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refactor: add MOSuite as a subtree (#1)
* refactor: load local MOSuite * Squashed 'code/MOSuite/' content from commit c09ee39 git-subtree-dir: code/MOSuite git-subtree-split: c09ee39f9b282237f13d88dcf4cdfed965209c68 * `air format` (GitHub Actions) * chore: update changelog * ci: add tests gha * chore: create .gitattributes * test: create basic tests * `air format` (GitHub Actions) * refactor: use MOSuite-minimal docker --------- Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
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‎.codeocean/environment.json‎

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{
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"version": 1,
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"base_image": "codeocean/mosuite:v0.3.0",
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"base_image": "codeocean/mosuite-minimal:v0.3.1",
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"post_install": true,
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"options": {
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"registry_host_arg": true,

‎.gitattributes‎

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/code/MOSuite linguist-vendored

.github/workflows/test.yml renamed to .github/workflows/tests.yml

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name: test
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name: tests
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on:
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push:
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branches: [ main, dev ]
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jobs:
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test:
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tests:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v3

‎CHANGELOG.md‎

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# Code Ocean capsule - MOSuite - Plot Volcano Summary
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## dev version
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- The MOSuite package is now available in `code/MOSuite`. (#1)
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- Use MOSuite v0.3.1.
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## v3.0
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- Use MOSuite v0.3.0.

‎code/MOSuite/.Rbuildignore‎

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^renv$
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^renv\.lock$
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^_pkgdown\.yml$
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^\.github$
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^\.lintr$
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^\.pre-commit-config\.yaml$
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^\.prettierignore$
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^\.prettierrc$
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^\.Rproj\.user$
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^CITATION\.cff$
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^codemeta\.json$
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^data-raw$
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^doc$
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^Dockerfile$
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^docker$
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^docs$
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^figures$
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^LICENSE\.md$
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^Meta$
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^MOSuite\.Rproj$
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^pkgdown$
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^README\.Rmd$
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^README\.html$
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^README_files$
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^Rplots\.pdf$
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^moo_input\.rds$
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^plot-volc-enh\.json$
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^volc-sum-params\.json$
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^report_files$
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^inst/quarto/report_files$
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^tests/figures$
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^vignettes/figures/$
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^vignettes/memory\.Rmd$
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^vignettes/cli\.Rmd$
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VennDiagram.*\.log
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^[.]?air[.]toml$
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^\.vscode$

‎code/MOSuite/.gitattributes‎

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CITATION.cff linguist-generated
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codemeta.json linguist-generated
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NAMESPACE linguist-generated
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man/ linguist-generated

‎code/MOSuite/.github/.Rprofile‎

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rlang::global_entrace()

