Metadata-Version: 2.1
Name: biopragmatics
Version: 0.0.1
Summary: Biomedical semantics and pragmatics.
Author-email: Charles Tapley Hoyt <cthoyt@gmail.com>
Maintainer-email: Charles Tapley Hoyt <cthoyt@gmail.com>
License: MIT License
        
        Copyright (c) 2024 Charles Tapley Hoyt
        
        Permission is hereby granted, free of charge, to any person obtaining a copy
        of this software and associated documentation files (the "Software"), to deal
        in the Software without restriction, including without limitation the rights
        to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
        copies of the Software, and to permit persons to whom the Software is
        furnished to do so, subject to the following conditions:
        
        The above copyright notice and this permission notice shall be included in all
        copies or substantial portions of the Software.
        
        THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
        IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
        FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
        AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
        LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
        OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
        SOFTWARE.
        
Project-URL: Bug Tracker, https://github.com/cthoyt/biopragmatics/issues
Project-URL: Homepage, https://github.com/cthoyt/biopragmatics
Project-URL: Repository, https://github.com/cthoyt/biopragmatics.git
Project-URL: Documentation, https://biopragmatics.readthedocs.io
Keywords: snekpack,cookiecutter
Classifier: Development Status :: 1 - Planning
Classifier: Environment :: Console
Classifier: Intended Audience :: Developers
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Classifier: Framework :: Pytest
Classifier: Framework :: tox
Classifier: Framework :: Sphinx
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Classifier: Programming Language :: Python :: 3.12
Classifier: Programming Language :: Python :: 3 :: Only
Requires-Python: >=3.10
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: more-itertools
Requires-Dist: tqdm
Requires-Dist: click
Requires-Dist: more-click
Provides-Extra: docs
Requires-Dist: sphinx >=8 ; extra == 'docs'
Requires-Dist: sphinx-rtd-theme >=3.0 ; extra == 'docs'
Requires-Dist: sphinx-click ; extra == 'docs'
Requires-Dist: sphinx-automodapi ; extra == 'docs'
Provides-Extra: tests
Requires-Dist: pytest ; extra == 'tests'
Requires-Dist: coverage ; extra == 'tests'

<!--
<p align="center">
  <img src="https://github.com/cthoyt/biopragmatics/raw/main/docs/source/logo.png" height="150">
</p>
-->

<h1 align="center">
  Biopragmatics
</h1>

<p align="center">
    <a href="https://github.com/cthoyt/biopragmatics/actions/workflows/tests.yml">
        <img alt="Tests" src="https://github.com/cthoyt/biopragmatics/actions/workflows/tests.yml/badge.svg" /></a>
    <a href="https://pypi.org/project/biopragmatics">
        <img alt="PyPI" src="https://img.shields.io/pypi/v/biopragmatics" /></a>
    <a href="https://pypi.org/project/biopragmatics">
        <img alt="PyPI - Python Version" src="https://img.shields.io/pypi/pyversions/biopragmatics" /></a>
    <a href="https://github.com/cthoyt/biopragmatics/blob/main/LICENSE">
        <img alt="PyPI - License" src="https://img.shields.io/pypi/l/biopragmatics" /></a>
    <a href='https://biopragmatics.readthedocs.io/en/latest/?badge=latest'>
        <img src='https://readthedocs.org/projects/biopragmatics/badge/?version=latest' alt='Documentation Status' /></a>
    <a href="https://codecov.io/gh/cthoyt/biopragmatics/branch/main">
        <img src="https://codecov.io/gh/cthoyt/biopragmatics/branch/main/graph/badge.svg" alt="Codecov status" /></a>  
    <a href="https://github.com/cthoyt/cookiecutter-python-package">
        <img alt="Cookiecutter template from @cthoyt" src="https://img.shields.io/badge/Cookiecutter-snekpack-blue" /></a>
    <a href="https://github.com/astral-sh/ruff">
        <img src="https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/v2.json" alt="Ruff" style="max-width:100%;"></a>
    <a href="https://github.com/cthoyt/biopragmatics/blob/main/.github/CODE_OF_CONDUCT.md">
        <img src="https://img.shields.io/badge/Contributor%20Covenant-2.1-4baaaa.svg" alt="Contributor Covenant"/></a>
</p>

Biomedical semantics and pragmatics.

