[cctbxbb] some thoughts on cctbx and pip
Billy Poon
BKPoon at lbl.gov
Fri Jan 10 08:39:53 PST 2020
Hi Gergely,
So for your base environment, the std::__cxx11::basic_string error is
caused by the boost package coming from the cctbx channel. I built that
copy of boost to support older compilers (developer environments may use
GCC versions that are different than the one used for building conda-forge
packages), but I'll just move it to another channel so it's less confusing.
I'm surprised that the dependency resolution step kept that package instead
of replacing it with the version from conda-forge.
What shell are you using? The LIBTBX_BUILD environment variable should be
set for sh and csh type shells. What files exist in
$CONDA_PREFIX/etc/conda/activate.d ?
Thanks for testing!
--
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 Tue, Jan 7, 2020 at 12:54 AM Gergely Katona <gkatona at gmail.com> wrote:
> Ah, an there is no sign of the mentioned file in
> PYTHON_VERSION_MAJOR_MINOR in /home/gergely/anaconda3/lib before I
> forget.
>
> Gergely
>
> On Tue, Jan 7, 2020 at 9:37 AM Gergely Katona <gkatona at gmail.com> wrote:
> >
> > Hi Billy,
> >
> > Here come the package lists from conda. I will do more testing with
> > the cleaned condas installation. Indeed, the boost packages came from
> > the conda-forge channel but for some odd reason in the test
> > environment not in the base.
> >
> > Best wishes,
> >
> > Gergely
> >
> > On Fri, Jan 3, 2020 at 9:05 PM Billy Poon <BKPoon at lbl.gov> wrote:
> > >
> > > Hi Gergely,
> > >
> > > Happy New Year!
> > >
> > > Can you provide the output to "conda list" for each environment?
> > >
> > > I suspect that the old version of cctbx might still be around. Is
> there a file named PYTHON_VERSION_MAJOR_MINOR in
> "/home/gergely/anaconda3/lib"? If so, delete that file. To make sure you
> are downloading a new copy of the package, clear the cache where conda
> keeps copies of all the packages. To do that, you can run "conda clean -y
> --all". You can remove the "-y" flag if you want to see what will be
> deleted. The hash for the new linux package should be h8b68381_0.
> > >
> > > The last error looks like an incompatible version of boost or gcc
> library was installed. The output from "conda list" should show the boost
> and boost-cpp packages coming from conda-forge. I would avoid installing
> into the root or base environment because that usually pulls from the
> default channels. All the dependencies should be pulled from the
> conda-forge channel.
> > >
> > > --
> > > 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 Fri, Jan 3, 2020 at 2:20 PM Gergely Katona <gkatona at gmail.com>
> wrote:
> > >>
> > >> I found some other errors when using the test environment.
> > >>
> > >>
> > >>
> ---------------------------------------------------------------------------
> > >> RuntimeError Traceback (most recent call
> last)
> > >> <ipython-input-1-fe308b345b3f> in <module>
> > >> 10 import scipy as sp
> > >> 11 from scipy import linalg
> > >> ---> 12 import iotbx.pdb
> > >> 13 import cctbx
> > >> 14 import pandas as pd
> > >>
> > >>
> ~/anaconda3/envs/test/lib/python3.8/site-packages/iotbx/pdb/__init__.py
> > >> in <module>
> > >> 8
> > >> 9 import iotbx.pdb.records
> > >> ---> 10 import iotbx.pdb.hierarchy
> > >> 11 from scitbx import matrix
> > >> 12
> > >>
> > >>
> ~/anaconda3/envs/test/lib/python3.8/site-packages/iotbx/pdb/hierarchy.py
> > >> in <module>
> > >> 14 from six.moves import cStringIO as StringIO
> > >> 15 from iotbx.pdb import hy36encode, hy36decode
> > >> ---> 16 import iotbx.cif.model
> > >> 17 from cctbx import crystal
> > >> 18 from libtbx import group_args
> > >>
> > >>
> ~/anaconda3/envs/test/lib/python3.8/site-packages/iotbx/cif/__init__.py
> > >> in <module>
> > >> 19
> > >> 20 from cctbx.array_family import flex
> > >> ---> 21 from cctbx import miller
> > >> 22 from iotbx.cif import model, builders, geometry
> > >> 23 from libtbx.containers import OrderedDict
> > >>
> > >>
> ~/anaconda3/envs/test/lib/python3.8/site-packages/cctbx/miller/__init__.py
> > >> in <module>
> > >> 11
> > >> 12 from cctbx import crystal
> > >> ---> 13 from cctbx import maptbx
> > >> 14 from cctbx import sgtbx
> > >> 15 from cctbx.sgtbx import lattice_symmetry
> > >>
> > >>
> ~/anaconda3/envs/test/lib/python3.8/site-packages/cctbx/maptbx/__init__.py
> > >> in <module>
> > >> 15 from libtbx import adopt_init_args
> > >> 16 from libtbx.utils import Sorry
> > >> ---> 17 import libtbx.load_env
> > >> 18 import math
> > >> 19 import sys, os
> > >>
> > >> ~/anaconda3/envs/test/lib/python3.8/site-packages/libtbx/load_env.py
> in <module>
> > >> 3 import libtbx.env_config
> > >> 4 import os
> > >> ----> 5 libtbx.env = libtbx.env_config.unpickle()
> > >> 6 libtbx.env.set_os_environ_all_dist()
> > >> 7 libtbx.env.dispatcher_name =
> os.environ.get("LIBTBX_DISPATCHER_NAME")
> > >>
> > >> ~/anaconda3/envs/test/lib/python3.8/site-packages/libtbx/env_config.py
> > >> in unpickle()
> > >> 2736 env = pickle.load(libtbx_env)
> > >> 2737 if (env.python_version_major_minor != sys.version_info[:2]):
> > >> -> 2738 env.raise_python_version_incompatible()
> > >> 2739 if (op.realpath(build_path) !=
> op.realpath(abs(env.build_path))):
> > >> 2740 env.build_path.reset(build_path)
> > >>
> > >> ~/anaconda3/envs/test/lib/python3.8/site-packages/libtbx/env_config.py
> > >> in raise_python_version_incompatible(self, prev_pvmm)
> > >> 469 if (prev_pvmm is None):
> > >> 470 prev_pvmm = "%d.%d" % self.python_version_major_minor
> > >> --> 471 raise RuntimeError("Python version incompatible with this
> build:\n"
> > >> 472 + " Build directory: %s\n" %
> show_string(abs(self.build_path))
> > >> 473 + " Python version used initially: %s\n" % prev_pvmm
> > >>
> > >> RuntimeError: Python version incompatible with this build:
> > >> Build directory: "/home/gergely/anaconda3"
> > >> Python version used initially: 3.6
> > >> Python version in use now: 3.8
> > >>
> > >>
> > >> Interestingly in the base environment all import worked, but I got an
> error at:
> > >>
> > >>
> > >> ArgumentError Traceback (most recent call
> last)
> > >> <ipython-input-4-5bc71c36e121> in <module>
> > >> 33 atm_odd.set_b(0)
> > >> 34
> > >> ---> 35 odd.write_pdb_file("bdiff_in_even_000.pdb") #skriver ny pdb
> > >> med dessa inkluderade
> > >> 36 dfWBvals=pd.DataFrame(rows_list)
> > >>
> > >> ~/anaconda3/lib/python3.6/site-packages/iotbx/pdb/__init__.py in
> > >> write_pdb_file(self, file_name, open_append, crystal_symmetry,
> > >> cryst1_z, write_scale_records, append_end, atom_hetatm, sigatm,
> > >> anisou, siguij)
> > >> 930 siguij=True):
> > >> 931 if (crystal_symmetry is Auto):
> > >> --> 932 crystal_symmetry = self.crystal_symmetry()
> > >> 933 if (cryst1_z is Auto):
> > >> 934 cryst1_z = self.extract_cryst1_z_columns()
> > >>
> > >> ~/anaconda3/lib/python3.6/site-packages/iotbx/pdb/__init__.py in
> > >> crystal_symmetry(self, crystal_symmetry, weak_symmetry)
> > >> 1218 crystal_symmetry=None,
> > >> 1219 weak_symmetry=False):
> > >> -> 1220 self_symmetry = self.crystal_symmetry_from_cryst1()
> > >> 1221 if (self_symmetry is None):
> > >> 1222 self_symmetry =
> self._crystal_symmetry_from_cns_remark_sg()
> > >>
> > >> ~/anaconda3/lib/python3.6/site-packages/iotbx/pdb/__init__.py in
> > >> crystal_symmetry_from_cryst1(self)
> > >> 1195 for line in self.crystallographic_section():
> > >> 1196 if (line.startswith("CRYST1")):
> > >> -> 1197 return
> > >> cryst1_interpretation.crystal_symmetry(cryst1_record=line)
> > >> 1198 return None
> > >> 1199
> > >>
> > >>
> ~/anaconda3/lib/python3.6/site-packages/iotbx/pdb/cryst1_interpretation.py
> > >> in crystal_symmetry(cryst1_record)
> > >> 136 space_group_info=None)
> > >> 137 space_group_info =
> categorize(cryst1_record.sgroup).space_group_info(
