https://github.com/j535d165/scisort
Sort files in research project folders in a scientific order
https://github.com/j535d165/scisort
directory-lister directory-listing file-sorting python research research-data-management science sorting utrecht-university
Last synced: 3 months ago
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Sort files in research project folders in a scientific order
- Host: GitHub
- URL: https://github.com/j535d165/scisort
- Owner: J535D165
- License: mit
- Created: 2022-09-23T20:10:59.000Z (about 3 years ago)
- Default Branch: main
- Last Pushed: 2022-10-30T22:34:41.000Z (almost 3 years ago)
- Last Synced: 2024-10-08T14:12:16.478Z (about 1 year ago)
- Topics: directory-lister, directory-listing, file-sorting, python, research, research-data-management, science, sorting, utrecht-university
- Language: Python
- Homepage:
- Size: 53.7 KB
- Stars: 3
- Watchers: 2
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
- Citation: CITATION.cff
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README
# Scisort - Sort files in research projects
 [](https://zenodo.org/badge/latestdoi/540602039)
Scisort is a Python package for sorting files in research projects and
scientific (data) repositories. Files and folders are sorted in such a way
that inspecting folders in research projects is more intuitive. See the
[philosophy of scisort](#philosophy-of-scisort) to understand the sorting algorithm.
---
Since scisort is a low-level API, most researchers, developers, and data
scientists may be more interested in [`scitree`](https://github.com/J535D165/scitree).
Scitree is a smart recursive directory listing program that makes use of scisort.
---
## Philosophy of scisort
Philosophy of scisort and [scitree](https://github.com/J535D165/scitree):
- Read the README first, therefore I'm on top
- Before I install or use the content, I open the [LICENSE](https://choosealicense.com/).
- Files first, folders second
- Numbered files are [naturally sorted](https://en.wikipedia.org/wiki/Natural_sort_order)
- I love [intuitive and reproducible project structures](https://doi.org/10.1371/journal.pcbi.1005510)
- Follow the order of execution where possible
- I ignore, what git ignores\*
*\* Only for [`scitree`](https://github.com/J535D165/scitree).*
For more information about the structure, see [scisort/scisort/keygen.py](https://github.com/J535D165/scisort/blob/main/scisort/keygen.py).
## Installation
Scisort requires Python 3.6 or later.
```sh
pip install scisort
```
## Getting started
### Traditional sorting
Consider the following project folder structure. It's a mixture of files and
folders. The folder is sorted on the file or folder name. Some reasons why
this sort is not intuitive:
```python
files = ['LICENSE.txt',
'README.md',
'data',
'data/Bos_2018.csv',
'jobs.sh',
'output',
'output/simulation',
'output/simulation/Bos_2018',
'output/simulation/Bos_2018/descriptives',
'output/simulation/Bos_2018/descriptives/data_stats_Bos_2018.json',
'output/simulation/Bos_2018/descriptives/wordcloud_Bos_2018.png',
'output/simulation/Bos_2018/descriptives/wordcloud_irrelevant_Bos_2018.png',
'output/simulation/Bos_2018/descriptives/wordcloud_relevant_Bos_2018.png',
'output/simulation/Bos_2018/metrics_sim_Bos_2018_0.json',
'output/simulation/Bos_2018/metrics_sim_Bos_2018_1640.json',
'output/simulation/Bos_2018/metrics_sim_Bos_2018_3154.json',
'output/simulation/Bos_2018/metrics_sim_Bos_2018_3518.json',
'output/simulation/Bos_2018/metrics_sim_Bos_2018_3519.json',
'output/simulation/Bos_2018/metrics_sim_Bos_2018_3721.json',
'output/simulation/Bos_2018/metrics_sim_Bos_2018_4612.json',
'output/simulation/Bos_2018/metrics_sim_Bos_2018_4699.json',
'output/simulation/Bos_2018/metrics_sim_Bos_2018_559.json',
'output/simulation/Bos_2018/metrics_sim_Bos_2018_5673.json',
'output/simulation/Bos_2018/metrics_sim_Bos_2018_6.json',
'output/simulation/Bos_2018/plot_recall_sim_Bos_2018.png',
'output/simulation/Bos_2018/state_files',
'output/simulation/Bos_2018/state_files/sim_Bos_2018_0.asreview',
'output/simulation/Bos_2018/state_files/sim_Bos_2018_1640.asreview',
'output/simulation/Bos_2018/state_files/sim_Bos_2018_3154.asreview',
'output/simulation/Bos_2018/state_files/sim_Bos_2018_3518.asreview',
'output/simulation/Bos_2018/state_files/sim_Bos_2018_3519.asreview',
'output/simulation/Bos_2018/state_files/sim_Bos_2018_3721.asreview',
'output/simulation/Bos_2018/state_files/sim_Bos_2018_4612.asreview',
'output/simulation/Bos_2018/state_files/sim_Bos_2018_4699.asreview',
'output/simulation/Bos_2018/state_files/sim_Bos_2018_559.asreview',
'output/simulation/Bos_2018/state_files/sim_Bos_2018_5673.asreview',
'output/simulation/Bos_2018/state_files/sim_Bos_2018_6.asreview',
'output/tables',
'output/tables/data_descriptives.csv',
'output/tables/data_descriptives.xlsx',
'output/tables/data_metrics.csv',
'output/tables/data_metrics.xlsx',
'scripts',
'scripts/get_plot.py',
'scripts/merge_descriptives.py',
'scripts/merge_metrics.py']
```
The files and folders are real research output created with `ASReview-makita`
(see [examples](examples)).
