Hi Billy, brilliant. We will try the cctbx-nightly in due course. Actually, it would be useful to us to have a minimal cctbx conda package. The equivalent of the build option cctbx-light would be perfect. It is all we need and it would minimise the risk of conflicts. Conda/mamba is very good but not invulnerable as our recent problems at Bruker shows. Eventually, this is not utterly critical because both the Anaconda people and you guys in charge of cctbx are amazing. So things get sorted out quickly enough. But still, I don’t like Damocles swords! Best wishes, Luc

On 24 Feb 2024, at 14:34, Billy Poon wrote:

Hi Luc,

There are currently nightly conda packages for Python 3.12 on the cctbx-nightly channel (https://anaconda.org/cctbx-nightly/ https://anaconda.org/cctbx-nightly/). The nightly tests are also run on that version (https://github.com/cctbx/cctbx_project?tab=readme-ov-file#nightly-checks-of-... https://github.com/cctbx/cctbx_project?tab=readme-ov-file#nightly-checks-of-...). There is a holdup to the migration on conda-forge because the pyside2 package is not available for Python 3.12. We will move that dependency to pyside6 (probably in a month or so) so that the migration can proceed. I removed the GUI packages (wxpython and pyside2, wxpython Python 3.12 support is available now) from the cctbx-nightly cctbx package so that I could build the Python 3.12 packages. Once the conda-forge package is migrated, I can add back the GUI dependencies to our nightly builds.

If you test the nightly packages, let me know if you find any issues on Python 3.12. Thanks!

-- Billy K. Poon Research Scientist, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory 1 Cyclotron Road, M/S 33R0345 Berkeley, CA 94720 Fax: (510) 486-5909 Web: https://phenix-online.org https://phenix-online.org/

On Wed, Feb 21, 2024 at 12:35 AM Luc Bourhis mailto:[email protected]> wrote: Hi,

I see in the commit that you guys are working on supporting Python 3.12. With the latest version of Python 3.11 on Anaconda, we have a compatibility issue between Qt that we use and ICU 70.1 that cctbx requires. The problem is solved by moving to Python 3.12, hence my question: when can we hope to see a release with Python 3.12? No pressure! Just trying to plan ahead.

Best wishes,

Luc

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Hi Luc, Thanks! Which package are you using? cctbx is cctbx-base plus some additional dependencies (mainly, wxPython, pyside2, and ipython). If you do not need those dependencies (or want to manually specify extra dependencies), then cctbx-base should be the one to use. I guess we can strip out some more dependencies for a cctbx-light. The package recipes are in cctbx-base-feedstock, and I can add a cctbx-light package as an additional output that has fewer dependencies. The cctbx package is an output in the meta.yaml file that adds extra dependencies to cctbx-base. So things like reportlab and biopython or even matplotlib could be removed for cctbx-light. Or do you mean to remove certain modules from cctbx-base for cctbx-light? That would be possible, but I could probably do it in the second half of this year. I'm already building all of Phenix as a giant conda package and I've been splitting parts of it off into smaller packages to help with making the builds more manageable on Azure (e.g. chem_data is 7 GB and does not need to be in every platform package since it's platform independent). -- Billy K. Poon Research Scientist, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory 1 Cyclotron Road, M/S 33R0345 Berkeley, CA 94720 Fax: (510) 486-5909 Web: https://phenix-online.org On Mon, Feb 26, 2024 at 1:15 AM Luc Bourhis wrote:

I have a question about the conda packages actually: I found out that cctbx-base is build with `—builder=cctbx`, by reading the recipe on the subrepository cctbx-base-feedstock on the conda-forge repo. But I can’t find a subrepo for the conda package cctbx. What is the exact difference between cctbx-base and cctbx?

On 26 Feb 2024, at 09:42, Luc Bourhis wrote:

Hi Billy,

brilliant. We will try the cctbx-nightly in due course. Actually, it would be useful to us to have a minimal cctbx conda package. The equivalent of the build option cctbx-light would be perfect. It is all we need and it would minimise the risk of conflicts. Conda/mamba is very good but not invulnerable as our recent problems at Bruker shows. Eventually, this is not utterly critical because both the Anaconda people and you guys in charge of cctbx are amazing. So things get sorted out quickly enough. But still, I don’t like Damocles swords!

Best wishes,

Luc

On 24 Feb 2024, at 14:34, Billy Poon wrote:

Hi Luc,

There are currently nightly conda packages for Python 3.12 on the cctbx-nightly channel (https://anaconda.org/cctbx-nightly/). The nightly tests are also run on that version ( https://github.com/cctbx/cctbx_project?tab=readme-ov-file#nightly-checks-of-...). There is a holdup to the migration on conda-forge because the pyside2 package is not available for Python 3.12. We will move that dependency to pyside6 (probably in a month or so) so that the migration can proceed. I removed the GUI packages (wxpython and pyside2, wxpython Python 3.12 support is available now) from the cctbx-nightly cctbx package so that I could build the Python 3.12 packages. Once the conda-forge package is migrated, I can add back the GUI dependencies to our nightly builds.

If you test the nightly packages, let me know if you find any issues on Python 3.12. Thanks!

-- Billy K. Poon Research Scientist, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory 1 Cyclotron Road, M/S 33R0345 Berkeley, CA 94720 Fax: (510) 486-5909 Web: https://phenix-online.org

On Wed, Feb 21, 2024 at 12:35 AM Luc Bourhis wrote:

...

Hi,

I see in the commit that you guys are working on supporting Python 3.12. With the latest version of Python 3.11 on Anaconda, we have a compatibility issue between Qt that we use and ICU 70.1 that cctbx requires. The problem is solved by moving to Python 3.12, hence my question: when can we hope to see a release with Python 3.12? No pressure! Just trying to plan ahead.

Best wishes,

Luc

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Hi Billy, I apologise for my very late response: I got a nasty cold and then I got swamped by work when I came back.

Thanks! Which package are you using? cctbx is cctbx-base plus some additional dependencies (mainly, wxPython, pyside2, and ipython). If you do not need those dependencies (or want to manually specify extra dependencies), then cctbx-base should be the one to use.

We are using cctbx. We should really be using cctbx-base then. We just went for the obvious name without giving much thought to it!

I guess we can strip out some more dependencies for a cctbx-light. The package recipes are in cctbx-base-feedstock, and I can add a cctbx-light package as an additional output that has fewer dependencies. The cctbx package is an output in the meta.yaml file that adds extra dependencies to cctbx-base. So things like reportlab and biopython or even matplotlib could be removed for cctbx-light.

Or do you mean to remove certain modules from cctbx-base for cctbx-light? That would be possible, but I could probably do it in the second half of this year. I'm already building all of Phenix as a giant conda package and I've been splitting parts of it off into smaller packages to help with making the builds more manageable on Azure (e.g. chem_data is 7 GB and does not need to be in every platform package since it's platform independent).

I had in mind the former. Precisely the —builder=cctbx-light option.

By the way, what were the problems you experienced?

Actually, it turns out the cctbx was not the root cause. We thought it was because removing it from the conda .yml spec made the resulting environment work. But eventually we have found out that the root cause was that we mixed the default and conda-forge channels. Using only conda-forge works with the cctbx. So I am afraid, sorry for the noise! But that triggered a useful discussion, at least from our point of view, so there is that! Thanks again for your time, Best wishes, Luc