Recommend pinning cytominer-database to v0.3.3 to avoid unexpected behaviors

[gwaybio]

A quick note to mention that @d33bs and I needed to perform two hotfixes of cytominer-database versions (v0.3.5) to accommodate pycytominer upload to conda-forge. You can see the change in #134

[Dave, please correct me if I’m wrong] If you have cytominer-database pipelines we recommend pinning to v0.3.3.

We aren’t quite there yet, but we also envision sunsetting cytominer-database in pycytominer in the near future, given cytominer-database deprecation and the steady march of python version EOLs.

cc @shntnu @bethac07

[shntnu]

We aren’t quite there yet, but we also envision sunsetting cytominer-database in pycytominer in the near future, given cytominer-database deprecation and the steady march of python version EOLs.

IIUC that would mean deprecating collate but nothing else, correct?

[gwaybio]

We'll pull out cytominer-database entirely (which I believe only includes collate, yes). We haven't decided when, but when we do, earlier pycytominer versions (at least <=1.2.0) will continue to support.

It's probably a good idea to continue this conversation over in cytomining/pycytominer#202

[d33bs]

[Dave, please correct me if I’m wrong] If you have cytominer-database pipelines we recommend pinning to v0.3.3.

I think pinning to v0.3.4 or v0.3.3 would be a good idea. We plan for v0.3.5 to merge changes from v0.3.4 with the master branch (#135) and also drop support for backports.tempfile (#134).

[d33bs]

Related note: cytominer-database v0.3.5 is now released on PyPI and conda-forge.