Dear All,

I could run successfully the example plot_bands.py
but noticed that after logging out of ipython I get the next error:
pymatgen.util.io_utils.FileLockException: /Users/temok/.abinit/abipy/nodecounter.lock: Timeout occurred.

Probably this issue is related to Issue #27 .

Thanks,
Temok

FULL LOG FILE FOR EXAMPLE plot_bands.py

_ls_
si_nscf_WFK-etsf.nc
plot_bands.py
plot_bands.py.log

cat plot_bands.py.log

In [1]: run plot_bands.py
/sw/lib/python2.7/site-packages/abipy-0.1.0-py2.7.egg/abipy/profile.py:192: UserWarning: Abipy configuration file /Users/temok/.abinit/abipy/abipyrc does not exist!
  warn("Abipy configuration file %s does not exist!" % filename)
ksampling {'kptopt': None, 'shifts': None, 'kptrlatt': None, 'mpdivs': None}
ksampling {'kptopt': None, 'shifts': None, 'kptrlatt': None, 'mpdivs': None}
old_fermie 0.0 eV, new fermie 5.59831252669

#############################
#  and the plot pops up, great!!! :)
#############################

In [2]: exit
Error in atexit._run_exitfuncs:
Traceback (most recent call last):
  File "/sw/lib/python2.7/atexit.py", line 24, in _run_exitfuncs
    func(*targs, **kargs)
  File "/sw/lib/python2.7/site-packages/pymatgen/io/abinitio/tasks.py", line 625, in save_lastnode_id
    with FileLock(_COUNTER_FILE) as lock:
  File "/sw/lib/python2.7/site-packages/pymatgen/util/io_utils.py", line 205, in __enter__
    self.acquire()
  File "/sw/lib/python2.7/site-packages/pymatgen/util/io_utils.py", line 184, in acquire
    self.lockfile)
FileLockException: /Users/temok/.abinit/abipy/nodecounter.lock: Timeout occured.
Error in sys.exitfunc:
Traceback (most recent call last):
  File "/sw/lib/python2.7/atexit.py", line 24, in _run_exitfuncs
    func(*targs, **kargs)
  File "/sw/lib/python2.7/site-packages/pymatgen/io/abinitio/tasks.py", line 625, in save_lastnode_id
    with FileLock(_COUNTER_FILE) as lock:
  File "/sw/lib/python2.7/site-packages/pymatgen/util/io_utils.py", line 205, in __enter__
    self.acquire()
  File "/sw/lib/python2.7/site-packages/pymatgen/util/io_utils.py", line 184, in acquire
    self.lockfile)
pymatgen.util.io_utils.FileLockException: /Users/temok/.abinit/abipy/nodecounter.lock: Timeout occured.

I have tried to install the stable release of abipy through pip but unfortunately pip cannot found the package.
The download link is absent at the pypi page https://pypi.python.org/pypi/abipy/0.1.0

So I resorted to build the latest version from git by following the instructions given on the page.
But then I faced some errors when I run the tests:

[root@comsics abipy]# nosetests
EEEEEEEEE...EE....E..EEEEEEE.EEEEEEEEEEEEEE......SSE.....S...EEE............EEEEEEEEEEEEE
======================================================================
ERROR: Failure: ImportError (cannot import name phonon_conv_flow)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/share/apps/estools/python/2.7.9/lib/python2.7/site-packages/nose/loader.py", line 420, in loadTestsFromName
    addr.filename, addr.module)
  File "/share/apps/estools/python/2.7.9/lib/python2.7/site-packages/nose/importer.py", line 47, in importFromPath
    return self.importFromDir(dir_path, fqname)
  File "/share/apps/estools/python/2.7.9/lib/python2.7/site-packages/nose/importer.py", line 94, in importFromDir
    mod = load_module(part_fqname, fh, filename, desc)
  File "/home/sheng/Desktop/program/Abinit/abipy/abipy/abilab.py", line 13, in <module>
    from pymatgen.io.abinitio.flows import (Flow, G0W0WithQptdmFlow, bandstructure_flow,
ImportError: cannot import name phonon_conv_flow

....

Is the problem lies in pymatgen version? (my pymatgen version is the latest 3.0.13)
Is the stable release through pip still available?
Thank you.

currently it returns the correction not the corrected value, which seems more intuitive

Dear developers,

I am new to abipy and try to use this tool to do high-throughput computation. I have downloaded a lot cif files from ICSD to prepare the input files for abinit. In the beginning, I need to optimize all the structures . However, I do not find how to create input files with optimization by abinp.py , and only the following calculations are considered:

    gs                  Build Abinit input for ground-state calculation.
    ebands              Build Abinit input for band structure calculations.
    phonons             Build Abinit input for phonon calculations.
    g0w0                Generate input files for G0W0 calculations.
    anaph               Build Anaddb input file for the computation of phonon
                        bands DOS.
    wannier90           Build wannier90 template input file from Abinit
                        input/output file. possibly with electron bands
    lobster             Build and print Lobster input file from directory with
                        files file (for pseudos) and GSR.nc output file
                        (multidatasets are not allowed). Supports also
                        directory with vasprun.xml and POTCAR file.

So, my question is how can i add calculation method into abinp.py (for example, generating input files for structure optimization)? Can you give me some guides?

Regards.

Pin.

When I test the example in the website:http://abinit.github.io/abipy/flow_gallery/run_phonons.html#sphx-glr-flow-gallery-run-phonons-py, I find that the high symmetry line of the phonon band structure of AlAs is different with the high symmetry line of the phonon band structure of AlAs from the website:https://www.materialsproject.org/materials/mp-2172/.
It seems that the right high symmetry line is Gamma-X-W-K-Gamma-L-U-W-L-K | U-X, which is followed the reference: Setyawan, W. & Curtarolo, S. High-throughput electronic band structure calculations: Challenges and tools. Computational Materials Science 49, 299 – 312 (2010)
Is this a bug? How can I fix it?

This similar bug is also found in the example (band structure of Si) of the website :http://abinit.github.io/abipy/flow_gallery/run_ht_si_ebands.html#sphx-glr-flow-gallery-run-ht-si-ebands-py
The version of abipy which I use is 0.5.0

hi,dear
when i test this example http://pythonhosted.org/abipy/examples/plot/plot_bz.html
It give me this message:
`ImportError Traceback (most recent call last)
in ()
----> 1 from abipy.abilab import abiopen
2 import abipy.data as abidata
3
4 # Open the WKF file.
5 wfk_file = abiopen(abidata.ref_file("si_scf_WFK.nc"))

/opt/anaconda2/lib/python2.7/site-packages/abipy/init.py in ()
16 #-----------------------------------------------------------------------------
17
---> 18 from abipy.core import release
19 #from abipy.profile import abipy_env
20 #from abipy.htc import Launcher, MassLauncher, AbinitInput

/opt/anaconda2/lib/python2.7/site-packages/abipy/core/init.py in ()
1 """Core objects."""
----> 2 from .kpoints import *
3 from .structure import *
4 from .symmetries import *
5 from .gsphere import *

/opt/anaconda2/lib/python2.7/site-packages/abipy/core/kpoints.py in ()
14 from monty.functools import lazy_property
15 from pymatgen.core.lattice import Lattice
---> 16 from pymatgen.serializers.json_coders import pmg_serialize
17 from pymatgen.serializers.pickle_coders import SlotPickleMixin
18 from abipy.iotools import ETSF_Reader

ImportError: No module named serializers.json_coders`

The pymatgen is already installed,
pip show pymatgen
Name: pymatgen Version: 2017.12.16 Summary: Python Materials Genomics is a robust materials analysis code that defines core object representations for structures and molecules with support for many electronic structure codes. It is currently the core analysis code powering the Materials Project (https://www.materialsproject.org). Home-page: http://www.pymatgen.org Author: Shyue Ping Ong Author-email: [email protected] License: MIT Location: /opt/anaconda2/lib/python2.7/site-packages Requires: numpy, six, requests, ruamel.yaml, monty, scipy, pydispatcher, tabulate, spglib, matplotlib, palettable, sympy, pandas, enum34
could you tell me how to solve it. thank you very much!

Hi,
I would like to test the phonon band structure convergence with ngkpt.
I would like to know if there is a way to choose the grid. It looks like that abinp.py does not take into account the ngkpt value from the input file.
Thank you for the code. It is really amazing !
All the best,
Luis

Code to reproduce this error:

import abipy.electrons as abielectrons 
abielectrons.ebands.ElectronBands.from_mpid('mp-565814',line_mode = True)

Produces the error:

ValueError                                Traceback (most recent call last)
/var/folders/pr/lgdp8dd12l5gbq5jhlzwtjlm0000gn/T/ipykernel_1625/626718764.py in <module>
      1 import abipy.electrons as abielectrons
----> 2 abielectrons.ebands.ElectronBands.from_mpid('mp-565814',line_mode = True)

~/.local/lib/python3.8/site-packages/abipy/electrons/ebands.py in from_mpid(cls, material_id, api_key, endpoint, nelect, has_timerev, nspinor, nspden, line_mode)
    481                 #print("iv_up", iv_up, "nelect: ", nelect)
    482                 if pmgb.is_spin_polarized:
--> 483                     iv_down = max(d["band_index"][PmgSpin.down])
    484                     assert iv_down == iv_up
    485 

ValueError: max() arg is an empty sequence

Any help would be greatly appreciated!

Ubuntu 13.04, the following error encountered with "pip install abipy",

Any ideas? Thanks!

$ sudo pip install abipy

Requirement already satisfied (use --upgrade to upgrade): abipy in /usr/local/lib/python2.7/dist-packages/abipy-0.1.0-py2.7.egg
Downloading/unpacking pymatgen>=2.7.3 (from abipy)
Running setup.py egg_info for package pymatgen

no previously-included directories found matching '*/*/tests'
no previously-included directories found matching '*/*/*/tests'

Requirement already satisfied (use --upgrade to upgrade): matplotlib>=1.1 in /usr/lib/pymodules/python2.7 (from abipy)
Requirement already satisfied (use --upgrade to upgrade): scipy>=0.10 in /usr/lib/python2.7/dist-packages (from abipy)
Requirement already satisfied (use --upgrade to upgrade): numpy>=1.5 in /usr/lib/python2.7/dist-packages (from abipy)
Downloading/unpacking netCDF4 (from abipy)
Running setup.py egg_info for package netCDF4

HDF5_DIR environment variable not set, checking some standard locations ..
checking /home/sherchy ...
checking /usr/local ...
checking /sw ...
checking /opt ...
checking /opt/local ...
checking /usr ...
HDF5 found in /usr

NETCDF4_DIR environment variable not set, checking standard locations..
checking /home/sherchy ...
checking /usr/local ...
checking /sw ...
checking /opt ...
checking /opt/local ...
checking /usr ...
Traceback (most recent call last):
  File "<string>", line 16, in <module>
  File "/tmp/pip-build-root/netCDF4/setup.py", line 198, in <module>
    raise ValueError('did not find netCDF version 4 headers')
ValueError: did not find netCDF version 4 headers
Complete output from command python setup.py egg_info:

HDF5_DIR environment variable not set, checking some standard locations ..

checking /home/sherchy ...

checking /usr/local ...

checking /sw ...

checking /opt ...

checking /opt/local ...

checking /usr ...

HDF5 found in /usr

NETCDF4_DIR environment variable not set, checking standard locations..

checking /home/sherchy ...

checking /usr/local ...

checking /sw ...

checking /opt ...

checking /opt/local ...

checking /usr ...

Traceback (most recent call last):

File "", line 16, in

File "/tmp/pip-build-root/netCDF4/setup.py", line 198, in

raise ValueError('did not find netCDF version 4 headers')

ValueError: did not find netCDF version 4 headers

Command python setup.py egg_info failed with error code 1 in /tmp/pip-build-root/netCDF4
Storing complete log in /home/sherchy/.pip/pip.log

Abipy imports monty.dict2namedtuple in a few places; this no longer exists in the
latest (official?) version of monty. This breaks Abipy.

Does abipy have a discussion forum or mailing list, where ideas can be exchanged, and/or questions can be asked and answered?

I specifically have two questions:

• Is there a way to utilize only the post-processing facilities of abipy on a local computer, assuming ABINIT calculations are completed on a remote cluster, and all the data has been transferred back to local computer?

• In general, abipy has data managers that allow you to specify how to run ABINIT on a cluster. However, it appears that the assumption is that the whole python scientific stack, jupyter notebooks, as well as abipy is installed on the cluster. My use case is such that I only want ABINIT on the cluster, while everything related to python, notebooks, and abipy is on my local computer. How to make such a setup work? I know there will have to be some scripts on the cluster that manage the execution of ABINIT, but I want those scripts to be as minimal as possible, only there to manage the ABINIT execution, while all the input/flow preparation, and post-processing happens on local computer. Any comments?

Thanks in advance

I run calculations in bunches and analyze the results in bunches.

I can connect and analyze the results of only the last flow in Jupiter notebook.

Is there a way to connect to the previously ran and closed flow for analyzing the results ?
Like saving all the calculations and close jupyter notebook and then come later to analyse the flow.

how can i get a picture on centos.Or structure.plot to a file. thank you

Hello!

I'm trying to run the example plot_bands.py from http://pythonhosted.org/abipy/examples/plot/plot_bands.html and gets the following error message:

python2.7 getbands.py
Traceback (most recent call last):
File "getbands.py", line 5, in
from abipy.abilab import abiopen
File "/usr/local/lib/python2.7/dist-packages/abipy-0.1.0-py2.7.egg/abipy/init.py", line 18, in
from abipy.core import release
File "/usr/local/lib/python2.7/dist-packages/abipy-0.1.0-py2.7.egg/abipy/core/init.py", line 2, in
from .kpoints import *
File "/usr/local/lib/python2.7/dist-packages/abipy-0.1.0-py2.7.egg/abipy/core/kpoints.py", line 15, in
from pymatgen.serializers.pickle_coders import SlotPickleMixin
ImportError: cannot import name SlotPickleMixin

I just changed the script name to getbands.py. After searching in pymatgen source I found that in the file

/usr/local/lib/python2.7/dist-packages/pymatgen/serializers/pickle_coders.py

the function SlotPickleMixin is not defined. So, I'm wondering if I'm using the wrong or incompatible version of pymatgen. Thanks in advance,

Camilo.

Dear Abipy Community,

I am having a hard time to install abipy on a mac laptop.
After doing
sudo /sw/bin/pip install --upgrade pip
Then searching for abipy
/sw/bin/pip search abipy
results in
abipy - ('Set of python modules and scripts to analyze the results of ABINIT computations.',)
Then doing
sudo /sw/bin/pip --log abipy.log -v -v -v install abipy
gives me
DistributionNotFound: No distributions at all found for abipy
I wonder if you would have an advice on this.

My pip version is
/sw/bin/pip --version
pip 1.5.4 from /sw/lib/python2.7/site-packages/pip-1.5.4-py2.7.egg (python 2.7)

The full [verbose] log file is at the end of this message,
With regards,
Temok

Downloading/unpacking abipy
Getting page https://pypi.python.org/simple/abipy/
URLs to search for versions for abipy:
https://pypi.python.org/simple/abipy/
Analyzing links from page https://pypi.python.org/simple/abipy/
Could not find any downloads that satisfy the requirement abipy
Cleaning up...
Removing temporary dir /private/tmp/pip_build_root...
No distributions at all found for abipy
Exception information:
Traceback (most recent call last):
File "/sw/lib/python2.7/site-packages/pip-1.5.4-py2.7.egg/pip/basecommand.py", line 122, in main
status = self.run(options, args)
File "/sw/lib/python2.7/site-packages/pip-1.5.4-py2.7.egg/pip/commands/install.py", line 278, in run
requirement_set.prepare_files(finder, force_root_egg_info=self.bundle, bundle=self.bundle)
File "/sw/lib/python2.7/site-packages/pip-1.5.4-py2.7.egg/pip/req.py", line 1177, in prepare_files
url = finder.find_requirement(req_to_install, upgrade=self.upgrade)
File "/sw/lib/python2.7/site-packages/pip-1.5.4-py2.7.egg/pip/index.py", line 277, in find_requirement
raise DistributionNotFound('No distributions at all found for %s' % req)
DistributionNotFound: No distributions at all found for abipy

Storing debug log for failure in /Users/temok/.pip/pip.log

Hi,
After successfully following the steps in the "Anaconda Howto" section (http://abinit.github.io/abipy/installation.html#contents), I got the following "strange" error message when trying to install abipy:

[ogando@PedroBala:~]$ conda install abipy -c abinit
Solving environment: failed

PackagesNotFoundError: The following packages are not available from current channels:

• abipy
• prettytable
• abipy
• pymatgen==2018.3.14

Current channels:

• https://conda.anaconda.org/abinit/linux-64
• https://conda.anaconda.org/abinit/noarch
• https://repo.anaconda.com/pkgs/main/linux-64
• https://repo.anaconda.com/pkgs/main/noarch
• https://repo.anaconda.com/pkgs/free/linux-64
• https://repo.anaconda.com/pkgs/free/noarch
• https://repo.anaconda.com/pkgs/r/linux-64
• https://repo.anaconda.com/pkgs/r/noarch
• https://repo.anaconda.com/pkgs/pro/linux-64
• https://repo.anaconda.com/pkgs/pro/noarch

To search for alternate channels that may provide the conda package you're
looking for, navigate to

https://anaconda.org

and use the search bar at the top of the page.

