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Initial merge: Dash sequence viewer #8

Merged
merged 121 commits into from
Nov 27, 2018
Merged

Initial merge: Dash sequence viewer #8

merged 121 commits into from
Nov 27, 2018

Commits on Sep 18, 2018

  1. Add sequence viewer to package.json.

    Shammamah Hossain committed Sep 18, 2018
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  2. Add React wrapper for sequence viewer component.

    Shammamah Hossain committed Sep 18, 2018
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Commits on Sep 19, 2018

  1. Add in requirements to package.json; add in selection feature for seq… 

    …uence viewer.
    Shammamah Hossain committed Sep 19, 2018
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  2. Implement coverage feature.

    Shammamah Hossain committed Sep 19, 2018
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  3. Add testing code for sequence viewer.

    Shammamah Hossain committed Sep 19, 2018
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Commits on Sep 22, 2018

  1. Update progress; setProps still undefined.

    Shammamah Hossain committed Sep 22, 2018
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Commits on Sep 24, 2018

  1. Back to working state; setProps still is not defined as a function.

    Shammamah Hossain committed Sep 24, 2018
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  2. Fix issue with setProps; all onclick functions work now for coverage.

    Shammamah Hossain committed Sep 24, 2018
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  3. Change deprecated ComponentWillMount to ComponentDidMount.

    Shammamah Hossain committed Sep 24, 2018
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  4. Use Insulin for Dash app.

    Shammamah Hossain committed Sep 24, 2018
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  5. Add error handling for updating coverage.

    Shammamah Hossain committed Sep 24, 2018
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  6. First attempt at implementing mouse selection and subpart selection.

    Shammamah Hossain committed Sep 24, 2018
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  7. Add sections for testing all aspects of coverage and selection.

    Shammamah Hossain committed Sep 24, 2018
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  8. Add descriptions of all prop types.

    Shammamah Hossain committed Sep 24, 2018
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  9. Implement and show example of legend.

    Shammamah Hossain committed Sep 24, 2018
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Commits on Sep 25, 2018

  1. onMouseSelection and onSubpartSelected correctly work with the consol… 

    …e, but not with setProps.
    Shammamah Hossain committed Sep 25, 2018
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  2. Remove some unnecessary lines of code and add TODO for ShouldComponen… 

    …tUpdate.
    Shammamah Hossain committed Sep 25, 2018
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Commits on Sep 26, 2018

  1. Fix issue with rerendering in the middle of searching for a sequence;… 

    … implement subpart selection and mouse selection.
    Shammamah Hossain committed Sep 26, 2018
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  2. Modify usage.py to demonstrate subpart selection.

    Shammamah Hossain committed Sep 26, 2018
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  3. Minor typo corrections; note that onMouseSelection and onclick events… 

    … for coverage cannot work together for some reason.
    Shammamah Hossain committed Sep 26, 2018
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  4. Add beginnings of app styling.

    Shammamah Hossain committed Sep 26, 2018
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Commits on Sep 27, 2018

  1. Implement shouldComponentUpdate to deal with issue of re-rendering up… 

    …on seach.
    Shammamah Hossain committed Sep 27, 2018
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  2. First draft of demo app for meeting.

    Shammamah Hossain committed Sep 27, 2018
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Commits on Sep 28, 2018

  1. Add fix for webpack issue described on dash-component-boilerplate rep… 

    …ository.
    Shammamah Hossain committed Sep 28, 2018
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  2. Add dash_bio and package-lock.

    Shammamah Hossain committed Sep 28, 2018
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Commits on Oct 3, 2018

  1. Add in a helper script to parse .fasta files, and incorporate these c… 

    …hanges into usage.py.
    Shammamah Hossain committed Oct 3, 2018
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Commits on Oct 4, 2018

  1. Add functionality for multiple proteins in single fasta file.

    Shammamah Hossain committed Oct 4, 2018
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  2. Always return a list of proteins in protein reader.

    Shammamah Hossain committed Oct 4, 2018
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  3. Modify to allow reading a raw data string as well as reading from a f… 

    …ile; reading contents of file will make application work when running on Heroku.
    Shammamah Hossain committed Oct 4, 2018
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  4. Add docstrings and clean up code.

    Shammamah Hossain committed Oct 4, 2018
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Commits on Oct 11, 2018

  1. Add test app for sequence viewer.

    Shammamah Hossain committed Oct 11, 2018
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  2. Remove protein files and folder.

    Shammamah Hossain committed Oct 11, 2018
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  3. Delete ExampleComponent.py

    Shammamah Hossain committed Oct 11, 2018
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Commits on Oct 17, 2018

  1. Fix merge conflicts when merging master back in.

    Shammamah Hossain committed Oct 17, 2018
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  2. Update code to reflect dependencies for this app.

    Shammamah Hossain committed Oct 17, 2018
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Commits on Oct 18, 2018

  1. Make some changes as suggested in PR.

    Shammamah Hossain committed Oct 18, 2018
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  2. Add coverage option into demo app.

