Refactor as a python package

.github/CONTRIBUTING.md

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+# Contributing to CCBR Tools
+
+## Proposing changes with issues
+
+If you want to make a change, it's a good idea to first
+[open an issue](https://code-review.tidyverse.org/issues/)
+and make sure someone from the team agrees that it’s needed.
+
+If you've decided to work on an issue,
+[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)
+so others will know you're working on it.
+
+## Pull request process
+
+We use [GitHub Flow](https://docs.github.com/en/get-started/using-github/github-flow)
+as our collaboration process.
+Follow the steps below for detailed instructions on contributing changes to
+CCBR Tools.
+
+![GitHub Flow diagram](./img/GitHub-Flow_bg-white.png)
+
+### Clone the repo
+
+If you are a member of [CCBR](https://github.com/CCBR),
+you can clone this repository to your computer or development environment.
+Otherwise, you will first need to
+[fork](https://docs.github.com/en/pull-requests/collaborating-with-pull-requests/working-with-forks/fork-a-repo)
+the repo and clone your fork. You only need to do this step once.
+
+```sh
+git clone https://github.com/CCBR/tools
+```
+
+> Cloning into 'tools'... <br>
+> remote: Enumerating objects: 1136, done. <br>
+> remote: Counting objects: 100% (463/463), done. <br>
+> remote: Compressing objects: 100% (357/357), done. <br>
+> remote: Total 1136 (delta 149), reused 332 (delta 103), pack-reused 673 <br>
+> Receiving objects: 100% (1136/1136), 11.01 MiB | 9.76 MiB/s, done. <br>
+> Resolving deltas: 100% (530/530), done. <br>
+
+```sh
+cd tools
+```
+
+### If this is your first time cloning the repo, you may need to install dependencies
+
+- Install the python dependencies with pip
+
+  ```sh
+  pip install .[[dev,test]]
+  ```
+
+- Install [`pre-commit`](https://pre-commit.com/#install) if you don't already
+  have it. Then from the repo's root directory, run
+
+  ```sh
+  pre-commit install
+  ```
+
+  This will install the repo's pre-commit hooks.
+  You'll only need to do this step the first time you clone the repo.
+
+### Create a branch
+
+Create a Git branch for your pull request (PR). Give the branch a descriptive
+name for the changes you will make, such as `iss-10` if it is for a specific
+issue.
+
+```sh
+# create a new branch and switch to it
+git branch iss-10
+git switch iss-10
+```
+
+> Switched to a new branch 'iss-10'
+
+### Make your changes
+
+Edit the code, write and run tests, and update the documentation as needed.
+
+#### test
+
+Changes to the **python package** code will also need unit tests to demonstrate
+that the changes work as intended.
+We write unit tests with pytest and store them in the `tests/` subdirectory.
+Run the tests with `python -m pytest`.
+
+#### document
+
+If you have added a new feature or changed the API of an existing feature,
+you will likely need to update the documentation in `docs/`.
+
+### Commit and push your changes
+
+If you're not sure how often you should commit or what your commits should
+consist of, we recommend following the "atomic commits" principle where each
+commit contains one new feature, fix, or task.
+Learn more about atomic commits here:
+<https://www.freshconsulting.com/insights/blog/atomic-commits/>
+
+First, add the files that you changed to the staging area:
+
+```sh
+git add path/to/changed/files/
+```
+
+Then make the commit.
+Your commit message should follow the
+[Conventional Commits](https://www.conventionalcommits.org/en/v1.0.0/)
+specification.
+Briefly, each commit should start with one of the approved types such as
+`feat`, `fix`, `docs`, etc. followed by a description of the commit.
+Take a look at the [Conventional Commits specification](https://www.conventionalcommits.org/en/v1.0.0/#summary)
+for more detailed information about how to write commit messages.
+
+```sh
+git commit -m 'feat: create function for awesome feature'
+```
+
+pre-commit will enforce that your commit message and the code changes are
+styled correctly and will attempt to make corrections if needed.
+
+> Check for added large files..............................................Passed <br>
+> Fix End of Files.........................................................Passed <br>
+> Trim Trailing Whitespace.................................................Failed <br>
+>
+> - hook id: trailing-whitespace <br>
+> - exit code: 1 <br>
+> - files were modified by this hook <br> > <br>
+>   Fixing path/to/changed/files/file.txt <br> > <br>
+>   codespell................................................................Passed <br>
+>   style-files..........................................(no files to check)Skipped <br>
+>   readme-rmd-rendered..................................(no files to check)Skipped <br>
+>   use-tidy-description.................................(no files to check)Skipped <br>