Could you, please, help me ?
All the best,
Luis

Hello abipy developers,

I have the following error when running the example code plot_bands.py (http://pythonhosted.org/abipy/examples/plot/plot_bands.html)

-----error-info-------------------------------------------------------------------------
TypeError Traceback (most recent call last)
in ()
8
9 # Open the GSR file and extract the band structure.
---> 10 with abiopen(filename) as ncfile:
11 ebands = ncfile.ebands
12

/Users/wzb/repos/abipy/abipy/abilab.py in abiopen(filepath)
189
190 cls = abifile_subclass_from_filename(filepath)
--> 191 return cls.from_file(filepath)
192
193

/Users/wzb/repos/abipy/abipy/electrons/gsr.py in from_file(cls, filepath)
42 def from_file(cls, filepath):
43 """Initialize the object from a Netcdf file"""
---> 44 return cls(filepath)
45
46 def init(self, filepath):

/Users/wzb/repos/abipy/abipy/electrons/gsr.py in init(self, filepath)
50
51 # Initialize the electron bands from file
---> 52 self._ebands = r.read_ebands()
53
54 # Add forces to structure

/Users/wzb/repos/abipy/abipy/electrons/ebands.py in read_ebands(self)
2358 nelect=self.read_nelect(),
2359 nspinor=self.read_nspinor(),
-> 2360 nspden=self.read_nspden(),
2361 nband_sk=self.read_nband_sk(),
2362 smearing=self.read_smearing(),

/Users/wzb/repos/abipy/abipy/electrons/ebands.py in read_nspden(self)
2374 """Number of spin-density components"""
2375 # FIXME: default 1 is needed for SIGRES files (abinit8)
-> 2376 return self.read_dimvalue("number_of_components", default=1)
2377
2378

TypeError: read_dimvalue() got an unexpected keyword argument 'default'

Could you pls do me favor to look into this problem?
I am using Abipy-0.1.0 and Abinit-7.10.5

Thanks
Zhenbin

When I do the band calculation，it always gives this：
“UserWarning:
The input structure does not match the expected standard primitive! The path can be incorrect. Use at your own risk.”

So，I check it carefully，use these code：
1. first step:

`import abipy.abilab as abilab
from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
import numpy as np

structure = abilab.Structure.from_file('Si_mp-149_computed.cif')
spg_a =SpacegroupAnalyzer(structure)
primitive_standard_structure=spg_a.get_primitive_standard_structure(international_monoclinic=False)
primitive_standard_structure.to(fmt='cif', filename='Si_mp-149_primitive_standard_structure.cif')
print(np.allclose(structure.lattice.matrix,structure.hsym_kpath.prim.lattice.matrix))
print(structure.lattice.matrix)
print(primitive_standard_structure.lattice.matrix)
print(structure.hsym_kpath.prim.lattice.matrix)`

output:
False
[[3.34889826 0. 1.93348731]
[1.11629942 3.15737156 1.93348731]
[0. 0. 3.86697462]]
[[4.39719264e-16 2.73436398e+00 2.73436398e+00]
[2.73436398e+00 0.00000000e+00 2.73436398e+00]
[2.73436398e+00 2.73436398e+00 3.34863009e-16]]
[[4.39719264e-16 2.73436398e+00 2.73436398e+00]
[2.73436398e+00 0.00000000e+00 2.73436398e+00]
[2.73436398e+00 2.73436398e+00 3.34863009e-16]]

2. second step:
`import abipy.abilab as abilab
from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
import numpy as np

structure = abilab.Structure.from_file('Si_mp-149_primitive_standard_structure.cif')
spg_analy =SpacegroupAnalyzer(structure)
primitive_standard_structure=spg_analy.get_primitive_standard_structure(international_monoclinic=False)
print(np.allclose(structure.lattice.matrix,structure.hsym_kpath.prim.lattice.matrix))
print(structure.lattice.matrix)
print(primitive_standard_structure.lattice.matrix)
print(structure.hsym_kpath.prim.lattice.matrix)`

output:
False
[[3.34889826 0. 1.93348731]
[1.11629942 3.15737156 1.93348731]
[0. 0. 3.86697462]]
[[4.39719264e-16 2.73436398e+00 2.73436398e+00]
[2.73436398e+00 0.00000000e+00 2.73436398e+00]
[2.73436398e+00 2.73436398e+00 3.34863009e-16]]
[[4.39719264e-16 2.73436398e+00 2.73436398e+00]
[2.73436398e+00 0.00000000e+00 2.73436398e+00]
[2.73436398e+00 2.73436398e+00 3.34863009e-16]]

Why "np.allclose(structure.lattice.matrix,structure.hsym_kpath.prim.lattice.matrix)" give "False" in the step 2 ?
The structure file download from here:
Si_mp-149_computed.cif
The abipy version is 0.6.0
The pymatgen version is 2019.3.13

Dear Abinit developers,

I have posted this issue on the pseudo_dojo branch as well as on abinit forum 9 days ago, but so far this has not been resolved yet. Can someone here help? Thanks!

Issue:
For elements Ge, Sb, Te, the PBEsol version of fully-relativistic, UPF pseudopotentials on pseudo dojo are of the wrong format (the file extension is ".upf", but the content is of the psp8 format). This is the case for both standard and stringent pseudos.

Best regards,
Jingyang

I get a parse error in abipy:

In [3]: abipy.abilab.abicheck()
AbiPy Manager:
[Qadapter 0]
ShellAdapter:localhost
Hardware:
   num_nodes: 1, sockets_per_node: 1, cores_per_socket: 2, mem_per_node 4096,
Qadapter selected: 0

---------------------------------------------------------------------------
KeyError                                  Traceback (most recent call last)
<ipython-input-3-a999053d8689> in <module>()
----> 1 abipy.abilab.abicheck()

/usr/local/lib/python3.6/dist-packages/abipy/abilab.py in abicheck(verbose)
    334     if manager is not None:
    335         cprint("AbiPy Manager:\n%s\n" % str(manager), color="green")
--> 336         build = AbinitBuild(manager=manager)
    337         if not build.has_netcdf: app("Abinit executable does not support netcdf")
    338         cprint("Abinitbuild:\n%s" % str(build), color="magenta")

/usr/local/lib/python3.6/dist-packages/abipy/flowtk/tasks.py in __init__(self, workdir, manager)
   1163                 self.has_netcdf = "netcdf" in line
   1164             if "openMP support" in line: self.has_omp = yesno2bool(line)
-> 1165             if "Parallel build" in line: self.has_mpi = yesno2bool(line)
   1166             if "Parallel I/O" in line: self.has_mpiio = yesno2bool(line)
   1167 

/usr/local/lib/python3.6/dist-packages/abipy/flowtk/tasks.py in yesno2bool(line)
   1155         def yesno2bool(line):
   1156             ans = line.split()[-1].lower()
-> 1157             return dict(yes=True, no=False, auto=True)[ans]
   1158 
   1159         # Parse info.

KeyError: ':'

I think this is because

antoine@beta ~/abipy $ abinit -b
 DATA TYPE INFORMATION: 
 REAL:      Data type name: REAL(DP) 
            Kind value:      8
            Precision:      15
            Smallest nonnegligible quantity relative to 1: 0.22204460E-015
            Smallest positive number:                      0.22250739E-307
            Largest representable number:                  0.17976931E+309
 INTEGER:   Data type name: INTEGER(default) 
            Kind value: 4
            Bit size:   32
            Largest representable number: 2147483647
 LOGICAL:   Data type name: LOGICAL 
            Kind value: 4
 CHARACTER: Data type name: CHARACTER             Kind value: 1
  MPI-IO support is OFF

 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
 CPP options activated during the build:

                    CC_GNU                   CXX_GNU                    FC_GNU
 
 HAVE_FC_ALLOCATABLE_DT...             HAVE_FC_ASYNC         HAVE_FC_BACKTRACE
 
  HAVE_FC_COMMAND_ARGUMENT      HAVE_FC_COMMAND_LINE        HAVE_FC_CONTIGUOUS
 
           HAVE_FC_CPUTIME              HAVE_FC_EXIT             HAVE_FC_FLUSH
 
             HAVE_FC_GAMMA            HAVE_FC_GETENV   HAVE_FC_IEEE_ARITHMETIC
 
   HAVE_FC_IEEE_EXCEPTIONS          HAVE_FC_INT_QUAD             HAVE_FC_IOMSG
 
     HAVE_FC_ISO_C_BINDING  HAVE_FC_ISO_FORTRAN_2008        HAVE_FC_LONG_LINES
 
        HAVE_FC_MOVE_ALLOC  HAVE_FC_ON_THE_FLY_SHAPE           HAVE_FC_PRIVATE
 
         HAVE_FC_PROTECTED           HAVE_FC_SHIFTLR         HAVE_FC_STREAM_IO
 
            HAVE_FC_SYSTEM                HAVE_FFTW3        HAVE_FFTW3_THREADS
 
          HAVE_FORTRAN2003                 HAVE_HDF5        HAVE_LIBPAW_ABINIT
 
      HAVE_LIBTETRA_ABINIT                HAVE_LIBXC         HAVE_LINALG_AXPBY
 
        HAVE_LINALG_GEMM3M               HAVE_NETCDF       HAVE_NETCDF_FORTRAN
 
                HAVE_NUMPY             HAVE_OS_LINUX         HAVE_TIMER_ABINIT
 
 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++


 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

 === Build Information === 
  Version       : 9.0.3
  Build target  : x86_64_linux_gnu7.5
  Build date    : 20200429

 === Compiler Suite === 
  C compiler       : gnu7.5
  C++ compiler     : gnu7.5
  Fortran compiler : gnu7.5
  CFLAGS           : -g -O2 -mtune=native -march=native
  CXXFLAGS         : -g -O2 -mtune=native -march=native
  FCFLAGS          : -g -ffree-line-length-none     -I/usr//include  -I/usr//include
  FC_LDFLAGS       : 

 === Optimizations === 
  Debug level        : @abi_debug_flavor@
  Optimization level : @abi_optim_flavor@
  Architecture       : unknown_unknown

 === Multicore === 
  Parallel build : 
  Parallel I/O   : 
  openMP support : 
  GPU support    : 

 === Connectors / Fallbacks === 
  LINALG flavor  : netlib+openblas
  FFT flavor     : fftw3-threads
  HDF5           : yes
  NetCDF         : yes
  NetCDF Fortran : yes
  LibXC          : yes
  Wannier90      : no

 === Experimental features === 
  Exports             : 
  GW double-precision : 

 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++


 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
 Default optimizations:
   -O2 -mtune=native -march=native


 Optimizations for 43_ptgroups:
   -O0


 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

and it's failing to parse the "multicore" section.

This is for abinit 9.0.3.

I having problem in setting fermi energy to zero in my band structure plot. I followed the official abipy plot example plot_bands.py, with the figure having its fermi level as computed in Abinit. I notice that in the ebands module there is a function _fix_fermie(), which should use efermi as the energy zero.

How should I modify the code so the data is shifted to that of zero fermi energy?

hello, I want to use abinit-6.8.1，but I can not find it. It seems like it is been erased from the abinit website, could you tell me how to get it. thank you very much!

Hello,

One of our users is trying to plot a band structure using Abipy:

from abipy.abilab import abiopen
import abipy.data as abidata

filename="big_GSR.nc"

with abiopen(filename) as ncfile:
    ebands = ncfile.ebands

ebands.plot(with_gaps=True, title="Band structure", show=False, savefig="bands.png")

ebands.kpoints.plot(show=False, savefig="kpoints.png")

This works for most inputs but he is getting an error with the big_GSR.nc file attached:

~/.conda/envs/abipy/lib/python3.7/site-packages/pymatgen/symmetry/kpath.py:180: UserWarning: The input structure does not match the expected standard primitive! The path can be incorrect. Use at your own risk.
  "The input structure does not match the expected standard primitive! "
Traceback (most recent call last):
  File "plot_ebands_user.py", line 9, in <module>
    ebands.plot(with_gaps=True, title="Silicon band structure", show=False, savefig="bands.png")
  File "~/.conda/envs/abipy/lib/python3.7/site-packages/pymatgen/util/plotting.py", line 573, in wrapper
    fig = func(*args, **kwargs)
  File "~/.conda/envs/abipy/lib/python3.7/site-packages/abipy/electrons/ebands.py", line 1967, in plot
    self.decorate_ax(ax, klabels=klabels)
  File "~/.conda/envs/abipy/lib/python3.7/site-packages/abipy/electrons/ebands.py", line 2256, in decorate_ax
    ticks, labels = self._make_ticks_and_labels(klabels)
  File "~/.conda/envs/abipy/lib/python3.7/site-packages/abipy/electrons/ebands.py", line 2410, in _make_ticks_and_labels
    d = self._auto_klabels
  File "~/.conda/envs/abipy/lib/python3.7/site-packages/monty/functools.py", line 238, in __get__
    value = self.__func(inst)
  File "~/.conda/envs/abipy/lib/python3.7/site-packages/abipy/electrons/ebands.py", line 560, in _auto_klabels
    name = kpoint.name if kpoint.name is not None else self.structure.findname_in_hsym_stars(kpoint)
  File "~/.conda/envs/abipy/lib/python3.7/site-packages/abipy/core/structure.py", line 1185, in findname_in_hsym_stars
    for star in self.hsym_stars:
  File "~/.conda/envs/abipy/lib/python3.7/site-packages/monty/functools.py", line 238, in __get__
    value = self.__func(inst)
  File "~/.conda/envs/abipy/lib/python3.7/site-packages/abipy/core/structure.py", line 1152, in hsym_stars
    return [kpoint.compute_star(self.abi_spacegroup.fm_symmops) for kpoint in self.hsym_kpoints]
  File "~/.conda/envs/abipy/lib/python3.7/site-packages/monty/functools.py", line 238, in __get__
    value = self.__func(inst)
  File "~/.conda/envs/abipy/lib/python3.7/site-packages/abipy/core/structure.py", line 1105, in hsym_kpoints
    name2frac_coords = self.hsym_kpath.kpath["kpoints"]
TypeError: 'NoneType' object is not subscriptable

The warning at the beginning might be relevant but it also appears for other input files for which the plots are successfully generated.

Best regards,
Rémi Lacroix

I try to plot DOS+BANDS from my GSR file, and i give in pycharm this error:

ValueError: Kpoint weights should sum up to one while sum_weights is 0.000
The list of kpoints does not represent a homogeneous sampling of the BZ
<class 'abipy.core.kpoints.Kpath'>
K-path contains 3 lines. Number of k-points in each line: [11, 13, 17]

I am trying to run the post process scripts (with AbinitGUI) to create Density of States and the band structure, and I encountered this error:

bsanddos(args.inputDos,args.inputBand,args.outputDos,args.outputBand,args.outputBoth,args.titleBS,args.titleDOS,args.show);
File "./H2/scripts/band+dos.py", line 9, in bsanddos
ebands = abipy.ebands.ElectronBands.from_ncfile(inputBand)
AttributeError: 'module' object has no attribute 'ebands'
!

Quick search suggested that an object 'ebands' exists in 'electrons' object, I tried that as well, did not work!

I'm a newbie, what should I do?

Dear devs,
While trying to use a Flow from the gallery using PhononWork, I've encountered an issue that the DDB files are only merged if you use scheduler, not if you use rapid to call tasks.

I'm trying to find a workaround to merge DDB files without using the scheduler.
I didn't find a way to create a task at the end of my PhononWork to merge files nor I find a way to artificially call on_all_ok(self).

Best regards,
Olivier

The abinit.pc file says

Libs: -L${libdir} -lab7_parser
Cflags: -I${includedir}/abinit

but no headers and libraries are installed.

OS: FreeBSD
Version: 8.8.2

Dear devs,
I'm trying to run the example flow run_mgb2_phonons_nkpt_tsmear.py. However, the second work fails, because the symbolic links for the wavefunctions do not have the proper netCDF file extension. The work w0 completes without problems, but the task w1/t0 fails with the error message:

--- !ERROR
src_file: m_nctk.F90
src_line: 896
mpi_rank: 0
message: |
    nf90_open_par: /home/antonius/Projects/AbipyTests/Production/130-phonons/flow_mgb2_phonons_nkpt_tsmear/w1/t0/indata/in_WFK.nc - NetCDF library returned:  NetCDF:   Error initializing for parallel access

Indeed, the symbolic link created in flow_mgb2_phonons_nkpt_tsmear/w1/t0/indata/ is called in_WFK but points to the file flow_mgb2_phonons_nkpt_tsmear/w0/t0/outdata/out_WFK.nc. Thus, it is missing the .nc extension and abinit complains about it.

Is there a quick way to fix this?

Hello,

I find that nosetests fail to execute a kpoint test, as you can see below.

• Is this a known issue? Is there a known fix?
• Are others experiencing this problem, or am I seeing malicious version+compilation+machine+OS interference?
• Is my analysis below correct?

Cheers!

Analysis:

My limited understanding of ABIPY leads me to think that the error is due to the fact that the decorator @returns_None_onfail on the reading routines in class KpointsReaderMixin isn't catching undefined variables in the netcdf file.

ABIPY tries to determine if a file contains a PATH or an IRR. BZ, but assumes an IRR. BZ by default. All variables are defined in the netcdf file, but when a PATH is present, the variables monkhorst_pack_folding, kpoint_grid_shift and kpoint_grid_vectors are not set.

ABIPY fails to catch that these variables are not set, reads their values on disk, which I guess are a set of binary zeros (for signed int32, - 1/2 (2**32)+1 = -2147483647, a value that appears below). ABIPY then fails to realize it is dealing with a PATH, which crashes the nosetest!

Failure output:

====================================================================FAIL: Test the reading of Kpoints from netcdf files.