    Shammamah Hossain committed Oct 18, 2018
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Commits on Oct 22, 2018

  1. Add files for DDS.

    Shammamah Hossain committed Oct 22, 2018
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  2. Add tarball.

    Shammamah Hossain committed Oct 22, 2018
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  3. Fix double declaration of dash in requirements.txt.

    Shammamah Hossain committed Oct 22, 2018
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  4. Remove base64 from requirements.txt.

    Shammamah Hossain committed Oct 22, 2018
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  5. Add server variable for DDS to usage.py.

    Shammamah Hossain committed Oct 22, 2018
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  6. Include entire event details for mouse selection event.

    Shammamah Hossain committed Oct 22, 2018
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  7. Fix control box height.

    Shammamah Hossain committed Oct 22, 2018
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  8. Ensure that component updates when a new sequence is loaded.

    Shammamah Hossain committed Oct 22, 2018
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  9. Fix issue with coverage not being enabled.

    Shammamah Hossain committed Oct 22, 2018
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  10. Update tarball.

    Shammamah Hossain committed Oct 22, 2018
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  11. Fix issue with selection and/or coverage not having a length due to b… 

    …eing null.
    Shammamah Hossain committed Oct 22, 2018
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  12. Update tarball.

    Shammamah Hossain committed Oct 22, 2018
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  13. Update tarball to fix error with initializing selection and coverage … 

    …to null.
    Shammamah Hossain committed Oct 22, 2018
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Commits on Oct 24, 2018

  1. Initialize coverage and selection to be empty lists instead of null.

    Shammamah Hossain committed Oct 24, 2018
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  2. Fix issue with trying to access 'selection' key in a NoneType variable.

    Shammamah Hossain committed Oct 24, 2018
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  3. Add support for selecting a different protein in the same file.

    Shammamah Hossain committed Oct 24, 2018
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  4. Update tarball to reflect changes in component.

    Shammamah Hossain committed Oct 24, 2018
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  5. Update tarball again.

    Shammamah Hossain committed Oct 24, 2018
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  6. Modify protein reader to use Bio.SeqIO for parsing; clean up usage.py… 

    … code.
    Shammamah Hossain committed Oct 24, 2018
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  7. add biopython to requirements.

    Shammamah Hossain committed Oct 24, 2018
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Commits on Oct 30, 2018

  1. Regenerate package-lock.

    Shammamah Hossain committed Oct 30, 2018
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  2. Alphabetize requirements.

    Shammamah Hossain committed Oct 30, 2018
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  3. Remove onMouseSelection and onSubpartSelected functions from componen… 

    …t's props.
    Shammamah Hossain committed Oct 30, 2018
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  4. Provide default prop values.

    Shammamah Hossain committed Oct 30, 2018
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  5. condense declaration of constants in render method.

    Shammamah Hossain committed Oct 30, 2018
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  6. Remove null initialization of selection in usage.py, and remove condi… 

    …tional for checking if selection and/or coverage is null in render method.
    Shammamah Hossain committed Oct 30, 2018
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  7. Use "some" functions to filter through selection and coverage in shou… 

    …ldComponentUpdate, and remove checking for null values. Fix usage.py to not return None as value of selection.
    Shammamah Hossain committed Oct 30, 2018
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  8. Change 'var' to 'let'.

    Shammamah Hossain committed Oct 30, 2018
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  9. Put sequenceMaxHeight in defaultProps.

    Shammamah Hossain committed Oct 30, 2018
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Commits on Nov 5, 2018

  1. Clean up code and fix stylesheet to be specific to sequence viewer co… 

    …mponent.
    Shammamah Hossain committed Nov 5, 2018
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  2. Add sequence viewer test app.

    Shammamah Hossain committed Nov 5, 2018
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  3. Add new stylesheet.

    Shammamah Hossain committed Nov 5, 2018
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Commits on Nov 6, 2018

  1. Redeploy to DDS

    Shammamah Hossain committed Nov 6, 2018
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  2. Re-add usage.py.

    Shammamah Hossain committed Nov 6, 2018
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  3. Add parsing for other databases.

    Shammamah Hossain committed Nov 6, 2018
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Commits on Nov 7, 2018

  1. Add default props to sequence viewer component.

    Shammamah Hossain committed Nov 7, 2018
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Commits on Nov 8, 2018

  1. Test out empty component

    Shammamah Hossain committed Nov 8, 2018
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  2. Merge branch 'master' into dash-sequence-viewer

    Shammamah Hossain committed Nov 8, 2018
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  3. Merge branch 'master' into dash-sequence-viewer

    Shammamah Hossain committed Nov 8, 2018
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  4. rename test app.

    Shammamah Hossain committed Nov 8, 2018
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  5. merge master back and resolve conflicts.

