Install optional boltztrap, vampire and openbabel in CI #3985

DanielYang59 · 2024-08-09T05:07:52Z

Summary

Install more optional dependencies in CI, follow up Install optional boltztrap2 and pygraphviz in CI #3786 (originally [Dev] Multiple dependencies for CI missing #3684)

Installed

x_trans: https://www.tuwien.at/en/tch/tc/theoretical-materials-chemistry/boltztrap
vampire: https://vampire.york.ac.uk/download/ Ubuntu test split 3
OBAlign: Use the openbabel-wheel unofficial prebuilt wheels instead

Caution

[Need help] Broken unit tests revealed

electronic_structure.plotter: Install optional boltztrap, vampire and openbabel in CI #3985 (comment)
command_line.vampire_caller: Install optional boltztrap, vampire and openbabel in CI #3985 (comment)
io.qchem.outputs: Install optional boltztrap, vampire and openbabel in CI #3985 (comment)
A dozen tests for openbabel are failing for Windows

Future PR

critic2: https://aoterodelaroza.github.io/critic2/installation/
zeo/pyzeo: http://www.zeoplusplus.org/download.html (last update 2017)
Properly test no ASE (mock ASE not installed):

pymatgen/tests/io/test_ase.py

Lines 356 to 357 in cadcae4

@pytest.mark.skipif(ase is not None, reason="ase is present")

def test_no_ase_err():

DanielYang59 · 2024-08-09T12:28:45Z

tests/electronic_structure/test_plotter.py

@@ -317,7 +317,7 @@ def test_plot_complexity_factor_mu(self):

    def test_plot_conductivity_dop(self):
        ax = self.plotter.plot_conductivity_dop()
-        assert len(ax.get_lines()) == 8, "wrong number of lines"
+        assert len(ax.get_lines()) == 16, f"wrong number of lines, got {len(ax.get_lines())}"


@janosh Perhaps you could help me verify eb7978d and f6a3fc7? #3237 seems to have broken some tests, and these commits just "fix" those tests, but I'm not sure if it's done properly.

Sorry I missed some, a8d04f9 and 1d104cb might need a closer look as well (changes made to electronic_structure.plotter).

there's definitely something broken here but probably older and not caused by you. just tried running plot_seebeck_dop. looks like the lines aren't applied to the right axes

Thanks for validation!

The tests were completely broken at feaadc0 (you have to fix the path in test file see a8d04f9 to get the following error log). changes on electronic_structure.plotter (not unit test) in this PR were made to get them back to run without any guarantee to generate proper plots :( I assume they were broken by #3237 (fig -> ax) 🙈 .

Looks like we got quite some work to do.

Full run log:

