Comments (27)
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by hacking: horton-2.1.0/horton/grid/cext.pyx
I managed to get it compiled and installed, but I get quite a number of errors when I run nosetests... I will have a look at the conda version.
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The fix is already available in the master branch. See #268
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from horton.
Fine by me but I'd suggest to make a maintenance branch rather releasing the current master as 2.1.1 (many backward incompatible changes). It may be worth skimming through the commits to look for other small fixes and improvements.
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I managed to compile and install the master branch, but when I run nosetests -v horton
I have 110 errors. Is that to be expected?
from horton.
No, but keep in mind that the master branch contains some rather severe backward-incompatible changes w.r.t. to the 2.1.0 release. These were mostly experimental changes we did to explore our future options. Normally the tests should run, but you need to link to libxc3.
from horton.
I think it was picking up stuff from previous installs, after cleaning everything I am left with:
horton.meanfield.test.test_libxc.test_dot_hessian_o3lyp_cs_polynomial ... SKIP: We should use more robust tests for derivatives.
horton.part.test.test_proatomdb.test_db_basics ... FAIL
horton.part.test.test_proatomdb.test_io_group ... FAIL
horton.part.test.test_proatomdb.test_io_filename ... FAIL
horton.part.test.test_proatomdb.test_compute_radii ... ERROR
horton.part.test.test_proatomdb.test_get_spline ... ERROR
horton.scripts.test.test_atomdb.test_plot_atoms ... FAIL
FAILED (SKIP=1, errors=2, failures=4)
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Can you also paste the details of the test fails and errors?
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======================================================================
ERROR: horton.part.test.test_proatomdb.test_compute_radii
----------------------------------------------------------------------
Traceback (most recent call last):
File "/usr/lib/python2.7/site-packages/nose/case.py", line 197, in runTest
self.test(*self.arg)
File "/home/maaren/.local/lib/python2.7/site-packages/horton/part/test/test_pr
oatomdb.py", line 128, in test_compute_radii
record = padb.get_record(6, 0)
File "/home/maaren/.local/lib/python2.7/site-packages/horton/part/proatomdb.py
", line 358, in get_record
return self._map[(number, charge)]
KeyError: (6, 0)
======================================================================
ERROR: horton.part.test.test_proatomdb.test_get_spline
----------------------------------------------------------------------
Traceback (most recent call last):
File "/usr/lib/python2.7/site-packages/nose/case.py", line 197, in runTest
self.test(*self.arg)
File "/home/maaren/.local/lib/python2.7/site-packages/horton/part/test/test_pr
oatomdb.py", line 172, in test_get_spline
spline = padb.get_spline(6)
File "/home/maaren/.local/lib/python2.7/site-packages/horton/part/proatomdb.py
", line 597, in get_spline
rho, deriv = self.get_rho(number, parameters, combine, do_deriv=True)
File "/home/maaren/.local/lib/python2.7/site-packages/horton/part/proatomdb.py
", line 547, in get_rho
record = self.get_record(number, charge)
File "/home/maaren/.local/lib/python2.7/site-packages/horton/part/proatomdb.py", line 358, in get_record
return self._map[(number, charge)]
KeyError: (6, 0)
======================================================================
FAIL: horton.part.test.test_proatomdb.test_db_basics
----------------------------------------------------------------------
Traceback (most recent call last):
File "/usr/lib/python2.7/site-packages/nose/case.py", line 197, in runTest
self.test(*self.arg)
File "/home/maaren/.local/lib/python2.7/site-packages/horton/part/test/test_proatomdb.py", line 32, in test_db_basics
assert padb.get_numbers() == [1, 8]
AssertionError
======================================================================
FAIL: horton.part.test.test_proatomdb.test_io_group
----------------------------------------------------------------------
Traceback (most recent call last):
File "/usr/lib/python2.7/site-packages/nose/case.py", line 197, in runTest
self.test(*self.arg)
File "/home/maaren/.local/lib/python2.7/site-packages/horton/part/test/test_proatomdb.py", line 103, in test_io_group
assert padb1.size == 5
AssertionError
======================================================================
FAIL: horton.part.test.test_proatomdb.test_io_filename
----------------------------------------------------------------------
Traceback (most recent call last):
File "/usr/lib/python2.7/site-packages/nose/case.py", line 197, in runTest
self.test(*self.arg)
File "/home/maaren/.local/lib/python2.7/site-packages/horton/part/test/test_proatomdb.py", line 116, in test_io_filename
assert keys == [(1, 0), (6, 0), (6, 1)]
AssertionError
======================================================================
FAIL: horton.scripts.test.test_atomdb.test_plot_atoms
----------------------------------------------------------------------
Traceback (most recent call last):
File "/usr/lib/python2.7/site-packages/nose/case.py", line 197, in runTest
self.test(*self.arg)
File "/home/maaren/.local/lib/python2.7/site-packages/horton/scripts/test/test_atomdb.py", line 209, in test_plot_atoms
check_files(dn, fns)
File "/home/maaren/.local/lib/python2.7/site-packages/horton/scripts/test/common.py", line 39, in check_files
assert os.path.isfile(os.path.join(dn, fn)), "Missing %s" % fn
AssertionError: Missing dens_001__h.png
----------------------------------------------------------------------
from horton.
