits into from
Dec 3, 2024

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amytangzheng
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Pull Request Template:
If you are merging in a feature or other major change, use this template to check your pull request!

Basic Info

What's this pull request about?

Allowing users to customize aggregation at the conversation and user level, allowing users to customize the columns and functions they want aggregated.

My PR Adds or Improves Documentation

If your feature is about documentation, ensure that you check the boxes relevant to you.

Docstrings

  • Docstrings: I have followed the proper documentation format (https://www.sphinx-doc.org/en/master/usage/extensions/napoleon.html; Google Format recommended).
  • Docstrings: Every function in the file has a block quote comment with a description of the feature.
  • Docstrings: Every input argument is documented.
  • Docstrings: The output type is documented, along with a description of what the output is for.
  • Docstrings: I have linked the feature under the Table of Contents (docs/source/features/index.rst)

Feature Wiki

  • Conceptual Wiki: I made a copy of the TEMPLATE (docs/source/features_conceptual/TEMPLATE.rst)
  • Conceptual Wiki: I replaced the word TEMPLATE at the top of the file with the name of the feature (.. _TEMPLATE:) Please do NOT delete any of the punctuation (the .._ and :) in the header, as this is important for referencing the feature in the Table of Contents!
  • Conceptual Wiki: I have answered the six sections of the template to the best of my ability.
  • Conceptual Wiki: I have linked the feature under the Table of Contents (docs/source/features_conceptual/index.rst).

General Documentation

  • My documentation is linked in a toctree.
  • I have confirmed that make clean and make html do not generate breaking errors.

My PR is About Adding a New Feature to the Code Repository

Adding Feature to the Feature Dictionary

  • I have edited the feature_dictionary.py file with an appropriate entry for my feature. Below is a sample entry; I confirm that all fields are accurately filled out.
  "Function Word Accommodation": {
    "columns": ["function_word_accommodation"],
    "file": "./features/word_mimicry.py",
    "level": "Chat",
    "semantic_grouping": "Variance",
    "description": "The total number of function words used in a given turn that were also used in the previous turn. Function words are defined as a list of 190 words from the source paper.",
    "references": "(Ranganath et al., 2013)",
    "wiki_link": "https://github.com/Watts-Lab/team-process-map/wiki/C.9-Mimicry:-Function-word,-Content-word,-BERT,-Moving",
    "function": ChatLevelFeaturesCalculator.calculate_word_mimicry,
    "dependencies": [],
    "preprocess": [],
    "vect_data": False,
    "bert_sentiment_data": False
  }
  • If my feature is at the chat level, my dictionary entry is in the top half of the file; if my feature is at the conversation level, my dictionary entry is in the bottom half of the file (below the comment that says, ### Conversation Level).

Documentation

Did you document your feature? You should follow the same requirements as above:

  • Docstrings: I have followed the proper documentation format (https://www.sphinx-doc.org/en/master/usage/extensions/napoleon.html; Google Format recommended).
  • Docstrings: Every function in the file has a block quote comment with a description of the feature.
  • Docstrings: Every input argument is documented.
  • Docstrings: The output type is documented, along with a description of what the output is for.
  • Docstrings: I have linked the feature under the Table of Contents (docs/source/features/index.rst)

Code Basics

  • My feature is a .py file.
  • My feature uses snake case in the name. That means the name of the format is my_feature, NOT myFeature (camel case).
  • My feature has the name, NAME_features.py, where NAME is the name of my feature.
  • My feature is located in src/features/.

Testing

  • I have thought about test cases for my features, with inputs and expected outputs.
  • I have added test cases for my feature under the tests/ folder.
  • My feature passes the automated testing suite.

