| Name | drugbank-downloader JSON |
| Version |
0.2.0
JSON |
| download |
| home_page | None |
| Summary | A tool for reproducibly downloading and extracting DrugBank data |
| upload_time | 2024-09-19 13:37:09 |
| maintainer | None |
| docs_url | None |
| author | None |
| requires_python | >=3.9 |
| 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. |
| keywords |
snekpack
cookiecutter
|
| VCS |
 |
| bugtrack_url |
|
| requirements |
No requirements were recorded.
|
| Travis-CI |
No Travis.
|
| coveralls test coverage |
No coveralls.
|
<!--
<p align="center">
<img src="https://github.com/cthoyt/drugbank-downloader/raw/main/docs/source/logo.png" height="150">
</p>
-->
<h1 align="center">
DrugBank Downloader
</h1>
<p align="center">
<a href="https://github.com/cthoyt/drugbank-downloader/actions/workflows/tests.yml">
<img alt="Tests" src="https://github.com/cthoyt/drugbank-downloader/actions/workflows/tests.yml/badge.svg" /></a>
<a href="https://pypi.org/project/drugbank_downloader">
<img alt="PyPI" src="https://img.shields.io/pypi/v/drugbank_downloader" /></a>
<a href="https://pypi.org/project/drugbank_downloader">
<img alt="PyPI - Python Version" src="https://img.shields.io/pypi/pyversions/drugbank_downloader" /></a>
<a href="https://github.com/cthoyt/drugbank-downloader/blob/main/LICENSE">
<img alt="PyPI - License" src="https://img.shields.io/pypi/l/drugbank_downloader" /></a>
<a href='https://drugbank_downloader.readthedocs.io/en/latest/?badge=latest'>
<img src='https://readthedocs.org/projects/drugbank_downloader/badge/?version=latest' alt='Documentation Status' /></a>
<a href="https://codecov.io/gh/cthoyt/drugbank-downloader/branch/main">
<img src="https://codecov.io/gh/cthoyt/drugbank-downloader/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/psf/black'>
<img src='https://img.shields.io/badge/code%20style-black-000000.svg' alt='Code style: black' /></a>
<a href="https://github.com/cthoyt/drugbank-downloader/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>
Don't worry about DrugBank licensing and distribution rules - just use ``drugbank_downloader`` to write code that knows
how to download it and use it automatically.
## Installation
```bash
$ pip install drugbank-downloader
```
## Download A Specific Version
```python
import os
from drugbank_downloader import download_drugbank
username = ... # suggestion: load from environment with os.getenv('DRUGBANK_USERNAME')
password = ...
path = download_drugbank(version='5.1.7', username=username, password=password)
# This is where it gets downloaded: ~/.data/drugbank/5.1.7/full database.xml.zip
expected_path = os.path.join(os.path.expanduser('~'), '.data', 'drugbank', '5.1.7', 'full database.xml.zip')
assert expected_path == path.as_posix()
```
After it's been downloaded once, it's smart and doesn't need to download again. It gets stored
using [`pystow`](https://github.com/cthoyt/pystow) automatically in the `~/.data/drugbank`
directory.
## Automating Configuration of DrugBank Credentials
There are two ways to automatically set the username and password so you don't have to worry about getting it and
passing it around in your python code:
1. Set `DRUGBANK_USERNAME` and `DRUGBANK_PASSWORD` in the environment
2. Create `~/.config/drugbank.ini` and set in the `[drugbank]` section a `username` and `password` key.
```python
from drugbank_downloader import download_drugbank
# Same path as before
path = download_drugbank(version='5.1.7')
```
The `username` and `password` keyword arguments are available for all functions in this package, but will be omitted in
the tutorial for brevity.
## Download the Latest Version
First, you'll have to install [`bioversions`](https://github.com/cthoyt/bioversions)
with `pip install bioversions`, whose job it is to look up the latest version of many databases. Then, you can modify
the previous code slightly by omitting the `version` keyword argument:
```python
import os
from drugbank_downloader import download_drugbank
path = download_drugbank()
# This is where it gets downloaded: ~/.data/drugbank/5.1.7/full database.xml.zip based on the latest
# version, as of December 14th, 2020.
expected_path = os.path.join(os.path.expanduser('~'), '.data', 'drugbank', '5.1.7', 'full database.xml.zip')
assert expected_path == path.as_posix()
```
The `version` keyword argument is available for all functions in this package, but like the username and password will
be omitted for brevity.