Traceback (most recent call last):
File ".../abipy/abipy/core/tests/test_kpoints.py", line 167, in test_reading
self.assertTrue(kpoints.is_path)
AssertionError: False is not true
-------------------- >> begin captured stdout << ---------------------
About to read file: .../abipy/abipy/data/runs/data_si_ebands/outdata/si_scf_GSR.nc
ksampling {'kptopt': None, 'shifts': array([ 9.96920997e+36, 9.96920997e+36, 9.96920997e+36]), 'kptrlatt': array([[ 9.96920997e+36, 9.96920997e+36, 9.96920997e+36],
[ 9.96920997e+36, 9.96920997e+36, 9.96920997e+36],
[ 9.96920997e+36, 9.96920997e+36, 9.96920997e+36]]), 'mpdivs': array([8, 8, 8], dtype=int32)}
About to read file: .../abipy/abipy/data/runs/data_si_ebands/outdata/si_nscf_GSR.nc
ksampling {'kptopt': None, 'shifts': array([ 9.96920997e+36, 9.96920997e+36, 9.96920997e+36]), 'kptrlatt': array([[ 9.96920997e+36, 9.96920997e+36, 9.96920997e+36],
[ 9.96920997e+36, 9.96920997e+36, 9.96920997e+36],

[ 9.96920997e+36, 9.96920997e+36, 9.96920997e+36]]), 'mpdivs': array([-2147483647, -2147483647, -2147483647], dtype=int32)}

