Documentation: Create guidance around making templates #295
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@manciniedoardo and @bundfussr what do you think? Feel free to edit. |
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This template vignette should additionally refer to the Programming Strategy vignette on admiraldev, as it explains lots of the code conventions that are used. |
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* #295 set up package extension guidance page * #295 fix vignetteindexentry * #295 chore: spellcheck * #295 chore: fix encoding issues in vignettes that prevented package from being built * #295: updates following review * #295 Chore: spellcheck * Update vignettes/package_extensions.Rmd Co-authored-by: Ross Farrugia <82581364+rossfarrugia@users.noreply.github.com> * #295 update to refer to admiraldev devel site * #295 Chore: spellcheck --------- Co-authored-by: Ross Farrugia <82581364+rossfarrugia@users.noreply.github.com>
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* feat: #295 add missing news entries * feat: #295 add missing news entries * fixed it * feat: add news entry for #306 * chore: #312 missing reference * chore: fix link that pointed to merged branch and use devel * Update NEWS.md --------- Co-authored-by: Zelos Zhu <zdz2101@github.com> Co-authored-by: Ben Straub <ben.x.straub@gsk.com>
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* docs: #283 update description and news * closes #286 commit messaging, new r-cmd vignette (#291) * docs: #286 commit messaging, new r-cmd vignette * chore: #286 spelling * docs: #286 squash and merge blurb * Update vignettes/git_usage.Rmd Co-authored-by: Zelos Zhu <zelos.zhu@atorusresearch.com> * chore: #286 news update --------- Co-authored-by: Zelos Zhu <zelos.zhu@atorusresearch.com> * Closes #271, #213, #260, #240 Documentation Update of get_datasets(); keep_source_vars argument; @family tag; compute_ functions (#287) * docs: #271 #213 clarify get_datasets and add keep_source_vars to prog strat * docs: #260 cleanup @family mentions * docs: #240 add blurb about compute functions * docs: #271 #213 #240 #260 add news blurb * adopt suggestion for family/keywords Co-authored-by: Ben Straub <ben.x.straub@gsk.com> * docs #271 adopt get_dataset feedback * docs: #213 #240 adopt recommendations from PR * chore: #240 add BMI to WORDLIST for spellcheck * chore: #271 #213 #260 adopt feedback --------- Co-authored-by: Zelos Zhu <zdz2101@github.com> Co-authored-by: Ben Straub <ben.x.straub@gsk.com> * Closes #264, #288 cleanup assertions and continue deprecation process (#289) * feat: #288 cleanup deprecation process * feat: #264 deprecate assert_function * test: #264 cleanup some tests in assert_function, confused how others would go * test: #264 rewrite tests in a more logical way * chore: #264 run styler/lintr * chore: #288 revert back to devel test file * chore: #288 properly fix assert_order_vars again * feat: #264 begin deprecation of redundant assertions * feat: #288 deprecate assert_named_exprs * deprecate assert_has_variables properly #264 * chore: #264 run styler * docs: #264 add blurb in news for the deprecated assertions * chore: #264 fix description version and remove deprecated examples --------- Co-authored-by: Zelos Zhu <zdz2101@github.com> * Propagate renv.lock from pharmaverse/admiralci (#294) renv update from pharmaverse/admiralci Co-authored-by: dgrassellyb <dgrassellyb@users.noreply.github.com> * Closes #22 #181 #201 #292 #298 Variety of small-scale general documentation updates (#303) * feat: #22 add documentation to friendly_type_of * feat: #181 add the appropriate URL * feat: #201 #292 add documentation about PR guidance and codeowners * chore: update wordlist for codeowners * chore: add NEWS --------- Co-authored-by: Zelos Zhu <zdz2101@github.com> * Closes #302 Adding Snapshot testing guidance to unit testing vignette (#308) * Update unit_test_guidance.Rmd * Update NEWS.md * Update NEWS.md * Closes #301: (#307) * #301: edoardo added as