[cctbxbb] conda cctbx on Mac 10.15.2 working with python3.8

5 Jan 2020

      Hi Tristan,

Thank you very much for the explanation and the suggested solution.
I needed both. 

When I tried your list comprehension in a Jupyter notebook with the orginal 
problem, it is too fast:

```
IOPub data rate exceeded.
The notebook server will temporarily stop sending output
to the client in order to avoid crashing it.
To change this limit, set the config variable
`--NotebookApp.iopub_data_rate_limit`.

Current values:
NotebookApp.iopub_data_rate_limit=1000000.0 (bytes/sec)
NotebookApp.rate_limit_window=3.0 (secs)
```

When I reduced the a and b edges by an order of magnitude (now 12,118 reflections),
your list comprehension is two orders of magnitude faster a for loop (no surprise).
It is also slightly faster than this generator expression coupled to a list 
comprehension, so there is no advantage to using the generator here. 

hklgen = (hkl for hkl in ms.indices()) 
print('\n'.join([str(hkl) for hkl in hklgen]))

Best regards,

Blaine

________________________________________
From: Tristan Croll [[email protected]]
Sent: Sunday, January 05, 2020 4:13 AM
To: cctbx mailing list
Cc: Mooers, Blaine H.M.  (HSC)
Subject: [EXTERNAL] Re: [cctbxbb] conda cctbx on Mac 10.15.2 working with python3.8

Hi Blaine,

The speed issue is probably because this list comprehension:

[print(hkl) for hkl in ms.indices()]

... is calling print() (and returning None) a million times over. I
think something like the following should be much faster:

print('\n'.join([str(hkl) for hkl in ms.indices()]))

Best regards,

Tristan

On 2020-01-04 22:00, Mooers, Blaine H.M.  (HSC) wrote:
...
Hi Billy,
Gergely's post yesterday stimulated me to check my conda cctbx setup.
I had earlier reported success with conda cctbx for Python3.6, 3.7, and
3.8.
This morning I found in my path an earlier python3.6 build of cctbx
that may
have given me false positives with my conda installs of cctbx.
After removing the old build of cctbx from my path, I modified my zshrc
file
as Gergely suggested. I can confirm that results that Gergely reported
yesterday.
I used a Mac OS X 10.15.2 with zsh as my shell and anaconda3 installed
as /opt/anaconda. I did my testing in a conda env named cctbx38.
I added 'export LIBTBX_BUILD=$CONDA_PREFIX' in my .zshrc file.
After sourcing my .zshrc file,  'echo $LIBTBX_BUILD' returns
'/opt/anaconda/envs/cctbx38' as expected.
The toy script  below prints the calculated Miller indices as a tuples
in a terminal window.
It was run using 'python https://urldefense.proofpoint.com/v2/url?u=http-3A__millerSet.py&d=DwICAg&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=qVi_X8RKqR9qAvj5zlpPK19KrpEm-gqysmWjKZEnfio&s=Tq8Ygnm_E0Kf1PWEK5NHF7K1TJSniqkF3PJ0JyLETLk&e= '.
Note that the printing of 1 million indices to a jupyter notebook cell
is disappointingly slow!!
Reduce each unit cell dimension by two orders of magnitude before
trying this at home!
The following code also worked with Python3.6 and Python3.7 in their
corresponding cctbx36 and cctbx37 envs.
from cctbx import crystal
from cctbx import miller
ms = miller.build_set(
    crystal_symmetry=crystal.symmetry(
        space_group_symbol='P4',
        unit_cell=(150.8,150.8,250.4,90.0,90.0,90.0)),
    anomalous_flag=False,
    d_min=1.4)
[print(hkl) for hkl in ms.indices()]
I used conda python3.8.0 built on November 22. Python3.8.1 does not
seem to be
available yet from Anaconda.
Best regards,
Blaine
Blaine Mooers, Ph.D.
Associate Professor
Department of Biochemistry and Molecular Biology
College of Medicine
University of Oklahoma Health Sciences Center
S.L. Young Biomedical Research Center (BRC) Rm. 466
975 NE 10th Street, BRC 466
Oklahoma City, OK 73104-5419
________________________________________
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[email protected] [[email protected]]
Sent: Saturday, January 04, 2020 2:00 PM
To: [email protected]
Subject: [EXTERNAL] cctbxbb Digest, Vol 130, Issue 2
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Today's Topics:
1. Re: some thoughts on cctbx and pip (Billy Poon)
----------------------------------------------------------------------
Message: 1
Date: Fri, 3 Jan 2020 21:04:25 +0100
From: Billy Poon 
To: cctbx mailing list 
Subject: Re: [cctbxbb] some thoughts on cctbx and pip
Message-ID:

