Managing Dependencies

AICSImageIO 4.3.0

This release has been published to begin the process of managing some of our dependencies and their licenses.

AICSImageIO is built off of many independent file format readers, each with their own licensing. For many of our supported formats, the library that provides us the capability to read the format is licensed under a permissive license such as MIT or BSD. However, some of our formats are released under GPL licenses. Previously, AICSImageIO has included all of these dependencies in our pip extra install options, and released our package under BSD license. However, after our latest release, we received push-back on this practice and as such, we have begun the process of stripping out the specific installation of GPL licensed dependencies.

This does not mean that AICSImageIO no longer supports the various file formats covered by GPL license. We still do, however we will no longer provide a pip extra install option for such formats and we will include specific reference to readers that utilize such GPL licenses.

In this release, the two readers that have had their extra install options removed are:

• LifReader -- was installed with pip install aicsimageio[lif] but must now be installed with pip install aicsimageio readlif>=0.6.4
• BioformatsReader -- was installed with pip install aicsimageio[bioformats] but must now be installed with pip install aicsimageio bioformats_jar

Both readlif and bioformats_jar are completely separate libraries that carry with them their own GPL licenses and as such, if you use either of these readers, be sure to see how your code should now be licensed and add these libraries to your own dependency list because our install option is no longer available.

Moving forward, we plan to use this same installation pattern for any more GPL licensed file format readers. AICSImageIO will make them generally available, but will document that the downstream user must install both aicsimageio and the supporting file format library independent so that AICSImageIO remains BSD licensed.

Changelog

• Support for reading LIF files must now be installed separately due to licensing conflicts. (pip install aicsimagieo readlif>=0.6.4) #332
• Support for reading Bio-Formats supported files must now be installed separately due to licensing conflicts. (pip install aicsimageio bioformats_jar) #329
• More detailed error message and documentation on how to configure BioFormats reading. #324
• Shortened reader import paths for any reader. #326

To review all changes made in this release please see our full CHANGELOG.

Contributors and Reviewers this Release (alphabetical)

Chris Allan (@chris-allan)
Sébastien Besson (@sbesson)
Jackson Maxfield Brown (@JacksonMaxfield)
Talley Lambert (@tlambert03)
Josh Moore (@joshmoore)
Peter Sobolewski (@psobolewskiPhD)
Madison Swain-Bowden (@AetherUnbound)
Jason Swedlow (@jrswedlow)
Dan Toloudis (@toloudis)