author, and author/contributor distinction implemented as in core admiral package * #301 chore: document * Propagate renv.lock from pharmaverse/admiralci (#310) * renv / codespaces update from pharmaverse/admiralci --------- Co-authored-by: galachad <galachad@users.noreply.github.com> Co-authored-by: Adam Foryś <adam.forys@gmail.com> * Closes #295 template documentation@devel (#300) * #295 set up package extension guidance page * #295 fix vignetteindexentry * #295 chore: spellcheck * #295 chore: fix encoding issues in vignettes that prevented package from being built * #295: updates following review * #295 Chore: spellcheck * Update vignettes/package_extensions.Rmd Co-authored-by: Ross Farrugia <82581364+rossfarrugia@users.noreply.github.com> * #295 update to refer to admiraldev devel site * #295 Chore: spellcheck --------- Co-authored-by: Ross Farrugia <82581364+rossfarrugia@users.noreply.github.com> * Closes #296 document_missing_value_s@devel (#311) * #296 - `missing_value` and `missing_values` added to the table of common arguments. * #296 - add in discussion of when to use singular vs plural arguments to programming strategy. * #296 - run checks required for PR and update NEWS.md. * #296 - Update according to requested changes. * #296 - revert the 'wrapped' changes in the programming strategy vignette * #296 - re-insert the new text into the programming strategy vignette, altered according to changes requested. * #296 - update NEWS.md with changes requested and run the required checks for PR. * Closes #282: Test Data Guidance vignette (#293) * #282: add test_data_guidance.Rmd, copy from admiraldata README devel * #282: update .yml * #282: add link for packages, remove SDTM, add naming conventions for program name * #282 spelling * #282: link to two data packages * #282: updated wordlist * #282: update pharmaverseadam description --------- Co-authored-by: Edoardo Mancini <53403957+manciniedoardo@users.noreply.github.com> * Propagate renv.lock from pharmaverse/admiralci (#314) renv / codespaces update from pharmaverse/admiralci Co-authored-by: galachad <galachad@users.noreply.github.com> * Propagate renv.lock from pharmaverse/admiralci (#315) * renv / codespaces update from pharmaverse/admiralci * renv / codespaces update from pharmaverse/admiralci --------- Co-authored-by: galachad <galachad@users.noreply.github.com> * Closes #306 argument descriptions added to table (#320) argument descriptions added to table Co-authored-by: Zelos Zhu <zelos.zhu@atorusresearch.com> * Closes #316 remove messaging that includes "-" as year not handled (#317) * feat: #316 remove messaging that includes "-" as year not handled * feat: #316 replace warning message * chore: #316 fix warning message and typos * chore: #316 add news blurb --------- Co-authored-by: Zelos Zhu <zdz2101@github.com> * Closes #318 #321 Documentation updates around admiral.test, staged dependencies, and function arguments (#323) * Fix hardcoded URL (#326) Resolves #325 * Closes #312 breakup wall of text (#319) * brick in the wall * remove special characters from image name * remove special characters from image name * replaced iframe with png * fixed image reference --------- Co-authored-by: Zelos Zhu <zelos.zhu@atorusresearch.com> * Closes #328 add missing news entries (#329) * feat: #295 add missing news entries * feat: #295 add missing news entries * fixed it * feat: add news entry for #306 * chore: #312 missing reference * chore: fix link that pointed to merged branch and use devel * Update NEWS.md --------- Co-authored-by: Zelos Zhu <zdz2101@github.com> Co-authored-by: Ben Straub <ben.x.straub@gsk.com> --------- Co-authored-by: Zelos Zhu <zdz2101@github.com> Co-authored-by: Ben Straub <ben.x.straub@gsk.com> Co-authored-by: pharmaverse-bot <113703390+pharmaverse-bot@users.noreply.github.com> Co-authored-by: dgrassellyb <dgrassellyb@users.noreply.github.com> Co-authored-by: Daniel Sjoberg <danield.sjoberg@gmail.com> Co-authored-by: Edoardo Mancini <53403957+manciniedoardo@users.noreply.github.com> Co-authored-by: galachad <galachad@users.noreply.github.com> Co-authored-by: Adam Foryś <adam.forys@gmail.com> Co-authored-by: Ross Farrugia <82581364+rossfarrugia@users.noreply.github.com> Co-authored-by: Sophie Shapcott <90790226+sophie-gem@users.noreply.github.com> Co-authored-by: Kangjie Zhang <47867131+kaz462@users.noreply.github.com> Co-authored-by: StefanThoma <40463122+StefanThoma@users.noreply.github.com> Co-authored-by: cicdguy <26552821+cicdguy@users.noreply.github.com>