........F......FFFFF.FFFFFFFFFFFFF..... [100%] ===================================================================== FAILURES ====================================================================== ___________________________________________________________ TestBSPlotter.test_get_ticks ____________________________________________________________ self = <electronic_structure.test_plotter.TestBSPlotter testMethod=test_get_ticks> def test_get_ticks(self): assert self.plotter.get_ticks()["label"][5] == "K", "wrong tick label" > assert self.plotter.get_ticks()["distance"][5] == 2.406607625322699, "wrong tick distance" E AssertionError: wrong tick distance /Users/yang/developer/pymatgen/tests/electronic_structure/test_plotter.py:156: AssertionError ______________________________________________________ TestBoltztrapPlotter.test_plot_carriers ______________________________________________________ self = <electronic_structure.test_plotter.TestBoltztrapPlotter testMethod=test_plot_carriers> def test_plot_carriers(self): > ax = self.plotter.plot_carriers() tests/electronic_structure/test_plotter.py:305: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ src/pymatgen/electronic_structure/plotter.py:3644: in plot_carriers ax.set_xticks(fontsize=25) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <Axes: xlabel='E-E$_f$ (eV)', ylabel='carrier concentration (cm-3)'>, args = (), kwargs = {'fontsize': 25} def wrapper(self, *args, **kwargs): > return get_method(self)(*args, **kwargs) E TypeError: Axis.set_ticks() missing 1 required positional argument: 'ticks' venv/lib/python3.12/site-packages/matplotlib/axes/_base.py:74: TypeError ________________________________________________ TestBoltztrapPlotter.test_plot_complexity_factor_mu ________________________________________________ eta = array([1.]), Lambda = 0.5 def seebeck_spb(eta, Lambda=0.5): """Seebeck analytic formula in the single parabolic model.""" try: > from fdint import fdk E ModuleNotFoundError: No module named 'fdint' src/pymatgen/electronic_structure/boltztrap.py:2257: ModuleNotFoundError During handling of the above exception, another exception occurred: self = <electronic_structure.test_plotter.TestBoltztrapPlotter testMethod=test_plot_complexity_factor_mu> def test_plot_complexity_factor_mu(self): > ax = self.plotter.plot_complexity_factor_mu() tests/electronic_structure/test_plotter.py:312: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ src/pymatgen/electronic_structure/plotter.py:2924: in plot_complexity_factor_mu cmplx_fact = self._bz.get_complexity_factor(output=output, temp=T, Lambda=Lambda) src/pymatgen/electronic_structure/boltztrap.py:1401: in get_complexity_factor sbk_mass = self.get_seebeck_eff_mass(output, temp, doping_levels=False, Lambda=Lambda) src/pymatgen/electronic_structure/boltztrap.py:1345: in get_seebeck_eff_mass sbk_mass.append(seebeck_eff_mass_from_seebeck_carr(abs(seebeck[idx]), concen, temp, Lambda)) src/pymatgen/electronic_structure/boltztrap.py:2302: in seebeck_eff_mass_from_seebeck_carr eta = eta_from_seebeck(seeb, Lambda) src/pymatgen/electronic_structure/boltztrap.py:2277: in eta_from_seebeck out = fsolve(lambda x: (seebeck_spb(x, Lambda) - abs(seeb)) ** 2, 1.0, full_output=True) venv/lib/python3.12/site-packages/scipy/optimize/_minpack_py.py:170: in fsolve res = _root_hybr(_wrapped_func, x0, args, jac=fprime, **options) venv/lib/python3.12/site-packages/scipy/optimize/_minpack_py.py:238: in _root_hybr shape, dtype = _check_func('fsolve', 'func', func, x0, args, n, (n,)) venv/lib/python3.12/site-packages/scipy/optimize/_minpack_py.py:23: in _check_func res = atleast_1d(thefunc(*((x0[:numinputs],) + args))) venv/lib/python3.12/site-packages/scipy/optimize/_minpack_py.py:158: in _wrapped_func return func(*fargs) src/pymatgen/electronic_structure/boltztrap.py:2277: in <lambda> out = fsolve(lambda x: (seebeck_spb(x, Lambda) - abs(seeb)) ** 2, 1.0, full_output=True) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ eta = array([1.]), Lambda = 0.5 def seebeck_spb(eta, Lambda=0.5): """Seebeck analytic formula in the single parabolic model.""" try: from fdint import fdk except ImportError: > raise BoltztrapError( "fdint module not found. Please, install it.