    Shammamah Hossain committed Nov 8, 2018
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  6. Fix conflicts with master and add description/image.

    Shammamah Hossain committed Nov 8, 2018
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  7. Update style to display properly in new gallery page.

    Shammamah Hossain committed Nov 8, 2018
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  8. Merge branch 'master' into dash-sequence-viewer

    Shammamah Hossain committed Nov 8, 2018
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Commits on Nov 9, 2018

  1. Merge branch 'master' into dash-sequence-viewer

    Shammamah Hossain committed Nov 9, 2018
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  2. Ignore changes to index

    Shammamah Hossain committed Nov 9, 2018
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Commits on Nov 13, 2018

  1. Remove JQuery dependency.

    Shammamah Hossain committed Nov 13, 2018
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  2. Remove unnecessary functionality from proteinReader.

    Shammamah Hossain committed Nov 13, 2018
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  3. Use Biopython to translate amino acid sequences.

    Shammamah Hossain committed Nov 13, 2018
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  4. Fix height of controls container.

    Shammamah Hossain committed Nov 13, 2018
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  5. Use Biopython for translation and add translation alphabet options.

    Shammamah Hossain committed Nov 13, 2018
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  6. change style and add logo to demo app.

    Shammamah Hossain committed Nov 13, 2018
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  7. Add logo to demo app.

    Shammamah Hossain committed Nov 13, 2018
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  8. Update index.py

    Shammamah Hossain committed Nov 13, 2018
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  9. Remove index.py from gitignore.

    Shammamah Hossain committed Nov 13, 2018
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Commits on Nov 14, 2018

  1. Remove whitespace and clean up code as per code review comments.

    Shammamah Hossain committed Nov 14, 2018
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Commits on Nov 15, 2018

  1. Merge master and resolve conflicts.

    Shammamah Hossain committed Nov 15, 2018
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  2. Add tarball.

    Shammamah Hossain committed Nov 15, 2018
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  3. Remove versions from requirements.

    Shammamah Hossain committed Nov 15, 2018
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Commits on Nov 16, 2018

  1. Merge master back into branch.

    Shammamah Hossain committed Nov 16, 2018
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  2. Fix index.py and package.json to include most current versions on mas… 

    …ter.
    Shammamah Hossain committed Nov 16, 2018
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  3. Regenerate tarball.

    Shammamah Hossain committed Nov 16, 2018
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Commits on Nov 19, 2018

  1. Fix whitespace errors in package.json; regenerate tarball.

    Shammamah Hossain committed Nov 19, 2018
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  2. tarball again

    Shammamah Hossain committed Nov 19, 2018
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  3. update folder

    Shammamah Hossain committed Nov 19, 2018
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  4. Change react-sequence-viewer dependency to come from git repository.

    Shammamah Hossain committed Nov 19, 2018
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Commits on Nov 20, 2018

  1. Update stylesheet to have component-specific scrollbar styling.

    Shammamah Hossain committed Nov 20, 2018
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  2. Remove usage.py

    Shammamah Hossain committed Nov 20, 2018
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  3. Add title to sequence viewer.

    Shammamah Hossain committed Nov 20, 2018
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  4. Move onclick function assignments for coverage outside of render meth… 

    …od (still buggy; onclick is assigned, but clicking doesn't register until changing to a different sequence and then changing back).
    Shammamah Hossain committed Nov 20, 2018
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  5. Add sample data and add support for adding coverage in-app.

    Shammamah Hossain committed Nov 20, 2018
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Commits on Nov 21, 2018

  1. Load default data and coverage.

    Shammamah Hossain committed Nov 21, 2018
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  2. Fix webkit scrollbar styling to be specific to app.

    Shammamah Hossain committed Nov 21, 2018
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  3. Fix bug in which multiples of 3 for subsequence selection would not a… 

    …ppear.
    Shammamah Hossain committed Nov 21, 2018
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  4. Rename SequenceViewerComponent to SequenceViewer.

    Shammamah Hossain committed Nov 21, 2018
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Commits on Nov 22, 2018

  1. Regenerate tarball.

    Shammamah Hossain committed Nov 22, 2018
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Commits on Nov 23, 2018

  1. Stylistic changes.

    Shammamah Hossain committed Nov 23, 2018
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  2. Regenerate tarball

    Shammamah Hossain committed Nov 23, 2018
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  3. Add specific sequence viewer commit ID.

    Shammamah Hossain committed Nov 23, 2018
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  4. Merge master back into branch.

    Shammamah Hossain committed Nov 23, 2018
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  5. Add or update descriptions for component and props.

    Shammamah Hossain committed Nov 23, 2018
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Commits on Nov 27, 2018

  1. Re-add selection to props in render.

    Shammamah Hossain committed Nov 27, 2018
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  2. Merge master back into branch and re-build package.

    Shammamah Hossain committed Nov 27, 2018
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  3. Remove inline styles.

    Shammamah Hossain committed Nov 27, 2018
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