### Scisort sorting
Scisort integrates with Python's `sorted` by supplying the sort key.
```python
from scisort import scisort_keygen
sorted(files, key=scisort_keygen())
```
```python
['README.md',
'LICENSE.txt',
'jobs.sh',
'data',
'data/Bos_2018.csv',
'scripts',
'scripts/get_plot.py',
'scripts/merge_descriptives.py',
'scripts/merge_metrics.py',
'output',
'output/simulation',
'output/simulation/Bos_2018',
'output/simulation/Bos_2018/metrics_sim_Bos_2018_0.json',
'output/simulation/Bos_2018/metrics_sim_Bos_2018_6.json',
'output/simulation/Bos_2018/metrics_sim_Bos_2018_559.json',
'output/simulation/Bos_2018/metrics_sim_Bos_2018_1640.json',
'output/simulation/Bos_2018/metrics_sim_Bos_2018_3154.json',
'output/simulation/Bos_2018/metrics_sim_Bos_2018_3518.json',
'output/simulation/Bos_2018/metrics_sim_Bos_2018_3519.json',
'output/simulation/Bos_2018/metrics_sim_Bos_2018_3721.json',
'output/simulation/Bos_2018/metrics_sim_Bos_2018_4612.json',
'output/simulation/Bos_2018/metrics_sim_Bos_2018_4699.json',
'output/simulation/Bos_2018/metrics_sim_Bos_2018_5673.json',
'output/simulation/Bos_2018/plot_recall_sim_Bos_2018.png',
'output/simulation/Bos_2018/descriptives',
'output/simulation/Bos_2018/descriptives/wordcloud_Bos_2018.png',
'output/simulation/Bos_2018/descriptives/wordcloud_irrelevant_Bos_2018.png',
'output/simulation/Bos_2018/descriptives/wordcloud_relevant_Bos_2018.png',
'output/simulation/Bos_2018/descriptives/data_stats_Bos_2018.json',
'output/simulation/Bos_2018/state_files',
'output/simulation/Bos_2018/state_files/sim_Bos_2018_0.asreview',
'output/simulation/Bos_2018/state_files/sim_Bos_2018_6.asreview',
'output/simulation/Bos_2018/state_files/sim_Bos_2018_559.asreview',
'output/simulation/Bos_2018/state_files/sim_Bos_2018_1640.asreview',
'output/simulation/Bos_2018/state_files/sim_Bos_2018_3154.asreview',
'output/simulation/Bos_2018/state_files/sim_Bos_2018_3518.asreview',
'output/simulation/Bos_2018/state_files/sim_Bos_2018_3519.asreview',
'output/simulation/Bos_2018/state_files/sim_Bos_2018_3721.asreview',
'output/simulation/Bos_2018/state_files/sim_Bos_2018_4612.asreview',
'output/simulation/Bos_2018/state_files/sim_Bos_2018_4699.asreview',
'output/simulation/Bos_2018/state_files/sim_Bos_2018_5673.asreview',
'output/tables',
'output/tables/data_descriptives.csv',
'output/tables/data_descriptives.xlsx',
'output/tables/data_metrics.csv',
'output/tables/data_metrics.xlsx']
```
### Third party support
Scisort also integrates with other libraries implementing sorting based on a
key.
#### Pandas
```python
import pandas as pd
from scisort import scisort_keygen_pandas
pd.Series(files).sort_values(key=scisort_keygen_pandas())
```
#### Natsort
```python
import natsort as ns
ns.natsorted(files, key=scisort_keygen())
```
## License
[MIT](/LICENSE)
## Contact
Feel free to reach out with questions, remarks, and suggestions. The
[issue tracker](/issues) is a good starting point. You can also email me at
[jonathandebruinos@gmail.com](mailto:jonathandebruinos@gmail.com).