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…y lines It's a binary stream where we don't care about lines, and iterating in tiny line-wise chunks (via the requests package) resulted in extremely slow `nextstrain remote upload` times when the destination was nextstrain.org.¹ When the destination was S3, the s3transfer package underlying boto3 took care of reading from the file handle in chunks instead of lines. ¹ https://bedfordlab.slack.com/archives/C01LCTT7JNN/p1648748118413089
On a ~200 MB example input (a real dataset JSON), the difference in compressed size of ~200 kB (6 MB vs. 6.2MB) seems not worth the difference in compression speed of ~4s (5.6s vs. 1.5s). I assume similar ratios for other inputs of different sizes but similar composition (dataset JSONs and narrative markdowns).
victorlin
approved these changes
Apr 1, 2022
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Tested manually. Dramatically improves upload speed to nextstrain.org. I performed a few ad-hoc benchmarks to ensure the compression level change was worth it.