From ec86f64539d17047c8582d28107f13da929d4714 Mon Sep 17 00:00:00 2001 From: Matteo Giantomassi Date: Sat, 30 Dec 2017 14:49:29 +0100 Subject: [PATCH] Add files for sphinx --- CHANGELOG.rst | 2 + docs/Makefile | 2 +- docs/changelog.rst | 7 ++ docs/conf.py | 66 ++++++++++- docs/index.rst | 4 +- docs/install_reqs.sh | 11 -- docs/installation.rst | 3 + docs/links.rst | 119 +++++++++++++++++++ docs/refs.bib | 265 ++++++++++++++++++++++++++++++++++++++++++ docs/requirements.txt | 10 ++ docs/whats_new.rst | 14 --- docs/zzbiblio.rst | 10 ++ requirements.txt | 13 +++ setup.py | 22 +--- 14 files changed, 496 insertions(+), 52 deletions(-) create mode 100644 CHANGELOG.rst create mode 100644 docs/changelog.rst delete mode 100755 docs/install_reqs.sh create mode 100644 docs/links.rst create mode 100644 docs/refs.bib create mode 100644 docs/requirements.txt delete mode 100644 docs/whats_new.rst create mode 100644 docs/zzbiblio.rst create mode 100644 requirements.txt diff --git a/CHANGELOG.rst b/CHANGELOG.rst new file mode 100644 index 0000000..8ac4c31 --- /dev/null +++ b/CHANGELOG.rst @@ -0,0 +1,2 @@ +* :release:`0.2.0 <2017-03-10>` +* :feature:`0` This is the first official release diff --git a/docs/Makefile b/docs/Makefile index defa5fa..64d1798 100644 --- a/docs/Makefile +++ b/docs/Makefile @@ -2,7 +2,7 @@ # # You can set these variables from the command line. -SPHINXOPTS = +SPHINXOPTS = -j4 SPHINXBUILD = sphinx-build PAPER = BUILDDIR = _build diff --git a/docs/changelog.rst b/docs/changelog.rst new file mode 100644 index 0000000..6a75ddb --- /dev/null +++ b/docs/changelog.rst @@ -0,0 +1,7 @@ +.. _changelog: + +********* +Changelog +********* + +.. include:: ../CHANGELOG.rst diff --git a/docs/conf.py b/docs/conf.py index 8cac922..9441a14 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -8,6 +8,7 @@ import sys import os +import shutil #import matplotlib as mpl #mpl.use("Agg") @@ -15,12 +16,24 @@ # add these directories to sys.path here. If the directory is relative to the # documentation root, use os.path.abspath to make it absolute, like shown here. -sys.path.insert(0, os.path.abspath('sphinxext')) +ABIFLOWS = os.path.abspath(os.path.join(os.path.dirname(os.path.abspath(__file__)), "..")) +print("ABIFLOWS", ABIFLOWS) + +sys.path.insert(0, ABIFLOWS) import imp -mod_name = "../abiflows/core/release.py" +mod_name = os.path.join(ABIFLOWS, "abiflows", "core", "release.py") relmod = imp.load_source(mod_name, mod_name) +on_rtd = os.environ.get('READTHEDOCS') == 'True' and os.environ.get("READTHEDOCS_PROJECT") +#if on_rtd: +# print("Preparing execution on READTHEDOCS server...") +# os.makedirs(os.path.expanduser("~/.abinit/abipy")) +# shutil.copy(os.path.join(ABIFLOWS, "data", "managers", "travis_scheduler.yml"), +# os.path.expanduser("~/.abinit/abipy/scheduler.yml")) +# shutil.copy(os.path.join(ABIFLOWS, "data", "managers", "travis_manager.yml"), +# os.path.expanduser("~/.abinit/abipy/manager.yml")) + # -- General configuration ----------------------------------------------------- # If your documentation needs a minimal Sphinx version, state it here. @@ -31,7 +44,6 @@ extensions = [ 'sphinx.ext.autodoc', 'sphinx.ext.doctest', - #'sphinx.ext.coverage', 'sphinx.ext.autosummary', 'sphinx.ext.intersphinx', 'sphinx.ext.todo', @@ -46,13 +58,15 @@ #'sphinx_gallery.gen_gallery', #"sphinxarg.ext", # CLI doc #'nbsphinx', + 'sphinxcontrib.bibtex', + "releases", ] # Add any Sphinx extension module names here, as strings. They can # be extensions coming with Sphinx (named 'sphinx.ext.