Collecting abipy
Downloading https://files.pythonhosted.org/packages/36/af/649c18c323504e445d22419fa6fcbf7f21a74f21b875340e7b0a5fe18303/abipy-0.5.0-py2.py3-none-any.whl (14.7MB)
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Requirement already satisfied: pandas in /usr/local/lib/python3.7/site-packages (from abipy) (0.23.1)
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Requirement already satisfied: netCDF4 in /usr/local/lib/python3.7/site-packages (from abipy) (1.4.0)
Collecting prettytable (from abipy)
Downloading https://files.pythonhosted.org/packages/ef/30/4b0746848746ed5941f052479e7c23d2b56d174b82f4fd34a25e389831f5/prettytable-0.7.2.tar.bz2
Collecting html2text (from abipy)
Downloading https://files.pythonhosted.org/packages/16/20/de2b458ef434713053dd83209a03a5431ebe0527c8e14d9ae7838ff67d8a/html2text-2018.1.9-py3-none-any.whl
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Collecting apscheduler==2.1.0 (from abipy)
Collecting pyyaml>=3.11 (from abipy)
Downloading https://files.pythonhosted.org/packages/4a/85/db5a2df477072b2902b0eb892feb37d88ac635d36245a72a6a69b23b383a/PyYAML-3.12.tar.gz (253kB)
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Collecting seaborn (from abipy)
Collecting pymatgen==2018.6.11 (from abipy)
Downloading https://files.pythonhosted.org/packages/e3/46/6d0a39b75776fc3297022ceb4997f2368fed8f8628388a0f1eeb43c851a4/pymatgen-2018.6.11.tar.gz (1.7MB)
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Collecting tqdm (from abipy)
Downloading https://files.pythonhosted.org/packages/93/24/6ab1df969db228aed36a648a8959d1027099ce45fad67532b9673d533318/tqdm-4.23.4-py2.py3-none-any.whl (42kB)
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Requirement already satisfied: mpmath>=0.19 in /usr/local/lib/python3.7/site-packages (from sympy->pymatgen==2018.6.11->abipy) (1.0.0)
Installing collected packages: prettytable, html2text, apscheduler, pyyaml, seaborn, pymatgen, tqdm, abipy
Running setup.py install for prettytable ... done
Running setup.py install for pyyaml ... error
Complete output from command /usr/local/opt/python/bin/python3.7 -u -c "import setuptools, tokenize;file='/private/tmp/pip-install-olko9aul/pyyaml/setup.py';f=getattr(tokenize, 'open', open)(file);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, file, 'exec'))" install --record /private/tmp/pip-record-3_n6shgj/install-record.txt --single-version-externally-managed --compile:
running install
running build
running build_py
creating build
creating build/lib.macosx-10.13-x86_64-3.7
creating build/lib.macosx-10.13-x86_64-3.7/yaml
copying lib3/yaml/scanner.py -> build/lib.macosx-10.13-x86_64-3.7/yaml
copying lib3/yaml/error.py -> build/lib.macosx-10.13-x86_64-3.7/yaml
copying lib3/yaml/constructor.py -> build/lib.macosx-10.13-x86_64-3.7/yaml
copying lib3/yaml/composer.py -> build/lib.macosx-10.13-x86_64-3.7/yaml
copying lib3/yaml/events.py -> build/lib.macosx-10.13-x86_64-3.7/yaml
copying lib3/yaml/init.py -> build/lib.macosx-10.13-x86_64-3.7/yaml
copying lib3/yaml/representer.py -> build/lib.macosx-10.13-x86_64-3.7/yaml
copying lib3/yaml/tokens.py -> build/lib.macosx-10.13-x86_64-3.7/yaml
copying lib3/yaml/dumper.py -> build/lib.macosx-10.13-x86_64-3.7/yaml
copying lib3/yaml/cyaml.py -> build/lib.macosx-10.13-x86_64-3.7/yaml
copying lib3/yaml/parser.py -> build/lib.macosx-10.13-x86_64-3.7/yaml
copying lib3/yaml/reader.py -> build/lib.macosx-10.13-x86_64-3.7/yaml
copying lib3/yaml/loader.py -> build/lib.macosx-10.13-x86_64-3.7/yaml
copying lib3/yaml/resolver.py -> build/lib.macosx-10.13-x86_64-3.7/yaml
copying lib3/yaml/serializer.py -> build/lib.macosx-10.13-x86_64-3.7/yaml
copying lib3/yaml/nodes.py -> build/lib.macosx-10.13-x86_64-3.7/yaml
copying lib3/yaml/emitter.py -> build/lib.macosx-10.13-x86_64-3.7/yaml
running build_ext
creating build/temp.macosx-10.13-x86_64-3.7
checking if libyaml is compilable
clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -I/usr/local/include -I/usr/local/opt/openssl/include -I/usr/local/opt/sqlite/include -I/usr/local/Cellar/python/3.7.0/Frameworks/Python.framework/Versions/3.7/include/python3.7m -c build/temp.macosx-10.13-x86_64-3.7/check_libyaml.c -o build/temp.macosx-10.13-x86_64-3.7/check_libyaml.o
checking if libyaml is linkable
clang build/temp.macosx-10.13-x86_64-3.7/check_libyaml.o -L/usr/local/lib -L/usr/local/opt/openssl/lib -L/usr/local/opt/sqlite/lib -lyaml -o build/temp.macosx-10.13-x86_64-3.7/check_libyaml
skipping 'ext/_yaml.c' Cython extension (up-to-date)
building '_yaml' extension
creating build/temp.macosx-10.13-x86_64-3.7/ext
clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -I/usr/local/include -I/usr/local/opt/openssl/include -I/usr/local/opt/sqlite/include -I/usr/local/Cellar/python/3.7.0/Frameworks/Python.framework/Versions/3.7/include/python3.7m -c ext/_yaml.c -o build/temp.macosx-10.13-x86_64-3.7/ext/_yaml.o
In file included from ext/_yaml.c:271:
ext/_yaml.h:10:9: warning: 'PyString_CheckExact' macro redefined [-Wmacro-redefined]
#define PyString_CheckExact PyBytes_CheckExact
^
ext/_yaml.c:139:11: note: previous definition is here
#define PyString_CheckExact PyUnicode_CheckExact
^
ext/_yaml.c:1410:17: warning: assigning to 'char *' from 'const char *' discards qualifiers [-Wincompatible-pointer-types-discards-qualifiers]
__pyx_v_value = yaml_get_version_string();
^ ~~~~~~~~~~~~~~~~~~~~~~~~~
ext/_yaml.c:2577:52: warning: incompatible pointer types passing 'int (void *, char *, size_t, size_t *)' (aka 'int (void *, char *, unsigned long, unsigned long *)') to parameter of type 'yaml_read_handler_t ' (aka 'int ()(void *, unsigned char *, unsigned long, unsigned long *)') [-Wincompatible-pointer-types]
yaml_parser_set_input((&__pyx_v_self->parser), __pyx_f_5_yaml_input_handler, ((void *)__pyx_v_self));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/local/include/yaml.h:1370:30: note: passing argument to parameter 'handler' here
yaml_read_handler_t *handler, void *data);
^
ext/_yaml.c:2818:59: warning: passing 'char *' to parameter of type 'const unsigned char *' converts between pointers to integer types with different sign [-Wpointer-sign]
yaml_parser_set_input_string((&__pyx_v_self->parser), PyString_AS_STRING(__pyx_v_stream), PyString_GET_SIZE(__pyx_v_stream));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ext/_yaml.h:11:29: note: expanded from macro 'PyString_AS_STRING'
#define PyString_AS_STRING PyBytes_AS_STRING
^
/usr/local/Cellar/python/3.7.0/Frameworks/Python.framework/Versions/3.7/include/python3.7m/bytesobject.h:87:31: note: expanded from macro 'PyBytes_AS_STRING'
#define PyBytes_AS_STRING(op) (assert(PyBytes_Check(op)),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/local/include/yaml.h:1344:30: note: passing argument to parameter 'input' here
const unsigned char *input, size_t size);
^
ext/_yaml.c:4572:38: warning: passing 'yaml_char_t *' (aka 'unsigned char *') to parameter of type 'const char *' converts between pointers to integer types with different sign [-Wpointer-sign]
__pyx_t_2 = PyUnicode_FromString(__pyx_v_token->data.tag_directive.handle); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 417, __pyx_L1_error)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/local/Cellar/python/3.7.0/Frameworks/Python.framework/Versions/3.7/include/python3.7m/unicodeobject.h:703:17: note: passing argument to parameter 'u' here
const char u / UTF-8 encoded string */
^
ext/_yaml.c:4584:38: warning: passing 'yaml_char_t *' (aka 'unsigned char *') to parameter of type 'const char *' converts between pointers to integer types with different sign [-Wpointer-sign]
__pyx_t_2 = PyUnicode_FromString(__pyx_v_token->data.tag_directive.prefix); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 418, __pyx_L1_error)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/local/Cellar/python/3.7.0/Frameworks/Python.framework/Versions/3.7/include/python3.7m/unicodeobject.h:703:17: note: passing argument to parameter 'u' here
const char u / UTF-8 encoded string */
^
ext/_yaml.c:5444:38: warning: passing 'yaml_char_t *' (aka 'unsigned char *') to parameter of type 'const char *' converts between pointers to integer types with different sign [-Wpointer-sign]
__pyx_t_2 = PyUnicode_FromString(__pyx_v_token->data.alias.value); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 448, __pyx_L1_error)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/local/Cellar/python/3.7.0/Frameworks/Python.framework/Versions/3.7/include/python3.7m/unicodeobject.h:703:17: note: passing argument to parameter 'u' here
const char u / UTF-8 encoded string */
^
ext/_yaml.c:5518:38: warning: passing 'yaml_char_t *' (aka 'unsigned char *') to parameter of type 'const char *' converts between pointers to integer types with different sign [-Wpointer-sign]
__pyx_t_2 = PyUnicode_FromString(__pyx_v_token->data.anchor.value); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 451, __pyx_L1_error)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/local/Cellar/python/3.7.0/Frameworks/Python.framework/Versions/3.7/include/python3.7m/unicodeobject.h:703:17: note: passing argument to parameter 'u' here
const char u / UTF-8 encoded string */
^
ext/_yaml.c:5592:38: warning: passing 'yaml_char_t *' (aka 'unsigned char *') to parameter of type 'const char *' converts between pointers to integer types with different sign [-Wpointer-sign]
__pyx_t_2 = PyUnicode_FromString(__pyx_v_token->data.tag.handle); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 454, __pyx_L1_error)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/local/Cellar/python/3.7.0/Frameworks/Python.framework/Versions/3.7/include/python3.7m/unicodeobject.h:703:17: note: passing argument to parameter 'u' here
const char u / UTF-8 encoded string */
^
ext/_yaml.c:5604:38: warning: passing 'yaml_char_t *' (aka 'unsigned char *') to parameter of type 'const char *' converts between pointers to integer types with different sign [-Wpointer-sign]
__pyx_t_2 = PyUnicode_FromString(__pyx_v_token->data.tag.suffix); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 455, __pyx_L1_error)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/local/Cellar/python/3.7.0/Frameworks/Python.framework/Versions/3.7/include/python3.7m/unicodeobject.h:703:17: note: passing argument to parameter 'u' here
const char u / UTF-8 encoded string */
^
ext/_yaml.c:5716:38: warning: passing 'yaml_char_t *' (aka 'unsigned char *') to parameter of type 'const char *' converts between pointers to integer types with different sign [-Wpointer-sign]
__pyx_t_2 = PyUnicode_DecodeUTF8(__pyx_v_token->data.scalar.value, __pyx_v_token->data.scalar.length, ((char *)"strict")); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 460, __pyx_L1_error)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/local/Cellar/python/3.7.0/Frameworks/Python.framework/Versions/3.7/include/python3.7m/unicodeobject.h:1299:17: note: passing argument to parameter 'string' here
const char string, / UTF-8 encoded string */
^
ext/_yaml.c:7424:42: warning: passing 'yaml_char_t *' (aka 'unsigned char *') to parameter of type 'const char *' converts between pointers to integer types with different sign [-Wpointer-sign]
__pyx_t_4 = PyUnicode_FromString(__pyx_v_tag_directive->handle); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 574, __pyx_L1_error)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/local/Cellar/python/3.7.0/Frameworks/Python.framework/Versions/3.7/include/python3.7m/unicodeobject.h:703:17: note: passing argument to parameter 'u' here
const char u / UTF-8 encoded string */
^
ext/_yaml.c:7436:42: warning: passing 'yaml_char_t *' (aka 'unsigned char *') to parameter of type 'const char *' converts between pointers to integer types with different sign [-Wpointer-sign]
__pyx_t_4 = PyUnicode_FromString(__pyx_v_tag_directive->prefix); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 575, __pyx_L1_error)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/local/Cellar/python/3.7.0/Frameworks/Python.framework/Versions/3.7/include/python3.7m/unicodeobject.h:703:17: note: passing argument to parameter 'u' here
const char u / UTF-8 encoded string */
^
ext/_yaml.c:7655:38: warning: passing 'yaml_char_t *' (aka 'unsigned char *') to parameter of type 'const char *' converts between pointers to integer types with different sign [-Wpointer-sign]
__pyx_t_4 = PyUnicode_FromString(__pyx_v_event->data.alias.anchor); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 586, __pyx_L1_error)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/local/Cellar/python/3.7.0/Frameworks/Python.framework/Versions/3.7/include/python3.7m/unicodeobject.h:703:17: note: passing argument to parameter 'u' here
const char u / UTF-8 encoded string */
^
ext/_yaml.c:7749:40: warning: passing 'yaml_char_t *' (aka 'unsigned char *') to parameter of type 'const char *' converts between pointers to integer types with different sign [-Wpointer-sign]
__pyx_t_4 = PyUnicode_FromString(__pyx_v_event->data.scalar.anchor); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 591, __pyx_L1_error)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/local/Cellar/python/3.7.0/Frameworks/Python.framework/Versions/3.7/include/python3.7m/unicodeobject.h:703:17: note: passing argument to parameter 'u' here
const char u / UTF-8 encoded string */
^
ext/_yaml.c:7790:40: warning: passing 'yaml_char_t *' (aka 'unsigned char *') to parameter of type 'const char *' converts between pointers to integer types with different sign [-Wpointer-sign]
__pyx_t_4 = PyUnicode_FromString(__pyx_v_event->data.scalar.tag); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 594, __pyx_L1_error)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/local/Cellar/python/3.7.0/Frameworks/Python.framework/Versions/3.7/include/python3.7m/unicodeobject.h:703:17: note: passing argument to parameter 'u' here
const char u / UTF-8 encoded string */
^
ext/_yaml.c:7811:38: warning: passing 'yaml_char_t *' (aka 'unsigned char *') to parameter of type 'const char *' converts between pointers to integer types with different sign [-Wpointer-sign]
__pyx_t_4 = PyUnicode_DecodeUTF8(__pyx_v_event->data.scalar.value, __pyx_v_event->data.scalar.length, ((char *)"strict")); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 595, __pyx_L1_error)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/local/Cellar/python/3.7.0/Frameworks/Python.framework/Versions/3.7/include/python3.7m/unicodeobject.h:1299:17: note: passing argument to parameter 'string' here
const char string, / UTF-8 encoded string */
^
ext/_yaml.c:8179:40: warning: passing 'yaml_char_t *' (aka 'unsigned char *') to parameter of type 'const char *' converts between pointers to integer types with different sign [-Wpointer-sign]
__pyx_t_4 = PyUnicode_FromString(__pyx_v_event->data.sequence_start.anchor); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 620, __pyx_L1_error)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/local/Cellar/python/3.7.0/Frameworks/Python.framework/Versions/3.7/include/python3.7m/unicodeobject.h:703:17: note: passing argument to parameter 'u' here
const char u / UTF-8 encoded string */
^
ext/_yaml.c:8220:40: warning: passing 'yaml_char_t *' (aka 'unsigned char *') to parameter of type 'const char *' converts between pointers to integer types with different sign [-Wpointer-sign]
__pyx_t_4 = PyUnicode_FromString(__pyx_v_event->data.sequence_start.tag); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 623, __pyx_L1_error)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/local/Cellar/python/3.7.0/Frameworks/Python.framework/Versions/3.7/include/python3.7m/unicodeobject.h:703:17: note: passing argument to parameter 'u' here
const char u / UTF-8 encoded string */
^
ext/_yaml.c:8449:40: warning: passing 'yaml_char_t *' (aka 'unsigned char *') to parameter of type 'const char *' converts between pointers to integer types with different sign [-Wpointer-sign]
__pyx_t_4 = PyUnicode_FromString(__pyx_v_event->data.mapping_start.anchor); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 637, __pyx_L1_error)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/local/Cellar/python/3.7.0/Frameworks/Python.framework/Versions/3.7/include/python3.7m/unicodeobject.h:703:17: note: passing argument to parameter 'u' here
const char u / UTF-8 encoded string */
^
ext/_yaml.c:8490:40: warning: passing 'yaml_char_t *' (aka 'unsigned char *') to parameter of type 'const char *' converts between pointers to integer types with different sign [-Wpointer-sign]
__pyx_t_4 = PyUnicode_FromString(__pyx_v_event->data.mapping_start.tag); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 640, __pyx_L1_error)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/local/Cellar/python/3.7.0/Frameworks/Python.framework/Versions/3.7/include/python3.7m/unicodeobject.h:703:17: note: passing argument to parameter 'u' here
const char u / UTF-8 encoded string */
^
ext/_yaml.c:10094:38: warning: passing 'yaml_char_t *' (aka 'unsigned char *') to parameter of type 'const char *' converts between pointers to integer types with different sign [-Wpointer-sign]
__pyx_t_3 = PyUnicode_FromString(__pyx_v_self->parsed_event.data.alias.anchor); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 734, __pyx_L1_error)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/local/Cellar/python/3.7.0/Frameworks/Python.framework/Versions/3.7/include/python3.7m/unicodeobject.h:703:17: note: passing argument to parameter 'u' here
const char u / UTF-8 encoded string */
^
ext/_yaml.c:10378:38: warning: passing 'yaml_char_t *' (aka 'unsigned char *') to parameter of type 'const char *' converts between pointers to integer types with different sign [-Wpointer-sign]
__pyx_t_6 = PyUnicode_FromString(__pyx_v_self->parsed_event.data.scalar.anchor); if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 750, __pyx_L1_error)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/local/Cellar/python/3.7.0/Frameworks/Python.framework/Versions/3.7/include/python3.7m/unicodeobject.h:703:17: note: passing argument to parameter 'u' here
const char u / UTF-8 encoded string */
^
ext/_yaml.c:10434:38: warning: passing 'yaml_char_t *' (aka 'unsigned char *') to parameter of type 'const char *' converts between pointers to integer types with different sign [-Wpointer-sign]
