Adds and runs extended pre-commit (#7)

.Rbuildignore

@@ -1,7 +1,8 @@
-^chef\.Rproj$
-^\.Rproj\.user$
 ^LICENSE\.md$
+^\.Rproj\.user$
+^\.github$
+^\.pre-commit-config\.yaml$
 ^_pkgdown\.yml$
+^chef\.Rproj$
 ^docs$
 ^pkgdown$
-^\.github$

.githooks/pre-commit

@@ -29,4 +29,4 @@ for branch in "${protected_branches[@]}"; do
 done
 
 
-exit 0
+exit 0

.github/workflows/Check.yaml

@@ -45,4 +45,3 @@ jobs:
   #   uses: ./.github/workflows/Roxygen.yaml
 
 
-

.github/workflows/PR_cleanup.yaml

@@ -10,4 +10,4 @@ jobs:
     steps:
       - uses: stefanluptak/delete-old-pr-artifacts@v1
         with:
-          workflow_filename: Check.yaml
+          workflow_filename: Check.yaml

.github/workflows/R-CMD-check.yaml

@@ -47,4 +47,4 @@ jobs:
 
       - uses: r-lib/actions/check-r-package@v2
         with:
-          upload-snapshots: true
+          upload-snapshots: true

.github/workflows/Roxygen.yaml

@@ -177,4 +177,4 @@
               }
               fi
             shell: bash
-            working-directory: ${{ github.event.repository.name }}/${{ inputs.package-subdirectory }}
+            working-directory: ${{ github.event.repository.name }}/${{ inputs.package-subdirectory }}

.github/workflows/Test.yaml

@@ -48,4 +48,4 @@ jobs:
         uses: actions/upload-artifact@v4
         with:
           name: coverage-test-failures
-          path: ${{ runner.temp }}/package
+          path: ${{ runner.temp }}/package

.pre-commit-config.yaml

@@ -0,0 +1,76 @@
+# All available hooks: https://pre-commit.com/hooks.html
+# R specific hooks: https://github.com/lorenzwalthert/precommit
+repos:
+-   repo: https://github.com/lorenzwalthert/precommit
+    rev: v0.3.2.9027
+    hooks: 
+    # -   id: style-files
+    #     args: [--style_pkg=styler, --style_fun=tidyverse_style]    
+    # -   id: roxygenize
+    # codemeta must be above use-tidy-description when both are used
+    # -   id: codemeta-description-updated
+    # -   id: use-tidy-description
+    # -   id: spell-check
+    #     exclude: >
+    #       (?x)^(
+    #       .*\.[rR]|
+    #       .*\.feather|
+    #       .*\.jpeg|
+    #       .*\.pdf|
+    #       .*\.png|
+    #       .*\.py|
+    #       .*\.RData|
+    #       .*\.rds|
+    #       .*\.Rds|
+    #       .*\.Rproj|
+    #       .*\.sh|
+    #       (.*/|)\.gitignore|
+    #       (.*/|)\.gitlab-ci\.yml|
+    #       (.*/|)\.lintr|
+    #       (.*/|)\.pre-commit-.*|
+    #       (.*/|)\.Rbuildignore|
+    #       (.*/|)\.Renviron|
+    #       (.*/|)\.Rprofile|
+    #       (.*/|)\.travis\.yml|
+    #       (.*/|)appveyor\.yml|
+    #       (.*/|)NAMESPACE|
+    #       (.*/|)renv/settings\.dcf|
+    #       (.*/|)renv\.lock|
+    #       (.*/|)WORDLIST|
+    #       \.github/workflows/.*|
+    #       data/.*|
+    #       )$
+    # -   id: lintr
+    -   id: readme-rmd-rendered
+    -   id: parsable-R
+    -   id: no-browser-statement
+    -   id: no-print-statement
+    -   id: no-debug-statement
+        exclude: "R/try_and_validate.R"
+    -   id: deps-in-desc
+        args: [--allow_private_imports]
+        exclude: "tests/testthat/test-fetch_db_data.R"
+    -   id: pkgdown
+-   repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v1.2.3
+    hooks: 
+    -   id: no-commit-to-branch
+        args: [--branch, staging, --branch, main, --branch, dev]
+    -   id: check-added-large-files
+        args: ['--maxkb=200']
+    # -   id: file-contents-sorter
+    #     files: '^\.Rbuildignore$'
+    -   id: end-of-file-fixer
+        exclude: >
+          '\.Rd'
+          'tests/testthat/_snaps'
+    - id: detect-private-key
+    # - id: detect-aws-credentials
+-   repo: local
+    hooks:
+    -   id: forbid-to-commit
+        name: Don't commit common R artifacts
+        entry: Cannot commit .Rhistory, .RData, .Rds or .rds.
+        language: fail
+        files: '\.(Rhistory|RData|Rds|rds)$'
+        # `exclude: <regex>` to allow committing specific files

