Changes in version 0.8.4 Bug fix - update_version_number only updates the protocol version number (#141) Changes in version 0.8.3 Bug fix - Unit tests failed on Windows due to issues with TeX installation Changes in version 0.8.2 Enhancement - Fixed a layout issue in the html version (DOI appearing in wrong place) - Fixed author names overflowing in the PDF version (#130) - Handle multiple reviewers in metadata table (#134) - Allow verbatim chunks (#136) Bug fix - Fix render_release failure in case of multiple reviewers (#137) - Fix parsing of Zenodo keywords (#132) Changes in version 0.8.1 Bug fix - protocolhelper:::update_doi() no longer removes the DOI when it is not published Changes in version 0.8.0 New features - Each protocol will be published to a protocol-specific Zenodo archive (#112). The protocol-specific Zenodo DOI is automatically added to protocol metadata (YAML section of the Index.Rmd file) and will be visible in the rendered versions. Bug fixes - Fixed rendering of authors in PDF version. Changes in version 0.7.0 Enhancements - create_protocol now works interactively (#117) - we make use of checklist::use_author() for author, reviewer and file_manager fields in YAML. Breaking change - the author, reviewer and file_manager YAML fields now have a different format Changes in version 0.6.1 Bug fixes - Overwriting placeholder headers resulted in false alarm from check_structure (issue #124) Enhancements - Added appendix chapters to spp templates (issue #121) Changes in version 0.6.0 Bug fixes - Updates were needed to LaTeX template to comply with pandoc 3.1.8+ (issue #122) Enhancements - internal reserved codes list has been augmented with codes from genetics lab - improved error and other messages for create_protocol() Changes in version 0.5.1 Enhancements - removed html comments from templates beneath part headers, which causes layout issues when rendering - automatically update version numbers in protocol-specific NEWS.md files Changes in version 0.5.0 New features - new function add_label for use with caption argument of pander tables Enhancements - better handle pre-existing protocol numbers Changes in version 0.4.13 Minor changes - internal function render_release() now also writes a .zenodo.json file - protocol authors are now added as contributors instead of creators in .zenodo.json file Changes in version 0.4.12 Minor changes - switched theme number of air and soil protocols Changes in version 0.4.11 Minor changes - removed unneeded docker file - improved layout of website overview tables Changes in version 0.4.10 Minor changes - improved code to generate metadata in templates Changes in version 0.4.9 Bug fixes - fixed a bug in protocol code check in check_frontmatter() Changes in version 0.4.8 Minor changes - various improvements to website homepage, including Dutch and English version Bug fixes - fixed bug in passing metadata to pandoc Changes in version 0.4.7 Minor changes - removed _bookdown.yml template files which are now created programmatically - website contains a NEWS page - each protocol now has a home button to return to protocols website homepage Bug fixes - fixes a problem that caused references to appear twice in bibliography in case of subprotocols Changes in version 0.4.6 Bug fixes - fixes a problem in check_structure when a subprotocol is present Changes in version 0.4.5 Minor changes - new function check_all which combines frontmatter and structure checks Bug fixes - fixes a problem in ´add_one_subprotocol()´ so the correct path to media and data is used - fixes a problem with bibliography field when a subprotocol is added - fixes a problem with figure and table cross-references in case of a subprotocol Changes in version 0.4.4 Minor changes - fixes a problem with checking of dates - improve error message when URL in NEWS.md is incorrect Changes in version 0.4.3 Minor changes - all (R)md template files are rewritten in canonical (pandoc) markdown format - fix check for code chunks which failed on html blocks Changes in version 0.4.2 Minor changes - better error handling in check_structure and check_frontmatter Changes in version 0.4.1 Minor changes - fixed a bug which occurred when check_structure and check_frontmatter ran on protocols based on the generic template - each template gains a template_name metadata field - added pandoc minimal system requirements to description - each template now has a path_to_protocol R object defined which resolves to the full path of the protocol Changes in version 0.4.0 breaking changes - reworked folder structure (src becomes source, thematic becomes sfp, project becomes spp) #82 New features - added a generic template which can be used as alternative to sfp, sip, sap and sop templates #78 - changed create_protocol to handle sap, sip, sop and generic templates - handle reserved (in use) protocol codes from lab and field work inventory lists which have not been migrated to protocolsource Minor changes - reworked internal function protocolhelper:::render_release to improve homepage of website #84 - fixed numerous spelling issues Changes in version 0.3.2 - patch to update checklist machinery Changes in version 0.3.1 Minor changes - update_version_number only commits a modified Index.Rmd - get_version_number temporarily stashes changes so they don't get lost when switching between branches Changes in version 0.3.0 New features - templates now also have a references.yaml file and corresponding bibliography fields in yaml front matter - added templates for standard analysis procedures (sap) - added templates for standard instrument procedures (sip) - added templates for standard operating procedures (sop) - added function check_structure() to check document structure of protocols - added function get_version_number() to determine version number Minor changes - various fixes to comply with new version of checklist package - improved checks when passing authors and orcids in create_protocol() - some template markdown files or chapter titles have been changed so that file name and chapter title are similar - functions clean_git and new_branch are now imported from checklist package Bug fixes - fix a problem with backslashes in path to media files after converting docx to markdown Changes in version 0.2.3 - fix problem in github action workflow (install more recent version of pandoc) Changes in version 0.2.2 New features - function to update a protocol (start development of a new version) - internal function to get protocol tags and optionally bump development version number (#27) - internal function to update .zenodo.json file (add new authors) (#25) Minor changes - fixed relative links in template NEWS.md html comments - removed function render_all(); it is superseded by the internal function protocolhelper:::render_release(). This function is internal because it should only be used by administrators as part of the workflow to publish a new protocol or update an existing protocol. The exported function protocolhelper::render_protocol() can be used to render an individual protocol. Bug fixes - fixed bugs in check_frontmatter() due to changes in the way YAML metadata are stored Changes in version 0.2.1 New features - protocol templates include CC-BY license Minor changes - arguments determining paths to save results of convert_docx_to_rmd() are reconsidered (#52 and #53) - change default of argument wrap in convert_docx_to_rmd() to NA - .emf files will converted to .png in convert_docx_to_rmd() Changes in version 0.2.0 Breaking changes - restructured yaml of skeleton.Rmd in templates: moved metadata under params section to top level of yaml - new YAML syntax to add dependencies to the params section the YAML New features - adds orcid information (#32) - adds a link to dependencies table when params are missing (#46) - adds a new function to aid adding dependencies to YAML header - adds a logo to the sidebar (#44) Bug fixes - remove unnecessary failing check from check on different OS (#49) Changes in version 0.1.5 - adds function add_captions() Changes in version 0.1.4 - fixes a bug introduced in 0.1.3 Changes in version 0.1.3 - When a protocol is created from an existing docx version, template files will be generated as well (and overwritten by the docx chapter if the filename is the same, i.e. confirms to current template standards) Changes in version 0.1.2 - removed redundant pkgdown workflow Changes in version 0.1.1 - Added a NEWS.md file to track changes to the package. - Minor code improvements to meet quality criteria of checklist::check_package() Changes in version 0.1.0 - Added new function add_subprotocols()