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Commits on Sep 2, 2025

• Merge pull request #210 from GilsonLabUCSD/jaketanderson-add-codacy

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Commits on Jun 16, 2025

• Pinned dependent actions to new releases w/ SHA

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• Changed actions' explicit versioning -> latest

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Commits on Jan 5, 2025

• Create codacy.yml

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Commits on Sep 16, 2024

• Merge pull request #202 from jaketanderson/github_actions

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Commits on Sep 7, 2024

• Undid pin to python 3.8 accidentally given in 9ad2d31

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• Yet another attempt at satisfying the linters

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• Cosmetic change to import order to stop flake8 from complaining during lint checks

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• Linted files with black

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• Moved pinned jax version to test_env.yaml from setup.py

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• Removed --no-deps flag from pip install inside CI workflow

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• Updated python & github actions versions for linting workflow

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• Modified setup.py install-requires s.t. python3.9 needs jax<=0.4.28

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• "Miniforge" doesn't work, "Miniforge3" may be the fix

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• Mambaforge --> Miniforge in ci.yaml

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• Raised versions for the github action

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• Removed testing on macos because pytraj does not support arm

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• Update action versions in CI

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• Merge pull request #201 from jaketanderson/maintenance_testing

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Commits on Sep 5, 2024

• Removed versioneer from test_env.yaml as it was only a one-time need

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• Updated codecov to v4 and falsified "fail_ci_if_error"

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• Cosmetic commit to prompt CI to run again in PR #201

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• Removed the specific jupyter packages from env file

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• Specifically require notebook

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• Removed numpy<2 criterion

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• cosmetic commit to kick CI

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• Linting

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• Attempt #1 at fixing versioneer issue

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Commits on Nov 29, 2023

• Merge pull request #197 from jaketanderson/avoid_tleap

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Commits on Oct 17, 2023

• Added myself as a contributor

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• Implemented changes recommended by @jeff231li except alterations to the manual pulling

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Commits on Oct 9, 2023

• Added to comment regarding improving the calculation

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• Added a tutorial notebook that does APR on sug-roc without using Tleap

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Commits on Aug 10, 2023

• Merge pull request #196 from jaketanderson/fix-window-import

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• Fixed some imports using old locations in tutorials

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