Re: [cctbxbb] [EXTERNAL] cctbxbb Digest, Vol 138, Issue 2

Hi Blaine, Sorry! You're right, the command should be "libtbx.run_tests_parallel" not "libtbx.run_tests_module". "module" is the keyword for command. -- 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 Wed, Sep 23, 2020 at 12:59 PM Mooers, Blaine H.M. (HSC) < [email protected]> wrote:

Hi Billy,

I installed cctbx in a new conda env called cctbx37:

conda create --name cctbx37 python=3.7 conda activate cctbx37 conda install -c conda-forge cctbx jupyterlab

I cannot find libtbx.run_tests_module.

I can only find libtbx.run_tests_parallel.

Best regards,

Blaine

Blaine Mooers, Ph.D. Associate Professor Department of Biochemistry and Molecular Biology College of Medicine University of Oklahoma Health Sciences Center S.L. Young Biomedical Research Center (BRC) Rm. 466 975 NE 10th Street, BRC 466 Oklahoma City, OK 73104-5419

________________________________________ From: [email protected] [[email protected]] on behalf of [email protected] [ [email protected]] Sent: Wednesday, September 23, 2020 2:00 PM To: [email protected] Subject: [EXTERNAL] cctbxbb Digest, Vol 138, Issue 2

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Today's Topics:

1. cctbx now available on conda-forge (Billy Poon)

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Message: 1 Date: Wed, 23 Sep 2020 11:22:03 -0700 From: Billy Poon To: cctbx mailing list , PHENIX user mailing list Subject: [cctbxbb] cctbx now available on conda-forge Message-ID: Content-Type: text/plain; charset="utf-8"

Hi everyone,

The conda-forge package for cctbx is now available. There are 2 packages, "cctbx-base" includes the base code and "cctbx" which includes "cctbx-base" and adds "wxPython", "PySide2", and "ipython". The commands for installing cctbx into your conda environment are

conda install -c conda-forge cctbx

or

conda install -c conda-forge cctbx-base

If you want to use Jupyter Lab, you can now easily do this with

conda install -c conda-forge cctbx-base jupyterlab jupyter lab

The existing documentation will be updated to reflect the easier installation procedure with conda.

After installing the conda package, you can also run some of the tests (in an empty directory) with

libtbx.run_tests_module module=libtbx module=cctbx nproc=<nproc>

I do know of a few issues that I want to fix in upcoming releases, but please submit issues to https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_cctbx_cctbx-5Fproject&d=DwICAg&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=6ECfX7MkBmhyld0TuhCVkFnEEf3aeFHIxM4znr2jCnY&s=Vn7Woa-V4O0G8CERBKscZ3z1ijUwBZ26YEU910l2nwE&e= with steps to reproduce the error.

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://urldefense.proofpoint.com/v2/url?u=https-3A__phenix-2Donline.org&d=DwICAg&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=6ECfX7MkBmhyld0TuhCVkFnEEf3aeFHIxM4znr2jCnY&s=0jI2Zk7EtFc6O96Dn_A4UuNMDiOZ1tNdA0jieZF0nCA&e=