Update README.md #7
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have a think about how to handle two people on the same project. There are details to using git in conjunction with another that can be tricky. It's a useful skill and well worth learning but will slow you down lots. Duplicating efforts across two repositories is not especially desirable either though. If you do choose to both use the same repo I can walk you through how to handle merge conflicts etc. |
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Do you have code written? If so, please push it to GitHub so that we can help out. |
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Great.
And no don't upload large files. A few small sample files/directory tree in
the tests directory so that you can write tests but otherwise no, git repos
shouldn't have large data files in them.
…On Wed, May 6, 2020 at 12:15 PM aob93 ***@***.***> wrote:
Hi John,
Thanks for getting in touch. Code is all written, just getting it uploaded
now.
My code takes a list of paths to files stored in our shared drives. Should
I also upload these files to github? (some are quite large)
~Aidan
From: john lee ***@***.***>
Reply-To: biof309/project_spring_2020 ***@***.***>
Date: Wednesday, May 6, 2020 at 12:12 PM
To: biof309/project_spring_2020 ***@***.***>
Cc: aob93 ***@***.***>, Author ***@***.***>
Subject: Re: [biof309/project_spring_2020] Update README.md (#7)
Do you have code written? If so, please push it to GitHub so that we can
help out.
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Hi Aidan, I just created a pull request of possible updates to your project repository. I have created a setup.py file (in order to package your code) which you should look at and fill out the necessary information. Additionally I changed your "code" directory to "project_code" and your "annotation.plot.py" file to "annotation_plot.py". I have also added an example test file (tests.py) to your tests directory to help start you start writing tests for you code. The example test just confirms that the "header" that you read in is a list. If you type in in your terminal you should be able to see that the test passes. These are just suggestions to help you start testing your code as well as package it. Let me know if you have any questions! |
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Hi Emily,
Thanks so much for your help here. Much appreciated. I'll take a look asap.
Aidan
Sent from Outlook Mobile<https://aka.ms/blhgte>
…________________________________
From: emily yaklich <[email protected]>
Sent: Thursday, May 7, 2020 12:33:16 AM
To: biof309/project_spring_2020 <[email protected]>
Cc: aob93 <[email protected]>; Author <[email protected]>
Subject: Re: [biof309/project_spring_2020] Update README.md (#7)
Hi Aidan,
I just created a pull request of possible updates to your project repository. I have created a setup.py file (in order to package your code) which you should look at and fill out the necessary information. Additionally I changed your "code" directory to "project_code" and your "annotation.plot.py" file to "annotation_plot.py".
I have also added an example test file (tests.py) to your tests directory to help start you start writing tests for you code. The example test just confirms that the "header" that you read in is a list. If you type in
pytest tests.py
in your terminal you should be able to see that the test passes.
These are just suggestions to help you start testing your code as well as package it.
Let me know if you have any questions!
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HI Aidan, One more suggestion, I think it may be easier to write unit tests for you code if divide your code up into multiple functions, instead of the one main function. Also, now that I think about it, it may be best to create a ''test_data" folder within your test directory (I basically just copied your data files over but it would be clearer to see a test directory with all of the data files) in order to organize your code. You can then read in the data from the directory as is currently done in the test. Also, I think a better test statement for the example test that I wrote is: because this would actually test that you are reading in what you think you are reading in from the datafile. |
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OK this sounds sensible. Basically just do the same things for each object being used in the function?
From: emily yaklich <[email protected]>
Reply-To: biof309/project_spring_2020 <[email protected]>
Date: Thursday, May 7, 2020 at 6:15 PM
To: biof309/project_spring_2020 <[email protected]>
Cc: aob93 <[email protected]>, Author <[email protected]>
Subject: Re: [biof309/project_spring_2020] Update README.md (#7)
HI Aidan,
One more suggestion, I think it may be easier to write unit tests for you code if divide your code up into multiple functions, instead of the one main function.
Also, now that I think about it, it may be best to create a ''test_data" folder within your test directory (I basically just copied your data files over but it would be clearer to see a test directory with all of the data files) in order to organize your code. You can then read in the data from the directory as is currently done in the test. Also, I think a better test statement for the example test that I wrote is:
assert header[0] == 'Chr'
because this would actually test that you are reading in what you think you are reading in from the datafile.
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Yes, basically, you want to test that your code is doing what you think it is doing with the tests. |
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I have a few more comments that may be useful: I think you also need to remove the 'sample_tests.py' from your test directory as there is a failing test in this script so it is causing issues. Additionally, filling out your package details in the 'setup.py' script (name, email, package name, etc.) will also be useful for you. |
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Hi Aidan, Well done on the project. You show a good understanding of Python and the use of NumPy and Pandas is nice as well as the creation of a plot using matplotlib. In the future, I would suggest modularizing your code into multiple functions which will then make it easier to debug as you think about writing tests. Also, I suggest adding files like .ipynb_checkpoints to your .gitignore file. Overall, the project is great, good work! Cheers, Emily |
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