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…333) * docs: #283 update description and news * closes #286 commit messaging, new r-cmd vignette (#291) * docs: #286 commit messaging, new r-cmd vignette * chore: #286 spelling * docs: #286 squash and merge blurb * Update vignettes/git_usage.Rmd Co-authored-by: Zelos Zhu <zelos.zhu@atorusresearch.com> * chore: #286 news update --------- Co-authored-by: Zelos Zhu <zelos.zhu@atorusresearch.com> * Closes #271, #213, #260, #240 Documentation Update of get_datasets(); keep_source_vars argument; @family tag; compute_ functions (#287) * docs: #271 #213 clarify get_datasets and add keep_source_vars to prog strat * docs: #260 cleanup @family mentions * docs: #240 add blurb about compute functions * docs: #271 #213 #240 #260 add news blurb * adopt suggestion for family/keywords Co-authored-by: Ben Straub <ben.x.straub@gsk.com> * docs #271 adopt get_dataset feedback * docs: #213 #240 adopt recommendations from PR * chore: #240 add BMI to WORDLIST for spellcheck * chore: #271 #213 #260 adopt feedback --------- Co-authored-by: Zelos Zhu <zdz2101@github.com> Co-authored-by: Ben Straub <ben.x.straub@gsk.com> * Closes #264, #288 cleanup assertions and continue deprecation process (#289) * feat: #288 cleanup deprecation process * feat: #264 deprecate assert_function * test: #264 cleanup some tests in assert_function, confused how others would go * test: #264 rewrite tests in a more logical way * chore: #264 run styler/lintr * chore: #288 revert back to devel test file * chore: #288 properly fix assert_order_vars again * feat: #264 begin deprecation of redundant assertions * feat: #288 deprecate assert_named_exprs * deprecate assert_has_variables properly #264 * chore: #264 run styler * docs: #264 add blurb in news for the deprecated assertions * chore: #264 fix description version and remove deprecated examples --------- Co-authored-by: Zelos Zhu <zdz2101@github.com> * Propagate renv.lock from pharmaverse/admiralci (#294) renv update from pharmaverse/admiralci Co-authored-by: dgrassellyb <dgrassellyb@users.noreply.github.com> * Closes #22 #181 #201 #292 #298 Variety of small-scale general documentation updates (#303) * feat: #22 add documentation to friendly_type_of * feat: #181 add the appropriate URL * feat: #201 #292 add documentation about PR guidance and codeowners * chore: update wordlist for codeowners * chore: add NEWS --------- Co-authored-by: Zelos Zhu <zdz2101@github.com> * Closes #302 Adding Snapshot testing guidance to unit testing vignette (#308) * Update unit_test_guidance.Rmd * Update NEWS.md * Update NEWS.md * Closes #301: (#307) * #301: edoardo added as author, and author/contributor distinction implemented as in core admiral package * #301 chore: document * Propagate renv.lock from pharmaverse/admiralci (#310) * renv / codespaces update from pharmaverse/admiralci --------- Co-authored-by: galachad <galachad@users.noreply.github.com> Co-authored-by: Adam Foryś <adam.forys@gmail.com> * Closes #295 template documentation@devel (#300) * #295 set up package extension guidance page * #295 fix vignetteindexentry * #295 chore: spellcheck * #295 chore: fix encoding issues in vignettes that prevented package from being built * #295: updates following review * #295 Chore: spellcheck * Update vignettes/package_extensions.Rmd Co-authored-by: Ross Farrugia <82581364+rossfarrugia@users.noreply.github.com> * #295 update to refer to admiraldev devel site * #295 Chore: spellcheck --------- Co-authored-by: Ross Farrugia <82581364+rossfarrugia@users.noreply.github.com> * Closes #296 document_missing_value_s@devel (#311) * #296 - `missing_value` and `missing_values` added to the table of common arguments. * #296 - add in discussion of when to use singular vs plural arguments to programming strategy. * #296 - run checks required for PR and update NEWS.md. * #296 - Update according to requested changes. * #296 - revert the 'wrapped' changes in the programming strategy vignette * #296 - re-insert the new text into the programming strategy vignette, altered according to changes requested. * #296 - update NEWS.md with changes requested and run the required checks for PR. * Closes #282: Test Data Guidance vignette (#293) * #282: add test_data_guidance.Rmd, copy from admiraldata README devel * #282: update .yml * #282: add link for packages, remove SDTM, add naming conventions for program name * #282 spelling * #282: link to two data packages * #282: updated wordlist * #282: update pharmaverseadam description --------- Co-authored-by: Edoardo Mancini <53403957+manciniedoardo@users.noreply.github.com> * Propagate renv.lock from pharmaverse/admiralci (#314) renv / codespaces update from pharmaverse/admiralci Co-authored-by: galachad <galachad@users.noreply.github.com> * Propagate renv.lock from pharmaverse/admiralci (#315) * renv / codespaces update from pharmaverse/admiralci * renv / codespaces update from pharmaverse/admiralci --------- Co-authored-by: galachad <galachad@users.noreply.github.com> * Closes #306 argument descriptions added to table (#320) argument descriptions added to table Co-authored-by: Zelos Zhu <zelos.zhu@atorusresearch.com> * Closes #316 remove messaging that includes "-" as year not handled (#317) * feat: #316 remove messaging that includes "-" as year not handled * feat: #316 replace warning message * chore: #316 fix warning message and typos * chore: #316 add news blurb --------- Co-authored-by: Zelos Zhu <zdz2101@github.com> * Closes #318 #321 Documentation updates around admiral.test, staged dependencies, and function arguments (#323) * Fix hardcoded URL (#326) Resolves #325 * Closes #312 breakup wall of text (#319) * brick in the wall * remove special characters from image name * remove special characters from image name * replaced iframe with png * fixed image reference --------- Co-authored-by: Zelos Zhu <zelos.zhu@atorusresearch.com> * Closes #328 add missing news entries (#329) * feat: #295 add missing news entries * feat: #295 add missing news entries * fixed it * feat: add news entry for #306 * chore: #312 missing reference * chore: fix link that pointed to merged branch and use devel * Update NEWS.md --------- Co-authored-by: Zelos Zhu <zdz2101@github.com> Co-authored-by: Ben Straub <ben.x.straub@gsk.com> * feat: #233 documentation for quoting * feat: #324 add footnotes blurb * feat: #332 add blurb for roxygen standardization * feat: #233 #324 #332 adopt feedback * italicize phrase * skip line to make markdown look correct * chore: run use_verion("dev") * feat: adding post-release cleanup stuff too * forgot line * accidental push * chore: fix tests * always is only a `deprecate_warn()` argument * .github folder updates * yaml syntax * fix link --------- Co-authored-by: Zelos Zhu <zdz2101@github.com> Co-authored-by: Ben Straub <ben.x.straub@gsk.com> Co-authored-by: pharmaverse-bot <113703390+pharmaverse-bot@users.noreply.github.com> Co-authored-by: dgrassellyb <dgrassellyb@users.noreply.github.com> Co-authored-by: Daniel Sjoberg <danield.sjoberg@gmail.com> Co-authored-by: Edoardo Mancini <53403957+manciniedoardo@users.noreply.github.com> Co-authored-by: galachad <galachad@users.noreply.github.com> Co-authored-by: Adam Foryś <adam.forys@gmail.com> Co-authored-by: Ross Farrugia <82581364+rossfarrugia@users.noreply.github.com> Co-authored-by: Sophie Shapcott <90790226+sophie-gem@users.noreply.github.com> Co-authored-by: Kangjie Zhang <47867131+kaz462@users.noreply.github.com> Co-authored-by: StefanThoma <40463122+StefanThoma@users.noreply.github.com> Co-authored-by: cicdguy <26552821+cicdguy@users.noreply.github.com>
