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Feature Request: Clean up assertions #264

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bundfussr opened this issue Apr 26, 2023 · 5 comments · Fixed by #289
Closed

Feature Request: Clean up assertions #264

bundfussr opened this issue Apr 26, 2023 · 5 comments · Fixed by #289
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@zdz2101
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enhancement New feature or request programming release Q3-2023

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@bundfussr
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Feature Idea

The assertion functions should be reviewed and duplicates and functions which are no longer used should be removed. For example assert_function() covers assert_function_params().

Relevant Input

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Relevant Output

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Reproducible Example/Pseudo Code

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@bundfussr bundfussr mentioned this issue Apr 26, 2023
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14 tasks
@zdz2101 zdz2101 self-assigned this May 3, 2023
@zdz2101
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zdz2101 commented May 3, 2023 •
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Currently in admiraldev, checked box indicates used in admiral:

  • assert_atomic_vector
    • used in admiraldev::get_duplciates() which is used in admiral::params()
  • assert_character_scalar
  • assert_character_vector
  • assert_data_frame
  • assert_date_var
  • assert_date_vector
  • assert_db_requirements
    • in admiral not admiraldev
  • assert_expr
  • assert_expr_list
  • assert_filter_cond
  • assert_function
  • assert_function_param
  • assert_has_variables
  • assert_integer_scalar
  • assert_list_element
  • assert_list_of
  • assert_logical_scalar
  • assert_named
  • assert_named_exprs
  • assert_numeric_vector
  • assert_one_to_one
  • assert_order_vars
  • assert_param_does_not_exist
  • assert_s3_class
  • assert_same_type
  • assert_symbol
  • assert_terms
    • in admiral not admiraldev
  • assert_unit
  • assert_valid_queries
    • in admiral not admiraldev
  • assert_vars
  • assert_varval_list

@zdz2101 zdz2101 mentioned this issue Jun 19, 2023
Closed
2 tasks
@zdz2101 zdz2101 linked a pull request Jun 19, 2023 that will close this issue
Closes #264, #288 cleanup assertions and continue deprecation process #289
Merged
14 tasks
zdz2101 pushed a commit that referenced this issue Jun 20, 2023
feat: #264 deprecate assert_function
2aeec90
zdz2101 pushed a commit that referenced this issue Jun 20, 2023
test: #264 cleanup some tests in assert_function, confused how others…
1d6a9ac 
… would go
zdz2101 pushed a commit that referenced this issue Jun 20, 2023
test: #264 rewrite tests in a more logical way
ee6d738
zdz2101 pushed a commit that referenced this issue Jun 20, 2023
chore: #264 run styler/lintr
006d7f3
@zdz2101
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zdz2101 commented Jun 23, 2023 •
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@pharmaverse/admiral, what do you all think? Ping me for mural access (didn't want to link it on this github issue)

Looks like

  1. assert_function() covers assert_function_params()
  2. assert_date_var() and assert_date_vector() do relatively similar things, ie check for is.instant() most likely can be consolidated?
  3. assert_date_frame() 's argument required_vars looks like it covers assert_has_variables()
  4. assert_named_expr() is only used in admiral::derive_basetype_records(), but looks like it can be swapped with assert_expr_list()

Proposed decision is the deprecate:

  • assert_function_params()
  • one of assert_date_var()/assert_date_vector() (based on naming convention I like _vector more)
  • assert_has_variables()
  • assert_named_expr()

@bms63
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bms63 commented Jun 23, 2023 •
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@pharmaverse/admiral, what do you all think? Ping me for mural access (didn't want to link it on this github issue)

Looks like

  1. assert_function() covers assert_function_params()
  2. assert_date_var() and assert_date_vector() do relatively similar things, ie check for is.instant() most likely can be consolidated?
  3. assert_date_frame() 's argument required_vars looks like it covers assert_has_variables()
  4. assert_named_expr() is only used in admiral::derive_basetype_records(), but looks like it can be swapped with assert_expr_list()

Proposed decision is the deprecate:

  • assert_function_params()

sounds good to me

  • one of assert_date_var()/assert_date_vector() (based on naming convention I like _vector more)

I like vector more as well

  • assert_has_variables()

umm...do you think we might need this...i can't think of any reason...

  • assert_named_expr()

sounds good to me

zdz2101 pushed a commit that referenced this issue Jun 23, 2023
feat: #264 begin deprecation of redundant assertions
bdbcc27
zdz2101 pushed a commit that referenced this issue Jun 26, 2023
deprecate assert_has_variables properly #264
715aab8
zdz2101 pushed a commit that referenced this issue Jun 26, 2023
chore: #264 run styler
5c16fca
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zdz2101 commented Jun 26, 2023

image

@pharmaverse/admiral After investigating a little more into how each of assert_date_var/assert_date_vector is used in admiral, there are slightly different use cases, side-by-side screenshot of code for reference above.

  • assert_date_var is used frequently in loops where there are multiple source datasets, in which the assertion becomes useful in providing messaging for indexing which columns from which dataframes there might be an issue with date/datetime
  • assert_date_vector is used frequently in compute_ function where there's no direct tie to a dataframe in the arguments

As such, I'm unsure if there is a need to deprecate the assert_date_* functions although I can't help but think these two still can be combined somehow, perhaps a better task would be to leave better documentation when to use each one?

@zdz2101 zdz2101 mentioned this issue Jun 26, 2023
Closed
zdz2101 pushed a commit that referenced this issue Jun 27, 2023
docs: #264 add blurb in news for the deprecated assertions
b1f4b68
zdz2101 pushed a commit that referenced this issue Jun 28, 2023
chore: #264 fix description version and remove deprecated examples
3b6bb5a
bms63 pushed a commit that referenced this issue Jun 29, 2023
@zdz2101
Closes #264, #288 cleanup assertions and continue deprecation process (…
80dcf7f 
…#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>
@bundfussr
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@zdz2101 , what about assert_varval_list()? I wonder if it should be deprecated in favor of assert_expr_list().

bms63 added a commit that referenced this issue Sep 10, 2023
@zdz2101 @bms63
@pharmaverse-bot @dgrassellyb @ddsjoberg @manciniedoardo @galachad @rossfarrugia @sophie-gem @kaz462 @StefanThoma @cicdguy
admiraldev v.0.5.0 (#327)
696a0f2 
* 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>
zdz2101 added a commit that referenced this issue Oct 11, 2023
@zdz2101 @bms63
@pharmaverse-bot @dgrassellyb @ddsjoberg @manciniedoardo @galachad @rossfarrugia @sophie-gem @kaz462 @StefanThoma @cicdguy
Closes #233 #324 #332 admiraldev miscellanous documentation updates (#…
aafdf33 
…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>
bms63 added a commit that referenced this issue Nov 17, 2023
@ddsjoberg @zdz2101
@bms63 @pharmaverse-bot @dgrassellyb @manciniedoardo @galachad @rossfarrugia @sophie-gem @kaz462 @StefanThoma @cicdguy
GitHub flow (#349)
76fee62 
* 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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@zdz2101 zdz2101

Labels
enhancement New feature or request programming release Q3-2023
Projects
admiral (sdtm/adam, dev, ci, template, core)
Status: Archive
Milestone
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Development

Successfully merging a pull request may close this issue.

Closes #264, #288 cleanup assertions and continue deprecation process pharmaverse/admiraldev
3 participants
@bms63 @zdz2101 @bundfussr