Merge branch 'development' into polishing-for-release

VERSION

@@ -1 +1 @@
-v3.0.0-alpha2-415-g09c2d7f3f
+v3.0.0-alpha2-421-ge96352b0e

python/damask/_colormap.py

@@ -223,25 +223,46 @@ class Colormap(mpl.colors.ListedColormap):
         return Colormap(np.array(rev.colors),rev.name[:-4] if rev.name.endswith('_r_r') else rev.name)
 
 
+    def _get_file_handle(self,fname,extension):
+        """
+        Provide file handle.
+
+        Parameters
+        ----------
+        fname : file, str, pathlib.Path, or None
+            Filename or filehandle, will be name of the colormap+extension if None.
+
+        extension: str
+            Extension of the filename.
+
+        Returns
+        -------
+        f
+            File handle
+
+        """
+        if fname is None:
+            fhandle = open(self.name.replace(' ','_')+'.'+extension,'w',newline='\n')
+        else:
+            try:
+                fhandle = open(fname,'w',newline='\n')
+            except TypeError:
+                fhandle = fname
+
+        return fhandle
+
+
     def save_paraview(self,fname=None):
         """
         Save as JSON file for use in Paraview.
 
         Parameters
         ----------
-        fname : file, str, or pathlib.Path, optional.
+        fname : file, str, or pathlib.Path, optional
             Filename to store results. If not given, the filename will
             consist of the name of the colormap and extension '.json'.
 
         """
-        if fname is None:
-            fhandle = None
-        else:
-            try:
-                fhandle = open(fname,'w')
-            except TypeError:
-                fhandle = fname
-
         colors = []
         for i,c in enumerate(np.round(self.colors,6).tolist()):
             colors+=[i]+c
@@ -254,8 +275,7 @@ class Colormap(mpl.colors.ListedColormap):
                 'RGBPoints':colors
                }]
 
-        with open(self.name.replace(' ','_')+'.json', 'w') if fhandle is None else fhandle as f:
+        json.dump(out,self._get_file_handle(fname,'json'),indent=4)
-            json.dump(out, f,indent=4)
 
 
     def save_ASCII(self,fname=None):
@@ -264,24 +284,14 @@ class Colormap(mpl.colors.ListedColormap):
 
         Parameters
         ----------
-        fname : file, str, or pathlib.Path, optional.
+        fname : file, str, or pathlib.Path, optional
             Filename to store results. If not given, the filename will
             consist of the name of the colormap and extension '.txt'.
 
         """
-        if fname is None:
-            fhandle = None
-        else:
-            try:
-                fhandle = open(fname,'w')
-            except TypeError:
-                fhandle = fname
-
         labels = {'RGBA':4} if self.colors.shape[1] == 4 else {'RGB': 3}
         t = Table(self.colors,labels,f'Creator: {util.execution_stamp("Colormap")}')
-
+        t.save(self._get_file_handle(fname,'txt'))
-        with open(self.name.replace(' ','_')+'.txt', 'w') if fhandle is None else fhandle as f:
-            t.save(f)
 
 
     def save_GOM(self,fname=None):
@@ -290,26 +300,19 @@ class Colormap(mpl.colors.ListedColormap):
 
         Parameters
         ----------
-        fname : file, str, or pathlib.Path, optional.
+        fname : file, str, or pathlib.Path, optional
             Filename to store results. If not given, the filename will
             consist of the name of the colormap and extension '.legend'.
 
         """
-        if fname is None:
-            fhandle = None
-        else:
-            try:
-                fhandle = open(fname,'w')
-            except TypeError:
-                fhandle = fname
         # ToDo: test in GOM
         GOM_str = '1 1 {name} 9 {name} '.format(name=self.name.replace(" ","_")) \
                 +  '0 1 0 3 0 0 -1 9 \\ 0 0 0 255 255 255 0 0 255 ' \
                 + f'30 NO_UNIT 1 1 64 64 64 255 1 0 0 0 0 0 0 3 0 {len(self.colors)}' \
                 + ' '.join([f' 0 {c[0]} {c[1]} {c[2]} 255 1' for c in reversed((self.colors*255).astype(int))]) \
                 + '\n'
-        with open(self.name.replace(' ','_')+'.legend', 'w') if fhandle is None else fhandle as f:
+
-            f.write(GOM_str)
+        self._get_file_handle(fname,'legend').write(GOM_str)
 
 
     def save_gmsh(self,fname=None):
@@ -318,24 +321,16 @@ class Colormap(mpl.colors.ListedColormap):
 