*') or your custom ones. import matplotlib extensions += [ - 'matplotlib.sphinxext.mathmpl', + #'matplotlib.sphinxext.mathmpl', 'matplotlib.sphinxext.only_directives', 'matplotlib.sphinxext.plot_directive', 'IPython.sphinxext.ipython_directive', @@ -114,7 +128,7 @@ # List of patterns, relative to source directory, that match files and # directories to ignore when looking for source files. -exclude_patterns = ['_build', '**.ipynb_checkpoints'] +exclude_patterns = ['_build', '**.ipynb_checkpoints', "links.rst"] # The reST default role (used for this markup: `text`) to use for all documents. #default_role = None @@ -363,9 +377,51 @@ "scipy": ("https://docs.scipy.org/doc/scipy/reference/", None), 'pandas': ("http://pandas-docs.github.io/pandas-docs-travis/", None), 'matplotlib': ('http://matplotlib.org/', None), + "monty": ("http://pythonhosted.org/monty/", None), "pymatgen": ("http://pymatgen.org/", None), + "fireworks": ("https://materialsproject.github.io/fireworks/", None), + "abipy": ("http://pythonhosted.org/abipy/", None), } # If true, Sphinx will warn about all references where the target cannot be found. # Default is False. You can activate this mode temporarily using the -n command-line switch. #nitpicky = True + +# A string of reStructuredText that will be included at the end of every source file that is read. +# This is the right place to add substitutions that should be available in every file. +with open("links.rst", "rt") as fh: + rst_epilog = fh.read() + +# http://www.sphinx-doc.org/en/stable/ext/extlinks.html#confval-extlinks +# :abivar:`ecut` +#ABINIT_DOCS_URL = +#extlinks = {' +# "abivar" : (ABINIT_DOC_ULRS + '/abinit/%s', "") +# api_url' : (settings.BASE_URL + '%s', settings.BASE_URL) +#} + +autodoc_member_order = "bysource" + +#'members', 'undoc-members', 'private-members', 'special-members', 'inherited-members' and 'show-inheritance'. +#autodoc_default_flags = ["show-inheritance", "inherited-members", "special-members"] + +# From https://sphinxcontrib-bibtex.readthedocs.io/en/latest/usage.html#custom-formatting-sorting-and-labelling +# 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 +# +#class MyStyle(UnsrtStyle): +# +# def format_XXX(self, e): +# template = toplevel [ +# # etc. +# ] +# return template.format_data(e) +# +#register_plugin('pybtex.style.formatting', 'mystyle', MyStyle) + +# This is for releases http://releases.readthedocs.io/en/latest/usage.html +releases_github_path = "abinit/abipy" diff --git a/docs/index.rst b/docs/index.rst index 3c4680e..2622659 100644 --- a/docs/index.rst +++ b/docs/index.rst @@ -1,5 +1,4 @@ .. htmlonly:: - :Release: |version| :Date: |today| @@ -24,7 +23,8 @@ Getting Started features installation - whats_new + changelog + zzbiblio API diff --git a/docs/install_reqs.sh b/docs/install_reqs.sh deleted file mode 100755 index 33d6056..0000000 --- a/docs/install_reqs.sh +++ /dev/null @@ -1,11 +0,0 @@ -#!