Support Entity management

.Rbuildignore

@@ -11,7 +11,6 @@
 ^CONTRIBUTING\.md$
 ^ISSUE_TEMPLATE\.md$
 ^SUPPORT\.md$
-^\.github$
 ^man-roxygen$
 ^appveyor\.yml$
 codemeta.json
@@ -25,3 +24,8 @@ codemeta.json
 ^tic\.R$
 ^Dockerfile$
 ^codemeta\.json$
+^\.devcontainer
+^\.github
+^\.vscode
+^.lintr
+^\.pre-commit-config\.yaml$

.devcontainer/Dockerfile

@@ -0,0 +1,25 @@
+FROM ghcr.io/rocker-org/devcontainer/r-ver:4.2
+
+# non interactive frontend for locales
+ENV DEBIAN_FRONTEND=noninteractive
+
+# installing texlive and utils
+RUN apt-get update && \
+ apt-get -y install --no-install-recommends \
+ libudunits2-dev libxtst6 libxt6 libmagick++-dev \
+ libxml2-dev libjq-dev libudunits2-dev libgdal-dev libgeos-dev libproj-dev \
+ libicu-dev libv8-dev libjq-dev libprotobuf-dev protobuf-compiler libgit2-dev \
+ rsync mdbtools cargo libavfilter-dev libfontconfig1-dev libopenblas-dev \
+ freetds-common libct4 libsybdb5 freetds-bin freetds-dev libsybdb5 tdsodbc \
+ unixodbc make git procps locales curl && \
+ rm -rf /var/lib/apt/lists/*
+
+# generating locales
+RUN sed -i -e 's/# en_GB.UTF-8 UTF-8/en_GB.UTF-8 UTF-8/' /etc/locale.gen && \
+ dpkg-reconfigure --frontend=noninteractive locales && \
+ update-locale LANG=en_GB.UTF-8
+ENV LANGUAGE=en_GB.UTF-8 LANG=en_GB.UTF-8 LC_ALL=en_GB.UTF-8
+
+# installing cpanm & missing latexindent dependencies
+RUN curl -L http://cpanmin.us | perl - --self-upgrade && \
+ cpanm Log::Dispatch::File YAML::Tiny File::HomeDir

.devcontainer/devcontainer.json

@@ -0,0 +1,40 @@
+{
+ "name": "R (rocker/r-ver base)",
+ "dockerFile": "Dockerfile",
+ "features": {
+ "ghcr.io/rocker-org/devcontainer-features/quarto-cli:1": {
+ "version": "prerelease"
+ },
+ "ghcr.io/rocker-org/devcontainer-features/apt-packages:1": {
+ "packages": "libudunits2-dev,libxtst6,libxt6,libmagick++-dev"
+ },
+ "ghcr.io/rocker-org/devcontainer-features/r-packages:1": {
+ "packages": "github::rstudio/renv,tidyverse,git2r,knitr,spelling,languageserver,precommit,clisymbols,crayon,dplyr,fs,glue,httr,httr2,janitor,lifecycle,lubridate,magrittr,purrr,readr,rlang,stringr,semver,tibble,tidyr,xml2,covr,DT,ggplot2,here,knitr,lattice,leaflet,listviewer,leafpop,leafem,mapview,rmarkdown,roxygen2,sf,terra,testthat,tmap,usethis"
+ },
+ "ghcr.io/devcontainers-contrib/features/pre-commit:2": {}
+ },
+ "mounts": [
+ "source=${localEnv:HOME}${localEnv:USERPROFILE}/.gitconfig,target=~/.gitconfig,type=bind,consistency=cached"
+ ],
+ "onCreateCommand": "pre-commit install && pre-commit run",
+ "customizations": {
+ "vscode": {
+ "extensions": [
+ "mechatroner.rainbow-csv",
+ "REditorSupport.r",
+ "RDebugger.r-debugger",
+ "ms-azuretools.vscode-docker",
+ "usernamehw.errorlens",
+ "christian-kohler.path-intellisense",
+ "ms-vscode.live-server"
+ ]
+ },
+ "codespaces": {
+ "openFiles": [
+ "DESCRIPTION",
+ "NEWS.md",
+ "data-raw/make_release.R"
+ ]
+ }
+ }
+}

.github/ISSUE_TEMPLATE/bug_report.md

@@ -8,34 +8,34 @@ assignees: florianm
 ---
 
 ## Problem
-<!-- 
+<!--
  Please briefly describe your problem.
 -->
 ## ruODK function(s) used
-<!-- 
+<!--
  The most important bit - which ruODK functions did you use?
 -->
 
 ## Unexpected behaviour
-<!-- 
+<!--
  Run the failing commands with verbose=TRUE and provide any error messages,
  and the time elapsed. Did the command fail straight away or run for a while?
  Could this be a networking issue or performance issues on the ODK Central server?
 -->
 
