conda run adds an extra newline to the output

[jmarshall]

Checklist

• I added a descriptive title
• I searched open reports and couldn't find a duplicate

What happened?

Running a command via conda run adds an extra newline (when the output is non-empty):

(base) $ conda run true
(base) $ conda run echo hello
hello

(base) $ 

When shell redirection is naively applied to the conda run command (rather than to the subcommand to be executed, though getting that right would require careful and fragile quoting if it is possible at all), this leads to the captured output having an extra blank line at the end of it. Where that captured output is to be processed by another program, this can lead to syntax errors, e.g., as seen in lh3/bwa#371.

In that issue, this can be avoided by using the subcommand's -o option instead of redirecting output. But such options are not alway available, and users often use the familiar redirection even when the subcommand has such an option.

This can be avoided with --no-capture-output if the user knows about that option:

(base) $ conda run --no-capture-output echo hello
hello
(base) $ 

but it would be beneficial if conda run did not alter the output by default as well.

The code in question is in conda/cli/main_run.py:

conda/conda/cli/main_run.py

Lines 39 to 44 in 606f55f

	# display stdout/stderr if it was captured
	if not args.no_capture_output:
	if response.stdout:
	print(response.stdout, file=sys.stdout)
	if response.stderr:
	print(response.stderr, file=sys.stderr)

It would be a simple fix to add …, end='', … to the print calls, or, if it was preferred, to only add an extra newline if the last character of the (non-empty) output is not already a newline.

Conda Info

No response

Conda Config

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Conda list

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Additional Context

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