__pyx_t_6 = PyUnicode_FromString(__pyx_v_self->parsed_event.data.sequence_start.anchor); if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 753, __pyx_L1_error)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/local/Cellar/python/3.7.0/Frameworks/Python.framework/Versions/3.7/include/python3.7m/unicodeobject.h:703:17: note: passing argument to parameter 'u' here
const char u / UTF-8 encoded string */
^
ext/_yaml.c:10490:38: warning: passing 'yaml_char_t *' (aka 'unsigned char *') to parameter of type 'const char *' converts between pointers to integer types with different sign [-Wpointer-sign]
__pyx_t_6 = PyUnicode_FromString(__pyx_v_self->parsed_event.data.mapping_start.anchor); if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 756, __pyx_L1_error)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/local/Cellar/python/3.7.0/Frameworks/Python.framework/Versions/3.7/include/python3.7m/unicodeobject.h:703:17: note: passing argument to parameter 'u' here
const char u / UTF-8 encoded string */
^
ext/_yaml.c:11109:36: warning: passing 'yaml_char_t *' (aka 'unsigned char *') to parameter of type 'const char *' converts between pointers to integer types with different sign [-Wpointer-sign]
__pyx_t_2 = PyUnicode_DecodeUTF8(__pyx_v_self->parsed_event.data.scalar.value, __pyx_v_self->parsed_event.data.scalar.length, ((char *)"strict")); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 791, __pyx_L1_error)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/local/Cellar/python/3.7.0/Frameworks/Python.framework/Versions/3.7/include/python3.7m/unicodeobject.h:1299:17: note: passing argument to parameter 'string' here
const char string, / UTF-8 encoded string */
^
ext/_yaml.c:11310:38: warning: passing 'yaml_char_t *' (aka 'unsigned char *') to parameter of type 'const char *' converts between pointers to integer types with different sign [-Wpointer-sign]
__pyx_t_2 = PyUnicode_FromString(__pyx_v_self->parsed_event.data.scalar.tag); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 804, __pyx_L1_error)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/local/Cellar/python/3.7.0/Frameworks/Python.framework/Versions/3.7/include/python3.7m/unicodeobject.h:703:17: note: passing argument to parameter 'u' here
const char u / UTF-8 encoded string */
^
ext/_yaml.c:11841:38: warning: passing 'yaml_char_t *' (aka 'unsigned char *') to parameter of type 'const char *' converts between pointers to integer types with different sign [-Wpointer-sign]
__pyx_t_3 = PyUnicode_FromString(__pyx_v_self->parsed_event.data.sequence_start.tag); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 837, __pyx_L1_error)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/local/Cellar/python/3.7.0/Frameworks/Python.framework/Versions/3.7/include/python3.7m/unicodeobject.h:703:17: note: passing argument to parameter 'u' here
const char u / UTF-8 encoded string */
^
ext/_yaml.c:12435:38: warning: passing 'yaml_char_t *' (aka 'unsigned char *') to parameter of type 'const char *' converts between pointers to integer types with different sign [-Wpointer-sign]
__pyx_t_3 = PyUnicode_FromString(__pyx_v_self->parsed_event.data.mapping_start.tag); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 876, __pyx_L1_error)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/local/Cellar/python/3.7.0/Frameworks/Python.framework/Versions/3.7/include/python3.7m/unicodeobject.h:703:17: note: passing argument to parameter 'u' here
const char u / UTF-8 encoded string */
^
ext/_yaml.c:13141:87: warning: comparison of integers of different signs: 'int' and 'size_t' (aka 'unsigned long') [-Wsign-compare]
__pyx_t_3 = (((__pyx_v_parser->stream_cache_len - __pyx_v_parser->stream_cache_pos) < __pyx_v_size) != 0);
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ ~~~~~~~~~~~~
ext/_yaml.c:13630:53: warning: incompatible pointer types passing 'int (void *, char *, size_t)' (aka 'int (void *, char *, unsigned long)') to parameter of type 'yaml_write_handler_t ' (aka 'int ()(void *, unsigned char *, unsigned long)') [-Wincompatible-pointer-types]
yaml_emitter_set_output((&__pyx_v_self->emitter), __pyx_f_5_yaml_output_handler, ((void *)__pyx_v_self));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/local/include/yaml.h:1832:31: note: passing argument to parameter 'handler' here
yaml_write_handler_t *handler, void *data);
^
ext/_yaml.c:15002:44: warning: assigning to 'yaml_char_t *' (aka 'unsigned char *') from 'char *' converts between pointers to integer types with different sign [-Wpointer-sign]
__pyx_v_tag_directives_end->handle = PyString_AS_STRING(__pyx_v_handle);
^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ext/_yaml.c:15117:44: warning: assigning to 'yaml_char_t *' (aka 'unsigned char *') from 'char *' converts between pointers to integer types with different sign [-Wpointer-sign]
__pyx_v_tag_directives_end->prefix = PyString_AS_STRING(__pyx_v_prefix);
^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ext/_yaml.c:15454:62: warning: passing 'char *' to parameter of type 'yaml_char_t *' (aka 'unsigned char *') converts between pointers to integer types with different sign [-Wpointer-sign]
__pyx_t_2 = ((yaml_alias_event_initialize(__pyx_v_event, __pyx_v_anchor) == 0) != 0);
^~~~~~~~~~~~~~
/usr/local/include/yaml.h:555:63: note: passing argument to parameter 'anchor' here
yaml_alias_event_initialize(yaml_event_t *event, yaml_char_t *anchor);
^
ext/_yaml.c:16169:63: warning: passing 'char *' to parameter of type 'yaml_char_t *' (aka 'unsigned char *') converts between pointers to integer types with different sign [-Wpointer-sign]
__pyx_t_2 = ((yaml_scalar_event_initialize(__pyx_v_event, __pyx_v_anchor, __pyx_v_tag, __pyx_v_value, __pyx_v_length, __pyx_v_plain_implicit, __pyx_v_quoted_implicit, __pyx_v_scalar_style) == 0) != 0);
^~~~~~~~~~~~~~
/usr/local/include/yaml.h:581:22: note: passing argument to parameter 'anchor' here
yaml_char_t *anchor, yaml_char_t *tag,
^
ext/_yaml.c:16169:79: warning: passing 'char *' to parameter of type 'yaml_char_t *' (aka 'unsigned char *') converts between pointers to integer types with different sign [-Wpointer-sign]
__pyx_t_2 = ((yaml_scalar_event_initialize(__pyx_v_event, __pyx_v_anchor, __pyx_v_tag, __pyx_v_value, __pyx_v_length, __pyx_v_plain_implicit, __pyx_v_quoted_implicit, __pyx_v_scalar_style) == 0) != 0);
^~~~~~~~~~~
/usr/local/include/yaml.h:581:43: note: passing argument to parameter 'tag' here
yaml_char_t *anchor, yaml_char_t *tag,
^
ext/_yaml.c:16169:92: warning: passing 'char *' to parameter of type 'yaml_char_t *' (aka 'unsigned char *') converts between pointers to integer types with different sign [-Wpointer-sign]
__pyx_t_2 = ((yaml_scalar_event_initialize(__pyx_v_event, __pyx_v_anchor, __pyx_v_tag, __pyx_v_value, __pyx_v_length, __pyx_v_plain_implicit, __pyx_v_quoted_implicit, __pyx_v_scalar_style) == 0) != 0);
^~~~~~~~~~~~~
/usr/local/include/yaml.h:582:22: note: passing argument to parameter 'value' here
yaml_char_t *value, int length,
^
ext/_yaml.c:16603:71: warning: passing 'char *' to parameter of type 'yaml_char_t *' (aka 'unsigned char *') converts between pointers to integer types with different sign [-Wpointer-sign]
__pyx_t_3 = ((yaml_sequence_start_event_initialize(__pyx_v_event, __pyx_v_anchor, __pyx_v_tag, __pyx_v_implicit, __pyx_v_sequence_style) == 0) != 0);
^~~~~~~~~~~~~~
/usr/local/include/yaml.h:604:22: note: passing argument to parameter 'anchor' here
yaml_char_t *anchor, yaml_char_t *tag, int implicit,
^
ext/_yaml.c:16603:87: warning: passing 'char *' to parameter of type 'yaml_char_t *' (aka 'unsigned char *') converts between pointers to integer types with different sign [-Wpointer-sign]
__pyx_t_3 = ((yaml_sequence_start_event_initialize(__pyx_v_event, __pyx_v_anchor, __pyx_v_tag, __pyx_v_implicit, __pyx_v_sequence_style) == 0) != 0);
^~~~~~~~~~~
/usr/local/include/yaml.h:604:43: note: passing argument to parameter 'tag' here
yaml_char_t *anchor, yaml_char_t *tag, int implicit,
^
ext/_yaml.c:17037:70: warning: passing 'char *' to parameter of type 'yaml_char_t *' (aka 'unsigned char *') converts between pointers to integer types with different sign [-Wpointer-sign]
__pyx_t_2 = ((yaml_mapping_start_event_initialize(__pyx_v_event, __pyx_v_anchor, __pyx_v_tag, __pyx_v_implicit, __pyx_v_mapping_style) == 0) != 0);
^~~~~~~~~~~~~~
/usr/local/include/yaml.h:636:22: note: passing argument to parameter 'anchor' here
yaml_char_t *anchor, yaml_char_t *tag, int implicit,
^
ext/_yaml.c:17037:86: warning: passing 'char *' to parameter of type 'yaml_char_t *' (aka 'unsigned char *') converts between pointers to integer types with different sign [-Wpointer-sign]
__pyx_t_2 = ((yaml_mapping_start_event_initialize(__pyx_v_event, __pyx_v_anchor, __pyx_v_tag, __pyx_v_implicit, __pyx_v_mapping_style) == 0) != 0);
^~~~~~~~~~~
/usr/local/include/yaml.h:636:43: note: passing argument to parameter 'tag' here
yaml_char_t *anchor, yaml_char_t *tag, int implicit,
^
ext/_yaml.c:18516:42: warning: assigning to 'yaml_char_t *' (aka 'unsigned char *') from 'char *' converts between pointers to integer types with different sign [-Wpointer-sign]
__pyx_v_tag_directives_end->handle = PyString_AS_STRING(__pyx_v_handle);
^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ext/_yaml.c:18631:42: warning: assigning to 'yaml_char_t *' (aka 'unsigned char *') from 'char *' converts between pointers to integer types with different sign [-Wpointer-sign]
__pyx_v_tag_directives_end->prefix = PyString_AS_STRING(__pyx_v_prefix);
^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ext/_yaml.c:19491:65: warning: passing 'char *' to parameter of type 'yaml_char_t *' (aka 'unsigned char *') converts between pointers to integer types with different sign [-Wpointer-sign]
__pyx_t_2 = ((yaml_alias_event_initialize((&__pyx_v_event), __pyx_v_anchor) == 0) != 0);
^~~~~~~~~~~~~~
/usr/local/include/yaml.h:555:63: note: passing argument to parameter 'anchor' here
yaml_alias_event_initialize(yaml_event_t *event, yaml_char_t *anchor);
^
ext/_yaml.c:20240:68: warning: passing 'char *' to parameter of type 'yaml_char_t *' (aka 'unsigned char *') converts between pointers to integer types with different sign [-Wpointer-sign]
__pyx_t_2 = ((yaml_scalar_event_initialize((&__pyx_v_event), __pyx_v_anchor, __pyx_v_tag, __pyx_v_value, __pyx_v_length, __pyx_v_plain_implicit, __pyx_v_quoted_implicit, __pyx_v_scalar_style) == 0) != 0);
^~~~~~~~~~~~~~
/usr/local/include/yaml.h:581:22: note: passing argument to parameter 'anchor' here
yaml_char_t *anchor, yaml_char_t *tag,
^
ext/_yaml.c:20240:84: warning: passing 'char *' to parameter of type 'yaml_char_t *' (aka 'unsigned char *') converts between pointers to integer types with different sign [-Wpointer-sign]
__pyx_t_2 = ((yaml_scalar_event_initialize((&__pyx_v_event), __pyx_v_anchor, __pyx_v_tag, __pyx_v_value, __pyx_v_length, __pyx_v_plain_implicit, __pyx_v_quoted_implicit, __pyx_v_scalar_style) == 0) != 0);
^~~~~~~~~~~
/usr/local/include/yaml.h:581:43: note: passing argument to parameter 'tag' here
yaml_char_t *anchor, yaml_char_t *tag,
^
ext/_yaml.c:20240:97: warning: passing 'char *' to parameter of type 'yaml_char_t *' (aka 'unsigned char *') converts between pointers to integer types with different sign [-Wpointer-sign]
__pyx_t_2 = ((yaml_scalar_event_initialize((&__pyx_v_event), __pyx_v_anchor, __pyx_v_tag, __pyx_v_value, __pyx_v_length, __pyx_v_plain_implicit, __pyx_v_quoted_implicit, __pyx_v_scalar_style) == 0) != 0);
^~~~~~~~~~~~~
/usr/local/include/yaml.h:582:22: note: passing argument to parameter 'value' here
yaml_char_t *value, int length,
^
ext/_yaml.c:20605:76: warning: passing 'char *' to parameter of type 'yaml_char_t *' (aka 'unsigned char *') converts between pointers to integer types with different sign [-Wpointer-sign]
__pyx_t_2 = ((yaml_sequence_start_event_initialize((&__pyx_v_event), __pyx_v_anchor, __pyx_v_tag, __pyx_v_implicit, __pyx_v_sequence_style) == 0) != 0);
^~~~~~~~~~~~~~
/usr/local/include/yaml.h:604:22: note: passing argument to parameter 'anchor' here
yaml_char_t *anchor, yaml_char_t *tag, int implicit,
^
ext/_yaml.c:20605:92: warning: passing 'char *' to parameter of type 'yaml_char_t *' (aka 'unsigned char *') converts between pointers to integer types with different sign [-Wpointer-sign]
__pyx_t_2 = ((yaml_sequence_start_event_initialize((&__pyx_v_event), __pyx_v_anchor, __pyx_v_tag, __pyx_v_implicit, __pyx_v_sequence_style) == 0) != 0);
^~~~~~~~~~~
/usr/local/include/yaml.h:604:43: note: passing argument to parameter 'tag' here
yaml_char_t *anchor, yaml_char_t *tag, int implicit,
^
ext/_yaml.c:21113:75: warning: passing 'char *' to parameter of type 'yaml_char_t *' (aka 'unsigned char *') converts between pointers to integer types with different sign [-Wpointer-sign]
__pyx_t_2 = ((yaml_mapping_start_event_initialize((&__pyx_v_event), __pyx_v_anchor, __pyx_v_tag, __pyx_v_implicit, __pyx_v_mapping_style) == 0) != 0);
^~~~~~~~~~~~~~
/usr/local/include/yaml.h:636:22: note: passing argument to parameter 'anchor' here
yaml_char_t *anchor, yaml_char_t *tag, int implicit,
^
ext/_yaml.c:21113:91: warning: passing 'char *' to parameter of type 'yaml_char_t *' (aka 'unsigned char *') converts between pointers to integer types with different sign [-Wpointer-sign]
__pyx_t_2 = ((yaml_mapping_start_event_initialize((&__pyx_v_event), __pyx_v_anchor, __pyx_v_tag, __pyx_v_implicit, __pyx_v_mapping_style) == 0) != 0);
^~~~~~~~~~~
/usr/local/include/yaml.h:636:43: note: passing argument to parameter 'tag' here
yaml_char_t *anchor, yaml_char_t *tag, int implicit,
^
ext/_yaml.c:24143:21: error: no member named 'exc_type' in 'struct _ts'
*type = tstate->exc_type;
~~~~~~ ^
ext/_yaml.c:24144:22: error: no member named 'exc_value' in 'struct _ts'; did you mean 'curexc_value'?
*value = tstate->exc_value;
^~~~~~~~~
curexc_value
/usr/local/Cellar/python/3.7.0/Frameworks/Python.framework/Versions/3.7/include/python3.7m/pystate.h:237:15: note: 'curexc_value' declared here
PyObject *curexc_value;
^
ext/_yaml.c:24145:19: error: no member named 'exc_traceback' in 'struct _ts'; did you mean 'curexc_traceback'?
*tb = tstate->exc_traceback;
^~~~~~~~~~~~~
curexc_traceback
/usr/local/Cellar/python/3.7.0/Frameworks/Python.framework/Versions/3.7/include/python3.7m/pystate.h:238:15: note: 'curexc_traceback' declared here
PyObject *curexc_traceback;
^
ext/_yaml.c:24152:24: error: no member named 'exc_type' in 'struct _ts'
tmp_type = tstate->exc_type;
~~~~~~ ^
ext/_yaml.c:24153:25: error: no member named 'exc_value' in 'struct _ts'; did you mean 'curexc_value'?
tmp_value = tstate->exc_value;
^~~~~~~~~
curexc_value
/usr/local/Cellar/python/3.7.0/Frameworks/Python.framework/Versions/3.7/include/python3.7m/pystate.h:237:15: note: 'curexc_value' declared here
PyObject *curexc_value;
^
ext/_yaml.c:24154:22: error: no member named 'exc_traceback' in 'struct _ts'; did you mean 'curexc_traceback'?
tmp_tb = tstate->exc_traceback;
^~~~~~~~~~~~~
curexc_traceback
/usr/local/Cellar/python/3.7.0/Frameworks/Python.framework/Versions/3.7/include/python3.7m/pystate.h:238:15: note: 'curexc_traceback' declared here
PyObject *curexc_traceback;
^
ext/_yaml.c:24155:13: error: no member named 'exc_type' in 'struct _ts'
tstate->exc_type = type;
~~~~~~ ^
ext/_yaml.c:24156:13: error: no member named 'exc_value' in 'struct _ts'; did you mean 'curexc_value'?
tstate->exc_value = value;
^~~~~~~~~
curexc_value
/usr/local/Cellar/python/3.7.0/Frameworks/Python.framework/Versions/3.7/include/python3.7m/pystate.h:237:15: note: 'curexc_value' declared here
PyObject *curexc_value;
^
ext/_yaml.c:24157:13: error: no member named 'exc_traceback' in 'struct _ts'; did you mean 'curexc_traceback'?
tstate->exc_traceback = tb;
^~~~~~~~~~~~~
curexc_traceback
/usr/local/Cellar/python/3.7.0/Frameworks/Python.framework/Versions/3.7/include/python3.7m/pystate.h:238:15: note: 'curexc_traceback' declared here
PyObject *curexc_traceback;
^
ext/_yaml.c:24212:24: error: no member named 'exc_type' in 'struct _ts'
tmp_type = tstate->exc_type;
~~~~~~ ^
ext/_yaml.c:24213:25: error: no member named 'exc_value' in 'struct _ts'; did you mean 'curexc_value'?
tmp_value = tstate->exc_value;
^~~~~~~~~
curexc_value
/usr/local/Cellar/python/3.7.0/Frameworks/Python.framework/Versions/3.7/include/python3.7m/pystate.h:237:15: note: 'curexc_value' declared here
PyObject *curexc_value;
^
ext/_yaml.c:24214:22: error: no member named 'exc_traceback' in 'struct _ts'; did you mean 'curexc_traceback'?
tmp_tb = tstate->exc_traceback;
^~~~~~~~~~~~~
curexc_traceback
/usr/local/Cellar/python/3.7.0/Frameworks/Python.framework/Versions/3.7/include/python3.7m/pystate.h:238:15: note: 'curexc_traceback' declared here
PyObject *curexc_traceback;
^
ext/_yaml.c:24215:13: error: no member named 'exc_type' in 'struct _ts'
tstate->exc_type = local_type;
~~~~~~ ^
ext/_yaml.c:24216:13: error: no member named 'exc_value' in 'struct _ts'; did you mean 'curexc_value'?
tstate->exc_value = local_value;
^~~~~~~~~
curexc_value
/usr/local/Cellar/python/3.7.0/Frameworks/Python.framework/Versions/3.7/include/python3.7m/pystate.h:237:15: note: 'curexc_value' declared here
PyObject *curexc_value;
^
ext/_yaml.c:24217:13: error: no member named 'exc_traceback' in 'struct _ts'; did you mean 'curexc_traceback'?
tstate->exc_traceback = local_tb;
^~~~~~~~~~~~~
curexc_traceback
/usr/local/Cellar/python/3.7.0/Frameworks/Python.framework/Versions/3.7/include/python3.7m/pystate.h:238:15: note: 'curexc_traceback' declared here
PyObject *curexc_traceback;
^
51 warnings and 15 errors generated.
error: command 'clang' failed with exit status 1

----------------------------------------

Command "/usr/local/opt/python/bin/python3.7 -u -c "import setuptools, tokenize;file='/private/tmp/pip-install-olko9aul/pyyaml/setup.py';f=getattr(tokenize, 'open', open)(file);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, file, 'exec'))" install --record /private/tmp/pip-record-3_n6shgj/install-record.txt --single-version-externally-managed --compile" failed with error code 1 in /private/tmp/pip-install-olko9aul/pyyaml/

• abipy 0.7.0 pypi_0 pypi
• pymatgen 2022.0.8 py37h2527ec5_0 conda-forge

If I try to execute

abiopen.py graphene_o_DS2_GSR.nc --expose -sns=talk

I get the following error:

AttributeError: module 'pymatgen' has no attribute 'Structure'

It can be fixed be replacing pymatgen.Structure with pymatgen.core.Structure in abipy/core/structure.py and from pymatgen import SETTINGS with from pymatgen import SETTINGS in abipy/core/restapi.py

abirun.py path reset submits all the available jobs !

