Merge branch 'main' into streamline-release-process

.github/workflows/CRAN_checks.yml

@@ -22,11 +22,34 @@ permissions:
   packages: read
 
 jobs:
+  URL_check:
+    runs-on: ubuntu-22.04
+    name: Run URL checks
+    # runs-on: ubuntu-latest
+    container:
+      image: ${{ vars.CONTAINER_SOURCE }}/${{ vars.CONTAINER_RELEASE || 'debian/gcc/release' }}/abn:${{ vars.CONTAINER_VERSION || 'latest' }}
+      credentials:
+        username: ${{ github.actor }}
+        password: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - uses: actions/checkout@v4
+      - name: Disable renv
+        run: |
+            renv::deactivate()
+        shell: Rscript {0}
+      - name: Check for broken urls and redirects
+        run: |
+            library(urlchecker)
+            uc=url_check("./")
+            print(uc)
+            # uc=url_check("./");print(uc);print(uc$Status); if(any(uc$Status=="Error") || any(uc$Status=="403")) {q("no", status=1, FALSE)}
+        shell: Rscript {0}
+
   R-CMD-check:
     runs-on: ubuntu-22.04
     if: ${{ !startsWith(github.event.head_commit.message, 'noT') }}  # skip on commits starting with 'noT'
     container:
-      image: ${{ matrix.image-source }}/${{ matrix.os }}/${{ matrix.compiler }}/${{ matrix.r-version }}/abn:${{ vars.CONTAINER_VERSION || 'latest' }}
+      image: ${{ vars.CONTAINER_SOURCE }}/${{ matrix.os }}/${{ matrix.compiler }}/${{ matrix.r-version }}/abn:${{ vars.CONTAINER_VERSION || 'latest' }}
       credentials:
         username: ${{ github.actor }}
         password: ${{ secrets.GITHUB_TOKEN }}
@@ -35,7 +58,6 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        image-source: ["ghcr.io/furrer-lab/r-containers"]  # This is only here since container.image ignores env
         r-version: ['release' , 'devel', 'patched']  # ['3.6.3', '4.1.1']
         os: ['debian', 'fedora']
         compiler: ['gcc', 'clang']

.github/workflows/quick-testthat.yml

@@ -80,13 +80,6 @@ jobs:
         run: |
             install.packages('${{ env.BUILD_LOC }}/abn.tar.gz', repos=NULL, type="source")
         shell: Rscript {0}
-
-      - name: Check for broken urls and redirects
-        run: |
-            library(urlchecker)
-            uc=url_check("./");print(uc);print(uc$Status); if(any(uc$Status=="Error") || any(uc$Status=="403")) {q("no", status=1, FALSE)}
-        shell: Rscript {0}
-
       - name: Testthat!
         run: |
             # since on a test failure devtools::test does not exit with

