Release 4.0 append output for save_results #1225
Open
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
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