[Numpy-discussion] savetxt -> gzip: nondeterministic because of time stamp

Derek Homeier derek at astro.physik.uni-goettingen.de
Wed Apr 14 17:56:22 EDT 2021

On 14 Apr 2021, at 11:15 pm, Robert Kern <robert.kern at gmail.com> wrote:
> On Wed, Apr 14, 2021 at 4:37 PM Joachim Wuttke <j.wuttke at fz-juelich.de> wrote:
> Regarding numpy, I'd propose a bolder measure:
> To let savetxt(fname, X, ...) store exactly the same information in
> compressed and uncompressed files, always invoke gzip with mtime = 0.
> I agree.
I would caution though that relying on the checksum or similar of the compressed data still
does not seem a very robust check of the data itself - the compressed file would still definitely
change with any change in compression level, and quite possibly with changes in the
linked compression library (perhaps even a simple version update).

Shouldn’t you better verify the data buffers themselves? Outside of Python, the lzma utility
xzcmp for example allows binary comparison of the content of compressed files independently
from the timestamp or even compression method, and it handles gzip and bzip2 files as well.

> I would like to follow up with a pull request, but I am unable to
> find out how numpy.savetxt is invoking gzip.
> `savetxt` uses the abstractions in this module to invoke gzip when the filename calls for it:
> https://github.com/numpy/numpy/blob/main/numpy/lib/_datasource.py#L115
One obstacle would be that this is setting gzip.open as _file_opener, which does not have the
mtime option; getting this replaced with gzip.GzipFile to work in text mode would require to
somehow replicate gzip.open’s io.TextIOWrapper wrapping of GzipFile.


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