Skip to content

Commit

Permalink
Adds min package version (#1012)
Browse files Browse the repository at this point in the history 
WIP :: parent issue:
insightsengineering/nestdevs-tasks#7

Supersede:
* #957

### 🔴 Checklist for PR Reviewer

[![Scheduled
🕰️](https://github.com/insightsengineering/tern/actions/workflows/scheduled.yaml/badge.svg?branch=verdepcheck_action)](https://github.com/insightsengineering/tern/actions/workflows/scheduled.yaml)
_(~~max strategy fails due to
tidyverse/ggplot2#5436 corrected upstream)_

- [ ] Tag yourself next to this repo on
insightsengineering/nestdevs-tasks#7
- [ ] Package versions are the same or higher than `main`
- [ ] Package list is the same
  - Only exception is `rmarkdown` (may have been removed on `Suggests`)
- [ ] All packages in `Imports`, `Depends` & `Suggests` are in new
section `Config/Needs/verdepcheck`
- [ ] Added entry to `NEWS.md`
- [ ] Last `scheduled.yaml` action was run succesfully _(all 4
strategies)_
- important: it's not the last commit, it's the one that runs 4
`Scheduled 🕰️ / Dependency` actions
- [ ] `scheduled.yaml` SHOULD NOT have any push on any branches

### 🔴 What's needed before merging?

This PR depends on some upstream changes that need to be
finalized/merged before being ready to review.

#### Change in code

* `verdepcheck.yml` action (see comments)
  - [x] Remove `on: push` section 
  - [x] Change branch to main

#### PRS

- [x] verdepcheck
  * insightsengineering/verdepcheck#24
  * insightsengineering/verdepcheck#26
- [x] verdepcheck-action
  * insightsengineering/r-verdepcheck-action#16

### Changes description

* Adds minimum version for packages `DESCRIPTION`
* Adds `Config/Need/verdepcheck` section in `DESCRIPTION`
* Updates verdepcheck action

---------

Signed-off-by: André Veríssimo <[email protected]>
Co-authored-by: Pawel Rucki <[email protected]>
  • Loading branch information
@averissimo @pawelru
averissimo and pawelru authored Oct 23, 2023
1 parent 9ec685b commit ae1a386
Show file tree
Hide file tree
Showing 3 changed files with 83 additions and 53 deletions.
2 changes: 1 addition & 1 deletion .github/workflows/scheduled.yaml
View file
Original file line number Diff line number Diff line change
Expand Up @@ -11,7 +11,7 @@ jobs:
strategy:
fail-fast: false
matrix:
test-strategy: ["min", "release", "max"]
test-strategy: ["min_cohort", "min_isolated", "release", "max"]
uses: insightsengineering/r.pkg.template/.github/workflows/verdepcheck.yaml@main
name: Dependency Test - ${{ matrix.test-strategy }} 🔢
secrets:
Expand Down
71 changes: 49 additions & 22 deletions DESCRIPTION
View file
Original file line number Diff line number Diff line change
Expand Up @@ -23,44 +23,71 @@ Depends:
R (>= 3.6),
rtables (>= 0.6.5)
Imports:
broom,
car,
checkmate,
cowplot,
dplyr,
emmeans (>= 1.4.5),
broom (>= 0.5.4),
car (>= 3.0-13),
checkmate (>= 2.1.0),
cowplot (>= 0.7.0),
dplyr (>= 1.0.0),
emmeans (>= 1.8.0),
forcats (>= 1.0.0),
formatters (>= 0.5.4),
ggplot2 (>= 3.4.0),
grid,
gridExtra,
gtable,
gridExtra (>= 2.0.0),
gtable (>= 0.3.0),
labeling,
lifecycle,
magrittr,
lifecycle (>= 0.2.0),
magrittr (>= 1.5),
methods,
Rdpack,
rlang,
scales,
Rdpack (>= 2.4),
rlang (>= 1.1.0),
scales (>= 1.2.0),
stats,
survival (>= 3.2-13),
tibble,
tidyr,
tibble (>= 2.0.0),
tidyr (>= 0.8.3),
utils
Suggests:
knitr,
lattice,
lubridate,
knitr (>= 1.42),
lattice (>= 0.18-4),
lubridate (>= 1.7.9),
nestcolor (>= 0.1.1),
rmarkdown,
stringr,
testthat (>= 3.0),
vdiffr (>= 1.0.0)
rmarkdown (>= 2.19),
stringr (>= 1.4.1),
testthat (>= 3.1.9),
vdiffr (>= 1.0.7)
VignetteBuilder:
knitr
RdMacros:
lifecycle,
Rdpack
Config/Needs/verdepcheck:
insightsengineering/rtables,
tidymodels/broom,
cran/car,
mllg/checkmate,
wilkelab/cowplot,
tidyverse/dplyr,
rvlenth/emmeans,
tidyverse/forcats,
insightsengineering/formatters,
tidyverse/ggplot2,
r-lib/gtable,
r-lib/lifecycle,
tidyverse/magrittr,
GeoBosh/Rdpack,
r-lib/rlang,
r-lib/scales,
tidyverse/tibble,
tidyverse/tidyr,
yihui/knitr,
deepayan/lattice,
tidyverse/lubridate,
insightsengineering/nestcolor,
rstudio/rmarkdown,
tidyverse/stringr,
r-lib/testthat,
r-lib/vdiffr
Config/Needs/website: insightsengineering/nesttemplate
Config/testthat/edition: 3
Encoding: UTF-8
Expand Down
63 changes: 33 additions & 30 deletions NEWS.md
View file
Original file line number Diff line number Diff line change
@@ -1,5 +1,8 @@
# tern 0.9.2.9000