Could you please deactivate this fact, I would prefer "reset" just to reset the jobs, not to run all the available jobs. My scheduler will do it more accurately ! Or even rapid if I want to submit all.

Thanks !

Dear Abipy Community,

After installing abipy from source, i.e.
download abipy-master.zip
cd abipy-master
sudo /sw/bin/python2.7 setup.py build
sudo /sw/bin/python2.7 setup.py install

and then doing either
/sw/bin/python2.7 or /sw/bin/ipython
import abipy

leads to the errors appended at the end of this message.
I would appreciate any suggestions,

With regards,
Temok

_p.s.1: During the install, setup.py automatically installed 'paramiko_1.13' but afterwards it complained itself that paramiko < 1.13 is required. Hence I installed paramiko_1.12 via pip.
_p.s.2: Then setup.py installed " PyCifRW 3.6.2.linux-i686", but then caused:
Processing PyCifRW-3.6.2.linux-i686.tar.gz
error: Couldn't find a setup script in /tmp/easy_install-TK4ob1/PyCifRW-3.6.2.linux-i686.tar.gz
Hence I installed PyCifRW with
sudo /sw/bin/pip install https://pypi.python.org/packages/source/P/PyCifRW/PyCifRW-3.6.2.tar.gz#md5=3f1f6ea26ba3654d6a361a89b1fea480

And then finally setup.py finalized install, but importing abipy fails.

Appendixes:
(1) Errors from "import abipy"
(2) Log file from "setup.py install"

_(1) Errors from "import abipy"_

/sw/bin/python2.7
or
/sw/bin/ipython
then
import abipy

Traceback (most recent call last):
File "", line 1, in
File "abipy/init.py", line 18, in
from abipy.core import release
File "abipy/core/init.py", line 3, in
from .kpoints import *
File "abipy/core/kpoints.py", line 9, in
from abipy.iotools import as_etsfreader, ETSF_Reader
File "abipy/iotools/init.py", line 5, in
from .files import *
File "abipy/iotools/files.py", line 9, in
from pymatgen.io.abinitio.events import EventsParser
File "/sw/lib/python2.7/site-packages/pymatgen/io/abinitio/init.py", line 5, in
from .tasks import *
File "/sw/lib/python2.7/site-packages/pymatgen/io/abinitio/tasks.py", line 605, in
_COUNTER = int(fh.read())
ValueError: invalid literal for int() with base 10: ''

_Log file from "setup.py install"_

sudo /sw/bin/python2.7 setup.py install >& setup.install.log

running install
running bdist_egg
running egg_info
creating abipy.egg-info
writing requirements to abipy.egg-info/requires.txt
writing abipy.egg-info/PKG-INFO
writing top-level names to abipy.egg-info/top_level.txt
writing dependency_links to abipy.egg-info/dependency_links.txt
writing manifest file 'abipy.egg-info/SOURCES.txt'
reading manifest file 'abipy.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
warning: no files found matching '.json' under directory 'abipy'
warning: no files found matching '.py' under directory 'scripts'
no previously-included directories found matching '///tests'
warning: no files found matching '' under directory 'cython'
writing manifest file 'abipy.egg-info/SOURCES.txt'
installing library code to build/bdist.macosx-10.9-x86_64/egg
running install_lib
running build_py
creating build/bdist.macosx-10.9-x86_64/egg
creating build/bdist.macosx-10.9-x86_64/egg/abipy
copying build/lib/abipy/init.py -> build/bdist.macosx-10.9-x86_64/egg/abipy
copying build/lib/abipy/abilab.py -> build/bdist.macosx-10.9-x86_64/egg/abipy
creating build/bdist.macosx-10.9-x86_64/egg/abipy/abitools
copying build/lib/abipy/abitools/init.py -> build/bdist.macosx-10.9-x86_64/egg/abipy/abitools
copying build/lib/abipy/abitools/fftprof.py -> build/bdist.macosx-10.9-x86_64/egg/abipy/abitools
creating build/bdist.macosx-10.9-x86_64/egg/abipy/abitools/tests
copying build/lib/abipy/abitools/tests/init.py -> build/bdist.macosx-10.9-x86_64/egg/abipy/abitools/tests
creating build/bdist.macosx-10.9-x86_64/egg/abipy/core
copying build/lib/abipy/core/init.py -> build/bdist.macosx-10.9-x86_64/egg/abipy/core
copying build/lib/abipy/core/constants.py -> build/bdist.macosx-10.9-x86_64/egg/abipy/core
copying build/lib/abipy/core/exceptions.py -> build/bdist.macosx-10.9-x86_64/egg/abipy/core
copying build/lib/abipy/core/fields.py -> build/bdist.macosx-10.9-x86_64/egg/abipy/core
copying build/lib/abipy/core/func1d.py -> build/bdist.macosx-10.9-x86_64/egg/abipy/core
copying build/lib/abipy/core/gsphere.py -> build/bdist.macosx-10.9-x86_64/egg/abipy/core
copying build/lib/abipy/core/irrepsdb.py -> build/bdist.macosx-10.9-x86_64/egg/abipy/core
copying build/lib/abipy/core/kpoints.py -> build/bdist.macosx-10.9-x86_64/egg/abipy/core
copying build/lib/abipy/core/mesh3d.py -> build/bdist.macosx-10.9-x86_64/egg/abipy/core
copying build/lib/abipy/core/perl.py -> build/bdist.macosx-10.9-x86_64/egg/abipy/core
copying build/lib/abipy/core/release.py -> build/bdist.macosx-10.9-x86_64/egg/abipy/core
copying build/lib/abipy/core/structure.py -> build/bdist.macosx-10.9-x86_64/egg/abipy/core
copying build/lib/abipy/core/symmetries.py -> build/bdist.macosx-10.9-x86_64/egg/abipy/core
copying build/lib/abipy/core/tensor.py -> build/bdist.macosx-10.9-x86_64/egg/abipy/core
copying build/lib/abipy/core/testing.py -> build/bdist.macosx-10.9-x86_64/egg/abipy/core
creating build/bdist.macosx-10.9-x86_64/egg/abipy/core/tests
copying build/lib/abipy/core/tests/init.py -> build/bdist.macosx-10.9-x86_64/egg/abipy/core/tests
copying build/lib/abipy/core/tests/test_density.py -> build/bdist.macosx-10.9-x86_64/egg/abipy/core/tests
copying build/lib/abipy/core/tests/test_func1d.py -> build/bdist.macosx-10.9-x86_64/egg/abipy/core/tests
copying build/lib/abipy/core/tests/test_gsphere.py -> build/bdist.macosx-10.9-x86_64/egg/abipy/core/tests
copying build/lib/abipy/core/tests/test_kpoints.py -> build/bdist.macosx-10.9-x86_64/egg/abipy/core/tests
copying build/lib/abipy/core/tests/test_mesh3d.py -> build/bdist.macosx-10.9-x86_64/egg/abipy/core/tests
copying build/lib/abipy/core/tests/test_structure.py -> build/bdist.macosx-10.9-x86_64/egg/abipy/core/tests
copying build/lib/abipy/core/tests/test_symmetries.py -> build/bdist.macosx-10.9-x86_64/egg/abipy/core/tests
copying build/lib/abipy/core/tests/test_tensor.py -> build/bdist.macosx-10.9-x86_64/egg/abipy/core/tests
creating build/bdist.macosx-10.9-x86_64/egg/abipy/data
copying build/lib/abipy/data/init.py -> build/bdist.macosx-10.9-x86_64/egg/abipy/data
creating build/bdist.macosx-10.9-x86_64/egg/abipy/data/benchmarks
copying build/lib/abipy/data/benchmarks/init.py -> build/bdist.macosx-10.9-x86_64/egg/abipy/data/benchmarks
copying build/lib/abipy/data/benchmarks/bench_gs_cgwf.py -> build/bdist.macosx-10.9-x86_64/egg/abipy/data/benchmarks
copying build/lib/abipy/data/benchmarks/taskmanager.yml -> build/bdist.macosx-10.9-x86_64/egg/abipy/data/benchmarks
creating build/bdist.macosx-10.9-x86_64/egg/abipy/data/cifs
copying build/lib/abipy/data/cifs/si.cif -> build/bdist.macosx-10.9-x86_64/egg/abipy/data/cifs
copying build/lib/abipy/data/PROF_fourwf_cplex0_option3_istwfk1 -> build/bdist.macosx-10.9-x86_64/egg/abipy/data
creating build/bdist.macosx-10.9-x86_64/egg/abipy/data/pseudos
copying build/lib/abipy/data/pseudos/12mg.pspnc -> build/bdist.macosx-10.9-x86_64/egg/abipy/data/pseudos
copying build/lib/abipy/data/pseudos/13al.981214.fhi -> build/bdist.macosx-10.9-x86_64/egg/abipy/data/pseudos
copying build/lib/abipy/data/pseudos/14si.pspnc -> build/bdist.macosx-10.9-x86_64/egg/abipy/data/pseudos
copying build/lib/abipy/data/pseudos/26fe.pspnc -> build/bdist.macosx-10.9-x86_64/egg/abipy/data/pseudos
copying build/lib/abipy/data/pseudos/28ni.paw -> build/bdist.macosx-10.9-x86_64/egg/abipy/data/pseudos
copying build/lib/abipy/data/pseudos/31ga.pspnc -> build/bdist.macosx-10.9-x86_64/egg/abipy/data/pseudos
copying build/lib/abipy/data/pseudos/33as.pspnc -> build/bdist.macosx-10.9-x86_64/egg/abipy/data/pseudos
copying build/lib/abipy/data/pseudos/5b.pspnc -> build/bdist.macosx-10.9-x86_64/egg/abipy/data/pseudos
copying build/lib/abipy/data/pseudos/6c.pspnc -> build/bdist.macosx-10.9-x86_64/egg/abipy/data/pseudos
copying build/lib/abipy/data/pseudos/8o.2.paw -> build/bdist.macosx-10.9-x86_64/egg/abipy/data/pseudos
copying build/lib/abipy/data/pseudos/8o.pspnc -> build/bdist.macosx-10.9-x86_64/egg/abipy/data/pseudos
copying build/lib/abipy/data/pseudos/Si.GGA_PBE-JTH-paw.xml -> build/bdist.macosx-10.9-x86_64/egg/abipy/data/pseudos
copying build/lib/abipy/data/QPSC_SIGRES.nc -> build/bdist.macosx-10.9-x86_64/egg/abipy/data
creating build/bdist.macosx-10.9-x86_64/egg/abipy/data/runs
copying build/lib/abipy/data/runs/init.py -> build/bdist.macosx-10.9-x86_64/egg/abipy/data/runs
copying build/lib/abipy/data/runs/_run_all.py -> build/bdist.macosx-10.9-x86_64/egg/abipy/data/runs
creating build/bdist.macosx-10.9-x86_64/egg/abipy/data/runs/data_si_ebands
creating build/bdist.macosx-10.9-x86_64/egg/abipy/data/runs/data_si_ebands/outdata
copying build/lib/abipy/data/runs/data_si_ebands/outdata/si_DEN-etsf.nc -> build/bdist.macosx-10.9-x86_64/egg/abipy/data/runs/data_si_ebands/outdata
copying build/lib/abipy/data/runs/data_si_ebands/outdata/si_nscf_GSR.nc -> build/bdist.macosx-10.9-x86_64/egg/abipy/data/runs/data_si_ebands/outdata
copying build/lib/abipy/data/runs/data_si_ebands/outdata/si_nscf_WFK-etsf.nc -> build/bdist.macosx-10.9-x86_64/egg/abipy/data/runs/data_si_ebands/outdata
copying build/lib/abipy/data/runs/data_si_ebands/outdata/si_scf_GSR.nc -> build/bdist.macosx-10.9-x86_64/egg/abipy/data/runs/data_si_ebands/outdata
copying build/lib/abipy/data/runs/data_si_ebands/outdata/si_scf_WFK-etsf.nc -> build/bdist.macosx-10.9-x86_64/egg/abipy/data/runs/data_si_ebands/outdata
creating build/bdist.macosx-10.9-x86_64/egg/abipy/data/runs/data_si_g0w0
creating build/bdist.macosx-10.9-x86_64/egg/abipy/data/runs/data_si_g0w0/outdata
copying build/lib/abipy/data/runs/data_si_g0w0/outdata/si_g0w0ppm_nband10_SIGRES.nc -> build/bdist.macosx-10.9-x86_64/egg/abipy/data/runs/data_si_g0w0/outdata
copying build/lib/abipy/data/runs/data_si_g0w0/outdata/si_g0w0ppm_nband20_SIGRES.nc -> build/bdist.macosx-10.9-x86_64/egg/abipy/data/runs/data_si_g0w0/outdata
copying build/lib/abipy/data/runs/data_si_g0w0/outdata/si_g0w0ppm_nband30_SIGRES.nc -> build/bdist.macosx-10.9-x86_64/egg/abipy/data/runs/data_si_g0w0/outdata
copying build/lib/abipy/data/runs/events_parser.py -> build/bdist.macosx-10.9-x86_64/egg/abipy/data/runs
copying build/lib/abipy/data/runs/extract_docs.py -> build/bdist.macosx-10.9-x86_64/egg/abipy/data/runs
copying build/lib/abipy/data/runs/qptdm_workflow.py -> build/bdist.macosx-10.9-x86_64/egg/abipy/data/runs
copying build/lib/abipy/data/runs/README.rst -> build/bdist.macosx-10.9-x86_64/egg/abipy/data/runs
copying build/lib/abipy/data/runs/run_deltafactor.py -> build/bdist.macosx-10.9-x86_64/egg/abipy/data/runs
copying build/lib/abipy/data/runs/run_fe_ebands.py -> build/bdist.macosx-10.9-x86_64/egg/abipy/data/runs
copying build/lib/abipy/data/runs/run_gwconv_ecuteps.py -> build/bdist.macosx-10.9-x86_64/egg/abipy/data/runs
copying build/lib/abipy/data/runs/run_ht_si_bsemdf.py -> build/bdist.macosx-10.9-x86_64/egg/abipy/data/runs
copying build/lib/abipy/data/runs/run_ht_si_ebands.py -> build/bdist.macosx-10.9-x86_64/egg/abipy/data/runs
copying build/lib/abipy/data/runs/run_ht_si_g0w0ppm.py -> build/bdist.macosx-10.9-x86_64/egg/abipy/data/runs
copying build/lib/abipy/data/runs/run_ldaus.py -> build/bdist.macosx-10.9-x86_64/egg/abipy/data/runs
copying build/lib/abipy/data/runs/run_mgb2_edoses.py -> build/bdist.macosx-10.9-x86_64/egg/abipy/data/runs
copying build/lib/abipy/data/runs/run_optic.py -> build/bdist.macosx-10.9-x86_64/egg/abipy/data/runs
copying build/lib/abipy/data/runs/run_phfrozen_bands.py -> build/bdist.macosx-10.9-x86_64/egg/abipy/data/runs
copying build/lib/abipy/data/runs/run_phonons.py -> build/bdist.macosx-10.9-x86_64/egg/abipy/data/runs
copying build/lib/abipy/data/runs/run_qptdmscr.py -> build/bdist.macosx-10.9-x86_64/egg/abipy/data/runs
copying build/lib/abipy/data/runs/run_raman.py -> build/bdist.macosx-10.9-x86_64/egg/abipy/data/runs
copying build/lib/abipy/data/runs/run_raman_optic.py -> build/bdist.macosx-10.9-x86_64/egg/abipy/data/runs
copying build/lib/abipy/data/runs/run_relax.py -> build/bdist.macosx-10.9-x86_64/egg/abipy/data/runs
copying build/lib/abipy/data/runs/run_si_ebands.py -> build/bdist.macosx-10.9-x86_64/egg/abipy/data/runs
copying build/lib/abipy/data/runs/run_si_g0w0.py -> build/bdist.macosx-10.9-x86_64/egg/abipy/data/runs
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copying build/lib/abipy/data/runs/scheduler.yml -> build/bdist.macosx-10.9-x86_64/egg/abipy/data/runs
copying build/lib/abipy/data/runs/taskmanager.yml -> build/bdist.macosx-10.9-x86_64/egg/abipy/data/runs
copying build/lib/abipy/data/runs/wykoff.py -> build/bdist.macosx-10.9-x86_64/egg/abipy/data/runs
copying build/lib/abipy/data/tbs_4o_DS2_MDF.nc -> build/bdist.macosx-10.9-x86_64/egg/abipy/data
copying build/lib/abipy/data/tgw1_9o_DS4_SIGRES.nc -> build/bdist.macosx-10.9-x86_64/egg/abipy/data
copying build/lib/abipy/data/tgw2_4o_SIGRES.nc -> build/bdist.macosx-10.9-x86_64/egg/abipy/data
copying build/lib/abipy/data/trf2_5.out_PHBST.nc -> build/bdist.macosx-10.9-x86_64/egg/abipy/data
copying build/lib/abipy/data/trf2_5.out_PHDOS.nc -> build/bdist.macosx-10.9-x86_64/egg/abipy/data
copying build/lib/abipy/data/ucells.py -> build/bdist.macosx-10.9-x86_64/egg/abipy/data
creating build/bdist.macosx-10.9-x86_64/egg/abipy/electrons
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copying build/lib/abipy/electrons/bse.py -> build/bdist.macosx-10.9-x86_64/egg/abipy/electrons
copying build/lib/abipy/electrons/ebands.py -> build/bdist.macosx-10.9-x86_64/egg/abipy/electrons
copying build/lib/abipy/electrons/edos.py -> build/bdist.macosx-10.9-x86_64/egg/abipy/electrons
copying build/lib/abipy/electrons/gsr.py -> build/bdist.macosx-10.9-x86_64/egg/abipy/electrons
copying build/lib/abipy/electrons/gw.py -> build/bdist.macosx-10.9-x86_64/egg/abipy/electrons
copying build/lib/abipy/electrons/scissors.py -> build/bdist.macosx-10.9-x86_64/egg/abipy/electrons
creating build/bdist.macosx-10.9-x86_64/egg/abipy/electrons/tests
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copying build/lib/abipy/electrons/tests/test_bse.py -> build/bdist.macosx-10.9-x86_64/egg/abipy/electrons/tests
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copying build/lib/abipy/electrons/tests/test_gsr.py -> build/bdist.macosx-10.9-x86_64/egg/abipy/electrons/tests
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copying build/lib/abipy/extensions/test_kpoints.py -> build/bdist.macosx-10.9-x86_64/egg/abipy/extensions
creating build/bdist.macosx-10.9-x86_64/egg/abipy/gui
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creating build/bdist.macosx-10.9-x86_64/egg/abipy/gui/awx
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copying build/lib/abipy/gui/awx/apps.py -> build/bdist.macosx-10.9-x86_64/egg/abipy/gui/awx
copying build/lib/abipy/gui/awx/core.py -> build/bdist.macosx-10.9-x86_64/egg/abipy/gui/awx
copying build/lib/abipy/gui/awx/dialogs.py -> build/bdist.macosx-10.9-x86_64/egg/abipy/gui/awx
copying build/lib/abipy/gui/awx/eggs.py -> build/bdist.macosx-10.9-x86_64/egg/abipy/gui/awx
copying build/lib/abipy/gui/awx/func1dframe.py -> build/bdist.macosx-10.9-x86_64/egg/abipy/gui/awx
copying build/lib/abipy/gui/awx/grids.py -> build/bdist.macosx-10.9-x86_64/egg/abipy/gui/awx
creating build/bdist.macosx-10.9-x86_64/egg/abipy/gui/awx/images
copying build/lib/abipy/gui/awx/images/abipy.png -> build/bdist.macosx-10.9-x86_64/egg/abipy/gui/awx/images
copying build/lib/abipy/gui/awx/images/abipy0.png -> build/bdist.macosx-10.9-x86_64/egg/abipy/gui/awx/images
copying build/lib/abipy/gui/awx/images/abipy1.png -> build/bdist.macosx-10.9-x86_64/egg/abipy/gui/awx/images
copying build/lib/abipy/gui/awx/images/abipy2.png -> build/bdist.macosx-10.9-x86_64/egg/abipy/gui/awx/images
copying build/lib/abipy/gui/awx/images/abipy3.png -> build/bdist.macosx-10.9-x86_64/egg/abipy/gui/awx/images
copying build/lib/abipy/gui/awx/images/abipy4.png -> build/bdist.macosx-10.9-x86_64/egg/abipy/gui/awx/images
copying build/lib/abipy/gui/awx/images/abipy5.png -> build/bdist.macosx-10.9-x86_64/egg/abipy/gui/awx/images
copying build/lib/abipy/gui/awx/images/abipy6.png -> build/bdist.macosx-10.9-x86_64/egg/abipy/gui/awx/images
copying build/lib/abipy/gui/awx/images/abipy7.png -> build/bdist.macosx-10.9-x86_64/egg/abipy/gui/awx/images
copying build/lib/abipy/gui/awx/images/abipy8.png -> build/bdist.macosx-10.9-x86_64/egg/abipy/gui/awx/images
copying build/lib/abipy/gui/awx/images/browse.png -> build/bdist.macosx-10.9-x86_64/egg/abipy/gui/awx/images
copying build/lib/abipy/gui/awx/images/bs.png -> build/bdist.macosx-10.9-x86_64/egg/abipy/gui/awx/images
copying build/lib/abipy/gui/awx/images/bz.png -> build/bdist.macosx-10.9-x86_64/egg/abipy/gui/awx/images
copying build/lib/abipy/gui/awx/images/chk.png -> build/bdist.macosx-10.9-x86_64/egg/abipy/gui/awx/images
copying build/lib/abipy/gui/awx/images/crystal.png -> build/bdist.macosx-10.9-x86_64/egg/abipy/gui/awx/images
copying build/lib/abipy/gui/awx/images/dos.png -> build/bdist.macosx-10.9-x86_64/egg/abipy/gui/awx/images
copying build/lib/abipy/gui/awx/images/empty.png -> build/bdist.macosx-10.9-x86_64/egg/abipy/gui/awx/images
copying build/lib/abipy/gui/awx/images/env.png -> build/bdist.macosx-10.9-x86_64/egg/abipy/gui/awx/images
copying build/lib/abipy/gui/awx/images/in.png -> build/bdist.macosx-10.9-x86_64/egg/abipy/gui/awx/images
copying build/lib/abipy/gui/awx/images/jdos.png -> build/bdist.macosx-10.9-x86_64/egg/abipy/gui/awx/images
copying build/lib/abipy/gui/awx/images/log.png -> build/bdist.macosx-10.9-x86_64/egg/abipy/gui/awx/images
copying build/lib/abipy/gui/awx/images/log_evt.png -> build/bdist.macosx-10.9-x86_64/egg/abipy/gui/awx/images
copying build/lib/abipy/gui/awx/images/out.png -> build/bdist.macosx-10.9-x86_64/egg/abipy/gui/awx/images
copying build/lib/abipy/gui/awx/images/out_evt.png -> build/bdist.macosx-10.9-x86_64/egg/abipy/gui/awx/images
copying build/lib/abipy/gui/awx/images/qpmarkers.png -> build/bdist.macosx-10.9-x86_64/egg/abipy/gui/awx/images
copying build/lib/abipy/gui/awx/images/qpresults.png -> build/bdist.macosx-10.9-x86_64/egg/abipy/gui/awx/images
copying build/lib/abipy/gui/awx/images/qpscissor.png -> build/bdist.macosx-10.9-x86_64/egg/abipy/gui/awx/images
copying build/lib/abipy/gui/awx/images/refresh.png -> build/bdist.macosx-10.9-x86_64/egg/abipy/gui/awx/images
copying build/lib/abipy/gui/awx/images/run.png -> build/bdist.macosx-10.9-x86_64/egg/abipy/gui/awx/images