 ## Reproducible example
-<!-- 
- If this issue refers to a bug or unexpected behaviour of ruODK, 
- please include a minimal reproducible example 
- ([reprex](https://reprex.tidyverse.org/), see also 
- <https://www.tidyverse.org/help/#reprex>). 
- 
- Note: If this issue involves an authenticated web request, 
+<!--
+ If this issue refers to a bug or unexpected behaviour of ruODK,
+ please include a minimal reproducible example
+ ([reprex](https://reprex.tidyverse.org/), see also
+ <https://www.tidyverse.org/help/#reprex>).
+
+ Note: If this issue involves an authenticated web request,
  do not include your credentials, server address, or any identifying
- information. 
+ information.
  Instead, run ru_setup() with environment variables.
  Make sure to sanitise any output of credentials, too.
- 
+
  The failing function and the (sanitised) error output alone
  will be a welcome help to narrow down the problem.
 -->
@@ -47,12 +47,12 @@ assignees: florianm
 <details>
 <summary><strong>Session Info</strong></summary>
 
-<!-- 
+<!--
  Append "version.txt" to your ODK Central URL
 -->
 ODK Central version:
- 
-<!-- 
+
+<!--
  R versions: R, ruODK, loaded packages
 -->
 ```{r}

.lintr

@@ -0,0 +1,7 @@
+linters: linters_with_defaults(
+ line_length_linter(120),
+ object_name_linter = NULL,
+ line_length_linter = NULL,
+ commented_code_linter = NULL
+ )
+exclusions: list()

.pre-commit-config.yaml

@@ -0,0 +1,53 @@
+exclude: "/migrations/|^venv/|/email/subject/"
+default_stages: [commit]
+
+repos:
+ - repo: https://github.com/pre-commit/pre-commit-hooks
+ rev: v4.6.0
+ hooks:
+ - id: trailing-whitespace
+ name: Drop trailing whitespace
+ exclude: man
+ - id: end-of-file-fixer
+ name: Fix end of files
+ - id: check-yaml
+ name: Check YAML syntax
+ - id: check-toml
+ name: Check TOML syntax
+ # - id: pretty-format-json
+ # name: Format JSON
+ - id: check-added-large-files
+ name: Prevent adding large files
+ args: ['--maxkb=1024']
+ - id: check-merge-conflict
+ name: Check for unhandled merge conflicts
+ - id: debug-statements
+ name: Check for debug statements
+ - id: detect-private-key
+ name: Detect private keys
+
+ - repo: https://github.com/lorenzwalthert/precommit
+ rev: v0.4.2
+ hooks:
+ - id: style-files
+ name: Style code to tidyverse conventions
+ args: [--scope=spaces]
+ - id: readme-rmd-rendered
+ name: Ensure README.md is up to date
+ - id: no-debug-statement
+ name: Ensure that no debug() statement is committed
+ - id: no-browser-statement
+ name: Ensure that no browser() statement is committed
+ # - id: spell-check
+ # name: Spellcheck
+ - id: deps-in-desc
+ name: Ensure that DESCRIPTION lists all dependencies
+ args: [--allow_private_imports, --root=R]
+ - id: use-tidy-description
+ name: Format DESCRIPTION
+ - id: pkgdown
+ name: Validate pkgdown.yml
+ # - id: lintr
+ # name: Lint code but emit only warnings
+ # args: [--warn_only]
+ # verbose: true

CODE_OF_CONDUCT.md

@@ -1,6 +1,6 @@
 # Contributor Code of Conduct
 
-As contributors and maintainers of this project, we pledge to respect all people who 
+As contributors and maintainers of this project, we pledge to respect all people who
 contribute through reporting issues, posting feature requests, updating documentation,
 submitting pull requests or patches, and other activities.
 
@@ -13,13 +13,13 @@ imagery, derogatory comments or personal attacks, trolling, public or private ha
 insults, or other unprofessional conduct.
 
 Project maintainers have the right and responsibility to remove, edit, or reject comments,
-commits, code, wiki edits, issues, and other contributions that are not aligned to this 
-Code of Conduct. Project maintainers who do not follow the Code of Conduct may be removed 
+commits, code, wiki edits, issues, and other contributions that are not aligned to this
+Code of Conduct. Project maintainers who do not follow the Code of Conduct may be removed
 from the project team.
 
-Instances of abusive, harassing, or otherwise unacceptable behaviour may be reported by 
+Instances of abusive, harassing, or otherwise unacceptable behaviour may be reported by
 opening an issue or contacting one or more of the project maintainers.
 
-This Code of Conduct is adapted from the Contributor Covenant 
-(<http://contributor-covenant.org>), version 1.0.0, available at 
+This Code of Conduct is adapted from the Contributor Covenant
+(<http://contributor-covenant.org>), version 1.0.0, available at
 <http://contributor-covenant.org/version/1/0/0/>