from muesr.io to muesr.i-o

bonfus · Feb 1, 2017 · d8b8119 · d8b8119
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diff --git a/README.md b/README.md
@@ -39,6 +39,11 @@ Known problems
 Please not that the code is still under heavy development. 
 You'll probably find bugs so please report them!
 
+Authors
+-------
+
+Pietro Bonfa', Ifeanyi John Onuorah and Roberto De Renzi.
+
 Notes
 -----
 

diff --git a/docs/Install.rst b/docs/Install.rst
@@ -26,12 +26,12 @@ installed to use *all* features of Muesr:
 ========= ========= =============================================== =========================================
 Package   Version   Required for                                    Package URL
 ========= ========= =============================================== =========================================
-YAML      >= 2.0.0  :mod:`muesr.io.sampleIO`                        http://pyyaml.org/
+YAML      >= 2.0.0  :mod:`muesr.i_o.sampleIO`                       http://pyyaml.org/
 Spglib    >= 1.6    :mod:`muesr.utilities.symsearch`                http://atztogo.github.io/spglib/
 Sympy     >= 1.0    :mod:`muesr.core.magmodel.SMM`                  http://sympy.org
 appdirs   >= 1.1    :mod:`muesr.settings`               
-XCrysDen  >= 1.0    :mod:`muesr.io.xsf.xsf.show_cell` ,             http://www.xcrysden.org
-                    :mod:`muesr.io.xsf.xsf.show_supercell`          
+XCrysDen  >= 1.0    :mod:`muesr.i_o.xsf.xsf.show_cell` ,            http://www.xcrysden.org
+                    :mod:`muesr.i_o.xsf.xsf.show_supercell`          
 ========= ========= =============================================== =========================================
 
 .. note::

diff --git a/docs/LiFePO4.rst b/docs/LiFePO4.rst
@@ -36,7 +36,7 @@ The sample object holds the following information:
 The lattice structure is orthorhombic, with *Pnma* symmetry and
 lattice parameters :math:`a=10.3244(2), b=6.0064(3), c=4.6901(5)`.
 We can import these data from a CIF file using the function
-:py:func:`~muesr.io.cif.cif.load_cif`:
+:py:func:`~muesr.i_o.cif.cif.load_cif`:
 
 .. literalinclude:: ../examples/LiFePO4/run_example.py
    :lines: 31

diff --git a/docs/Tutorial.rst b/docs/Tutorial.rst
@@ -46,24 +46,24 @@ files. Here's a few examples:
 .. code-block:: python
     
     >>> # load data from XCrysden .xsf file
-    >>> from muesr.io.xsf.xsf import load_xsf
+    >>> from muesr.i_o.xsf.xsf import load_xsf
     >>> 
     >>> load_xsf(mysample, "/path/to/file.xsf")
     >>> 
     >>> 
     >>> # load data from .cif file
-    >>> from muesr.io.cif.cif import load_cif
+    >>> from muesr.i_o.cif.cif import load_cif
     >>> 
     >>> load_cif(mysample, "/path/to/file.cif")
     >>> 
     >>> 
     >>> # load data from .mcif file
-    >>> from muesr.io.cif.cif import load_mcif
+    >>> from muesr.i_o.cif.cif import load_mcif
     >>> 
     >>> load_mcif(mysample, "/path/to/file.mcif")
 
 
-The :py:func:`~muesr.io.cif.cif.load_cif` function will also load symmetry information. 
+The :py:func:`~muesr.i_o.cif.cif.load_cif` function will also load symmetry information. 
 Please note that only a single lattice structure at a time can be
 defined so each load function will remove the previous lattice structure
 definition.

diff --git a/docs/Usage.rst b/docs/Usage.rst
@@ -33,9 +33,9 @@ However this can be tedious and error prone. Therefore you are strongly
 suggested to load the lattice information from a file using use one of
 these functions:
 
- - :py:func:`~muesr.io.cif.cif.load_cif` for Crystallographic Information Files
- - :py:func:`~muesr.io.cif.cif.load_mcif` for Magnetic Crystallographic Information Files
- - :py:func:`~muesr.io.xsf.xsf.load_xsf` for XCrysDen files.
+ - :py:func:`~muesr.i_o.cif.cif.load_cif` for Crystallographic Information Files
+ - :py:func:`~muesr.i_o.cif.cif.load_mcif` for Magnetic Crystallographic Information Files
+ - :py:func:`~muesr.i_o.xsf.xsf.load_xsf` for XCrysDen files.
 
