Change bibtex style

abipy/core/symmetries.py

@@ -742,11 +742,12 @@ class AbinitSpaceGroup(OpSequence):
         """
         Test whether two k-points in fractional coordinates are symmetry equivalent
         i.e. if there's a symmetry operations TO (including time-reversal T, if present)
-        such that:
+	such that::
 
             TO(k1) = k2 + G0
 
-        Return: namedtuple with:
+	Return: namedtuple with::
+
             isym: The index of the symmetry operation such that TS(k1) = k2 + G0
                 Set to -1 if k1 and k2 are not related by symmetry.
             op: Symmetry operation.

abipy/dfpt/ddb.py

@@ -1265,14 +1265,16 @@ class DdbFile(TextFile, Has_Structure, NotebookWriter):
         return DielectricTensorGenerator.from_files(os.path.join(task.workdir, "run.abo_PHBST.nc"),
                                                     os.path.join(task.workdir, "anaddb.nc"))
 
-    def anaget_elastic(self, relaxed_ion="automatic", piezo="automatic", dde=False, stress_correction=False,
-			asr=2, chneut=1, mpi_procs=1, workdir=None, manager=None, verbose=0, retpath=False):
+    def anaget_elastic(self, relaxed_ion="automatic", piezo="automatic",
+                        dde=False, stress_correction=False, asr=2, chneut=1,
+                        mpi_procs=1, workdir=None, manager=None, verbose=0, retpath=False):
         """
         Call anaddb to compute elastic and piezoelectric tensors. Require DDB with strain terms.
 
 	By default, this method sets the anaddb input variables automatically
 	by looking at the 2nd-order derivatives available in the DDB file.
-	This behaviour can be changed by setting explicitly the value of: `relaxed_ion` and `piezo`.
+	This behaviour can be changed by setting explicitly the value of:
+        `relaxed_ion` and `piezo`.
 
         Args:
             relaxed_ion: Activate computation of relaxed-ion tensors.

abipy/dfpt/gruneisen.py

@@ -780,7 +780,6 @@ class GrunsNcFile(AbinitNcFile, Has_Structure, NotebookWriter):
         """
         Splits the values of the finite differences gruneisen along a path like for the phonon bands
         """
-
         try:
             return self._split_gruns_fd
         except AttributeError:
@@ -965,6 +964,7 @@ def calculate_gruns_finite_differences(phfreqs, eig, iv0, volume, dv):
     """
     Calculates the Gruneisen parameters from finite differences on the phonon frequencies. Uses the eigenvectors
     to match the frequencies at different volumes.
+
     Args:
         phfreqs: numpy array with the phonon frequencies at different volumes. Shape (nvols, nqpts, 3*natoms)
         eig: numpy array with the phonon eigenvectors at the different volumes. Shape (nvols, nqpts, 3*natoms, 3*natoms)
@@ -972,6 +972,7 @@ def calculate_gruns_finite_differences(phfreqs, eig, iv0, volume, dv):
         iv0: index of the 0 volume.
         volume: volume of the structure at the central volume.
         dv: volume variation.
+
     Returns:
         A numpy array with the gruneisen parameters. Shape (nqpts, 3*natoms)
     """

abipy/electrons/ebands.py

@@ -632,8 +632,7 @@ class ElectronBands(Has_Structure):
         that underestimates the Fermi energy because e.g. the IBZ sampling
         is shifted whereas the true VMB is at Gamma.
 
-        Return:
-            New fermi energy in eV.
+        Return: New fermi energy in eV.
 
