Functionality in convert_output for WHAM #192
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* Merge newer dev branch into old (#148) * Minor grammatical changes just to set up new dev-1.1 branch (changed quarto --> Quarto) * Feat(vignettes): -added tables of contents to vignettes -added tip for how to edit rda files to a11y vignette -added link to faqs vignette to a11y vignette re: how to edit alt text and captions --------- Co-authored-by: sbreitbart-NOAA <sophie.breitbart@noaa.gov> * Custom template fixes (#143) * update(create_template): comment out skeleton pop up at the end * update(add_section): add functionality for putting new subsection into section * Update(add_section): fix pathing for locating section to place code and change from add_chunk to add_child * update(create_template): select only custom_sections when user wants to make a different outline of report custom must = TRUE otherwise copies all files * Fix(create_template): adjust if statement argument for custom_sections * Add nmfspalette package back in * removed add_theme and associated test and documentation * remove static NOAA Fishies in authorship * update NOAA fisheries affiliations Co-authored-by: Schiano-NOAA <Schiano-NOAA@users.noreply.github.com> --------- Co-authored-by: sbreitbart-NOAA <sophie.breitbart@noaa.gov> Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Schiano-NOAA <Schiano-NOAA@users.noreply.github.com> * update(create_template): custom_sections adds all selected plus refs, acknow, and tables and figs if desired * create(create_yaml): initial commit for fxn and remove from create_template * update(create_template): remove yaml code from fxn and begin to sparse for rerender_skeleton arg * update(create_template): code to find previous skeleton format in yaml * update(create_template): begin to build foundation for rerender skeleton * update(create_template): add authors if selected on rerender skeleton * update(create_template): option to include additional parameters to yaml * update(create_template): option to add bib file - cannot remove old one * update(rerender): make improvements to functioning of rerender_skeleton arg in create_template after minimal testing * update(create-template): fix issue with citation not created when skeleton is rerendered; can now add new section when skeleton is rerendered and keep those sectioning when skeleton is rerendered at a later time * update(package): finish updates and checks for rerender skeleton arg; update documentation and other package needs * update(rerender skeleton): update create_template to include other ways skeleton could be updated especially from blank; update yaml respectively * update(create_template): finish going through fxn to adjust based on rerender_skeleton option * update(create_template: allow users to update their results when they had initially run a blank template * update(create_template): add condition for when results files need to be updated in the yaml, add question if old skeleton should be deleted * test change to check PR * remove test sentence * test integration into new dev branch (minor grammatical change) * update(create_template): add condition for when results files need to be updated in the yaml, add question if old skeleton should be deleted * update(create_yaml): adjust fxn so that parameters are included or changed when indicated * update(fxns): adjust issues with preamble incorrectly being added and sections into the new skeleton * fix(create_yaml): remove trailing extra space at the end of the authors formatting * update(create_yaml): fix issue when rerendering and params are kept from old call * update function per group discussion * fix(create_template): fix issue where authors are duplicated if the previous function was run with small changes to authors * fix(create_template-rerender_skeleton): fix issue with new skeleton name wrongly produced when species name and other info is not present * improve(create_template): add new message for rerender_skeleton for directions at the end of fxn * improve(create_template): add new message for rerender_skeleton for directions at the end of fxn * Feature: add draft watermark to default docs (#174) * feature(draft): initial commit to add in features to create_template where by default there is a draft watermark over the document, remove_draft created so user can remove the mark at the end * fix(format_quarto): error in notation for includes in header for pdf - also fix remove_draft where the default was finding the tex file rather than the qmd file * update(documentation): properly document remove_draft an update other various documentation around the functions modified for this feature * improve(create_template): add new message for rerender_skeleton for directions at the end of fxn * improve(create_template): add new message for rerender_skeleton for directions at the end of fxn --------- Co-authored-by: sbreitbart-NOAA <sophie.breitbart@noaa.gov> Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Schiano-NOAA <Schiano-NOAA@users.noreply.github.com>
