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Scisort - Sort files in research projects
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 to understand the sorting algorithm.
Since scisort is a low-level API, most researchers, developers, and data
scientists may be more interested in scitree.
Scitree is a smart recursive directory listing program that makes use of scisort.
Philosophy of scisort
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
Scisort requires Python 3.6 or later.
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:
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).
Scisort sorting
Scisort integrates with Python's sorted by supplying the sort key.
from scisort import scisort_keygen
sorted(files, key=scisort_keygen())
['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
import pandas as pd
from scisort import scisort_keygen_pandas
pd.Series(files).sort_values(key=scisort_keygen_pandas())
Natsort
import natsort as ns
ns.natsorted(files, key=scisort_keygen())
License
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.
FAQs
Smart sorting algorithm for files and folders in research projects and repositories
We found that scisort demonstrated a healthy version release cadence and project activity because the last version was released less than a year ago. It has 1 open source maintainer collaborating on the project.
Did you know?
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