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K cl #98

Merged
merged 46 commits into from Apr 26, 2019
Merged

K cl #98

merged 46 commits into from Apr 26, 2019

Commits on Jan 10, 2019

  1. Remove custom precommit hook

    @slochower
    slochower committed Jan 10, 2019
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  2. Add intersphinx to ParmEd

    @slochower
    slochower committed Jan 10, 2019
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Commits on Feb 8, 2019

  1. First migration of cookie-cutter

    @slochower
    slochower committed Feb 8, 2019
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  2. Forgot to migrate dotfiles

    @slochower
    slochower committed Feb 8, 2019
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  3. Add versioneer.py

    @slochower
    slochower committed Feb 8, 2019
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  4. Fixed a few imports and first test working

    @slochower
    slochower committed Feb 8, 2019
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  5. Updates test_tleap.py

    @slochower
    slochower committed Feb 8, 2019
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  6. Rename restraints_json to io

    @slochower
    slochower committed Feb 8, 2019
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Commits on Feb 9, 2019

  1. Updates test_io (from test_json) and implements pytest.fixture

    @slochower
    slochower committed Feb 9, 2019
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  2. Removed efficiency testing

    @slochower
    slochower committed Feb 9, 2019
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Commits on Feb 10, 2019

  1. Add separate file to test for Amber/OpenMM imports and executables.

    @slochower
    slochower committed Feb 10, 2019
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  2. Add separate file to test for Amber/OpenMM imports and executables.

    @slochower
    slochower committed Feb 10, 2019
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  3. DS_Store be gone

    @slochower
    slochower committed Feb 10, 2019
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  4. OpenMM tests working, but need reference values

    @slochower
    slochower committed Feb 10, 2019
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Commits on Feb 11, 2019

  1. Rename reference data, optimize imports, and fix analysis

    @slochower
    slochower committed Feb 11, 2019
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  2. Run black on tests/ directory

    @slochower
    slochower committed Feb 11, 2019
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  3. Debugging paths

    @slochower
    slochower committed Feb 11, 2019
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  4. Debugging Travis paths

    @slochower
    slochower committed Feb 11, 2019
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  5. Testing before_script

    @slochower
    slochower committed Feb 11, 2019
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  6. Change in test directory

    @slochower
    slochower committed Feb 11, 2019
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Commits on Feb 12, 2019

  1. Much better, more robust, path handling in tests

    @slochower
    slochower committed Feb 12, 2019
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  2. Much better, more robust, path handling in tests

    @slochower
    slochower committed Feb 12, 2019
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  3. Add ParmEd dependency

    @slochower
    slochower committed Feb 12, 2019
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  4. Add Pytraj dependency

    @slochower
    slochower committed Feb 12, 2019
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  5. Add ambermd to dependencies, in addition to ambertools/conda

    @slochower
    slochower committed Feb 12, 2019
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  6. Bump ambertools=18, remove explicit pytraj

    @slochower
    slochower committed Feb 12, 2019
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Commits on Feb 13, 2019

  1. Disable Python 3.7 testing until is updated

    @slochower
    slochower committed Feb 13, 2019
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  2. Merge branch 'cookiecutter' of ssh://github.com/slochower/pAPRika int… 

    …o cookiecutter
    @slochower
    slochower committed Feb 13, 2019
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  3. Adjust reference value

    @slochower
    slochower committed Feb 13, 2019
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Commits on Feb 14, 2019

  1. Reduce atol to get tests to pass

    @slochower
    slochower committed Feb 14, 2019
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  2. Adjust atol for AMBER

    @slochower
    slochower committed Feb 14, 2019
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  3. Remove half-baked K-Cl test

    @slochower
    slochower committed Feb 14, 2019
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  4. Better path handling

    @slochower
    slochower committed Feb 14, 2019
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  5. Adjust path for filecmp

    @slochower
    slochower committed Feb 14, 2019
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Commits on Feb 15, 2019

  1. Explicitly set neutralize=False for tleap (more strict with ambertool… 

    …s=18)
    @slochower
    slochower committed Feb 15, 2019
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  2. Add K-Cl reference data

    @slochower
    slochower committed Feb 15, 2019
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  3. Change file comparison to np.allclose()

    @slochower
    slochower committed Feb 15, 2019
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Commits on Feb 19, 2019

  1. Update .gitignore and more inclusive JSON serialization

    @slochower
    slochower committed Feb 19, 2019
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  2. Add quick outline of how to perform a K-Cl calculation

    @slochower
    slochower committed Feb 19, 2019
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Commits on Apr 25, 2019

  1. Begin test cleanup

    @slochower
    slochower committed Apr 25, 2019
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  2. Add utility tests

    @slochower
    slochower committed Apr 25, 2019
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  3. Update test_align

    @slochower
    slochower committed Apr 25, 2019
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  4. Strip half-backed OpenMM stuff out for now

    @slochower
    slochower committed Apr 25, 2019
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  5. Extract TSCC script for running k-cl calculations

    @slochower
    slochower committed Apr 25, 2019
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  6. Add K-Cl input files (modified charge) from the gold-standard calcula… 

    …tion
    @slochower
    slochower committed Apr 25, 2019
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  7. Test cleanup and switch from CB6-BUT to K-Cl for simple cases

    @slochower
    slochower committed Apr 25, 2019
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