PyStow

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

💪 Getting Started

Get a directory for your application.

```python 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

pykeenexperimentsdirectory = pystow.join('pykeen', 'experiments')

You can go as deep as you want

pykeendeepdirectory = pystow.join('pykeen', 'experiments', 'a', 'b', 'c') ```

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

```python 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

pykeenexperimentsdirectory = pykeen_module.join('experiments')

You can go as deep as you want past the original "pykeen" module

pykeendeepdirectory = 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.

```python import pystow

Get a directory (as a pathlib.Path) for ~/.data/indra/database.tsv

indradatabasepath = pystow.join('indra', 'database', name='database.tsv') ```

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

```python 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):

```python 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):

```python import pystow import pandas as pd

url = 'https://raw.githubusercontent.com/cthoyt/pystow/main/tests/resources/test1.csv' df: pd.DataFrame = pystow.ensurecsv('pykeen', 'datasets', 'nations', url=url, readcsvkwargs=dict(sep=",")) ```

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

```python import pystow import rdflib

url = 'https://ftp.expasy.org/databases/rhea/rdf/rhea.rdf.gz' rdfgraph: rdflib.Graph = pystow.ensurerdf('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:

```python import numpy as np import pystow

url = "https://cloud.enterprise.informatik.uni-leipzig.de/index.php/s/LHPbMCre7SLqajB/download/MultiKEDY15KV1.zip"

the path inside the archive to the file you want

innerpath = "MultiKE/DY15KV1/7215fold/1/20210219183115/entembeds.npy" with pystow.ensureopenzip("kiez", url=url, innerpath=innerpath) 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:

```python 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:

```python 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 uv:

console $ uv pip install pystow

or with pip:

console $ python3 -m pip install pystow

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

console $ uv pip install git+https://github.com/cthoyt/pystow.git

or with pip:

console $ 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: ```console $ git clone git+https://github.com/cthoyt/pystow.git $ cd pystow $ uv pip install -e . ``` Alternatively, install using pip: ```console $ 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. Install cruft with either `uv tool install cruft` or `python3 -m pip install cruft` then run: ```console $ 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 `uv tool install tox --with tox-uv` or `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/pystow/actions?query=workflow%3ATests). ### 📖 Building the Documentation The documentation can be built locally using the following: ```console $ 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`](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/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)](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. ```console $ 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 `uv tool install tox --with tox-uv` or `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/pystow/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 [`uv publish`](https://docs.astral.sh/uv/guides/publish/#publishing-your-package). 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.