> > >> --> 138 unit_cell=u)
> > >> 139 return crystal.symmetry(unit_cell=u,
> > >> space_group_info=space_group_info)
> > >>
> > >>
> ~/anaconda3/lib/python3.6/site-packages/iotbx/pdb/cryst1_interpretation.py
> > >> in space_group_info(self, unit_cell)
> > >> 85 if (self.symbol is None): return None
> > >> 86 if (self.category is None):
> > >> ---> 87 try: return sgtbx.space_group_info(self.symbol)
> > >> 88 except RuntimeError: return None
> > >> 89 if (isinstance(unit_cell, uctbx.ext.unit_cell)):
> > >>
> > >> ~/anaconda3/lib/python3.6/site-packages/cctbx/sgtbx/__init__.py in
> > >> __init__(self, symbol, table_id, group, number, space_group_t_den)
> > >> 100 assert group is None
> > >> 101 if (table_id is None):
> > >> --> 102 symbols = space_group_symbols(symbol)
> > >> 103 else:
> > >> 104 if (isinstance(symbol, int)): symbol = str(symbol)
> > >>
> > >> ArgumentError: Python argument types in
> > >> space_group_symbols.__init__(space_group_symbols, str)
> > >> did not match C++ signature:
> > >> __init__(_object*, int space_group_number)
> > >> __init__(_object*, int space_group_number,
> > >> std::__cxx11::basic_string<char, std::char_traits<char>,
> > >> std::allocator<char> > extension='')
> > >> __init__(_object*, int space_group_number,
> > >> std::__cxx11::basic_string<char, std::char_traits<char>,
> > >> std::allocator<char> > extension='', std::__cxx11::basic_string<char,
> > >> std::char_traits<char>, std::allocator<char> > table_id='')
> > >> __init__(_object*, std::__cxx11::basic_string<char,
> > >> std::char_traits<char>, std::allocator<char> > symbol)
> > >> __init__(_object*, std::__cxx11::basic_string<char,
> > >> std::char_traits<char>, std::allocator<char> > symbol,
> > >> std::__cxx11::basic_string<char, std::char_traits<char>,
> > >> std::allocator<char> > table_id='')
> > >>
> > >>
> > >> Gergely
> > >>
> > >>
> > >>
> > >> On Fri, Jan 3, 2020 at 1:44 PM Gergely Katona <gkatona at gmail.com>
> wrote:
> > >> >
> > >> > Dear Billy,
> > >> >
> > >> > I did some tests installing in my base conda was not troublefree in
> > >> > python 3.8. Running iotbx.fetch_pdb --all --mtz 1kp8 resulted in
> boost
> > >> > related error when converting to mtz. Installing into a test
> > >> > environment went fine with iotbx.fetch_pdb --all --mtz 1kp8 running
> > >> > successfully. I could add pymc3, jupyter and seaborn and iotbx still
> > >> > did not break. My LIBTBX_BUILD is not set however in the test
> > >> > environment, which breaks miller when I was trying to import it.
> > >> > Manually setting the LIBTBX_BUILD to CONDA_PREFIX (setenv
> LIBTBX_BUILD
> > >> > $CONDA_PREFIX) fixes this and one of my script works fine! I will
> come
> > >> > back if I find some problems with my other scripts, but so far this
> > >> > looks promising!
> > >> >
> > >> >
> > >> > Happy new year!
> > >> >
> > >> > Gergely
> > >> >
> > >> >
> > >> >
> > >> >
> > >> >
> > >> > On Fri, Dec 20, 2019 at 8:16 PM Billy Poon <BKPoon at lbl.gov> wrote:
> > >> > >
> > >> > > Hi everyone,
> > >> > >
> > >> > > I updated the conda packages on the cctbx-dev channel and there
> are also now packages for macOS. The old packages have been removed so you
> can create a new environment with
> > >> > >
> > >> > > conda create -n test -c cctbx-dev cctbx python=2.7
> > >> > > conda activate test
> > >> > >
> > >> > > where "test" is the environment name and 2.7 is the python
> version. For the python version, you can also pick 3.6, 3.7, or 3.8. I
> think the latest conda will install 3.8 as the default python if the python
> argument is not provided. Or install into an existing environment (with
> python already installed) with the same command as before,
> > >> > >
> > >> > > conda install -c cctbx-dev cctbx
> > >> > >
> > >> > > Again, your .condarc file should have conda-forge as the first
> channel so that dependencies can be pulled correctly.
> > >> > >
> > >> > > The dispatchers should work now and $LIBTBX_BUILD will be set on
> activation of an environment (and unset on environment deactivation) or
> after installing into an existing environment, so you can do more
> interesting things like
> > >> > >
> > >> > > iotbx.fetch_pdb --all --mtz 1kp8
> > >> > >
> > >> > > However, this package does not install databases, so
> > >> > >
> > >> > > molprobity.molprobity 1kp8.pdb 1kp8.mtz
> > >> > >
> > >> > > will fail because the database is not available (also probe and
> reduce are not built).
> > >> > >
> > >> > > Some known issues in no particular order,
> > >> > >
> > >> > > 1) You can run "libtbx.run_tests_parallel module=cctbx
> nproc=Auto" to run tests, but not all the test files were copied, so I got
> 30 failures here. The final package will probably not have the test files.
> > >> > > 2) The other python dispatchers, like "cctbx.python", were not
> updated, so those will fail. But you can just run "python" in the active
> environment.
> > >> > > 3) Parts of mmtbx still need to be updated for Python 3.
> > >> > > 4) The LIBTBX_BUILD variable should be set for sh and csh shells.
> Let me know if it's not working for your shell (i.e. "echo $LIBTBX_BUILD"
> should show the same thing as $CONDA_PREFIX).
> > >> > > 5) One future step is to enable building other CCTBX-like modules
> with this conda package. This will require some bookkeeping updates so that
> modules in the conda environment and the modules being built are tracked
> properly. Also, making sure that all the necessary headers exist in
> $PREFIX/include.
> > >> > >
> > >> > > Gergely, let me know if your scripts are working.
> > >> > >
> > >> > > Happy holidays!
> > >> > >
> > >> > > --
> > >> > > 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, Dec 18, 2019 at 11:25 AM Billy Poon <BKPoon at lbl.gov>
> wrote:
> > >> > >>
> > >> > >> Hi Gergely,
> > >> > >>
> > >> > >> That's the other information that hasn't been updated yet in the
> conda package. :)
> > >> > >>
> > >> > >> For LIBTBX_BUILD, I can set up environment variables sort of how
> the conda gcc package sets up environment variables. I have to double check
> to see if they're set after installation of the package and after
> activation of an environment. The variable will just be a copy of
> $CONDA_PREFIX.
> > >> > >>
> > >> > >> The libtbx_env file is a file that exists in $LIBTBX_BUILD that
> basically stores configuration information. I'll have to modify the
> contents to update the locations of the different modules since the conda
> package will not have a "modules" directory.
> > >> > >>
> > >> > >> --
> > >> > >> 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, Dec 18, 2019 at 2:08 AM Gergely Katona <
> gkatona at gmail.com> wrote:
> > >> > >>>
> > >> > >>> Hi Billy,
> > >> > >>>
> > >> > >>> Conda install went fine with your instructions after
> rearranging the
> > >> > >>> channels by putting cctbx last. I removed all environmental
> variables
> > >> > >>> and previous build of cctbx.
> > >> > >>>
> > >> > >>> import sys
> > >> > >>> print (sys.path, sys.prefix)
> > >> > >>>
> > >> > >>> ['/home/gergely/anaconda3/lib/python36.zip',
> > >> > >>> '/home/gergely/anaconda3/lib/python3.6',
> > >> > >>> '/home/gergely/anaconda3/lib/python3.6/lib-dynload', '',
> > >> > >>> '/home/gergely/anaconda3/lib/python3.6/site-packages',
> > >> > >>>
> '/home/gergely/anaconda3/lib/python3.6/site-packages/IPython/extensions',
> > >> > >>> '/home/gergely/.ipython'] /home/gergely/anaconda3
> > >> > >>>
> > >> > >>> Many imports went fine including pymc3, but I encountered
> problems
> > >> > >>> with these three:
> > >> > >>>
> > >> > >>> from cctbx import miller
> > >> > >>> import iotbx.pdb
> > >> > >>> from iotbx import reflection_file_reader, mtz
> > >> > >>>
> > >> > >>>
> > >> > >>> I also got type error when handling space groups.