## Don't Bother Unpacking - read `full database.xml.zip` Directly
DrugBank is a single XML (could be JSON in a better future) file inside a zip archive. Normally, people manually unzip
this folder then do something with the resulting file. Don't do this, it's not reproducible!
Instead, it can be opened as a file object in Python with the following code.
```python
import zipfile
from drugbank_downloader import download_drugbank
path = download_drugbank()
with zipfile.ZipFile(path) as zip_file:
with zip_file.open('full database.xml') as file:
pass # do something with the file
```
You don't have time to remember this. Just use `drugbank_downloader.open_drugbank()` instead:
```python
from drugbank_downloader import open_drugbank
with open_drugbank() as file:
pass # do something with the file, same as above
```
## Reading DrugBank's XML
After you've opened the file, you probably want to read it with an XML parser like:
```python
from xml.etree import ElementTree
from drugbank_downloader import open_drugbank
with open_drugbank() as file:
tree = ElementTree.parse(file)
```
You don't have time to remember this either. Just use `drugbank_downloader.parse_drugbank()` instead:
```python
from xml.etree import ElementTree
from drugbank_downloader import parse_drugbank
tree = parse_drugbank()
root = tree.getroot()
```
If your first thing to do to the tree is always to get its root, just use
`drugbank_downloader.get_drugbank_root()`:
```python
from drugbank_downloader import get_drugbank_root
root = get_drugbank_root()
```
You now know everything I can teach you. Please use these tools to do re-usable, reproducible
science!
## Store in a Different Place
If you want to store the data elsewhere using `pystow` (e.g., in [`pyobo`](https://github.com/pyobo/pyobo)
I also keep a copy of this file), you can use the `prefix` argument.
```python
import os
from drugbank_downloader import download_drugbank
path = download_drugbank(prefix=['pyobo', 'raw', 'drugbank'])
# This is where it gets downloaded: ~/.data/pyobo/raw/drugbank/5.1.7/full database.xml.zip
expected_path = os.path.join(os.path.expanduser('~'), '.data', 'pyobo', 'raw', 'drugbank', '5.1.7',
'full database.xml.zip')
assert expected_path == path.as_posix()
```
See the `pystow` [documentation](https://github.com/cthoyt/pystow#%EF%B8%8F-configuration) on configuring the storage
location further.
## Download via CLI
After installing, run the following CLI command to ensure it and send the path to stdout
```bash
$ drugbank_downloader
```
If you haven't pre-configured the username and password, you can specify them with the `--username` and `--password`
options.
## 👐 Contributing
Contributions, whether filing an issue, making a pull request, or forking, are appreciated. See
[CONTRIBUTING.md](https://github.com/cthoyt/drugbank-downloader/blob/master/.github/CONTRIBUTING.md)
for more information on getting involved.
## 👋 Attribution
### ⚖️ License
The code in this package is licensed under the MIT License.
### 🍪 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:
```bash
git clone git+https://github.com/cthoyt/drugbank-downloader.git
cd drugbank-downloader
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:
```shell
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 `pip install tox tox-uv`,
the unit tests in the `tests/` folder can be run reproducibly with:
```shell
tox -e py
```
Additionally, these tests are automatically re-run with each commit in a
[GitHub Action](https://github.com/cthoyt/drugbank-downloader/actions?query=workflow%3ATests).
