Add stdin support to the tskit CLI#3469
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Nice, thanks. LGTM, but maybe someone else could check it over too? |
Codecov Report✅ All modified and coverable lines are covered by tests. Additional details and impacted files@@ Coverage Diff @@
## main #3469 +/- ##
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Coverage 91.67% 91.67%
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Files 38 38
Lines 32186 32188 +2
Branches 5150 5151 +1
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+ Hits 29505 29509 +4
+ Misses 2348 2346 -2
Partials 333 333
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Thanks @chris-a-talbot - I'll have a good look at this in the next few days |
Update changelog to reflect stdin CLI feature
Update the CLI tests to cover reading a tree sequence from stdin when the positional path argument is omitted, replacing the stale tests written for the earlier '-' convention. Adds in-process equivalence tests across all loading subcommands, stdin error-path tests, and end-to-end subprocess tests that exercise a real non-seekable pipe. Also removes a dead comment in cli.py and updates the changelog to describe the omit-argument behaviour.
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jeromekelleher
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Jun 23, 2026
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I updated this to use the convention we usually use of "no file means read from stdin" instead of having "-" mean stdin. I also added more thorough tests and simplified the implementation.
Thanks again for picking this up @chris-a-talbot
The info command prints unicode box-drawing characters, which crash the child process with a UnicodeEncodeError when stdout is a pipe on platforms defaulting to a non-UTF-8 codec (e.g. Windows). Set PYTHONIOENCODING=utf-8 in the subprocess environment.
jeromekelleher
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Jun 25, 2026
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Closes #3468.
CLI commands that load a tree sequence now accept
-as the input path to read from stdin. This allows workflows such asto convert a
.tszfile to VCF.