> > >> > >>>
> > >> > >>>
> > >> > >>>
> > >> > >>>
> ---------------------------------------------------------------------------
> > >> > >>> KeyError Traceback (most
> recent call last)
> > >> > >>> <ipython-input-5-cedbd4f84f3d> in <module>
> > >> > >>> 25 from cctbx import uctbx
> > >> > >>> 26 from cctbx import sgtbx
> > >> > >>> ---> 27 from cctbx import miller
> > >> > >>> 28 #from iotbx import reflection_file_reader, mtz
> > >> > >>> 29 sns.set_context("poster")
> > >> > >>>
> > >> > >>>
> ~/anaconda3/lib/python3.6/site-packages/cctbx/miller/__init__.py in <module>
> > >> > >>> 11
> > >> > >>> 12 from cctbx import crystal
> > >> > >>> ---> 13 from cctbx import maptbx
> > >> > >>> 14 from cctbx import sgtbx
> > >> > >>> 15 from cctbx.sgtbx import lattice_symmetry
> > >> > >>>
> > >> > >>>
> ~/anaconda3/lib/python3.6/site-packages/cctbx/maptbx/__init__.py in <module>
> > >> > >>> 15 from libtbx import adopt_init_args
> > >> > >>> 16 from libtbx.utils import Sorry
> > >> > >>> ---> 17 import libtbx.load_env
> > >> > >>> 18 import math
> > >> > >>> 19 import sys, os
> > >> > >>>
> > >> > >>> ~/anaconda3/lib/python3.6/site-packages/libtbx/load_env.py in
> <module>
> > >> > >>> 3 import libtbx.env_config
> > >> > >>> 4 import os
> > >> > >>> ----> 5 libtbx.env = libtbx.env_config.unpickle()
> > >> > >>> 6 libtbx.env.set_os_environ_all_dist()
> > >> > >>> 7 libtbx.env.dispatcher_name =
> os.environ.get("LIBTBX_DISPATCHER_NAME")
> > >> > >>>
> > >> > >>> ~/anaconda3/lib/python3.6/site-packages/libtbx/env_config.py in
> unpickle()
> > >> > >>> 2603
> > >> > >>> 2604 def unpickle():
> > >> > >>> -> 2605 build_path = os.environ["LIBTBX_BUILD"]
> > >> > >>> 2606
> set_preferred_sys_prefix_and_sys_executable(build_path=build_path)
> > >> > >>> 2607 libtbx_env = open(op.join(build_path, "libtbx_env"),
> "rb")
> > >> > >>>
> > >> > >>> ~/anaconda3/lib/python3.6/os.py in __getitem__(self, key)
> > >> > >>> 667 except KeyError:
> > >> > >>> 668 # raise KeyError with the original key value
> > >> > >>> --> 669 raise KeyError(key) from None
> > >> > >>> 670 return self.decodevalue(value)
> > >> > >>> 671
> > >> > >>>
> > >> > >>> KeyError: 'LIBTBX_BUILD'
> > >> > >>>
> > >> > >>>
> > >> > >>>
> > >> > >>>
> ---------------------------------------------------------------------------
> > >> > >>> ArgumentError Traceback (most
> recent call last)
> > >> > >>> <ipython-input-7-2acd3a9ce26a> in <module>
> > >> > >>> 26 return
> ms,msnam,mscent,msacent,msnamacent,msnamcent,msnamacent_dstar
> > >> > >>> 27
> > >> > >>> ---> 28
> ms,msnam,mscent,msacent,msnamacent,msnamcent,msnamacent_dstar=initializecrystal()
> > >> > >>>
> > >> > >>> <ipython-input-7-2acd3a9ce26a> in initializecrystal()
> > >> > >>> 11 uc = uctbx.unit_cell(unit_cell)
> > >> > >>> 12 wavelength = 1.54980
> > >> > >>> ---> 13 xtal_symm = crystal.symmetry(unit_cell=unit_cell,
> > >> > >>> space_group_symbol="P 43 21 2")
> > >> > >>> 14
> > >> > >>> 15 ms =
> > >> > >>> miller.build_set(crystal_symmetry=xtal_symm,anomalous_flag=True,
> > >> > >>> d_min=1.61)
> > >> > >>>
> > >> > >>>
> ~/anaconda3/lib/python3.6/site-packages/cctbx/crystal/__init__.py in
> > >> > >>> __init__(self, unit_cell, space_group_symbol, space_group_info,
> > >> > >>> space_group, correct_rhombohedral_setting_if_necessary,
> > >> > >>> assert_is_compatible_unit_cell,
> raise_sorry_if_incompatible_unit_cell,
> > >> > >>> force_compatible_unit_cell)
> > >> > >>> 74 if (space_group_symbol is not None):
> > >> > >>> 75 self._space_group_info = sgtbx.space_group_info(
> > >> > >>> ---> 76 symbol=space_group_symbol)
> > >> > >>> 77 elif (space_group is not None):
> > >> > >>> 78 if (isinstance(space_group, sgtbx.space_group)):
> > >> > >>>
> > >> > >>> ~/anaconda3/lib/python3.6/site-packages/cctbx/sgtbx/__init__.py
> in
> > >> > >>> __init__(self, symbol, table_id, group, number,
> space_group_t_den)
> > >> > >>> 100 assert group is None
> > >> > >>> 101 if (table_id is None):
> > >> > >>> --> 102 symbols = space_group_symbols(symbol)
> > >> > >>> 103 else:
> > >> > >>> 104 if (isinstance(symbol, int)): symbol =
> str(symbol)
> > >> > >>>
> > >> > >>> ArgumentError: Python argument types in
> > >> > >>> space_group_symbols.__init__(space_group_symbols, str)
> > >> > >>> did not match C++ signature:
> > >> > >>> __init__(_object*, int space_group_number)
> > >> > >>> __init__(_object*, int space_group_number,
> > >> > >>> std::__cxx11::basic_string<char, std::char_traits<char>,
> > >> > >>> std::allocator<char> > extension='')
> > >> > >>> __init__(_object*, int space_group_number,
> > >> > >>> std::__cxx11::basic_string<char, std::char_traits<char>,
> > >> > >>> std::allocator<char> > extension='',
> std::__cxx11::basic_string<char,
> > >> > >>> std::char_traits<char>, std::allocator<char> > table_id='')
> > >> > >>> __init__(_object*, std::__cxx11::basic_string<char,
> > >> > >>> std::char_traits<char>, std::allocator<char> > symbol)
> > >> > >>> __init__(_object*, std::__cxx11::basic_string<char,
> > >> > >>> std::char_traits<char>, std::allocator<char> > symbol,
> > >> > >>> std::__cxx11::basic_string<char, std::char_traits<char>,
> > >> > >>> std::allocator<char> > table_id='')
> > >> > >>>
> > >> > >>>
> > >> > >>> When I tried to set LIBTBX_BUILD to /home/gergely/anaconda3
> (this is
> > >> > >>> sys.prefix on my system), I got other problems when importing.
> Can
> > >> > >>> LIBTBX_BUILD be set in the conda package?
> > >> > >>>
> > >> > >>>
> > >> > >>>
> > >> > >>>
> ---------------------------------------------------------------------------
> > >> > >>> FileNotFoundError Traceback (most
> recent call last)
> > >> > >>> <ipython-input-1-7e2b144826cc> in <module>
> > >> > >>> 26 from cctbx import sgtbx
> > >> > >>> 27 #from cctbx import miller
> > >> > >>> ---> 28 from iotbx import reflection_file_reader, mtz
> > >> > >>> 29 sns.set_context("poster")
> > >> > >>> 30 plt.rcParams.update({'figure.autolayout': True})
> > >> > >>>
> > >> > >>>
> ~/anaconda3/lib/python3.6/site-packages/iotbx/reflection_file_reader.py
> > >> > >>> in <module>
> > >> > >>> 53
> > >> > >>> 54 from __future__ import absolute_import, division,
> print_function
> > >> > >>> ---> 55 from iotbx import mtz
> > >> > >>> 56 from iotbx.scalepack import merge as scalepack_merge
> > >> > >>> 57 from iotbx.scalepack import no_merge_original_index as
> > >> > >>> scalepack_no_merge
> > >> > >>>
> > >> > >>> ~/anaconda3/lib/python3.6/site-packages/iotbx/mtz/__init__.py
> in <module>
> > >> > >>> 9 import iotbx_mtz_ext as ext
> > >> > >>> 10
> > >> > >>> ---> 11 from iotbx.mtz import extract_from_symmetry_lib
> > >> > >>> 12 from cctbx import xray
> > >> > >>> 13 import cctbx.xray.observation_types
> > >> > >>>
> > >> > >>>
> ~/anaconda3/lib/python3.6/site-packages/iotbx/mtz/extract_from_symmetry_lib.py
> > >> > >>> in <module>
> > >> > >>> 1 from __future__ import absolute_import, division,
> print_function
> > >> > >>> 2 from cctbx import sgtbx
> > >> > >>> ----> 3 import libtbx.load_env
> > >> > >>> 4 import os.path as op
> > >> > >>> 5 from six.moves import range
> > >> > >>>
> > >> > >>> ~/anaconda3/lib/python3.6/site-packages/libtbx/load_env.py in
> <module>
> > >> > >>> 3 import libtbx.env_config
> > >> > >>> 4 import os
> > >> > >>> ----> 5 libtbx.env = libtbx.env_config.unpickle()
> > >> > >>> 6 libtbx.env.set_os_environ_all_dist()
> > >> > >>> 7 libtbx.env.dispatcher_name =
> os.environ.get("LIBTBX_DISPATCHER_NAME")
> > >> > >>>
> > >> > >>> ~/anaconda3/lib/python3.6/site-packages/libtbx/env_config.py in
> unpickle()
> > >> > >>> 2605 build_path = os.environ["LIBTBX_BUILD"]
> > >> > >>> 2606
> set_preferred_sys_prefix_and_sys_executable(build_path=build_path)
> > >> > >>> -> 2607 libtbx_env = open(op.join(build_path, "libtbx_env"),
> "rb")
> > >> > >>> 2608 env = pickle.load(libtbx_env)
> > >> > >>> 2609 if (env.python_version_major_minor !=
> sys.version_info[:2]):
> > >> > >>>
> > >> > >>> FileNotFoundError: [Errno 2] No such file or directory:
> > >> > >>> '/home/gergely/anaconda3/libtbx_env'
> > >> > >>>
> > >> > >>> On Wed, Dec 18, 2019 at 9:10 AM Billy Poon <BKPoon at lbl.gov>
> wrote:
> > >> > >>> >
> > >> > >>> > Hi Gergely,
> > >> > >>> >
> > >> > >>> > I've uploaded linux packages to a new channel, cctbx-dev, and
> you can install it with
> > >> > >>> >
> > >> > >>> > conda install -c cctbx-dev cctbx
> > >> > >>> >
> > >> > >>> > in your current environment. You should set your ~/.condarc
> file to pull the other dependencies from the conda-forge channel first, so
> put conda-forge above cctbx. Mine looks like
> > >> > >>> >
> > >> > >>> > channels:
> > >> > >>> > - conda-forge
> > >> > >>> > - defaults
> > >> > >>> > - cctbx
> > >> > >>> >
> > >> > >>> > Do you need dxtbx for your scripts? This package does not
> build that part. I think the plan is to build a separate conda package for
> dxtbx so that it can be updated more frequently. I can rebuild the packages
> to include it for testing, but the one being submitted to conda-forge will
> not have it.