### Miscellaneous
* Specified minimal version of package dependencies.

# tern 0.9.2

### New Features
Expand Down Expand Up @@ -65,7 +68,7 @@
### Enhancements
* Added `ylim` argument to `g_km` to allow the user to set custom limits for the y-axis.
* Added assertion to `g_km` which checks whether there is one arm present in the data when `annot_coxph` is true.
* Added `flag_labels` argument to `s_count_patients_with_flags` to enable more label handling options in `count_patients_by_flags`.
* Added `flag_labels` argument to `s_count_patients_with_flags` to enable more label handling options in `count_patients_by_flags`.
* Added the `nested` argument to `analyze` wrapper functions `count_abnormal`, `count_abnormal_by_baseline`, `count_abnormal_by_marked`, `count_abnormal_by_worst_grade`, `count_abnormal_lab_worsen_by_baseline`, `count_cumulative`, `count_missed_doses`, `count_occurrences`, `count_occurrences_by_grade`, `count_patients_with_event`, `count_patients_with_flags`, `count_values`, `estimate_multinomial_response`, `estimate_proportion`, `estimate_incidence_rate`, `estimate_odds_ratio`, `estimate_proportion_diff`, `test_proportion_diff`, `summarize_ancova`, `summarize_change`, `summarize_glm_count`, `analyze_num_patients`, `coxph_pairwise`, `surv_time`, and `surv_timepoint`.

## Miscellaneous
Expand Down Expand Up @@ -139,19 +142,19 @@
### Enhancements
* Added `summarize_glm_count` function to analyze count data using a linear model.
* Added legend to `g_step`.
* Added formatting functions `format_fraction_fixed_dp` and
* Added formatting functions `format_fraction_fixed_dp` and
`format_count_fraction_fixed_dp` with fixed single decimal place in percentages.
* Added `na_level` and `labelstr` arguments to `summarize_vars_in_cols`.
* Added `analyze_num_patients` to include summary at the beginning that does not
repeat when paginating.
* Added `h_row_first_values` function as a more general helper function to retrieve
first values from specific rows.
* Added option to remove `"(n)"` suffix from `unique_count` labels for `s_num_patients`.
* Added options to `g_km` to annotate with statistics (`annot_stats`) and add corresponding
* Added options to `g_km` to annotate with statistics (`annot_stats`) and add corresponding
vertical lines (`annot_stats_lines`).