### 📖 Building the Documentation
The documentation can be built locally using the following:
```shell
git clone git+https://github.com/cthoyt/drugbank-downloader.git
cd drugbank-downloader
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/drugbank-downloader
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 `pip install tox tox-uv`,
run the following from the shell:
```shell
tox -e finish
```
This script does the following:
1. Uses [Bump2Version](https://github.com/c4urself/bump2version) to switch the version number in
the `pyproject.toml`, `CITATION.cff`, `src/drugbank_downloader/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 [`build`](https://github.com/pypa/build)
3. Uploads to PyPI using [`twine`](https://github.com/pypa/twine).
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/drugbank-downloader/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>
Raw data
{
"_id": null,
"home_page": null,
"name": "drugbank-downloader",
"maintainer": null,
"docs_url": null,
"requires_python": ">=3.9",
"maintainer_email": "Charles Tapley Hoyt <cthoyt@gmail.com>",
"keywords": "snekpack, cookiecutter",
"author": null,
"author_email": "Charles Tapley Hoyt <cthoyt@gmail.com>",
"download_url": "https://files.pythonhosted.org/packages/fa/da/1e4a08c3e6cf726d3c75e4af59d82c4df8af31ffb86ce81e91a2522ccc72/drugbank_downloader-0.2.0.tar.gz",
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"description": "<!--\n<p align=\"center\">\n <img src=\"https://github.com/cthoyt/drugbank-downloader/raw/main/docs/source/logo.png\" height=\"150\">\n</p>\n-->\n\n<h1 align=\"center\">\n DrugBank Downloader\n</h1>\n\n<p align=\"center\">\n <a href=\"https://github.com/cthoyt/drugbank-downloader/actions/workflows/tests.yml\">\n <img alt=\"Tests\" src=\"https://github.com/cthoyt/drugbank-downloader/actions/workflows/tests.yml/badge.svg\" /></a>\n <a href=\"https://pypi.org/project/drugbank_downloader\">\n <img alt=\"PyPI\" src=\"https://img.shields.io/pypi/v/drugbank_downloader\" /></a>\n <a href=\"https://pypi.org/project/drugbank_downloader\">\n <img alt=\"PyPI - Python Version\" src=\"https://img.shields.io/pypi/pyversions/drugbank_downloader\" /></a>\n <a href=\"https://github.com/cthoyt/drugbank-downloader/blob/main/LICENSE\">\n <img alt=\"PyPI - License\" src=\"https://img.shields.io/pypi/l/drugbank_downloader\" /></a>\n <a href='https://drugbank_downloader.readthedocs.io/en/latest/?badge=latest'>\n <img src='https://readthedocs.org/projects/drugbank_downloader/badge/?version=latest' alt='Documentation Status' /></a>\n <a href=\"https://codecov.io/gh/cthoyt/drugbank-downloader/branch/main\">\n <img src=\"https://codecov.io/gh/cthoyt/drugbank-downloader/branch/main/graph/badge.svg\" alt=\"Codecov status\" /></a> \n <a href=\"https://github.com/cthoyt/cookiecutter-python-package\">\n <img alt=\"Cookiecutter template from @cthoyt\" src=\"https://img.shields.io/badge/Cookiecutter-snekpack-blue\" /></a>\n <a href='https://github.com/psf/black'>\n <img src='https://img.shields.io/badge/code%20style-black-000000.svg' alt='Code style: black' /></a>\n <a href=\"https://github.com/cthoyt/drugbank-downloader/blob/main/.github/CODE_OF_CONDUCT.md\">\n <img src=\"https://img.shields.io/badge/Contributor%20Covenant-2.1-4baaaa.svg\" alt=\"Contributor Covenant\"/></a>\n</p>\n\nDon't worry about DrugBank licensing and distribution rules - just use ``drugbank_downloader`` to write code that knows\nhow to download it and use it automatically.\n\n## Installation\n\n```bash\n$ pip install drugbank-downloader\n```\n\n## Download A Specific Version\n\n```python\nimport os\nfrom drugbank_downloader import download_drugbank\n\nusername = ... # suggestion: load from environment with os.getenv('DRUGBANK_USERNAME')\npassword = ...\n\npath = download_drugbank(version='5.1.7', username=username, password=password)\n\n# This is where it gets downloaded: ~/.data/drugbank/5.1.7/full database.xml.zip\nexpected_path = os.path.join(os.path.expanduser('~'), '.data', 'drugbank', '5.1.7', 'full database.xml.zip')\nassert expected_path == path.as_posix()\n```\n\nAfter it's been downloaded once, it's smart and doesn't need to download again. It gets stored\nusing [`pystow`](https://github.com/cthoyt/pystow) automatically in the `~/.data/drugbank`\ndirectory.