The location of my tests are here:

[PASTE LINK HERE]

If you check all the boxes above, then you ready to merge!

amytangzheng and others added 30 commits September 11, 2024 14:44
* Add Examples Notebook (#294)

* Urgent fix to remove LIWC lexicons from public repo (#279)

* delete small test lexicons

* move .pkl files to assets and remove from GH

* filesystem cleanup

* update certainty pickle location

* remove unpickling certainty

* remove lexicons from pyproject

* change lexical pkl path

* add error handling when lexicons are not found

* update warning message

* add legal caveat and update name of certainty pkl to be correct

* ensure lexicons are ignored

* Update Documentation (Complete Conceptual Documentation, Document Assumptions) (#289)

* new docs

* lexicons hotfix

* emilys doc edits

* update deprecated github actions to latest

* update last remaining text features

* update index

* update docs

* update index

* update docs

* update docs and the feature dictionary

* add basics.rst

* add new basics page

* update docs

---------

Co-authored-by: Xinlan Emily Hu <[email protected]>
Co-authored-by: Xinlan Emily Hu <[email protected]>

* update torch requirements to resolve compatibility issue on torch end (#290)

* Update Website (#291)

* website updates

* renaming tpm-website to website

* deploying via gh-pages

* changed from tpm-website to website

* deployed website

* copyright and team

* team headshots and footer

* edits to the pages

* website updates

* updated links

* updated homepage

* link updates

* mobile compatibility

* mobile adjustments

* navbar mobile updates

* whitespace edits

* homepage updates

* feature table

* website updates

* renaming tpm-website to website

* deploying via gh-pages

* changed from tpm-website to website

* edits to the pages

* website updates

* updated links

* updated homepage

* link updates

* mobile compatibility

* mobile adjustments

* navbar mobile updates

* homepage updates

* add table of features

* updated team page titles

* include flask in requirements.txt

* updates to table of features

* load pages from top

* fix to 404 issues

* moved build under website folder

* updates to package launch

* hyperlink ./setup.sh

* fix nav bar sizing and hamburger logo

* include preprint

* updates to "getting started"

* update team

---------

Co-authored-by: amytangzheng <[email protected]>

* update documentation for clarity and correct typos in positivity z-score and information exchange and liwc

* add demo notebook

* update notebook and add information to docs

* update documentation

---------

Co-authored-by: Shruti Agarwal <[email protected]>
Co-authored-by: amytangzheng <[email protected]>

* Bump path-to-regexp and express in /website

Bumps [path-to-regexp](https://github.com/pillarjs/path-to-regexp) and [express](https://github.com/expressjs/express). These dependencies needed to be updated together.

Updates `path-to-regexp` from 0.1.7 to 0.1.10
- [Release notes](https://github.com/pillarjs/path-to-regexp/releases)
- [Changelog](https://github.com/pillarjs/path-to-regexp/blob/master/History.md)
- [Commits](pillarjs/path-to-regexp@v0.1.7...v0.1.10)

Updates `express` from 4.19.2 to 4.21.0
- [Release notes](https://github.com/expressjs/express/releases)
- [Changelog](https://github.com/expressjs/express/blob/4.21.0/History.md)
- [Commits](expressjs/express@4.19.2...4.21.0)

---
updated-dependencies:
- dependency-name: path-to-regexp
  dependency-type: indirect
- dependency-name: express
  dependency-type: indirect
...

Signed-off-by: dependabot[bot] <[email protected]>

---------

Signed-off-by: dependabot[bot] <[email protected]>
Co-authored-by: Xinlan Emily Hu <[email protected]>
Co-authored-by: Shruti Agarwal <[email protected]>
Co-authored-by: amytangzheng <[email protected]>
Co-authored-by: Xinlan Emily Hu <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
* Add Examples Notebook (#294)

* Urgent fix to remove LIWC lexicons from public repo (#279)

* delete small test lexicons

* move .pkl files to assets and remove from GH

* filesystem cleanup

* update certainty pickle location

* remove unpickling certainty

* remove lexicons from pyproject

* change lexical pkl path

* add error handling when lexicons are not found

* update warning message

* add legal caveat and update name of certainty pkl to be correct

* ensure lexicons are ignored

* Update Documentation (Complete Conceptual Documentation, Document Assumptions) (#289)

