Changelog • protocolhelper

Bug fixes

Overwriting placeholder headers resulted in false alarm from check_structure (issue #124)

Enhancements

Added appendix chapters to spp templates (issue #121)

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()

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

New features

new function add_label for use with caption argument of pander tables

Enhancements

better handle pre-existing protocol numbers

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

Minor changes

switched theme number of air and soil protocols

Minor changes

removed unneeded docker file
improved layout of website overview tables

Minor changes

improved code to generate metadata in templates

Bug fixes

fixed a bug in protocol code check in check_frontmatter()

Minor changes

various improvements to website homepage, including Dutch and English version

Bug fixes

fixed bug in passing metadata to pandoc

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

Bug fixes

fixes a problem in check_structure when a subprotocol is present

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

Minor changes

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

Minor changes

all (R)md template files are rewritten in canonical (pandoc) markdown format
fix check for code chunks which failed on html blocks

Minor changes

better error handling in check_structure and check_frontmatter

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

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

patch to update checklist machinery

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

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

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

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

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()

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)

adds function add_captions()

fixes a bug introduced in 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)

removed redundant pkgdown workflow

Added a NEWS.md file to track changes to the package.
Minor code improvements to meet quality criteria of checklist::check_package()

Added new function add_subprotocols()