‎code/MOSuite/.github/.gitignore‎

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*.html

‎code/MOSuite/.github/CONTRIBUTING.md‎

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# Contributing to MOSuite
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## Proposing changes with issues
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If you want to make a change, it's a good idea to first
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[open an issue](https://github.com/CCBR/MOSuite/issues)
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and make sure someone from the team agrees that it’s needed.
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Before opening an issue, check the existing issues to make sure you're not
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opening a duplicate, and follow these guidelines to ensure your issue will be
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high-quality:
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<https://code-review.tidyverse.org/issues/>.
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If you've decided to work on an issue,
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[assign yourself to the issue](https://docs.github.com/en/issues/tracking-your-work-with-issues/assigning-issues-and-pull-requests-to-other-github-users#assigning-an-individual-issue-or-pull-request)
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so others will know you're working on it.
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## Pull request process
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We use [GitHub Flow](https://docs.github.com/en/get-started/using-github/github-flow)
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as our collaboration process.
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Follow the steps below for detailed instructions on contributing changes to
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MOSuite.
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![GitHub Flow diagram](https://raw.githubusercontent.com/CCBR/CCBR_NextflowTemplate/main/.github/img/GitHub-Flow_bg-white.png)
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### Clone the repo
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If you are a member of [CCBR](https://github.com/CCBR),
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you can clone this repository to your computer or development environment.
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Otherwise, you will first need to
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[fork](https://docs.github.com/en/pull-requests/collaborating-with-pull-requests/working-with-forks/fork-a-repo)
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the repo and clone your fork. You only need to do this step once.
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```sh
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git clone https://github.com/CCBR/MOSuite
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```
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> Cloning into 'MOSuite'... <br>
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> remote: Enumerating objects: 1136, done. <br>
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> remote: Counting objects: 100% (463/463), done. <br>
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> remote: Compressing objects: 100% (357/357), done. <br>
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> remote: Total 1136 (delta 149), reused 332 (delta 103), pack-reused 673 <br>
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> Receiving objects: 100% (1136/1136), 11.01 MiB | 9.76 MiB/s, done. <br>
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> Resolving deltas: 100% (530/530), done. <br>
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```sh
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cd MOSuite
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```
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### If this is your first time cloning the repo, install dependencies
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- In an R console, install the R development dependencies with
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`devtools::install_dev_deps()`, and then make sure the package passes R CMD
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check by running `devtools::check()`. If R CMD check doesn't pass cleanly,
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it's a good idea to ask for help before continuing.
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- Install [`pre-commit`](https://pre-commit.com/#install) if you don't already
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have it. Then from the repo's root directory, run
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```sh
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pre-commit install
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```
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This will install the repo's pre-commit hooks.
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You'll only need to do this step the first time you clone the repo.
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### Create a branch
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Create a Git branch for your pull request (PR). Give the branch a descriptive
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name for the changes you will make, such as `iss-10` if it is for a specific
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issue.
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```sh
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# create a new branch and switch to it
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git branch iss-10
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git switch iss-10
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```
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> Switched to a new branch 'iss-10'
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### Make your changes
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Edit the code, write unit tests, and update the documentation as needed.
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#### style
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New code should follow the [tidyverse style guide](https://style.tidyverse.org).
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You can use the [styler](https://CRAN.R-project.org/package=styler) package to
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apply these styles, but please don't restyle code that has nothing to do with
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your PR.
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A brief overview of conventions according to the tidyverse style guide:
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- most object names (variables and functions) should be in [snake_case](https://style.tidyverse.org/syntax.html#sec-objectnames)
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- function names should use [verbs](https://style.tidyverse.org/functions.html#naming) where possible
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- use `<-` for assignment
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- use [pipes](https://style.tidyverse.org/pipes.html) to chain operations on a single object
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Please see the [tidyverse style guide](https://style.tidyverse.org) for more details.
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#### test
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Most changes to the code will also need unit tests to demonstrate that the
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changes work as intended.
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Use [`testthat`](https://testthat.r-lib.org/) to create your unit tests and test
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the code.
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Test files are organized as described in
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<https://style.tidyverse.org/tests.html>.
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Take a look at the existing code in this package for examples.
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#### document
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If you have written a new function or changed the API of an existing function,
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you will need to update the function's documentation using
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[roxygen2](https://cran.r-project.org/package=roxygen2) with
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[Markdown syntax](https://roxygen2.r-lib.org/articles/rd-formatting.html).
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See instructions on writing roxygen2 comments here:
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<https://r-pkgs.org/man.html>.
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If the function is used in a vignette, you may also need to update the vignette.
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#### check
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After making your changes, run `devtools::check()` from an R console to make
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sure the package still passes R CMD check.
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### Commit and push your changes
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If you're not sure how often you should commit or what your commits should
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consist of, we recommend following the "atomic commits" principle where each
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commit contains one new feature, fix, or task.
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Learn more about atomic commits here:
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<https://www.freshconsulting.com/insights/blog/atomic-commits/>
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First, add the files that you changed to the staging area:
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```sh
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git add path/to/changed/files/
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```
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Then make the commit.
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Your commit message should follow the
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[Conventional Commits](https://www.conventionalcommits.org/en/v1.0.0/)
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specification.
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Briefly, each commit should start with one of the approved types such as
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`feat`, `fix`, `docs`, etc. followed by a description of the commit.
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Take a look at the [Conventional Commits specification](https://www.conventionalcommits.org/en/v1.0.0/#summary)
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for more detailed information about how to write commit messages.
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```sh
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git commit -m 'feat: create function for awesome feature'
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```
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pre-commit will enforce that your commit message and the code changes are
