Modern numpy compatibility

Makes bioread work with numpy >= 1.20

Also remove last references to the GPL

Also also bump CI test versions (now python 3.7, 3.9, and 3.11)

Also also also update copyright to 2023

Change license to MIT

This release changes the license from GPL v2 to MIT.

Additionally, copyright is updated to 2022.

No other functionality is changed in this release.

Fix crash on reading marker dates

Some marker timestamps don't make sense to me; in this case, ignore the timestamps instead of crashing.

Hopefully make file reading more robust

Replace a dodgy "read X bytes ahead" magic number hack with a hopefully-less-dodgy "seek for the channel data type headers" procedure.

This seems more robust in practice.

Improve file reading

This adds support for version 4 files that have foreign data. (No, I don't know what that is.)

It also trades one set of gross hacks for another, maybe less gross hack.

With these changes, we're back to "reading all known files" status!

Autodetecting encodings! Data-only conversions! Yay!

This release will, with any luck at all, be the end of character encoding issues. (Fie on you, µV!) Files from before Acqknowledge 4.0 are assumed to be using latin-1 encoding, while 4.0 and on are assumed to be using UTF-8. This strikes me as likely true, but if it seems not to be, let me know. I can't run old versions of Acqknowledge any more, so I'm relying on examples people send in. Thanks to @benoitvalery and others who have done exactly that.

Also, if you're going to be publishing data, acq2hdf5 and acq2mat have a new option that may make you happy: --data-only. With that option, event markers and the journal (both of which can contain identifiers such as visit dates) will not be written into the output files.

Go forth! Read data! Wear a mask!

Version 2.0!

Now supports Python 3.6 and up! No more weird unicode issues!

Thanks to @pvelasco, we now know when event markers were created, as long as data files are from Acq 4.4.0 or newer. In addition, we've added Datafile.earliest_marker_created_at which reports the earliest date for an event marker, which will usually be the created_at time for the file — Acq automatically creates an apnd marker when recording starts.

Also, packaging was improved by @smoia, so bioread should install properly on clean systems and docker / singularity images.

Along the same lines (and thanks again to @smoia), optional installation dependencies for h5py and scipy are specified. You won't need them for basic library support, so they aren't installed all the time. Get them with:

# Just h5py
pip install bioread[hdf5]
# Just scipy
pip install bioread[mat]
# The whole shebang
pip install bioread[all]

Also also now uses Github Actions to run tests automatically on push. Pretty great! Python 3.6, 3.7, and 3.8 on ubuntu-latest are being tested at the moment, if you want to do testing on other platforms, let me know or make a PR.

Also also also removes vendor/ in favor of install-time dependencies. If we're gonna depend on numpy, we can depend on docopt.

That's a wrap, I think! I have effectively no roadmap for future versions, so this should be stable for a long time.

v1.0.4

First official Github release! Now with a Zenodo record!