+
+In the example above, one of the hooks modified a file in the proposed commit,
+so the pre-commit check failed. You can run `git diff` to see the changes that
+pre-commit made and `git status` to see which files were modified. To proceed
+with the commit, re-add the modified file(s) and re-run the commit command:
+
+```sh
+git add path/to/changed/files/file.txt
+git commit -m 'feat: create function for awesome feature'
+```
+
+This time, all the hooks either passed or were skipped
+(e.g. hooks that only run on R code will not run if no R files were
+committed).
+When the pre-commit check is successful, the usual commit success message
+will appear after the pre-commit messages showing that the commit was created.
+
+> Check for added large files..............................................Passed <br>
+> Fix End of Files.........................................................Passed <br>
+> Trim Trailing Whitespace.................................................Passed <br>
+> codespell................................................................Passed <br>
+> style-files..........................................(no files to check)Skipped <br>
+> readme-rmd-rendered..................................(no files to check)Skipped <br>
+> use-tidy-description.................................(no files to check)Skipped <br>
+> Conventional Commit......................................................Passed <br> > [iss-10 9ff256e] feat: create function for awesome feature <br>
+> 1 file changed, 22 insertions(+), 3 deletions(-) <br>
+
+Finally, push your changes to GitHub:
+
+```sh
+git push
+```
+
+If this is the first time you are pushing this branch, you may have to
+explicitly set the upstream branch:
+
+```sh
+git push --set-upstream origin iss-10
+```
+
+> Enumerating objects: 7, done. <br>
+> Counting objects: 100% (7/7), done. <br>
+> Delta compression using up to 10 threads <br>
+> Compressing objects: 100% (4/4), done. <br>
+> Writing objects: 100% (4/4), 648 bytes | 648.00 KiB/s, done. <br>
+> Total 4 (delta 3), reused 0 (delta 0), pack-reused 0 <br>
+> remote: Resolving deltas: 100% (3/3), completed with 3 local objects. <br>
+> remote: <br>
+> remote: Create a pull request for 'iss-10' on GitHub by visiting: <br>
+> remote: https://github.com/CCBR/tools/pull/new/iss-10 <br>
+> remote: <br>
+> To https://github.com/CCBR/tools <br> > <br> > [new branch] iss-10 -> iss-10 <br>
+> branch 'iss-10' set up to track 'origin/iss-10'. <br>
+
+We recommend pushing your commits often so they will be backed up on GitHub.
+You can view the files in your branch on GitHub at
+`https://github.com/CCBR/tools/tree/<your-branch-name>`
+(replace `<your-branch-name>` with the actual name of your branch).
+
+### Create the PR
+
+Once your branch is ready, create a PR on GitHub:
+<https://github.com/CCBR/tools/pull/new/>
+
+Select the branch you just pushed:
+
+![Create a new PR from your branch](./img/new-PR.png)
+
+Edit the PR title and description.
+The title should briefly describe the change.
+Follow the comments in the template to fill out the body of the PR, and
+you can delete the comments (everything between `<!--` and `-->`) as you go.
+Be sure to fill out the checklist, checking off items as you complete them or
+striking through any irrelevant items.
+When you're ready, click 'Create pull request' to open it.
+
+![Open the PR after editing the title and description](./img/create-PR.png)
+
+Optionally, you can mark the PR as a draft if you're not yet ready for it to
+be reviewed, then change it later when you're ready.
+
+### Wait for a maintainer to review your PR
+
+We will do our best to follow the tidyverse code review principles:
+<https://code-review.tidyverse.org/>.
+The reviewer may suggest that you make changes before accepting your PR in
+order to improve the code quality or style.
+If that's the case, continue to make changes in your branch and push them to
+GitHub, and they will appear in the PR.
+
+Once the PR is approved, the maintainer will merge it and the issue(s) the PR
+links will close automatically.
+Congratulations and thank you for your contribution!
+
+### After your PR has been merged
+
+After your PR has been merged, update your local clone of the repo by
+switching to the main branch and pulling the latest changes:
+
+```sh
+git checkout main
+git pull
+```
+
+It's a good idea to run `git pull` before creating a new branch so it will
+start from the most recent commits in main.
+
+## Helpful links for more information
+
+- [GitHub Flow](https://docs.github.com/en/get-started/using-github/github-flow)
+- [semantic versioning guidelines](https://semver.org/)
+- [changelog guidelines](https://keepachangelog.com/en/1.1.0/)
+- [tidyverse code review principles](https://code-review.tidyverse.org)
+- [reproducible examples](https://www.tidyverse.org/help/#reprex)

