[cctbxbb] Python3 / scons / non-conda builds

Sun May 12 22:55:01 PDT 2019

Thanks Billy, I will give this a go later on

Best wishes Graeme

On 13 May 2019, at 04:14, Billy Poon <bkpoon at lbl.gov<mailto:bkpoon at lbl.gov>> wrote:

Hi Graeme,

I recently checked in a change that should help. If the "scons" directory does not exist and SCons is importable, the installed SCons will be used instead. This is also helpful for conda builds since I want to move SCons into the conda environment.

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Billy K. Poon
Research Scientist, Molecular Biophysics and Integrated Bioimaging
Lawrence Berkeley National Laboratory
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On Wed, May 8, 2019 at 1:02 AM Graeme.Winter at Diamond.ac.uk<mailto:Graeme.Winter at Diamond.ac.uk> <Graeme.Winter at diamond.ac.uk<mailto:Graeme.Winter at diamond.ac.uk>> wrote:
Dear All,

Back in the mists of time, one could build cctbx modules without bootstrap or conda by having the right modules available yourself - a so-called baseless install which I think is still important in X-fel land?

Anyhow, trying this with Python3 suggests that we have some special constraints which are perhaps too tight regarding module locations - for example scons -

Grey-Area p3_compile :( $ pip3 install scons
Collecting scons
  Downloading https://files.pythonhosted.org/packages/65/41/ac58638421414acc64e26fc120c81c12bc2b1ebcea9e7e0939149878f0a3/scons-3.0.5-py2.py3-none-any.whl (831kB)
    100% |████████████████████████████████| 839kB 14.3MB/s
Installing collected packages: scons
Successfully installed scons-3.0.5
You are using pip version 19.0.1, however version 19.1.1 is available.
You should consider upgrading via the 'pip install --upgrade pip' command.
Grey-Area p3_compile :) $ make
./bin/libtbx.scons -j "`./bin/libtbx.show_number_of_processors`"
ModuleNotFoundError: No module named 'SCons'

During handling of the above exception, another exception occurred:

Sorry: SCons is not available.
  A possible solution is to unpack a SCons distribution in
  one of these directories:
    "/Users/graeme/svn/scr"
    "/Users/graeme/svn/scr/cctbx_project"
  SCons distributions are available at this location:
    http://www.scons.org/
  It may be necessary to rename the unpacked distribution, e.g.:
    mv scons-0.96.1 scons
make: *** [default] Error 1
Grey-Area p3_compile :( $ which scons
/Library/Frameworks/Python.framework/Versions/3.7/bin/scons

Should we require that scons is installed as part of cctbx when it is already installed on the system?

If we *do* have to have this constraint, maybe that should be checked at configure time (where it complains about six and future)

Thoughts?

In other news - the syntax changing branch referenced in https://github.com/cctbx/cctbx_project/pull/325 now compiles correctly on Python3 (note: not run, just compile but this means that it’s purpose is done) for the modules which it intends to touch and has no conflicts right now…

Best wishes Graeme

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