PyStow

👜 Easily pick a place to store data for your Python code

💪 Getting Started

Get a directory for your application.

import pystow

# Get a directory (as a pathlib.Path) for ~/.data/pykeen
pykeen_directory = pystow.join('pykeen')

# Get a subdirectory (as a pathlib.Path) for ~/.data/pykeen/experiments
pykeen_experiments_directory = pystow.join('pykeen', 'experiments')

# You can go as deep as you want
pykeen_deep_directory = pystow.join('pykeen', 'experiments', 'a', 'b', 'c')

If you reuse the same directory structure a lot, you can save them in a module:

import pystow

pykeen_module = pystow.module("pykeen")

# Access the module's directory with .base
assert pystow.join("pykeen") == pystow.module("pykeen").base

# Get a subdirectory (as a pathlib.Path) for ~/.data/pykeen/experiments
pykeen_experiments_directory = pykeen_module.join('experiments')

# You can go as deep as you want past the original "pykeen" module
pykeen_deep_directory = pykeen_module.join('experiments', 'a', 'b', 'c')

Get a file path for your application by adding the name keyword argument. This is made explicit so PyStow knows which parent directories to automatically create. This works with pystow or any module you create with pystow.module.

import pystow

# Get a directory (as a pathlib.Path) for ~/.data/indra/database.tsv
indra_database_path = pystow.join('indra', 'database', name='database.tsv')

Ensure a file from the internet is available in your application's directory:

import pystow

url = 'https://raw.githubusercontent.com/pykeen/pykeen/master/src/pykeen/datasets/nations/test.txt'
path = pystow.ensure('pykeen', 'datasets', 'nations', url=url)

Ensure a tabular data file from the internet and load it for usage (requires pip install pandas):

import pystow
import pandas as pd

url = 'https://raw.githubusercontent.com/pykeen/pykeen/master/src/pykeen/datasets/nations/test.txt'
df: pd.DataFrame = pystow.ensure_csv('pykeen', 'datasets', 'nations', url=url)

Ensure a comma-separated tabular data file from the internet and load it for usage (requires pip install pandas):

import pystow
import pandas as pd

url = 'https://raw.githubusercontent.com/cthoyt/pystow/main/tests/resources/test_1.csv'
df: pd.DataFrame = pystow.ensure_csv('pykeen', 'datasets', 'nations', url=url, read_csv_kwargs=dict(sep=","))

Ensure a RDF file from the internet and load it for usage (requires pip install rdflib)

import pystow
import rdflib

url = 'https://ftp.expasy.org/databases/rhea/rdf/rhea.rdf.gz'
rdf_graph: rdflib.Graph = pystow.ensure_rdf('rhea', url=url)

Also see pystow.ensure_excel(), pystow.ensure_rdf(), pystow.ensure_zip_df(), and pystow.ensure_tar_df().

If your data comes with a lot of different files in an archive, you can ensure the archive is downloaded and get specific files from it:

import numpy as np
import pystow

url = "https://cloud.enterprise.informatik.uni-leipzig.de/index.php/s/LHPbMCre7SLqajB/download/MultiKE_D_Y_15K_V1.zip"
# the path inside the archive to the file you want
inner_path = "MultiKE/D_Y_15K_V1/721_5fold/1/20210219183115/ent_embeds.npy"
with pystow.ensure_open_zip("kiez", url=url, inner_path=inner_path) as file:
    emb = np.load(file)

Also see pystow.module.ensure_open_lzma(), pystow.module.ensure_open_tarfile() and pystow.module.ensure_open_gz().

⚙️️ Configuration

By default, data is stored in the $HOME/.data directory. By default, the <app> app will create the $HOME/.data/<app> folder.

If you want to use an alternate folder name to .data inside the home directory, you can set the PYSTOW_NAME environment variable. For example, if you set PYSTOW_NAME=mydata, then the following code for the pykeen app will create the $HOME/mydata/pykeen/ directory:

import os
import pystow

# Only for demonstration purposes. You should set environment
# variables either with your .bashrc or in the command line REPL.
os.environ['PYSTOW_NAME'] = 'mydata'

# Get a directory (as a pathlib.Path) for ~/mydata/pykeen
pykeen_directory = pystow.join('pykeen')

If you want to specify a completely custom directory that isn't relative to your home directory, you can set the PYSTOW_HOME environment variable. For example, if you set PYSTOW_HOME=/usr/local/, then the following code for the pykeen app will create the /usr/local/pykeen/ directory:

import os
import pystow

# Only for demonstration purposes. You should set environment
# variables either with your .bashrc or in the command line REPL.
os.environ['PYSTOW_HOME'] = '/usr/local/'

# Get a directory (as a pathlib.Path) for /usr/local/pykeen
pykeen_directory = pystow.join('pykeen')

Note: if you set PYSTOW_HOME, then PYSTOW_NAME is disregarded.

X Desktop Group (XDG) Compatibility

While PyStow's main goal is to make application data less opaque and less hidden, some users might want to use the XDG specifications for storing their app data.

If you set the environment variable PYSTOW_USE_APPDIRS to true or True, then the appdirs package will be used to choose the base directory based on the user data dir option. This can still be overridden by PYSTOW_HOME.

🚀 Installation

The most recent release can be installed from PyPI with:

python3 -m pip install pystow

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

python3 -m pip install git+https://github.com/cthoyt/pystow.git

👐 Contributing

Contributions, whether filing an issue, making a pull request, or forking, are appreciated. See 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's cookiecutter package using @cthoyt's cookiecutter-snekpack template.

🛠️ For Developers

See developer instructions

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:

git clone git+https://github.com/cthoyt/pystow.git
cd pystow
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:

python3 -m pip install cruft
cruft update

More info on Cruft's update command is available here.

🥼 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:

tox -e py

Additionally, these tests are automatically re-run with each commit in a GitHub Action.

📖 Building the Documentation

The documentation can be built locally using the following:

git clone git+https://github.com/cthoyt/pystow.git
cd pystow
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. sphinx plugins like texext can be added there. Additionally, they need to be added to the extensions list in docs/source/conf.py.

The documentation can be deployed to ReadTheDocs using this guide. The .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.

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 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/pystow 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)
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). 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.

$ uv tool install keyring
$ keyring set https://upload.pypi.org/legacy/ __token__
$ keyring set https://test.pypi.org/legacy/ __token__

Note that this deprecates previous workflows using .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:

tox -e finish

This script does the following:

1. Uses bump-my-version to switch the version number in the pyproject.toml, CITATION.cff, src/pystow/version.py, and 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
3. Uploads to PyPI using uv publish.
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/pystow/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.