Content-Type: text/plain; charset="utf-8"
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://urldefense.proofpoint.com/v2/url?u=https-3A__phenix-2Donline.org&d=DwICAg&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=9IjF95nqsrMq_R_HHQ4nsTpGpSpiU2e4ynF8kN3qTHY&s=c-5sC2_Edn5Vxnj97Qf6f-IoSGnKKf5ZC1fy_jJS77k&e=
On Fri, Jan 3, 2020 at 2:20 PM Gergely Katona 
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/https://urldefense.proofpoint.com/v2/url?u=http-3A__-5F-5Finit-5F-5F.py&d=DwICAg&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=9IjF95nqsrMq_R_HHQ4nsTpGpSpiU2e4ynF8kN3qTHY&s=9NiF4LTTyEpDCh-vdb5bXVIJ4i9E6HmD6eWJg_3SjzE&e=
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/https://urldefense.proofpoint.com/v2/url?u=http-3A__hierarchy.py&d=DwICAg&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=9IjF95nqsrMq_R_HHQ4nsTpGpSpiU2e4ynF8kN3qTHY&s=QlonHINbJqyu1vTwlBJWKyChCMCCJxpIWIaT5_rrkLc&e=
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/https://urldefense.proofpoint.com/v2/url?u=http-3A__-5F-5Finit-5F-5F.py&d=DwICAg&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=9IjF95nqsrMq_R_HHQ4nsTpGpSpiU2e4ynF8kN3qTHY&s=9NiF4LTTyEpDCh-vdb5bXVIJ4i9E6HmD6eWJg_3SjzE&e=
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/https://urldefense.proofpoint.com/v2/url?u=http-3A__-5F-5Finit-5F-5F.py&d=DwICAg&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=9IjF95nqsrMq_R_HHQ4nsTpGpSpiU2e4ynF8kN3qTHY&s=9NiF4LTTyEpDCh-vdb5bXVIJ4i9E6HmD6eWJg_3SjzE&e=
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/https://urldefense.proofpoint.com/v2/url?u=http-3A__-5F-5Finit-5F-5F.py&d=DwICAg&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=9IjF95nqsrMq_R_HHQ4nsTpGpSpiU2e4ynF8kN3qTHY&s=9NiF4LTTyEpDCh-vdb5bXVIJ4i9E6HmD6eWJg_3SjzE&e=
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/https://urldefense.proofpoint.com/v2/url?u=http-3A__load-5Fenv.py&d=DwICAg&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=9IjF95nqsrMq_R_HHQ4nsTpGpSpiU2e4ynF8kN3qTHY&s=rJbfdPr3ymiz7Ir508_VGIhspAKCOwozKhY5I6OXux0&e=
 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/https://urldefense.proofpoint.com/v2/url?u=http-3A__env-5Fconfig.py&d=DwICAg&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=9IjF95nqsrMq_R_HHQ4nsTpGpSpiU2e4ynF8kN3qTHY&s=UrsFhQ0dxNNuzXmOT3D6pnGJ5lXko4mfrKceNgBaQV4&e=
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/https://urldefense.proofpoint.com/v2/url?u=http-3A__env-5Fconfig.py&d=DwICAg&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=9IjF95nqsrMq_R_HHQ4nsTpGpSpiU2e4ynF8kN3qTHY&s=UrsFhQ0dxNNuzXmOT3D6pnGJ5lXko4mfrKceNgBaQV4&e=
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/https://urldefense.proofpoint.com/v2/url?u=http-3A__-5F-5Finit-5F-5F.py&d=DwICAg&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=9IjF95nqsrMq_R_HHQ4nsTpGpSpiU2e4ynF8kN3qTHY&s=9NiF4LTTyEpDCh-vdb5bXVIJ4i9E6HmD6eWJg_3SjzE&e=
 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/https://urldefense.proofpoint.com/v2/url?u=http-3A__-5F-5Finit-5F-5F.py&d=DwICAg&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=9IjF95nqsrMq_R_HHQ4nsTpGpSpiU2e4ynF8kN3qTHY&s=9NiF4LTTyEpDCh-vdb5bXVIJ4i9E6HmD6eWJg_3SjzE&e=
 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/https://urldefense.proofpoint.com/v2/url?u=http-3A__-5F-5Finit-5F-5F.py&d=DwICAg&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=9IjF95nqsrMq_R_HHQ4nsTpGpSpiU2e4ynF8kN3qTHY&s=9NiF4LTTyEpDCh-vdb5bXVIJ4i9E6HmD6eWJg_3SjzE&e=
 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/https://urldefense.proofpoint.com/v2/url?u=http-3A__cryst1-5Finterpretation.py&d=DwICAg&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=9IjF95nqsrMq_R_HHQ4nsTpGpSpiU2e4ynF8kN3qTHY&s=3OchLb18AMp3YpXOuEb8BDOwhl2XLrV1QAfZByH-l2E&e=
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/https://urldefense.proofpoint.com/v2/url?u=http-3A__cryst1-5Finterpretation.py&d=DwICAg&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=9IjF95nqsrMq_R_HHQ4nsTpGpSpiU2e4ynF8kN3qTHY&s=3OchLb18AMp3YpXOuEb8BDOwhl2XLrV1QAfZByH-l2E&e=
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/https://urldefense.proofpoint.com/v2/url?u=http-3A__-5F-5Finit-5F-5F.py&d=DwICAg&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=9IjF95nqsrMq_R_HHQ4nsTpGpSpiU2e4ynF8kN3qTHY&s=9NiF4LTTyEpDCh-vdb5bXVIJ4i9E6HmD6eWJg_3SjzE&e=