\nIt is needed to calculate Fermi integral quickly." ) E pymatgen.electronic_structure.boltztrap.BoltztrapError: fdint module not found. Please, install it. E It is needed to calculate Fermi integral quickly. src/pymatgen/electronic_structure/boltztrap.py:2259: BoltztrapError __________________________________________________ TestBoltztrapPlotter.test_plot_conductivity_dop __________________________________________________ self = <electronic_structure.test_plotter.TestBoltztrapPlotter testMethod=test_plot_conductivity_dop> def test_plot_conductivity_dop(self): > ax = self.plotter.plot_conductivity_dop() tests/electronic_structure/test_plotter.py:319: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ src/pymatgen/electronic_structure/plotter.py:3450: in plot_conductivity_dop ax.set_xticks(fontsize=25) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <Axes: title={'center': 'n-type'}, xlabel='Doping concentration ($cm^{-3}$)', ylabel='conductivity $\\sigma$ (1/($\\Omega$ m))'>, args = () kwargs = {'fontsize': 25} def wrapper(self, *args, **kwargs): > return get_method(self)(*args, **kwargs) E TypeError: Axis.set_ticks() missing 1 required positional argument: 'ticks' venv/lib/python3.12/site-packages/matplotlib/axes/_base.py:74: TypeError __________________________________________________ TestBoltztrapPlotter.test_plot_conductivity_mu ___________________________________________________ self = <electronic_structure.test_plotter.TestBoltztrapPlotter testMethod=test_plot_conductivity_mu> def test_plot_conductivity_mu(self): > ax = self.plotter.plot_conductivity_mu() tests/electronic_structure/test_plotter.py:326: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ src/pymatgen/electronic_structure/plotter.py:3025: in plot_conductivity_mu ax.set_xticks(fontsize=25) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <Axes: xlabel='E-E$_f$ (eV)', ylabel='conductivity,\n $\\Sigma$ (1/($\\Omega$ m))'>, args = (), kwargs = {'fontsize': 25} def wrapper(self, *args, **kwargs): > return get_method(self)(*args, **kwargs) E TypeError: Axis.set_ticks() missing 1 required positional argument: 'ticks' venv/lib/python3.12/site-packages/matplotlib/axes/_base.py:74: TypeError _________________________________________________ TestBoltztrapPlotter.test_plot_conductivity_temp __________________________________________________ self = <electronic_structure.test_plotter.TestBoltztrapPlotter testMethod=test_plot_conductivity_temp> def test_plot_conductivity_temp(self): > ax = self.plotter.plot_conductivity_temp() tests/electronic_structure/test_plotter.py:333: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ src/pymatgen/electronic_structure/plotter.py:3202: in plot_conductivity_temp ax.set_xticks(fontsize=25) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <Axes: title={'center': 'n-type'}, xlabel='Temperature (K)', ylabel='conductivity $\\sigma$ (1/($\\Omega$ m))'>, args = () kwargs = {'fontsize': 25} def wrapper(self, *args, **kwargs): > return get_method(self)(*args, **kwargs) E TypeError: Axis.set_ticks() missing 1 required positional argument: 'ticks' venv/lib/python3.12/site-packages/matplotlib/axes/_base.py:74: TypeError ____________________________________________________ TestBoltztrapPlotter.test_plot_eff_mass_dop ____________________________________________________ self = <electronic_structure.test_plotter.TestBoltztrapPlotter testMethod=test_plot_eff_mass_dop> def test_plot_eff_mass_dop(self): > ax = self.plotter.plot_eff_mass_dop() tests/electronic_structure/test_plotter.py:347: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ src/pymatgen/electronic_structure/plotter.py:3606: in plot_eff_mass_dop ax.set_xticks(fontsize=25) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <Axes: title={'center': 'n-type'}, xlabel='Doping concentration ($cm^{-3}$)', ylabel='Effective mass (m$_e$)'>, args = () kwargs = {'fontsize': 25} def wrapper(self, *args, **kwargs): > return get_method(self)(*args, **kwargs) E TypeError: Axis.set_ticks() missing 1 required positional argument: 'ticks' venv/lib/python3.12/site-packages/matplotlib/axes/_base.py:74: TypeError ___________________________________________________ TestBoltztrapPlotter.test_plot_eff_mass_temp ____________________________________________________ self = <electronic_structure.test_plotter.TestBoltztrapPlotter testMethod=test_plot_eff_mass_temp> def test_plot_eff_mass_temp(self): ax = self.plotter.plot_eff_mass_temp() > assert len(ax.get_lines()) == 6, "wrong number of lines" E AssertionError: wrong number of lines tests/electronic_structure/test_plotter.py:355: AssertionError ___________________________________________________ TestBoltztrapPlotter.test_plot_hall_carriers ____________________________________________________ self = <electronic_structure.test_plotter.TestBoltztrapPlotter testMethod=test_plot_hall_carriers> def test_plot_hall_carriers(self): > ax = self.plotter.plot_hall_carriers() tests/electronic_structure/test_plotter.py:361: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ src/pymatgen/electronic_structure/plotter.py:3667: in plot_hall_carriers ax.set_xticks(fontsize=25) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <Axes: xlabel='E-E$_f$ (eV)', ylabel='Hall carrier concentration (cm-3)'>, args = (), kwargs = {'fontsize': 25} def