[cctbxbb] Is there a schedule for the python3 migration or can cctbx.python already be built to be/use a python3 interpreter?

[Billy Poon]

Hi Jan,

Do you need to build cctbx from scratch? The cctbx has been available for
Python 3 for a while now, but is using conda packages (
https://docs.conda.io/en/latest/) for managing dependencies. Building the
dependencies from scratch for multiple versions of Python 3 for multiple
platforms was getting too complicated.

You can install cctbx as a conda package for Python 3.6 through 3.9 with
support for macOS (Intel and Apple Silicon), linux, and Windows.
Instructions can be found here (
https://github.com/cctbx/cctbx_project#installation), but essentially it is
just

conda install -c conda-forge cctbx-base

to get it into an existing environment. The smtbx module will be available,
but not fast_linalg yet.

Note that with a conda environment, you do not need to run any of the
"setpaths" scripts to set it up. Just activate the environment and cctbx
will be available in python.

There are also nightly builds of the conda packages on a separate channel (
https://github.com/cctbx/cctbx_project#nightly-builds). The command above
becomes

conda install -c cctbx-nightly -c conda-forge cctbx-base

You can also build cctbx with Python 3 using conda packages as dependencies
(https://github.com/cctbx/cctbx_project#building-a-development-version).
The bootstrap.py command becomes

python bootstrap.py --use-conda --python 38

This will install miniconda if conda is not already available on your
system.

You can run

python bootstrap.py --help

to see more options.

There are monthly releases and I will make announcements on this bulletin
board from now on to help spread the word.

--
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 Fri, Jul 9, 2021 at 4:57 AM Jan M. Simons <marten at ifk.rwth-aachen.de>
wrote:

> Hi Oleg,
>
> Am 09.07.21 um 13:16 schrieb Oleg Dolomanov:
> > Hi Jan,
> >
> > which way have you been using to build cctbx?
>
> I've been following https://cctbx.github.io/installation.html
>
> (as https://cci.lbl.gov/cctbx_docs/installation.html seems to be the
> older/outdated documentation which should perhaps redirect to the newer
> one instead.)
>
> Is this not the right documentation on how to build it on a bare bones
> linux distribution? (I'm using sabayon, a gentoo derivative)
>
> So right now I've re-tried to execute an up-to-date bootstrap.py with my
> system supplied python3.7 and on first attempt it still built python2.7
> and then failed with
>
> Installing h5py 2.10.0...
> Read and write HDF5 files from Python
>   log file is /home/jan/Arbeit/cctbx-dev/base_tmp/h5py_install_log
> Traceback (most recent call last):
>   File
> "modules/cctbx_project/libtbx/auto_build/install_base_packages.py", line
> 1682, in <module>
>     installer(args=sys.argv, log=sys.stdout)
>   File
> "modules/cctbx_project/libtbx/auto_build/install_base_packages.py", line
> 256, in __init__
>     self.build_dependencies(packages=packages)
>   File
> "modules/cctbx_project/libtbx/auto_build/install_base_packages.py", line
> 782, in build_dependencies
>     getattr(self, 'build_%s'%i)()
>   File
> "modules/cctbx_project/libtbx/auto_build/install_base_packages.py", line
> 1220, in build_h5py
>     confirm_import_module='h5py', extra_options=["--no-binary=h5py"])
>   File
> "modules/cctbx_project/libtbx/auto_build/install_base_packages.py", line
> 694, in build_python_module_pip
>     log=log)
>   File
> "modules/cctbx_project/libtbx/auto_build/install_base_packages.py", line
> 359, in call
>     return call(args, log=log, verbose=self.verbose, **kwargs)
>   File
>
> "/home/jan/Arbeit/cctbx-dev/modules/cctbx_project/libtbx/auto_build/installer_utils.py",
> line 55, in call
>     raise RuntimeError("Call to '%s' failed with exit code %d" % (args,
> rc))
> RuntimeError: Call to '/home/jan/Arbeit/cctbx-dev/base/bin/python -m pip
> install  "h5py==2.10.0" --no-binary=h5py' failed with exit code 1
> Process failed with return code 1
>
> Then calling
> $ python3 ./bootstrap.py
> again it is still compiling, but from the paths I suppose that it's
> continuing to only build the python2.7 version (like before).
>
>
> So, I suppose I'm missing some bit of documentation on how to get it
> working with python3.
>
> Thanks for your support
> Jan
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