copying build/lib/abipy/gui/awx/images/script.png -> build/bdist.macosx-10.9-x86_64/egg/abipy/gui/awx/images
copying build/lib/abipy/gui/awx/images/struct.png -> build/bdist.macosx-10.9-x86_64/egg/abipy/gui/awx/images
copying build/lib/abipy/gui/awx/images/term.png -> build/bdist.macosx-10.9-x86_64/egg/abipy/gui/awx/images
copying build/lib/abipy/gui/awx/images/timer.png -> build/bdist.macosx-10.9-x86_64/egg/abipy/gui/awx/images
copying build/lib/abipy/gui/awx/images/vers.png -> build/bdist.macosx-10.9-x86_64/egg/abipy/gui/awx/images
copying build/lib/abipy/gui/awx/images/wave.png -> build/bdist.macosx-10.9-x86_64/egg/abipy/gui/awx/images
copying build/lib/abipy/gui/awx/images/wfk.png -> build/bdist.macosx-10.9-x86_64/egg/abipy/gui/awx/images
copying build/lib/abipy/gui/awx/panels.py -> build/bdist.macosx-10.9-x86_64/egg/abipy/gui/awx
copying build/lib/abipy/gui/awx/threads.py -> build/bdist.macosx-10.9-x86_64/egg/abipy/gui/awx
copying build/lib/abipy/gui/baseviewer.py -> build/bdist.macosx-10.9-x86_64/egg/abipy/gui
copying build/lib/abipy/gui/browser.py -> build/bdist.macosx-10.9-x86_64/egg/abipy/gui
copying build/lib/abipy/gui/comparison.py -> build/bdist.macosx-10.9-x86_64/egg/abipy/gui
copying build/lib/abipy/gui/converter.py -> build/bdist.macosx-10.9-x86_64/egg/abipy/gui
copying build/lib/abipy/gui/editor.py -> build/bdist.macosx-10.9-x86_64/egg/abipy/gui
copying build/lib/abipy/gui/electronswx.py -> build/bdist.macosx-10.9-x86_64/egg/abipy/gui
copying build/lib/abipy/gui/eos.py -> build/bdist.macosx-10.9-x86_64/egg/abipy/gui
copying build/lib/abipy/gui/events.py -> build/bdist.macosx-10.9-x86_64/egg/abipy/gui
copying build/lib/abipy/gui/fftprof.py -> build/bdist.macosx-10.9-x86_64/egg/abipy/gui
copying build/lib/abipy/gui/flowsdb.py -> build/bdist.macosx-10.9-x86_64/egg/abipy/gui
copying build/lib/abipy/gui/flowviewer.py -> build/bdist.macosx-10.9-x86_64/egg/abipy/gui
copying build/lib/abipy/gui/gsrviewer.py -> build/bdist.macosx-10.9-x86_64/egg/abipy/gui
copying build/lib/abipy/gui/kpoints.py -> build/bdist.macosx-10.9-x86_64/egg/abipy/gui
copying build/lib/abipy/gui/mdfviewer.py -> build/bdist.macosx-10.9-x86_64/egg/abipy/gui
copying build/lib/abipy/gui/mixins.py -> build/bdist.macosx-10.9-x86_64/egg/abipy/gui
copying build/lib/abipy/gui/popupmenus.py -> build/bdist.macosx-10.9-x86_64/egg/abipy/gui
copying build/lib/abipy/gui/scissors.py -> build/bdist.macosx-10.9-x86_64/egg/abipy/gui
copying build/lib/abipy/gui/sigresviewer.py -> build/bdist.macosx-10.9-x86_64/egg/abipy/gui
copying build/lib/abipy/gui/structure.py -> build/bdist.macosx-10.9-x86_64/egg/abipy/gui
copying build/lib/abipy/gui/timer.py -> build/bdist.macosx-10.9-x86_64/egg/abipy/gui
copying build/lib/abipy/gui/wfkviewer.py -> build/bdist.macosx-10.9-x86_64/egg/abipy/gui
copying build/lib/abipy/gui/wxapps.py -> build/bdist.macosx-10.9-x86_64/egg/abipy/gui
copying build/lib/abipy/gui/wxncview.py -> build/bdist.macosx-10.9-x86_64/egg/abipy/gui
creating build/bdist.macosx-10.9-x86_64/egg/abipy/htc
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copying build/lib/abipy/htc/abinitfiles.py -> build/bdist.macosx-10.9-x86_64/egg/abipy/htc
copying build/lib/abipy/htc/abinitinput.py -> build/bdist.macosx-10.9-x86_64/egg/abipy/htc
copying build/lib/abipy/htc/abivars.py -> build/bdist.macosx-10.9-x86_64/egg/abipy/htc
copying build/lib/abipy/htc/abivars_db.py -> build/bdist.macosx-10.9-x86_64/egg/abipy/htc
copying build/lib/abipy/htc/clusters.py -> build/bdist.macosx-10.9-x86_64/egg/abipy/htc
copying build/lib/abipy/htc/filesfile.py -> build/bdist.macosx-10.9-x86_64/egg/abipy/htc
copying build/lib/abipy/htc/input.py -> build/bdist.macosx-10.9-x86_64/egg/abipy/htc
copying build/lib/abipy/htc/inputfile.py -> build/bdist.macosx-10.9-x86_64/egg/abipy/htc
copying build/lib/abipy/htc/jobfile.py -> build/bdist.macosx-10.9-x86_64/egg/abipy/htc
copying build/lib/abipy/htc/launcher.py -> build/bdist.macosx-10.9-x86_64/egg/abipy/htc
copying build/lib/abipy/htc/robots.py -> build/bdist.macosx-10.9-x86_64/egg/abipy/htc
creating build/bdist.macosx-10.9-x86_64/egg/abipy/htc/tests
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copying build/lib/abipy/htc/tests/test_filesfile.py -> build/bdist.macosx-10.9-x86_64/egg/abipy/htc/tests
copying build/lib/abipy/htc/tests/test_input.py -> build/bdist.macosx-10.9-x86_64/egg/abipy/htc/tests
copying build/lib/abipy/htc/tests/test_inputfile.py -> build/bdist.macosx-10.9-x86_64/egg/abipy/htc/tests
copying build/lib/abipy/htc/tests/test_jobfile.py -> build/bdist.macosx-10.9-x86_64/egg/abipy/htc/tests
copying build/lib/abipy/htc/utils.py -> build/bdist.macosx-10.9-x86_64/egg/abipy/htc
copying build/lib/abipy/htc/variable.py -> build/bdist.macosx-10.9-x86_64/egg/abipy/htc
creating build/bdist.macosx-10.9-x86_64/egg/abipy/iotools
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copying build/lib/abipy/iotools/files.py -> build/bdist.macosx-10.9-x86_64/egg/abipy/iotools
copying build/lib/abipy/iotools/visualizer.py -> build/bdist.macosx-10.9-x86_64/egg/abipy/iotools
copying build/lib/abipy/iotools/xsf.py -> build/bdist.macosx-10.9-x86_64/egg/abipy/iotools
creating build/bdist.macosx-10.9-x86_64/egg/abipy/phonons
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copying build/lib/abipy/phonons/eph.py -> build/bdist.macosx-10.9-x86_64/egg/abipy/phonons
copying build/lib/abipy/phonons/phbands.py -> build/bdist.macosx-10.9-x86_64/egg/abipy/phonons
copying build/lib/abipy/phonons/phdos.py -> build/bdist.macosx-10.9-x86_64/egg/abipy/phonons
creating build/bdist.macosx-10.9-x86_64/egg/abipy/phonons/tests
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copying build/lib/abipy/phonons/tests/test_phonons.py -> build/bdist.macosx-10.9-x86_64/egg/abipy/phonons/tests
copying build/lib/abipy/profile.py -> build/bdist.macosx-10.9-x86_64/egg/abipy
copying build/lib/abipy/scissors.py -> build/bdist.macosx-10.9-x86_64/egg/abipy
creating build/bdist.macosx-10.9-x86_64/egg/abipy/tools
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copying build/lib/abipy/tools/animator.py -> build/bdist.macosx-10.9-x86_64/egg/abipy/tools
copying build/lib/abipy/tools/decorators.py -> build/bdist.macosx-10.9-x86_64/egg/abipy/tools
copying build/lib/abipy/tools/derivatives.py -> build/bdist.macosx-10.9-x86_64/egg/abipy/tools
copying build/lib/abipy/tools/design_patterns.py -> build/bdist.macosx-10.9-x86_64/egg/abipy/tools
copying build/lib/abipy/tools/devtools.py -> build/bdist.macosx-10.9-x86_64/egg/abipy/tools
copying build/lib/abipy/tools/generic.py -> build/bdist.macosx-10.9-x86_64/egg/abipy/tools
copying build/lib/abipy/tools/iotools.py -> build/bdist.macosx-10.9-x86_64/egg/abipy/tools
copying build/lib/abipy/tools/numtools.py -> build/bdist.macosx-10.9-x86_64/egg/abipy/tools
copying build/lib/abipy/tools/plotting_utils.py -> build/bdist.macosx-10.9-x86_64/egg/abipy/tools
creating build/bdist.macosx-10.9-x86_64/egg/abipy/tools/tests
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copying build/lib/abipy/tools/text.py -> build/bdist.macosx-10.9-x86_64/egg/abipy/tools
creating build/bdist.macosx-10.9-x86_64/egg/abipy/waves
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copying build/lib/abipy/waves/pwwave.py -> build/bdist.macosx-10.9-x86_64/egg/abipy/waves
creating build/bdist.macosx-10.9-x86_64/egg/abipy/waves/tests
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copying build/lib/abipy/waves/tests/test_pwwave.py -> build/bdist.macosx-10.9-x86_64/egg/abipy/waves/tests
copying build/lib/abipy/waves/tests/test_wfkfile.py -> build/bdist.macosx-10.9-x86_64/egg/abipy/waves/tests
copying build/lib/abipy/waves/wfkfile.py -> build/bdist.macosx-10.9-x86_64/egg/abipy/waves
byte-compiling build/bdist.macosx-10.9-x86_64/egg/abipy/init.py to init.pyc
byte-compiling build/bdist.macosx-10.9-x86_64/egg/abipy/abilab.py to abilab.pyc
byte-compiling build/bdist.macosx-10.9-x86_64/egg/abipy/abitools/init.py to init.pyc
byte-compiling build/bdist.macosx-10.9-x86_64/egg/abipy/abitools/fftprof.py to fftprof.pyc
byte-compiling build/bdist.macosx-10.9-x86_64/egg/abipy/abitools/tests/init.py to init.pyc
byte-compiling build/bdist.macosx-10.9-x86_64/egg/abipy/core/init.py to init.pyc
byte-compiling build/bdist.macosx-10.9-x86_64/egg/abipy/core/constants.py to constants.pyc
byte-compiling build/bdist.macosx-10.9-x86_64/egg/abipy/core/exceptions.py to exceptions.pyc
byte-compiling build/bdist.macosx-10.9-x86_64/egg/abipy/core/fields.py to fields.pyc
byte-compiling build/bdist.macosx-10.9-x86_64/egg/abipy/core/func1d.py to func1d.pyc
byte-compiling build/bdist.macosx-10.9-x86_64/egg/abipy/core/gsphere.py to gsphere.pyc
byte-compiling build/bdist.macosx-10.9-x86_64/egg/abipy/core/irrepsdb.py to irrepsdb.pyc
byte-compiling build/bdist.macosx-10.9-x86_64/egg/abipy/core/kpoints.py to kpoints.pyc
byte-compiling build/bdist.macosx-10.9-x86_64/egg/abipy/core/mesh3d.py to mesh3d.pyc
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File "build/bdist.macosx-10.9-x86_64/egg/abipy/data/runs/run_sic_relax.py", line 26
workdir = options.workdir:
^
SyntaxError: invalid syntax

byte-compiling build/bdist.macosx-10.9-x86_64/egg/abipy/data/runs/wykoff.py to wykoff.pyc
byte-compiling build/bdist.macosx-10.9-x86_64/egg/abipy/data/ucells.py to ucells.pyc
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byte-compiling build/bdist.macosx-10.9-x86_64/egg/abipy/gui/flowsdb.py to flowsdb.pyc
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byte-compiling build/bdist.macosx-10.9-x86_64/egg/abipy/gui/gsrviewer.py to gsrviewer.pyc
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byte-compiling build/bdist.macosx-10.9-x86_64/egg/abipy/htc/init.py to init.pyc
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byte-compiling build/bdist.macosx-10.9-x86_64/egg/abipy/htc/tests/init.py to init.pyc
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byte-compiling build/bdist.macosx-10.9-x86_64/egg/abipy/htc/variable.py to variable.pyc
byte-compiling build/bdist.macosx-10.9-x86_64/egg/abipy/iotools/init.py to init.pyc
byte-compiling build/bdist.macosx-10.9-x86_64/egg/abipy/iotools/files.py to files.pyc
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byte-compiling build/bdist.macosx-10.9-x86_64/egg/abipy/phonons/init.py to init.pyc
byte-compiling build/bdist.macosx-10.9-x86_64/egg/abipy/phonons/eph.py to eph.pyc
byte-compiling build/bdist.macosx-10.9-x86_64/egg/abipy/phonons/phbands.py to phbands.pyc
byte-compiling build/bdist.macosx-10.9-x86_64/egg/abipy/phonons/phdos.py to phdos.pyc
byte-compiling build/bdist.macosx-10.9-x86_64/egg/abipy/phonons/tests/init.py to init.pyc
byte-compiling build/bdist.macosx-10.9-x86_64/egg/abipy/phonons/tests/test_phonons.py to test_phonons.pyc
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byte-compiling build/bdist.macosx-10.9-x86_64/egg/abipy/tools/plotting_utils.py to plotting_utils.pyc
byte-compiling build/bdist.macosx-10.9-x86_64/egg/abipy/tools/tests/init.py to init.pyc
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byte-compiling build/bdist.macosx-10.9-x86_64/egg/abipy/tools/text.py to text.pyc
byte-compiling build/bdist.macosx-10.9-x86_64/egg/abipy/waves/init.py to init.pyc
byte-compiling build/bdist.macosx-10.9-x86_64/egg/abipy/waves/pwwave.py to pwwave.pyc
byte-compiling build/bdist.macosx-10.9-x86_64/egg/abipy/waves/tests/init.py to init.pyc
byte-compiling build/bdist.macosx-10.9-x86_64/egg/abipy/waves/tests/test_pwwave.py to test_pwwave.pyc
byte-compiling build/bdist.macosx-10.9-x86_64/egg/abipy/waves/tests/test_wfkfile.py to test_wfkfile.pyc
byte-compiling build/bdist.macosx-10.9-x86_64/egg/abipy/waves/wfkfile.py to wfkfile.pyc
creating build/bdist.macosx-10.9-x86_64/egg/EGG-INFO
installing scripts to build/bdist.macosx-10.9-x86_64/egg/EGG-INFO/scripts
running install_scripts
running build_scripts
creating build/bdist.macosx-10.9-x86_64/egg/EGG-INFO/scripts
copying build/scripts-2.7/abicheck.py -> build/bdist.macosx-10.9-x86_64/egg/EGG-INFO/scripts
copying build/scripts-2.7/abiinsp.py -> build/bdist.macosx-10.9-x86_64/egg/EGG-INFO/scripts
copying build/scripts-2.7/abiopen.py -> build/bdist.macosx-10.9-x86_64/egg/EGG-INFO/scripts
copying build/scripts-2.7/abirun.py -> build/bdist.macosx-10.9-x86_64/egg/EGG-INFO/scripts
copying build/scripts-2.7/abistruct.py -> build/bdist.macosx-10.9-x86_64/egg/EGG-INFO/scripts
copying build/scripts-2.7/cif2spg.py -> build/bdist.macosx-10.9-x86_64/egg/EGG-INFO/scripts
copying build/scripts-2.7/mrgddb.py -> build/bdist.macosx-10.9-x86_64/egg/EGG-INFO/scripts
changing mode of build/bdist.macosx-10.9-x86_64/egg/EGG-INFO/scripts/abicheck.py to 755
changing mode of build/bdist.macosx-10.9-x86_64/egg/EGG-INFO/scripts/abiinsp.py to 755
changing mode of build/bdist.macosx-10.9-x86_64/egg/EGG-INFO/scripts/abiopen.py to 755
changing mode of build/bdist.macosx-10.9-x86_64/egg/EGG-INFO/scripts/abirun.py to 755
changing mode of build/bdist.macosx-10.9-x86_64/egg/EGG-INFO/scripts/abistruct.py to 755
changing mode of build/bdist.macosx-10.9-x86_64/egg/EGG-INFO/scripts/cif2spg.py to 755
changing mode of build/bdist.macosx-10.9-x86_64/egg/EGG-INFO/scripts/mrgddb.py to 755
copying abipy.egg-info/PKG-INFO -> build/bdist.macosx-10.9-x86_64/egg/EGG-INFO
copying abipy.egg-info/SOURCES.txt -> build/bdist.macosx-10.9-x86_64/egg/EGG-INFO
copying abipy.egg-info/dependency_links.txt -> build/bdist.macosx-10.9-x86_64/egg/EGG-INFO
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zip_safe flag not set; analyzing archive contents...
abipy.profile: module references file
abipy.data.init: module references file
abipy.data.runs.init: module references file
abipy.data.runs.init: module MAY be using inspect.stack
abipy.data.runs._run_all: module references file
abipy.data.runs.extract_docs: module references file
abipy.data.runs.run_deltafactor: module references file
abipy.data.runs.run_fe_ebands: module references file
abipy.data.runs.run_gwconv_ecuteps: module references file
abipy.data.runs.run_ht_si_bsemdf: module references file
abipy.data.runs.run_ht_si_ebands: module references file
abipy.data.runs.run_ht_si_g0w0ppm: module references file
abipy.data.runs.run_ldaus: module references file
abipy.data.runs.run_mgb2_edoses: module references file
abipy.data.runs.run_optic: module references file
abipy.data.runs.run_phfrozen_bands: module references file
abipy.data.runs.run_phonons: module references file
abipy.data.runs.run_qptdmscr: module references file
abipy.data.runs.run_raman: module references file
abipy.data.runs.run_raman_optic: module references file
abipy.data.runs.run_relax: module references file
abipy.data.runs.run_si_ebands: module references file
abipy.data.runs.run_si_g0w0: module references file
abipy.data.runs.wykoff: module references file
abipy.gui.awx.core: module references file
creating 'dist/abipy-0.1.0-py2.7.egg' and adding 'build/bdist.macosx-10.9-x86_64/egg' to it
removing 'build/bdist.macosx-10.9-x86_64/egg' (and everything under it)
Processing abipy-0.1.0-py2.7.egg
creating /sw/lib/python2.7/site-packages/abipy-0.1.0-py2.7.egg
Extracting abipy-0.1.0-py2.7.egg to /sw/lib/python2.7/site-packages
File "/sw/lib/python2.7/site-packages/abipy-0.1.0-py2.7.egg/abipy/data/runs/run_sic_relax.py", line 26
workdir = options.workdir:
^
SyntaxError: invalid syntax

Adding abipy 0.1.0 to easy-install.pth file
Installing abicheck.py script to /sw/bin
Installing abiinsp.py script to /sw/bin
Installing abiopen.py script to /sw/bin
Installing abirun.py script to /sw/bin
Installing abistruct.py script to /sw/bin
Installing cif2spg.py script to /sw/bin
Installing mrgddb.py script to /sw/bin

Installed /sw/lib/python2.7/site-packages/abipy-0.1.0-py2.7.egg
Processing dependencies for abipy==0.1.0
Searching for Jinja2==2.7.1
Best match: Jinja2 2.7.1
Adding Jinja2 2.7.1 to easy-install.pth file

Using /sw/lib/python2.7/site-packages
Searching for pyzmq==13.1.0
Best match: pyzmq 13.1.0
Adding pyzmq 13.1.0 to easy-install.pth file

Using /sw/lib/python2.7/site-packages
Searching for ipython==2.0.0
Best match: ipython 2.0.0
Adding ipython 2.0.0 to easy-install.pth file

Using /sw/lib/python2.7/site-packages
Searching for wxmplot==unknown
Best match: wxmplot unknown
Processing wxmplot-unknown-py2.7.egg
wxmplot unknown is already the active version in easy-install.pth

Using /sw/lib/python2.7/site-packages/wxmplot-unknown-py2.7.egg
Searching for paramiko==1.12.0
Best match: paramiko 1.12.0
Adding paramiko 1.12.0 to easy-install.pth file

Using /sw/lib/python2.7/site-packages
Searching for Fabric==1.8.3
Best match: Fabric 1.8.3
Processing Fabric-1.8.3-py2.7.egg
Fabric 1.8.3 is already the active version in easy-install.pth
Installing fab script to /sw/bin

Using /sw/lib/python2.7/site-packages/Fabric-1.8.3-py2.7.egg
Searching for pymatgen==2.9.5
Best match: pymatgen 2.9.5
Adding pymatgen 2.9.5 to easy-install.pth file

Using /sw/lib/python2.7/site-packages
Searching for netCDF4==1.0.8
Best match: netCDF4 1.0.8
Processing netCDF4-1.0.8-py2.7-macosx-10.9-x86_64.egg
netCDF4 1.0.8 is already the active version in easy-install.pth
Installing nc4tonc3 script to /sw/bin
Installing nc3tonc4 script to /sw/bin
Installing ncinfo script to /sw/bin

Using /sw/lib/python2.7/site-packages/netCDF4-1.0.8-py2.7-macosx-10.9-x86_64.egg
Searching for PyYAML==3.11
Best match: PyYAML 3.11
Processing PyYAML-3.11-py2.7-macosx-10.9-x86_64.egg
PyYAML 3.11 is already the active version in easy-install.pth

Using /sw/lib/python2.7/site-packages/PyYAML-3.11-py2.7-macosx-10.9-x86_64.egg
Searching for matplotlib==1.3.1
Best match: matplotlib 1.3.1
Adding matplotlib 1.3.1 to easy-install.pth file

Using /sw/lib/python2.7/site-packages
Searching for scipy==0.13.2
Best match: scipy 0.13.2
Adding scipy 0.13.2 to easy-install.pth file

Using /sw/lib/python2.7/site-packages
Searching for numpy==1.8.0
Best match: numpy 1.8.0
Adding numpy 1.8.0 to easy-install.pth file

Using /sw/lib/python2.7/site-packages
Searching for PyDispatcher==2.0.3
Best match: PyDispatcher 2.0.3
Processing PyDispatcher-2.0.3-py2.7.egg
PyDispatcher 2.0.3 is already the active version in easy-install.pth

Using /sw/lib/python2.7/site-packages/PyDispatcher-2.0.3-py2.7.egg
Searching for APScheduler==2.1.2
Best match: APScheduler 2.1.2
Processing APScheduler-2.1.2-py2.7.egg
APScheduler 2.1.2 is already the active version in easy-install.pth

Using /sw/lib/python2.7/site-packages/APScheduler-2.1.2-py2.7.egg
