Scitree - Like tree, but optimized for science

In computing, tree is a recursive directory listing command or program that produces a depth-indented listing of files. Wikipedia, 2022.

Scitree is like tree, but different. Instead of sorting content on its name, scitree sorts and highlights given opiniated scientific principles. In this way, you can inspect directory listings more easily.

Scitree is based on scisort, a Python package to sort file paths based on scientific principles.

Philosophy

Philosophy of scisort and scitree:

• Read the README first, therefore I'm on top
• Before I install or use the content, I open the LICENSE.
• Files first, folders second
• Numbered files are naturally sorted
• I love intuitive and reproducible project structures
• Follow the order of execution where possible
• I ignore, what git ignores*

* Only for scitree.

For more information about the structure, see scisort/scisort/keygen.py.

Installation

Scitree requires Python 3.6 or later.

pip install scitree

Getting started

scitree command

Scittree command on the command line outputs a tree.

scitree

./
├── README.md
├── LICENSE.txt
├── jobs.sh
├── data/
│   └── Bos_2018.csv
├── scripts/
│   ├── get_plot.py
│   ├── merge_descriptives.py
│   └── merge_metrics.py
└── output/
    ├── simulation/
    │   └── Bos_2018/
    │       ├── metrics_sim_Bos_2018_0.json
    │       ├── metrics_sim_Bos_2018_6.json
    │       ├── metrics_sim_Bos_2018_559.json
    │       ├── metrics_sim_Bos_2018_1640.json
    │       ├── metrics_sim_Bos_2018_3154.json
    │       ├── metrics_sim_Bos_2018_3518.json
    │       ├── metrics_sim_Bos_2018_3519.json
    │       ├── metrics_sim_Bos_2018_3721.json
    │       ├── metrics_sim_Bos_2018_4612.json
    │       ├── metrics_sim_Bos_2018_4699.json
    │       ├── metrics_sim_Bos_2018_5673.json
    │       ├── plot_recall_sim_Bos_2018.png
    │       ├── descriptives/
    │       │   ├── wordcloud_Bos_2018.png
    │       │   ├── wordcloud_irrelevant_Bos_2018.png
    │       │   ├── wordcloud_relevant_Bos_2018.png
    │       │   └── data_stats_Bos_2018.json
    │       └── state_files/
    │           ├── sim_Bos_2018_0.asreview
    │           ├── sim_Bos_2018_6.asreview
    │           ├── sim_Bos_2018_559.asreview
    │           ├── sim_Bos_2018_1640.asreview
    │           ├── sim_Bos_2018_3154.asreview
    │           ├── sim_Bos_2018_3518.asreview
    │           ├── sim_Bos_2018_3519.asreview
    │           ├── sim_Bos_2018_3721.asreview
    │           ├── sim_Bos_2018_4612.asreview
    │           ├── sim_Bos_2018_4699.asreview
    │           └── sim_Bos_2018_5673.asreview
    └── tables/
        ├── data_descriptives.csv
        ├── data_descriptives.xlsx
        ├── data_metrics.csv
        └── data_metrics.xlsx

8 directories, 38 files

scitree function for Python

The scitree function in Python prints the tree for the current folder (".").

from scitree import scitree

scitree()

License

MIT

Contact

Feel free to reach out with questions, remarks, and suggestions. The issue tracker is a good starting point. You can also email me at jonathandebruinos@gmail.com.