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Changelog

Source: NEWS.md

Version 1.5.3

Bug Fixes

  1. Fixed the path to search for DESCRIPTION file in a package directory.
  2. Moved clean up function to on.exit(), instead of sequential execution.
  3. Fixed issue #99 where a Lua filter would not work with newer pandoc version.

Version 1.5.0

CRAN release: 2024-10-15

Feature Updates

  1. Included CodeCov code coverage workflow closing issue #70.
  2. Included custom JavaScript for auto-numbering equations independent of number_sections: option, fixing issue #83 and issue #86.
  3. Optional automatic equation numbering with a custom pandoc Lua filter, fixing issue #68.
  4. New option to convert figures into R markdown code chunks instead of regular markdown syntax, somewhat fixing issue #80.
  5. New option to convert most table structures into a csv data file, which is included into the article using kable() in a code block.
  6. New option to suppress package start up messages in the generated document, fixing issue #81.
  7. New options for vignette output styles including bookdown,litedown and biocstyle, closing issue #76.
  8. Use of pseudocodejs for rendering Algorithm environment in the R markdown files, closing issue #69.
  9. texor::rnw_to_rmd() now also modifies the DESCRIPTION file (if available) with Dependency Suggests and VignetteBuilder if missing (#94)

Bug Fixes

  1. Fixed Issue #78 where references are not hyperlinked.
  2. Fixed Issue #67 where unlabeled tables were not numbered.
  3. Updated example Sweave file.
  4. Added support for some jss style LaTeX macros under issue #77.
  5. Partially fixed Issue #84 renaming bibliography file more appropriately.
  6. Fixed Issue #79 where \vspace*{},\hspace*{} are ignored.
  7. Removed web_only parameter from yaml front matter, adapting to changes in rjtools package.
  8. Using updated table_code_chunk pandoc Lua filter, which preserves the table data more effectively, see supported types for more information.
  9. texor::rnw_to_rmd(): front_matter_type parameter is now called output_format with no defaults (#91).
  10. To support offline math in bookdown format, math_method option is now set to katex (better for accessibility) by default, in case of equation numbering it is set to mathjax (#92,#90).
  11. Fixed Relative Paths Issue in texor::rnw_to_rmd() (#93).
  12. VignetteEngine in bookdown format is now knitr::rmarkdown (#94).
  13. Removed excess print() statements from Lua Filters.
  14. If the figure/table referenced to a sweave code chunk is labelled with the prefix (fig:,tab:,table:) then the references will be transformed to bookdown style label.

Version 1.4.0

Feature Updates

  1. Initial Support for Sweave (.Rnw) article conversion.
  2. A new Hex-sticker for the package.
  3. Simplification of Readme file.

Bug Fixes

  1. Fixed Rd files with LaTeX like syntax to conform with recent R changes.
  2. Removed redundant comments regarding pandoc version checks from examples.
  3. Updates warning messages and notes in Rd section.

Version 1.3.0

CRAN release: 2023-09-27

Feature Updates

  1. Equations are better handled and equation references are edited to match bookdown format.
  2. Knitting of Rmarkdown is now done outside the temp folder to avoid PDF compilation errors.
  3. Added workaround macros for \nameref{} and \autoref{}.
  4. Added workaround macros for \scalebox{}, \fbox{}, \adjustbox{}, \framebox{}.
  5. Option to set DPI when invoking convert_to_png function.

Bug Fixes

  1. CodeBlocks and WideTables are now back to the original form.
  2. Algorithm get separate numbering in references.
  3. Removed unnecessary warnings.
  4. Better mechanism to remove leftover text after processing tikz.
  5. Package names using \pkg{} are now bold.
  6. Reduced DPI of raster images to reduce file sizes.
  7. Algorithmic not treated as figures.
  8. Fixes in lua filters for equation which now adds basic support for tabular and removes nested inline math.
  9. Fixing logic in table reference numbering.

Accessibility Feature Updates

  1. All images processed are set with a default alt-text : ‘graphic without alt text’

Version 1.2.0

Feature Updates

  1. CodeBlock and WideTable get their own numbering (but they share references with figures), Enhancement #51.
  2. added support for \command{..} macro.
  3. Included dummy slug and citation_url, Issue #50.
  4. Included a constructor for sample article, Enhancement #52.
  5. Added support for \file{},\var{},\env{},\option{},\dfn{}, \cpkg{} and \samp{} macro.
  6. Asking user for Inputs in interactive_mode, Enhancement #53.

Bug Fixes

  1. Modified the workflow to avoid missing Images.
  2. Modified Lua filters to suppress numbering widetables in captions.
  3. Fixed Issue #49 where some text of algorithms were left behind.
  4. Updated pdf conversion functions with poppler version check and note in man pages.
  5. Fixed copying markdown files back in temp_mode.
  6. Set unlink() as on.exit() function in temp_mode
  7. Removed table Numbering for images gridded in a table environment within a Figure environment.

Version 1.1.0

Feature Updates

  1. New mechanism to convert articles without wrapper files.
  2. Support for non-standard named RJwrapper files.
  3. Support for files with inclusive articles, however only articles included in the main article are included.
  4. Support for smallexample code environment
  5. Enhancement #47 : temporary mode for conversions to keep the original LaTeX article untouched.
  6. Bumped up pandoc version requirement from 2.17 to 3.1 (minimum), latest (recommended)

Bug Fixes

  1. Figure Environment wont be numbered if there is no Image in it.
  2. Now tikz images can be hot reloaded, no need to remove \includegraphics{} line manually.
  3. Fixed #46 where tikz style blocks would persist.
  4. Fixed #45 with Enhancement #47.
  5. Closed #41 momentarily.
  6. Default issue and year is now based on current date.
  7. Fixed #48 - in Lua filter added check for DisplayMath for equation numbering.
  8. Closed #40 as most of the issues have been fixed.

