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Functions to plot networkx graphs of topology objects #492

Merged
merged 81 commits into from
May 11, 2021
Merged

Functions to plot networkx graphs of topology objects #492

merged 81 commits into from
May 11, 2021

Commits on Jan 9, 2021

  1. Include angle and dihedral information on conversion of topology to n… 

    …etworkx
    @CalCraven
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Commits on Jan 10, 2021

  1. create gmso/formats/networkx.py

    @CalCraven
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Commits on Jan 12, 2021

  1. Add _get_angles_for and _get_dihedrals_for methods for a topology. Se… 

    …lects angles/dihedrals for a particular Site
    @CalCraven
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Commits on Jan 14, 2021

  1. Add functions to clean up networkx plotting, and plot missing angle a… 

    …nd bond types
    @CalCraven
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Commits on Jan 15, 2021

  1. Add unit tests for _get_x_for where x is bonds, angles, and dihedrals… 

    …. Add _get_bonds_for method in topology.py
    @CalCraven
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  2. Merge branch 'convert_nx' of https://github.com/CalCraven/gmso into v… 

    …is_atype

"merge new methods to convert angles and dihedrals from the _get_angles,dihderals_for methods in topology.py"
    @CalCraven
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Commits on Jan 20, 2021

  1. Fix import * and add soft import for matplotlib

    @CalCraven
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Commits on Jan 21, 2021

  1. Add unit tests for selecting atomtype parameters, and soft imports fo… 

    …r matplotlib and networkx to io.py
    @CalCraven
    CalCraven committed Jan 21, 2021
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  2. change to

    @CalCraven
    CalCraven committed Jan 21, 2021
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Commits on Jan 28, 2021

  1. update to current master branch

    @CalCraven
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  2. add interactive features to networkx.py

    @CalCraven
    CalCraven committed Jan 28, 2021
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  3. update to master

    @CalCraven
    CalCraven committed Jan 28, 2021
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  4. fix bugs with importing networkx.py functions

    @CalCraven
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Commits on Feb 4, 2021

  1. Merge branch 'master' into vis_atype

    @daico007
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  2. Convert charge units, clean up if statements for selecting angles and… 

    … dihedrals
    @CalCraven
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Commits on Feb 10, 2021

  1. Merge branch 'vis_atype' of https://github.com/CalCraven/gmso into vi… 

    …s_atype

"Merge to changes made to master need to be merged"
    @CalCraven
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  2. Clean up layout for plotting molecules

    @CalCraven
    CalCraven committed Feb 10, 2021
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  3. update charges

    @CalCraven
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  4. Merge branch 'master' of https://github.com/mosdef-hub/gmso 

    "update to master"
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  5. Merge branch 'master' of https://github.com/CalCraven/gmso into vis_a… 

    …type
    @CalCraven
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  6. remove Ipython.Display import

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Commits on Feb 15, 2021

  1. Add messages and support for gmso.topology objects that are missing a… 

    …ttributes such as parameters and atomtypes
    @CalCraven
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Commits on Feb 22, 2021

  1. Unit tests that are still failing

    @CalCraven
    CalCraven committed Feb 22, 2021
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  2. Passing test_highlight_edges

    @CalCraven
    CalCraven committed Feb 22, 2021
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  3. unit tests passing for selecting_parameters

    @CalCraven
    CalCraven committed Feb 22, 2021
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Commits on Feb 24, 2021

  1. update to master

    @CalCraven
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  2. Fix unused import, and improve import of test_networkx.py functions

    @CalCraven
    CalCraven committed Feb 24, 2021
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  3. increase unit test coverage

    @CalCraven
    CalCraven committed Feb 24, 2021
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  4. Merge branch 'master' of https://github.com/mosdef-hub/gmso into vis_… 

    …atype

"Update to master"
    @CalCraven
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  5. Add ipywidgets to requirements-test.txt

    @CalCraven
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Commits on Feb 25, 2021

  1. Fill out unit tests

    @CalCraven
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  2. Merge branch 'master' of https://github.com/mosdef-hub/gmso into vis_… 

    …atype

"update to master"
    @CalCraven
    CalCraven committed Feb 25, 2021
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Commits on Feb 26, 2021

  1. parameter and get_edges unit tests

    @CalCraven
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Commits on Mar 11, 2021

  1. Update to master

    @CalCraven
    CalCraven committed Mar 11, 2021
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  2. Fix merge issue, update test_return_labels_for_nodes

    @CalCraven
    CalCraven committed Mar 11, 2021
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  3. create gmso/formats/networkx.py

    @CalCraven
    CalCraven committed Mar 11, 2021
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  4. Add functions to clean up networkx plotting, and plot missing angle a… 

    …nd bond types
    @CalCraven
    CalCraven committed Mar 11, 2021
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  5. Add _get_angles_for and _get_dihedrals_for methods for a topology. Se… 

    …lects angles/dihedrals for a particular Site
    @CalCraven
    CalCraven committed Mar 11, 2021
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  6. Add unit tests for _get_x_for where x is bonds, angles, and dihedrals… 

    …. Add _get_bonds_for method in topology.py
    @CalCraven
    CalCraven committed Mar 11, 2021
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  7. Fix import * and add soft import for matplotlib

