[phenixbb] New cctbx conda packages for testing

[Billy Poon]

Hi everyone,

The cctbx package needs dependencies from the conda-forge channel, so your
~/.condarc should have conda-forge somewhere in there. For example, it
should have an entry that looks like,

channels:
  - conda-forge
  - defaults

That causes conda to look for dependencies in conda-forge before the
default channels.

--
Billy K. Poon
Research Scientist, Molecular Biophysics and Integrated Bioimaging
Lawrence Berkeley National Laboratory
1 Cyclotron Road, M/S 33R0345
Berkeley, CA 94720
Tel: (510) 486-5709
Fax: (510) 486-5909
Web: https://phenix-online.org


On Fri, Mar 20, 2020 at 12:41 AM Billy Poon <BKPoon at lbl.gov> wrote:

> Hi everyone,
>
> Sorry for the long delay, the current Phenix release and helping out with
> an experiment at SACLA earlier in the year, took priority. But I have been
> able to clean up the cctbx conda packages that I built at the end of last
> year. The major differences are as follows.
>
> 1) Windows packages are available for Python 2.7, 3.6, and 3.7. It's not
> clear why conda-build is having issues with Python 3.8, so I'm still
> sorting it out.
> 2) The full repositories are copied now. As a consequence, you'll be able
> to run some tests like "libtbx.run_tests_parallel module=cctbx nproc=24"
> and all the tests will run.
> 3) The LIBTBX_BUILD environment variable is no longer needed, so it is not
> set on activation of the conda environment.
> 4) The libtbx.configure and libtbx.refresh commands are removed from the
> conda package until the ability to configure/build against the conda
> installation of cctbx is available. Currently, those commands will break
> the environment.
>
> The linux and macOS packages support Python 2.7, 3.6, 3.7, and 3.8, just
> like before. The command to create a new environment is,
>
> conda create -n test -c cctbx-dev cctbx python=<python version>
>
> If "python=<python version>" is left out, the default Python version will
> be 3.8. To install cctbx into the currently active conda environment, the
> command is,
>
> conda install -c cctbx-dev cctbx
>
> The packages are currently on the cctbx-dev channel, but the goal is to
> get official packages into conda-forge. To get the cctbx recipe into
> conda-forge (https://github.com/conda-forge/staged-recipes/pull/10021),
> we'll need an official release. I've opened up an issue on GitHub (
> https://github.com/cctbx/cctbx_project/issues/451). Please provide any
> feedback on the versioning system, release schedule, and anything release
> related.
>
> Let us know if you're scripts are not working with these packages. Thanks!
>
> --
> Billy K. Poon
> Research Scientist, Molecular Biophysics and Integrated Bioimaging
> Lawrence Berkeley National Laboratory
> 1 Cyclotron Road, M/S 33R0345
> Berkeley, CA 94720
> Tel: (510) 486-5709
> Fax: (510) 486-5909
> Web: https://phenix-online.org
>
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