 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 extension='')
    __init__(_object*, int space_group_number,
std::__cxx11::basic_string extension='', std::__cxx11::basic_string table_id='')
    __init__(_object*, std::__cxx11::basic_string symbol)
    __init__(_object*, std::__cxx11::basic_string symbol,
std::__cxx11::basic_string table_id='')
Gergely
On Fri, Jan 3, 2020 at 1:44 PM Gergely Katona 
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  wrote:
...
Hi everyone,
I updated the conda packages on the cctbx-dev channel and there are
...
...
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
...
...
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
...
...
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://urldefense.proofpoint.com/v2/url?u=https-3A__phenix-2Donline.org&d=DwICAg&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=9IjF95nqsrMq_R_HHQ4nsTpGpSpiU2e4ynF8kN3qTHY&s=c-5sC2_Edn5Vxnj97Qf6f-IoSGnKKf5ZC1fy_jJS77k&e=
On Wed, Dec 18, 2019 at 11:25 AM Billy Poon  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
also now packages for macOS. The old packages have been removed so you
can
create a new environment with
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,
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.
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://urldefense.proofpoint.com/v2/url?u=https-3A__phenix-2Donline.org&d=DwICAg&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=9IjF95nqsrMq_R_HHQ4nsTpGpSpiU2e4ynF8kN3qTHY&s=c-5sC2_Edn5Vxnj97Qf6f-IoSGnKKf5ZC1fy_jJS77k&e=
On Wed, Dec 18, 2019 at 2:08 AM Gergely Katona 
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/https://urldefense.proofpoint.com/v2/url?u=http-3A__python36.zip&d=DwICAg&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=9IjF95nqsrMq_R_HHQ4nsTpGpSpiU2e4ynF8kN3qTHY&s=cUHL8qgeloeUO3oYTQcr9d56RegJk01wJ2i-c3Zo6oE&e= ',
'/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/https://urldefense.proofpoint.com/v2/url?u=http-3A__-5F-5Finit-5F-5F.py&d=DwICAg&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=9IjF95nqsrMq_R_HHQ4nsTpGpSpiU2e4ynF8kN3qTHY&s=9NiF4LTTyEpDCh-vdb5bXVIJ4i9E6HmD6eWJg_3SjzE&e=  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/https://urldefense.proofpoint.com/v2/url?u=http-3A__-5F-5Finit-5F-5F.py&d=DwICAg&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=9IjF95nqsrMq_R_HHQ4nsTpGpSpiU2e4ynF8kN3qTHY&s=9NiF4LTTyEpDCh-vdb5bXVIJ4i9E6HmD6eWJg_3SjzE&e=  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/https://urldefense.proofpoint.com/v2/url?u=http-3A__load-5Fenv.py&d=DwICAg&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=9IjF95nqsrMq_R_HHQ4nsTpGpSpiU2e4ynF8kN3qTHY&s=rJbfdPr3ymiz7Ir508_VGIhspAKCOwozKhY5I6OXux0&e=  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/https://urldefense.proofpoint.com/v2/url?u=http-3A__env-5Fconfig.py&d=DwICAg&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=9IjF95nqsrMq_R_HHQ4nsTpGpSpiU2e4ynF8kN3qTHY&s=UrsFhQ0dxNNuzXmOT3D6pnGJ5lXko4mfrKceNgBaQV4&e=  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/https://urldefense.proofpoint.com/v2/url?u=http-3A__os.py&d=DwICAg&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=9IjF95nqsrMq_R_HHQ4nsTpGpSpiU2e4ynF8kN3qTHY&s=hA1zo5wap0c9wK3DrlWIKqYBIqqbfKXca5jQ9aX5pYU&e=  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/https://urldefense.proofpoint.com/v2/url?u=http-3A__-5F-5Finit-5F-5F.py&d=DwICAg&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=9IjF95nqsrMq_R_HHQ4nsTpGpSpiU2e4ynF8kN3qTHY&s=9NiF4LTTyEpDCh-vdb5bXVIJ4i9E6HmD6eWJg_3SjzE&e=  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/https://urldefense.proofpoint.com/v2/url?u=http-3A__-5F-5Finit-5F-5F.py&d=DwICAg&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=9IjF95nqsrMq_R_HHQ4nsTpGpSpiU2e4ynF8kN3qTHY&s=9NiF4LTTyEpDCh-vdb5bXVIJ4i9E6HmD6eWJg_3SjzE&e=  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 extension='')
    __init__(_object*, int space_group_number,
std::__cxx11::basic_string extension='', std::__cxx11::basic_string table_id='')
    __init__(_object*, std::__cxx11::basic_string symbol)
    __init__(_object*, std::__cxx11::basic_string symbol,
std::__cxx11::basic_string 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})
...
in <module>
     53
     54 from __future__ import absolute_import, division,