\n\n## Automating Configuration of DrugBank Credentials\n\nThere are two ways to automatically set the username and password so you don't have to worry about getting it and\npassing it around in your python code:\n\n1. Set `DRUGBANK_USERNAME` and `DRUGBANK_PASSWORD` in the environment\n2. Create `~/.config/drugbank.ini` and set in the `[drugbank]` section a `username` and `password` key.\n\n```python\nfrom drugbank_downloader import download_drugbank\n\n# Same path as before\npath = download_drugbank(version='5.1.7')\n```\n\nThe `username` and `password` keyword arguments are available for all functions in this package, but will be omitted in\nthe tutorial for brevity.\n\n## Download the Latest Version\n\nFirst, you'll have to install [`bioversions`](https://github.com/cthoyt/bioversions)\nwith `pip install bioversions`, whose job it is to look up the latest version of many databases. Then, you can modify\nthe previous code slightly by omitting the `version` keyword argument:\n\n```python\nimport os\nfrom drugbank_downloader import download_drugbank\n\npath = download_drugbank()\n\n# This is where it gets downloaded: ~/.data/drugbank/5.1.7/full database.xml.zip based on the latest\n# version, as of December 14th, 2020.\nexpected_path = os.path.join(os.path.expanduser('~'), '.data', 'drugbank', '5.1.7', 'full database.xml.zip')\nassert expected_path == path.as_posix()\n```\n\nThe `version` keyword argument is available for all functions in this package, but like the username and password will\nbe omitted for brevity.\n\n## Don't Bother Unpacking - read `full database.xml.zip` Directly\n\nDrugBank is a single XML (could be JSON in a better future) file inside a zip archive. Normally, people manually unzip\nthis folder then do something with the resulting file. Don't do this, it's not reproducible!\nInstead, it can be opened as a file object in Python with the following code.\n\n```python\nimport zipfile\nfrom drugbank_downloader import download_drugbank\n\npath = download_drugbank()\n\nwith zipfile.ZipFile(path) as zip_file:\n with zip_file.open('full database.xml') as file:\n pass # do something with the file\n```\n\nYou don't have time to remember this. Just use `drugbank_downloader.open_drugbank()` instead:\n\n```python\nfrom drugbank_downloader import open_drugbank\n\nwith open_drugbank() as file:\n pass # do something with the file, same as above\n```\n\n## Reading DrugBank's XML\n\nAfter you've opened the file, you probably want to read it with an XML parser like:\n\n```python\nfrom xml.etree import ElementTree\nfrom drugbank_downloader import open_drugbank\n\nwith open_drugbank() as file:\n tree = ElementTree.parse(file)\n```\n\nYou don't have time to remember this either. Just use `drugbank_downloader.parse_drugbank()` instead:\n\n```python\nfrom xml.etree import ElementTree\nfrom drugbank_downloader import parse_drugbank\n\ntree = parse_drugbank()\nroot = tree.getroot()\n```\n\nIf your first thing to do to the tree is always to get its root, just use\n`drugbank_downloader.get_drugbank_root()`:\n\n```python\nfrom drugbank_downloader import get_drugbank_root\n\nroot = get_drugbank_root()\n```\n\nYou now know everything I can teach you. Please use these tools to do re-usable, reproducible \nscience!\n\n## Store in a Different Place\n\nIf you want to store the data elsewhere using `pystow` (e.g., in [`pyobo`](https://github.com/pyobo/pyobo)\nI also keep a copy of this file), you can use the `prefix` argument.\n\n```python\nimport os\nfrom drugbank_downloader import download_drugbank\n\npath = download_drugbank(prefix=['pyobo', 'raw', 'drugbank'])\n\n# This is where it gets downloaded: ~/.data/pyobo/raw/drugbank/5.1.7/full database.xml.zip\nexpected_path = os.path.join(os.path.expanduser('~'), '.data', 'pyobo', 'raw', 'drugbank', '5.1.7',\n 'full database.xml.zip')\nassert expected_path == path.as_posix()\n```\n\nSee the `pystow` [documentation](https://github.com/cthoyt/pystow#%EF%B8%8F-configuration) on configuring the storage\nlocation further.