[ase-users] Installation error using macOS Sierra 10.12.1

[M. Avicenna Naradipa]

Dear ASE Developers,

Hi, I'm currently trying to install ASE on my Macbook Pro 2015 running
macOS Sierra 10.12.1, Python 2.7.10. I've been unable to install it due to
a path variable error that I cannot seem to fix.

The location of all ASE installations are located in
~/Library/Python/2.7/bin. These include the ase-gui, ase-build, and so on.
Based on the tutorial, I have create both a ~/.bashrc and ~/.cshrc files
that follows the command to include a new path.

This did not work as I used "echo PATH" and it is not actually added in the
list of paths. Then, creating another ~/.bash_profile file, I added the
same commands as the ~/.bashrc file and ran "source ~/.bash_profile". This
confirms the path location has been added. Here are the results:

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

Cennas-Mac:test_ase cennanaradipa$ echo $PATH

/Users/cennaradipa/Library/Python/2.7/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin:/Users/cennaradipa/Library/Python/2.7/bin

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

Inside the path the contents of the folder are:

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

Cennas-Mac:test_ase cennanaradipa$ cd ~/Library/Python/2.7/bin/

Cennas-Mac:bin cennanaradipa$ ls

ase-build ase-gui ase-run

ase-db ase-info f2py

Cennas-Mac:bin cennanaradipa$

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

I have tried to run the test, both at a random location and an empty folder
in terminal, and it shows the same results:

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

Cennas-Mac:test_ase cennanaradipa$ python -m ase.test

platform        Darwin-16.1.0-x86_64-i386-64bit

python-2.7.10   /usr/bin/python

ase-3.12.0
/Users/cennanaradipa/Library/Python/2.7/lib/python/site-packages/ase/

numpy-1.11.2
/Users/cennanaradipa/Library/Python/2.7/lib/python/site-packages/numpy/

scipy-0.18.1
/Users/cennanaradipa/Library/Python/2.7/lib/python/site-packages/scipy/

test-dir
/var/folders/vn/pgvk15v53hn9k_9b5j459n080000gn/T/ase-test-rqXv06


Ag-Cu100.py ... ok

CO2_Au111.py ... ok

COCu111_2.py ... ok

aff.py ... ok

ag.py ... ok

atom.py ... ok

atoms_distance.py ... ok

atoms_get_duplicates.py ... ok

atoms_info_copy.py ... ok

bader.py ... ok

bandgap.py ... ok

bandstructure.py ...
/Users/cennanaradipa/Library/Python/2.7/lib/python/site-packages/matplotlib/font_manager.py:273:
UserWarning: Matplotlib is building the font cache using fc-list. This may
take a moment.

  warnings.warn('Matplotlib is building the font cache using fc-list. This
may take a moment.')