~/anaconda3/lib/python3.6/site-packages/iotbx/https://urldefense.proofpoint.com/v2/url?u=http-3A__reflection-5Ffile-5Freader.py&d=DwICAg&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=9IjF95nqsrMq_R_HHQ4nsTpGpSpiU2e4ynF8kN3qTHY&s=U5BvLmuCgufvN_LRxQw9n78p33jNaRrXVbH1BRSXgxg&e=
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/https://urldefense.proofpoint.com/v2/url?u=http-3A__-5F-5Finit-5F-5F.py&d=DwICAg&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=9IjF95nqsrMq_R_HHQ4nsTpGpSpiU2e4ynF8kN3qTHY&s=9NiF4LTTyEpDCh-vdb5bXVIJ4i9E6HmD6eWJg_3SjzE&e=  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
...
in <module>
      1 from __future__ import absolute_import, division,
~/anaconda3/lib/python3.6/site-packages/iotbx/mtz/https://urldefense.proofpoint.com/v2/url?u=http-3A__extract-5Ffrom-5Fsymmetry-5Flib.py&d=DwICAg&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=9IjF95nqsrMq_R_HHQ4nsTpGpSpiU2e4ynF8kN3qTHY&s=k3WR6VZd4-PDULPXl4O0Vwz9q3LCaocUUhK_ehTn9UE&e=
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/https://urldefense.proofpoint.com/v2/url?u=http-3A__load-5Fenv.py&d=DwICAg&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=9IjF95nqsrMq_R_HHQ4nsTpGpSpiU2e4ynF8kN3qTHY&s=rJbfdPr3ymiz7Ir508_VGIhspAKCOwozKhY5I6OXux0&e=  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/https://urldefense.proofpoint.com/v2/url?u=http-3A__env-5Fconfig.py&d=DwICAg&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=9IjF95nqsrMq_R_HHQ4nsTpGpSpiU2e4ynF8kN3qTHY&s=UrsFhQ0dxNNuzXmOT3D6pnGJ5lXko4mfrKceNgBaQV4&e=  in
...
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  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
...
>
> channels:
>   - conda-forge
>   - defaults
>   - cctbx
>
> Do you need dxtbx for your scripts? This package does not build
...
>
> Also, your error message is probably due to version of HDF5 that
...
>
> Lastly, the dispatchers will not work in these packages because
...
>
> 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://urldefense.proofpoint.com/v2/url?u=https-3A__phenix-2Donline.org&d=DwICAg&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=9IjF95nqsrMq_R_HHQ4nsTpGpSpiU2e4ynF8kN3qTHY&s=c-5sC2_Edn5Vxnj97Qf6f-IoSGnKKf5ZC1fy_jJS77k&e=
>
>
> On Tue, Dec 17, 2019 at 5:39 AM Gergely Katona 
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
...
>> 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@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 
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
...
>> >
>> > 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 https://urldefense.proofpoint.com/v2/url?u=http-3A__bootstrap.py&d=DwICAg&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=9IjF95nqsrMq_R_HHQ4nsTpGpSpiU2e4ynF8kN3qTHY&s=bt_bS5majJbOBt0MQ5A0UJNxCAHR9nzX5sOsNeglug8&e=  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 https://urldefense.proofpoint.com/v2/url?u=http-3A__bootstrap.py&d=DwICAg&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=9IjF95nqsrMq_R_HHQ4nsTpGpSpiU2e4ynF8kN3qTHY&s=bt_bS5majJbOBt0MQ5A0UJNxCAHR9nzX5sOsNeglug8&e=  file handles that with SCons.
>> >
>> > 3) Running. After building, there should be a https://urldefense.proofpoint.com/v2/url?u=http-3A__setpaths.sh&d=DwICAg&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=9IjF95nqsrMq_R_HHQ4nsTpGpSpiU2e4ynF8kN3qTHY&s=jdLrRP40_yWUf0wRYzKtzCKGcxskN9ROwtX498mqAOM&e=  (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
...
>> >
>> > 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
...
>> >
>> > --
>> > 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://urldefense.proofpoint.com/v2/url?u=https-3A__phenix-2Donline.org&d=DwICAg&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=9IjF95nqsrMq_R_HHQ4nsTpGpSpiU2e4ynF8kN3qTHY&s=c-5sC2_Edn5Vxnj97Qf6f-IoSGnKKf5ZC1fy_jJS77k&e=
>> >
>> >
>> > On Mon, Dec 16, 2019 at 2:53 AM Gergely Katona <
[email protected]> 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
...
>> >> when using these flags:
>> >> python https://urldefense.proofpoint.com/v2/url?u=http-3A__bootstrap.py&d=DwICAg&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=9IjF95nqsrMq_R_HHQ4nsTpGpSpiU2e4ynF8kN3qTHY&s=bt_bS5majJbOBt0MQ5A0UJNxCAHR9nzX5sOsNeglug8&e=  --use-conda --python3 --nproc=12
>> >>
>> >> Then I probably did the unorthodox thing and sourced these
...
>> >>
>> >> 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 