\n\n## Download via CLI\n\nAfter installing, run the following CLI command to ensure it and send the path to stdout\n\n```bash\n$ drugbank_downloader\n```\n\nIf you haven't pre-configured the username and password, you can specify them with the `--username` and `--password`\noptions.\n\n## \ud83d\udc50 Contributing\n\nContributions, whether filing an issue, making a pull request, or forking, are appreciated. See\n[CONTRIBUTING.md](https://github.com/cthoyt/drugbank-downloader/blob/master/.github/CONTRIBUTING.md)\nfor more information on getting involved.\n\n## \ud83d\udc4b Attribution\n\n### \u2696\ufe0f License\n\nThe code in this package is licensed under the MIT License.\n\n### \ud83c\udf6a Cookiecutter\n\nThis package was created with [@audreyfeldroy](https://github.com/audreyfeldroy)'s\n[cookiecutter](https://github.com/cookiecutter/cookiecutter) package using [@cthoyt](https://github.com/cthoyt)'s\n[cookiecutter-snekpack](https://github.com/cthoyt/cookiecutter-snekpack) template.\n\n## \ud83d\udee0\ufe0f For Developers\n\n<details>\n <summary>See developer instructions</summary>\n\nThe final section of the README is for if you want to get involved by making a code contribution.\n\n### Development Installation\n\nTo install in development mode, use the following:\n\n```bash\ngit clone git+https://github.com/cthoyt/drugbank-downloader.git\ncd drugbank-downloader\npip install -e .\n```\n\n### Updating Package Boilerplate\n\nThis project uses `cruft` to keep boilerplate (i.e., configuration, contribution guidelines, documentation\nconfiguration)\nup-to-date with the upstream cookiecutter package. Update with the following:\n\n```shell\npip install cruft\ncruft update\n```\n\nMore info on Cruft's update command is\navailable [here](https://github.com/cruft/cruft?tab=readme-ov-file#updating-a-project).\n\n### \ud83e\udd7c Testing\n\nAfter cloning the repository and installing `tox` with `pip install tox tox-uv`, \nthe unit tests in the `tests/` folder can be run reproducibly with:\n\n```shell\ntox -e py\n```\n\nAdditionally, these tests are automatically re-run with each commit in a\n[GitHub Action](https://github.com/cthoyt/drugbank-downloader/actions?query=workflow%3ATests).\n\n### \ud83d\udcd6 Building the Documentation\n\nThe documentation can be built locally using the following:\n\n```shell\ngit clone git+https://github.com/cthoyt/drugbank-downloader.git\ncd drugbank-downloader\ntox -e docs\nopen docs/build/html/index.html\n``` \n\nThe documentation automatically installs the package as well as the `docs`\nextra specified in the [`pyproject.toml`](pyproject.toml). `sphinx` plugins\nlike `texext` can be added there. Additionally, they need to be added to the\n`extensions` list in [`docs/source/conf.py`](docs/source/conf.py).\n\nThe documentation can be deployed to [ReadTheDocs](https://readthedocs.io) using\n[this guide](https://docs.readthedocs.io/en/stable/intro/import-guide.html).\nThe [`.readthedocs.yml`](.readthedocs.yml) YAML file contains all the configuration you'll need.\nYou can also set up continuous integration on GitHub to check not only that\nSphinx can build the documentation in an isolated environment (i.e., with ``tox -e docs-test``)\nbut also that [ReadTheDocs can build it too](https://docs.readthedocs.io/en/stable/pull-requests.html).\n\n#### Configuring ReadTheDocs\n\n1. Log in to ReadTheDocs with your GitHub account to install the integration\n at https://readthedocs.org/accounts/login/?next=/dashboard/\n2. Import your project by navigating to https://readthedocs.org/dashboard/import then clicking the plus icon next to\n your repository\n3. You can rename the repository on the next screen using a more stylized name (i.e., with spaces and capital letters)\n4. Click next, and you're good to go!\n\n### \ud83d\udce6 Making a Release\n\n#### Configuring Zenodo\n\n[Zenodo](https://zenodo.org) is a long-term archival system that assigns a DOI to each release of your package.