Avoid inspect.getfullargspec to maintain compatibility with py2.7 (m…

…aterialsproject#986)

* Use set_prop_cycle

* Import pymatgen.util.serialization

* Fix DeprecationWarning

* Add Hdr.to_string

* Minor changes

* Add is_ngqpt option to PhononWork class methods

* Better error message if disordered structure is passed to to_abivars

* Workaround for pandas issue 18021

* Fix typo

* Init build.version

* Minor changes

* Add Flow.get_task_cycles method

* Use universal_newlines in Popen if py3k

* Enforce in NscfTask same FFT mesh as in GSTask

* Add repr for DFPT tasks

* Begin removing deprecated functions

* update pseudos

* Use universal_newlines if py3k

* Add tests

* Add tests

* Add mpi_runner_options

* Count number of jobs in the queue without contacting the resource manager

* Add CyclesPlotter and new methods for RelaxationCycle, EOSFit.plot_ax + tests

* add methods and classes to __all__

* Just to trigger travis build

* This to check if travis gets stuck due to matplotlib

* Indent RST table in add_fix_kwargs decorator

* Remove logger.debug call

* Minor fix in NscfTask

* add class to __all__

* one more class in __all__

* remove introspection in dict methods

* Remove unused import

pymatgen/io/abinit/events.py

@@ -15,7 +15,6 @@
 import six
 import abc
 import logging
-import inspect
 import numpy as np
 
 from monty.string import indent, is_string, list_strings
@@ -36,7 +35,9 @@
     "ScfConvergenceWarning",
     "NscfConvergenceWarning",
     "RelaxConvergenceWarning",
-    "Correction"
+    "Correction",
+    "DilatmxError",
+    "DilatmxErrorHandler"
 ]
 
 
@@ -566,19 +567,20 @@ def handle_task_event(self, task, event):
 
     @pmg_serialize
     def as_dict(self):
-        #@Guido this introspection is nice but it's not safe
+        """
+        Basic implementation of as_dict if __init__ has no arguments. Subclasses may need to overwrite.
+        """
+
         d = {}
-        if hasattr(self, "__init__"):
-            for c in inspect.getfullargspec(self.__init__).args:
-                if c != "self":
-                    d[c] = self.__getattribute__(c)
         return d
 
     @classmethod
     def from_dict(cls, d):
-        kwargs = {k: v for k, v in d.items()
-                  if k in inspect.getfullargspec(cls.__init__).args}
-        return cls(**kwargs)
+        """
+        Basic implementation of from_dict if __init__ has no arguments. Subclasses may need to overwrite.
+        """
+
+        return cls()
 
     @classmethod
     def compare_inputs(cls, new_input, old_input):
@@ -721,6 +723,14 @@ class DilatmxErrorHandler(ErrorHandler):
     def __init__(self, max_dilatmx=1.3):
         self.max_dilatmx = max_dilatmx
 
+    @pmg_serialize
+    def as_dict(self):
+        return {'max_dilatmx': self.max_dilatmx}
+
+    @classmethod
+    def from_dict(cls, d):
+        return cls(max_dilatmx=d['max_dilatmx'])
+
     def handle_task_event(self, task, event):
         # Read the last structure dumped by ABINIT before aborting.
         filepath = task.outdir.has_abiext("DILATMX_STRUCT.nc")
@@ -777,6 +787,14 @@ class TolSymErrorHandler(ErrorHandler):
     def __init__(self, max_nfixes=3):
         self.max_nfixes = max_nfixes
 
+    @pmg_serialize
+    def as_dict(self):
+        return {'max_nfixes': self.max_nfixes}
+
+    @classmethod
+    def from_dict(cls, d):
+        return cls(max_nfixes=d['max_nfixes'])
+
     def handle_task_event(self, task, event):
         # TODO: Add limit on the number of fixes one can do for the same error
         # For example in this case, the scheduler will stop after 20 submissions

pymatgen/io/abinit/flows.py

@@ -2563,7 +2563,7 @@ def from_scf_input(cls, workdir, scf_input, ph_ngqpt, with_becs=True, manager=No
             raise ValueError("ph_ngqpt %s should be a sub-mesh of scf_ngkpt %s" % (ph_ngqpt, scf_ngkpt))
 
         # Get the q-points in the IBZ from Abinit
-        qpoints = scf_input.abiget_ibz(ngkpt=ph_ngqpt, shiftk=(0,0,0), kptopt=1).points
+        qpoints = scf_input.abiget_ibz(ngkpt=ph_ngqpt, shiftk=(0, 0, 0), kptopt=1).points
 
         # Create a PhononWork for each q-point. Add DDK and E-field if q == Gamma and with_becs.
         for qpt in qpoints:

pymatgen/io/abinit/qadapters.py

@@ -946,7 +946,7 @@ def optimize_params(self, qnodes=None):
         This method is called in get_subs_dict. Return a dict with parameters to be added to qparams
         Subclasses may provide a specialized version.
         """
-        logger.debug("optimize_params of baseclass --> no optimization available!!!")
+        #logger.debug("optimize_params of baseclass --> no optimization available!!!")
         return {}
 
     def get_subs_dict(self, qnodes=None):

pymatgen/io/abinit/tasks.py

@@ -3227,10 +3227,14 @@ def setup(self):
         (in principle, it's possible to interpolate inside Abinit but tests revealed some numerical noise
         Here we change the input file of the NSCF task to have the same FFT mesh.
         """
-        assert len(self.deps) == 1
-        dep = self.deps[0]
-        parent_task = dep.node
         # TODO: This won't work if parent_node is a file
+        for dep in self.deps:
+            if "DEN" in dep.exts:
+                parent_task = dep.node
+                break
+        else:
+            raise RuntimeError("Cannot find parent node producing DEN file")
+
         with parent_task.open_gsr() as gsr:
             den_mesh = 3 * [None]
             den_mesh[0] = gsr.reader.read_dimvalue("number_of_grid_points_vector1")

pymatgen/util/plotting.py

@@ -385,19 +385,21 @@ def wrapper(*args, **kwargs):
         return fig
 
     # Add docstring to the decorated method.
-    s = "\n" + """\
-    keyword arguments controlling the display of the figure:
-
-    ================  ====================================================
-    kwargs            Meaning
-    ================  ====================================================
-    title             Title of the plot (Default: None).
-    show              True to show the figure (default: True).
-    savefig           'abc.png' or 'abc.eps' to save the figure to a file.
-    size_kwargs       Dictionary with options passed to fig.set_size_inches
-                      example: size_kwargs=dict(w=3, h=4)
-    tight_layout      True to call fig.tight_layout (default: False)
-    ================  ===================================================="""
+    s = "\n\n" + """\
+        Keyword arguments controlling the display of the figure:
+
+        ================  ====================================================
+        kwargs            Meaning
+        ================  ====================================================
+        title             Title of the plot (Default: None).
+        show              True to show the figure (default: True).
+        savefig           "abc.png" or "abc.eps" to save the figure to a file.
+        size_kwargs       Dictionary with options passed to fig.set_size_inches
+                          e.g. size_kwargs=dict(w=3, h=4)
+        tight_layout      True to call fig.tight_layout (default: False)
+        ================  ====================================================
+
+"""
 
     if wrapper.__doc__ is not None:
         # Add s at the end of the docstring.