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Add / revise vignettes #216

Merged
merged 19 commits into from
Jan 28, 2023
Merged

Add / revise vignettes #216

merged 19 commits into from
Jan 28, 2023

Commits on Jan 28, 2023

  1. CLN: Fix default user_data_dir in data module 

    so that paths from readthedocs infra don't appear
in the docs

Instead of setting the default to a constant,
set it to None for all the functions,
and then if it is None, set it to that constant
inside the function
    @NickleDave
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  2. DOC/CLN: Clean up/revise docstrings in seq/simple.py

    @NickleDave
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  3. Add doc/data/giraudon-et-al-2021/.gitkeep

    @NickleDave
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  4. Change paths in doc/tutorial.md to use data sub-dir

    @NickleDave
    NickleDave committed Jan 28, 2023
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  5. DEV: Specify ipython != 8.7.0 in pyproject.toml 

    to avoid bug ipython/ipython#13845
    @NickleDave
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  6. DOC/BUG: Add .md to source suffixes in doc/conf.py 

    so that myst-nb executes jupyter notebook in .md format.

Not clear to me why renders worked before without this.
    @NickleDave
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  7. DOC: Add doc/nitpick-ignore.txt

    @NickleDave
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  8. DOC: Config nitpicky mode in conf.py w/astropy approach 

    adapted from
https://stackoverflow.com/a/30624034/4906855
    @NickleDave
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  9. CLN: Fix extract_data_files to not error if files already extracted

    @NickleDave
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  10. Set 'show_toc_level' to 1 in html_theme_options

    @NickleDave
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  11. Revise index.md

    @NickleDave
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  12. ENH: Add ability to convert GenericSeq to DataFrame 

    in crowsetta/formats/seq/generic.py.
- Refactor `annot2csv` function into `annot2df` function
  that return the pandas.Dataframe, and `annot2csv`
  that now just calls `annot2df` and then saves the result.
- Add `to_df` method on `GenericSeq` class that uses `annot2df`.
    @NickleDave
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  13. TST: Add unit tests for annot2df, GenericSeq.to_df

    @NickleDave
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  14. DEV/DOC: enable myst extension 'dollarmath' in conf.py

    @NickleDave
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  15. Revise doc/howto/convert-generic-seq.md

    @NickleDave
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  16. Add doc/howto/convert-simple-seq.md, fixes #152

    @NickleDave
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  17. Add howto/convert-simple-seq to toctree in doc/howto.md

    @NickleDave
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  18. Add doc/howto/remove-silent-labels-textgrid.md, fixes #197

    @NickleDave
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  19. Add remove-silent-labels-textgrid to toc in howto.md

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