\n\n1. Log in to Zenodo via GitHub with this link: https://zenodo.org/oauth/login/github/?next=%2F. This brings you to a\n page that lists all of your organizations and asks you to approve installing the Zenodo app on GitHub. Click \"grant\"\n next to any organizations you want to enable the integration for, then click the big green \"approve\" button. This\n step only needs to be done once.\n2. Navigate to https://zenodo.org/account/settings/github/, which lists all of your GitHub repositories (both in your\n username and any organizations you enabled). Click the on/off toggle for any relevant repositories. When you make\n a new repository, you'll have to come back to this\n\nAfter these steps, you're ready to go! After you make \"release\" on GitHub (steps for this are below), you can navigate\nto https://zenodo.org/account/settings/github/repository/cthoyt/drugbank-downloader\nto see the DOI for the release and link to the Zenodo record for it.\n\n#### Registering with the Python Package Index (PyPI)\n\nYou only have to do the following steps once.\n\n1. Register for an account on the [Python Package Index (PyPI)](https://pypi.org/account/register)\n2. Navigate to https://pypi.org/manage/account and make sure you have verified your email address. A verification email\n might not have been sent by default, so you might have to click the \"options\" dropdown next to your address to get to\n the \"re-send verification email\" button\n3. 2-Factor authentication is required for PyPI since the end of 2023 (see\n this [blog post from PyPI](https://blog.pypi.org/posts/2023-05-25-securing-pypi-with-2fa/)). This means\n you have to first issue account recovery codes, then set up 2-factor authentication\n4. Issue an API token from https://pypi.org/manage/account/token\n\n#### Configuring your machine's connection to PyPI\n\nYou have to do the following steps once per machine. Create a file in your home directory called\n`.pypirc` and include the following:\n\n```ini\n[distutils]\nindex-servers =\n pypi\n testpypi\n\n[pypi]\nusername = __token__\npassword = <the API token you just got>\n\n# This block is optional in case you want to be able to make test releases to the Test PyPI server\n[testpypi]\nrepository = https://test.pypi.org/legacy/\nusername = __token__\npassword = <an API token from test PyPI>\n```\n\nNote that since PyPI is requiring token-based authentication, we use `__token__` as the user, verbatim.\nIf you already have a `.pypirc` file with a `[distutils]` section, just make sure that there is an `index-servers`\nkey and that `pypi` is in its associated list. More information on configuring the `.pypirc` file can\nbe found [here](https://packaging.python.org/en/latest/specifications/pypirc).\n\n#### Uploading to PyPI\n\nAfter installing the package in development mode and installing\n`tox` with `pip install tox tox-uv`,\nrun the following from the shell:\n\n```shell\ntox -e finish\n```\n\nThis script does the following:\n\n1. Uses [Bump2Version](https://github.com/c4urself/bump2version) to switch the version number in\n the `pyproject.toml`, `CITATION.cff`, `src/drugbank_downloader/version.py`,\n and [`docs/source/conf.py`](docs/source/conf.py) to not have the `-dev` suffix\n2. Packages the code in both a tar archive and a wheel using [`build`](https://github.com/pypa/build)\n3. Uploads to PyPI using [`twine`](https://github.com/pypa/twine).\n4. Push to GitHub. You'll need to make a release going with the commit where the version was bumped.\n5. Bump the version to the next patch. If you made big changes and want to bump the version by minor, you can\n use `tox -e bumpversion -- minor` after.\n\n#### Releasing on GitHub\n\n1. Navigate\n to https://github.com/cthoyt/drugbank-downloader/releases/new\n to draft a new release\n2. Click the \"Choose a Tag\" dropdown and select the tag corresponding to the release you just made\n3. Click the \"Generate Release Notes\" button to get a quick outline of recent changes. Modify the title and description\n as you see fit\n4. Click the big green \"Publish Release\" button\n\nThis will trigger Zenodo to assign a DOI to your release as well.\n\n</details>\n",
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"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. ",
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