wrapper(self, *args, **kwargs): > return get_method(self)(*args, **kwargs) E TypeError: Axis.set_ticks() missing 1 required positional argument: 'ticks' venv/lib/python3.12/site-packages/matplotlib/axes/_base.py:74: TypeError __________________________________________________ TestBoltztrapPlotter.test_plot_power_factor_dop __________________________________________________ self = <electronic_structure.test_plotter.TestBoltztrapPlotter testMethod=test_plot_power_factor_dop> def test_plot_power_factor_dop(self): > ax = self.plotter.plot_power_factor_dop() tests/electronic_structure/test_plotter.py:368: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ src/pymatgen/electronic_structure/plotter.py:3498: in plot_power_factor_dop ax.set_xticks(fontsize=25) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <Axes: title={'center': 'n-type'}, xlabel='Doping concentration ($cm^{-3}$)', ylabel='Power Factor ($\\mu$W/(mK$^2$))'>, args = () kwargs = {'fontsize': 25} def wrapper(self, *args, **kwargs): > return get_method(self)(*args, **kwargs) E TypeError: Axis.set_ticks() missing 1 required positional argument: 'ticks' venv/lib/python3.12/site-packages/matplotlib/axes/_base.py:74: TypeError __________________________________________________ TestBoltztrapPlotter.test_plot_power_factor_mu ___________________________________________________ self = <electronic_structure.test_plotter.TestBoltztrapPlotter testMethod=test_plot_power_factor_mu> def test_plot_power_factor_mu(self): > ax = self.plotter.plot_power_factor_mu() tests/electronic_structure/test_plotter.py:375: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ src/pymatgen/electronic_structure/plotter.py:3064: in plot_power_factor_mu ax.set_xticks(fontsize=25) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <Axes: xlabel='E-E$_f$ (eV)', ylabel='Power factor, ($\\mu$W/(mK$^2$))'>, args = (), kwargs = {'fontsize': 25} def wrapper(self, *args, **kwargs): > return get_method(self)(*args, **kwargs) E TypeError: Axis.set_ticks() missing 1 required positional argument: 'ticks' venv/lib/python3.12/site-packages/matplotlib/axes/_base.py:74: TypeError _________________________________________________ TestBoltztrapPlotter.test_plot_power_factor_temp __________________________________________________ self = <electronic_structure.test_plotter.TestBoltztrapPlotter testMethod=test_plot_power_factor_temp> def test_plot_power_factor_temp(self): > ax = self.plotter.plot_power_factor_temp() tests/electronic_structure/test_plotter.py:382: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ src/pymatgen/electronic_structure/plotter.py:3257: in plot_power_factor_temp ax.set_xticks(fontsize=25) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <Axes: title={'center': 'n-type'}, xlabel='Temperature (K)', ylabel='Power Factor ($\\mu$W/(mK$^2$))'>, args = (), kwargs = {'fontsize': 25} def wrapper(self, *args, **kwargs): > return get_method(self)(*args, **kwargs) E TypeError: Axis.set_ticks() missing 1 required positional argument: 'ticks' venv/lib/python3.12/site-packages/matplotlib/axes/_base.py:74: TypeError ____________________________________________________ TestBoltztrapPlotter.test_plot_seebeck_dop _____________________________________________________ self = <electronic_structure.test_plotter.TestBoltztrapPlotter testMethod=test_plot_seebeck_dop> def test_plot_seebeck_dop(self): > ax = self.plotter.plot_seebeck_dop() tests/electronic_structure/test_plotter.py:389: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ src/pymatgen/electronic_structure/plotter.py:3397: in plot_seebeck_dop ax.set_xticks(fontsize=25) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <Axes: title={'center': 'n-type'}, xlabel='Doping concentration (cm$^{-3}$)', ylabel='Seebeck coefficient ($\\mu$V/K)'>, args = () kwargs = {'fontsize': 25} def wrapper(self, *args, **kwargs): > return get_method(self)(*args, **kwargs) E TypeError: Axis.set_ticks() missing 1 required positional argument: 'ticks' venv/lib/python3.12/site-packages/matplotlib/axes/_base.py:74: TypeError ________________________________________________ TestBoltztrapPlotter.test_plot_seebeck_eff_mass_mu _________________________________________________ eta = array([1.]), Lambda = 0.5 def seebeck_spb(eta, Lambda=0.5): """Seebeck analytic formula in the single parabolic model.""" try: > from fdint import fdk E ModuleNotFoundError: No module named 'fdint' src/pymatgen/electronic_structure/boltztrap.py:2257: ModuleNotFoundError During handling of the above exception, another exception occurred: self = <electronic_structure.test_plotter.TestBoltztrapPlotter testMethod=test_plot_seebeck_eff_mass_mu> def test_plot_seebeck_eff_mass_mu(self): > ax = self.plotter.plot_seebeck_eff_mass_mu() tests/electronic_structure/test_plotter.py:396: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ src/pymatgen/electronic_structure/plotter.py:2864: in plot_seebeck_eff_mass_mu sbk_mass = self._bz.get_seebeck_eff_mass(output=output, temp=temp, Lambda=0.5) src/pymatgen/electronic_structure/boltztrap.py:1345: in get_seebeck_eff_mass sbk_mass.append(seebeck_eff_mass_from_seebeck_carr(abs(seebeck[idx]), concen, temp, Lambda)) src/pymatgen/electronic_structure/boltztrap.py:2302: in seebeck_eff_mass_from_seebeck_carr eta = eta_from_seebeck(seeb, Lambda) src/pymatgen/electronic_structure/boltztrap.py:2277: in eta_from_seebeck out = fsolve(lambda x: (seebeck_spb(x, Lambda) - abs(seeb)) ** 2, 1.0, full_output=True) venv/lib/python3.12/site-packages/scipy/optimize/_minpack_py.py:170: in fsolve res = _root_hybr(_wrapped_func, x0, args, jac=fprime, **options) venv/lib/python3.12/site-packages/scipy/optimize/_minpack_py.py:238: in _root_hybr shape, dtype = _check_func('fsolve', 'func', func, x0, args, n, (n,)) venv/lib/python3.12/site-packages/scipy/optimize/_minpack_py.py:23: in _check_func res = atleast_1d(thefunc(*((x0[:numinputs],) + args))) venv/lib/python3.12/site-packages/scipy/optimize/_minpack_py.py:158: in _wrapped_func return func(*fargs) src/pymatgen/electronic_structure/boltztrap.py:2277: in <lambda> out = fsolve(lambda x: (seebeck_spb(x, Lambda) - abs(seeb)) ** 2, 1.0, full_output=True) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ eta = array([1.]), Lambda = 0.5 def seebeck_spb(eta, Lambda=0.5): """Seebeck analytic formula in the single parabolic model.""" try: from fdint import fdk except ImportError: > raise BoltztrapError( "fdint module not found. Please, install it.\nIt is needed to calculate Fermi integral quickly." ) E pymatgen.electronic_structure.boltztrap.BoltztrapError: fdint module not found. Please, install it. E It is needed to calculate Fermi integral quickly. src/pymatgen/electronic_structure/boltztrap.py:2259: BoltztrapError _____________________________________________________ TestBoltztrapPlotter.test_plot_seebeck_mu _____________________________________________________ self = <electronic_structure.test_plotter.TestBoltztrapPlotter testMethod=test_plot_seebeck_mu> def test_plot_seebeck_mu(self): > ax = self.plotter.plot_seebeck_mu() tests/electronic_structure/test_plotter.py:403: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ src/pymatgen/electronic_structure/plotter.py:2987: in plot_seebeck_mu ax.set_xticks(fontsize=25) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <Axes: xlabel='E-E$_f$ (eV)', ylabel='Seebeck \n coefficient ($\\mu$V/K)'>, args = (), kwargs = {'fontsize': 25} def wrapper(self, *args, **kwargs): > return get_method(self)(*args, **kwargs) E TypeError: Axis.set_ticks() missing 1 required positional argument: 'ticks' venv/lib/python3.12/site-packages/matplotlib/axes/_base.py:74: TypeError ____________________________________________________ TestBoltztrapPlotter.test_plot_seebeck_temp ____________________________________________________ self = <electronic_structure.test_plotter.TestBoltztrapPlotter testMethod=test_plot_seebeck_temp> def test_plot_seebeck_temp(self): > ax = self.plotter.plot_seebeck_temp() tests/electronic_structure/test_plotter.py:410: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ src/pymatgen/electronic_structure/plotter.py:3148: in plot_seebeck_temp ax.set_xticks(fontsize=25) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <Axes: title={'center': 'n-type'}, xlabel='Temperature (K)', ylabel='Seebeck \n coefficient ($\\mu$V/K)'>, args = () kwargs = {'fontsize': 25} def wrapper(self, *args, **kwargs): > return get_method(self)(*args, **kwargs) E TypeError: Axis.set_ticks() missing 1 required positional argument: 'ticks' venv/lib/python3.12/site-packages/matplotlib/axes/_base.py:74: TypeError _______________________________________________________ TestBoltztrapPlotter.test_plot_zt_dop _______________________________________________________ self = <electronic_structure.test_plotter.TestBoltztrapPlotter testMethod=test_plot_zt_dop> def test_plot_zt_dop(self): > ax = self.plotter.plot_zt_dop() tests/electronic_structure/test_plotter.py:417: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ src/pymatgen/electronic_structure/plotter.py:3552: in plot_zt_dop ax.set_xticks(fontsize=25) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <Axes: title={'center': 'n-type'}, xlabel='Doping concentration ($cm^{-3}$)', ylabel='zT'>, args = (), kwargs = {'fontsize': 25} def wrapper(self, *args, **kwargs): > return get_method(self)(*args, **kwargs) E TypeError: Axis.set_ticks() missing 1 required positional argument: 'ticks' venv/lib/python3.12/site-packages/matplotlib/axes/_base.py:74: TypeError _______________________________________________________ TestBoltztrapPlotter.test_plot_zt_mu ________________________________________________________ self = <electronic_structure.test_plotter.TestBoltztrapPlotter testMethod=test_plot_zt_mu> def test_plot_zt_mu(self): > ax = self.plotter.plot_zt_mu() tests/electronic_structure/test_plotter.py:424: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ src/pymatgen/electronic_structure/plotter.py:3101: in plot_zt_mu ax.set_xticks(fontsize=25) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <Axes: xlabel='E-E$_f$ (eV)', ylabel='ZT'>, args = (), kwargs = {'fontsize': 25} def wrapper(self, *args, **kwargs): > return get_method(self)(*args, **kwargs) E TypeError: Axis.set_ticks() missing 1 required positional argument: 'ticks' venv/lib/python3.12/site-packages/matplotlib/axes/_base.py:74: TypeError ______________________________________________________ TestBoltztrapPlotter.test_plot_zt_temp _______________________________________________________ self = <electronic_structure.test_plotter.TestBoltztrapPlotter testMethod=test_plot_zt_temp> def test_plot_zt_temp(self): > ax = self.plotter.plot_zt_temp() tests/electronic_structure/test_plotter.py:431: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ src/pymatgen/electronic_structure/plotter.py:3311: in plot_zt_temp ax.set_xticks(fontsize=25) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <Axes: title={'center': 'n-type'}, xlabel='Temperature (K)', ylabel='zT'>, args = (), kwargs = {'fontsize': 25} def wrapper(self, *args, **kwargs): > return get_method(self)(*args, **kwargs) E TypeError: Axis.set_ticks() missing 1 required positional argument: 'ticks' venv/lib/python3.12/site-packages/matplotlib/axes/_base.py:74: TypeError =============================================================== slowest 30 durations ================================================================ 10.97s call tests/electronic_structure/test_plotter.py::TestBSPlotterProjected::test_methods 4.33s call tests/electronic_structure/test_plotter.py::TestBoltztrapPlotter::test_plot_conductivity_mu 2.23s call tests/electronic_structure/test_plotter.py::TestBSDOSPlotter::test_methods 2.18s call tests/electronic_structure/test_plotter.py::TestBSPlotter::test_get_plot 0.61s call tests/electronic_structure/test_plotter.py::TestBoltztrapPlotter::test_plot_zt_mu 0.57s call tests/electronic_structure/test_plotter.py::TestBSPlotter::test_add_bs 0.56s call tests/electronic_structure/test_plotter.py::TestBSPlotter::test_get_ticks 0.54s call tests/electronic_structure/test_plotter.py::TestBoltztrapPlotter::test_plot_hall_carriers 0.53s call tests/electronic_structure/test_plotter.py::TestBoltztrapPlotter::test_plot_eff_mass_temp 0.52s call tests/electronic_structure/test_plotter.py::TestBoltztrapPlotter::test_plot_power_factor_mu 0.52s call tests/electronic_structure/test_plotter.py::TestBoltztrapPlotter::test_plot_seebeck_eff_mass_mu 0.51s call tests/electronic_structure/test_plotter.py::TestBSPlotter::test_bs_plot_data 0.51s call tests/electronic_structure/test_plotter.py::TestBoltztrapPlotter::test_plot_zt_dop 0.51s call tests/electronic_structure/test_plotter.py::TestBoltztrapPlotter::test_plot_zt_temp 0.50s call tests/electronic_structure/test_plotter.py::TestBoltztrapPlotter::test_plot_seebeck_mu 0.50s call tests/electronic_structure/test_plotter.py::TestBSPlotter::test_get_branch_steps 0.49s call tests/electronic_structure/test_plotter.py::TestBSPlotter::test_rescale_distances 0.48s call tests/electronic_structure/test_plotter.py::TestBSPlotter::test_interpolate_bands 0.47s call tests/electronic_structure/test_plotter.py::TestBoltztrapPlotter::test_plot_power_factor_temp 0.46s call tests/electronic_structure/test_plotter.py::TestBoltztrapPlotter::test_plot_seebeck_dop 0.45s call tests/electronic_structure/test_plotter.py::TestBoltztrapPlotter::test_plot_seebeck_temp 0.45s call tests/electronic_structure/test_plotter.py::TestBoltztrapPlotter::test_plot_power_factor_dop 0.45s call tests/electronic_structure/test_plotter.py::TestBoltztrapPlotter::test_plot_conductivity_temp 0.44s call tests/electronic_structure/test_plotter.py::TestBoltztrapPlotter::test_plot_dos 0.42s call tests/electronic_structure/test_plotter.py::TestBoltztrapPlotter::test_plot_eff_mass_dop 0.34s call tests/electronic_structure/test_plotter.py::TestDosPlotter::test_get_plot_limits 0.33s call tests/electronic_structure/test_plotter.py::TestBoltztrapPlotter::test_plot_complexity_factor_mu 0.32s call tests/electronic_structure/test_plotter.py::TestBoltztrapPlotter::test_plot_conductivity_dop 0.32s call tests/electronic_structure/test_plotter.py::TestBoltztrapPlotter::test_plot_carriers 0.28s call tests/electronic_structure/test_plotter.py::TestDosPlotter::test_get_plot 19 failed, 20 passed in 34.70s