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://urldefense.proofpoint.com/v2/url?u=https-3A__phenix-2Donline.org&d=DwICAg&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=9IjF95nqsrMq_R_HHQ4nsTpGpSpiU2e4ynF8kN3qTHY&s=c-5sC2_Edn5Vxnj97Qf6f-IoSGnKKf5ZC1fy_jJS77k&e=
>> >> >
>> >> >
>> >> > On Fri, Dec 13, 2019 at 5:44 AM Gergely Katona <
[email protected]> 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 
wrote:
>> >> >> >
>> >> >> > Hi all,
>> >> >> >
>> >> >> > For a brief update, I have submitted a recipe for
cctbxlite to conda-forge (
https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_conda-2Dforge_staged-2Drecipes_pull_10021&d=DwICAg&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=9IjF95nqsrMq_R_HHQ4nsTpGpSpiU2e4ynF8kN3qTHY&s=uPteSh0sovoqW00_UboKZdbEomi9DvxJcyFGCL-3XGw&e=
) and support for
Python 3.7 and 3.8 is being added (
https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_cctbx_cctbx-5Fproject_pull_409&d=DwICAg&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=9IjF95nqsrMq_R_HHQ4nsTpGpSpiU2e4ynF8kN3qTHY&s=vJRw_RsofbmTidC7cfMBgYyjBBnPVLTqqDjSQqWhbI8&e=
). With some fixes for
Windows
(https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_cctbx_cctbx-5Fproject_pull_416&d=DwICAg&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=9IjF95nqsrMq_R_HHQ4nsTpGpSpiU2e4ynF8kN3qTHY&s=-In07B2uX5dd1lZsYqkki89edSNt_RGyn8Exkj_P22s&e=
), 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
...
>> >> >> >
>> >> >> > --
>> >> >> > 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://urldefense.proofpoint.com/v2/url?u=https-3A__phenix-2Donline.org&d=DwICAg&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=9IjF95nqsrMq_R_HHQ4nsTpGpSpiU2e4ynF8kN3qTHY&s=c-5sC2_Edn5Vxnj97Qf6f-IoSGnKKf5ZC1fy_jJS77k&e=
>> >> >> >
>> >> >> >
>> >> >> > On Sun, Aug 25, 2019 at 2:33 PM Tristan Croll <
[email protected]> 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 <
[email protected]> wrote:
>> >> >> >> >
>> >> >> >> > Hi Tristan,
>> >> >> >> >
>> >> >> >> > cctbx could be built to use your ChimeraX python, now
...
>> >> >> >> >
>> >> >> >> > Best wishes,
>> >> >> >> >
>> >> >> >> > Luc
>> >> >> >> >
>> >> >> >> >
>> >> >> >> >> On 23 Aug 2019, at 19:02, Tristan Croll <
[email protected]> 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 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
...
>> >> >> >> >>
>> >> >> >> >> 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
...
>> >> >> >> >>> (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
...
>> >> >> >> >>> 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,
[email protected]  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 <
[email protected]mailto:[email protected]> wrote:
>> >> >> >> >>>> Hi,
>> >> >> >> >>>> Even if we managed to ship our the boost dynamic
...
>> >> >> >> >>>> Best wishes,
>> >> >> >> >>>> Luc
>> >> >> >> >>>> On 16 Aug 2019, at 22:47, Luc Bourhis <
[email protected]mailto:[email protected]> 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
...
>> >> >> >> >>>> Best wishes,
>> >> >> >> >>>> Luc
>> >> >> >> >>>> On 16 Aug 2019, at 21:45, Aaron Brewster <
[email protected]mailto:[email protected]> wrote:
>> >> >> >> >>>> Hi, to avoid clouding Dorothee's documentation
email thread, which I think is a highly useful enterprise, here's some
...
>> >> >> >> >>>> All that said, we could build a manylinux1 version
of cctbx and upload it to PyPi (I'm just learning about this).  For a
...
>> >> >> >> >>>> There is also a manylinux2010 standard, which is
...
>> >> >> >> >>>> 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
...
>> >> >> >> >>>> Further, we need to think about how dials and other
cctbx-based packages interact.  If pip install cctbx is set up, how
does
...
>> >> >> >> >>>> Finally, there's the option of providing a source
...
>> >> >> >> >>>> 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
>> >> >> >> >>>> [email protected]
>> >> >> >> >>>> https://urldefense.proofpoint.com/v2/url?u=http-3A__phenix-2Donline.org_mailman_listinfo_cctbxbb&d=DwICAg&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=9IjF95nqsrMq_R_HHQ4nsTpGpSpiU2e4ynF8kN3qTHY&s=Ti1nnpC9106KFO2KdIcwPujIFcsZwVLMx7pKoumCBx0&e=
>> >> >> >> >>>> _______________________________________________
>> >> >> >> >>>> cctbxbb mailing list
>> >> >> >> >>>> [email protected]
