Merge pull request #323 from eitsupi/super-linter

.github/workflows/linting.yml

@@ -6,31 +6,23 @@ on:
       - "master"
 
 jobs:
-  # yamllint:
-  #   runs-on: ubuntu-latest
-  #   steps:
-  #     - name: Check out code
-  #       uses: actions/checkout@v2
-  #     - name: Run yaml Lint
-  #       uses: actionshub/yamllint@main
-
-  mdl:
+  linter:
+    name: Lint Code Base
     runs-on: ubuntu-latest
-    steps:
-      - name: Check out code
-        uses: actions/checkout@v2
-      - name: Run Markdown Lint
-        uses: actionshub/markdownlint@main
 
-  shellcheck:
-    runs-on: ubuntu-latest
     steps:
-      - name: Check out code
+      - name: Checkout Code
         uses: actions/checkout@v2
-      - name: Run ShellCheck
-        uses: ludeeus/action-shellcheck@master
         with:
-          ignore: scripts
+          fetch-depth: 0
+
+      - name: Lint Code Base
+        uses: github/super-linter@v4
+        env:
+          VALIDATE_ALL_CODEBASE: false
+          DEFAULT_BRANCH: master
+          LINTER_RULES_PATH: .
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
 
   make_test:
     runs-on: ubuntu-latest

.hadolint.yaml

@@ -0,0 +1,3 @@
+ignored:
+  - "DL3006"
+  - "DL3059"

.jscpd.json

@@ -0,0 +1,10 @@
+{
+  "threshold": 0,
+  "reporters": [
+    "consoleFull"
+  ],
+  "ignore": [
+    "**/stacks/*.json"
+  ],
+  "absolute": true
+}

.lintr

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

.markdownlint.yaml

@@ -0,0 +1,13 @@
+default: true
+
+MD013:
+  line_length: 120
+  heading_line_length: 120
+  code_block_line_length: 120
+  tables: false
+
+MD024:
+  allow_different_nesting: true
+
+MD033:
+  allowed_elements: ["img"]

.yamllint → .yaml-lint.yml

@@ -1,7 +1,7 @@
----
 extends: default
+
 rules:
   line-length:
-    max: 256
+    max: 120
     level: warning
   document-start: disable

NEWS.md

@@ -4,12 +4,16 @@
 
 ### Changes in rocker_scripts
 
-- `userconf.sh`, which is executed when RStudio Server is launched, has been split into `init_set_env.sh` and `init_userconf.sh`. `init_set_env.sh` is also executed when Shiny Server is launched. ([#320](https://github.com/rocker-org/rocker-versioned2/pull/320))
+- `userconf.sh`, which is executed when RStudio Server is launched, has been split into `init_set_env.sh` and `init_userconf.sh`.
+  `init_set_env.sh` is also executed when Shiny Server is launched.
+  ([#320](https://github.com/rocker-org/rocker-versioned2/pull/320))
 
 ### Changes in pre-built images
 
 - Environment variables set in the container are now reflected in the sessions on Shiny Server. ([#320](https://github.com/rocker-org/rocker-versioned2/pull/320))
-- Change the date of the CRAN mirrors that were set for the R 4.0.0, R 4.0.1, R 4.0.2, and R 4.0.3 images. This reconfiguration was done mechanically, selecting the mirrors just before the release date of the next version of R. ([#328](https://github.com/rocker-org/rocker-versioned2/pull/328))
+- Change the date of the CRAN mirrors that were set for the R 4.0.0, R 4.0.1, R 4.0.2, and R 4.0.3 images.
+  This reconfiguration was done mechanically, selecting the mirrors just before the release date of the next version of R.
+  ([#328](https://github.com/rocker-org/rocker-versioned2/pull/328))
   - R 4.0.0: 2020-06-08 to 2020-06-04 (The next version, R 4.0.1 was released on 2020-06-06)
   - R 4.0.1: 2020-06-25 to 2020-06-18 (The next version, R 4.0.2 was released on 2020-06-22)
   - R 4.0.2: 2020-10-07 to 2020-10-09 (The next version, R 4.0.3 was released on 2020-10-10)
@@ -19,18 +23,22 @@
 
 ### Changes in pre-built images
 
-- In the newly built images, the default password for RStudio Server will be randomly generated when the server is started. ([#298](https://github.com/rocker-org/rocker-versioned2/pull/298))
+- In the newly built images, the default password for RStudio Server will be randomly generated when the server is started.
+  ([#298](https://github.com/rocker-org/rocker-versioned2/pull/298))
 