OK, that should be easy to fix. Can you try the following: http://theochem.github.io/horton/2.1.0/tech_dev_git.html#reference-atoms
from horton.
Thanks Toon! Apart from one SKIP, everything is ok now.
from horton.
Great. Be careful with the master branch because it contains a lot of experimental changes, some of which are definitely for the better. E.g. we stripped a lot of redundant infrastructure code relative to the 2.1.0 release. If you build the documentation from the master branch, it should also be in sync with the changes in the code.
from horton.
OK, I will try to build the documentation too.
I was wondering if install_libxc-3.0.0.sh
and install_libint-2.0.3.sh
are still required on fedora f26/f27? The libs libint2-2.1.0
and libxc-3.0.1
are available in the OS repo.
from horton.
I'm not sure if that will work for LibInt. For LibXC, this should just work.
from horton.
I tried it on my f27 system, and it seems to work:
$ ldd ~/.local/lib/python2.7/site-packages/horton/gbasis/cext.so | grep libint2
libint2-beta.so.2 => /lib64/libint2-beta.so.2 (0x00007fcad1900000)
$ ldd ~/.local/lib/python2.7/site-packages/horton/meanfield/cext.so | grep libxc
libxc.so.4 => /lib64/libxc.so.4 (0x00007f0ad1f3a000)
$ nosetests -v horton
...
OK (SKIP=1)
from horton.
Nice. Thanks for letting us know.
from horton.
I assume you are aware, but there is a hard-coded dependency on qaworkdir/cached/libxc-x.x.x
to build the documentation. I think there are also some javascript files missing under doc/_static (I downloaded doctools.js, jquery.js & underscore.js manually to get the equations to render)
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Yes, there is no other way to extrac the list of functionals from LibXC. (There is no API to get the full list from a compiled instance of the library, as far as I know.)
It should normally not be needed to include these javascripts. At least, I haven't noticed the need yet. I just double checked on my machine and documentation builds without adding these scripts. Could it be one of the dependencies that is missing? There are additional dependencies for building the documentation. See http://theochem.github.io/horton/2.1.0/tech_dev_git.html#building-the-documentation
from horton.
I am doing this on f27, and the dependencies are there:
Package python2-sphinx-1:1.6.5-1.fc27.noarch is already installed, skipping.
Package python2-sphinx_rtd_theme-0.2.4-2.fc27.noarch is already installed, skipping.
Package doxygen-1:1.8.13-10.fc27.x86_64 is already installed, skipping.
Package python2-breathe-4.7.3-1.fc27.noarch is already installed, skipping.
Package python2-docutils-0.13.1-6.fc27.noarch is already installed, skipping.
Everything seems to be generated OK, only the _static
directory only contained custom.css
, and the equations did not render. I checked the HTML code and noticed:
$ grep _static _build/html/user_postproc_espfit.html
<link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
<link rel="stylesheet" href="_static/custom.css" type="text/css" />
<script src="_static/js/modernizr.min.js"></script>
<img src="_static/horton.png" class="logo" />
<script type="text/javascript" src="_static/jquery.js"></script>
<script type="text/javascript" src="_static/underscore.js"></script>
<script type="text/javascript" src="_static/doctools.js"></script>
<script type="text/javascript" src="_static/js/theme.js"></script>
After I downloaded:
http://theochem.github.io/horton/2.1.0/_static/jquery.js
http://theochem.github.io/horton/2.1.0/_static/underscore.js
http://theochem.github.io/horton/2.1.0/_static/doctools.js
the equations rendered. I have not tried them individually to figure out if all are required. modernizr.min.js
and js/theme.js
don't seem to be necessary.
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from horton.