>> >> >> >> >>>> https://urldefense.proofpoint.com/v2/url?u=http-3A__phenix-2Donline.org_mailman_listinfo_cctbxbb&d=DwICAg&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=9IjF95nqsrMq_R_HHQ4nsTpGpSpiU2e4ynF8kN3qTHY&s=Ti1nnpC9106KFO2KdIcwPujIFcsZwVLMx7pKoumCBx0&e=
>> >> >> >> >>>> _______________________________________________
>> >> >> >> >>>> cctbxbb mailing list
>> >> >> >> >>>> [email protected]
>> >> >> >> >>>> https://urldefense.proofpoint.com/v2/url?u=http-3A__phenix-2Donline.org_mailman_listinfo_cctbxbb&d=DwICAg&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=9IjF95nqsrMq_R_HHQ4nsTpGpSpiU2e4ynF8kN3qTHY&s=Ti1nnpC9106KFO2KdIcwPujIFcsZwVLMx7pKoumCBx0&e=
>> >> >> >> >>>> --
>> >> >> >> >>>> This e-mail and any attachments may contain
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...
>> >> >> >> >>>> Any opinions expressed within this e-mail are those
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>> >> >> >> >>>> Diamond Light Source Ltd. cannot guarantee that
unpickle()
put
conda-forge above cctbx. Mine looks like
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.
the development build installs. The
https://urldefense.proofpoint.com/v2/url?u=http-3A__bootstrap.py&d=DwICAg&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=9IjF95nqsrMq_R_HHQ4nsTpGpSpiU2e4ynF8kN3qTHY&s=bt_bS5majJbOBt0MQ5A0UJNxCAHR9nzX5sOsNeglug8&e=
 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.
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
linked.
process, though, which is summarized as follows.
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.
packages.
What is the conflict with hdf5? That's something that should be fixed.
Thanks!
problem
directories:
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.
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.
the other in that form... well, I don't think I'm a good enough
programmer
to really know where to start.
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).
particular task
people interested by
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/https://urldefense.proofpoint.com/v2/url?u=http-3A__env-5Fconfig.py&d=DwICAg&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=9IjF95nqsrMq_R_HHQ4nsTpGpSpiU2e4ynF8kN3qTHY&s=UrsFhQ0dxNNuzXmOT3D6pnGJ5lXko4mfrKceNgBaQV4&e=
 so that we can hardwire LIBTBX_BUILD in there when pip
installs?
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
https://urldefense.proofpoint.com/v2/url?u=http-3A__Anaconda.org&d=DwICAg&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=9IjF95nqsrMq_R_HHQ4nsTpGpSpiU2e4ynF8kN3qTHY&s=9CHcyWn3-LWReM2OUP6nG0zWCa7YC98zlDOEBrLkbes&e=
<https://urldefense.proofpoint.com/v2/url?u=http-3A__anaconda.org_&d=DwICAg&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=9IjF95nqsrMq_R_HHQ4nsTpGpSpiU2e4ynF8kN3qTHY&s=HOVPiVxtqw3cPaIPsgyGuTEhL-dzqPTi3R8R9WraZ-0&e=
, and then to advertise it hard to
every potential user out there.
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://urldefense.proofpoint.com/v2/url?u=https-3A__wiki.wxpython.org_How-2520to-2520install-2520wxPython-23Installing-5FwxPython-2DPhoenix-5Fusing-5Fpip&d=DwICAg&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=9IjF95nqsrMq_R_HHQ4nsTpGpSpiU2e4ynF8kN3qTHY&s=D7zSUB-oAgRewijSj2GVWIC9iZor67suNQAfHV4I8dA&e=
).
MPI libraries are system dependent.  If cctbx were a pure python
package,
pip would be fine, but cctbx is not.
pip
package to be portable (which is a requirement for cctbx), it needs to
conform to PEP513, the manylinux1 standard (
https://urldefense.proofpoint.com/v2/url?u=https-3A__www.python.org_dev_peps_pep-2D0513_&d=DwICAg&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=9IjF95nqsrMq_R_HHQ4nsTpGpSpiU2e4ynF8kN3qTHY&s=CjakQKmcA0apMQME2kkx69X-T8nuUgqRCmbL4WrFPSI&e=
).  For example, numpy is built
according to this standard (see
https://urldefense.proofpoint.com/v2/url?u=https-3A__pypi.org_project_numpy_-23files&d=DwICAg&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=9IjF95nqsrMq_R_HHQ4nsTpGpSpiU2e4ynF8kN3qTHY&s=9tTcpapBSq5VuQfr6JwVg_MGJJnJZ_Q3ul7KFs4_SoE&e=
,
where you'll see the manylinux1 wheel).  Note, the manylinux1 standard
is
built with Centos 5.11 which we no longer support.
based on Centos 6
(https://urldefense.proofpoint.com/v2/url?u=https-3A__www.python.org_dev_peps_pep-2D0571_&d=DwICAg&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=9IjF95nqsrMq_R_HHQ4nsTpGpSpiU2e4ynF8kN3qTHY&s=bkliO9EJWFKQrM-uTVswT_jOd9v0ZZw-5-DCexzX7BQ&e=