DESCRIPTION

@@ -30,7 +30,8 @@ Imports:
     tarchetypes,
     usethis,
     utils,
-    crew
+    crew,
+    purrr
 Suggests:
     covr,
     fs,
@@ -53,4 +54,3 @@ Config/testthat/edition: 3
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.3.1
-

R/apply_stats.R

@@ -103,5 +103,3 @@ apply_stats <-
     ep_cp[, .SD, .SDcols = keep]
 
   }
-
-

R/mk_userdef_fn_dt.R

@@ -87,6 +87,3 @@ generate_function_table_row <- function(fn_type, fn, fn_name, fn_hash, env){
 
   return(out_row)
 }
-
-
-

R/validate_endpoints_def.R

@@ -150,4 +150,3 @@ error_not_fn <- function(x, i) {
     )
   }
 }
-

README.Rmd

@@ -30,6 +30,18 @@ Behind the scenes, {chef} uses the {[targets](https://books.ropensci.org/targets
 
 ## Install githooks
 
-```
+This project supports two styles of githooks.
+
+1.  The first style is to use the githooks provided in the `.githooks` directory. To use these hooks, run the following command in the root of the project:
+  - These hooks are very simple just blocking the commit to protected branches.
+``
 git config --local core.hooksPath .githooks/
-```
+```
+
+2. The second is to install the precommit tool (for linux) [precommit](https://pre-commit.com/). 
+  - These are much more powerful and can be used to run checks on the code before it is committed.
+```
+pipx install pre-commit
+# Then run in the root of repo:
+pre-commit install
+```

README.md

@@ -1,4 +1,7 @@
 
+<!-- Insert badges here -->
+
+[![R-CMD-check](https://github.com/hta-pharma/chef/actions/workflows/package-check-test.yaml/badge.svg)](https://github.com/hta-pharma/chef/actions/workflows/package-check-test.yaml)
 <!-- README.md is generated from README.Rmd. Please edit that file -->
 
 # chef
@@ -37,4 +40,20 @@ pipelines.
 
 ## Install githooks
 
-    git config --local core.hooksPath .githooks/
+This project supports two styles of githooks.
+
+1.  The first style is to use the githooks provided in the `.githooks`
+    directory. To use these hooks, run the following command in the root
+    of the project:
+
+- These hooks are very simple just blocking the commit to protected
+  branches. \`\` git config –local core.hooksPath .githooks/
+
+<!-- -->
+
+
+    2. The second is to install the precommit tool (for linux) [precommit](https://pre-commit.com/). 
+      - These are much more powerful and can be used to run checks on the code before it is committed.
+
+pipx install pre-commit \# Then run in the root of repo: pre-commit
+install \`\`\`

tests/testthat/_snaps/targets.md

@@ -677,4 +677,3 @@
       10: SEX == "M"...  1-0001-000...  4, 5, 6, 7,45,46,... <data.table[1x4]>
       11: SEX == "F"...  1-0001-000... 11,12,54,55,56,57,... <data.table[1x4]>
       12: SEX == "M"...  1-0001-000...  8, 9,70,71,72,73,... <data.table[1x4]>
-

tests/testthat/helper-custom_expect.R

@@ -52,4 +52,3 @@ expect_same_items <- function(actual, expected, ...) {
   }
   invisible(actual)
 }
-

tests/testthat/test-apply_criterion_by_strata.R

@@ -543,4 +543,3 @@ test_that("strata_var remains a character variable when some endpoint have been
   expect_equal(typeof(actual[["strata_var"]]), "character")
 
 })
-

tests/testthat/test-apply_stats.R

@@ -691,4 +691,3 @@ test_that("Complex application of stats functions",
   expect_true(all(ep_stat[ep_stat$fn_type == "stat_across_strata_across_trt"][["value"]] == 158))
 
 })
-

tests/testthat/test-prepare_for_stats.R

@@ -464,5 +464,3 @@ test_that("base - dataprep", {
     regexp = "'arg' should be one of"
   )
 })
-
-

tests/testthat/test-unnest_endpoint_functions.R

@@ -245,4 +245,3 @@ test_that("Unnest adam and adsl functions", {
                            return(x[["fn_type"]] == lookup[[x[["fn_name"]]]])
                          })), TRUE)
 })
-

vignettes/ep_overview.Rmd

@@ -118,5 +118,3 @@ The parameters of each endpoint specification can be grouped in to the sets belo
         <td>`stat_across_strata_across_trt`</td>
     </tr>
 </table>
-
-

vignettes/methods_criteria.Rmd

@@ -385,8 +385,3 @@ endpoint_XYZ <- mk_endpoint_str(
 )
 
 ```
-
-
-
-
-

vignettes/methods_stat.Rmd

@@ -543,26 +543,3 @@ mk_endpoint_def <- function() {
               )
 }
 ```
-
-
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