Skip problematic tests

abipy/abio/tests/test_outputs.py

@@ -1,6 +1,7 @@
 # coding: utf-8
 """Test for output files"""
 import os
+import pytest
 import abipy.data as abidata
 
 from abipy import abilab

abipy/core/tests/test_restapi.py

@@ -1,5 +1,6 @@
 """Tests for core.restapi module"""
 import contextlib
+import pytest
 import abipy.data as abidata
 
 from abipy import abilab
@@ -10,18 +11,10 @@
 class TestMpRestApi(AbipyTest):
     """Test interfaces with the Materials Project REST API."""
 
+    @pytest.mark.skip(reason="Interface with MP rester is broken")
     def test_mprester(self):
         """Testing MP Rest API wrappers."""
 
-        #with restapi.get_mprester() as rest:
-        #    #pdr = rest.get_phasediagram_results("Li-Fe-O".split("-"))
-        #    pdr = rest.get_phasediagram_results("Ga-Ge-As".split("-"))  # This one is faster.
-        #    repr(pdr); str(pdr)
-        #    pdr.print_dataframes(verbose=2)
-        #    if self.has_matplotlib():
-        #        plotter = pdr.plot(show_unstable=True, show=False)
-        #        assert hasattr(plotter, "show")
-
         # Test mp_search
         mp = abilab.mp_search("MgB2")
         repr(mp); str(mp)

abipy/ml/aseml.py

@@ -1258,7 +1258,7 @@ class MyAlignnCalculator(_MyMlCalculator, AlignnAtomwiseCalculator):
         raise ValueError(f"Invalid {self.nn_type=}")
 
 
-class _MlBase:
+class MlBase:
     """
     Base class for all Ml subclasses providing helper methods to
     perform typical tasks such as writing files in the workdir
@@ -1411,7 +1411,7 @@ def _finalize(self) -> None:
         print("\nResults available in directory:", self.workdir)
 
 
-class MlRelaxer(_MlBase):
+class MlRelaxer(MlBase):
     """
     Relax structure with ASE and ML-potential.
     """
@@ -1625,7 +1625,7 @@ def run(self):
         return relax
 
 
-class MlMd(_MlBase):
+class MlMd(MlBase):
     """Perform MD calculations with ASE and ML potential."""
 
     def __init__(self, atoms: Atoms, temperature, timestep, steps, loginterval,
@@ -1728,7 +1728,7 @@ def run(self) -> None:
         #                   label=f"xdatcar with relaxation generated by {self.__class__.__name__}")
 
 
-class _MlNebBase(_MlBase):
+class _MlNebBase(MlBase):
     """
     Base class for Neb calculations
     """
@@ -2117,7 +2117,7 @@ def make_ase_neb(initial: Atoms, final: Atoms, nimages: int,
     return neb
 
 
-class MlOrderer(_MlBase):
+class MlOrderer(MlBase):
     """
     Order a disordered structure using pymatgen and ML potential.
     """
@@ -2582,7 +2582,7 @@ def traj_to_qepos(traj_filepath: str, pos_filepath: str) -> None:
 
 
 
-class MlAsePhonons(_MlBase):
+class MlAsePhonons(MlBase):
     """
     Compute phonons with ASE and ML potential.
     """
@@ -2705,107 +2705,3 @@ def run(self) -> None:
         self.savefig("phonons.png", fig, info=title)
 
         self._finalize()
-
-
-class MlPhononsWithDDB(_MlBase):
-    """
-    Compute phonons with phonopy and a set of ML potentials starting from a DDB file.
-    """
-
-    def __init__(self, ddb_filepath: str, supercell, qmesh, asr, nqpath,
-                 relax_mode, fmax, pressure, steps, optimizer, nn_name,
-                 verbose, workdir, prefix=None):
-        """
-        Args:
-            ddb_filepath: DDB filename.
-            supercell: tuple with supercell dimension.
-            qmesh: q-mesh for phonon-DOS
-            asr: Enforce acoustic sum-rule.
-            nqpath: Number of q-point along the q-path.
-            relax_mode: "ions" to relax ions only, "cell" for ions + cell, "no" for no relaxation.
-            fmax: tolerance for relaxation convergence. Here fmax is a sum of force and stress forces.
-            verbose: whether to print stdout.
-            optimizer: name of the ASE optimizer to use for relaxation.
-            nn_name: String defining the NN potential. See also CalcBuilder.
-            verbose: Verbosity level.
-            workdir:
-            prefix:
-        """
-        super().__init__(workdir, prefix)
-        from abipy.dfpt.ddb import DdbFile
-        self.ddb = DdbFile(ddb_file)
-        self.initial_atoms = get_atoms(ddb.structure)
-        self.supercell = supercell
-        self.qmesh = qmesh
-        self.asr = asr
-        self.nqpath = nqpath
-        self.relax_mode = relax_mode
-        RX_MODE.validate(self.relax_mode)
-        self.fmax = fmax
-        self.pressure = pressure
-        self.steps = steps
-        self.optimizer = optimizer
-        self.nn_name = nn_name
-        self.verbose = verbose
-
-    def to_string(self, verbose=0):
-        """String representation with verbosity level `verbose`."""
-        s = f"""\
-
-{self.__class__.__name__} parameters:
-
-     ddb_path   = {self.ddb.filepath}
-     supercell  = {self.supercell}
-     qmesh      = {self.qmesh}
-     asr        = {self.asr}
-     nqpath     = {self.nqpath}
-     relax_mode = {self.relax_mode}
-     fmax       = {self.fmax}
-     steps      = {self.steps}
-     optimizer  = {self.optimizer}
-     pressure   = {self.pressure}
-     nn_names   = {self.nn_names}
-     workdir    = {self.workdir}
-     verbose    = {self.verbose}
-
-=== ATOMS ===
-
-{self.initial_atoms}
-"""
-        return s
-
-    def run(self) -> None:
-        """Run MlPhononsWithDDB."""
-        workdir = self.workdir
-
-        atoms = self.initial_atoms.copy()
-        calculator = CalcBuilder(self.nn_name).get_calculator()
-        atoms.calc = calculator
-
-        if self.relax != RX_MODE.no:
-            print(f"Relaxing DDB atoms with relax mode: {self.relax_mode}.")
-            relax_kws = dict(optimizer=self.optimizer,
-                             relax_mode=self.relax_mode,
-                             fmax=self.fmax,
-                             pressure=self.pressure,
-                             steps=self.steps,
-                             traj_path=self.get_path("relax.traj", "ASE relax trajectory"),
-                             verbose=self.verbose,
-                            )
-
-            relax = relax_atoms(atoms, **relax_kws)
-            r0, r1 = AseResults.from_traj_inds(relax.traj, 0, -1)
-            df = dataframe_from_results_list(["DDB_initial", "DDB_relaxed"], [r0, r1])
-            print(df, end=2*"\n")
-
-        # Call phonopy to compute phonons with finite difference and ML potential.
-        # Include non-analytical term if dipoles are available in the DDB file.
-        if self.dbb.has_lo_to_data:
-            print("Activating dipolar term in phonopy calculation using BECS and Zeff taken from DDB.")
-
-        # Call anaddb to compute ab-initio phonon frequencies from the DDB.
-        #self.ddb.anaget_phmodes_at_qpoints(
-        #   qpoints=None, asr=2, chneut=1, dipdip=1, dipquad=1, quadquad=1,
-        #   ifcflag=0, ngqpt=None, workdir=None, mpi_procs=1, manager=None, verbose=0,
-        #   lo_to_splitting=False,
-        #   spell_check=True, directions=None, anaddb_kwargs=None, return_input=False)