         Parameters
         ----------
-        fname : file, str, or pathlib.Path, optional.
+        fname : file, str, or pathlib.Path, optional
             Filename to store results. If not given, the filename will
             consist of the name of the colormap and extension '.msh'.
 
         """
-        if fname is None:
-            fhandle = None
-        else:
-            try:
-                fhandle = open(fname,'w')
-            except TypeError:
-                fhandle = fname
         # ToDo: test in gmsh
         gmsh_str = 'View.ColorTable = {\n' \
                  +'\n'.join([f'{c[0]},{c[1]},{c[2]},' for c in self.colors[:,:3]*255]) \
                  +'\n}\n'
-        with open(self.name.replace(' ','_')+'.msh', 'w') if fhandle is None else fhandle as f:
+        self._get_file_handle(fname,'msh').write(gmsh_str)
-            f.write(gmsh_str)
 
 
     @staticmethod

python/damask/_config.py

@@ -75,7 +75,7 @@ class Config(dict):
 
         """
         try:
-            fhandle = open(fname,'w')
+            fhandle = open(fname,'w',newline='\n')
         except TypeError:
             fhandle = fname
 

python/damask/_result.py

@@ -1287,7 +1287,7 @@ class Result:
                                                                                                       np.prod(shape))}
                                 data_items[-1].text=f'{os.path.split(self.fname)[1]}:{name}'
 
-        with open(self.fname.with_suffix('.xdmf').name,'w') as f:
+        with open(self.fname.with_suffix('.xdmf').name,'w',newline='\n') as f:
             f.write(xml.dom.minidom.parseString(ET.tostring(xdmf).decode()).toprettyxml())
 
 

python/damask/_table.py

@@ -26,7 +26,7 @@ class Table:
         comments_ = [comments] if isinstance(comments,str) else comments
         self.comments = [] if comments_ is None else [c for c in comments_]
         self.data = pd.DataFrame(data=data)
-        self.shapes = { k:(v,) if isinstance(v,(np.int,int)) else v for k,v in shapes.items() }
+        self.shapes = { k:(v,) if isinstance(v,(np.int64,np.int32,int)) else v for k,v in shapes.items() }
         self._label_uniform()
 
     def __repr__(self):
@@ -380,7 +380,7 @@ class Table:
                   [f'# {comment}' for comment in self.comments]
 
         try:
-            fhandle = open(fname,'w')
+            fhandle = open(fname,'w',newline='\n')
         except TypeError:
             fhandle = fname
 

python/damask/solver/_marc.py

@@ -66,7 +66,7 @@ class Marc:
 
         if logfile is not None:
             try:
-                f = open(logfile,'w+')
+                f = open(logfile,'w+',newline='\n')
             except TypeError:
                 f = logfile
         else:

src/IO.f90

@@ -65,8 +65,8 @@ end subroutine IO_init
 function IO_readlines(fileName) result(fileContent)
 
   character(len=*),          intent(in)                :: fileName
-
   character(len=pStringLen), dimension(:), allocatable :: fileContent                               !< file content, separated per lines
+
   character(len=pStringLen)                            :: line
   character(len=:),                        allocatable :: rawData
   integer ::  &
@@ -75,6 +75,7 @@ function IO_readlines(fileName) result(fileContent)
     l
   logical :: warned
 
+
   rawData = IO_read(fileName)
 
 !--------------------------------------------------------------------------------------------------
@@ -112,16 +113,21 @@ end function IO_readlines
 