* new docs

* lexicons hotfix

* emilys doc edits

* update deprecated github actions to latest

* update last remaining text features

* update index

* update docs

* update index

* update docs

* update docs and the feature dictionary

* add basics.rst

* add new basics page

* update docs

---------

Co-authored-by: Xinlan Emily Hu <[email protected]>
Co-authored-by: Xinlan Emily Hu <[email protected]>

* update torch requirements to resolve compatibility issue on torch end (#290)

* Update Website (#291)

* website updates

* renaming tpm-website to website

* deploying via gh-pages

* changed from tpm-website to website

* deployed website

* copyright and team

* team headshots and footer

* edits to the pages

* website updates

* updated links

* updated homepage

* link updates

* mobile compatibility

* mobile adjustments

* navbar mobile updates

* whitespace edits

* homepage updates

* feature table

* website updates

* renaming tpm-website to website

* deploying via gh-pages

* changed from tpm-website to website

* edits to the pages

* website updates

* updated links

* updated homepage

* link updates

* mobile compatibility

* mobile adjustments

* navbar mobile updates

* homepage updates

* add table of features

* updated team page titles

* include flask in requirements.txt

* updates to table of features

* load pages from top

* fix to 404 issues

* moved build under website folder

* updates to package launch

* hyperlink ./setup.sh

* fix nav bar sizing and hamburger logo

* include preprint

* updates to "getting started"

* update team

---------

Co-authored-by: amytangzheng <[email protected]>

* update documentation for clarity and correct typos in positivity z-score and information exchange and liwc

* add demo notebook

* update notebook and add information to docs

* update documentation

---------

Co-authored-by: Shruti Agarwal <[email protected]>
Co-authored-by: amytangzheng <[email protected]>

* Bump nltk from 3.8.1 to 3.9

Bumps [nltk](https://github.com/nltk/nltk) from 3.8.1 to 3.9.
- [Changelog](https://github.com/nltk/nltk/blob/develop/ChangeLog)
- [Commits](nltk/nltk@3.8.1...3.9)

---
updated-dependencies:
- dependency-name: nltk
  dependency-type: direct:production
...

Signed-off-by: dependabot[bot] <[email protected]>

* Update pyproject.toml

* Update requirements.txt

* Update download_resources.py

---------

Signed-off-by: dependabot[bot] <[email protected]>
Co-authored-by: Xinlan Emily Hu <[email protected]>
Co-authored-by: Shruti Agarwal <[email protected]>
Co-authored-by: amytangzheng <[email protected]>
Co-authored-by: Xinlan Emily Hu <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
* Add Examples Notebook (#294)

* Urgent fix to remove LIWC lexicons from public repo (#279)

* delete small test lexicons

* move .pkl files to assets and remove from GH

* filesystem cleanup

* update certainty pickle location

* remove unpickling certainty

* remove lexicons from pyproject

* change lexical pkl path

* add error handling when lexicons are not found

* update warning message

* add legal caveat and update name of certainty pkl to be correct

* ensure lexicons are ignored

* Update Documentation (Complete Conceptual Documentation, Document Assumptions) (#289)

* new docs

* lexicons hotfix

* emilys doc edits

* update deprecated github actions to latest

* update last remaining text features

* update index

* update docs

* update index

* update docs

* update docs and the feature dictionary

* add basics.rst

* add new basics page

* update docs

---------

Co-authored-by: Xinlan Emily Hu <[email protected]>
Co-authored-by: Xinlan Emily Hu <[email protected]>

* update torch requirements to resolve compatibility issue on torch end (#290)

* Update Website (#291)

* website updates

* renaming tpm-website to website

* deploying via gh-pages

* changed from tpm-website to website

* deployed website

* copyright and team

* team headshots and footer

* edits to the pages

* website updates

* updated links

* updated homepage

* link updates

* mobile compatibility

* mobile adjustments

* navbar mobile updates

* whitespace edits

* homepage updates

* feature table

* website updates

* renaming tpm-website to website

* deploying via gh-pages

* changed from tpm-website to website

* edits to the pages

* website updates

* updated links

* updated homepage

* link updates

* mobile compatibility

* mobile adjustments

* navbar mobile updates

* homepage updates

* add table of features

* updated team page titles

* include flask in requirements.txt

* updates to table of features

* load pages from top

* fix to 404 issues

* moved build under website folder

* updates to package launch

* hyperlink ./setup.sh

* fix nav bar sizing and hamburger logo

* include preprint

* updates to "getting started"

