Merge some infrastructure files from main-R to master

.Rbuildignore

@@ -0,0 +1,24 @@
+^source-linkage-files\.Rproj$
+^\.Rproj\.user$
+^_pkgdown\.yml$
+^docs$
+^pkgdown$
+^\.github$
+^copy_slf\.sh$
+^00-Sort_BI_Extracts\.py$
+^LICENSE\.md$
+^Reablement changes\.html$
+^hc_data_issues\.Rmd$
+^hc_data_issues\.html$
+^hc_methodology\.Rmd$
+^hc_methodology\.html$
+^hc_methodology_simple\.html$
+^hc_methodology_simple\.Rmd$
+^missing_derived_hours\.html$
+^R_development_SOP\.md$
+^codecov\.yml$
+^Rmarkdown$
+^\.lintr$
+^_targets\.R$
+^_targets\.yaml$
+^_SPSS_archived$

.github/actions/spelling/allow.txt

@@ -1,4 +1,11 @@
-github
-https
-ssh
-ubuntu
+Dunbartonshire
+Eilean
+Eileanan
+Inverclyde
+Jennifer
+McBride
+McMahon
+Moohan
+Scougal
+Tayside
+Zihao

.github/actions/spelling/excludes.txt

@@ -5,7 +5,6 @@
 (?:^|/)go\.sum$
 (?:^|/)package(?:-lock|)\.json$
 (?:^|/)vendor/
-ignore$
 \.a$
 \.ai$
 \.avi$
@@ -56,3 +55,6 @@ ignore$
 \.zip$
 ^\.github/actions/spelling/
 ^\Q.github/workflows/spelling.yml\E$
+^\Q/tmp/check-spelling/Public-Health-Scotland/source-linkage-files/commits/f13483ca341940e8549dc23c930da2f23dd0ac43.message\E$
+^\Q/tmp/check-spelling/Public-Health-Scotland/source-linkage-files/pull-request/613/summary.txt\E$
+ignore$

.github/actions/spelling/expect.txt

@@ -1,83 +1,201 @@
+Accom
+admloc
+admtype
+ADPE
+adtf
+arrivalmode
+arth
+attendcat
 aut
+bedday
 beddays
 birthtime
+bodyloc
 boxi
+callr
+Canx
+carehome
+careinspectorate
+cattend
+CCYY
+cennum
+chp
+chpstart
+cij
+Classificat
+cls
 cmh
+CNWs
+commhosp
+congen
+costmonthnum
+costsfy
 covr
 cph
 createslf
+dataframe
+datamart
 datazone
+datediff
+dateformat
+dateop
 datetime
+daycase
 dbconnect
 dbplyr
+deathdiag
 demog
+disch
+dischloc
+dischto
+disdest
+dminutes
+dna
+dnas
 dontrun
+downup
 dplyr
 dsn
 dtplyr
 DVPROD
 dvprod
 envir
+feb
+fileext
+Finalise
+fst
+ftm
 fyear
 fyyear
+geogs
+ggplot
+GLS
+gms
+GPOo
 gpprac
+gss
 hbnames
+hbpraccode
+hbrescode
+hbtreatcode
+hbtreatname
+hci
+HCP
+HHG
 hhg
+hjust
 hms
 homecare
 hscp
 hscpnames
+infyyear
+ipdc
 itle
-jennifer
+iwalk
+jaccard
+jan
+jul
 keydate
 keyring
+keytime
+keytimex
+los
 ltc
+ltcs
 lubridate
 magrittr
-Mcbride
-mcmahon
+MMMYY
+monthflag
+mpat
+multiday
+multisession
 multistaff
+NAs
+nhs
+nhshosp
+NRS
 nrs
 nsu
 odbc
+oldtadm
+opendata
+openxl
 openxlsx
 ORCID
 outfile
+patflow
+pattype
 phs
 phsmethods
 phsopendata
+placeinc
+plics
+PMS
+postcodes
+PPAs
+Prac
+prac
+praccode
+ptypes
 purrr
 quickstart
+Rbuildignore
 rds
 reablement
 readcode
 readr
 readxl
+reasonwait
 recid
+refsource
 rlang
 rmarkdown
 roxygen
 Rprofile
+Rscript
+rspm
+RStudio
 rstudioapi
+Rtype
+seealso
+selfharm
+Siar
+sigfac
 simd
-SLF
 slf
 slfhelper
 smr
 SMRA
 smrtype
+SPARRA
 sparra
 spd
+SPSS
+spss
+stadm
+stefanzweifel
+stringdist
 stringr
+submis
+tadm
+tarchetypes
 tbl
 telecare
 testthat
 thom
 tibble
 tidyr
 tidyselect
+TODOs
 uid
 ungroup
+Unicode
 updown
+upi
+vline
+xintercept
 xlsx
-zihao
+yearstay
+YYYYQX
+zsav
+zstd

.github/workflows/spelling.yml

@@ -82,6 +82,7 @@ jobs:
         extra_dictionary_limit: 10
         extra_dictionaries:
            cspell:r/src/r.txt
+           cspell:cpp/src/cpp.txt
            cspell:software-terms/src/software-terms.txt
         check_commit_messages: commits title description
 

.github/workflows/style.yaml

@@ -38,7 +38,7 @@ jobs:
         id: styler-location
         run: |
           cat(
-            "location=", 
+            "location=",
             styler::cache_info(format = "tabular")$location,
             "\n",
             file = Sys.getenv("GITHUB_OUTPUT"),
@@ -57,23 +57,15 @@ jobs:
             ${{ runner.os }}-
 
       - name: Style standard package functions and tests
-        run: styler::style_pkg(filetype = c(".R", ".Rmd", ".Rmarkdown", ".Rnw"))
+        run: styler::style_pkg()
         shell: Rscript {0}
 
-      - name: Style production scripts
-        run: styler::style_dir("Production_scripts/")
+      - name: Style the targets file
+        run: styler::style_file("_targets.R")
         shell: Rscript {0}
 
       - name: Style other scripts
-        run: styler::style_dir("Make_R_files/")
-        shell: Rscript {0}
-
-      - name: Style Rmarkdown files
-        run: styler::style_dir("Rmarkdown/")
-        shell: Rscript {0}
-
-      - name: Style older scripts
-        run: styler::style_dir("All_years/")
+        run: styler::style_dir(".")
         shell: Rscript {0}
 
       - name: Commit and push changes

LICENSE

@@ -0,0 +1,2 @@
+YEAR: 2022
+COPYRIGHT HOLDER: Public Health Scotland

LICENSE.md

@@ -0,0 +1,21 @@
+# MIT License
+
+Copyright (c) 2022 Public Health Scotland
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

README.md

@@ -1,3 +1,8 @@
+  <!-- badges: start -->
+  [![R-CMD-check](https://github.com/Public-Health-Scotland/source-linkage-files/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/Public-Health-Scotland/source-linkage-files/actions/workflows/R-CMD-check.yaml)
+  [![Codecov test coverage](https://codecov.io/gh/Public-Health-Scotland/source-linkage-files/branch/master/graph/badge.svg)](https://app.codecov.io/gh/Public-Health-Scotland/source-linkage-files?branch=master)
+  <!-- badges: end -->
+
 # source-linkage-files
 This repo is for the SPSS syntax used for the PHS Source Linkage File (SLF) project.