> > >> > >>> >
> > >> > >>> > Also, your error message is probably due to version of HDF5
> that the development build installs. The bootstrap.py script will install
> 1.10.4, but your other dependency is looking for 1.10.5. Installing this
> cctbx conda package should install 1.10.5, which should fix the issue.
> Also, I'm updating those environments and 1.10.5 will be the new default
> version.
> > >> > >>> >
> > >> > >>> > Lastly, the dispatchers will not work in these packages
> because the old paths during the build process are still in them and many
> of them expect some additional information that has not been updated in the
> packages yet. I'm in the process of doing that and will update the
> cctbx-dev channel when that's done. However, by starting python, you can
> import cctbx modules. So you can run commands like
> > >> > >>> >
> > >> > >>> > from scitbx.array_family import flex
> > >> > >>> > a = flex.random_double(1000000)
> > >> > >>> > b = flex.min_max_mean_double(a)
> > >> > >>> > b.min
> > >> > >>> > b.max
> > >> > >>> > b.mean
> > >> > >>> >
> > >> > >>> > 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://phenix-online.org
> > >> > >>> >
> > >> > >>> >
> > >> > >>> > On Tue, Dec 17, 2019 at 5:39 AM Gergely Katona <
> gkatona at gmail.com> wrote:
> > >> > >>> >>
> > >> > >>> >> Dear Billy,
> > >> > >>> >>
> > >> > >>> >> Thank you for the detailed explanation, I look forward to do
> further
> > >> > >>> >> testing! I aim to pool all modules under the same
> environment, if
> > >> > >>> >> there are conflicts then I just try to reshuffle the order
> of imports.
> > >> > >>> >> So far this did not cause problems for me even when I was
> using system
> > >> > >>> >> python, but of course it is not the most prudent thing to
> do. With
> > >> > >>> >> anaconda everything is much more standardized and isolated
> already and
> > >> > >>> >> without being superuser I can have my familiar environment
> at any
> > >> > >>> >> synchrotron based cluster. It is great that cctbx will be an
> integral
> > >> > >>> >> part of this ecosystem and this was also the last thing
> holding me
> > >> > >>> >> back from adopting python3. About hdf5, pymc3 requires it and
> > >> > >>> >> importing causes a kernel restart with the following error
> messages,
> > >> > >>> >> curiously if I import h5py first this can be avoided.
> > >> > >>> >>
> > >> > >>> >> Best wishes,
> > >> > >>> >>
> > >> > >>> >> Gergely
> > >> > >>> >>
> > >> > >>> >> import pymc3 as pm
> > >> > >>> >>
> > >> > >>> >> Warning! ***HDF5 library version mismatched error***
> > >> > >>> >> The HDF5 header files used to compile this application do
> not match
> > >> > >>> >> the version used by the HDF5 library to which this
> application is linked.
> > >> > >>> >> Data corruption or segmentation faults may occur if the
> application continues.
> > >> > >>> >> This can happen when an application was compiled by one
> version of HDF5 but
> > >> > >>> >> linked with a different version of static or shared HDF5
> library.
> > >> > >>> >> You should recompile the application or check your shared
> library related
> > >> > >>> >> settings such as 'LD_LIBRARY_PATH'.
> > >> > >>> >> You can, at your own risk, disable this warning by setting
> the environment
> > >> > >>> >> variable 'HDF5_DISABLE_VERSION_CHECK' to a value of '1'.
> > >> > >>> >> Setting it to 2 or higher will suppress the warning messages
> totally.
> > >> > >>> >> Headers are 1.10.4, library is 1.10.5
> > >> > >>> >> SUMMARY OF THE HDF5 CONFIGURATION
> > >> > >>> >> =================================
> > >> > >>> >>
> > >> > >>> >> General Information:
> > >> > >>> >> -------------------
> > >> > >>> >> HDF5 Version: 1.10.5
> > >> > >>> >> Configured on: Tue Oct 22 12:02:13 UTC 2019
> > >> > >>> >> Configured by: conda at 16247e67ecd5
> > >> > >>> >> Host system: x86_64-conda_cos6-linux-gnu
> > >> > >>> >> Uname information: Linux 16247e67ecd5
> 4.15.0-1059-azure
> > >> > >>> >> #64-Ubuntu SMP Fri Sep 13 17:02:44 UTC 2019 x86_64 x86_64
> x86_64
> > >> > >>> >> GNU/Linux
> > >> > >>> >> Byte sex: little-endian
> > >> > >>> >> Installation point: /home/gergely/anaconda3
> > >> > >>> >>
> > >> > >>> >> Compiling Options:
> > >> > >>> >> ------------------
> > >> > >>> >> Build Mode: production
> > >> > >>> >> Debugging Symbols: no
> > >> > >>> >> Asserts: no
> > >> > >>> >> Profiling: no
> > >> > >>> >> Optimization Level: high
> > >> > >>> >>
> > >> > >>> >> Linking Options:
> > >> > >>> >> ----------------
> > >> > >>> >> Libraries: static, shared
> > >> > >>> >> Statically Linked Executables:
> > >> > >>> >> LDFLAGS: -Wl,-O2 -Wl,--sort-common
> > >> > >>> >> -Wl,--as-needed -Wl,-z,relro -Wl,-z,now
> -Wl,--disable-new-dtags
> > >> > >>> >> -Wl,--gc-sections -Wl,-rpath,/home/gergely/anaconda3/lib
> > >> > >>> >> -Wl,-rpath-link,/home/gergely/anaconda3/lib
> > >> > >>> >> -L/home/gergely/anaconda3/lib
> > >> > >>> >> H5_LDFLAGS:
> > >> > >>> >> AM_LDFLAGS:
> -L/home/gergely/anaconda3/lib
> > >> > >>> >> Extra libraries: -lrt -lpthread -lz -ldl -lm
> > >> > >>> >> Archiver:
> > >> > >>> >>
> /home/conda/feedstock_root/build_artifacts/hdf5_split_1571745596770/_build_env/bin/x86_64-conda_cos6-linux-gnu-ar
> > >> > >>> >> AR_FLAGS: cr
> > >> > >>> >> Ranlib:
> > >> > >>> >>
> /home/conda/feedstock_root/build_artifacts/hdf5_split_1571745596770/_build_env/bin/x86_64-conda_cos6-linux-gnu-ranlib
> > >> > >>> >>
> > >> > >>> >> Languages:
> > >> > >>> >> ----------
> > >> > >>> >> C: yes
> > >> > >>> >> C Compiler:
> > >> > >>> >>
> /home/conda/feedstock_root/build_artifacts/hdf5_split_1571745596770/_build_env/bin/x86_64-conda_cos6-linux-gnu-cc
> > >> > >>> >> CPPFLAGS: -DNDEBUG
> -D_FORTIFY_SOURCE=2 -O2
> > >> > >>> >> -I/home/gergely/anaconda3/include
> > >> > >>> >> H5_CPPFLAGS: -D_GNU_SOURCE
> > >> > >>> >> -D_POSIX_C_SOURCE=200809L -DNDEBUG -UH5_DEBUG_API
> > >> > >>> >> AM_CPPFLAGS:
> -I/home/gergely/anaconda3/include
> > >> > >>> >> C Flags: -march=nocona -mtune=haswell
> > >> > >>> >> -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2
> > >> > >>> >> -ffunction-sections -pipe -I/home/gergely/anaconda3/include
> > >> > >>> >>
> -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/hdf5_split_1571745596770/work=/usr/local/src/conda/hdf5_split-1.10.5
> > >> > >>> >>
> -fdebug-prefix-map=/home/gergely/anaconda3=/usr/local/src/conda-prefix
> > >> > >>> >> H5 C Flags: -std=c99 -pedantic -Wall
> -Wextra
> > >> > >>> >> -Wbad-function-cast -Wc++-compat -Wcast-align -Wcast-qual
> -Wconversion
> > >> > >>> >> -Wdeclaration-after-statement -Wdisabled-optimization
> -Wfloat-equal
> > >> > >>> >> -Wformat=2 -Winit-self -Winvalid-pch -Wmissing-declarations
> > >> > >>> >> -Wmissing-include-dirs -Wmissing-prototypes -Wnested-externs
> > >> > >>> >> -Wold-style-definition -Wpacked -Wpointer-arith
> -Wredundant-decls
> > >> > >>> >> -Wshadow -Wstrict-prototypes -Wswitch-default -Wswitch-enum
> -Wundef