/bin/bash -set -ev # exit on first error, print each command - -#conda config --set always_yes yes --set changeps1 no -conda install sphinx matplotlib ipython -pip install sphinxcontrib.napoleon -#pip install sphinxcontrib-programoutput -#pip install sphinx-gallery -#pip install sphinx-argparse -pip install sphinx_bootstrap_theme -#pip install nbsphinx diff --git a/docs/installation.rst b/docs/installation.rst index a64af10..85a2883 100644 --- a/docs/installation.rst +++ b/docs/installation.rst @@ -2,6 +2,9 @@ Getting AbiFlows ================ +.. contents:: + :backlinks: top + -------------- Stable version -------------- diff --git a/docs/links.rst b/docs/links.rst new file mode 100644 index 0000000..ece8838 --- /dev/null +++ b/docs/links.rst @@ -0,0 +1,119 @@ +.. Links to websites +.. _Sphinx: http://sphinx.pocoo.org +.. _Abinit: https://www.abinit.org +.. _abiconfig: https://github.com/abinit/abiconfig +.. _abiflows: https://github.com/abinit/abiflows +.. _abitutorials: https://github.com/abinit/abitutorials +.. _abiconda: https://github.com/abinit/abiconda +.. _pseudo-dojo: http://www.pseudo-dojo.org/ +.. _pseudo-dojo repository: https://github.com/abinit/pseudo_dojo +.. _pymatgen: http://www.pymatgen.org +.. _fireworks: https://materialsproject.github.io/fireworks/ +.. _mongodb: https://www.mongodb.com/ +.. _mongoengine: http://mongoengine.org/ +.. _`materials project`: https://materialsproject.org/ +.. _conda: https://conda.io/docs/ +.. _Anaconda: https://continuum.io/downloads +.. _abinit-channel: https://anaconda.org/abinit +.. _matsci: http://materials.sh/ +.. _spack: https://github.com/LLNL/spack +.. _matplotlib: http://matplotlib.org +.. _pandas: http://pandas.pydata.org +.. _scipy: https://www.scipy.org/ +.. _numpy: http://www.numpy.org/ +.. _seaborn: https://seaborn.pydata.org/ +.. _simpy: https://simpy.readthedocs.io/en/latest/ +.. _networkx: https://networkx.github.io/ +.. _pytest: https://docs.pytest.org/en/latest/contents.html +.. _netcdf4-python: http://unidata.github.io/netcdf4-python/ +.. _nbformat: https://github.com/jupyter/nbformat +.. _pip: https://pypi.python.org/pypi/pip +.. _ipython: https://ipython.org/index.html +.. _jupyter: http://jupyter.org/ +.. _Python: http://www.python.org/ +.. _spglib: https://atztogo.github.io/spglib/ +.. _bader: http://theory.cm.utexas.edu/henkelman/code/bader/ +.. _ase: https://wiki.fysik.dtu.dk/ase/ +.. _COD: http://www.crystallography.net/cod/ +.. _CIF: http://www.iucr.org/resources/cif +.. _vesta: http://jp-minerals.org/vesta/en/ +.. _xcrysden: http://www.xcrysden.org/ +.. _xmgrace: http://plasma-gate.weizmann.ac.il/Grace/ +.. _gnuplot: http://www.gnuplot.info/ +.. _ovito: https://ovito.org/ +.. _v_sim: http://inac.cea.fr/L_Sim/V_Sim/ +.. _mayavi: http://docs.enthought.com/mayavi/mayavi/ +.. _avogadro: https://avogadro.cc/ +.. _nbjsmol: https://github.com/gmatteo/nbjsmol +.. _phononwebsite: http://henriquemiranda.github.io/phononwebsite/ +.. _phonopy: https://atztogo.github.io/phonopy/ +.. _netcdf: https://www.unidata.ucar.edu/software/netcdf/docs/faq.html#whatisit +.. _ipywidgets: https://github.com/jupyter-widgets/ipywidgets +.. _YAML: https://en.wikipedia.org/wiki/YAML +.. _JSON: https://en.wikipedia.org/wiki/JSON +.. _slurm: https://slurm.schedmd.com/ +.. _pbspro: http://pbspro.org/ +.. _sge: http://gridscheduler.sourceforge.net/howto/GridEngineHowto.html +.. _torque: http://www.adaptivecomputing.com/products/open-source/torque/ +.. _moab: http://www.adaptivecomputing.com/products/hpc-products/moab-hpc-basic-edition/ +.. _loadleveler: https://www.ibm.com/support/knowledgecenter/en/SSFJTW + +.. Links to important python objects. +.. _POSCAR: http://cms.mpi.univie.ac.at/vasp/guide/node59.html +.. _DataFrame: https://pandas.pydata.org/pandas-docs/stable/generated/pandas.DataFrame.html +.. _DataFrames: https://pandas.pydata.org/pandas-docs/stable/generated/pandas.DataFrame.html + +.. Links to jupyter notebooks associated to AbiPy files available at + https://nbviewer.jupyter.org/github/abinit/abitutorials/blob/master/abitutorials/index.ipynb?flush_cache=true +.. _AbipyStructure: https://nbviewer.jupyter.org/github/abinit/abitutorials/blob/master/abitutorials/structure.ipynb +.. _AbinitInput: https://nbviewer.jupyter.org/github/abinit/abitutorials/blob/master/abitutorials/abinit_input.ipynb +.. _GSR.nc: https://nbviewer.jupyter.org/github/abinit/abitutorials/blob/master/abitutorials/gsr.ipynb +.. _HIST.nc: https://nbviewer.jupyter.org/github/abinit/abitutorials/blob/master/abitutorials/hist.ipynb +.. _FATBANDS.nc: https://nbviewer.jupyter.org/github/abinit/abitutorials/blob/master/abitutorials/efatbands.ipynb +.. _DDB: https://nbviewer.jupyter.org/github/abinit/abitutorials/blob/master/abitutorials/ddb.ipynb +.. _SIGRES.nc: https://nbviewer.jupyter.org/github/abinit/abitutorials/blob/master/abitutorials/sigres.ipynb + +.. Important Abipy objects. +.. |AttrDict| replace:: :class:`monty.collections.AttrDict` +.. |Function1D| replace:: :class:`abipy.core.func1d.Function1D` +.. |Mesh3d| replace:: :class:`abipy.core.mesh3d.Mesh3d` +.. |GSphere| replace:: :class:`abipy.core.gsphere.GSphere` +.. |Kpoint| replace:: :class:`abipy.core.kpoints.Kpoint` +.. |KpointList| replace:: :class:`abipy.core.kpoints.KpointList` +.. |Kpath| replace:: :class:`abipy.core.kpoints.Kpath` +.. |IrredZone| replace:: :class:`abipy.core.kpoints.IrredZone` +.. |KpointStar| replace:: :class:`abipy.core.kpoints.KpointStar` +.. |Structure| replace:: :class:`abipy.core.structure.Structure` +.. |pymatgen-Structure| replace:: :class:`pymatgen.core.structure.Structure` +.. |Lattice| replace:: :class:`pymatgen.core.lattice.Lattice` +.. |AbinitInput| replace:: :class:`abipy.abio.inputs.AbinitInput` +.. |MultiDataset| replace:: :class:`abipy.abio.inputs.MultiDataset` +.. |ElectronBands| replace:: :class:`abipy.electrons.ebands.ElectronBands` +.. |SkwInterpolator| replace:: :class:`abipy.core.skw.SkwInterpolator` +.. |ElectronDos| replace:: :class:`abipy.electrons.ebands.ElectronDos` +.. |PhononBands| replace:: :class:`abipy.dfpt.phonons.PhononBands` +.. |Task| replace:: :class:`pymatgen.io.abinit.tasks.Task` +.. |ScfTask| replace:: :class:`pymatgen.io.abinit.tasks.ScfTask` +.. |NscfTask| replace:: :class:`pymatgen.io.abinit.tasks.NscfTask` +.. |Flow| replace:: :class:`pymatgen.io.abinit.flows.Flow` +.. |Work| replace:: :class:`pymatgen.io.abinit.works.Work` +.. |TaskManager| replace:: :class:`pymatgen.io.abinit.tasks.TaskManager` +.. |GsrFile| replace:: :class:`abipy.electrons.gsr.GsrFile` +.. |GsrRobot| replace:: :class:`abipy.electrons.gsr.GsrRobot` +.. |DdbFile| replace:: :class:`abipy.dfpt.ddb.DdbFile` +.. |DdbRobot| replace:: :class:`abipy.dfpt.ddb.DdbRobot` +.. |PhbstFile| replace:: :class:`abipy.dfpt.phonons.PhbstFile` +.. |PhdosFile| replace:: :class:`abipy.dfpt.phonons.PhdosFile` +.. |PhononDos| replace:: :class:`abipy.dfpt.phonons.PhononDos` +.. |PhononBandsPlotter| replace:: :class:`abipy.dfpt.phonons.PhononBandsPlotter` +.. |PhononDosPlotter| replace:: :class:`abipy.dfpt.phonons.PhononDosPlotter` +.. |Pseudo| replace:: :class:`pymatgen.io.abinit.pseudos.Pseudo` +.. |PseudoTable| replace:: :class:`pymatgen.io.abinit.pseudos.PseudoTable` +.. |Visualizer| replace:: :class:`abipy.iotools.visualizer.Visualizer` + +.. Important