* update team

---------

Co-authored-by: amytangzheng <[email protected]>

* update documentation for clarity and correct typos in positivity z-score and information exchange and liwc

* add demo notebook

* update notebook and add information to docs

* update documentation

---------

Co-authored-by: Shruti Agarwal <[email protected]>
Co-authored-by: amytangzheng <[email protected]>

* Bump body-parser and express in /website

Bumps [body-parser](https://github.com/expressjs/body-parser) and [express](https://github.com/expressjs/express). These dependencies needed to be updated together.

Updates `body-parser` from 1.20.2 to 1.20.3
- [Release notes](https://github.com/expressjs/body-parser/releases)
- [Changelog](https://github.com/expressjs/body-parser/blob/master/HISTORY.md)
- [Commits](expressjs/body-parser@1.20.2...1.20.3)

Updates `express` from 4.19.2 to 4.21.0
- [Release notes](https://github.com/expressjs/express/releases)
- [Changelog](https://github.com/expressjs/express/blob/4.21.0/History.md)
- [Commits](expressjs/express@4.19.2...4.21.0)

---
updated-dependencies:
- dependency-name: body-parser
  dependency-type: indirect
- dependency-name: express
  dependency-type: indirect
...

Signed-off-by: dependabot[bot] <[email protected]>

---------

Signed-off-by: dependabot[bot] <[email protected]>
Co-authored-by: Xinlan Emily Hu <[email protected]>
Co-authored-by: Shruti Agarwal <[email protected]>
Co-authored-by: amytangzheng <[email protected]>
Co-authored-by: Xinlan Emily Hu <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
* Add Examples Notebook (#294)

* Urgent fix to remove LIWC lexicons from public repo (#279)

* delete small test lexicons

* move .pkl files to assets and remove from GH

* filesystem cleanup

* update certainty pickle location

* remove unpickling certainty

* remove lexicons from pyproject

* change lexical pkl path

* add error handling when lexicons are not found

* update warning message

* add legal caveat and update name of certainty pkl to be correct

* ensure lexicons are ignored

* Update Documentation (Complete Conceptual Documentation, Document Assumptions) (#289)

* new docs

* lexicons hotfix

* emilys doc edits

* update deprecated github actions to latest

* update last remaining text features

* update index

* update docs

* update index

* update docs

* update docs and the feature dictionary

* add basics.rst

* add new basics page

* update docs

---------

Co-authored-by: Xinlan Emily Hu <[email protected]>
Co-authored-by: Xinlan Emily Hu <[email protected]>

* update torch requirements to resolve compatibility issue on torch end (#290)

* Update Website (#291)

* website updates

* renaming tpm-website to website

* deploying via gh-pages

* changed from tpm-website to website

* deployed website

* copyright and team

* team headshots and footer

* edits to the pages

* website updates

* updated links

* updated homepage

* link updates

* mobile compatibility

* mobile adjustments

* navbar mobile updates

* whitespace edits

* homepage updates

* feature table

* website updates

* renaming tpm-website to website

* deploying via gh-pages

* changed from tpm-website to website

* edits to the pages

* website updates

* updated links

* updated homepage

* link updates

* mobile compatibility

* mobile adjustments

* navbar mobile updates

* homepage updates

* add table of features

* updated team page titles

* include flask in requirements.txt

* updates to table of features

* load pages from top

* fix to 404 issues

* moved build under website folder

* updates to package launch

* hyperlink ./setup.sh

* fix nav bar sizing and hamburger logo

* include preprint

* updates to "getting started"

* update team

---------

Co-authored-by: amytangzheng <[email protected]>

* update documentation for clarity and correct typos in positivity z-score and information exchange and liwc

