Correctd setup.py and added requirements.txt. New logic for mago_add …

…and now I/O functions return True on succees.

MANIFEST.in

@@ -1,5 +1,6 @@
 include MANIFEST.in
 include LICENSE README.md
+include requirements.txt
 include muesr/core/spacegroup.dat
 recursive-include muesr/tests/structures *
 recursive-include docs *

docs/Install.rst

@@ -79,8 +79,9 @@ and to activate the environment (linux and OsX) ::
    cd muesr-env
    source bin/activate
    
-now you can install Muesr in the virtualenv with the command ::
+now you can install LFC and Muesr in the virtualenv with the commands ::
 
+   pip install https://github.com/bonfus/muLFC/archive/master.tar.gz
    pip install https://github.com/bonfus/muesr/archive/master.tar.gz
    
 this will only provide the minimal dependencies. To have access to all 

muesr/i_o/sampleIO.py

@@ -23,16 +23,17 @@
 
 
 
-def save_sample(sample, filename="", fileobj=None):
+def save_sample(sample, filename="", fileobj=None, overwrite=False):
     """
     This function saves the sample provided in YAML format.
     
     :param sample: the sample object
     :param str filename: the filename used to store data.
     :param file fileobj: a file object used in place of filename.
+    :param overwrite bool: if selected file should be overwritten.
     :return: None
     :rtype: None
-    :raises: TypeError
+    :raises: TypeError, ValueError, IsADirectoryError
     """        
 
 
@@ -112,18 +113,18 @@ def save_sample(sample, filename="", fileobj=None):
         if filename == "":
             raise ValueError("Specify filename or provide a file object")
 
-        while os.path.isfile(filename):
-            if not ninput('Do you really want to overwite ' + 
-                    os.path.basename(filename) + '?', parse_bool):
-                filename = ninput('New file name: ')
-            else:
-                break
+        if os.path.isfile(filename) and (not overwrite):
+            warnings.warn('File not (over)written.', RuntimeWarning)
+            return False
+
 
-        # TODO: check overwrite and handle errors
         with open(filename,'w') as f:
             f.write(output)
+        return True
+
     else:
         fileobj.write(output)
+        return True
 
 
 def load_sample(filename="", fileobj=None):
@@ -136,10 +137,7 @@ def load_sample(filename="", fileobj=None):
                          supersede the filename input.
     :return: a sample object
     :rtype: :py:class:`~Sample` object or None
-    :raises: ValueError
-    
-    .. note::
-       Overwrite is not checked!  
+    :raises: ValueError, FileNotFoundError, IsADirectoryError
     
     """      
 

muesr/utilities/ms.py

@@ -14,7 +14,7 @@
 
 
 
-def mago_set_k(sample, kvalue=None,mm=None):
+def mago_set_k(sample, kvalue=None, mm=None):
 
     """
     Set propagation with respect to the conventional reciprocal cell
@@ -36,7 +36,7 @@ def mago_set_k(sample, kvalue=None,mm=None):
         if not kvalue is None:
             if isinstance(kvalue, np.ndarray) and ( kvalue.shape == (3,)):
                 smm.k = kvalue
-                return
+                return True
         else:
             try:
                 if kvalue is None:
@@ -46,37 +46,48 @@ def mago_set_k(sample, kvalue=None,mm=None):
 
             except EOFError:
                 nprint("Ok.")
-                return
+                return False
             except TypeError:
                 nprint("Cannot parse position.",'warn')
                 return
             smm.k=np.array(kval,dtype=np.float)
-            return
+            return True
 
 
-def mago_add(sample, coordinates='b-c'):
+def mago_add(sample, coordinates='b-c', fcs=None, kvalue=None):
     """
-    Add a magnetic model (fourier components and K vector).
-    
+    Adds a magnetic model (fourier components and K vector).
     The order is automatically selected if succesfully added.
     
+    :param sample: A sample object.
+    :param string coordinates: coordinates of Fourier components
+    :param np.complex fcs: Fourier components in coordinate system 
+                          (default: Bohr magnetoc/ Cartesian coordinates)
+    :param np.ndarray kvalue: Propagation vector in r.l.u.
+    :returns: True if successful, False otherwise.
+    :rtype: bool
     
-    returns: None
     """        
 
     nmm = MM(sample.cell.get_number_of_atoms(),sample.cell.get_cell())
 
-    mago_set_k(sample, mm=nmm)
-    mago_set_FC(sample, mm=nmm, inputConvention=coordinates)
+    ret = mago_set_k(sample, mm=nmm, kvalue=kvalue)
+    if not ret:
+        return False
+
+    ret = mago_set_FC(sample, mm=nmm, inputConvention=coordinates, fcs=fcs)
+    if not ret:
+        return False
+
     sample.mm = nmm
-
+    return True
 
 
 
-def mago_set_FC(sample, fcs= None, atoms_types = None, mm=None, inputConvention='b-c'):
+def mago_set_FC(sample, fcs = None, atoms_types = None, mm=None, inputConvention='b-c'):
     """
-    defines fourier components for the unit cell.
-    Values are given in CARTESIAN coordinates (this is different from mcif convention)
+    Defines fourier components for the unit cell.
+    
     """
 
