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https://github.com/AmeliaES/code-review-workshop/issues

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Materials for Code Review in Academia Workshop. Contribute to AmeliaES/code-review-workshop development by creating an account on GitHub.

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Materials for Code Review in Academia Workshop. Contribute to AmeliaES/code-review-workshop development by creating an account on GitHub.

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How can we encourage coding review within our lab?

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How can we encourage coding review within our lab?

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could show an example of expected JSON input structure

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could show an example of expected JSON input structure

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since dplyr is used, could use bind_rows() instead of do.call(rbind, .)

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since dplyr is used, could use bind_rows() instead of do.call(rbind, .)

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lubridate and hms provide similar functions. are they both needed?

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lubridate and hms provide similar functions. are they both needed?

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Line 73 you use the number 10. You could define this as a variable at the top of the script.

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Line 73 you use the number 10. You could define this as a variable at the top of the script.

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Don't include comments with actual counts of individuals when you are working with sensitive data.

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Don't include comments with actual counts of individuals when you are working with sensitive data.

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The script uses a lot of interactive commands. It may be helpful to run this in a notebook.

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The script uses a lot of interactive commands. It may be helpful to run this in a notebook.

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The column name CRP is in double quotes (Line 73)

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The column name CRP is in double quotes (Line 73)

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Internal checks of the data were useful, however, more comments would aid the understandability of the code.

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Internal checks of the data were useful, however, more comments would aid the understandability of the code.

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There are a lot of modules that are imported but not used.

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There are a lot of modules that are imported but not used.

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At the end of the Python script there are three functions that could be combined and simplified

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At the end of the Python script there are three functions that could be combined and simplified

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You used the absolute path. This may make it difficult for other users to load in the data.

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You used the absolute path. This may make it difficult for other users to load in the data.

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It would be good to have a comment about what the input data looks like. Then how it looks when you have cleaned it up at each step.

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It would be good to have a comment about what the input data looks like. Then how it looks when you have cleaned it up at each step.

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The data is called 'data' which isn't very descriptive. There is also a function in R called 'data' which may also cause confusion.

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The data is called 'data' which isn't very descriptive. There is also a function in R called 'data' which may also cause confusion.

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Some of the code was repeated and could be turned into functions to make it more succinct

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Some of the code was repeated and could be turned into functions to make it more succinct

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The indentations of some of the functions weren't always very clear

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The indentations of some of the functions weren't always very clear

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We liked that some of the code was written in the actual colours

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We liked that some of the code was written in the actual colours

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The quality of the comments were a little inconsistent (sometimes very detailed, sometimes not). Sometimes they explained what the code was doing, and sometimes they explained why the code was being used.

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The quality of the comments were a little inconsistent (sometimes very detailed, sometimes not). Sometimes they explained what the code was doing, and sometimes they explained why the code was being used.

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We liked the comments that were next to the packages. It was helpful to see why each package was needed. However, some of the packages look like they may do similar things and may not be needed.

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We liked the comments that were next to the packages. It was helpful to see why each package was needed. However, some of the packages look like they may do similar things and may not be needed.

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Excellent resource for learning git/GitHub 

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Excellent resource for learning git/GitHub 

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I reccomend data and software carpentries. They run some events in Edinburgh too. They teach good coding practices. Here is one on git and GitHub: https://datacarpentry.github.io/rr-version-control/01-git-github/index.html

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Reproducible Research Version Control: Version Control via Git and Github

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Version control is a system that records changes to a file or set of files over time so that you can recall specific versions later.

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Look for code that doesn't get executed, functions or packages that are not used

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How can we make file paths useable by different coders?

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How can we make file paths useable by different coders?

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A basic linter for Python.

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How can we name/structure folders and files in an understandable way?

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How can we name/structure folders and files in an understandable way?

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Is chatGPT a helpful tool to review code?

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Is chatGPT a helpful tool to review code?

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What are your thoughts?

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Do industry/particular organisations use a common coding style to help with coding review?

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Do industry/particular organisations use a common coding style to help with coding review?

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Code formatters (such as black for Python) can automatically check/apply style rules.

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For examples see: https://github.com/OxfordCodeReviewNet/forum

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GitHub - OxfordCodeReviewNet/forum: A central repository to coordinate code reviews between researchers at the University of Oxford

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A central repository to coordinate code reviews between researchers at the University of Oxford - OxfordCodeReviewNet/forum

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Talked about how industry uses pull requests