.github/ISSUE_TEMPLATE/bug_report.yml

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+name: Bug report
+description: Report something that is broken or incorrect
+labels: bug
+body:
+  - type: markdown
+    attributes:
+      value: |
+        Before you post this issue, please check the documentation:
+
+        <https://ccbr.github.io/CCBR/Tools>
+
+  - type: textarea
+    id: description
+    attributes:
+      label: Description of the bug
+      description: A clear and concise description of what the bug is.
+    validations:
+      required: true
+
+  - type: textarea
+    id: command_used
+    attributes:
+      label: Command used and terminal output
+      description: Steps to reproduce the behaviour. Please paste the code you used
+      render: console
+      placeholder: |
+        $ ccbr_tools ...
+
+        Some output where something broke
+
+  - type: textarea
+    id: files
+    attributes:
+      label: Relevant files
+      description: |
+        Please drag and drop any relevant files here. Create a `.zip` archive if the extension is not allowed.
+
+  - type: textarea
+    id: system
+    attributes:
+      label: System information
+      description: |
+        - Version of CCBR Tools _(eg. 1.0, 1.8.2)_
+        - Python version _(eg. 3.11)_
+        - Environment _(eg. local macOS, biowulf HPC)_

.github/ISSUE_TEMPLATE/config.yml

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+contact_links:
+  - name: Discussions
+    url: https://github.com/CCBR/Tools/discussions
+    about: Please ask and answer questions here.

.github/ISSUE_TEMPLATE/feature_request.yml

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+name: Feature request
+description: Suggest an idea for the tool
+labels: enhancement
+body:
+  - type: textarea
+    id: description
+    attributes:
+      label: Description of feature
+      description: Please describe your suggestion for a new feature. It might help to describe a problem or use case, plus any alternatives that you have considered.
+    validations:
+      required: true

.github/PULL_REQUEST_TEMPLATE.md

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+## Changes
+
+<!--
+Provide a summary of what is included in this Pull Request (PR).
+-->
+
+## Issues
+
+<!--
+Reference any issues related to this PR.
+If this PR fixes any issues, [use a keyword](https://docs.github.com/en/issues/tracking-your-work-with-issues/linking-a-pull-request-to-an-issue#linking-a-pull-request-to-an-issue-using-a-keyword)
+when referring to the issue.
+-->
+
+## PR Checklist
+
+(~Strikethrough~ any points that are not applicable.)
+
+- [ ] This comment contains a description of changes with justifications, with any relevant issues linked.
+- [ ] Write unit tests for any new features, bug fixes, or other code changes.
+- [ ] Update docs if there are any API changes.
+- [ ] Update `CHANGELOG.md` with a short description of any user-facing changes and reference the PR number. Guidelines: https://keepachangelog.com/en/1.1.0/

.github/workflows/auto-format.yml

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+name: auto-format
+
+on:
+  workflow_dispatch:
+  pull_request:
+    paths:
+      - "src/**"
+      - "README.qmd"
+
+env:
+  GH_TOKEN: ${{ github.token }}
+
+jobs:
+  auto-format:
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.11"]
+
+    steps:
+      - uses: actions/checkout@v4
+        if: github.event_name == 'pull_request'
+        with:
+          fetch-depth: 0
+          ref: ${{ github.event.pull_request.head.ref }}
+
+      - uses: actions/checkout@v4
+        if: github.event_name == 'push'
+        with:
+          fetch-depth: 0
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+          cache: "pip"
+      - name: Install dependencies
+        run: |
+          python -m pip install .[dev] --upgrade pip
+      - name: format
+        uses: psf/black@stable
+        with:
+          options: "--verbose"
+          use_pyproject: true
+      - name: commit & push
+        run: |
+          git config --global user.name "github-actions[bot]"
+          git config --global user.email "41898282+github-actions[bot]@users.noreply.github.com"
+          git add .
+          git commit -m "ci: 🤖 black formatting" && git push || echo "nothing to commit"
+      - uses: quarto-dev/quarto-actions/setup@v2
+        with:
+          version: 1.4.515
+      - name: quarto render readme
+        run: |
+          quarto render README.qmd
+          git add README.md
+          git commit -m "ci: 🤖 render readme" && git push || echo "nothing to commit"