).  This is
likely a more attainable target (note though by default C++11 is not
supported on Centos 6).
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.
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 :)
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.
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...
>> >> >> >> >>>> Diamond Light Source Limited (company no. 4375679).
Registered in England and Wales with its registered office at Diamond
House, Harwell Science and Innovation Campus, Didcot, Oxfordshire,
OX11
0DE, United Kingdom
>> >> >> >> >>>> _______________________________________________
>> >> >> >> >>>> cctbxbb mailing list
>> >> >> >> >>>> [email protected]
>> >> >> >> >>>> https://urldefense.proofpoint.com/v2/url?u=http-3A__phenix-2Donline.org_mailman_listinfo_cctbxbb&d=DwICAg&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=9IjF95nqsrMq_R_HHQ4nsTpGpSpiU2e4ynF8kN3qTHY&s=Ti1nnpC9106KFO2KdIcwPujIFcsZwVLMx7pKoumCBx0&e=
>> >> >> >> >>> _______________________________________________
>> >> >> >> >>> cctbxbb mailing list
>> >> >> >> >>> [email protected]
>> >> >> >> >>> https://urldefense.proofpoint.com/v2/url?u=http-3A__phenix-2Donline.org_mailman_listinfo_cctbxbb&d=DwICAg&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=9IjF95nqsrMq_R_HHQ4nsTpGpSpiU2e4ynF8kN3qTHY&s=Ti1nnpC9106KFO2KdIcwPujIFcsZwVLMx7pKoumCBx0&e=
>> >> >> >> >>
>> >> >> >> >>
>> >> >> >> >> _______________________________________________
>> >> >> >> >> cctbxbb mailing list
>> >> >> >> >> [email protected]
>> >> >> >> >> https://urldefense.proofpoint.com/v2/url?u=http-3A__phenix-2Donline.org_mailman_listinfo_cctbxbb&d=DwICAg&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=9IjF95nqsrMq_R_HHQ4nsTpGpSpiU2e4ynF8kN3qTHY&s=Ti1nnpC9106KFO2KdIcwPujIFcsZwVLMx7pKoumCBx0&e=
>> >> >> >> >
>> >> >> >> >
>> >> >> >> > _______________________________________________
>> >> >> >> > cctbxbb mailing list
>> >> >> >> > [email protected]
>> >> >> >> > https://urldefense.proofpoint.com/v2/url?u=http-3A__phenix-2Donline.org_mailman_listinfo_cctbxbb&d=DwICAg&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=9IjF95nqsrMq_R_HHQ4nsTpGpSpiU2e4ynF8kN3qTHY&s=Ti1nnpC9106KFO2KdIcwPujIFcsZwVLMx7pKoumCBx0&e=
>> >> >> >>
>> >> >> >>
>> >> >> >> _______________________________________________
>> >> >> >> cctbxbb mailing list
>> >> >> >> [email protected]
>> >> >> >> https://urldefense.proofpoint.com/v2/url?u=http-3A__phenix-2Donline.org_mailman_listinfo_cctbxbb&d=DwICAg&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=9IjF95nqsrMq_R_HHQ4nsTpGpSpiU2e4ynF8kN3qTHY&s=Ti1nnpC9106KFO2KdIcwPujIFcsZwVLMx7pKoumCBx0&e=
>> >> >> >
>> >> >> > _______________________________________________
>> >> >> > cctbxbb mailing list
>> >> >> > [email protected]
>> >> >> > https://urldefense.proofpoint.com/v2/url?u=http-3A__phenix-2Donline.org_mailman_listinfo_cctbxbb&d=DwICAg&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=9IjF95nqsrMq_R_HHQ4nsTpGpSpiU2e4ynF8kN3qTHY&s=Ti1nnpC9106KFO2KdIcwPujIFcsZwVLMx7pKoumCBx0&e=
>> >> >>
>> >> >>
>> >> >>
>> >> >> --
>> >> >> Gergely Katona, PhD
>> >> >> Associate Professor
>> >> >> Department of Chemistry and Molecular Biology, University
of Gothenburg
>> >> >> Box 462, 40530 G?teborg, Sweden
>> >> >> Tel: +46-31-786-3959 / M: +46-70-912-3309 / Fax:
+46-31-786-3910
>> >> >> Web: https://urldefense.proofpoint.com/v2/url?u=http-3A__katonalab.eu&d=DwICAg&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=9IjF95nqsrMq_R_HHQ4nsTpGpSpiU2e4ynF8kN3qTHY&s=V-FcxiRTC7MtbnraHvP-9rEwfelDcisXMb0j8rpaCF8&e= , Email: [email protected]
>> >> >>
>> >> >> _______________________________________________
>> >> >> cctbxbb mailing list
>> >> >> [email protected]
>> >> >> https://urldefense.proofpoint.com/v2/url?u=http-3A__phenix-2Donline.org_mailman_listinfo_cctbxbb&d=DwICAg&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=9IjF95nqsrMq_R_HHQ4nsTpGpSpiU2e4ynF8kN3qTHY&s=Ti1nnpC9106KFO2KdIcwPujIFcsZwVLMx7pKoumCBx0&e=
>> >> >
>> >> > _______________________________________________
>> >> > cctbxbb mailing list
>> >> > [email protected]
>> >> > https://urldefense.proofpoint.com/v2/url?u=http-3A__phenix-2Donline.org_mailman_listinfo_cctbxbb&d=DwICAg&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=9IjF95nqsrMq_R_HHQ4nsTpGpSpiU2e4ynF8kN3qTHY&s=Ti1nnpC9106KFO2KdIcwPujIFcsZwVLMx7pKoumCBx0&e=