* Merge newer dev branch into old (#148) * Minor grammatical changes just to set up new dev-1.1 branch (changed quarto --> Quarto) * Feat(vignettes): -added tables of contents to vignettes -added tip for how to edit rda files to a11y vignette -added link to faqs vignette to a11y vignette re: how to edit alt text and captions --------- Co-authored-by: sbreitbart-NOAA <sophie.breitbart@noaa.gov> * Custom template fixes (#143) * update(create_template): comment out skeleton pop up at the end * update(add_section): add functionality for putting new subsection into section * Update(add_section): fix pathing for locating section to place code and change from add_chunk to add_child * update(create_template): select only custom_sections when user wants to make a different outline of report custom must = TRUE otherwise copies all files * Fix(create_template): adjust if statement argument for custom_sections * Add nmfspalette package back in * removed add_theme and associated test and documentation * remove static NOAA Fishies in authorship * update NOAA fisheries affiliations Co-authored-by: Schiano-NOAA <Schiano-NOAA@users.noreply.github.com> --------- Co-authored-by: sbreitbart-NOAA <sophie.breitbart@noaa.gov> Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Schiano-NOAA <Schiano-NOAA@users.noreply.github.com> * update(create_template): custom_sections adds all selected plus refs, acknow, and tables and figs if desired * create(create_yaml): initial commit for fxn and remove from create_template * update(create_template): remove yaml code from fxn and begin to sparse for rerender_skeleton arg * update(create_template): code to find previous skeleton format in yaml * update(create_template): begin to build foundation for rerender skeleton * update(create_template): add authors if selected on rerender skeleton * update(create_template): option to include additional parameters to yaml * update(create_template): option to add bib file - cannot remove old one * update(rerender): make improvements to functioning of rerender_skeleton arg in create_template after minimal testing * update(create-template): fix issue with citation not created when skeleton is rerendered; can now add new section when skeleton is rerendered and keep those sectioning when skeleton is rerendered at a later time * update(package): finish updates and checks for rerender skeleton arg; update documentation and other package needs * update(rerender skeleton): update create_template to include other ways skeleton could be updated especially from blank; update yaml respectively * update(create_template): finish going through fxn to adjust based on rerender_skeleton option * update(create_template: allow users to update their results when they had initially run a blank template * update(create_template): add condition for when results files need to be updated in the yaml, add question if old skeleton should be deleted * test change to check PR * remove test sentence * test integration into new dev branch (minor grammatical change) * update(create_template): add condition for when results files need to be updated in the yaml, add question if old skeleton should be deleted * update(create_yaml): adjust fxn so that parameters are included or changed when indicated * update(fxns): adjust issues with preamble incorrectly being added and sections into the new skeleton * fix(create_yaml): remove trailing extra space at the end of the authors formatting * update(create_yaml): fix issue when rerendering and params are kept from old call * update function per group discussion * fix(create_template): fix issue where authors are duplicated if the previous function was run with small changes to authors * fix(create_template-rerender_skeleton): fix issue with new skeleton name wrongly produced when species name and other info is not present * improve(create_template): add new message for rerender_skeleton for directions at the end of fxn * improve(create_template): add new message for rerender_skeleton for directions at the end of fxn * Feature: add draft watermark to default docs (#174) * feature(draft): initial commit to add in features to create_template where by default there is a draft watermark over the document, remove_draft created so user can remove the mark at the end * fix(format_quarto): error in notation for includes in header for pdf - also fix remove_draft where the default was finding the tex file rather than the qmd file * update(documentation): properly document remove_draft an update other various documentation around the functions modified for this feature * improve(create_template): add new message for rerender_skeleton for directions at the end of fxn * improve(create_template): add new message for rerender_skeleton for directions at the end of fxn --------- Co-authored-by: sbreitbart-NOAA <sophie.breitbart@noaa.gov> Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Schiano-NOAA <Schiano-NOAA@users.noreply.github.com>
…ion per work done in quarto-accessibility-reprex repo
…r and add in script for testing and developing functionality - wham.R
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