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Release 4.0 append output for save_results #1225
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Codecov Report
@@ Coverage Diff @@
## release-4.0 #1225 +/- ##
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Coverage 100.00% 100.00%
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Files 157 157
Lines 6759 6767 +8
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+ Hits 6759 6767 +8
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@all-contributors please add @afinit for code, doc, test. |
I've put up a pull request to add @afinit! 🎉 |
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Describe your changes
I expect changes, but this seems like a good start for discussion.
outformat
paramTrue
with
to open csv fileBefore this PR, neither json nor csv files would append data. The json path reads in the existing data, but throws away the observations and only keeps the metadata.
The part that needs some discussion:
With this PR, existing json and csv data are treated differently. When json data is appended, we overwrite any observations that have the same sample name as our new data. When csv data is appended, we are strictly appending without any consideration of the data that is already in the file.
I don't like this difference in behavior
Options for fixing the differences
There are probably other options, but these are the 2 ideas I came up with to resolve the current difference in behavior
Option 1
Read existing CSV data with pandas and remove any rows with the same sample name as the new data
Option 2
Read existing data for both json and csv. Modify conflicting sample names to have an appended
_###
where we autoincrement that number for new data. This would look something like:Type of update
new feature
Associated issues
Addresses #886
For the reviewer
See this page for instructions on how to review the pull request.
plantcv/mkdocs.yml
updating.md