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* docs: #283 update description and news * closes #286 commit messaging, new r-cmd vignette (#291) * docs: #286 commit messaging, new r-cmd vignette * chore: #286 spelling * docs: #286 squash and merge blurb * Update vignettes/git_usage.Rmd Co-authored-by: Zelos Zhu <zelos.zhu@atorusresearch.com> * chore: #286 news update --------- Co-authored-by: Zelos Zhu <zelos.zhu@atorusresearch.com> * Closes #271, #213, #260, #240 Documentation Update of get_datasets(); keep_source_vars argument; @family tag; compute_ functions (#287) * docs: #271 #213 clarify get_datasets and add keep_source_vars to prog strat * docs: #260 cleanup @family mentions * docs: #240 add blurb about compute functions * docs: #271 #213 #240 #260 add news blurb * adopt suggestion for family/keywords Co-authored-by: Ben Straub <ben.x.straub@gsk.com> * docs #271 adopt get_dataset feedback * docs: #213 #240 adopt recommendations from PR * chore: #240 add BMI to WORDLIST for spellcheck * chore: #271 #213 #260 adopt feedback --------- Co-authored-by: Zelos Zhu <zdz2101@github.com> Co-authored-by: Ben Straub <ben.x.straub@gsk.com> * Closes #264, #288 cleanup assertions and continue deprecation process (#289) * feat: #288 cleanup deprecation process * feat: #264 deprecate assert_function * test: #264 cleanup some tests in assert_function, confused how others would go * test: #264 rewrite tests in a more logical way * chore: #264 run styler/lintr * chore: #288 revert back to devel test file * chore: #288 properly fix assert_order_vars again * feat: #264 begin deprecation of redundant assertions * feat: #288 deprecate assert_named_exprs * deprecate assert_has_variables properly #264 * chore: #264 run styler * docs: #264 add blurb in news for the deprecated assertions * chore: #264 fix description version and remove deprecated examples --------- Co-authored-by: Zelos Zhu <zdz2101@github.com> * Propagate renv.lock from pharmaverse/admiralci (#294) renv update from pharmaverse/admiralci Co-authored-by: dgrassellyb <dgrassellyb@users.noreply.github.com> * Closes #22 #181 #201 #292 #298 Variety of small-scale general documentation updates (#303) * feat: #22 add documentation to friendly_type_of * feat: #181 add the appropriate URL * feat: #201 #292 add documentation about PR guidance and codeowners * chore: update wordlist for codeowners * chore: add NEWS --------- Co-authored-by: Zelos Zhu <zdz2101@github.com> * Closes #302 Adding Snapshot testing guidance to unit testing vignette (#308) * Update unit_test_guidance.Rmd * Update NEWS.md * Update NEWS.md * Closes #301: (#307) * #301: edoardo added as author, and author/contributor distinction implemented as in core admiral package * #301 chore: document * Propagate renv.lock from pharmaverse/admiralci (#310) * renv / codespaces update from pharmaverse/admiralci --------- Co-authored-by: galachad <galachad@users.noreply.github.com> Co-authored-by: Adam Foryś <adam.forys@gmail.com> * Closes #295 template documentation@devel (#300) * #295 set up package extension guidance page * #295 fix vignetteindexentry * #295 chore: spellcheck * #295 chore: fix encoding issues in vignettes that prevented package from being built * #295: updates following review * #295 Chore: spellcheck * Update vignettes/package_extensions.Rmd Co-authored-by: Ross Farrugia <82581364+rossfarrugia@users.noreply.github.com> * #295 update to refer to admiraldev devel site * #295 Chore: spellcheck --------- Co-authored-by: Ross Farrugia <82581364+rossfarrugia@users.noreply.github.com> * Closes #296 document_missing_value_s@devel (#311) * #296 - `missing_value` and `missing_values` added to the table of common arguments. * #296 - add in discussion of when to use singular vs plural arguments to programming strategy. * #296 - run checks required for PR and update NEWS.md. * #296 - Update according to requested changes. * #296 - revert the 'wrapped' changes in the programming strategy