Version 1.0.5

Feature Updates

  1. A new Lua Filter to check for possible issues in LaTeX file during conversion
  2. New function to check multiple labels used in an environment

Bug Fixes

  1. Updated Image caption Lua filter which was broken by pandoc v3 (Figure update)
  2. Updated pkgdown website theme
  3. Fixed a Lua Filter to add extensions to some LaTeX Figure elements

Version 1.0.3

CRAN release: 2023-06-13

Bug Fixes

  1. Fixed a test case where it was attempting to write in user-library.

Version 1.0.2

CRAN release: 2023-06-11

Bug Fixes

  1. Added a pre-check before reading a file in texor::check_markdown_file().
  2. Fixed a bug where empty lines could not be filtered out.
  3. Usage of file.exists() before actual readLines().

Version 1.0.1

CRAN release: 2023-06-08

Feature Updates

  1. Algorithm figures are now numbered.
  2. Added boxedverbatim support for code environments.
  3. Included web_only parameter for embedding PDF or using Rmarkdown to produce HTML.
  4. Updated to MathJax Version3 and added -tex_math_single_backslash extension to pandoc for better math handling.
  5. Support for sample articles without the directory structure as required for RJ articles.
  6. Updated Instructions and examples (hence closing GitHub Issue #23).
  7. Updated contributor information.
  8. More examples and test cases.
  9. Pandoc Version checker for better compatibility and experience.
  10. Markdown checker for better compatibility and experience.
  11. CRAN release.

Bug Fixes

  1. Using xfun::normalize_path() instead of normalizePath() for relative/absolute path handling
  2. Stream editor also works on algorithm environments.
  3. Fixed image sizing paramaters.
  4. New algorithm to find, convert and copy images appropriately.
  5. Fixed a bug where, if the metadata$address is missing then metadata$author will be used as author name.
  6. Removes RJournal.sty file as it conflicts with inner workings of pandoc.
  7. Fixed file extension editing using xfun::with_ext() instead of gsub().
  8. More precise title and description.
  9. Added rebib as a dependency given it is now available on cran(hence closing #38)
  10. Fixed bugs related to copying files and images (Github Issue #36 and #34)

Version 0.6.9

Feature Updates

  1. Added algorithm2e graphics support (beta) (GitHub Issue #32)
  2. Added tikz graphics support (GitHub Issue #7)
  3. Added automation workflow with a separate logger for logging success and failure of conversion.

Bug Fixes

  1. Fixing equation labeling issue with , ., _ in equations and also added eq: before equation starts if not present.
  2. Added support for relative paths
  3. Fixed bugs in figure parser with new regex.
  4. Fixed tikz lib extraction method

Deprecated Features

  1. Removing old bibliographic parser/converter from texor in favour of new implementation in rebib which supports many more features.

Version 0.6.7

Feature Updates

  1. Equation labeling and numbering
  2. Code/table/equation/figure pre-processors
  3. fixed many meta data related issues
  4. We now use Mathjax V3
  5. New testthat test cases
  6. pkgdown website
  7. texor::latex_to_web() for a single article
  8. new stat tools for some metrics and conversion coverage check
  9. environment/word count for pandoc convert

Bug Fixes

  1. Support for absolute paths
  2. Fixed a lot of logic errors
  3. Fixed incompatibilities
  4. removed unnecessary code and features
  5. R-CMD-check passing
  6. Github workflows should work now
  7. Improved stat filter which exports pre and post conversion stats yaml file
  8. namespaces in logger
  9. URL fix for non http:// web Links
  10. Figure max width : 100% extra option added to figures.
  11. fixed pre processing of tikz
  12. fixed problems in journal volume
  13. comment filter mechanism for latex
  14. improved lua filter for numbering and centering figures
  15. fixed slug issue

Version 0.5.9

Feature Updates

  1. Automated orchestration of conversion
  2. New stream editor in R
  3. Using stream editor instead of lua filter for code
  4. Using stream editor instead of GNU sed for table
  5. changes in lua filter for R code
  6. Using stream editor for figure environment patching
  7. Automatic fetching of volume and issue from folder

Bug Fixes

  1. Support for absolute paths fixed(in almost all functions)
  2. Fixed some logic errors
  3. Fixes in metafix.sty

Version 0.5.5

Update Highlights :

  1. Placeholder abstract text for articles missing abstract
  2. \CRANpkg(),\BIOpkg() and CRAN_TASK_VIEWS are supported
  3. Tables have numbering
  4. A new lua filter for numbering tables
  5. Patched Metafix.sty
  6. More vignettes

Version 0.5.2

This package matures at this point where almost all features are working, and soon will be ready for CRAN deployment. The following are the features working:

  1. LaTeX macros such as \pkg,\CRANpkg,\code are supported.
  2. Reading Metadata from LaTeX file as well as DESCRIPTION.
  3. Reading bibliography from bibtex files and ignoring \thebibliography
  4. A parser to read and convert inbuilt \thebibliography to bibtex
  5. Supports code environments like Sinput,Soutput, example ,example*,verbatim with code highlight.
  6. Supports graphics included as PDF,PNG,JPG.
  7. Functions to convert PDF graphics to PNG.
  8. Almost all tables are converted with a few exceptions.
  9. Other things like citations,links,footnotes,math(limited) are also supported.