Hi Aaron,
Thank you for those amendments to bootstrap. I just tested cctbxlite with
amendments to also build phaser from bootstrap. It simplifies the build
steps for building phaser so sometime soon I'd like to add a separate
builder to bootstrap that builds phaser only. Perhaps cctbxlite could form
the basis for a python wheel installer.
Rob
From: Aaron Brewster
Sent: Saturday, February 10, 2018 12:58 AM
To: Asmit Bhowmick
Cc: cctbx mailing list ; R.D. Oeffner ; Luc Bourhis
Subject: Re: [cctbxbb] Revisiting cctbx/iotbx/dxtbx dependencies
Hi folks, you can now run python bootstrap.py --builder=cctbxlite to get a
lite version of cctbx. It will follow the steps listed above, skipping
hdf5, cbflib and dxtbx.
I'd like to close issues 125 and 126 unless someone objects.
https://github.com/cctbx/cctbx_project/issues/125
https://github.com/cctbx/cctbx_project/issues/126
Thanks!
-Aaron
On Thu, Feb 8, 2018 at 8:50 PM, Asmit Bhowmick wrote:
For the 2nd step that Aaron mentioned, if certain packages are to be skipped
during the base step, you can also run bootstrap.py with the
flag --skip-base-packages and specify the packages to be skipped separated
by a comma. For example
python bootstrap.py base --builder=cctbx --skip-base-packages
hdf5,lz4_plugin
Best Wishes
Asmit
On Wed, Feb 7, 2018 at 3:08 PM, Aaron Brewster wrote:
Hey folks, especially Rob and Luc. So after a quick change to
iotbx/libtbx_config, it turns out there's a way to get a super minimum
version of cctbx, without configuring dxtbx, and it takes advantage of
existing mechanisms:
python bootstrap.py --builder=cctbx hot update
python modules/cctbx_project/libtbx/auto_build/install_base_packages.py
openssl python python_compatibility certifi numpy cython png libsvm pytest
pythonextra jinja2 junitxml biopython docutils sphinx pyopengl misc freetype
matplotlib pillow gettext glib expat fontconfig render pixman tiff cairo gtk
fonts wxpython
mkdir build; cd build
../base/bin/python ../modules/cctbx_project/libtbx/configure.py cctbx iotbx
make
Now, some details as to why this works. First, the cctbx builder in
boostrap.py doesn't download cbflib so cbflib is never configured. Next,
the base step of bootstrap.py is simply a call to install_base_packages.py
with a list of required packages. You can just run it standalone and get
the packages you need. Here, I ran "python bootstrap.py --builder=cctbx
base", killed it after I saw the list of packages it was going to install,
then ran install_base_packages manually after removing hdf5 and lz4 (which
depends on hdf5) from the list. One could imagine removing other packages
depending on your use case. With that, I could run configure.py directly.
I can't use cctbx by itself as the cctbx/maptbx/SConscript file has a
dependency on iotbx, but configuring cctbx and iotbx together seems to work.
The key trick was to make iotbx only depend on dxtbx if dxtbx is explicitly
configured. I used a keyword in libtbx_configure added by Luc a bit ago:
optional_modules_only_if_explicit_request. I committed that change just
now.
Outstanding questions:
Is there interest in making this a builder? It would be straightforward to
add a builder named cctbx_minimal which would just do the above steps
Is there further need for making cbflib and hdf5 optional in dxtbx? I
purport there is not as the above procedure seems to satisfy the use case,
but I can be persuaded otherwise.
Thanks,
-Aaron
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Molecular Biophysics & Integrated Bioimaging Division
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