> > >> > >>> >> -Wunused-macros -Wunsafe-loop-optimizations -Wwrite-strings
> > >> > >>> >> -finline-functions -s -Wno-inline -Wno-aggregate-return
> > >> > >>> >> -Wno-missing-format-attribute -Wno-missing-noreturn -O
> > >> > >>> >> AM C Flags:
> > >> > >>> >> Shared C Library: yes
> > >> > >>> >> Static C Library: yes
> > >> > >>> >>
> > >> > >>> >>
> > >> > >>> >> Fortran: yes
> > >> > >>> >> Fortran Compiler:
> > >> > >>> >>
> /home/conda/feedstock_root/build_artifacts/hdf5_split_1571745596770/_build_env/bin/x86_64-conda_cos6-linux-gnu-gfortran
> > >> > >>> >> Fortran Flags:
> > >> > >>> >> H5 Fortran Flags: -pedantic -Wall -Wextra
> -Wunderflow
> > >> > >>> >> -Wimplicit-interface -Wsurprising -Wno-c-binding-type -s -O2
> > >> > >>> >> AM Fortran Flags:
> > >> > >>> >> Shared Fortran Library: yes
> > >> > >>> >> Static Fortran Library: yes
> > >> > >>> >>
> > >> > >>> >> C++: yes
> > >> > >>> >> C++ Compiler:
> > >> > >>> >>
> /home/conda/feedstock_root/build_artifacts/hdf5_split_1571745596770/_build_env/bin/x86_64-conda_cos6-linux-gnu-c++
> > >> > >>> >> C++ Flags: -fvisibility-inlines-hidden
> > >> > >>> >> -std=c++17 -fmessage-length=0 -march=nocona -mtune=haswell
> > >> > >>> >> -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2
> > >> > >>> >> -ffunction-sections -pipe -I/home/gergely/anaconda3/include
> > >> > >>> >>
> -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/hdf5_split_1571745596770/work=/usr/local/src/conda/hdf5_split-1.10.5
> > >> > >>> >>
> -fdebug-prefix-map=/home/gergely/anaconda3=/usr/local/src/conda-prefix
> > >> > >>> >> H5 C++ Flags: -pedantic -Wall -W
> -Wundef -Wshadow
> > >> > >>> >> -Wpointer-arith -Wcast-qual -Wcast-align -Wwrite-strings
> -Wconversion
> > >> > >>> >> -Wredundant-decls -Winline -Wsign-promo -Woverloaded-virtual
> > >> > >>> >> -Wold-style-cast -Weffc++ -Wreorder -Wnon-virtual-dtor
> > >> > >>> >> -Wctor-dtor-privacy -Wabi -finline-functions -s -O
> > >> > >>> >> AM C++ Flags:
> > >> > >>> >> Shared C++ Library: yes
> > >> > >>> >> Static C++ Library: yes
> > >> > >>> >>
> > >> > >>> >> Java: no
> > >> > >>> >>
> > >> > >>> >>
> > >> > >>> >> Features:
> > >> > >>> >> ---------
> > >> > >>> >> Parallel HDF5: no
> > >> > >>> >> Parallel Filtered Dataset Writes: no
> > >> > >>> >> Large Parallel I/O: no
> > >> > >>> >> High-level library: yes
> > >> > >>> >> Threadsafety: yes
> > >> > >>> >> Default API mapping: v110
> > >> > >>> >> With deprecated public symbols: yes
> > >> > >>> >> I/O filters (external): deflate(zlib)
> > >> > >>> >> MPE: no
> > >> > >>> >> Direct VFD: no
> > >> > >>> >> dmalloc: no
> > >> > >>> >> Packages w/ extra debug output: none
> > >> > >>> >> API tracing: no
> > >> > >>> >> Using memory checker: yes
> > >> > >>> >> Memory allocation sanity checks: no
> > >> > >>> >> Function stack tracing: no
> > >> > >>> >> Strict file format checks: no
> > >> > >>> >> Optimization instrumentation: no
> > >> > >>> >>
> > >> > >>> >> On Tue, Dec 17, 2019 at 8:35 AM Billy Poon <BKPoon at lbl.gov>
> wrote:
> > >> > >>> >> >
> > >> > >>> >> > Hi Gergely,
> > >> > >>> >> >
> > >> > >>> >> > Let me build the test package tomorrow. All the gritty
> details for building with conda is being finalized and the official
> documentation will be updated to describe the steps. It would be too
> confusing to keep changing the documentation as the process evolves. You do
> have the general process, though, which is summarized as follows.
> > >> > >>> >> >
> > >> > >>> >> > 1) Installing dependencies. The cctbx_dependencies
> metapackage was an initial approach for managing the CCTBX dependencies,
> but after contacting the conda-forge folks, they recommended using the
> --only-deps flag. So when the CCTBX conda package is available, you'll be
> able to get a set of dependencies with,
> > >> > >>> >> >
> > >> > >>> >> > conda install -c conda-forge --only-deps cctbx
> > >> > >>> >> >
> > >> > >>> >> > By default, the bootstrap.py file will automatically
> install a set of dependencies in the "conda_base" directory (and a conda
> installation if one is not found). It just uses standard conda environment
> files located in libtbx/auto_build/conda_envs, so you do not need to
> install cctbx_dependencies as a separate step. The environment files avoid
> channel issues by explicitly defining the channel to pull the packages from
> and the cctbx channel just stores copies of packages from conda-forge.
> There were issues earlier where the conda-forge packages would sometimes be
> moved to a different label. The --use-conda flag also accepts a path to
> $CONDA_PREFIX if you want to use a specific environment for testing.
> > >> > >>> >> >
> > >> > >>> >> > 2) Building. The bootstrap.py file handles that with SCons.
> > >> > >>> >> >
> > >> > >>> >> > 3) Running. After building, there should be a setpaths.sh
> (and .csh) file that adds build/bin to your path. The build/bin directory
> has our dispatchers, which are just scripts that set up the environment
> variables for you. This prevents other programs from loading our libraries,
> whose versions may conflict. You should see that there is a "python"
> dispatcher, which is a convenience for developers. Otherwise, you can use
> libtbx.python, which will be able to import CCTBX modules.
> > >> > >>> >> >
> > >> > >>> >> > The running part is where the conda package for CCTBX will
> be different than this build. Since our Python files and extensions modules
> will be in the "site-packages" directory for Python, the PYTHONPATH
> variable will not be needed (and conda suggests that that variable not be
> set). The other CCTBX libraries will be in $CONDA_PREFIX/lib, so
> LD_LIBRARY_PATH is not needed. In an active environment, PATH will already
> be modified. And then our LIBTBX_BUILD directory can be set to sys.prefix.
> > >> > >>> >> >
> > >> > >>> >> > So with the conda package, you would only need to activate
> your conda environment and CCTBX should integrate with other conda
> packages. What is the conflict with hdf5? That's something that should be
> fixed. 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://phenix-online.org
> > >> > >>> >> >
> > >> > >>> >> >
> > >> > >>> >> > On Mon, Dec 16, 2019 at 2:53 AM Gergely Katona <
> gkatona at gmail.com> wrote:
> > >> > >>> >> >>
> > >> > >>> >> >> Dear Billy,
> > >> > >>> >> >>
> > >> > >>> >> >> Thank you for this update and for your efforts! I found a
> solution and
> > >> > >>> >> >> indeed most things already work in anaconda3. The steps I
> took (even
> > >> > >>> >> >> if these instructions will have short expiry date):
> > >> > >>> >> >>
> > >> > >>> >> >> Modified .condarc with:
> > >> > >>> >> >> channels:
> > >> > >>> >> >> - cctbx
> > >> > >>> >> >> - conda-forge
> > >> > >>> >> >> - defaults
> > >> > >>> >> >>
> > >> > >>> >> >> run
> > >> > >>> >> >> conda conda install cctbx_dependencies python=3.6
> > >> > >>> >> >>
> > >> > >>> >> >> I expect this will work without python=3.6 in the near
> future.