 .. note ::
    For CIF files the symmetry is automatically parsed and set from the file.
@@ -326,8 +326,8 @@ Exceptions are only raised in core components.
 Saving and loading sample details to/from file
 ----------------------------------------------
 
-To save a sample use :py:func:`~muesr.io.sampleIO.save_sample`. To load
-a saved sample use :py:func:`~muesr.io.sampleIO.load_sample`.
+To save a sample use :py:func:`~muesr.i_o.sampleIO.save_sample`. To load
+a saved sample use :py:func:`~muesr.i_o.sampleIO.load_sample`.
 
 Data is stored in an YAML file. It is possible (but error prone) to write
 an input file by hand. When loaded, the file will undergo a minimal 

diff --git a/examples/Fe_bcc/run_example.py b/examples/Fe_bcc/run_example.py
@@ -5,9 +5,9 @@
 
 import numpy as np
 from muesr.core.sample import Sample                   # Retains all the sample info.
-from muesr.io.cif.cif import load_cif                  # For loading the structure from cif files
-from muesr.io.xsf.xsf import load_xsf                  # For loading the structure from xsf files
-from muesr.io.xsf.xsf import show_supercell, show_cell # For visualisation with xcrysden (http://www.xcrysden.org/)
+from muesr.i_o.cif.cif import load_cif                  # For loading the structure from cif files
+from muesr.i_o.xsf.xsf import load_xsf                  # For loading the structure from xsf files
+from muesr.i_o.xsf.xsf import show_supercell, show_cell # For visualisation with xcrysden (http://www.xcrysden.org/)
 from muesr.utilities.ms import mago_add                # For magnetic structure description
 from muesr.engines.clfc import locfield                # Does the sum and returns the local field in its diff. contributions
 from muesr.engines.clfc import find_largest_sphere     # Aids in the calculation of the sphere's radius for the lattice sum.

diff --git a/examples/LaFeAsO/run_example.py b/examples/LaFeAsO/run_example.py
@@ -4,7 +4,7 @@
 np.set_printoptions(precision=3,suppress=True)
 
 from muesr.core.sample import Sample
-from muesr.io.cif.cif import load_mcif
+from muesr.i_o.cif.cif import load_mcif
 from muesr.utilities.symsearch import symsearch
 from muesr.utilities import  muon_find_equiv
 from muesr.engines.clfc import locfield

diff --git a/examples/LiFePO4/run_example.py b/examples/LiFePO4/run_example.py
@@ -12,7 +12,7 @@
 import os          # join path on windows.  
 
 from muesr.core import Sample            # this object contains all the info on our sample
-from muesr.io import load_cif            # loads lattice and symmetry from CIF file
+from muesr.i_o import load_cif            # loads lattice and symmetry from CIF file
 from muesr.utilities import  mago_add    # this function provides a CLI for inserting the MAGnetic Order
 from muesr.engines.clfc import locfield  # this is the function which actually performs the sum and returns
                                          #  the local fields.

diff --git a/examples/MnSi/run_example.py b/examples/MnSi/run_example.py
@@ -1,7 +1,7 @@
 # coding: utf-8
 import numpy as np
 from muesr.core.sample import Sample
-from muesr.io import load_cif
+from muesr.i_o import load_cif
 from muesr.utilities import print_cell, muon_find_equiv
 from muesr.engines.clfc import locfield
 from matplotlib import pyplot as plt

diff --git a/muesr/io/__init__.py → muesr/i_o/__init__.py b/muesr/io/__init__.py → muesr/i_o/__init__.py
diff --git a/muesr/io/cif/__init__.py → muesr/i_o/cif/__init__.py b/muesr/io/cif/__init__.py → muesr/i_o/cif/__init__.py
diff --git a/muesr/io/cif/cell.py → muesr/i_o/cif/cell.py b/muesr/io/cif/cell.py → muesr/i_o/cif/cell.py
diff --git a/muesr/io/cif/cif.py → muesr/i_o/cif/cif.py b/muesr/io/cif/cif.py → muesr/i_o/cif/cif.py
@@ -15,9 +15,9 @@
 from muesr.core.spg import Spacegroup
 from muesr.core.nprint import nprint, nprintmsg
 
-from muesr.io.cif.crystal import crystal
+from muesr.i_o.cif.crystal import crystal
 from muesr.core.spg import spacegroup_from_data
-from muesr.io.cif.cell import cellpar_to_cell
+from muesr.i_o.cif.cell import cellpar_to_cell
 