 !--------------------------------------------------------------------------------------------------
 !> @brief Read whole file.
-!> @details ensures that the string ends with a new line (expected UNIX behavior)
+!> @details ensures that the string ends with a new line (expected UNIX behavior) and rejects
+! windows (CRLF) line endings
 !--------------------------------------------------------------------------------------------------
 function IO_read(fileName) result(fileContent)
 
   character(len=*),  intent(in) :: fileName
   character(len=:), allocatable :: fileContent
+
   integer ::  &
     fileLength, &
     fileUnit, &
-    myStat
+    myStat, &
+    firstEOL
+  character, parameter :: CR = achar(13)
+
 
   inquire(file = fileName, size=fileLength)
   open(newunit=fileUnit, file=fileName, access='stream',&
@@ -137,8 +143,12 @@ function IO_read(fileName) result(fileContent)
   if(myStat /= 0) call IO_error(102,ext_msg=trim(fileName))
   close(fileUnit)
 
+
   if(fileContent(fileLength:fileLength) /= IO_EOL) fileContent = fileContent//IO_EOL                ! ensure EOL@EOF
 
+  firstEOL = index(fileContent,IO_EOL)
+  if(scan(fileContent(firstEOL:firstEOL),CR) /= 0) call IO_error(115)
+
 end function IO_read
 
 
@@ -151,6 +161,7 @@ logical pure function IO_isBlank(string)
 
   integer :: posNonBlank
 
+
   posNonBlank = verify(string,IO_WHITESPACE)
   IO_isBlank = posNonBlank == 0 .or. posNonBlank == scan(string,IO_COMMENT)
 
@@ -170,6 +181,7 @@ pure function IO_stringPos(string)
 
   integer                      :: left, right
 
+
   allocate(IO_stringPos(1), source=0)
   right = 0
 
@@ -249,6 +261,7 @@ pure function IO_lc(string)
 
   integer :: i,n
 
+
   do i=1,len(string)
     n = index(UPPER,string(i:i))
     if(n/=0) then
@@ -271,6 +284,7 @@ function IO_rmComment(line)
   character(len=:), allocatable :: IO_rmComment
   integer :: split
 
+
   split = index(line,IO_COMMENT)
 
   if (split == 0) then
@@ -292,6 +306,7 @@ integer function IO_stringAsInt(string)
   integer                      :: readStatus
   character(len=*), parameter  :: VALIDCHARS = '0123456789+- '
 
+
   valid: if (verify(string,VALIDCHARS) == 0) then
     read(string,*,iostat=readStatus) IO_stringAsInt
     if (readStatus /= 0) call IO_error(111,ext_msg=string)
@@ -313,6 +328,7 @@ real(pReal) function IO_stringAsFloat(string)
   integer                      :: readStatus
   character(len=*), parameter  :: VALIDCHARS = '0123456789eE.+- '
 
+
   valid: if (verify(string,VALIDCHARS) == 0) then
     read(string,*,iostat=readStatus) IO_stringAsFloat
     if (readStatus /= 0) call IO_error(112,ext_msg=string)
@@ -331,6 +347,7 @@ logical function IO_stringAsBool(string)
 
   character(len=*), intent(in) :: string                                                            !< string for conversion to int value
 
+
   if     (trim(adjustl(string)) == 'True' .or.  trim(adjustl(string)) == 'true') then
     IO_stringAsBool = .true.
   elseif (trim(adjustl(string)) == 'False' .or. trim(adjustl(string)) == 'false') then
@@ -356,6 +373,7 @@ subroutine IO_error(error_ID,el,ip,g,instance,ext_msg)
   character(len=:), allocatable :: msg
   character(len=pStringLen)     :: formatString
 
+
   select case (error_ID)
 
 !--------------------------------------------------------------------------------------------------
@@ -382,6 +400,9 @@ subroutine IO_error(error_ID,el,ip,g,instance,ext_msg)
       msg = 'invalid character for logical:'
     case (114)
       msg = 'cannot decode base64 string:'
+    case (115)
+      msg = 'found CR. Windows file endings (CRLF) are not supported.'
+
 
 !--------------------------------------------------------------------------------------------------
 ! lattice error messages