Changelog

Source: NEWS.md

protocolhelper 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

protocolhelper 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)

protocolhelper 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()

protocolhelper 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

protocolhelper 0.5.0

New features

• new function add_label for use with caption argument of pander tables

Enhancements

• better handle pre-existing protocol numbers

protocolhelper 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

protocolhelper 0.4.12

Minor changes

• switched theme number of air and soil protocols

protocolhelper 0.4.11

Minor changes

• removed unneeded docker file
• improved layout of website overview tables

protocolhelper 0.4.10

Minor changes

• improved code to generate metadata in templates

protocolhelper 0.4.9

Bug fixes

• fixed a bug in protocol code check in check_frontmatter()

protocolhelper 0.4.8

Minor changes

• various improvements to website homepage, including Dutch and English version

Bug fixes

• fixed bug in passing metadata to pandoc

protocolhelper 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

protocolhelper 0.4.6

Bug fixes

• fixes a problem in check_structure when a subprotocol is present

protocolhelper 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

protocolhelper 0.4.4

Minor changes

• fixes a problem with checking of dates
• improve error message when URL in NEWS.md is incorrect

protocolhelper 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

protocolhelper 0.4.2

Minor changes

• better error handling in check_structure and check_frontmatter

protocolhelper 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

protocolhelper 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

protocolhelper 0.3.2

• patch to update checklist machinery

protocolhelper 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

protocolhelper 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

protocolhelper 0.2.3

• fix problem in github action workflow (install more recent version of pandoc)

protocolhelper 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

protocolhelper 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()

protocolhelper 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)

protocolhelper 0.1.5

• adds function add_captions()

protocolhelper 0.1.4

• fixes a bug introduced in 0.1.3

protocolhelper 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)

protocolhelper 0.1.2

• removed redundant pkgdown workflow

protocolhelper 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()

protocolhelper 0.1.0

• Added new function add_subprotocols()