## 💪 Getting Started

> TODO show in a very small amount of space the **MOST** useful thing your package can do.
> Make it as short as possible! You have an entire set of docs for later.

### Command Line Interface

The biopragmatics command line tool is automatically installed. It can
be used from the console with the `--help` flag to show all subcommands:

```console
biopragmatics --help
```

> TODO show the most useful thing the CLI does! The CLI will have documentation auto-generated
> by `sphinx`.

## 🚀 Installation

<!-- Uncomment this section after your first ``tox -e finish``
The most recent release can be installed from
[PyPI](https://pypi.org/project/biopragmatics/) with:

```console
python3 -m pip install biopragmatics
```
-->

The most recent code and data can be installed directly from GitHub with:

```console
python3 -m pip install git+https://github.com/cthoyt/biopragmatics.git
```

## 👐 Contributing

Contributions, whether filing an issue, making a pull request, or forking, are appreciated. See
[CONTRIBUTING.md](https://github.com/cthoyt/biopragmatics/blob/master/.github/CONTRIBUTING.md)
for more information on getting involved.

## 👋 Attribution

### ⚖️ License

The code in this package is licensed under the MIT License.

<!--
### 📖 Citation

Citation goes here!
-->

<!--
### 🎁 Support

This project has been supported by the following organizations (in alphabetical order):

- [Biopragmatics Lab](https://biopragmatics.github.io)

-->

<!--
### 💰 Funding

This project has been supported by the following grants:

| Funding Body  | Program                                                      | Grant Number |
|---------------|--------------------------------------------------------------|--------------|
| Funder        | [Grant Name (GRANT-ACRONYM)](https://example.com/grant-link) | ABCXYZ       |
-->

### 🍪 Cookiecutter

This package was created with [@audreyfeldroy](https://github.com/audreyfeldroy)'s
[cookiecutter](https://github.com/cookiecutter/cookiecutter) package using [@cthoyt](https://github.com/cthoyt)'s
[cookiecutter-snekpack](https://github.com/cthoyt/cookiecutter-snekpack) template.

## 🛠️ For Developers

<details>
  <summary>See developer instructions</summary>

The final section of the README is for if you want to get involved by making a code contribution.

### Development Installation

To install in development mode, use the following:

```console
git clone git+https://github.com/cthoyt/biopragmatics.git
cd biopragmatics
python3 -m pip install -e .
```

### Updating Package Boilerplate

This project uses `cruft` to keep boilerplate (i.e., configuration, contribution guidelines, documentation
configuration)
up-to-date with the upstream cookiecutter package. Update with the following:

```console
python3 -m pip install cruft
cruft update
```

More info on Cruft's update command is
available [here](https://github.com/cruft/cruft?tab=readme-ov-file#updating-a-project).

### 🥼 Testing

After cloning the repository and installing `tox` with
`python3 -m pip install tox tox-uv`,
the unit tests in the `tests/` folder can be run reproducibly with:

```console
tox -e py
```

Additionally, these tests are automatically re-run with each commit in a
[GitHub Action](https://github.com/cthoyt/biopragmatics/actions?query=workflow%3ATests).

### 📖 Building the Documentation

The documentation can be built locally using the following:

```console
git clone git+https://github.com/cthoyt/biopragmatics.git
cd biopragmatics
tox -e docs
open docs/build/html/index.html
```

The documentation automatically installs the package as well as the `docs`
extra specified in the [`pyproject.toml`](pyproject.toml). `sphinx` plugins
like `texext` can be added there. Additionally, they need to be added to the
`extensions` list in [`docs/source/conf.py`](docs/source/conf.py).

The documentation can be deployed to [ReadTheDocs](https://readthedocs.io) using
[this guide](https://docs.readthedocs.io/en/stable/intro/import-guide.html).
The [`.readthedocs.yml`](.readthedocs.yml) YAML file contains all the configuration you'll need.
You can also set up continuous integration on GitHub to check not only that
Sphinx can build the documentation in an isolated environment (i.e., with `tox -e docs-test`)
but also that [ReadTheDocs can build it too](https://docs.readthedocs.io/en/stable/pull-requests.html).