         .. warning:
 
@@ -649,11 +648,9 @@ class ElectronBands(Has_Structure):
 
          Args:
             edos: |ElectronDos| object.
-            nelect: Number of electrons.
-                If None, the number of electrons in self. is used
+            nelect: Number of electrons. If None, the number of electrons in self. is used
 
-        Return:
-            New fermi energy in eV.
+        Return: New fermi energy in eV.
         """
         if nelect is None:
             new_fermie = edos.find_mu(self.nelect)

abipy/integration_tests/TODO.md

@@ -2,7 +2,7 @@ TODO list:
 
 ## High priority
 
-* DONE Remove all the abiview commands that are now implemented in abiopen. 
+* Get rid of readthedocs
 
 * DONE Add ebands.method to fix the fermi level in semiconductors
   Remember that ebands is immutable
@@ -16,12 +16,6 @@ TODO list:
 * introduce new staus WAITING_FOR_RESTART
   so that we don't have to restart task in callbacks
 
-* DONE Check PJDOS in abinit@gitlab
-
-* DONE Add mpirun_args see e.g nic4 and mpirun --bind-to None
-
-* DONE Re-implement max_njobs in the queue using a counter local to the Launcher.
-
 * Fix annoying warnings about k-point sampling.
 
 * Reorganize modules in flowtk to prepare future migration. Modules with gs_works, dfpt_works ...
@@ -31,8 +25,7 @@ TODO list:
 
 * Almost DONE: Add support for https://mybinder.readthedocs.io/en/latest/sample_repos.html#conda-environment-with-environment-yml
 
-* ALMOST DONE Add https://github.com/mcmtroffaes/sphinxcontrib-bibtex
-  Change bibtex style.
+* DONE Add https://github.com/mcmtroffaes/sphinxcontrib-bibtex Change bibtex style.
 
 * DONE Add support for DVDV, DDB in plot_networkx (but graphviz is much better)
 
@@ -52,7 +45,7 @@ TODO list:
 
 * remove phononflow
 
-* Add DOS to GSR file (useful if tetra)  Create Dosfile ?
+* Add DOS to GSR file (useful if tetra)  Create Dosfile ? Fortran exec?
 
 * Add with_becs to PhononWork
 
@@ -73,8 +66,6 @@ TODO list:
 
 * DONE Solve problem with visualize in jupyter notebooks (files should be produced in workdir)
 
-* DONE Change shifts default value in g0w0_with_ppmodel_inputs
-
 * Scheduler should report info on exceptions (especially if at the end when on_all_ok is invoked)
 
 * ALMOST DONE: Replace core.tensor with pymatgen tensor
@@ -102,13 +93,9 @@ TODO list:
 
 * XG remarks:
 
-    - Improve abipy/docs/README.rst mentions 
+    - Improve abipy/docs/README.rst
     - Change bibtex style (use same format as abidocs)
 
-	open _build/html/index.html
-
-    - Band structure and Fermi level
-
 ## Low priority
 
 * Use parser subclass to avoid boiler plate code.

abipy/scripts/abiview.py

@@ -419,7 +419,7 @@ def get_parser(with_epilog=False):
         help="Use the row index as x-value in the plot. By default the plotter uses the first column as x-values")
 
     # Subparser for abo command.
-    p_abo = subparsers.add_parser('abo', parents=[copts_parser], help=abiview_abo.__doc__)
+    #p_abo = subparsers.add_parser('abo', parents=[copts_parser], help=abiview_abo.__doc__)
 
     # Subparser for log command.
     p_dirviz = subparsers.add_parser('dirviz', parents=[copts_parser], help=abiview_dirviz.__doc__)

dev_scripts/runtests.sh

@@ -18,7 +18,6 @@ if [[ "${ABIPY_PYTEST}" == "yes" ]]; then
 	    --ignore=abipy/integration_tests --ignore=abipy/data/refs --ignore=abipy/scripts/ \
 	    --ignore=abipy/examples/plot --ignore=abipy/examples/flows --ignore=abipy/gui 
     else
-	#pytest --cov-config=.coveragerc --cov=abipy -v --doctest-modules abipy \
 	pytest -n 2 --cov-config=.coveragerc --cov=abipy -v --doctest-modules abipy \
 	    --ignore=abipy/integration_tests --ignore=abipy/data/refs --ignore=abipy/scripts/ \
 	    --ignore=abipy/examples/plot --ignore=abipy/examples/flows --ignore=abipy/gui 
@@ -29,7 +28,6 @@ fi
 # integration_tests are excluded in setup.cfg
 if [[ "${ABIPY_COVERALLS}" == "yes" ]]; then 
     pytest -n 2 --cov-config=.coveragerc --cov=abipy --cov-append -v abipy/integration_tests 
-    #pytest --cov-config=.coveragerc --cov=abipy --cov-append -v abipy/integration_tests 
 fi
 