### Bug Fixes
* Fixed bug causing incorrect ordering of numeric grade levels when missing
* Fixed bug causing incorrect ordering of numeric grade levels when missing
grades are present in `s_count_occurrences_by_grade`.
* Refactored `summarize_vars_in_cols` to work with pagination machinery.
* Fixed bug to allow passing of `conf_level` argument to `emmeans::contrast()` in `s_ancova`.
Expand All @@ -166,11 +169,11 @@
* Added more tests to increase code coverage.
* Created separate documentation files for functions in different sections of `pkgdown` reference.
* Created separate `.R` files for logistic regression and cox regression helper functions.
* Fixed table tests using `analyze_num_patients` to generate an initial summary so there is no
* Fixed table tests using `analyze_num_patients` to generate an initial summary so there is no
repetition when paginating.
* Updated tests to use `testthat` 3rd edition and replaced applicable tests with snapshot testing.
* Updated `summarize_ancova` examples to use `iris` dataset instead of `scda` data.
* Created vignette which saves cached synthetic `CDISC` dataset files to the `data/` folder and
* Created vignette which saves cached synthetic `CDISC` dataset files to the `data/` folder and
generated cached synthetic datasets.
* Updated all examples/tests to use datasets from the `data/` folder instead of `scda` datasets.
* Removed all template tests from `tern`. These tests are in internal repo `scda.test`.
Expand All @@ -189,40 +192,40 @@
### New Features
* Added stratified `Newcombe` and stratified Wilson statistics to `estimate_proportion` and
`estimate_proportion_diff` with relative tests.
* Added `stat_mean_pval`, a new summary statistic to calculate the p-value of
* Added `stat_mean_pval`, a new summary statistic to calculate the p-value of
the mean.
* Added statistic `mean_se` (mean with standard error) for `summarize_variables`
* Added statistic `mean_se` (mean with standard error) for `summarize_variables`
and related functions.
* Introduced again `Rdpack` for references.

### Enhancements
* Redesign of data handling in tests by removing repetitive data loads and
### Enhancements
* Redesign of data handling in tests by removing repetitive data loads and
library calls.
* Added `DescTools::BinomDiffCI` function within `tern`.
* Added new parameter to `summarize_logistic` to specify which pivoted value
* Added new parameter to `summarize_logistic` to specify which pivoted value
to use during analysis.
* Updated `s_coxph_pairwise` to generate log-rank p-value using original
* Updated `s_coxph_pairwise` to generate log-rank p-value using original
log-rank test instead of Cox Proportional-Hazards Model.
* Implemented `nestcolor` in all examples by adapting `g_km`, `g_ipp`,
* Implemented `nestcolor` in all examples by adapting `g_km`, `g_ipp`,
`g_waterfall`, `g_step`, `g_lineplot`, and `g_forest`.
* Added parameters `interaction_y` and `interaction_item` in `ANCOVA` to make the
* Added parameters `interaction_y` and `interaction_item` in `ANCOVA` to make the
interaction calculations available.
* Added new parameter `footnotes` to add footnotes to `g_km`.

### Migration from `assertthat` to `checkmate`
* Implemented `checkmate::assert_vector`, `checkmate::assert_set_equal`, and
* Implemented `checkmate::assert_vector`, `checkmate::assert_set_equal`, and
`checkmate::assert_int` to check vector type, length, and values.
* Replaced with standard assertions from `checkmate` the following functions:
`all_elements_in_ref`, `is_df_with_nlevels_factor`, `is_df_with_no_na_level`,
`is_proportion_vector`, `is_quantiles_vector`, `is_character_or_factor`,
`is_nonnegative_count`, `is_valid_character`, `assert_character_or_factor`,
`all_elements_in_ref`, `is_df_with_nlevels_factor`, `is_df_with_no_na_level`,
`is_proportion_vector`, `is_quantiles_vector`, `is_character_or_factor`,
`is_nonnegative_count`, `is_valid_character`, `assert_character_or_factor`,
`assert_equal_length` and `has_tabletree_colnames`.
* Modified `is_proportion`, `is_equal_length`, `is_df_with_no_na_level`,
`is_df_with_nlevels_factor`, `is_variables`, `is_df_with_variables`,
* Modified `is_proportion`, `is_equal_length`, `is_df_with_no_na_level`,
`is_df_with_nlevels_factor`, `is_variables`, `is_df_with_variables`,
`is_df_with_factors`, `is_valid_factor` to use assertion logic.
* Added more verbose warnings from `as_factor_keep_attributes`.
* Made `assert_df_with_factors` and `assert_proportion_value` internal functions.
* Renamed `assertthat.R` and `test-assertthat.R` to `utils_checkmate.R` and
* Renamed `assertthat.R` and `test-assertthat.R` to `utils_checkmate.R` and
`test-utils_checkmate.R`.

### Documentation and NAMESPACE Polishing
Expand Down Expand Up @@ -252,7 +255,7 @@
`estimate_multinomial_rsp`, `decorate_grob_set`, `extreme_format`, `fit_rsp_step`,
`fit_survival_step`, `footnotes`, `footnotes-set`,
`format_count_fraction`, `format_fraction_threshold`, `formatting_functions`,
`format_fraction`, `combination_function` (S4 method), `compare_variables` (S3 method),
`format_fraction`, `combination_function` (S4 method), `compare_variables` (S3 method),
`kaplan_meier`.
* Internal keywords added, export removed, `_pkgdown.yml` updated, and `tern:::` added for
tests/examples/vignettes where present for the following functions:
Expand Down Expand Up @@ -287,24 +290,24 @@
* Fixed empty vector exception for `cut_quantile_bins`.
* Fixed exception error when empty strings are present in pivoted columns (`rtables` split
functions)
* Fixed bug in `s_ancova` causing an error when the first level of the arm
factor is not the control arm.
* Fixed bug in `s_ancova` causing an error when the first level of the arm
factor is not the control arm.
* Fixed bug in `s_abnormal_by_worst_grade` when there is one `PARAM` level.
* Fixed bug in `prop_diff_wald` when selecting all responders, updated tests accordingly.
* Fixed bug in `h_ancova` that caused an error when deselecting all covariates.

### Miscellaneous
* Added deprecated badge to `g_mmrm`.
* Removed internal function calls in examples (`tern:::`) and added `dontrun`
* Removed internal function calls in examples (`tern:::`) and added `dontrun`
to internal function examples.
* Removed warnings and messages to console occurring in examples and tests.
* Deprecated functions `color_palette` and `h_set_nest_theme` in favor of
* Deprecated functions `color_palette` and `h_set_nest_theme` in favor of
`nestcolor::color_palette` and `nestcolor::theme_nest`, respectively.
* Removed deprecated functions: `color_palette`, `color_palette_core`,
* Removed deprecated functions: `color_palette`, `color_palette_core`,
`h_set_nest_theme`, `s_cox_univariate`.
* Removed deprecated `mmrm` functions: `fit_mmrm`, `g_mmrm_diagnostic`,
`g_mmrm_lsmeans`, `as.rtable.mmrm`, `h_mmrm_fixed`, `h_mmrm_cov`,
`h_mmrm_diagnostic`, `tidy.mmrm`, `s_mmrm_lsmeans`, `s_mmrm_lsmeans_single`,
* Removed deprecated `mmrm` functions: `fit_mmrm`, `g_mmrm_diagnostic`,
`g_mmrm_lsmeans`, `as.rtable.mmrm`, `h_mmrm_fixed`, `h_mmrm_cov`,
`h_mmrm_diagnostic`, `tidy.mmrm`, `s_mmrm_lsmeans`, `s_mmrm_lsmeans_single`,
`summarize_lsmeans`.
* Renamed functions `arm` to `study_arm` and `extract` to `extract_by_name`.
* Renamed `rtables.R` to `utils_rtables.R`.
Expand Down

0 comments on commit ae1a386

Please sign in to comment.