objects provided by libraries. +.. |matplotlib-Figure| replace:: :class:`matplotlib.figure.Figure` +.. |matplotlib-Axes| replace:: :class:`matplotlib.axes.Axes` +.. |pandas-DataFrame| replace:: :class:`pandas.DataFrame` +.. |pandas-DataFrames| replace:: :class:`pandas.DataFrame` +.. |numpy-array| replace:: :class:`numpy.ndarray` diff --git a/docs/refs.bib b/docs/refs.bib new file mode 100644 index 0000000..5033f05 --- /dev/null +++ b/docs/refs.bib @@ -0,0 +1,265 @@ +@article{Gonze2016, + author = {Gonze, X. and Jollet, F. and Abreu Araujo, F. and Adams, D. and Amadon, B. and Applencourt, T. and Audouze, C. and Beuken, J.-M. and Bieder, J. and Bokhanchuk, A. and Bousquet, E. and Bruneval, F. and Caliste, D. and Côté, M. and Dahm, F. and Da Pieve, F. and Delaveau, M. and Di Gennaro, M. and Dorado, B. and Espejo, C. and Geneste, G. and Genovese, L. and Gerossier, A. and Giantomassi, M. and Gillet, Y. and Hamann, D.R. and He, L. and Jomard, G. and Laflamme Janssen, J. and Le Roux, S. and Levitt, A. and Lherbier, A. and Liu, F. and Lukačević, I. and Martin, A. and Martins, C. and Oliveira, M.J.T. and Poncé, S. and Pouillon, Y. and Rangel, T. and Rignanese, G.-M. and Romero, A.H. and Rousseau, B. and Rubel, O. and Shukri, A.A. and Stankovski, M. and Torrent, M. and Van Setten, M.J. and Van Troeye, B. and Verstraete, M.J. and Waroquiers, D. and Wiktor, J. and Xu, B. and Zhou, A. and Zwanziger, J.W.}, + doi = {10.1016/j.cpc.2016.04.003}, + pages = {106-131}, + source = {Crossref}, + url = {http://dx.doi.org/10.1016/j.cpc.2016.04.003}, + volume = {205}, + journal = {Computer Physics Communications}, + publisher = {Elsevier BV}, + title = {Recent developments in the {ABINIT} software package}, + issn = {0010-4655}, + year = {2016}, + month = aug, +} +@article{Setyawan2010, + author = {Setyawan, Wahyu and Curtarolo, Stefano}, + doi = {10.1016/j.commatsci.2010.05.010}, + number = {2}, + pages = {299-312}, + source = {Crossref}, + url = {http://dx.doi.org/10.1016/j.commatsci.2010.05.010}, + volume = {49}, + journal = {Computational Materials Science}, + publisher = {Elsevier BV}, + title = {High-throughput electronic band structure calculations: {Challenges} and tools}, + issn = {0927-0256}, + year = {2010}, + month = aug, +} +@article{Ong2013, + author = {Ong, Shyue Ping and Richards, William Davidson and Jain, Anubhav and Hautier, Geoffroy and Kocher, Michael and Cholia, Shreyas and Gunter, Dan and Chevrier, Vincent L. and Persson, Kristin A. and Ceder, Gerbrand}, + doi = {10.1016/j.commatsci.2012.10.028}, + pages = {314-319}, + source = {Crossref}, + url = {http://dx.doi.org/10.1016/j.commatsci.2012.10.028}, + volume = {68}, + journal = {Computational Materials Science}, + publisher = {Elsevier BV}, + title = {Python Materials Genomics (pymatgen): {A} robust, open-source python library for materials analysis}, + issn = {0927-0256}, + year = {2013}, + month = feb, +} +@article{Caliste2008, + author = {Caliste, D. and Pouillon, Y. and Verstraete, M.J. and Olevano, V. and Gonze, X.