 ### Changes in rocker_scripts
 
-- The default locale, `LANG=en_US.UTF-8`, is now set [as recommended](https://github.com/docker-library/docs/tree/master/ubuntu#locales) by the official ubuntu image. ([#302](https://github.com/rocker-org/rocker-versioned2/issues/302), [#313](https://github.com/rocker-org/rocker-versioned2/pull/313))
+- The default locale, `LANG=en_US.UTF-8`,
+  is now set [as recommended](https://github.com/docker-library/docs/tree/master/ubuntu#locales) by the official ubuntu image.
+  ([#302](https://github.com/rocker-org/rocker-versioned2/issues/302), [#313](https://github.com/rocker-org/rocker-versioned2/pull/313))
 
 ## 2021-11
 
 ### Changes in rocker_scripts
 
 - `install_tidyverse.sh` now assumes that the `install2.r` command has the `--skipmissing` option. ([#283](https://github.com/rocker-org/rocker-versioned2/pull/283))
-- The [duckdb](https://github.com/duckdb/duckdb) package is added to the R packages installed by running `install_tidyverse.sh`. ([#283](https://github.com/rocker-org/rocker-versioned2/pull/283))
+- The [duckdb](https://github.com/duckdb/duckdb) package is added to the R packages installed by running `install_tidyverse.sh`.
+  ([#283](https://github.com/rocker-org/rocker-versioned2/pull/283))
 
 ### Changes in pre-built images
 
@@ -40,19 +48,33 @@
 
 ### Changes in rocker_scripts
 
-- Add a new script `install_quarto.sh`, to install [quarto-cli](https://github.com/quarto-dev/quarto-cli) and the quarto R package. ([#253](https://github.com/rocker-org/rocker-versioned2/pull/253))
-- Add a new script `install_julia.sh`, to install the Julia Language and two R packages which call Julia from R; [JuliaCall](https://github.com/Non-Contradiction/JuliaCall) and [JuliaConnectoR](https://github.com/stefan-m-lenz/JuliaConnectoR). ([#269](https://github.com/rocker-org/rocker-versioned2/pull/269))
-- A new script `install2.r`, copied from [eddelbuettel/littler](https://github.com/eddelbuettel/littler) and slightly modified, has been added in the `bin` directory. And add a new script `patch_install_command.sh`, to replace the symbolic link of `install2.r` command with rocker script version of `install2.r`. ([#275](https://github.com/rocker-org/rocker-versioned2/pull/275))
+- Add a new script `install_quarto.sh`,
+  to install [quarto-cli](https://github.com/quarto-dev/quarto-cli) and the quarto R package.
+  ([#253](https://github.com/rocker-org/rocker-versioned2/pull/253))
+- Add a new script `install_julia.sh`, to install the Julia Language and two R packages which call Julia from R;
+  [JuliaCall](https://github.com/Non-Contradiction/JuliaCall) and [JuliaConnectoR](https://github.com/stefan-m-lenz/JuliaConnectoR).
+  ([#269](https://github.com/rocker-org/rocker-versioned2/pull/269))
+- A new script `install2.r`, copied from [eddelbuettel/littler](https://github.com/eddelbuettel/littler) and slightly modified,
+  has been added in the `bin` directory. And add a new script `patch_install_command.sh`,
+  to replace the symbolic link of `install2.r` command with rocker script version of `install2.r`.
+  ([#275](https://github.com/rocker-org/rocker-versioned2/pull/275))
 - `install2.r` gets a new option `--skipmissing`. ([#275](https://github.com/rocker-org/rocker-versioned2/pull/275))
 
 ### Changes in pre-built images
 
-- New builds of `rocker/verse` and `rocker/ml-verse` for R >= 4.1.0 will install [quarto-cli](https://github.com/quarto-dev/quarto-cli) and the quarto R package. ([#253](https://github.com/rocker-org/rocker-versioned2/pull/253))
+- New builds of `rocker/verse` and `rocker/ml-verse` for R >= 4.1.0 will install [quarto-cli](https://github.com/quarto-dev/quarto-cli)
+  and the quarto R package.
+  ([#253](https://github.com/rocker-org/rocker-versioned2/pull/253))
 - The `install2.r` command has been replaced by rocker scripts version of `install2.r`. ([#275](https://github.com/rocker-org/rocker-versioned2/pull/275))
 
 ## 2021-06
 
 ### Changes in pre-built images
 
-- The time zone setting for R, which was hardcoded as `TZ=Etc/UTC` in `Renviron.site`, has been removed. The environment variable `TZ` set in the container will be used instead. ([#151](https://github.com/rocker-org/rocker-versioned2/issues/151), [#186](https://github.com/rocker-org/rocker-versioned2/pull/186))
-- Environment variables set in the container are now reflected in the sessions on RStudio Server. ([#186](https://github.com/rocker-org/rocker-versioned2/pull/186), [#189](https://github.com/rocker-org/rocker-versioned2/pull/189), [#190](https://github.com/rocker-org/rocker-versioned2/pull/190))
+- The time zone setting for R, which was hardcoded as `TZ=Etc/UTC` in `Renviron.site`, has been removed.
+  The environment variable `TZ` set in the container will be used instead.
+  ([#151](https://github.com/rocker-org/rocker-versioned2/issues/151), [#186](https://github.com/rocker-org/rocker-versioned2/pull/186))
+- Environment variables set in the container are now reflected in the sessions on RStudio Server.
+  ([#186](https://github.com/rocker-org/rocker-versioned2/pull/186),
+  [#189](https://github.com/rocker-org/rocker-versioned2/pull/189),
+  [#190](https://github.com/rocker-org/rocker-versioned2/pull/190))