Are you sure? After make clean
I get:
$ make html > make-html.log 2>&1
$ ls _static/
custom.css
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I don't have the javascripts in my source tree under doc/_static
and still the documentation works, with equations rendered with mathjax. These files do not need to be present in the source tree. Instead they are added automatically in doc/_build/html/_static
when you compile the docs.
@matt-chan: can you remove them again from MANIFEST.in
?
@maaren: can you copy the output of the setup.py
script with the list of dependencies?
This is what I have:
Version of dependencies:
breathe: 4.7.3
coverage: /bin/sh: coverage: command not found
cppcheck: Cppcheck 1.80
curl: curl 7.55.1 (x86_64-redhat-linux-gnu) libcurl/7.55.1 OpenSSL/1.1.0g zlib/1.2.11 libidn2/2.0.4 libpsl/0.18.0 (+libidn2/2.0.3) libssh2/1.8.0 nghttp2/1.25.0
cython: Cython version 0.26.1
docutils: 0.13.1
doxygen: 1.8.13
gcc: gcc (GCC) 7.2.1 20170915 (Red Hat 7.2.1-2)
git: git version 2.14.3
gitpython: -- not found --
h5py: 2.7.1
matplotlib: 2.0.0
nose: nosetests version 1.3.7
numpy: 1.13.1
pip: pip 9.0.1 from /usr/lib/python2.7/site-packages (python 2.7)
pycodestyle: 2.3.1
pydocstyle: 2.0.0
pylint: pylint 1.7.2, astroid 1.5.3
python: Python 2.7.14
scipy: 0.19.1
sphinx: Sphinx (sphinx-build) 1.6.5
sphinx_rtd_theme: 0.2.4
sympy: 1.1.1
Especially the sphinx version could be relevant.
from horton.
Mmm, I am not sure what I have done, but it seems to work now...
I had the issue on f27. So I tried it on my f26 system and it worked fine. So I tried again on the f27 system, and everything is rendering now. These are the dependencies on f26:
Version of dependencies:
breathe: 3.1.0
coverage: Coverage.py, version 4.4.1 with C extension
cppcheck: -- not found --
curl: curl 7.53.1 (x86_64-redhat-linux-gnu) libcurl/7.53.1 NSS/3.33 zlib/1.2.11 libidn2/2.0.4 libpsl/0.18.0 (+libidn2/2.0.3) libssh2/1.8.0 nghttp2/1.21.1
cython: Cython version 0.27.3
docutils: 0.13.1
doxygen: 1.8.13
gcc: gcc (GCC) 7.2.1 20170915 (Red Hat 7.2.1-2)
git: git version 2.13.6
gitpython: 2.1.7
h5py: 2.7.1
matplotlib: 2.0.0
nose: nosetests version 1.3.7
numpy: 1.12.1
pip: pip 9.0.1 from /usr/lib/python2.7/site-packages (python 2.7)
pycodestyle: -- not found --
pydocstyle: -- not found --
pylint:
python: Python 2.7.14
scipy: 0.19.1
sphinx: Sphinx (sphinx-build) 1.5.5
sphinx_rtd_theme: 0.2.4
sympy: 1.1.1
And these on f27:
Version of dependencies:
breathe: -- not found --
coverage: Coverage.py, version 4.4.2 with C extension
cppcheck: -- not found --
curl: curl 7.55.1 (x86_64-redhat-linux-gnu) libcurl/7.55.1 OpenSSL/1.1.0g zlib/1.2.11 libidn2/2.0.4 libpsl/0.18.0 (+libidn2/2.0.3) libssh2/1.8.0 nghttp2/1.25.0
cython: Cython version 0.27.3
docutils: 0.13.1
doxygen: 1.8.13
gcc: gcc (GCC) 7.2.1 20170915 (Red Hat 7.2.1-2)
git: git version 2.14.3
gitpython: -- not found --
h5py: 2.7.1
matplotlib: 2.0.0
nose: nosetests version 1.3.7
numpy: 1.13.3
pip: pip 9.0.1 from /usr/lib/python2.7/site-packages (python 2.7)
pycodestyle: -- not found --
pydocstyle: -- not found --
pylint:
python: Python 2.7.14
scipy: 0.19.1
sphinx: Sphinx (sphinx-build) 1.6.5
sphinx_rtd_theme: 0.2.4
sympy: -- not found --
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OK. on f27, part of the documentation should look better with the package python-breathe installed. Other than that, I can't really recommend anything. If all works and you have no further questions, feel free to close the issue.
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Thanks, everything seems to be working at the moment, so I will close the issue.
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I just made a bugfix release (horton 2.1.1) that contains the fix for this problem.
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