>> >>
>> >>
>> >>
>> >> --
>> >> Gergely Katona, PhD
>> >> Associate Professor
>> >> Department of Chemistry and Molecular Biology, University of
Gothenburg
>> >> Box 462, 40530 G?teborg, Sweden
>> >> Tel: +46-31-786-3959 / M: +46-70-912-3309 / Fax:
+46-31-786-3910
>> >> Web: https://urldefense.proofpoint.com/v2/url?u=http-3A__katonalab.eu&d=DwICAg&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=9IjF95nqsrMq_R_HHQ4nsTpGpSpiU2e4ynF8kN3qTHY&s=V-FcxiRTC7MtbnraHvP-9rEwfelDcisXMb0j8rpaCF8&e= , Email: [email protected]
>> >>
>> >> _______________________________________________
>> >> cctbxbb mailing list
>> >> [email protected]
>> >> https://urldefense.proofpoint.com/v2/url?u=http-3A__phenix-2Donline.org_mailman_listinfo_cctbxbb&d=DwICAg&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=9IjF95nqsrMq_R_HHQ4nsTpGpSpiU2e4ynF8kN3qTHY&s=Ti1nnpC9106KFO2KdIcwPujIFcsZwVLMx7pKoumCBx0&e=
>> >
>> > _______________________________________________
>> > cctbxbb mailing list
>> > [email protected]
>> > https://urldefense.proofpoint.com/v2/url?u=http-3A__phenix-2Donline.org_mailman_listinfo_cctbxbb&d=DwICAg&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=9IjF95nqsrMq_R_HHQ4nsTpGpSpiU2e4ynF8kN3qTHY&s=Ti1nnpC9106KFO2KdIcwPujIFcsZwVLMx7pKoumCBx0&e=
>>
>>
>>
>> --
>> Gergely Katona, PhD
>> Associate Professor
>> Department of Chemistry and Molecular Biology, University of
Gothenburg
>> Box 462, 40530 G?teborg, Sweden
>> Tel: +46-31-786-3959 / M: +46-70-912-3309 / Fax: +46-31-786-3910
>> Web: https://urldefense.proofpoint.com/v2/url?u=http-3A__katonalab.eu&d=DwICAg&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=9IjF95nqsrMq_R_HHQ4nsTpGpSpiU2e4ynF8kN3qTHY&s=V-FcxiRTC7MtbnraHvP-9rEwfelDcisXMb0j8rpaCF8&e= , Email: [email protected]
>>
>> _______________________________________________
>> cctbxbb mailing list
>> [email protected]
>> https://urldefense.proofpoint.com/v2/url?u=http-3A__phenix-2Donline.org_mailman_listinfo_cctbxbb&d=DwICAg&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=9IjF95nqsrMq_R_HHQ4nsTpGpSpiU2e4ynF8kN3qTHY&s=Ti1nnpC9106KFO2KdIcwPujIFcsZwVLMx7pKoumCBx0&e=
>
> _______________________________________________
> cctbxbb mailing list
> [email protected]
> https://urldefense.proofpoint.com/v2/url?u=http-3A__phenix-2Donline.org_mailman_listinfo_cctbxbb&d=DwICAg&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=9IjF95nqsrMq_R_HHQ4nsTpGpSpiU2e4ynF8kN3qTHY&s=Ti1nnpC9106KFO2KdIcwPujIFcsZwVLMx7pKoumCBx0&e=
--
Gergely Katona, PhD
Associate Professor
Department of Chemistry and Molecular Biology, University of
Gothenburg
Box 462, 40530 G?teborg, Sweden
Tel: +46-31-786-3959 / M: +46-70-912-3309 / Fax: +46-31-786-3910
Web: https://urldefense.proofpoint.com/v2/url?u=http-3A__katonalab.eu&d=DwICAg&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=9IjF95nqsrMq_R_HHQ4nsTpGpSpiU2e4ynF8kN3qTHY&s=V-FcxiRTC7MtbnraHvP-9rEwfelDcisXMb0j8rpaCF8&e= , Email: [email protected]
_______________________________________________
cctbxbb mailing list
[email protected]
https://urldefense.proofpoint.com/v2/url?u=http-3A__phenix-2Donline.org_mailman_listinfo_cctbxbb&d=DwICAg&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=9IjF95nqsrMq_R_HHQ4nsTpGpSpiU2e4ynF8kN3qTHY&s=Ti1nnpC9106KFO2KdIcwPujIFcsZwVLMx7pKoumCBx0&e=
_______________________________________________
cctbxbb mailing list
[email protected]
https://urldefense.proofpoint.com/v2/url?u=http-3A__phenix-2Donline.org_mailman_listinfo_cctbxbb&d=DwICAg&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=9IjF95nqsrMq_R_HHQ4nsTpGpSpiU2e4ynF8kN3qTHY&s=Ti1nnpC9106KFO2KdIcwPujIFcsZwVLMx7pKoumCBx0&e=
--
Gergely Katona, Professor
Department of Chemistry and Molecular Biology, University of Gothenburg
Box 462, 40530 G?teborg, Sweden
Tel: +46-31-786-3959 / M: +46-70-912-3309 / Fax: +46-31-786-3910
Web: https://urldefense.proofpoint.com/v2/url?u=http-3A__katonalab.eu&d=DwICAg&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=9IjF95nqsrMq_R_HHQ4nsTpGpSpiU2e4ynF8kN3qTHY&s=V-FcxiRTC7MtbnraHvP-9rEwfelDcisXMb0j8rpaCF8&e= , Email: [email protected]
--
Gergely Katona, Professor
Department of Chemistry and Molecular Biology, University of
Gothenburg
Box 462, 40530 G?teborg, Sweden
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