wadoh-raccoon 0.4.0
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Requires Python: >=3.11

# wadoh_raccoon

A Python package for transforming and linking pathogen sequencing/subtyping metadata.

See our github page for function references and docs https://nw-page.github.io/wadoh_raccoon/ 

# How to install the package

Open PowerShell terminal (or Ubuntu bash terminal)

1. Make a new folder
2. `pip install uv`
3. `uv venv --python 3.11`
4.  `.\.venv\Scripts\activate`
5. `uv pip install git+https://github.com/NW-PaGe/wadoh_raccoon.git#egg=wadoh_raccoon`

To install a specific version, find the git tag noted in the GitHub Release section (something like `v0.2.5`) and then put it in the install statement like `.git@v0.2.5`:

```bash
uv pip install git+https://github.com/NW-PaGe/wadoh_raccoon.git@v0.2.5#egg=wadoh_raccoon
```

here's what it looks like when updating the install version:

![image](https://github.com/user-attachments/assets/ac571054-4918-40a1-b601-000869b97866)



# How to test it
create a script called `main.py` in your folder and run this code:

```python

from wadoh_raccoon.utils import helpers
import polars as pl


df = pl.DataFrame({
    'date': [
        '2022-01-03',
        '01-02-2020',
        '44115',
        None,
        "2022-12-27 08:26:49",
        # "2022-12-27T08:26:49",
        '01/02/1995',
        '2/3/2022',
        '2/16/2022'
    ]
})

df_output = (
    df
    .with_columns(
        output_date = helpers.date_format('date')
    )
    .select('output_date')
)

print(df_output)
```

it should give you this output

```python
>>> print(df_output)
shape: (8, 1)
┌─────────────┐
│ output_date │
│ ---         │
│ date        │
╞═════════════╡
│ 2022-01-03  │
│ 2020-01-02  │
│ null        │
│ null        │
│ 2022-12-27  │
│ 1995-01-02  │
│ 2022-02-03  │
│ 2022-02-16  │
└─────────────┘
```


# For Devs

## how to create a package with uv
1. In a new repo, run `uv init --package <package_name>`
	It gives you this:
```bash
.
├── LICENSE
├── README.md
└── test_package
    ├── README.md
    ├── pyproject.toml
    └── src
        └── test_package
            └── __init__.py

3 directories, 5 files

```
2. Create a venv with `uv venv`
  a. This creates a venv you can activate (called your package name)
	b. Creates a  `uv.lock` file 
	c. `Uv sync` to install and update your venv
3. Run `uv build` and it will build your package, adding a `dist/` folder with a `.tar.gz` file of the package.
	a. Amazing
	b. [follow these docs](https://docs.astral.sh/uv/guides/package/#publishing-your-package) to publish it to pypi or somewhere else privately 
4. To install from github: `uv pip install git+https://github.com/NW-PaGe/wadoh_raccoon.git#egg=wadoh_raccoon`
If you get python version error, add python version to your .venv with `uv python install 3.11` or rebuild the venv with `uv venv --python 3.11`

5. for dev packages that you need but aren't package dependencies, like `pytest`, you can add them to the project with [development dependencies](https://docs.astral.sh/uv/concepts/projects/dependencies/#development-dependencies) like this:

```bash
uv add --dev pytest
```

and that will add pytest to the `uv.lock` and `pyproject.toml` but as a separate dependency from the actual packages. In other words, the package won't be dependent on `pytest`, but it will be installed for devs that want to run the unit tests.

## how to build the package automatically with CI/CD

this repo has a github action that automatically runs unit tests, builds the package, and outputs a changelog for a github release.

The github action has two steps:

### 1. unit-tests

This step will install `uv`, install python, and then run the unit tests in the `tests` folder.

```yaml
unit-tests:
    name: Build and Test Python Package
    runs-on: ubuntu-latest

    steps:
      - uses: actions/checkout@v4

      - name: Install uv
        uses: astral-sh/setup-uv@v5
        with:
          version: "0.6.5" # pin a specific version is best practice
          enable-cache: true

      # install python in 
      - name: "Set up Python"
        uses: actions/setup-python@v5
        with:
          python-version-file: "pyproject.toml"

      - name: Run tests
        # For example, using `pytest`
        run: uv run pytest tests
```

### 2. build-and-release

This step is dependent on the first step above. If any unit-tests fail, then this build/release will not run.

The build step works like this:

1. Scan the code for conventional commit messages (like `fix:`, `feat:`, etc) and render a changelog based on the commits
2. Create a GitHub Release (git tags) that bump up the version of the codebase (like `v1.0.0` to `v1.1.0`)
3. Build the python package and have its version match the git tag version. `uv` currently doesn't have a built in way to do this, but [they are currently working on it](https://github.com/astral-sh/uv/issues/6298). In the meantime, that link has a way to link the python package version to the git release like this:

```yaml
# install uv
- name: Set up uv
  run: curl -LsSf https://astral.sh/uv/install.sh | sh

- name: Build package
  if: ${{ steps.changelog.outputs.skipped == 'false' }}
  run: |
    VERSION=$(uvx dunamai from any --no-metadata --style pep440) # find the version of the git tag for the python package
    echo $VERSION
    uvx --from=toml-cli toml set --toml-path=pyproject.toml project.version $VERSION # update the version in the pyproject.toml
    uv build # build the package

```

so it will update the `pyproject.toml` to have the most up to date version that matches the git tag version and then build the package with `uv build`. The [build function](https://docs.astral.sh/uv/concepts/projects/build/#using-uv-build) builds the package and outputs a `dist/` folder with a `.tar.gz` file and a `.whl` file, both of which are source files for installing the package.


I also wanted to take the `.tar.gz` and `.whl` files and add them to the `Assets` in the changelog for GitHub. That way we can always save copies of our package whenever we make a new release, just to be safe.

```yaml
# Attach the build assets to the GitHub release (only if changelog creation was successful)
- name: Upload sdist to GitHub release
  run: gh release upload $TAG $FILES --clobber
  env:
    GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
    TAG: ${{ steps.changelog.outputs.tag }} # this is pulled from the changelog step where it creates the git tag
    FILES: dist/*.tar.gz dist/*.whl # these files are created in the build step
```