    @CalCraven
    CalCraven committed Mar 11, 2021
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  8. Add unit tests for selecting atomtype parameters, and soft imports fo… 

    …r matplotlib and networkx to io.py
    @CalCraven
    CalCraven committed Mar 11, 2021
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  9. change to

    @CalCraven
    CalCraven committed Mar 11, 2021
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  10. remove merge conflicts

    @CalCraven
    CalCraven committed Mar 11, 2021
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  11. rebase to master

    @CalCraven
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  12. rebase to fee3df2

    @CalCraven
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Commits on Mar 15, 2021

  1. Add tests for select_params_on_networkx and select_angles_from_sites

    @CalCraven
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  2. unit tests for select_parameters_on_networkx missing angles and dihed… 

    …rals
    @CalCraven
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Commits on Mar 18, 2021

  1. remove interact fixtures to improve ease for writing unit tests

    @CalCraven
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  2. unit tests for call_interactive_sites

    @CalCraven
    CalCraven committed Mar 18, 2021
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Commits on Mar 24, 2021

  1. Merge branch 'master' into vis_atype

    @daico007
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Commits on Mar 25, 2021

  1. add tests for select_edges and show_bond_info

    @CalCraven
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  2. add tests to call_interactive sites

    @CalCraven
    CalCraven committed Mar 25, 2021
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Commits on Apr 2, 2021

  1. apply black to clean up code formatting

    @CalCraven
    CalCraven committed Apr 2, 2021
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Commits on Apr 6, 2021

  1. Update gmso/formats/networkx.py 

    update docstrings

Co-authored-by: Umesh Timalsina <umesh.timalsina@vanderbilt.edu>
    @CalCraven @umesh-timalsina
    CalCraven and umesh-timalsina authored Apr 6, 2021
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  2. Update gmso/formats/networkx.py 

    update docstrings

Co-authored-by: Umesh Timalsina <umesh.timalsina@vanderbilt.edu>
    @CalCraven @umesh-timalsina
    CalCraven and umesh-timalsina authored Apr 6, 2021
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  3. Update gmso/formats/networkx.py 

    use .items method to simplify code

Co-authored-by: Umesh Timalsina <umesh.timalsina@vanderbilt.edu>
    @CalCraven @umesh-timalsina
    CalCraven and umesh-timalsina authored Apr 6, 2021
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  4. add selectable_dict_for_edges_from_labels function

    @CalCraven
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  5. fixed an issue with the widgets dropdown not being selectable as a li… 

    …st of tuples, and fixed the selection methods for angles from two and three specified atoms
    @CalCraven
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Commits on Apr 7, 2021

  1. fix behavior with missing atom_types so parameters can still be visua… 

    …lized
    @CalCraven
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  2. update docstrings for interactive methods

    @CalCraven
    CalCraven committed Apr 7, 2021
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  3. apply black

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    CalCraven committed Apr 7, 2021
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Commits on Apr 8, 2021

  1. Update gmso/formats/networkx.py 

    Co-authored-by: Umesh Timalsina <umesh.timalsina@vanderbilt.edu>
    @CalCraven @umesh-timalsina
    CalCraven and umesh-timalsina authored Apr 8, 2021
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Commits on Apr 11, 2021

  1. Merge branch 'master' into vis_atype

    @daico007
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Commits on Apr 15, 2021

  1. Merge branch 'master' into vis_atype

    @CalCraven
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Commits on Apr 19, 2021

  1. Merge branch 'master' of https://github.com/mosdef-hub/gmso

    @CalCraven
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Commits on Apr 28, 2021

  1. Merge branch 'master' of https://github.com/mosdef-hub/gmso

    @CalCraven
    CalCraven committed Apr 28, 2021
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  2. update to master

    @CalCraven
    CalCraven committed Apr 28, 2021
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  3. remove requirements-test.txt

    @CalCraven
    CalCraven committed Apr 28, 2021
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  4. checks for installation of matplotlib and ipywidgets

    @CalCraven
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  5. change ipywidgets to widgets

    @CalCraven
    CalCraven committed Apr 28, 2021
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  6. update testing with soft imports

    @CalCraven
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  7. put functions meant to be implemented by users on top, add checks for… 

    … operations within a jupyter notebook
    @CalCraven
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  8. add matplotlib and ipywidgets for unit testing

    @CalCraven
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  9. skip tests that need a jupyter notebook to run

    @CalCraven
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  10. Merge branch 'master' into vis_atype

    @CalCraven
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Commits on Apr 29, 2021

  1. switch interactive functions to not be covered by codecov, create gms… 

    …o/utils/nx_utils.py for functions used by interactive visualization
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  2. Merge branch 'vis_atype' of https://github.com/CalCraven/gmso into vi… 

    …s_atype
    @CalCraven
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Commits on May 3, 2021

  1. Merge branch 'master' into vis_atype

    @CalCraven
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  2. add calls to io/nx_utils for functions in formats/networkx.py

    @CalCraven
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Commits on May 6, 2021

  1. fix __init__.py for importing networkx functionality

    @CalCraven
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Commits on May 11, 2021

  1. improve logic for unit tests

    @CalCraven
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