thanks for checking, i suspected the same! the only good news is the fix shouldn't require much code changes...

This reverts commit 6b19836.

.github/workflows/test.yml

janosh · 2024-08-22T11:07:33Z

tests/electronic_structure/test_plotter.py

@@ -317,7 +317,7 @@ def test_plot_complexity_factor_mu(self):

    def test_plot_conductivity_dop(self):
        ax = self.plotter.plot_conductivity_dop()
-        assert len(ax.get_lines()) == 8, "wrong number of lines"
+        assert len(ax.get_lines()) == 16, f"wrong number of lines, got {len(ax.get_lines())}"


there's definitely something broken here but probably older and not caused by you. just tried running plot_seebeck_dop. looks like the lines aren't applied to the right axes

tests/transformations/test_advanced_transformations.py

This reverts commit e2ff5fa.

This reverts commit 1d104cb.

This reverts commit a8d04f9.

This reverts commit eb7978d.

This reverts commit f6a3fc7.

DanielYang59 · 2024-09-06T03:54:20Z

@janosh I decide to separate the BoltztrapPlotter issue (it's not broken by this PR), and all changed made on BoltztrapPlotter in this PR has been reverted. It would take some effort to manually inspect the generated plot, instead of relying on passing of unit test.

janosh

thanks so much for this PR @DanielYang59! anything that increases coverage is super useful! 👍

one minor nitpick

janosh · 2024-09-06T11:00:05Z

tests/analysis/test_functional_groups.py

@@ -110,6 +111,7 @@ def test_get_all_functional_groups(self):
        assert len(all_func) == (len(link) + len(basics))
        assert sorted(all_func) == sorted(link + basics)

+    @pytest.mark.skipif(os.name == "nt", reason="Tests for openbabel failing on Win")


i think sys.platform == 'windows' is more readable and seems to be generally preferred to os.name

Wonderful! Would do that.

I'm sure it's a typo, sys.platform should return win32, and platform.system() would return Windows

Perhaps just use platform.system() because sys.platform also returns win32 in 64-bit machines, which is a bit misleading.

Side note, just looked into the source code, and it turns out platform.system() is "almost" an alias to os.uname (when there is uname recording):

def uname(): """ Fairly portable uname interface. Returns a tuple of strings (system, node, release, version, machine, processor) identifying the underlying platform. Note that unlike the os.uname function this also returns possible processor information as an additional tuple entry. Entries which cannot be determined are set to ''. """ global _uname_cache if _uname_cache is not None: return _uname_cache # Get some infos from the builtin os.uname API... try: system, node, release, version, machine = infos = os.uname() except AttributeError: system = sys.platform node = _node() release = version = machine = '' infos = () if not any(infos): # uname is not available # Try win32_ver() on win32 platforms if system == 'win32': release, version, csd, ptype = win32_ver() machine = machine or _get_machine_win32() # Try the 'ver' system command available on some # platforms if not (release and version): system, release, version = _syscmd_ver(system) # Normalize system to what win32_ver() normally returns # (_syscmd_ver() tends to return the vendor name as well) if system == 'Microsoft Windows': system = 'Windows' elif system == 'Microsoft' and release == 'Windows': # Under Windows Vista and Windows Server 2008, # Microsoft changed the output of the ver command. The # release is no longer printed. This causes the # system and release to be misidentified. system = 'Windows' if '6.0' == version[:3]: release = 'Vista' else: release = '' # In case we still don't know anything useful, we'll try to # help ourselves if system in ('win32', 'win16'): if not version: if system == 'win32': version = '32bit' else: version = '16bit' system = 'Windows' elif system[:4] == 'java': release, vendor, vminfo, osinfo = java_ver() system = 'Java' version = ', '.join(vminfo) if not version: version = vendor # System specific extensions if system == 'OpenVMS': # OpenVMS seems to have release and version mixed up if not release or release == '0': release = version version = '' # normalize name if system == 'Microsoft' and release == 'Windows': system = 'Windows' release = 'Vista' vals = system, node, release, version, machine # Replace 'unknown' values with the more portable '' _uname_cache = uname_result(*map(_unknown_as_blank, vals)) return _uname_cache

janosh

great work @DanielYang59! 👍 🧪

DanielYang59 · 2024-09-06T13:04:48Z

Thanks for reviewing!

