phab-utils

Data processing tools and knowledge base of Centre for Earth Evolution and Dynamics and its successor Centre for Planetary Habitability.

Original project name was uio-exoplanet-group, which later got renamed to phab-utils (on 2025-01-29).

• Installing
  • From PyPI
  • From sources
    • Building a wheel
• Data
• Documentation
  • API
  • wiki
• Tests

Installing

From PyPI

$ pip install phab-utils

If you need an older version from the original uio-exoplanet-group package, those are still available here.

From sources

$ cd /path/to/phab-utils/
$ pip install .

Add an -e argument, if you'd like to automatically update your locally installed package by pulling from the repository or/and if you intend to modify the sources:

$ pip install -e .

Building a wheel

You can also build a wheel and distribute/install that instead:

$ cd /path/to/phab-utils/
$ python -m build
$ pip install ./dist/phab_utils-*.whl

Data

Wherever you see a reference to some data files in documentation, examples, comments or anywhere else, for example some function taking a path like ./data/systems-528n.pkl, check the data folder - chances are, that file will be provided there.

Documentation

There are two different pieces of documentation.

API

Located in documentation. This is the package API documentation, which is published here.

It is generated with pdoc:

$ pip install pdoc

$ cd /path/to/phab-utils
$ rm -r ./documentation/_deploy/*

$ PHAB_PACKAGE_VERSION=$(git rev-parse --short HEAD) pdoc ./src/phab/utils ./src/phab/tasks \
    --template-directory ./documentation/_templates/ \
    --edit-url="utils=https://github.com/retifrav/phab-utils/blob/master/src/phab/utils/" \
    --edit-url="tasks=https://github.com/retifrav/phab-utils/blob/master/src/phab/tasks/" \
    --output-directory ./documentation/_deploy/
$ cp ./documentation/{favicon.ico,phab.jpg} ./documentation/_deploy/

For now it's a blunt deployment of generated HTML, but later it probably will be better to rely on GitHub Actions (if it won't spend too much of free quota) by customizing this workflow.

If you'd like to browse generated documentation locally, you can just open the main index.html from ./documentation/_deploy/ in your browser. Alternatively, you can launch a basic Python server:

$ cd ./documentation/_deploy/
$ python -m http.server 8000

and open http://localhost:8000/.

wiki

Located in wiki. This is general purpose / technical manuals, articles, notes, etc: how to install/build various tools, dependencies, how to set-up environments and so on.

It is meant to be published somewhere else, but for now it will do being a part of repository. GitHub wikis could've been an option, but those are still quite bad in terms of organizing the content.

Tests

To run tests:

$ pip install pytest

$ python -m pytest ./src/phab/tests/*[^_*].py
$ python -m pytest ./src/phab/tests/databases.py
$ python -m pytest ./src/phab/tests/databases.py -k "test_get_parameters_that_are_double_in_nasa"