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Remove deprecated formats, update reader and writer backends #1191

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Remove deprecated formats, update reader and writer backends #1191

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Commits on Jul 2, 2024

  1. remove hoomdxml

    @chrisjonesBSU
    chrisjonesBSU committed Jul 2, 2024
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  2. remove protobuf

    @chrisjonesBSU
    chrisjonesBSU committed Jul 2, 2024
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  3. remove hoomd3 force writers

    @chrisjonesBSU
    chrisjonesBSU committed Jul 2, 2024
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  4. change backend for mol2 and xyz to gmso

    @chrisjonesBSU
    chrisjonesBSU committed Jul 2, 2024
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  5. remove protobuf from dev environments

    @chrisjonesBSU
    chrisjonesBSU committed Jul 2, 2024
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Commits on Jul 3, 2024

  1. add some TODO notes

    @chrisjonesBSU
    chrisjonesBSU committed Jul 3, 2024
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Commits on Aug 7, 2024

  1. Merge branch 'main' of github.com:mosdef-hub/mbuild into remove-dep

    @chrisjonesBSU
    chrisjonesBSU committed Aug 7, 2024
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Commits on Aug 19, 2024

  1. Merge branch 'main' of github.com:mosdef-hub/mbuild into remove-dep

    @chrisjonesBSU
    chrisjonesBSU committed Aug 19, 2024
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  2. Merge branch 'main' of github.com:mosdef-hub/mbuild into remove-dep

    @chrisjonesBSU
    chrisjonesBSU committed Aug 19, 2024
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Commits on Aug 20, 2024

  1. Merge branch 'main' of github.com:mosdef-hub/mbuild into remove-dep

    @chrisjonesBSU
    chrisjonesBSU committed Aug 20, 2024
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Commits on Aug 22, 2024

  1. change behavior of xyz test

    @chrisjonesBSU
    chrisjonesBSU committed Aug 22, 2024
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  2. Merge branch 'remove-dep' of github.com:chrisjonesBSU/mbuild into rem… 

    …ove-dep
    @chrisjonesBSU
    chrisjonesBSU committed Aug 22, 2024
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Commits on Aug 26, 2024

  1. Merge branch 'main' of github.com:mosdef-hub/mbuild into remove-dep

    @chrisjonesBSU
    chrisjonesBSU committed Aug 26, 2024
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  2. comment out test for elements

    @chrisjonesBSU
    chrisjonesBSU committed Aug 26, 2024
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  3. fix test based on expected behavior for xyz files, remove wrong n ato… 

    …ms tests, that is being tested for in GMSO test_xyz.py
    @chrisjonesBSU
    chrisjonesBSU committed Aug 26, 2024
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Commits on Aug 29, 2024

  1. remove lammpsdata and tests

    @chrisjonesBSU
    chrisjonesBSU committed Aug 29, 2024
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  2. Merge branch 'remove-dep' of github.com:chrisjonesBSU/mbuild into rem… 

    …ove-dep
    @chrisjonesBSU
    chrisjonesBSU committed Aug 29, 2024
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Commits on Sep 9, 2024

  1. remove duplicate benzene fixture that reads benzene from a mol2 file

    @chrisjonesBSU
    chrisjonesBSU committed Sep 9, 2024
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Commits on Sep 13, 2024

  1. update benzene naming to fix failing rigid tests

    @CalCraven
    CalCraven committed Sep 13, 2024
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  2. Merge branch 'main' of github.com:mosdef-hub/mbuild into remove-dep

    @chrisjonesBSU
    chrisjonesBSU committed Sep 13, 2024
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  3. add hoomd_writer file that has GSD and snapshot writer

    @chrisjonesBSU
    chrisjonesBSU committed Sep 13, 2024
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  4. fix typo

    @chrisjonesBSU
    chrisjonesBSU committed Sep 13, 2024
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  5. add else statement

    @chrisjonesBSU
    chrisjonesBSU committed Sep 13, 2024
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  6. move to_hoomdsnapshot to conversion, add method in Compound class. De… 

    …lete old snapshot and gsd writers
    @chrisjonesBSU
    chrisjonesBSU committed Sep 13, 2024
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  7. fix import

    @chrisjonesBSU
    chrisjonesBSU committed Sep 13, 2024
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  8. remove hoomd writer file, add TODO flags to conversion

    @chrisjonesBSU
    chrisjonesBSU committed Sep 13, 2024
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Commits on Sep 16, 2024

  1. add TODO notes, pass in overwrite to Topology.save(), comment out fil… 

    …e formats that require typed systems
    @chrisjonesBSU
    chrisjonesBSU committed Sep 16, 2024
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  2. remove tests for gsd, hoomd, cassandra and par writers, move tests fo… 

    …r loading xys into test_compound
    @chrisjonesBSU
    chrisjonesBSU committed Sep 16, 2024
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  3. [pre-commit.ci] auto fixes from pre-commit.com hooks 

    for more information, see https://pre-commit.ci
    @pre-commit-ci
    pre-commit-ci[bot] committed Sep 16, 2024
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  4. add check for charges back in save method

    @chrisjonesBSU
    chrisjonesBSU committed Sep 16, 2024
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  5. Merge branch 'remove-dep' of github.com:chrisjonesBSU/mbuild into rem… 

    …ove-dep
    @chrisjonesBSU
    chrisjonesBSU committed Sep 16, 2024
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  6. [pre-commit.ci] auto fixes from pre-commit.com hooks 

    for more information, see https://pre-commit.ci
    @pre-commit-ci
    pre-commit-ci[bot] committed Sep 16, 2024
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  7. add if statement before checking charge is neutral

    @chrisjonesBSU
    chrisjonesBSU committed Sep 16, 2024
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Commits on Sep 17, 2024

  1. remove .top from unit test

    @chrisjonesBSU
    chrisjonesBSU committed Sep 17, 2024
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Commits on Oct 3, 2024

  1. remove lammps and lammpsdata files from tests and support in conversi… 

    …on.py
    @chrisjonesBSU
    chrisjonesBSU committed Oct 3, 2024
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Commits on Oct 5, 2024

  1. Don't use gmso mol2 backend

    @chrisjonesBSU
    chrisjonesBSU committed Oct 5, 2024
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  2. Don't use gmso mol2 backend

    @chrisjonesBSU
    chrisjonesBSU committed Oct 5, 2024
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Commits on Oct 6, 2024

  1. remove gmso as backend for mol2 saver

    @chrisjonesBSU
    chrisjonesBSU committed Oct 6, 2024
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  2. remove Hoomd V3 test from CI

    @chrisjonesBSU
    chrisjonesBSU committed Oct 6, 2024
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  3. remove par writer and xyz reader/write

    @chrisjonesBSU
    chrisjonesBSU committed Oct 6, 2024
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