ok

basin.py ... ok

build.py ... ok

bulk.py ... ok

c60.py ... ok

center.py ... ok

checkpoint.py ... ok

com.py ... ok

coverage.py ... ok

crystal.py ... ok

*db.py ... /bin/sh: ase-build: command not found*

*/bin/sh: ase-run: command not found*

*ERROR*

db2.py ... ok

db_web.py ... skipped (no flask module) ok

dependency_gtk.py ... ok

dependency_matplotlib.py ... ok

dihedralconstraint.py ... ok

dimer.py ... ok

dimer_method.py ... ok

distance.py ... ok

distmom.py ... ok

doctests.py ... ok

eam_pot.py ... ok

eam_pot_test.py ... ok

eam_test.py ... ok

emt.py ... ok

emt1.py ... ok

emt2.py ... ok

emt_h3o2m.py ... ok

eos.py ... ok

example.py ... ok

external_force.py ... ok

filter.py ... ok

fire.py ... ok

fix_bond_length_mic.py ... ok

franck_condon.py ... ok

geometry.py ... ok

h2.py ... ok

hcp.py ... ok

hookean.py ... ok

idpp.py ... ok

kpts.py ... ok

langevin.py ... ok

maxwellboltzmann.py ... ok

md.py ... ok

mic.py ... ok

minimahop.py ... ok

mopac.py ... skipped (use --calculators=mopac to enable) ok

n2.py ... ok

neb.py ... ok

neb_tr.py ... ok

neighbor.py ... ok

niggli.py ... ok

noncollinear.py ... ok

pourbaix.py ... skipped ok

preconlbfgs.py ... ok

properties.py ... ok

pull.py ... ok

qmmm.py ... ok

quaternions.py ... ok

rattle.py ... ok

repeat_FixAtoms.py ... ok

replay.py ... ok

root_test.py ... ok

rotate.py ... ok

rotate_euler.py ... ok

s22.py ... ok

scaled_positions.py ... ok

scientificpython_bug.py ... skipped (no Scientific module) ok

set_get_angle.py ... ok

set_momenta.py ... ok

singlepointcalc.py ... ok

stm.py ... ok

strain.py ... ok

strain_emt.py ... ok

stress.py ... ok

surface.py ... ok

thermochemistry.py ... ok

things.py ... ok

tip3p.py ... ok

unitcellfilter.py ... ok

unitcellfilter2.py ... ok

units.py ... ok

vacancy.py ... ok

verlet.py ... ok

vib.py ... ok

abinit/abinit_Si.py ... skipped (use --calculators=abinit to enable) ok

abinit/abinit_cmdline.py ... ok

aims/H2O_aims.py ... skipped (use --calculators=aims to enable) ok

aims/aims_cmdline.py ... skipped (use --calculators=aims to enable) ok

calculator/al.py ... ok

calculator/bandgap.py ... ok

calculator/h2.py ... ok

calculator/kd2mp.py ... ok

calculator/traj.py ... ok

castep/castep_interface.py ... skipped (use --calculators=castep to enable)
ok

constraints/fixatoms.py ... ok

constraints/fixbonds.py ... ok

constraints/getindices.py ... ok

constraints/setpos.py ... ok

cp2k/cp2k_GeoOpt.py ... skipped ($ASE_CP2K_COMMAND not defined) ok

cp2k/cp2k_H2_LDA.py ... skipped ($ASE_CP2K_COMMAND not defined) ok

cp2k/cp2k_H2_LS.py ... skipped ($ASE_CP2K_COMMAND not defined) ok

cp2k/cp2k_H2_None.py ... skipped ($ASE_CP2K_COMMAND not defined) ok

cp2k/cp2k_H2_PBE.py ... skipped ($ASE_CP2K_COMMAND not defined) ok

cp2k/cp2k_H2_libxc.py ... skipped ($ASE_CP2K_COMMAND not defined) ok

cp2k/cp2k_MD.py ... skipped ($ASE_CP2K_COMMAND not defined) ok

cp2k/cp2k_O2.py ... skipped ($ASE_CP2K_COMMAND not defined) ok

cp2k/cp2k_restart.py ... skipped ($ASE_CP2K_COMMAND not defined) ok

cp2k/cp2k_stress.py ... skipped ($ASE_CP2K_COMMAND not defined) ok

demon/h2o.py ... skipped (use --calculators=demon to enable) ok

dftb/test_simple.py ... skipped (DFTB_COMMAND not defined) ok

dftb/test_tricky.py ... skipped (use --calculators=dftb to enable) ok

elk/Al_rmt.py ... skipped (ELK_SPECIES_PATH not set.) ok

elk/elk_cmdline.py ... skipped (use --calculators=elk to enable) ok

eon/eon_masses.py ... ok

eon/eon_readwrite.py ... ok

exciting/exciting.py ... skipped (no lxml module) ok

fio/abinit.py ... ok

fio/cfg.py ... ok

fio/extxyz.py ... ok

fio/info.py ... ok

fio/magmom.py ... ok

fio/netcdftrajectory.py ... skipped (No NetCDF module available
(netCDF4-python, scipy.io.netcdf)) ok