* add demo notebook

* update notebook and add information to docs

* update documentation

---------

Co-authored-by: Shruti Agarwal <[email protected]>
Co-authored-by: amytangzheng <[email protected]>

* update check embeddings with tqdm loading bar and BERT tokenization update

* (1) allow BERT sentiments to be generated from the messages with punctuation, rather than the preprocessed messages; (2) batch BERT sentiment generation to make it more efficient; (3) add loading bar for generation of chat-level features

---------

Co-authored-by: Shruti Agarwal <[email protected]>
Co-authored-by: amytangzheng <[email protected]>
* website updates

* renaming tpm-website to website

* deploying via gh-pages

* changed from tpm-website to website

* deployed website

* copyright and team

* team headshots and footer

* edits to the pages

* website updates

* updated links

* updated homepage

* link updates

* mobile compatibility

* mobile adjustments

* navbar mobile updates

* whitespace edits

* homepage updates

* feature table

* website updates

* renaming tpm-website to website

* deploying via gh-pages

* changed from tpm-website to website

* edits to the pages

* website updates

* updated links

* updated homepage

* link updates

* mobile compatibility

* mobile adjustments

* navbar mobile updates

* homepage updates

* add table of features

* updated team page titles

* include flask in requirements.txt

* updates to table of features

* load pages from top

* fix to 404 issues

* moved build under website folder

* updates to package launch

* hyperlink ./setup.sh

* fix nav bar sizing and hamburger logo

* include preprint

* updates to "getting started"

* update team

* gh actions and custom domain

* deploy to custom url

* deploy to custom url

* updates to cname

* changes to cname

* cname updates

* testing github actions

* updates to github-actions-website

* testing github actions

* updates to gh actions

* updates to github-actions

* update home for testing gh actions

* updates CNAME

* update testing email

* updates username/email

* updates to email in github-actions-website

* testing gh actions for feature_dict

* testing github-actions feature_dict

* updates to github-actions-feature_dict

* Update github-actions-feature_dict.yaml

* testing updates to feature_dict.py

* testing feature_dict updates

* testing updates to feature_dict.py

* testing feature_dict deployment

* Update github-actions-feature_dict.yaml

* testing feature_dict updates

* testing updates to feature_dict.py

* updates to feature_dict

* updates to github actions feature_dict

* testing auto updates to feature_dict

* Update feature_dict.py

* testing feature_dict auto updates

* testing feature_dict auto updates

* Update feature_dict.py

* testing feature_dict auto updates

* remove commented code in feature_dict.py

* Delete src/team_comm_tools/filtered_dict.json

delete test json file

* Update github-actions-website.yaml to deploy on update to dev

* put 'dev' in quotes

* Update github-actions-feature_dict.yaml to update upon dev

* re-add filtered dict

---------

Co-authored-by: Xinlan Emily Hu <[email protected]>
Co-authored-by: Xinlan Emily Hu <[email protected]>
* website updates

* renaming tpm-website to website

* deploying via gh-pages

* changed from tpm-website to website

* deployed website

* copyright and team

* team headshots and footer

* edits to the pages

* website updates

* updated links

* updated homepage

* link updates

* mobile compatibility

* mobile adjustments

* navbar mobile updates

* whitespace edits

* homepage updates

* feature table

* website updates

* renaming tpm-website to website

* deploying via gh-pages

* changed from tpm-website to website

* edits to the pages

* website updates

* updated links

* updated homepage

* link updates

* mobile compatibility

* mobile adjustments

* navbar mobile updates

* homepage updates

* add table of features

* updated team page titles

* include flask in requirements.txt

* updates to table of features

* load pages from top

* fix to 404 issues

* moved build under website folder

* updates to package launch

* hyperlink ./setup.sh

* fix nav bar sizing and hamburger logo

* include preprint

* updates to "getting started"