#### Configuring ReadTheDocs

1. Log in to ReadTheDocs with your GitHub account to install the integration
   at https://readthedocs.org/accounts/login/?next=/dashboard/
2. Import your project by navigating to https://readthedocs.org/dashboard/import then clicking the plus icon next to
   your repository
3. You can rename the repository on the next screen using a more stylized name (i.e., with spaces and capital letters)
4. Click next, and you're good to go!

### 📦 Making a Release

#### Configuring Zenodo

[Zenodo](https://zenodo.org) is a long-term archival system that assigns a DOI to each release of your package.

1. Log in to Zenodo via GitHub with this link: https://zenodo.org/oauth/login/github/?next=%2F. This brings you to a
   page that lists all of your organizations and asks you to approve installing the Zenodo app on GitHub. Click "grant"
   next to any organizations you want to enable the integration for, then click the big green "approve" button. This
   step only needs to be done once.
2. Navigate to https://zenodo.org/account/settings/github/, which lists all of your GitHub repositories (both in your
   username and any organizations you enabled). Click the on/off toggle for any relevant repositories. When you make
   a new repository, you'll have to come back to this

After these steps, you're ready to go! After you make "release" on GitHub (steps for this are below), you can navigate
to https://zenodo.org/account/settings/github/repository/cthoyt/biopragmatics
to see the DOI for the release and link to the Zenodo record for it.

#### Registering with the Python Package Index (PyPI)

You only have to do the following steps once.

1. Register for an account on the [Python Package Index (PyPI)](https://pypi.org/account/register)
2. Navigate to https://pypi.org/manage/account and make sure you have verified your email address. A verification email
   might not have been sent by default, so you might have to click the "options" dropdown next to your address to get to
   the "re-send verification email" button
3. 2-Factor authentication is required for PyPI since the end of 2023 (see
   this [blog post from PyPI](https://blog.pypi.org/posts/2023-05-25-securing-pypi-with-2fa/)). This means
   you have to first issue account recovery codes, then set up 2-factor authentication
4. Issue an API token from https://pypi.org/manage/account/token

#### Configuring your machine's connection to PyPI

You have to do the following steps once per machine. Create a file in your home directory called
`.pypirc` and include the following:

```ini
[distutils]
index-servers =
    pypi
    testpypi

[pypi]
username = __token__
password = <the API token you just got>

# This block is optional in case you want to be able to make test releases to the Test PyPI server
[testpypi]
repository = https://test.pypi.org/legacy/
username = __token__
password = <an API token from test PyPI>
```

Note that since PyPI is requiring token-based authentication, we use `__token__` as the user, verbatim.
If you already have a `.pypirc` file with a `[distutils]` section, just make sure that there is an `index-servers`
key and that `pypi` is in its associated list. More information on configuring the `.pypirc` file can
be found [here](https://packaging.python.org/en/latest/specifications/pypirc).

#### Uploading to PyPI

After installing the package in development mode and installing
`tox` with `python3 -m pip install tox tox-uv`,
run the following from the console:

```console
tox -e finish
```

This script does the following:

1. Uses [bump-my-version](https://github.com/callowayproject/bump-my-version) to switch the version number in
   the `pyproject.toml`, `CITATION.cff`, `src/biopragmatics/version.py`,
   and [`docs/source/conf.py`](docs/source/conf.py) to not have the `-dev` suffix
2. Packages the code in both a tar archive and a wheel using
   [`uv build`](https://docs.astral.sh/uv/guides/publish/#building-your-package)
3. Uploads to PyPI using [`twine upload`](https://github.com/pypa/twine).
   This will be replaced soon with `uv publish` (see https://github.com/cthoyt/cookiecutter-snekpack/issues/29)
4. Push to GitHub. You'll need to make a release going with the commit where the version was bumped.
5. Bump the version to the next patch. If you made big changes and want to bump the version by minor, you can
   use `tox -e bumpversion -- minor` after.

#### Releasing on GitHub

1. Navigate
   to https://github.com/cthoyt/biopragmatics/releases/new
   to draft a new release
2. Click the "Choose a Tag" dropdown and select the tag corresponding to the release you just made
3. Click the "Generate Release Notes" button to get a quick outline of recent changes. Modify the title and description
   as you see fit
4. Click the big green "Publish Release" button

This will trigger Zenodo to assign a DOI to your release as well.

</details>