Searching for termcolor==1.1.0
Best match: termcolor 1.1.0
Processing termcolor-1.1.0-py2.7.egg
termcolor 1.1.0 is already the active version in easy-install.pth

Using /sw/lib/python2.7/site-packages/termcolor-1.1.0-py2.7.egg
Searching for MarkupSafe==0.18
Best match: MarkupSafe 0.18
Adding MarkupSafe 0.18 to easy-install.pth file

Using /sw/lib/python2.7/site-packages
Searching for ecdsa==0.11
Best match: ecdsa 0.11
Processing ecdsa-0.11-py2.7.egg
ecdsa 0.11 is already the active version in easy-install.pth

Using /sw/lib/python2.7/site-packages/ecdsa-0.11-py2.7.egg
Searching for pycrypto==2.6.1
Best match: pycrypto 2.6.1
Processing pycrypto-2.6.1-py2.7-macosx-10.9-x86_64.egg
pycrypto 2.6.1 is already the active version in easy-install.pth

Using /sw/lib/python2.7/site-packages/pycrypto-2.6.1-py2.7-macosx-10.9-x86_64.egg
Searching for monty==0.2.2
Best match: monty 0.2.2
Processing monty-0.2.2-py2.7.egg
monty 0.2.2 is already the active version in easy-install.pth

Using /sw/lib/python2.7/site-packages/monty-0.2.2-py2.7.egg
Searching for pybtex==0.17
Best match: pybtex 0.17
Processing pybtex-0.17-py2.7.egg
pybtex 0.17 is already the active version in easy-install.pth
Installing pybtex script to /sw/bin
Installing pybtex-format script to /sw/bin
Installing pybtex-convert script to /sw/bin

Using /sw/lib/python2.7/site-packages/pybtex-0.17-py2.7.egg
Searching for requests==2.2.1
Best match: requests 2.2.1
Processing requests-2.2.1-py2.7.egg
requests 2.2.1 is already the active version in easy-install.pth

Using /sw/lib/python2.7/site-packages/requests-2.2.1-py2.7.egg
Searching for PyCifRW==3.6.2
Best match: PyCifRW 3.6.2
Adding PyCifRW 3.6.2 to easy-install.pth file

Using /sw/lib/python2.7/site-packages
Searching for pyhull==1.4.3
Best match: pyhull 1.4.3
Processing pyhull-1.4.3-py2.7-macosx-10.9-x86_64.egg
pyhull 1.4.3 is already the active version in easy-install.pth

Using /sw/lib/python2.7/site-packages/pyhull-1.4.3-py2.7-macosx-10.9-x86_64.egg
Searching for nose==1.3.0
Best match: nose 1.3.0
Adding nose 1.3.0 to easy-install.pth file
Installing nosetests script to /sw/bin
Installing nosetests-2.7 script to /sw/bin

Using /sw/lib/python2.7/site-packages
Searching for pyparsing==1.5.6
Best match: pyparsing 1.5.6
Adding pyparsing 1.5.6 to easy-install.pth file

Using /sw/lib/python2.7/site-packages
Searching for tornado==3.1.1
Best match: tornado 3.1.1
Adding tornado 3.1.1 to easy-install.pth file

Using /sw/lib/python2.7/site-packages
Searching for python-dateutil==1.5
Best match: python-dateutil 1.5
Adding python-dateutil 1.5 to easy-install.pth file

Using /sw/lib/python2.7/site-packages
Finished processing dependencies for abipy==0.1.0

Hi,

I've used abipy in the (distant) past, and I want to get back into it. I'm trying to run a simple example abipy/lessons/lesson_base1.py. I modified the script slightly to only have three tasks instead of 20, for debugging purposes.

The flow is created and executed, and all the jobs seem to run fine; however, the analyse_flow
routine yields

      Work #0: <Work, node_id=2573, workdir=flow_h/w0>, Finalized=False
    +------+-------------+-----------------+--------------+--------------+---------+---------------+----------+---------+
    | Task |    Status   |      Queue      |  MPI|Omp|Gb  | Err|Warn|Com |  Class  | Rest|Sub|Corr |   Time   | Node_ID |
    +------+-------------+-----------------+--------------+--------------+---------+---------------+----------+---------+
    |  t0  | AbiCritical | 76104@localhost |    1|  1|2.0 |   1|   0|  0 | ScfTask |   (0, 1, 0)   | 0:00:01Q |   2574  |
    |  t1  | AbiCritical | 76110@localhost |    1|  1|2.0 |   1|   0|  0 | ScfTask |   (0, 1, 0)   | 0:00:01Q |   2575  |
    |  t2  | AbiCritical | 76116@localhost |    1|  1|2.0 |   1|   0|  0 | ScfTask |   (0, 1, 0)   | 0:00:01Q |   2576  |
    +------+-------------+-----------------+--------------+--------------+---------+---------------+----------+---------+
    Total number of errors: 3

I understand abipy is under rapid development: is this example script supposed to work? Am I missing something subtle, like a proper command in the scheduler.yml, or manager.yml? Any hints you may have on how to fix this would be welcomed.

Cheers,
Bruno

Dear ABIPY Community,

I have a question that is indirectly related to abipy: following abipy, I have developed some python scripts for post-processing the wavefunction output from ABINIT. It works well for pseudo potential runs (HGH pseudopotentials).

Now I need to do PAW runs but it seems that ETSF-IO output (netCDF files) for PAW runs is not yet possible in ABINIT (production release 7.6.2).

Would anyone in this forum have an advice or workaround?
( I guess I could just modify my scripts to read the wavefunction in the old-binary format)

I have also posted this question in the ABINIT forum,
http://forum.abinit.org/viewtopic.php?f=7&t=2686

Thanks,
Temok

I installed abipy 0.6.0 devel version. I tried the lobster notebook tutorial for plotting cohp.

for this given command line in the jupyter notebook,

from abipy.abilab import LobsterAnalyzer

it is giving the below error:

ImportError: cannot import name 'LobsterAnalyzer'

Dear devs:

Hope everything is going well. I've been following your recipe to install abinit and abipy using Anaconda. I am able to download install numpy, scipy, netcdf4, abipy and abinit from the Anaconda cloud linked to by the recipe with no issues. But when I try to run
abinit --version
I get the error:

abinit: error while loading shared libraries: libnetcdf.so.15: cannot open shared object file: No such file or directory

When I search the shared library, I find libnetcdf.so.11 instead of libnetcdf.so.15. So it seems like abinit is not linking correctly to the shared library or I do not have the right version of netCDF in the shared library. I have tried both abinit 8.8.2 and 8.10.1 on the conda cloud to no avail. I am wondering if this is a issue with the abinit package on conda or if I am messing up the installation procedure. Is there any report of the same issue? What should I try next?

Best regards,
Alex

Dear Prof. Matteo,

My interest in abipy is because I would like to read and post process the expansion coefficients of the wavefunctions (the cg array in the ABINIT documentation, e.g. ~/ABINIT/doc/theory/wavefunction.pdf) from a WFK.nc; this is in order to implement a model Hamiltonian method.

If I understand well, the .nc file contains such coefficients in the variable called
reduced_coordinates_of_plane_waves.

Using abipy, how can I extract such array?
Is there something like:
abifile = abiopen("my_WFK.nc")
my_cg = abifile.something.somethingelse.reduced_coordinates_of_plane_waves ?

So far, I ran the example plot_bands.py , which reads si_nscf_WFK-etsf.nc, then I typed abifile followed by a double TAB, and obtain

abifile.basename abifile.get_wave abifile.nspinor abifile.classify_ebands abifile.gspheres abifile.nsppol abifile.ebands abifile.kindex abifile.plot_ebands abifile.export_structure abifile.kpoints abifile.reader abifile.export_ur2 abifile.mband abifile.show_bz abifile.fft_mesh abifile.nband_sk abifile.structure abifile.filepath abifile.ncdump abifile.tostring abifile.filestat abifile.nkpt abifile.visualize_structure_with abifile.filetype abifile.npwarr abifile.visualize_ur2 abifile.from_file abifile.nspden

But so far I haven't identify which could contain the cg coefficients.

I would appreciate your advice on reading these cg from abipy or from a another netcdf+python tool.
With regards,
Temok

$ sudo easy_install abipy
Searching for abipy
Reading https://pypi.python.org/simple/abipy/
No local packages or download links found for abipy
error: Could not find suitable distribution for Requirement.parse('abipy')

How do I get abipy to appear as a known package to install?

Hi,

I have just starting to experiment with abipy, which I plan to use to automate and optimize production calculations. I normally run ABINIT on a cluster without a queue system, and I would like to use the same method for running with abipy. Is there any way to specify the specific hosts I want to use with MPI without relying on a queue system?

Thanks,
Sean

when i install abipy by

pip install abipy

It ruturns

Collecting abipy
  Could not find a version that satisfies the requirement abipy (from versions: )
No matching distribution found for abipy

I recently received a DDB to start from called 'mrgdd.ddb.out'. When uploading this file in the 'dash app', following error occurs:

There was an error processing this file. Cannot find magic_start line: -outvars: echo values of preprocessed input variables --------

After seeing this very informative error message I realized that I could try to rename the file to e.g. 'mrgdd.ddb_DDB'. Then it works.

To check, abipy installation, I run abicheck.py and abicheck.py --with-flow. The former was passed but the latter didn't finished. Could you suggest how to solve this program?

Attached file is my manager.yml file.

manager.txt

Hello I just started study abinit and abipy and I am going through first base tutorial from abinit and when I wrote ( abiopen.py tbase1_1.out --expose) or something similar to it I will take memory error.
I have ubuntu 16.04 LTS also 8 gb RAW memory.
(base) vova@bobik:/Abinit/abinit-8.10.3/tests/tutorial/Input/work$ abiopen.py tbase1_1.out --expose
Traceback (most recent call last):
File "/home/vova/miniconda3/bin/abiopen.py", line 15, in
from abipy import abilab
File "/home/vova/miniconda3/lib/python3.7/site-packages/abipy/abilab.py", line 43, in
from abipy.electrons.ebands import (ElectronBands, ElectronBandsPlotter, ElectronDos, ElectronDosPlotter,
File "/home/vova/miniconda3/lib/python3.7/site-packages/abipy/electrons/init.py", line 4, in
from .gsr import *
File "/home/vova/miniconda3/lib/python3.7/site-packages/abipy/electrons/gsr.py", line 20, in
from abipy.tools.tensors import Stress
File "/home/vova/miniconda3/lib/python3.7/site-packages/abipy/tools/tensors.py", line 9, in
from pymatgen.analysis.elasticity.elastic import ElasticTensor # flake8: noqa
File "/home/vova/miniconda3/lib/python3.7/site-packages/pymatgen/analysis/elasticity/init.py", line 5, in
from .elastic import *
File "/home/vova/miniconda3/lib/python3.7/site-packages/pymatgen/analysis/elasticity/elastic.py", line 20, in
import sympy as sp
File "/home/vova/miniconda3/lib/python3.7/site-packages/sympy/init.py", line 19, in
import mpmath
File "/home/vova/miniconda3/lib/python3.7/site-packages/mpmath/init.py", line 5, in
from .ctx_fp import FPContext
File "/home/vova/miniconda3/lib/python3.7/site-packages/mpmath/ctx_fp.py", line 1, in
from .ctx_base import StandardBaseContext
File "/home/vova/miniconda3/lib/python3.7/site-packages/mpmath/ctx_base.py", line 3, in
from .libmp.backend import xrange
File "/home/vova/miniconda3/lib/python3.7/site-packages/mpmath/libmp/init.py", line 17, in
from .libmpc import (mpc_one, mpc_zero, mpc_two, mpc_half,
File "/home/vova/miniconda3/lib/python3.7/site-packages/mpmath/libmp/libmpc.py", line 23, in
from .libelefun import (
File "/home/vova/miniconda3/lib/python3.7/site-packages/mpmath/libmp/libelefun.py", line 76, in
cache_prec_steps += [min(2k,LOG_TAYLOR_PREC)+20] * 2(k-1)
MemoryError
(base) vova@bobik:/Abinit/abinit-8.10.3/tests/tutorial/Input/work$ abiopen.py tbase1_1.out --seaborn
Traceback (most recent call last):
File "/home/vova/miniconda3/bin/abiopen.py", line 15, in
from abipy import abilab
File "/home/vova/miniconda3/lib/python3.7/site-packages/abipy/abilab.py", line 43, in
from abipy.electrons.ebands import (ElectronBands, ElectronBandsPlotter, ElectronDos, ElectronDosPlotter,
File "/home/vova/miniconda3/lib/python3.7/site-packages/abipy/electrons/init.py", line 4, in
from .gsr import *
File "/home/vova/miniconda3/lib/python3.7/site-packages/abipy/electrons/gsr.py", line 20, in
from abipy.tools.tensors import Stress
File "/home/vova/miniconda3/lib/python3.7/site-packages/abipy/tools/tensors.py", line 9, in
from pymatgen.analysis.elasticity.elastic import ElasticTensor # flake8: noqa
File "/home/vova/miniconda3/lib/python3.7/site-packages/pymatgen/analysis/elasticity/init.py", line 5, in
from .elastic import *
File "/home/vova/miniconda3/lib/python3.7/site-packages/pymatgen/analysis/elasticity/elastic.py", line 20, in
import sympy as sp
File "/home/vova/miniconda3/lib/python3.7/site-packages/sympy/init.py", line 19, in
import mpmath
File "/home/vova/miniconda3/lib/python3.7/site-packages/mpmath/init.py", line 5, in
from .ctx_fp import FPContext
File "/home/vova/miniconda3/lib/python3.7/site-packages/mpmath/ctx_fp.py", line 1, in
from .ctx_base import StandardBaseContext
File "/home/vova/miniconda3/lib/python3.7/site-packages/mpmath/ctx_base.py", line 3, in
from .libmp.backend import xrange
File "/home/vova/miniconda3/lib/python3.7/site-packages/mpmath/libmp/init.py", line 17, in
from .libmpc import (mpc_one, mpc_zero, mpc_two, mpc_half,
File "/home/vova/miniconda3/lib/python3.7/site-packages/mpmath/libmp/libmpc.py", line 23, in
from .libelefun import (
File "/home/vova/miniconda3/lib/python3.7/site-packages/mpmath/libmp/libelefun.py", line 76, in
cache_prec_steps += [min(2k,LOG_TAYLOR_PREC)+20] * 2(k-1)
MemoryError

It looks like when I try to use non-primitive unit cells abiopen fails to load the output:

abilab.abiopen("al_100_relax/w0/t0/run.abo")

---------------------------------------------------------------------------
ValueError                                Traceback (most recent call last)
<ipython-input-123-daf00dd3f9ab> in <module>
      1 abo = abilab.abiopen("al_100_relax/w0/t0/run.abo")
----> 2 print(abo)

~/.conda/envs/surfascope/lib/python3.8/site-packages/abipy/abio/outputs.py in __str__(self)
    451 
    452     def __str__(self):
--> 453         return self.to_string()
    454 
    455     def to_string(self, verbose=0):

~/.conda/envs/surfascope/lib/python3.8/site-packages/abipy/abio/outputs.py in to_string(self, verbose)
    486 
    487         # Print dataframe with dimensions.
--> 488         df = self.get_dims_spginfo_dataframe(verbose=verbose)
    489         from abipy.tools.printing import print_dataframe
    490         strio = StringIO()

~/.conda/envs/surfascope/lib/python3.8/site-packages/abipy/abio/outputs.py in get_dims_spginfo_dataframe(self, verbose)
    501         Parse the section with the dimensions of the calculation. Return Dataframe.
    502         """
--> 503         dims_dataset, spginfo_dataset = self.get_dims_spginfo_dataset(verbose=verbose)
    504         rows = []
    505         for dtind, dims in dims_dataset.items():

~/.conda/envs/surfascope/lib/python3.8/site-packages/abipy/abio/outputs.py in get_dims_spginfo_dataset(self, verbose)
    605 
    606                     dims_dataset[dtindex] = dims = OrderedDict()
--> 607                     spginfo_dataset[dtindex] = parse_spgline(line)
    608                     continue
    609 

~/.conda/envs/surfascope/lib/python3.8/site-packages/abipy/abio/outputs.py in parse_spgline(line)
    571             # Could use regular expressions ...
    572             i = line.find("space group")
--> 573             spg_str, brav_str = line[i:].replace("space group", "").split(";")
    574             toks = spg_str.split()
    575             return {

ValueError: not enough values to unpack (expected 2, got 1)

Hi,

When using the Launcher object in python 3, there is a bug when writing the .sh file. I've submitted a PR #129 2 months ago that resolves this issue and I have not received any news. The details of the bug fix are located in the commits that comes with the PR.

Would it be possible to either merge this PR or resolve the issue?
Thanks

No matter what I try I get this error message which is annoying since I cannot make use of abipy due to this.

Traceback (most recent call last):
File "/home/universe/.local/bin/abiopen.py", line 15, in
from abipy import abilab
File "/home/universe/.local/lib/python3.7/site-packages/abipy/init.py", line 18, in
from abipy.core import release
File "/home/universe/.local/lib/python3.7/site-packages/abipy/core/init.py", line 3, in
from .kpoints import *
File "/home/universe/.local/lib/python3.7/site-packages/abipy/core/kpoints.py", line 18, in
from abipy.iotools import ETSF_Reader
File "/home/universe/.local/lib/python3.7/site-packages/abipy/iotools/init.py", line 4, in
import pymatgen.io.abinit.netcdf as ionc
File "/home/universe/.local/lib/python3.7/site-packages/pymatgen/io/abinit/init.py", line 6, in
from .netcdf import *
File "/home/universe/.local/lib/python3.7/site-packages/pymatgen/io/abinit/netcdf.py", line 41, in
import netCDF4
File "/home/universe/.local/lib/python3.7/site-packages/netCDF4/init.py", line 3, in
from ._netCDF4 import *
File "netCDF4/_netCDF4.pyx", line 1213, in init netCDF4._netCDF4
File "/home/universe/.local/lib/python3.7/site-packages/cftime/init.py", line 1, in
from ._cftime import utime, JulianDayFromDate, DateFromJulianDay
File "init.pxd", line 918, in init cftime._cftime
ValueError: numpy.ufunc size changed, may indicate binary incompatibility. Expected 216 from C header, got 192 from PyObject

Could you fix this issue in an update or let me know how to resolve it.
I use Fedora Scientific.

I'm working on a Spack package for abipy, but I'm not finding it for download on PyPI. Do you recommend that users download the latest commit from GitHub and build from source?

So i think it's so stupid question, but where can I find WFK.nc file, in outputs files if have only WFK file without filename extension?

Dear devs,
I cannot get abipy to launch a job on my computing server. I believed that I set up the manager.yml and scheduler.yml properly.

I adapted the run_relax.py script for my needs, which creates a flow_relax directory and the job submission script flow_relax/w0/t0/job.sh is well formed and could be manually submitted with sbatch. However, I want to get abirun.py to submit the whole flow.

I tried: abirun.py flow_relax single or abirun.py flow_relax rapid or abirun.py flow_relax scheduler. In either case, it results in AbiCritical status, with an error message in the file flow_relax/w0/t0/run.err complaining about missing SLURM lines in the job script. Indeed, I can see that the file flow_relax/w0/t0/job.sh has been overwritten, because all the SLURM preemble that was in this file is now gone.

What is going on? Am I missing the basic usage here?