DH Code Review #1
Conversation
update run_pydistinto_beginners.py and output folder
There was a problem hiding this comment.
- General remarks on
scripts/pipeline/calculate_simple.py- The file is relatively long (>250 LOC)
- Most methods have many positional arguments (more than 4) which make it hard to read
- Pandas Dataframes could be used to reduce complexity
- Docstrings should be more concise
- Parameters should not be passed as concatinated strings
- There is some code duplication (welsh_t, LLR, chi_squared, ranksumtest)
- Use automated tools to improve your code https://github.com/maehr/pydistinto/pull/1/files#diff-9a65b3c578318adb9006f0a948af12ef7d261f8bf00dea5003adeac29f79a5b7
- Use a code formatter like black, yapf or autopep to get more consistency
README.mdis missing important pieces: (Also check https://www.makeareadme.com/)- Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
- Example usage and data: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems). Do the authors include example data to be used to test the software?
- Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
LICENSE.mdis missing.- Functionality is hard to judge because of unconventional API (i.e.
parameters.txt) and missing documentation- Installation: Does installation proceed as outlined in the documentation?
- Functionality: Have the functional claims of the software been confirmed?
- Nice to Have things that are missing
- Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
- Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support?
| @@ -0,0 +1,371 @@ | |||
| # -*- coding: utf-8 -*- | |||
| """ | |||
There was a problem hiding this comment.
The filename does not indicate the functionality and there is very little information in the docstring. Checkout https://realpython.com/documenting-python-code/#package-and-module-docstrings
|
|
||
| @author: KeliDu | ||
| """ | ||
| # ================================= |
There was a problem hiding this comment.
The code is self-explanatory at this point. You can remove this comment.
|
|
||
| @author: KeliDu | ||
| """ | ||
| # ================================= |
There was a problem hiding this comment.
The code is self-explanatory at this point. You can remove this comment.
| # ================================= | ||
|
|
||
| import os | ||
| import re |
| # ================================= | ||
|
|
||
| import os | ||
| import re |
| tf_frame1 = tf_frame.T.filter(regex=ids1, axis=1) | ||
| tf_frame2 = tf_frame.T.filter(regex=ids2, axis=1) | ||
| print("\nbinary1\n", binary1.head()) | ||
| """ |
| """ | ||
| # Define logaddition and division-by-zero avoidance addition | ||
| logaddition = logaddition+1 | ||
| divaddition = 0.00000000001 |
There was a problem hiding this comment.
very unorthodox and not properly documented
| """ | ||
| # Define logaddition and division-by-zero avoidance addition | ||
| logaddition = logaddition+1 | ||
| divaddition = 0.00000000001 |
There was a problem hiding this comment.
very unorthodox and not properly documented
| return devprops | ||
|
|
||
|
|
||
| def calculate_scores(docprops1, docprops2, absolute1, absolute2, relfreqs1, relfreqs2, logaddition, segmentlength, idlists, tf_framefreqs1, tf_framefreqs2): |
| return devprops | ||
|
|
||
|
|
||
| def calculate_scores(docprops1, docprops2, absolute1, absolute2, relfreqs1, relfreqs2, logaddition, segmentlength, idlists, tf_framefreqs1, tf_framefreqs2): |
| @@ -0,0 +1,371 @@ | |||
| # -*- coding: utf-8 -*- | |||
| """ | |||
There was a problem hiding this comment.
The filename does not indicate the functionality and there is very little information in the docstring. Checkout https://realpython.com/documenting-python-code/#package-and-module-docstrings
|
@maehr this is great, thanks so much! What do you think the author should definitely address to get a code review completed badge? |
|
Most importantly documentation. But I recommend refactoring and simplifying of the code base to make it easier to understand (and maintain). |
The ticket for this code review is: DHCodeReview/DHCodeReview#3
This repository is ready for review.