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Trajectory visualizer #51

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wants to merge 21 commits into from
Closed

Trajectory visualizer #51

wants to merge 21 commits into from

Commits on Oct 29, 2019

  1. start migration towards aiida 1.0

     * structures.ipynb starts to work
       (at least the examples part)
       For some reason, upload button is not displayed
     * enable travis
    
     * fix versions of pre-commit packages
    ltalirz authored and yakutovicha committed Oct 29, 2019
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  2. Finish migration towards aiida 1.0

    * Migrate to python 3
    Also reemove aiida from the dependency list. This is needed to lock
    the dependencies using Pipfile: aiida-core -> circus -> pyzmq <17.0
    notebook -> pyzmq>=17
    * Apply pre-commit hooks to the code
    yakutovicha committed Oct 29, 2019
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  3. Add widgets from aiidalab-empa-surfaces:

    widgets are imported from the repository:
    https://github.com/cpignedoli/aiidalab-empa-surfaces
    
    List of widgets:
    1) structure browser widget
    2) metadata widget
    3) submit button widget
    
    Also remove functions introduced in fbc917f
    Since they weren't proven to be useful.
    yakutovicha committed Oct 29, 2019
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Commits on Oct 31, 2019

  1. Add custom pre-commit config files and fix most of the style problems

    Files added:
    1) .pre-commit-config.yaml
    2) .prospector.yaml
    3) .pylintrc
    4) .style.yapf
    
    Python3 compatibility:
    1) computers.py: fix utf-8 problems
    
    Code refactoring:
    1) Factor out predefine_settings, valid_arguments and put them into utils
    
    Silent some pylint warnings, where appropriate
    yakutovicha committed Oct 31, 2019
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Commits on Nov 1, 2019

  1. Prepare release 1.0.0a6

    yakutovicha committed Nov 1, 2019
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Commits on Nov 7, 2019

  1. Three new widgets + two fixes:

    * New widgets:
      1) ProgressBar
      2) ExportButton
      3) RunningCalcJobOutput
    
    * Fix download function in FolderData and StructureVisualizer widgets
    yakutovicha committed Nov 7, 2019
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  2. Prepare release 1.0.0a7

    yakutovicha committed Nov 7, 2019
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Commits on Dec 3, 2019

  1. Work on AiiDA objects viewers (#28)

    * Replace `aiidalab_display` function with a `viewer` function that returns a
    a viewer object able to display the given AiiDA object:
    * StructureVisualizer:
      1) Add thumbnail property
      2) Simplify and unify the conversion to cif, xyz and png formats
    yakutovicha authored Dec 3, 2019
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  2. CodeDropdown widget: add path_to_root parameter (#29)

    This parameter defines how many folders one should go up in order
    to arrive at the apps' root folder.
    yakutovicha authored Dec 3, 2019
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Commits on Dec 4, 2019

  1. Inject StructureBrowserWidget into StructureUploader (#30)

    Before StructureBrowserWidget was a stand-alone. To unify the access and
    simplify the usage I made it insertable into the StructureUploaderWidget.
    yakutovicha authored Dec 4, 2019
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Commits on Dec 6, 2019

  1. Introduce the concept of the ProcessFollower (#33)

    Add the `ProcessFollower` class that is able to follow a process until it is completed. At the
    creation time the `ProcessFollower` accepts a list of followers that can check a particular
    outcome of the running process and display it. The followers are specified at the moment of
    `ProcessFollower` creation. For the moment we have two followers: `ProgressBarWidget` that
    displays the progress and `RunningCalcJobOutputWidget` that displays the output of a running
    process.
    yakutovicha authored Dec 6, 2019
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Commits on Dec 18, 2019

  1. Refactor structures widgets and add SMILES importer (#35)

    * Move structure browser widget into structures.py
    
    * Initial implementation of SMILES importer.
    yakutovicha authored Dec 18, 2019
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  2. Refactor process widgets (#37)

    Move `SubmitButtonWidget` from a separate file into `process.py` where all process-related widgets are located
    yakutovicha authored Dec 18, 2019
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Commits on Dec 19, 2019

  1. Remove metadata widget (#39)

    As at the current state of things, the metadata widget can be be made general enough, it is better to not provide it as a part of the package.
    yakutovicha authored Dec 19, 2019
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Commits on Dec 24, 2019

  1. Work on structure widgets: (#40)

    Since the `StructureUploadWidget` has become a widget of more general-purpose, not only for
    uploading - it makes sense to rename it so that the name reflects it's nature. The widget has been
    renamed to `StructureManagerWidget`. The only purpose of the widget is to call other single-purpose
    widgets to upload structure, select structure from AiiDA database, upload structure from public
    databases, etc. Two single-purpose widgets were extracted from old `StructureUploadWidget`: new `StructureUploadWidget` that only allows uploading structures from a computer and `StructureExamplesWidget` that allows providing example structures.
    yakutovicha authored Dec 24, 2019
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Commits on Dec 30, 2019

  1. Reuse structure data viewer in StructureManagerWidget (#41)

    To avoid code duplication I used StructureViewerWidget to display structure
    in StructureManagerWidget. The code of the viewer has been improved
    thanks to the suggestions of @csadorf.
    yakutovicha authored Dec 30, 2019
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  2. Configuration menu
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Commits on Jan 16, 2020

  1. Make OpenBabel a soft dependency (#50)

    * Disable smiles widget if openbabel library is not present.
    
    Co-authored-by: Aliaksandr Yakutovich <[email protected]>
    csadorf and yakutovicha committed Jan 16, 2020
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  2. Remove py27 (#49)

    * Remove six module imports.
    * Remove __future__ imports.
    * Remove 'python-modernize' from git pre-commit installs.
    csadorf authored and yakutovicha committed Jan 16, 2020
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Commits on Jan 20, 2020

  1. Work on StructureDataViewer (#47)

    * Extract Base parts into a separate class that can be reused. It defines the basic outline
    and properties. Also, it adds a configuration panel. Finally, it contains the `selection` trait.  
    * Inherit `StructureDataViewer` widget from the base one. It adds `structure` trait.
    * Create CopyToClipboardButton widget that has `value` trait used for a copy.
    
    Co-authored-by: Carl Simon Adorf <[email protected]>
    yakutovicha and csadorf authored Jan 20, 2020
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  2. Working version of trajectory visualizer based on bqplot

    yakutovicha authored and Aliaksandr Yakutovich committed Jan 20, 2020
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