fio/nwchem.py ... skipped (use --calculators=nwchem to enable) ok

fio/oi.py ... ok

fio/oldtraj.py ... ok

fio/res.py ... ok

fio/trajectory.py ... ok

fio/v_sim.py ... ok

fio/vasp_out.py ... ok

fio/xsf_spec.py ... ok

fleur/fleur_cmdline.py ... skipped (use --calculators=fleur to enable) ok

ga/basic_example_create_database.py ... ok

ga/basic_example_main_run.py ... ok

ga/create_database.py ... ok

ga/cutandsplicepairing.py ... ok

ga/database_logic.py ... ok

ga/element_operators.py ... ok

ga/mutations.py ... ok

ga/particle_comparators.py ... ok

ga/particle_operators.py ... ok

ga/standardcomparator.py ... ok

gaussian/gaussian_cmdline.py ... skipped (use --calculators=gaussian to
enable) ok

gaussian/h2of.py ... skipped (use --calculators=gaussian to enable) ok

gaussian/water.py ... skipped (use --calculators=gaussian to enable) ok

gpaw/no_spin_and_spin.py ... skipped (no gpaw module) ok

gromacs/test_gromacs.py ... skipped (use --calculators=gromacs to enable) ok

jacapo/jacapo.py ... skipped (no Scientific module) ok

nwchem/nwchem_broken_symmetry.py ... skipped (use --calculators=nwchem to
enable) ok

nwchem/nwchem_cmdline.py ... skipped (use --calculators=nwchem to enable) ok

nwchem/nwchem_h3o2m.py ... skipped (use --calculators=nwchem to enable) ok

nwchem/nwchem_spin_symmetry.py ... skipped (use --calculators=nwchem to
enable) ok

nwchem/nwchem_strong_levelshift.py ... ok

octopus/big-test.py ... skipped (use --calculators=octopus to enable) ok

octopus/restart-octopus.py ... skipped (use --calculators=octopus to
enable) ok

octopus/test-octopus.py ... skipped (use --calculators=octopus to enable) ok

onetep/onetep.py ... skipped (use --calculators=onetep to enable) ok

siesta/siesta.py ... skipped (use --calculators=siesta to enable) ok

turbomole/turbomole_H2.py ... skipped (use --calculators=turbomole to
enable) ok

turbomole/turbomole_h3o2m.py ... skipped (use --calculators=turbomole to
enable) ok

vasp/vasp_Al_volrelax.py ... skipped (Neither VASP_COMMAND nor VASP_SCRIPT
defined) ok

vasp/vasp_co.py ... skipped (Neither VASP_COMMAND nor VASP_SCRIPT defined)
ok

vasp/vasp_kpoints.py ... skipped (use --calculators=vasp to enable) ok

vasp/vasp_xc.py ... skipped (use --calculators=vasp to enable) ok

vasp/vasp_xml.py ... skipped (Neither VASP_COMMAND nor VASP_SCRIPT defined)
ok

COCu111.py ... ok


======================================================================

ERROR: db.py

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

Traceback (most recent call last):

  File
"/Users/cennanaradipa/Library/Python/2.7/lib/python/site-packages/ase/test/__init__.py",
line 53, in testfile

    {'display': self.display})

  File
"/Users/cennanaradipa/Library/Python/2.7/lib/python/site-packages/ase/test/db.py",
line 21, in <module>

    cli(cmd.replace('y.json', name))

  File
"/Users/cennanaradipa/Library/Python/2.7/lib/python/site-packages/ase/test/__init__.py",
line 179, in cli

    raise RuntimeError('Failed running a shell command.  '

RuntimeError: Failed running a shell command.  Please set you $PATH
environment variable!


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

Ran 177 tests in 91.488s

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

The only error is "db.py" and it seems that it does not recognize the
ase-gui and ase-build, thinking that its location is in bin/sh (underline).
Copying these two files to the bin/sh would solve it but I do not think
that this is the right way to go, e.g. I already modified the PATH variable.

Is there something missing here? Or are there any more errors that should
be fixed? Thank you for your help
Sincerely,
M. Avicenna Naradipa (Cenna)
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