}, + doi = {10.1016/j.cpc.2008.05.007}, + number = {10}, + pages = {748-758}, + source = {Crossref}, + url = {http://dx.doi.org/10.1016/j.cpc.2008.05.007}, + volume = {179}, + journal = {Computer Physics Communications}, + publisher = {Elsevier BV}, + title = {Sharing electronic structure and crystallographic data with {ETSF_IO}}, + issn = {0010-4655}, + year = {2008}, + month = nov, +} +@article{Marques2012, + author = {Marques, Miguel A.L. and Oliveira, Micael J.T. and Burnus, Tobias}, + doi = {10.1016/j.cpc.2012.05.007}, + number = {10}, + pages = {2272-2281}, + source = {Crossref}, + url = {http://dx.doi.org/10.1016/j.cpc.2012.05.007}, + volume = {183}, + journal = {Computer Physics Communications}, + publisher = {Elsevier BV}, + title = {Libxc: {A} library of exchange and correlation functionals for density functional theory}, + issn = {0010-4655}, + year = {2012}, + month = oct, +} +@article{Ong2008, + author = {Ping Ong, Shyue and Wang, Lei and Kang, Byoungwoo and Ceder, Gerbrand}, + doi = {10.1021/cm702327g}, + number = {5}, + pages = {1798-1807}, + source = {Crossref}, + url = {http://dx.doi.org/10.1021/cm702327g}, + volume = {20}, + journal = {Chem. Mater.}, + publisher = {American Chemical Society (ACS)}, + title = {{Li−Fe−P−O2Phase} Diagram from First Principles Calculations}, + issn = {0897-4756, 1520-5002}, + year = {2008}, + month = mar, +} +@article{Ong2010, + author = {Ong, Shyue Ping and Jain, Anubhav and Hautier, Geoffroy and Kang, Byoungwoo and Ceder, Gerbrand}, + doi = {10.1016/j.elecom.2010.01.010}, + number = {3}, + pages = {427-430}, + source = {Crossref}, + url = {http://dx.doi.org/10.1016/j.elecom.2010.01.010}, + volume = {12}, + journal = {Electrochemistry Communications}, + publisher = {Elsevier BV}, + title = {Thermal stabilities of delithiated olivine {MPO4} {(M=Fe,} Mn) cathodes investigated using first principles calculations}, + issn = {1388-2481}, + year = {2010}, + month = mar, +} +@article{Jain2013, + author = {Jain, Anubhav and Ong, Shyue Ping and Hautier, Geoffroy and Chen, Wei and Richards, William Davidson and Dacek, Stephen and Cholia, Shreyas and Gunter, Dan and Skinner, David and Ceder, Gerbrand and Persson, Kristin A.}, + doi = {10.1063/1.4812323}, + number = {1}, + pages = {011002}, + source = {Crossref}, + url = {http://dx.doi.org/10.1063/1.4812323}, + volume = {1}, + journal = {APL Materials}, + publisher = {AIP Publishing}, + title = {Commentary: {The} Materials Project: {A} materials genome approach to accelerating materials innovation}, + issn = {2166-532X}, + year = {2013}, + month = jul, +} +@article{Ong2015, + author = {Ong, Shyue Ping and Cholia, Shreyas and Jain, Anubhav and Brafman, Miriam and Gunter, Dan and Ceder, Gerbrand and Persson, Kristin A.}, + doi = {10.1016/j.commatsci.2014.10.037}, + pages = {209-215}, + source = {Crossref}, + url = {http://dx.doi.org/10.1016/j.commatsci.2014.10.037}, + volume = {97}, + journal = {Computational Materials Science}, + publisher = {Elsevier BV}, + title = {The Materials Application Programming Interface {(API):} {A} simple, flexible and efficient {API} for materials data based on {REpresentational} State Transfer {(REST)} principles}, + issn = {0927-0256}, + year = {2015}, + month = feb, +} +@article{Grazulis2011, + author = {Gražulis, Saulius and Daškevič, Adriana and Merkys, Andrius and Chateigner, Daniel and Lutterotti, Luca and Quirós, Miguel and Serebryanaya, Nadezhda R. and Moeck, Peter and Downs, Robert T. and Le Bail, Armel}, + doi = {10.1093/nar/gkr900}, + number = {D1}, + pages = {D420-D427}, + source = {Crossref}, + url = {http://dx.doi.org/10.1093/nar/gkr900}, + volume = {40}, + journal = {Nucleic Acids Research}, + publisher = {Oxford University Press (OUP)}, + title = {Crystallography Open Database {(COD):} {An} open-access collection of crystal structures and platform for world-wide collaboration}, + issn = {1362-4962, 0305-1048}, + year = {2011}, + month = nov, +} +@article{Setten2017, + author = {van Setten, M. J. and Giantomassi, M. and Gonze, X. and Rignanese, G.