[cctbxbb] Revisiting cctbx/iotbx/dxtbx dependencies

[Aaron Brewster]

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 <abhowmick at lbl.gov> 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 <asbrewster at lbl.gov> 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:
>>
>>    1. 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
>>    2. 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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>>
>>
>
>
> --
> Asmit Bhowmick, Ph.D
> Molecular Biophysics & Integrated Bioimaging Division
> Lawrence Berkeley National Laboratory
> 1 Cyclotron Rd., Bldg. 33, Room 349B
> <https://maps.google.com/?q=1+Cyclotron+Rd.,+Bldg.+33,+Room+349B&entry=gmail&source=g>
> Berkeley, CA 94720
> Cell: 510.684.6011 <(510)%20684-6011>
>
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