README.md

@@ -1,12 +1,16 @@
+# Version-stable Rocker images <img src="https://avatars0.githubusercontent.com/u/9100160?v=3&s=200" align="right">
+
+<!-- badges: start -->
+
 [![license](https://img.shields.io/badge/license-GPLv2-blue.svg)](https://opensource.org/licenses/GPL-2.0)
 [![Project Status: Active – The project has reached a stable, usable state and is being actively developed.](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active)
 [![Update container definition files](https://github.com/rocker-org/rocker-versioned2/actions/workflows/dockerfiles.yml/badge.svg)](https://github.com/rocker-org/rocker-versioned2/actions/workflows/dockerfiles.yml)
 [![Build & Push Core images](https://github.com/rocker-org/rocker-versioned2/actions/workflows/core.yml/badge.svg)](https://github.com/rocker-org/rocker-versioned2/actions/workflows/core.yml)
 [![Build & Push R devel images and RStudio daily build images](https://github.com/rocker-org/rocker-versioned2/actions/workflows/devel.yml/badge.svg)](https://github.com/rocker-org/rocker-versioned2/actions/workflows/devel.yml)
 
-Visit [rocker-project.org](https://rocker-project.org) for more about available Rocker images, configuration, and use.
+<!-- badges: end -->
 
-# Version-stable Rocker images <img src="https://avatars0.githubusercontent.com/u/9100160?v=3&s=200" align="right">
+Visit [rocker-project.org](https://rocker-project.org) for more about available Rocker images, configuration, and use.
 
 ## Overview
 
@@ -69,7 +73,7 @@ and the `latest-daily` tag, which installs the RStudio daily build.
 
 ## Modifying and extending images
 
-Check the website for common methods for Rocker images. <https://www.rocker-project.org/use/extending/>
+Check the Rocker project site for common methods for Rocker images. <https://www.rocker-project.org/use/extending/>
 
 ### Install R packages
 
@@ -82,7 +86,8 @@ consider using `r-base` or [`rocker/r-bspm`](https://github.com/rocker-org/bspm)
 
 ### Rocker scripts
 
-The Docker images built from this repository describe the software installation method in standalone scripts rather than directly in the Dockerfiles.
+The Docker images built from this repository describe the software installation method in standalone scripts
+rather than directly in the Dockerfiles.
 These files are under [the `scripts` directory](./scripts/), and these files are copied in all Docker images,
 under a top-level `/rocker_scripts` directory.
 This allows users to extend images by selecting additional modules to install on top of any pre-built images.
@@ -95,7 +100,8 @@ FROM rocker/rstudio:4.0.0
 RUN /rocker_scripts/install_shiny_server.sh
 ```
 
-Install scripts can generally take a version as a first argument or ingest an environment variable to specify the version to install.
+Install scripts can generally take a version as a first argument or ingest an environment variable
+to specify the version to install.
 So to install fixed versions, one can use either of the following syntaxes:
 
 ```Dockerfile
@@ -109,17 +115,21 @@ FROM rocker/rstudio:4.0.0
 RUN /rocker_scripts/install_shiny_server.sh 1.5.14.948
 ```
 
-RStudio Server and Shiny Server are managed by [the S6 supervisor system](https://github.com/just-containers/s6-overlay), which allows containers to manage multiple background processes gracefully.
+RStudio Server and Shiny Server are managed by [the S6 supervisor system](https://github.com/just-containers/s6-overlay),
+which allows containers to manage multiple background processes gracefully.
 
 _Note: No longer support `ADD=` runtime triggers for installing Shiny or similar modules,
 which is used for R <= 3.6.3 images._
 
-## Build system
+## Build images
 
 ### Container definition files
 
-Dockerfiles and docker-bake.json files, which define the pre-built images, are in [the `dockerfiles` folder](./dockerfiles/) and [the `bakefiles` folder](./bakefiles/).
-And, these files are created from the JSON files under [the `stacks` folder](./stacks/) by the build scripts under [the `build` folder](./build/).
+Dockerfiles and docker-bake.json files, which define the pre-built images,
+are in [the `dockerfiles` folder](./dockerfiles/) and [the `bakefiles` folder](./bakefiles/).
+And,
+these files are created from the JSON files under [the `stacks` folder](./stacks/)
+by the build scripts under [the `build` folder](./build/).
 
 When a new version of R or RStudio is released, GitHub Actions will automatically create a Pull Request to update these files.