-M. and Hautier, G.}, + doi = {10.1103/physrevb.96.155207}, + number = {15}, + source = {Crossref}, + url = {http://dx.doi.org/10.1103/physrevb.96.155207}, + volume = {96}, + journal = {Phys. Rev. B}, + publisher = {American Physical Society (APS)}, + title = {Automation methodologies and large-scale validation for {GW} : {Towards} high-throughput {GW} calculations}, + issn = {2469-9950, 2469-9969}, + year = {2017}, + month = oct, +} +@article{Euwema1969, + author = {Euwema, R. N. and Stukel, D. J. and Collins, T. C. and Dewitt, J. S. and Shankland, D. G.}, + doi = {10.1103/physrev.178.1419}, + number = {3}, + pages = {1419-1423}, + source = {Crossref}, + url = {http://dx.doi.org/10.1103/physrev.178.1419}, + volume = {178}, + journal = {Phys. Rev.}, + publisher = {American Physical Society (APS)}, + title = {Crystalline Interpolation with Applications to {Brillouin}-Zone Averages and Energy-Band Interpolation}, + issn = {0031-899X}, + year = {1969}, + month = feb, +} +@article{Koelling1986, + author = {Koelling, D.D and Wood, J.H}, + doi = {10.1016/0021-9991(86)90261-5}, + number = {2}, + pages = {253-262}, + source = {Crossref}, + url = {http://dx.doi.org/10.1016/0021-9991(86)90261-5}, + volume = {67}, + journal = {Journal of Computational Physics}, + publisher = {Elsevier BV}, + title = {On the interpolation of eigenvalues and a resultant integration scheme}, + issn = {0021-9991}, + year = {1986}, + month = dec, +} +@article{Madsen2006, + author = {Madsen, Georg K.H. and Singh, David J.}, + doi = {10.1016/j.cpc.2006.03.007}, + number = {1}, + pages = {67-71}, + source = {Crossref}, + url = {http://dx.doi.org/10.1016/j.cpc.2006.03.007}, + volume = {175}, + journal = {Computer Physics Communications}, + publisher = {Elsevier BV}, + title = {{BoltzTraP.} A code for calculating band-structure dependent quantities}, + issn = {0010-4655}, + year = {2006}, + month = jul, +} +@article{Pickett1988, + author = {Pickett, Warren E. and Krakauer, Henry and Allen, Philip B.}, + doi = {10.1103/physrevb.38.2721}, + number = {4}, + pages = {2721-2726}, + source = {Crossref}, + url = {http://dx.doi.org/10.1103/physrevb.38.2721}, + volume = {38}, + journal = {Phys. Rev. B}, + publisher = {American Physical Society (APS)}, + title = {Smooth {Fourier} interpolation of periodic functions}, + issn = {0163-1829}, + year = {1988}, + month = aug, +} +@article{Giustino2017, + author = {Giustino, Feliciano}, + doi = {10.1103/revmodphys.89.015003}, + number = {1}, + source = {Crossref}, + url = {http://dx.doi.org/10.1103/revmodphys.89.015003}, + volume = {89}, + journal = {Rev. Mod. Phys.