CONTRIBUTING.md

@@ -0,0 +1,115 @@
+# Contributing to `abn`
+
+This outlines how to propose a change to `abn`.
+
+## The "Pull request" process
+
+In general all edits to the `abn` package go through the process of a
+[Pull request](https://docs.github.com/en/pull-requests/collaborating-with-pull-requests/proposing-changes-to-your-work-with-pull-requests/creating-a-pull-request).
+
+### Fixing typos
+
+If you spot typos or other language related errors in the documentation you may
+directly use the GitHub web interface to edit the source file.
+Simply click on the edit :pen: button and Github will guide you through the
+process of forking the repository and creating a pull request.
+
+### Beyond typos
+
+If you would like to contribute bigger changes please always refer to the
+[issue board](https://github.com/furrer-lab/abn/issues) first!
+
+> [!NOTE]
+> With the exception of simple typos, never open a pull request without an
+> existing issue that it relates to!
+>
+> If you want to link a pull request to an issue simply copy the link to the
+> issue into the description of the pull request.
+> If you are unsure how to to that have a look at the
+> official [Github documentation for pull requests](https://docs.github.com/en/issues/tracking-your-work-with-issues/linking-a-pull-request-to-an-issue) for further details.
+
+#### If you want to help,
+
+but have nothing specific in mind, simply head over to the [issue board](https://github.com/furrer-lab/abn/issues) where
+you will find open issues labelled with
+https://github.com/furrer-lab/abn/labels/help%20wanted.
+Feel free to comment on them if it is not clear to you what exactly the issue is about.
+Issues with the label
+https://github.com/furrer-lab/abn/labels/good%20first%20issue might be good
+starting points if you are new to `abn`.
+
+#### If you have a specific contribution
+that you would like to add first check the
+[issue board](https://github.com/furrer-lab/abn/issues)
+(also see the
+[closed issues](https://github.com/furrer-lab/abn/issues?q=is%3Aissue+is%3Aclosed))
+if you can find existing issues related to the contribution you plan to make.
+If yes, leave a comment on the related issue.
+If no, create a [new issue](https://github.com/furrer-lab/abn/issues/new) describing
+the feature you want to implement.
+For some inspiration on how to write a great issue refer to the
+[tidyteam code review prinicples](https://code-review.tidyverse.org/issues/).
+
+Once the foreseen edits are documented in an issue, create a pull request
+(to see how simply follow
+[Github's instructions on creating a Pull request](https://docs.github.com/en/pull-requests/collaborating-with-pull-requests/proposing-changes-to-your-work-with-pull-requests/creating-a-pull-request))
+and add your changes to the related branch.
+
+## Development
+
+We use [renv](https://rstudio.github.io/renv/index.html) for our development
+environment and would encourage you to do the same.
+Therefore, `abn` directly provides a development environment and we suggest the
+following workflow for development:
+
+*   Fork the package and clone it onto your computer.
+
+    _Note:_ You might do this with `usethis::create_from_github("furrer-lab/abn", fork = TRUE)`.
+
+*   Install `renv` with `install.packages("renv")`
+*   Restore the development environment with `renv::restore()`
+*   Create a new branch for your pull request.
+
+    _Note:_ You might use `usethis::pr_init("explicative-branch-name")`.
+
+    _See [Testing](#testing) for flags you can set in the branch name_
+
+*   Edit the code and commit your changes.
+
+    _Note:_ With `usethis` you would run: `usethis::pr_push()` and the follow 
+    the prompts.
+    The title of your pull request should briefly describe the change.
+    The body of your pull request should contain `Closes #issue-number`, where
+    `#issue-number` is the identifier of the related issue.
+
+## Testing
+
+The `abn` package uses several testing pipelines.
+When developing (i.e. not on the `main` branch) we recommend running the
+[quick-testthat.yml](https://github.com/furrer-lab/abn/blob/24-documentation-of-the-testing-procedure-noT/.github/workflows/quick-testthat.yml) action.
+This pipeline runs by default on push event on all branches other than `main`
+and executes all the test defined withing the `abn` package by calling
+[`devtools::test`](https://devtools.r-lib.org/reference/test.html).
+It does so in a docker container from the
+[r-containers](https://github.com/furrer-lab/r-containers) package which builds
+container images that are setup with all the required dependencies.
+
+By default, a container based on `Debian` using `clang` as compiler front-end
+and the current R development version version (`debian/clang/devel`) is used.
+However, [other configurations are available](https://github.com/orgs/furrer-lab/packages?repo_name=r-containers).
+
+If you want to change the container image to use for testing your branch against,
+you can append the desired configuration to the name of your branch with the
+prefix `'__'`.
+Hence, a branch named `my-awesome-branch__debian/gcc/release` would use the
+container image based on Debian, using `gcc` and the current release version of
+R to run the tests.
+
+You can also completely opt-out of testing by adding the flag `noT` to your
+branch name.
+It does not matter where you put the string `noT` in the branch name, so a
+branch named `"monoTestingBranch"` will also make you opt-out of testing.
+
+_Note:_ If you start a commit message with `"noT"` then the testing pipeline
+will also not run for this commit. In a commit message, however, the message
+has to start with `noT`, it will be ignored otherwise.