 # Generate documentation

docs/README.rst

@@ -1,7 +1,7 @@
 .. _documenting-abipy:
 
 Documenting AbiPy
-==================
+=================
 
 .. contents::
    :backlinks: top
@@ -10,16 +10,16 @@ Organization of documentation
 -----------------------------
 
 The documentation for AbiPy is generated from ReStructured Text using the Sphinx_ documentation generation tool. 
-The documentation sources are found in the :file:`~/docs/` directory in the repository. Major items : 
+The documentation sources are found in the :file:`~/docs/` directory in the repository. Major items:
 
 * index.rst - the top level include document for AbiPy docs
 * api - placeholders to automatically generate the api documentation
 * scripts - documentation for scripts
-* workflows - documentation for workflows 
+* flow_gallery/gallery - automatically generated by sphinx-gallery
+* workflows - Documentation about Abinit flows/works/tasks and TaskManager
 * README.rst - the present file
 * conf.py - the sphinx configuration
 * _static - used by the sphinx build system
-* _templates - used by the sphinx build system
 
 The main entry point is :file:`docs/index.rst`, which pulls in 
 the files for the users guide, developers guide, api reference. 
@@ -62,7 +62,7 @@ Use::
 
    ./ghp_import.py _build/html/ -n -p
 
-to deploy to gh-pages.
+to deploy to gh-pages (only for project leader)
 
 
 .. _formatting-abipy-docs:

docs/conf.py

@@ -17,7 +17,6 @@ import shutil
 # documentation root, use os.path.abspath to make it absolute, like shown here.
 
 ABIPY_ROOT = os.path.abspath(os.path.join(os.path.dirname(os.path.abspath(__file__)), ".."))
-#print(ABIPY_ROOT)
 
 sys.path.insert(0, ABIPY_ROOT)
 
@@ -442,22 +441,21 @@ autodoc_member_order = "bysource"
 # pybtex provides a very powerful way to create and register new styles, using setuptools entry points,
 # as documented here: http://docs.pybtex.org/api/plugins.html
 
-#from pybtex.style.formatting.unsrt import Style as UnsrtStyle
-#from pybtex.style.template import toplevel # ... and anything else needed
-#from pybtex.plugin import register_plugin
+from pybtex.style.formatting.plain import Style
+from pybtex.style.labels.alpha import LabelStyle
 
-#class MyStyle(UnsrtStyle):
-#    def format_label(self, entry):
-#        print("hello")
-#        return "APA"
-#
-#    #def format_XXX(self, e):
-#    #    template = toplevel [
-#    #        # etc.
-#    #    ]
-#    #    return template.format_data(e)
 
-#register_plugin('pybtex.style.formatting', 'mystyle', MyStyle)
+class AbiPyLabelStyle(LabelStyle):
+    def format_label(self, entry):
+        return entry.key
+
+class AbiPyStyle(Style):
+    default_label_style = 'abipy'
+
+from pybtex.plugin import register_plugin
+register_plugin('pybtex.style.labels', 'abipy', AbiPyLabelStyle)
+register_plugin('pybtex.style.formatting', 'abipystyle', AbiPyStyle)
+
 
 # This is for releases http://releases.readthedocs.io/en/latest/usage.html
 releases_github_path = "abinit/abipy"

docs/zzbiblio.rst

@@ -7,4 +7,5 @@ Bibliography
 .. rubric:: References
 
 .. bibliography:: refs.bib
+   :style: abipystyle
    :cited: