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Add tests and set up some Continuous Integration (CI) #104

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Tracked by #80
tacazares opened this issue Jun 8, 2022 · 0 comments
Open
Tracked by #80

Add tests and set up some Continuous Integration (CI) #104

tacazares opened this issue Jun 8, 2022 · 0 comments

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@tacazares tacazares mentioned this issue Jun 8, 2022
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@tacazares tacazares changed the title If possible add tests and set up some Continuous Integration (CI) Add tests and set up some Continuous Integration (CI) Jun 8, 2022
tacazares added a commit that referenced this issue Aug 24, 2022
@tacazares
#104 test data clean up, pytest req in setup.py, and #109 update aver…
0c4c309 
…age flags for consistency

The major changes were to the average function.

Changes include:

* The `--prefix` option for average was changed to `-n` and `-name`
* The optional names for chromosomes are `-c`, `--chroms`, and `--chromosomes`
* The optional names for chromosome_sizes are `-cs`,  `--chrom_sizes`, and `--chromosome_sizes`
* The default output directory is the current working directory and can be specified with `-o`
* A timer was added to track runtime
* Additional logging messages
* Cleaned up old test data
* Added a namespace class to system_tools.py to hold variables in tests
* Added pytest to setup.py
* Created tests for average.py with expected outputs.
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