vignette * #296 - re-insert the new text into the programming strategy vignette, altered according to changes requested. * #296 - update NEWS.md with changes requested and run the required checks for PR. * Closes #282: Test Data Guidance vignette (#293) * #282: add test_data_guidance.Rmd, copy from admiraldata README devel * #282: update .yml * #282: add link for packages, remove SDTM, add naming conventions for program name * #282 spelling * #282: link to two data packages * #282: updated wordlist * #282: update pharmaverseadam description --------- Co-authored-by: Edoardo Mancini <53403957+manciniedoardo@users.noreply.github.com> * Propagate renv.lock from pharmaverse/admiralci (#314) renv / codespaces update from pharmaverse/admiralci Co-authored-by: galachad <galachad@users.noreply.github.com> * Propagate renv.lock from pharmaverse/admiralci (#315) * renv / codespaces update from pharmaverse/admiralci * renv / codespaces update from pharmaverse/admiralci --------- Co-authored-by: galachad <galachad@users.noreply.github.com> * Closes #306 argument descriptions added to table (#320) argument descriptions added to table Co-authored-by: Zelos Zhu <zelos.zhu@atorusresearch.com> * Closes #316 remove messaging that includes "-" as year not handled (#317) * feat: #316 remove messaging that includes "-" as year not handled * feat: #316 replace warning message * chore: #316 fix warning message and typos * chore: #316 add news blurb --------- Co-authored-by: Zelos Zhu <zdz2101@github.com> * Closes #318 #321 Documentation updates around admiral.test, staged dependencies, and function arguments (#323) * Fix hardcoded URL (#326) Resolves #325 * Closes #312 breakup wall of text (#319) * brick in the wall * remove special characters from image name * remove special characters from image name * replaced iframe with png * fixed image reference --------- Co-authored-by: Zelos Zhu <zelos.zhu@atorusresearch.com> * Closes #328 add missing news entries (#329) * feat: #295 add missing news entries * feat: #295 add missing news entries * fixed it * feat: add news entry for #306 * chore: #312 missing reference * chore: fix link that pointed to merged branch and use devel * Update NEWS.md --------- Co-authored-by: Zelos Zhu <zdz2101@github.com> Co-authored-by: Ben Straub <ben.x.straub@gsk.com> * GitFlow Migration * rename to match repo/pkg name * Update release_strategy.Rmd * progress * chore: branch image and main * chore: images updated to our modern times * docs: new images, removed most of the action sections * chore: delete dev process * chore: new blurb for the people --------- Co-authored-by: Zelos Zhu <zdz2101@github.com> Co-authored-by: Zelos Zhu <zelos.zhu@atorusresearch.com> Co-authored-by: Ben Straub <ben.x.straub@gsk.com> Co-authored-by: pharmaverse-bot <113703390+pharmaverse-bot@users.noreply.github.com> Co-authored-by: dgrassellyb <dgrassellyb@users.noreply.github.com> Co-authored-by: Edoardo Mancini <53403957+manciniedoardo@users.noreply.github.com> Co-authored-by: galachad <galachad@users.noreply.github.com> Co-authored-by: Adam Foryś <adam.forys@gmail.com> Co-authored-by: Ross Farrugia <82581364+rossfarrugia@users.noreply.github.com> Co-authored-by: Sophie Shapcott <90790226+sophie-gem@users.noreply.github.com> Co-authored-by: Kangjie Zhang <47867131+kaz462@users.noreply.github.com> Co-authored-by: StefanThoma <40463122+StefanThoma@users.noreply.github.com> Co-authored-by: cicdguy <26552821+cicdguy@users.noreply.github.com>
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We do not provide any guidance to extension packages or to core team around creating a template for ADaMs.
Prep Work
Definition of Done
Quote from referenced issue #293 :
We provide several templates in
inst/templatesbut we do not have a guidance for these files, e.g., we do not describe when templates should be created, how they should be structured, which data they should use, ...Originally posted by @bundfussr in #293 (comment)
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