 
@@ -93,27 +104,27 @@ def mago_set_FC(sample, fcs= None, atoms_types = None, mm=None, inputConvention=
     inputConvEnum = -1
 
     if inputConvention.lower() in ['bohr-cartesian', 'b-c']:
-        nprint('Magnetic moments in bohr magnetons and cartesian coordinates.')
+        nprint('Magnetic moments in Bohr magnetons and cartesian coordinates.')
         inputConvEnum = 0
 
     elif inputConvention.lower() in ['bohr/angstrom-lattice', 'b/a-l']:
-        nprint('Magnetic moments in bohr magnetons/angstrom and lattice coordinates.')
+        nprint('Magnetic moments in Bohr magnetons/angstrom and lattice coordinates.')
         inputConvEnum = 1
 
     elif inputConvention.lower() in ['bohr-lattice','b-l']:
-        nprint('Magnetic moments in bohr magnetons and lattice coordinates.')
+        nprint('Magnetic moments in Bohr magnetons and lattice coordinates.')
         inputConvEnum = 2
 
     else:
-        nprint('Invalid Fourier Description method: ' + inputConvention.lower() ,'error')
-        return    
+        nprint('Invalid Fourier Description method: ' + inputConvention.lower() ,'error.')
+        return False
 
 
 
 
     if not fcs is None:
         smm.fc_set(fcs, inputConvEnum)
-        return
+        return True
 
 
 
@@ -122,7 +133,7 @@ def mago_set_FC(sample, fcs= None, atoms_types = None, mm=None, inputConvention=
 
 
     if atoms_types is None:
-        atoms_types=ninput('Which atom? (enter for all)').split()
+        atoms_types=ninput('Which atom? (enter for all): ').split()
 
     if atoms_types == []:
         set_this_fc = lambda x: True
@@ -154,8 +165,10 @@ def mago_set_FC(sample, fcs= None, atoms_types = None, mm=None, inputConvention=
 
     if gotEOS:
         nprint('Nothing set')
+        return False
     else:
         smm.fc_set(fcs, inputConvEnum)
+        return True
 
 
 

muesr/utilities/muon.py

@@ -26,18 +26,19 @@ def muon_set_frac(sample, arg = None):
 
         except EOFError:
             nprint("Ok.")
-            return
+            return False
         except TypeError:
             nprint("Cannot parse position.",'warn')
-            return
+            return False
 
         if (not isinstance(arg, np.ndarray)):
             pos = np.array(pos)
 
         sample.add_muon(pos)
-        return      
+        return True
     else:
-        nprintmsg('NS') 
+        #nprintmsg('NS')
+        return False
 
 
 
@@ -57,11 +58,12 @@ def muon_find_equiv(sample, eps=1.e-3):
     sample._reset(muon=True)
     for p in eqpoints:
         sample.add_muon(np.array(p))
-
+    return True
 
 def muon_reset(sample):
     """
-    Resets muon position.
-    returns: None
+    Removes all previously set muon positions.
+    returns: True
     """
     sample._reset(muon=True)
+    return True

muesr/utilities/printer.py

@@ -1,14 +1,14 @@
 from muesr.core.nprint import print_cell as pc
 
 
-
 
 def print_cell(sample):
     """
     Print base cell
     """
     if sample._check_lattice():
         pc(sample._cell)
+        return True
 
 
 

muesr/utilities/xcrysden.py

@@ -41,12 +41,14 @@ def show_structure(sample, supercell=[1,1,1], askConfirm=True, block=True):
 
     if ans:
         save_xsf(sample, os.path.join(config.XCrysTmp,'preview.xsf'),supercell=supercell)
-        run_xcrysden(os.path.join(config.XCrysTmp,'preview.xsf'),block)
+        return run_xcrysden(os.path.join(config.XCrysTmp,'preview.xsf'),block)
+    else:
+        return ans
 
 def run_xcrysden(fname, block=True):
     if config.XCrysExec == None:
         warnings.warn("XCrysDen executable not found. Check configs.")
-        return
+        return False
 
 
     spargs = dict(
@@ -66,4 +68,4 @@ def run_xcrysden(fname, block=True):
 
     if block:
         out, err = p.communicate()
-
+    return True

requirements.txt

@@ -0,0 +1,11 @@
+#
+####### muesr-requirements.txt #######
+#
+###### C Extension ######
+https://github.com/bonfus/muLFC/archive/master.tar.gz
+#
+###### Requirements for complete functionality ######
+#   See https://www.python.org/dev/peps/pep-0440/#version-specifiers
+spglib >= 1.9
+pyyaml >= 3.0
+

setup.py

@@ -20,9 +20,8 @@
                 ],
       include_package_data=True,
       package_dir={'muesr': 'muesr' },
-      requires=['numpy', 'LFC',],
       install_requires=[
-            'numpy',
+            'numpy >= 1.6',
       ],
       test_suite="muesr.tests",
      )