Cross-device link error when exporting to file with --output-format

When using qiime tools export with --output-format to export to a single file, a cross-device link error occurs if the qiime2 temporary directory is on a different device than the directory being exported to.

Here’s an example error message using qiime2-2018.11 installed via conda on macOS:

$ qiime tools export \
    --input-path tree.qza \
    --output-path tree.nwk \
    --output-format NewickFormat
OSError: [Errno 18] Cross-device link: '/var/folders/bt/rtfdzpmn0hz8mcgwgvy6m0000000gn/T/qiime2-archive-nzu4ozdw/e7904029-d9f0-405c-b376-9b6f681c620b/data/tree.nwk' -> '/Volumes/test-export/tree.nwk'

This happens because q2cli’s export_data function uses os.renames if the user provides an output_format and it’s exporting to a single file (see these lines). If output_format is omitted, or the data being exported is a directory, a different codepath is taken that works across devices.

A workaround is to set qiime2’s temporary directory to be on the same device as the output directory (e.g. setting TMPDIR environment variable). Another option is to omit --output-format from the command to use the default output format.

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Thanks for the report @jairideout!
I’ve created a PR to hopefully fix this here:

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