Merge pull request #16 from ukgovdatascience/feature/pre-commit-r

Feature: Pre-commit R

README.md

@@ -92,7 +92,8 @@ Here's a few changes you **must** do once you've created your new project:
 
 - Set up a Python virtual environment — there are **many** ways to [set up a virtual environment][pluralsight], so
   we'll let you decide what's best for you!
-- Git is not set up by default — open your terminal, navigate to your new project, run `git init` to set it up
+- Git is not set up by default — open your terminal, navigate to your new project, run `git init` in your shell to set it up.
+- Install the packages necessary by running `make requirements` in your shell.
 
 ## Changes to consider post-creation
 

cookiecutter.json

@@ -10,5 +10,7 @@
   "project_name": "Your new project name",
   "repo_name": "{{ cookiecutter.project_name.lower().replace(' ', '-') }}",
   "overview": "Brief overview of your project.",
-  "project_version": "0.0.1"
+  "project_version": "0.0.1",
+
+  "add_r_precommit_hooks": ["No", "Yes"]
 }

{{ cookiecutter.repo_name }}/.Rprofile

@@ -0,0 +1 @@
+source('startup.R')

{{ cookiecutter.repo_name }}/.gitignore

@@ -874,3 +874,7 @@ data/processed/*
 
 # Ignore the `.secrets` file
 .secrets
+
+# Ignore r artifacts
+*.Renviron
+*.Rhistory

{{ cookiecutter.repo_name }}/.lintr

@@ -0,0 +1,4 @@
+linters: with_defaults(
+    line_length_linter = line_length_linter(120),
+    commented_code_linter = NULL
+    )

{{ cookiecutter.repo_name }}/.pre-commit-config.yaml

@@ -26,4 +26,22 @@ repos:
     -   id: check-added-large-files
         args: ["--maxkb=5120"]
     -   id: end-of-file-fixer
+        exclude: '\.Rd'
     -   id: trailing-whitespace
+{% if cookiecutter.add_r_precommit_hooks == "Yes" %}
+# R specific hooks: https://github.com/lorenzwalthert/precommit
+-   repo: https://github.com/lorenzwalthert/precommit
+    rev: v0.1.2
+    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: lintr
+        exclude: renv/activate.R
+    -   id: readme-rmd-rendered
+    -   id: parsable-R
+    -   id: no-browser-statement
+{% endif -%}

{{ cookiecutter.repo_name }}/DESCRIPTION

@@ -0,0 +1,20 @@
+Package: {{ cookiecutter.repo_name }}
+Title: {{ cookiecutter.project_name }}
+Version: {{ cookiecutter.project_version }}
+Authors@R:
+    person(given = "{{ cookiecutter.organisation_name }}",
+           role = c("aut", "cre"),
+           email = "{{ cookiecutter.contact_email }}")
+Description: {{ cookiecutter.overview }}
+License: MIT + file LICENSE
+Imports:
+    docopt,
+    git2r,
+    lintr,
+    styler,
+    usethis
+Encoding: UTF-8
+Language: en-GB
+LazyData: true
+Roxygen: list(markdown = TRUE)
+RoxygenNote: 7.0.0

{{ cookiecutter.repo_name }}/README.md

@@ -13,7 +13,11 @@
 
 ## Getting started
 
-To be added.
+To start contributing to `{{ cookiecutter.repo_name }}`, run the following commands in your shell:
+
+``` shell script
+make requirements
+```
 
 ### Requirements
 

{{ cookiecutter.repo_name }}/docs/structure/README.md

@@ -35,7 +35,7 @@ coverage run -m pytest
 coverage html
 ```
 
-a code coverage report in HTML will be produced on the code in the `src` folder. This HTMl report can be accessed at
+a code coverage report in HTML will be produced on the code in the `src` folder. This HTML report can be accessed at
 `htmlcov/index.html`.
 
 ### `.envrc`
@@ -137,6 +137,19 @@ Alternatively, to install the requirements file along with pre-commit hooks, run
 make requirements
 ```
 
+### `DESCRIPTION`
+R-specific. Information related to the project including the name, authors and packages necessary for the project.
+
+### `startup.R`
+R-specific. Installs necessary packages specified in the `DESCRIPTION` file upon starting R via `.Rprofile`.
+
+### `.Rprofile`
+R-specific. Initialisation file that runs automatically when starting R.
+
+### `.lintr`
+R-specific. Configuration file for styling R code that's used by pre-commit hooks to check R code.
+
+
 [code-of-conduct]:../contributor_guide/CODE_OF_CONDUCT.md
 [contributing]: ../contributor_guide/CONTRIBUTING.md
 [coverage]: https://coverage.readthedocs.io/

{{ cookiecutter.repo_name }}/startup.R

@@ -0,0 +1,7 @@
+if (length(grep(pattern = "devtools", x = utils::installed.packages()[, 1])) == 0) {
+  Sys.setenv(R_PROFILE_USER = "/dev/null")
+  utils::install.packages(pkgs = "devtools", Ncpus = 1, repos = "https://cran.ma.imperial.ac.uk/")
+  # install packages from DESCRIPTION file
+  devtools::install()
+  Sys.unsetenv("R_PROFILE_USER")
+}