Merge branch 'develop' of https://github.com/abinit/abipy into develop

README.rst

@@ -81,7 +81,7 @@ in the form of pre-compiled packages that can be easily installed with e.g.::
 
 Create a new conda_ environment (let's call it ``abienv``) with::
 
-    conda create --name abienv
+    conda create --name abienv python=3.11
 
 and activate it with::
 
@@ -106,7 +106,10 @@ in the `anaconda howto <http://abinit.github.io/abipy/installation#anaconda-howt
 Developmental version
 ---------------------
 
-Getting the developmental version of AbiPy is easy.
+To install the developmental version of AbiPy with pip, use::
+
+    pip install git+https://github.com/abinit/abipy.git@develop
+
 Clone the `github repository <https://github.com/abinit/abipy>`_ with::
 
     git clone https://github.com/abinit/abipy
@@ -118,7 +121,7 @@ For pip, use::
 
 If you are using conda_ (see `Installing conda`_ to install conda itself), create a new environment (``abienv``) with::
 
-    conda create -n abienv
+    conda create -n abienv python=3.11
     source activate abienv
 
 Add ``conda-forge``, and ``abinit`` to your channels with::
@@ -143,22 +146,6 @@ or alternately::
 to install the package in developmental mode.
 This is the recommended approach, especially if you are planning to implement new features.
 
-Note, however, that the developmental version of AbiPy is kept in sync with the
-developmental version of pymatgen thus ```python setup.py develop``` may
-try to download new versions from the PyPi portal and then fail with e.g. the error message::
-
-    ...
-    processing dependencies for abipy==0.6.0.dev0
-    error: scipy 1.0.0 is installed but scipy>=1.0.1 is required by {'pymatgen'}
-
-due to inconsistent dependencies.
-To solve the problem, use conda to update scipy to a version >= 1.0.1 with::
-
-    conda install "scipy>=1.0.1"
-
-then issue again python setup.py develop. If this fails, supposing you were upgrading abipy inside 
-an already existing conda environment, try to restart by creating from scratch a fresh conda environment, see above.
-
 Also note that the BLAS/Lapack libraries provided by conda have multithreading support activated by default.
 Each process will try to use all of the cores on your machine, which quickly overloads things
 if there are multiple processes running.

abipy/abio/robots.py

@@ -817,36 +817,6 @@ def close(self) -> None:
                     print("Exception while closing: ", abifile.filepath)
                     print(exc)
 
-    #@classmethod
-    #def open(cls, obj, nids=None, **kwargs):
-    #    """
-    #    Flexible constructor. obj can be a :class:`Flow` or a string with the directory containing the Flow.
-    #    `nids` is an optional list of :class:`Node` identifiers used to filter the set of :class:`Task` in the Flow.
-    #    """
-    #    has_dirpath = False
-    #    if is_string(obj):
-    #        try:
-    #            from abipy.flowtk import Flow
-    #            obj = Flow.pickle_load(obj)
-    #        except:
-    #            has_dirpath = True
-
-    #    if not has_dirpath:
-    #        # We have a Flow. smeth is the name of the Task method used to open the file.
-    #        items = []
-    #        smeth = "open_" + cls.EXT.lower()
-    #        for task in obj.iflat_tasks(nids=nids): #, status=obj.S_OK):
-    #            open_method = getattr(task, smeth, None)
-    #            if open_method is None: continue
-    #            abifile = open_method()
-    #            if abifile is not None: items.append((task.pos_str, abifile))
-    #        return cls(*items)
-
-    #    else:
-    #        # directory --> search for files with the appropriate extension and open it with abiopen.
-    #        if nids is not None: raise ValueError("nids cannot be used when obj is a directory.")
-    #        return cls.from_dir(obj)
-
     #def get_attributes(self, attr_name, obj=None, retdict=False):
     #    od = OrderedDict()
     #    for label, abifile in self.items():
@@ -1241,10 +1211,14 @@ def get_baserobot_code_cells(self, title=None) -> list:
     @staticmethod
     def get_yvals_item_abifiles(item: Any, abifiles: list) -> np.ndarray:
         """Extract values for a list of Abinit files."""
+        def _float(obj):
+            if obj is None: return obj
+            return float(obj)
+
         if callable(item):
-            return np.array([float(item(a)) for a in abifiles])
+            return np.array([_float(item(a)) for a in abifiles])
         else:
-            return np.array([float(duck.getattrd(a, item)) for a in abifiles])
+            return np.array([_float(duck.getattrd(a, item)) for a in abifiles])
 
     @staticmethod
     def plot_xvals_or_xstr_ax(ax, xs, yvals, fontsize, **kwargs) -> list:

abipy/electrons/ebands.py

@@ -3933,7 +3933,7 @@ def boxplot(self, e0="fermie", brange=None, swarm=False, fontsize=8, **kwargs) -
         ax_list, fig, plt = get_axarray_fig_plt(None, nrows=nrows, ncols=ncols,
                                                 sharex=False, sharey=True, squeeze=False)
         ax_list = ax_list.ravel()
-        # don't show the last ax if numeb is odd.
+        # don't show the last ax if num_plots is odd.
         if num_plots % ncols != 0: ax_list[-1].axis("off")
 
         for (label, ebands), ax in zip(self.ebands_dict.items(), ax_list):

abipy/electrons/gwr.py

@@ -38,6 +38,7 @@
 class _MyQpkindsList(list):
     """Returned by find_qpkinds."""
 
+
 @dataclasses.dataclass
 class MinimaxMesh:
     """