> > >> > >>> >> >>
> > >> > >>> >> >> Then compiling cctbx with anaconda3 python went without
> any problem
> > >> > >>> >> >> when using these flags:
> > >> > >>> >> >> python bootstrap.py --use-conda --python3 --nproc=12
> > >> > >>> >> >>
> > >> > >>> >> >> Then I probably did the unorthodox thing and sourced
> these directories:
> > >> > >>> >> >>
> > >> > >>> >> >> setenv LIBTBX_BUILD /home/gergely/cctbx/build
> > >> > >>> >> >> setenv PATH ${PATH}:/home/gergely/cctbx/build/bin
> > >> > >>> >> >> setenv PYTHONPATH
> > >> > >>> >> >>
> /home/gergely/cctbx/modules/cctbx_project:/home/gergely/cctbx/modules:/home/gergely/cctbx/modules/cctbx_project/boost_adaptbx:/home/gergely/cctbx/build/lib:/home/gergely/cctbx/conda_base/lib/python3.6/site-packages:$PYTHONPATH
> > >> > >>> >> >> setenv LD_LIBRARY_PATH
> > >> > >>> >> >>
> /home/gergely/cctbx/conda_base/lib:/home/gergely/cctbx/build/lib:$LD_LIBRARY_PATH
> > >> > >>> >> >>
> > >> > >>> >> >> There is probably a better way to put this into conda
> environment.
> > >> > >>> >> >> With these steps I could run one of my scripts depending
> on cctbx. The
> > >> > >>> >> >> only problem I found is that hdf5 library had conflict
> with another
> > >> > >>> >> >> package in conda, but I does not find this as a
> showstopper.
> > >> > >>> >> >>
> > >> > >>> >> >> Best wishes,
> > >> > >>> >> >>
> > >> > >>> >> >> Gergely
> > >> > >>> >> >>
> > >> > >>> >> >>
> > >> > >>> >> >>
> > >> > >>> >> >>
> > >> > >>> >> >>
> > >> > >>> >> >>
> > >> > >>> >> >> On Fri, Dec 13, 2019 at 7:23 PM Billy Poon <
> BKPoon at lbl.gov> wrote:
> > >> > >>> >> >> >
> > >> > >>> >> >> > Hi Gergely,
> > >> > >>> >> >> >
> > >> > >>> >> >> > It's still a work in progress. I'm sorting out some
> Windows issues right now. I can probably build a test package on a separate
> channel for people that want to test it (let's say next week?). I'll
> provide instructions, but basically, the test conda package will be in its
> own separate channel and the dependencies will be pulled from the
> conda-forge channel. I want most things to be working correctly on Python
> 2.7, 3.6, 3.7, and 3.8 on all 3 platforms.
> > >> > >>> >> >> >
> > >> > >>> >> >> > 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://phenix-online.org
> > >> > >>> >> >> >
> > >> > >>> >> >> >
> > >> > >>> >> >> > On Fri, Dec 13, 2019 at 5:44 AM Gergely Katona <
> gkatona at gmail.com> wrote:
> > >> > >>> >> >> >>
> > >> > >>> >> >> >> Dear Billy,
> > >> > >>> >> >> >>
> > >> > >>> >> >> >> This sounds very promising and exciting. I am not sure
> if cctbx is
> > >> > >>> >> >> >> already functional as a conda package in anaconda3
> (Linux) or this is
> > >> > >>> >> >> >> still work in progress. My technical expertise does
> not allow me to
> > >> > >>> >> >> >> tell the difference. What I tried:
> > >> > >>> >> >> >>
> > >> > >>> >> >> >> Fresh install of anaconda3. Adding - cctbx and -
> conda-forge to
> > >> > >>> >> >> >> .condarc . Installing pyside2 with conda. Running
> conda install
> > >> > >>> >> >> >> conda_dependencies . I get a lot package version
> conflict, and I
> > >> > >>> >> >> >> cannot import cctbx or iotbx to anaconda python. Am I
> following the
> > >> > >>> >> >> >> right instructions? Or it is too early to expect that
> cctbx works when
> > >> > >>> >> >> >> installed through conda?
> > >> > >>> >> >> >>
> > >> > >>> >> >> >> Best wishes,
> > >> > >>> >> >> >>
> > >> > >>> >> >> >> Gergely
> > >> > >>> >> >> >>
> > >> > >>> >> >> >> On Wed, Nov 27, 2019 at 3:56 PM Billy Poon <
> BKPoon at lbl.gov> wrote:
> > >> > >>> >> >> >> >
> > >> > >>> >> >> >> > Hi all,
> > >> > >>> >> >> >> >
> > >> > >>> >> >> >> > For a brief update, I have submitted a recipe for
> cctbxlite to conda-forge (
> https://github.com/conda-forge/staged-recipes/pull/10021) and support for
> Python 3.7 and 3.8 is being added (
> https://github.com/cctbx/cctbx_project/pull/409). With some fixes for
> Windows (https://github.com/cctbx/cctbx_project/pull/416), all platforms
> (macOS, linux, and Windows) can build for Python 2.7, 3.6, 3.7, and 3.8.
> Some additional changes will be needed to get Windows to work with Python 3
> and for tests to pass with Boost 1.70.0. That will enable the conda-forge
> recipe to build for all platforms and for all supported versions of Python.
> > >> > >>> >> >> >> >
> > >> > >>> >> >> >> > Currently, the conda-forge recipe will install into
> the conda python and cctbx imports can be done without sourcing the
> environment scripts. It looks like a lot of the environment variables being
> set in the dispatchers can be removed since the Python files and C++
> extensions are in the right places. I'll update the libtbx_env file so that
> commands that load the environment can work correctly.
> > >> > >>> >> >> >> >
> > >> > >>> >> >> >> > --
> > >> > >>> >> >> >> > 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 Sun, Aug 25, 2019 at 2:33 PM Tristan Croll <
> tic20 at cam.ac.uk> wrote:
> > >> > >>> >> >> >> >>
> > >> > >>> >> >> >> >> Hi Luc,
> > >> > >>> >> >> >> >>
> > >> > >>> >> >> >> >> That sounds promising. From there, I’d need to work
> out how to make a fully-packaged installer (basically a modified wheel
> file) for the ChimeraX ToolShed - the aim is for the end user to not have
> to worry about any of this. That adds a couple of complications - e.g.
> $LIBTBX_BUILD would need to be set dynamically before first import - but
> doesn’t seem insurmountable.
> > >> > >>> >> >> >> >>
> > >> > >>> >> >> >> >> Thanks,
> > >> > >>> >> >> >> >>
> > >> > >>> >> >> >> >> Tristan
> > >> > >>> >> >> >> >>
> > >> > >>> >> >> >> >>
> > >> > >>> >> >> >> >>
> > >> > >>> >> >> >> >> Tristan Croll
> > >> > >>> >> >> >> >> Research Fellow
> > >> > >>> >> >> >> >> Cambridge Institute for Medical Research
> > >> > >>> >> >> >> >> University of Cambridge CB2 0XY
> > >> > >>> >> >> >> >>
> > >> > >>> >> >> >> >>
> > >> > >>> >> >> >> >>
> > >> > >>> >> >> >> >>
> > >> > >>> >> >> >> >> > On 25 Aug 2019, at 18:31, Luc Bourhis <
> luc_j_bourhis at mac.com> wrote:
> > >> > >>> >> >> >> >> >
> > >> > >>> >> >> >> >> > Hi Tristan,
> > >> > >>> >> >> >> >> >
> > >> > >>> >> >> >> >> > cctbx could be built to use your ChimeraX python,
> now that cctbx is moving to Python 3. The option —with-python is there for
> that with the bootstrap script. The specific environment setup boil down to
> setting two environment variable LIBTBX_BUILD and either LD_LIBRARY_PATH on
> Linux, PATH on Win32, or DYLIB_LIBRARY_PATH on MacOS. If you work within a
> framework such as ChimeraX, that should not be difficult to ensure those
> two variables are set.
> > >> > >>> >> >> >> >> >
> > >> > >>> >> >> >> >> > Best wishes,
> > >> > >>> >> >> >> >> >
> > >> > >>> >> >> >> >> > Luc
> > >> > >>> >> >> >> >> >
> > >> > >>> >> >> >> >> >
> > >> > >>> >> >> >> >> >> On 23 Aug 2019, at 19:02, Tristan Croll <
> tic20 at cam.ac.uk> wrote:
> > >> > >>> >> >> >> >> >>
> > >> > >>> >> >> >> >> >> To add my two cents on this: probably the
> second-most common question I've had about ISOLDE's implementation is, "why
> didn't you use CCTBX?". The honest answer to that is, "I didn't know how."
> > >> > >>> >> >> >> >> >>
> > >> > >>> >> >> >> >> >> Still don't, really - although the current
> developments are rather promising. The problem I've faced is that CCTBX was
> designed as its own self-contained Python (2.7, until very recently)
> environment, with its own interpreter and a lot of very specific
> environment setup. Meanwhile I'm developing ISOLDE in ChimeraX, which is
> *also* its own self-contained Python (3.7) environment. To plug one into
> the other in that form... well, I don't think I'm a good enough programmer
> to really know where to start.