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styled correctly and will attempt to make corrections if needed.
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> Check for added large files..............................................Passed <br>
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> Fix End of Files.........................................................Passed <br>
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> Trim Trailing Whitespace.................................................Failed <br>
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> - hook id: trailing-whitespace <br>
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> - exit code: 1 <br>
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> - files were modified by this hook <br>
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> <br>
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> Fixing path/to/changed/files/file.txt <br>
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> <br>
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> codespell................................................................Passed <br>
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> style-files..........................................(no files to check)Skipped <br>
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> readme-rmd-rendered..................................(no files to check)Skipped <br>
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> use-tidy-description.................................(no files to check)Skipped <br>
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In the example above, one of the hooks modified a file in the proposed commit,
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so the pre-commit check failed. You can run `git diff` to see the changes that
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pre-commit made and `git status` to see which files were modified. To proceed
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with the commit, re-add the modified file(s) and re-run the commit command:
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```sh
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git add path/to/changed/files/file.txt
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git commit -m 'feat: create function for awesome feature'
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```
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This time, all the hooks either passed or were skipped
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(e.g. hooks that only run on R code will not run if no R files were
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committed).
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When the pre-commit check is successful, the usual commit success message
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will appear after the pre-commit messages showing that the commit was created.
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> Check for added large files..............................................Passed <br>
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> Fix End of Files.........................................................Passed <br>
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> Trim Trailing Whitespace.................................................Passed <br>
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> codespell................................................................Passed <br>
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> style-files..........................................(no files to check)Skipped <br>
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> readme-rmd-rendered..................................(no files to check)Skipped <br>
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> use-tidy-description.................................(no files to check)Skipped <br>
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> Conventional Commit......................................................Passed <br>
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> [iss-10 9ff256e] feat: create function for awesome feature <br>
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> 1 file changed, 22 insertions(+), 3 deletions(-) <br>
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Finally, push your changes to GitHub:
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```sh
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git push
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```
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If this is the first time you are pushing this branch, you may have to
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explicitly set the upstream branch:
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```sh
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git push --set-upstream origin iss-10
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```
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> Enumerating objects: 7, done. <br>
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> Counting objects: 100% (7/7), done. <br>
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> Delta compression using up to 10 threads <br>
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> Compressing objects: 100% (4/4), done. <br>
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> Writing objects: 100% (4/4), 648 bytes | 648.00 KiB/s, done. <br>
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> Total 4 (delta 3), reused 0 (delta 0), pack-reused 0 <br>
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> remote: Resolving deltas: 100% (3/3), completed with 3 local objects. <br>
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> remote: <br>
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> remote: Create a pull request for 'iss-10' on GitHub by visiting: <br>
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> remote: https://github.com/CCBR/MOSuite/pull/new/iss-10 <br>
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> remote: <br>
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> To https://github.com/CCBR/MOSuite <br>
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> <br>
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> [new branch] iss-10 -> iss-10 <br>
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> branch 'iss-10' set up to track 'origin/iss-10'. <br>
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We recommend pushing your commits often so they will be backed up on GitHub.
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You can view the files in your branch on GitHub at
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`https://github.com/CCBR/MOSuite/tree/<your-branch-name>`
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(replace `<your-branch-name>` with the actual name of your branch).
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### Create the PR
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Once your branch is ready, create a PR on GitHub:
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<https://github.com/CCBR/MOSuite/pull/new/>
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Select the branch you just pushed:
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![Create a new PR from your branch](https://raw.githubusercontent.com/CCBR/CCBR_NextflowTemplate/main/.github/img/new-PR.png)
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Edit the PR title and description.
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The title should briefly describe the change.
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Follow the comments in the template to fill out the body of the PR, and
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you can delete the comments (everything between `<!--` and `-->`) as you go.
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When you're ready, click 'Create pull request' to open it.
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![Open the PR after editing the title and description](https://raw.githubusercontent.com/CCBR/CCBR_NextflowTemplate/main/.github/img/create-PR.png)
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Optionally, you can mark the PR as a draft if you're not yet ready for it to
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be reviewed, then change it later when you're ready.
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### Wait for a maintainer to review your PR
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We will do our best to follow the tidyverse code review principles:
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<https://code-review.tidyverse.org/>.
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The reviewer may suggest that you make changes before accepting your PR in
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order to improve the code quality or style.
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If that's the case, continue to make changes in your branch and push them to
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GitHub, and they will appear in the PR.
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Once the PR is approved, the maintainer will merge it and the issue(s) the PR
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links will close automatically.
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Congratulations and thank you for your contribution!
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### After your PR has been merged
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After your PR has been merged, update your local clone of the repo by
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switching to the main branch and pulling the latest changes:
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```sh
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git checkout main
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git pull
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```
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It's a good idea to run `git pull` before creating a new branch so it will
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start from the most recent commits in main.
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## Helpful links for more information
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- This contributing guide was adapted from the [tidyverse contributing guide](https://github.com/tidyverse/tidyverse/blob/main/.github/CONTRIBUTING.md)
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- [GitHub Flow](https://docs.github.com/en/get-started/using-github/github-flow)
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- [tidyverse style guide](https://style.tidyverse.org)
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- [tidyverse code review principles](https://code-review.tidyverse.org)
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- [reproducible examples](https://www.tidyverse.org/help/#reprex)
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- [R packages book](https://r-pkgs.org/)
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- packages:
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- [usethis](https://usethis.r-lib.org/)
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- [devtools](https://devtools.r-lib.org/)
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- [testthat](https://testthat.r-lib.org/)
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- [styler](https://styler.r-lib.org/)
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- [roxygen2](https://roxygen2.r-lib.org)

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