}, + publisher = {American Physical Society (APS)}, + title = {Electron-phonon interactions from first principles}, + issn = {0034-6861, 1539-0756}, + year = {2017}, + month = feb, +} +@article{Henkelman2006, + author = {Henkelman, Graeme and Arnaldsson, Andri and Jónsson, Hannes}, + doi = {10.1016/j.commatsci.2005.04.010}, + number = {3}, + pages = {354-360}, + source = {Crossref}, + url = {http://dx.doi.org/10.1016/j.commatsci.2005.04.010}, + volume = {36}, + journal = {Computational Materials Science}, + publisher = {Elsevier BV}, + title = {A fast and robust algorithm for Bader decomposition of charge density}, + issn = {0927-0256}, + year = {2006}, + month = jun, +} +@article{Jain2015, + author = {Jain, Anubhav and Ong, Shyue Ping and Chen, Wei and Medasani, Bharat and Qu, Xiaohui and Kocher, Michael and Brafman, Miriam and Petretto, Guido and Rignanese, Gian-Marco and Hautier, Geoffroy and Gunter, Daniel and Persson, Kristin A.}, + doi = {10.1002/cpe.3505}, + number = {17}, + pages = {5037-5059}, + source = {Crossref}, + url = {http://dx.doi.org/10.1002/cpe.3505}, + volume = {27}, + journal = {Concurrency Computat.: Pract. Exper.}, + publisher = {Wiley-Blackwell}, + title = {{FireWorks:} {A} dynamic workflow system designed for high-throughput applications}, + issn = {1532-0626}, + year = {2015}, + month = may, +} diff --git a/docs/requirements.txt b/docs/requirements.txt new file mode 100644 index 0000000..69764f6 --- /dev/null +++ b/docs/requirements.txt @@ -0,0 +1,10 @@ +ipython +sphinx +sphinxcontrib-napoleon +sphinxcontrib-programoutput +sphinx-gallery +sphinx-argparse +sphinx_bootstrap_theme +#nbsphinx +sphinxcontrib-bibtex +releases diff --git a/docs/whats_new.rst b/docs/whats_new.rst deleted file mode 100644 index e3e2129..0000000 --- a/docs/whats_new.rst +++ /dev/null @@ -1,14 +0,0 @@ -.. _whats-new: - -********************** -What's new in AbiFlows -********************** - -This page just covers the highlights -- for the full story, see the CHANGELOG - -.. _whats-new-0-2: - -abiflows-0.2 -============ - -This is the first official release in which we have reached a relatively stable API diff --git a/docs/zzbiblio.rst b/docs/zzbiblio.rst new file mode 100644 index 0000000..58636e4 --- /dev/null +++ b/docs/zzbiblio.rst @@ -0,0 +1,10 @@ +.. _bibliography: + +************* +Bibliography +************* + +.. rubric:: References + +.. bibliography:: refs.bib + :cited: diff --git a/requirements.txt b/requirements.txt new file mode 100644 index 0000000..0ba3804 --- /dev/null +++ b/requirements.txt @@ -0,0 +1,13 @@ +six +prettytable +numpy +#python-daemon +jinja2 +pymongo +mongoengine +flask +flask-mongoengine +paramiko +abipy>=0.2.0 +custodian +fireworks diff --git a/setup.py b/setup.py index cf29891..4516a71 100755 --- a/setup.py +++ b/setup.py @@ -77,10 +77,7 @@ def find_scripts(): def get_long_desc(): with open("README.md") as f: - long_desc = f.read() - #ind = long_desc.find("\n") - #long_desc = long_desc[ind + 1:] - return long_desc + return f.read() #----------------------------------------------------------------------------- @@ -101,21 +98,8 @@ def cleanup(): # List of external packages we rely on. # Note setup install will download them from Pypi if they are not available. -install_requires = [ - "six", - "prettytable", - "numpy", - #"python-daemon", - "jinja2", - "pymongo", - "mongoengine", - "flask", - "flask-mongoengine", - "paramiko", - "abipy>=0.2.0", - "custodian", - "fireworks", -] +with open("requirements.txt", "rt") as fh: + install_requires = [s.strip() for s in fh] #--------------------------------------------------------------------------- # Find all the packages, package data, and data_files