> > >> > >>> >> >> >> >> >>
> > >> > >>> >> >> >> >> >> The move to Conda and a more modular CCTBX
> architecture should make a lot more possible in that direction. Pip would
> be even better for me personally (ChimeraX can install directly from the
> PyPI, but doesn't interact with Conda) - but I understand pretty well the
> substantial challenge that would amount to (not least being that the PyPI
> imposes a limit - around 100MB from memory? - on the size of an individual
> package).
> > >> > >>> >> >> >> >> >>
> > >> > >>> >> >> >> >> >> Best regards,
> > >> > >>> >> >> >> >> >>
> > >> > >>> >> >> >> >> >> Tristan
> > >> > >>> >> >> >> >> >>
> > >> > >>> >> >> >> >> >>> On 2019-08-23 09:28, Luc Bourhis wrote:
> > >> > >>> >> >> >> >> >>> Hi Graeme,
> > >> > >>> >> >> >> >> >>> Yes, I know. But “black" is a program doing a
> very particular task
> > >> > >>> >> >> >> >> >>> (code formatting from the top of my head).
> Requiring to use a wrapper
> > >> > >>> >> >> >> >> >>> for python itself is another level. But ok, I
> think I am mellowing to
> > >> > >>> >> >> >> >> >>> the idea after all! Talking with people around
> me, and extrapolating,
> > >> > >>> >> >> >> >> >>> I would bet that, right now, a great majority
> of people interested by
> > >> > >>> >> >> >> >> >>> cctbx in pip have already used the cctbx, so
> they know about the
> > >> > >>> >> >> >> >> >>> Python wrapper, and they would not be too
> sanguine about that. My
> > >> > >>> >> >> >> >> >>> concern is for the future, when pip will be the
> first time some people
> > >> > >>> >> >> >> >> >>> use cctbx. Big fat warning notices on PyPI page
> and a better error
> > >> > >>> >> >> >> >> >>> message when cctbx fails because LIBTBX_BUILD
> is not set would be
> > >> > >>> >> >> >> >> >>> needed but that could be all right.
> > >> > >>> >> >> >> >> >>> If we do a pip installer, we should aim at a
> minimal install: cctbx,
> > >> > >>> >> >> >> >> >>> iotbx and their dependencies, and that’s it.
> > >> > >>> >> >> >> >> >>> Best wishes,
> > >> > >>> >> >> >> >> >>> Luc
> > >> > >>> >> >> >> >> >>>> On 23 Aug 2019, at 07:17,
> Graeme.Winter at Diamond.ac.uk <Graeme.Winter at diamond.ac.uk> wrote:
> > >> > >>> >> >> >> >> >>>> Without discussing the merits of this or
> whether we _choose_ to make the move to supporting PIP, I am certain it
> would be _possible_ - many other packages make dispatcher scripts when you
> pip install them e.g.
> > >> > >>> >> >> >> >> >>>> Silver-Surfer rescale_f2 :) $ which black; cat
> $(which black)
> > >> > >>> >> >> >> >> >>>>
> /Library/Frameworks/Python.framework/Versions/3.6/bin/black
> > >> > >>> >> >> >> >> >>>>
> #!/Library/Frameworks/Python.framework/Versions/3.6/bin/python3.6
> > >> > >>> >> >> >> >> >>>> # -*- coding: utf-8 -*-
> > >> > >>> >> >> >> >> >>>> import re
> > >> > >>> >> >> >> >> >>>> import sys
> > >> > >>> >> >> >> >> >>>> from black import main
> > >> > >>> >> >> >> >> >>>> if __name__ == '__main__':
> > >> > >>> >> >> >> >> >>>> sys.argv[0] =
> re.sub(r'(-script\.pyw?|\.exe)?$', '', sys.argv[0])
> > >> > >>> >> >> >> >> >>>> sys.exit(main())
> > >> > >>> >> >> >> >> >>>> So we _could_ work around the absence of
> LIBTBX_BUILD etc. in the system. Whether or not we elect to do the work is
> a different question, and it seems clear that here are very mixed opinions
> on this.
> > >> > >>> >> >> >> >> >>>> Best wishes Graeme
> > >> > >>> >> >> >> >> >>>> On 23 Aug 2019, at 01:21, Luc Bourhis <
> luc_j_bourhis at mac.com<mailto:luc_j_bourhis at mac.com>> wrote:
> > >> > >>> >> >> >> >> >>>> Hi,
> > >> > >>> >> >> >> >> >>>> Even if we managed to ship our the boost
> dynamic libraries with pip, it would still not be pip-like, as we would
> still need our python wrappers to set LIBTBX_BUILD and LD_LIBRARY_PATH.
> Normal pip packages work with the standard python exe. LD_LIBRARY_PATH, we
> could get around that by changing the way we compile, using -Wl,-R, which
> is the runtime equivalent of build time -L. That’s a significant change
> that would need to be tested. But there is no way around setting
> LIBTBX_BUILD right now. Leaving that to the user is horrible. Perhaps there
> is a way to hack libtbx/env_config.py so that we can hardwire LIBTBX_BUILD
> in there when pip installs?
> > >> > >>> >> >> >> >> >>>> Best wishes,
> > >> > >>> >> >> >> >> >>>> Luc
> > >> > >>> >> >> >> >> >>>> On 16 Aug 2019, at 22:47, Luc Bourhis <
> luc_j_bourhis at mac.com<mailto:luc_j_bourhis at mac.com>> wrote:
> > >> > >>> >> >> >> >> >>>> Hi,
> > >> > >>> >> >> >> >> >>>> I did look into that many years ago, and even
> toyed with building a pip installer. What stopped me is the exact
> conclusion you reached too: the user would not have the pip experience he
> expects. You are right that it is a lot of effort but is it worth it?
> Considering that remark, I don’t think so. Now, Conda was created
> specifically to go beyond pip pure-python-only support. Since cctbx has
> garnered support for Conda, the best avenue imho is to go the extra length
> to have a package on Anaconda.org<http://anaconda.org/>, and then to
> advertise it hard to every potential user out there.
> > >> > >>> >> >> >> >> >>>> Best wishes,
> > >> > >>> >> >> >> >> >>>> Luc
> > >> > >>> >> >> >> >> >>>> On 16 Aug 2019, at 21:45, Aaron Brewster <
> asbrewster at lbl.gov<mailto:asbrewster at lbl.gov>> wrote:
> > >> > >>> >> >> >> >> >>>> Hi, to avoid clouding Dorothee's documentation
> email thread, which I think is a highly useful enterprise, here's some
> thoughts about putting cctbx into pip. Pip doesn't install non-python
> dependencies well. I don't think boost is available as a package on pip
> (at least the package version we use). wxPython4 isn't portable through
> pip (
> https://wiki.wxpython.org/How%20to%20install%20wxPython#Installing_wxPython-Phoenix_using_pip).
> MPI libraries are system dependent. If cctbx were a pure python package,
> pip would be fine, but cctbx is not.
> > >> > >>> >> >> >> >> >>>> All that said, we could build a manylinux1
> version of cctbx and upload it to PyPi (I'm just learning about this). For
> a pip package to be portable (which is a requirement for cctbx), it needs
> to conform to PEP513, the manylinux1 standard (
> https://www.python.org/dev/peps/pep-0513/). For example, numpy is built
> according to this standard (see https://pypi.org/project/numpy/#files,
> where you'll see the manylinux1 wheel). Note, the manylinux1 standard is
> built with Centos 5.11 which we no longer support.
> > >> > >>> >> >> >> >> >>>> There is also a manylinux2010 standard, which
> is based on Centos 6 (https://www.python.org/dev/peps/pep-0571/). This
> is likely a more attainable target (note though by default C++11 is not
> supported on Centos 6).
> > >> > >>> >> >> >> >> >>>> If we built a manylinuxX version of cctbx and
> uploaded it to PyPi, the user would need all the non-python dependencies.
> There's no way to specify these in pip. For example, cctbx requires boost
> 1.63 or better. The user will need to have it in a place their python can
> find it, or we could package it ourselves and supply it, similar to how the
> pip h5py package now comes with an hd5f library, or how the pip numpy
> package includes an openblas library. We'd have to do the same for any
> packages we depend on that aren't on pip using the manylinux standards,
> such as wxPython4.
> > >> > >>> >> >> >> >> >>>> Further, we need to think about how dials and
> other cctbx-based packages interact. If pip install cctbx is set up, how
> does pip install dials work, such that any dials shared libraries can find
> the cctbx libraries? Can shared libraries from one pip package link
> against libraries in another pip package? Would each package need to
> supply its own boost? Possibly this is well understood in the pip field,
> but not by me :)
> > >> > >>> >> >> >> >> >>>> Finally, there's the option of providing a
> source pip package. This would require the full compiler toolchain for any
> given platform (macOS, linux, windows). These are likely available for
> developers, but not for general users.
> > >> > >>> >> >> >> >> >>>> Anyway, these are some of the obstacles. Not
> saying it isn't possible, it's just a lot of effort.
> > >> > >>> >> >> >> >> >>>> Thanks,
> > >> > >>> >> >> >> >> >>>> -Aaron
> > >> > >>> >> >> >> >> >>>> _______________________________________________
> > >> > >>> >> >> >> >> >>>> cctbxbb mailing list
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> cctbxbb at phenix-online.org>
> > >> > >>> >> >> >> >> >>>>
> http://phenix-online.org/mailman/listinfo/cctbxbb
> > >> > >>> >> >> >> >> >>>> _______________________________________________
> > >> > >>> >> >> >> >> >>>> cctbxbb mailing list
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> > >> > >>> >> >> >> >> >>>>
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> > >> > >>> >> >> >> >> >>>> _______________________________________________
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> > >> > >>> >> >> >> >> >>>>
> http://phenix-online.org/mailman/listinfo/cctbxbb
> > >> > >>> >> >> >> >> >>>> --
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> > >> > >>> >> >> >> >> >>>> _______________________________________________
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> > >> > >>> >> >> >> >> >>>>
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> > >> > >>> >> >> >> >> >>> _______________________________________________
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> > >> > >>> >> >> >> >> >>>
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> > >> > >>> >> >> >> >> >>
> > >> > >>> >> >> >> >> >>
> > >> > >>> >> >> >> >> >> _______________________________________________
> > >> > >>> >> >> >> >> >> cctbxbb mailing list
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> > >> > >>> >> >> >> >> >>
> http://phenix-online.org/mailman/listinfo/cctbxbb
> > >> > >>> >> >> >> >> >
> > >> > >>> >> >> >> >> >
> > >> > >>> >> >> >> >> > _______________________________________________
> > >> > >>> >> >> >> >> > cctbxbb mailing list
> > >> > >>> >> >> >> >> > cctbxbb at phenix-online.org
> > >> > >>> >> >> >> >> > http://phenix-online.org/mailman/listinfo/cctbxbb
> > >> > >>> >> >> >> >>
> > >> > >>> >> >> >> >>
> > >> > >>> >> >> >> >> _______________________________________________
> > >> > >>> >> >> >> >> cctbxbb mailing list
> > >> > >>> >> >> >> >> cctbxbb at phenix-online.org
> > >> > >>> >> >> >> >> http://phenix-online.org/mailman/listinfo/cctbxbb
> > >> > >>> >> >> >> >
> > >> > >>> >> >> >> > _______________________________________________
> > >> > >>> >> >> >> > cctbxbb mailing list
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> > >> > >>> >> >> >> > http://phenix-online.org/mailman/listinfo/cctbxbb
> > >> > >>> >> >> >>
> > >> > >>> >> >> >>
> > >> > >>> >> >> >>
> > >> > >>> >> >> >> --
> > >> > >>> >> >> >> Gergely Katona, PhD
> > >> > >>> >> >> >> Associate Professor
> > >> > >>> >> >> >> Department of Chemistry and Molecular Biology,
> University of Gothenburg
> > >> > >>> >> >> >> Box 462, 40530 Göteborg, Sweden
> > >> > >>> >> >> >> Tel: +46-31-786-3959 / M: +46-70-912-3309 / Fax:
> +46-31-786-3910
> > >> > >>> >> >> >> Web: http://katonalab.eu, Email: gergely.katona at gu.se
> > >> > >>> >> >> >>
> > >> > >>> >> >> >> _______________________________________________
> > >> > >>> >> >> >> cctbxbb mailing list
> > >> > >>> >> >> >> cctbxbb at phenix-online.org
> > >> > >>> >> >> >> http://phenix-online.org/mailman/listinfo/cctbxbb
> > >> > >>> >> >> >
> > >> > >>> >> >> > _______________________________________________
> > >> > >>> >> >> > cctbxbb mailing list
> > >> > >>> >> >> > cctbxbb at phenix-online.org
> > >> > >>> >> >> > http://phenix-online.org/mailman/listinfo/cctbxbb
> > >> > >>> >> >>
> > >> > >>> >> >>
> > >> > >>> >> >>
> > >> > >>> >> >> --
> > >> > >>> >> >> Gergely Katona, PhD
> > >> > >>> >> >> Associate Professor
> > >> > >>> >> >> Department of Chemistry and Molecular Biology, University
> of Gothenburg
> > >> > >>> >> >> Box 462, 40530 Göteborg, Sweden
> > >> > >>> >> >> Tel: +46-31-786-3959 / M: +46-70-912-3309 / Fax:
> +46-31-786-3910
> > >> > >>> >> >> Web: http://katonalab.eu, Email: gergely.katona at gu.se
> > >> > >>> >> >>
> > >> > >>> >> >> _______________________________________________
> > >> > >>> >> >> cctbxbb mailing list
> > >> > >>> >> >> cctbxbb at phenix-online.org
> > >> > >>> >> >> http://phenix-online.org/mailman/listinfo/cctbxbb
> > >> > >>> >> >
> > >> > >>> >> > _______________________________________________
> > >> > >>> >> > cctbxbb mailing list
> > >> > >>> >> > cctbxbb at phenix-online.org
> > >> > >>> >> > http://phenix-online.org/mailman/listinfo/cctbxbb
> > >> > >>> >>
> > >> > >>> >>
> > >> > >>> >>
> > >> > >>> >> --
> > >> > >>> >> Gergely Katona, PhD
> > >> > >>> >> Associate Professor
> > >> > >>> >> Department of Chemistry and Molecular Biology, University of
> Gothenburg
> > >> > >>> >> Box 462, 40530 Göteborg, Sweden
> > >> > >>> >> Tel: +46-31-786-3959 / M: +46-70-912-3309 / Fax:
> +46-31-786-3910
> > >> > >>> >> Web: http://katonalab.eu, Email: gergely.katona at gu.se
> > >> > >>> >>
> > >> > >>> >> _______________________________________________
> > >> > >>> >> cctbxbb mailing list
> > >> > >>> >> cctbxbb at phenix-online.org
> > >> > >>> >> http://phenix-online.org/mailman/listinfo/cctbxbb
> > >> > >>> >
> > >> > >>> > _______________________________________________
> > >> > >>> > cctbxbb mailing list
> > >> > >>> > cctbxbb at phenix-online.org
> > >> > >>> > http://phenix-online.org/mailman/listinfo/cctbxbb
> > >> > >>>
> > >> > >>>
> > >> > >>>
> > >> > >>> --
> > >> > >>> Gergely Katona, PhD
> > >> > >>> Associate Professor
> > >> > >>> Department of Chemistry and Molecular Biology, University of
> Gothenburg
> > >> > >>> Box 462, 40530 Göteborg, Sweden
> > >> > >>> Tel: +46-31-786-3959 / M: +46-70-912-3309 / Fax: +46-31-786-3910
> > >> > >>> Web: http://katonalab.eu, Email: gergely.katona at gu.se
> > >> > >>>
> > >> > >>> _______________________________________________
> > >> > >>> cctbxbb mailing list
> > >> > >>> cctbxbb at phenix-online.org
> > >> > >>> http://phenix-online.org/mailman/listinfo/cctbxbb
> > >> > >
> > >> > > _______________________________________________
> > >> > > cctbxbb mailing list
> > >> > > cctbxbb at phenix-online.org
> > >> > > http://phenix-online.org/mailman/listinfo/cctbxbb
> > >> >
> > >> >
> > >> >
> > >> > --
> > >> > Gergely Katona, Professor
> > >> > Department of Chemistry and Molecular Biology, University of
> Gothenburg
> > >> > Box 462, 40530 Göteborg, Sweden
> > >> > Tel: +46-31-786-3959 / M: +46-70-912-3309 / Fax: +46-31-786-3910
> > >> > Web: http://katonalab.eu, Email: gergely.katona at gu.se
> > >>
> > >>
> > >>
> > >> --
> > >> Gergely Katona, Professor
> > >> Department of Chemistry and Molecular Biology, University of
> Gothenburg
> > >> Box 462, 40530 Göteborg, Sweden
> > >> Tel: +46-31-786-3959 / M: +46-70-912-3309 / Fax: +46-31-786-3910
> > >> Web: http://katonalab.eu, Email: gergely.katona at gu.se
> > >>
> > >> _______________________________________________
> > >> cctbxbb mailing list
> > >> cctbxbb at phenix-online.org
> > >> http://phenix-online.org/mailman/listinfo/cctbxbb
> > >
> > > _______________________________________________
> > > cctbxbb mailing list
> > > cctbxbb at phenix-online.org
> > > http://phenix-online.org/mailman/listinfo/cctbxbb
> >
> >
> >
> > --
> > Gergely Katona, Professor
> > Department of Chemistry and Molecular Biology, University of Gothenburg
> > Box 462, 40530 Göteborg, Sweden
> > Tel: +46-31-786-3959 / M: +46-70-912-3309 / Fax: +46-31-786-3910
> > Web: http://katonalab.eu, Email: gergely.katona at gu.se
>
>
>
> --
> Gergely Katona, Professor
> Department of Chemistry and Molecular Biology, University of Gothenburg
> Box 462, 40530 Göteborg, Sweden
> Tel: +46-31-786-3959 / M: +46-70-912-3309 / Fax: +46-31-786-3910
> Web: http://katonalab.eu, Email: gergely.katona at gu.se
>
> _______________________________________________
> cctbxbb mailing list
> cctbxbb at phenix-online.org
> http://phenix-online.org/mailman/listinfo/cctbxbb
>
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