Output results as a dataframe + return short names, hctsa names and values as standard.

[joshuabmoore]

Modifying the original changes proposed by @anniegbryant in PR #21, this PR updates the catch22 output to a DataFrame and marks a transition away from long (HCTSA) feature names toward what has previously been called "short" feature names, as default, i.e., mode_5 instead of DN_HistogramMode_5, etc.

Breaking Changes:

Since these modifications will introduce breaking changes for the existing user base, this PR will constitute a new major version release (catch22 v1.0.0), with docs + README updated to reflect the new output format. Users will need to be made aware of the new output via clear documentation and a migration guide in the changelogs to avoid confusion.

Major changes

• Removal of short_names as an optional parameter in the catch22_all() function. Three columns will now be returned as standard: feature, hctsa_name and value. That is, catch22_all() now accepts only two arguments:

catch22_all(data, catch24=False)

• < = v0.4.5 catch22 features_short are now called features (or feature in the output DataFrame).
• < = v0.4.5 catch22 featureis now features_hctsa (or hctsa_name in the output DataFrame).
• catch22 results are now returned as a pandas DataFrame instead of a dict for improved readability:

df = catch22_all(data, catch24=False)

# print the first feature name
print(df.feature[0])

# print the first feature value
print(df.value[0])

# print the first feature HCTSA (long) name
print(df.hctsa_name[0])

• Added pandas and numpy dependencies.

Minor changes

• Added a security policy, SECURITY.md.
• Added a code of conduct, CODE_OF_CONDUCT.md
• Added a darkmode logo to the README.
• Added python unit testing + python version support badges to README.
• Updated usage guide in README to notify users of DataFrame output.
• Included support for python 3.12 unit test runners.
• Updated unit tests to support new DataFrame output.

[joshuabmoore]

Also, the changelogs will be more extensive and clearer about the breaking changes for users + new naming conventions with old short_names and names essentially swapping places.

[benfulcher]

@anniegbryant can you do a quick test?

[KieranOwens]

I tried the new catch22_all function with my workflow. The change in the dictionary/dataframe key from 'values' (old version) to 'value' (new version) breaks my code. Otherwise, it works fine.