 
 

diff --git a/muesr/io/cif/crystal.py → muesr/i_o/cif/crystal.py b/muesr/io/cif/crystal.py → muesr/i_o/cif/crystal.py
@@ -11,7 +11,7 @@
 
 from muesr.core.atoms import Atoms
 from muesr.core.spg import Spacegroup
-from muesr.io.cif.cell import cellpar_to_cell
+from muesr.i_o.cif.cell import cellpar_to_cell
 
 __all__ = ['crystal']
 

diff --git a/muesr/io/exportFPS.py → muesr/i_o/exportFPS.py b/muesr/io/exportFPS.py → muesr/i_o/exportFPS.py
diff --git a/muesr/io/sampleIO.py → muesr/i_o/sampleIO.py b/muesr/io/sampleIO.py → muesr/i_o/sampleIO.py
diff --git a/muesr/io/xsf/__init__.py → muesr/i_o/xsf/__init__.py b/muesr/io/xsf/__init__.py → muesr/i_o/xsf/__init__.py
diff --git a/muesr/io/xsf/xsf.py → muesr/i_o/xsf/xsf.py b/muesr/io/xsf/xsf.py → muesr/i_o/xsf/xsf.py
@@ -5,8 +5,8 @@
 
 from muesr.settings import config
 
-from muesr.io.xsf.xsfio import *
-from muesr.io.xsf.xsfrun import *
+from muesr.i_o.xsf.xsfio import *
+from muesr.i_o.xsf.xsfrun import *
 
 from muesr.core.sampleErrors import MuonError
 from muesr.core.parsers import *

diff --git a/muesr/io/xsf/xsfio.py → muesr/i_o/xsf/xsfio.py b/muesr/io/xsf/xsfio.py → muesr/i_o/xsf/xsfio.py
diff --git a/muesr/io/xsf/xsfrun.py → muesr/i_o/xsf/xsfrun.py b/muesr/io/xsf/xsfrun.py → muesr/i_o/xsf/xsfrun.py
diff --git a/muesr/io/ms_from_mcif.py b/muesr/io/ms_from_mcif.py
diff --git a/muesr/tests/io/test_sampleIO.py b/muesr/tests/io/test_sampleIO.py
@@ -9,7 +9,7 @@
 
 from muesr.core.sample import Sample
 from muesr.core.sampleErrors import *
-from muesr.io.sampleIO import *
+from muesr.i_o.sampleIO import *
 
 yaml_only_lattice = """
 Lattice:

diff --git a/muesr/tests/test_muesr.py b/muesr/tests/test_muesr.py
@@ -13,8 +13,8 @@
 from muesr.core.magmodel import MM, have_sympy
 if have_sympy:
     from muesr.core.magmodel import SMM
-from muesr.io.xsf.xsf import load_xsf
-from muesr.io.cif.cif import load_mcif
+from muesr.i_o.xsf.xsf import load_xsf
+from muesr.i_o.cif.cif import load_mcif
 from muesr.engines.clfc import locfield
 from muesr.utilities.muon import muon_reset, muon_set_frac
 

diff --git a/muesr/tests/utilities/test_dftgrid.py b/muesr/tests/utilities/test_dftgrid.py
@@ -9,7 +9,7 @@
 from muesr.core.sampleErrors import CellError, MuonError
 from muesr.core.sample import Sample
 from muesr.utilities.dft_grid import build_uniform_grid
-from muesr.io.cif.cif import read_cif
+from muesr.i_o.cif.cif import read_cif
 
 co_lattice = StringIO("""
 #------------------------------------------------------------------------------

diff --git a/muesr/tests/utilities/test_muon.py b/muesr/tests/utilities/test_muon.py
@@ -9,7 +9,7 @@
 from muesr.core.sampleErrors import CellError, MuonError
 from muesr.core.sample import Sample
 from muesr.utilities import muon_set_frac, muon_find_equiv, muon_reset
-from muesr.io.cif.cif import read_cif
+from muesr.i_o.cif.cif import read_cif
 
 co_lattice = StringIO("""
 #------------------------------------------------------------------------------

diff --git a/muesr/tests/utilities/test_symsearch.py b/muesr/tests/utilities/test_symsearch.py
@@ -9,7 +9,7 @@
 from muesr.core.sampleErrors import CellError, MuonError
 from muesr.core.sample import Sample
 from muesr.utilities.symsearch import symsearch, have_spg
-from muesr.io.cif.cif import read_cif
+from muesr.i_o.cif.cif import read_cif
 
 
 co_lattice = StringIO("""