[cctbxbb] New cctbx conda packages for testing

Luc Bourhis luc_j_bourhis at mac.com
Sat Mar 21 04:53:33 PDT 2020


Hi,

allow to state the obvious: some people might prefer to do

conda install -c conda-forge -c cctbx-dev cctbx

or

conda create -n xxxx -c conda-forge -c cctbx-dev cctbx python=yyyy

instead of having cctbx-forge systematically searched into behind their back.

Best wishes,

Luc


> On 20 Mar 2020, at 16:57, Billy Poon <bkpoon at lbl.gov> wrote:
> 
> 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 <https://phenix-online.org/>
> 
> On Fri, Mar 20, 2020 at 12:41 AM Billy Poon <BKPoon at lbl.gov <mailto: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 <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 <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 <https://phenix-online.org/>_______________________________________________
> cctbxbb mailing list
> cctbxbb at phenix-online.org
> http://phenix-online.org/mailman/listinfo/cctbxbb

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