* update team

* gh actions and custom domain

* deploy to custom url

* deploy to custom url

* updates to cname

* changes to cname

* cname updates

* testing github actions

* updates to github-actions-website

* testing github actions

* updates to gh actions

* updates to github-actions

* update home for testing gh actions

* updates CNAME

* update testing email

* updates username/email

* updates to email in github-actions-website

* testing gh actions for feature_dict

* testing github-actions feature_dict

* updates to github-actions-feature_dict

* Update github-actions-feature_dict.yaml

* testing updates to feature_dict.py

* testing feature_dict updates

* testing updates to feature_dict.py

* testing feature_dict deployment

* Update github-actions-feature_dict.yaml

* testing feature_dict updates

* testing updates to feature_dict.py

* updates to feature_dict

* updates to github actions feature_dict

* testing auto updates to feature_dict

* Update feature_dict.py

* testing feature_dict auto updates

* testing feature_dict auto updates

* Update feature_dict.py

* testing feature_dict auto updates

* remove commented code in feature_dict.py

* Delete src/team_comm_tools/filtered_dict.json

delete test json file

* Update github-actions-website.yaml to deploy on update to dev

* put 'dev' in quotes

* Update github-actions-feature_dict.yaml to update upon dev

* re-add filtered dict

* update packages for website

---------

Co-authored-by: amytangzheng <[email protected]>
* Update package-lock.json

* Update package.json
* address #306

* fix hedges reference and update dictionary
@amytangzheng amytangzheng requested a review from xehu November 6, 2024 02:14
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Please update the package requirements in requirements.txt and pyproject.toml and make sure the tests pass!

@xehu xehu changed the base branch from main to dev November 20, 2024 23:26
@@ -18,6 +18,9 @@
juries_df = pd.read_csv("./example_data/full_empirical_datasets/jury_conversations_with_outcome_var.csv", encoding='utf-8')
csop_df = pd.read_csv("./example_data/full_empirical_datasets/csop_conversations_withblanks.csv", encoding='utf-8')
csopII_df = pd.read_csv("./example_data/full_empirical_datasets/csopII_conversations_withblanks.csv", encoding='utf-8')
test_df = pd.read_csv("C:/Users/amyta/Documents/GitHub/team_comm_tools/tests/data/cleaned_data/test_package_aggregation.csv", encoding='utf-8')
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@amytangzheng I think this is a reference to a local path and it needs to be updated!

self.chat_features = list(itertools.chain(*[feature_dict[feature]["columns"] for feature in self.feature_names if feature_dict[feature]["level"] == "Chat"]))
self.conv_features_base = list(itertools.chain(*[feature_dict[feature]["columns"] for feature in self.feature_names if feature_dict[feature]["level"] == "Conversation"]))
self.conv_features_all = [col for col in self.conv_data if col not in self.orig_data and col != 'conversation_num']

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Note --- check this; we likely want the last line self.conv_features_all to appear AFTER we actually generate the features, so moving this line of code up may not work.

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UPDATE: fixed

:type regenerate_vectors: bool, optional

:param compute_vectors_from_preprocessed: If true, computes vectors using preprocessed text (that is, with capitalization and punctuation removed). This was the default behavior for v.0.1.3 and earlier, but we now default to computing metrics on the unpreprocessed text (which INCLUDES capitalization and punctuation). Defaults to False.
:type compute_vectors_from_preprocessed: bool, optional
:param custom_vect_path: If provided, features will be generated using custom vectors rather than default SBERT. Defaults to None.
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Note: need to update documentation

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RESOLVED

@@ -358,7 +392,24 @@ def __init__(
if not re.match(r"(.*\/|^)output\/", self.output_file_path_user_level):
self.output_file_path_user_level = re.sub(r'/user/', r'/output/user/', self.output_file_path_user_level)

self.vect_path = vector_directory + "sentence/" + ("turns" if self.turns else "chats") + "/" + base_file_name
if custom_vect_path is not None:
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Note: it seems like this PR build in some of the initial infrastructure for custom vectors (document this)

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RESOLVED -- custom vector infrastructure has been removed

@xehu xehu merged commit aa7b5f4 into dev Dec 3, 2024
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@xehu xehu deleted the amy/package_v2 branch December 3, 2024 22:50
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