Daniel Paley

I see the tst_commandline_anomrefine failure on Centos 8/python36, but I couldn't reproduce it in 300 trials in a VM. I know that was one of the builds affected by the...

Actually this only happens when `step_threshold` and `gradient_threshold` are set to 0. In that case it runs iterations until `actual_decrease` is identically 0; then it starts doing ``` else: self.non_linear_ls.step_backward()...

I think that is true although I'm not a cif expert. This page seems to agree: https://mmcif.wwpdb.org/docs/tutorials/mechanics/pdbx-mmcif-syntax.html How about accepting any of the following: -extension cif or mmcif -first non-blank,...

> Perhaps not only .gz, but also tgz, tar, tar.gz, zip, bzip, rar, bzip2, etc etc. I had an impression this is handled separately in cctbx. Pavel > […](#) Not...

> For now, set the version of `setuptools` to `

Alright, this is clearly a headache and is not fixing itself. I’ll look at it next week and try to figure out what’s going on.

Got some clarity on this from @abravalheri. It's apparently well known that importing `pip` will break `setuptools` because `setuptools` packages a modified `distutils` while `pip` requires the unmodified stdlib `distutils`....

On first glance I only see that `pip` is really needed in `pkg_utils.require`. @bkpoon any chance we can quarantine calls to `require` inside subprocesses so that we don't have to...

The problem more specifically is what levenberg_marquardt_iterations does to the damping factor when the user forces it to do a lot of iterations. This is the current code in scitbx/lstbx/normal_eqns_solving.py:...

Sorry, I had no luck reproducing this. When installing cctbx via conda on 10.15.7 with python=3.7.7, no segfault. Seems like Apple has made it harder to find old OSX installers,...