DanielYang59 added 15 commits August 9, 2024 13:06

remove unused read_cube import

ee93a65

tweak test.yml comments

388ab03

try to install BoltzTraP

9e9bf63

fix decompress command

e94df2f

make installation script modular

c823018

try to modify PATH, test split 4

feaadc0

fix boltztrap unit test

97f4aa4

use rtol

2cf3b86

properly skip unit test

54105bf

fix fig.xticks to ax migration in materialsproject#3237

a8d04f9

ax.gca -> plg.gca()

1d104cb

properly use ScalarFormatter

e2ff5fa

NEED CONFIRM: fix number of lines

eb7978d

NEED CONFIRM: fix unit test values

f6a3fc7

try to install open babel

47fadcc

DanielYang59 commented Aug 9, 2024

View reviewed changes

shyuep added 2 commits August 9, 2024 06:20

Merge branch 'master' into install-more-opt-ci-deps

9b4357b

Merge branch 'master' into install-more-opt-ci-deps

f091e80

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DanielYang59 added 6 commits August 9, 2024 22:35

NEED CONFIRM: include fdint

6b19836

Revert "NEED CONFIRM: include fdint"

684ad68

This reverts commit 6b19836.

skip tests if no fdint

8053e9d

try to install Vampire

eb57d13

make vampire executable

63dc112

Merge branch 'master' into install-more-opt-ci-deps

7a5975e

DanielYang59 changed the title ~~Install more optional dependencies in CI~~ Install optional boltztrap and vampire in CI Aug 13, 2024

DanielYang59 added 4 commits August 13, 2024 10:52

relocate attribute to class docstring

17684e7

try to use absolute path in PATH

a788b1b

use VAMPEXE

05e2277

mark vampire test for fix and skip for now

a21ddbb

janosh added ci Continuous integration help wanted Help wanted labels Aug 22, 2024

janosh reviewed Aug 22, 2024

View reviewed changes

tests/transformations/test_advanced_transformations.py Show resolved Hide resolved

DanielYang59 and others added 15 commits August 23, 2024 11:11

make ubuntu dep install inline

d76c585

Merge branch 'master' into install-more-opt-ci-deps

407d5d0

fix test skip and make module var all cap

77c2eaa

add TODO tags

b7a87a0

renames

f249306

Merge branch 'master' into install-more-opt-ci-deps

7af61e7

Merge branch 'master' into install-more-opt-ci-deps

1bda006

Merge branch 'master' into install-more-opt-ci-deps

e821215

Revert "properly use ScalarFormatter"

1d6527c

This reverts commit e2ff5fa.

Revert "ax.gca -> plg.gca()"

4e3a1ab

This reverts commit 1d104cb.

Revert "fix fig.xticks to ax migration in materialsproject#3237"

49bdd5f

This reverts commit a8d04f9.

Revert "NEED CONFIRM: fix number of lines"

310c97d

This reverts commit eb7978d.

Revert "NEED CONFIRM: fix unit test values"

d304380

This reverts commit f6a3fc7.

ruff fix

a5d11de

skip entire TestBoltztrapPlotter

5a97b98

DanielYang59 mentioned this pull request Sep 6, 2024

[BUG] Entire BoltztrapPlotter is broken #4045

Open

DanielYang59 requested a review from janosh September 6, 2024 03:54

janosh removed the help wanted Help wanted label Sep 6, 2024

janosh suggested changes Sep 6, 2024

View reviewed changes

DanielYang59 added 2 commits September 6, 2024 19:49

use platform.system() == "Windows" over os.name == "nt"

f28d8ac

use platform.system() == "Windows" over sys.platform == "win32"

322ae3f

janosh approved these changes Sep 6, 2024

View reviewed changes

janosh merged commit 5e208f4 into materialsproject:master Sep 6, 2024
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DanielYang59 deleted the install-more-opt-ci-deps branch September 6, 2024 13:04

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Install optional boltztrap, vampire and openbabel in CI #3985

Install optional boltztrap, vampire and openbabel in CI #3985

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	@pytest.mark.skipif(ase is not None, reason="ase is present")
	def test_no_ase_err():

Install optional boltztrap, vampire and openbabel in CI #3985

Install optional boltztrap, vampire and openbabel in CI #3985

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