mnt: ensured super calls on Siles._setup, fixed __iter__

Now __iter__ reads and returns the file, but will not close
the file-handle. This should be done by some other means.

Also moved the _completed variable into the _setup method
such that it is not a class variable.

sisl/io/bigdft/ascii.py

@@ -27,6 +27,7 @@ class asciiSileBigDFT(SileBigDFT):
 
     def _setup(self, *args, **kwargs):
         """ Initialize for `asciiSileBigDFT` """
+        super()._setup(*args, **kwargs)
         self._comment = ['#', '!']
 
     @sile_fh_open()

sisl/io/gulp/got.py

@@ -35,6 +35,7 @@ class gotSileGULP(SileGULP):
 
     def _setup(self, *args, **kwargs):
         """ Setup `gotSileGULP` after initialization """
+        super()._setup(*args, **kwargs)
         self._keys = dict()
         self.set_supercell_key('Cartesian lattice vectors')
         self.set_geometry_key('Final fractional coordinates')

sisl/io/openmx/omx.py

@@ -58,6 +58,7 @@ def file(self):
 
     def _setup(self, *args, **kwargs):
         """ Setup the `omxSileOpenMX` after initialization """
+        super()._setup(*args, **kwargs)
         # These are the comments
         self._comment = ['#']
 

sisl/io/pdb.py

@@ -23,6 +23,7 @@ class pdbSile(Sile):
 
     def _setup(self, *args, **kwargs):
         """ Instantiate counters """
+        super()._setup(*args, **kwargs)
         self._model = 1
         self._serial = 1
         self._wrote_header = False

sisl/io/siesta/fdf.py

@@ -96,6 +96,7 @@ class fdfSileSiesta(SileSiesta):
 
     def _setup(self, *args, **kwargs):
         """ Setup the `fdfSileSiesta` after initialization """
+        super()._setup(*args, **kwargs)
         self._comment = ['#', '!', ';']
 
         # List of parent file-handles used while reading

sisl/io/siesta/out.py

@@ -38,10 +38,14 @@ class outSileSiesta(SileSiesta):
 
     This enables reading the output quantities from the Siesta output.
     """
-    _completed = None
 
-    def readline(self):
-        line = super().readline()
+    def _setup(self, *args, **kwargs):
+        """ Ensure the class has a _completed tag """
+        super()._setup(*args, **kwargs)
+        self._completed = None
+
+    def readline(self, *args, **kwargs):
+        line = super().readline(*args, **kwargs)
         if 'Job completed' in line:
             self._completed = True
         return line

sisl/io/sile.py

@@ -628,8 +628,11 @@ def line_has_keys(line, keys, case=True):
         return found
 
     def __iter__(self):
-        r""" Iterator for file """
-        yield from self.fh
+        """ Reading the entire content, without regarding comments """
+        l = self.readline(comment=True)
+        while l:
+            yield l
+            l = self.readline(comment=True)
 
     def readline(self, comment=False):
         r""" Reads the next line of the file """

sisl/io/table.py

@@ -71,6 +71,7 @@ class tableSile(Sile):
 
     def _setup(self, *args, **kwargs):
         """ Setup the `tableSile` after initialization """
+        super()._setup(*args, **kwargs)
         self._comment = ['#']
 
     @sile_fh_open()

sisl/io/tbtrans/sile.py

@@ -17,6 +17,7 @@ class SileCDFTBtrans(SileCDF):
 
     # all netcdf output should not be masked
     def _setup(self, *args, **kwargs):
+        super()._setup(*args, **kwargs)
         # all NetCDF routines actually returns masked arrays
         # this is to prevent TBtrans CDF files from doing this.
         if hasattr(self, "fh"):

sisl/io/vasp/car.py

@@ -25,6 +25,7 @@ class carSileVASP(SileVASP):
 
     def _setup(self, *args, **kwargs):
         """ Setup the `carSile` after initialization """
+        super()._setup(*args, **kwargs)
         self._scale = 1.
 
     @sile_fh_open()

sisl/io/vasp/out.py

@@ -14,10 +14,14 @@
 @set_module("sisl.io.vasp")
 class outSileVASP(SileVASP):
     """ Output file from VASP """
-    _completed = None
 
-    def readline(self):
-        line = super().readline()
+    def _setup(self, *args, **kwargs):
+        """ Ensure the class has a _completed tag """
+        super()._setup(*args, **kwargs)
+        self._completed = None
+
+    def readline(self, *args, **kwargs):
+        line = super().readline(*args, **kwargs)
         if "General timing and accounting" in line:
             self._completed = True
         return line

sisl/io/wannier90/seedname.py

@@ -58,6 +58,7 @@ class winSileWannier90(SileWannier90):
 
     def _setup(self, *args, **kwargs):
         """ Setup `winSileWannier90` after initialization """
+        super()._setup(*args, **kwargs)
         self._comment = ['!', '#']
         self._seed = str(self.file).replace('.win', '')
 

sisl/io/xsf.py

@@ -32,6 +32,7 @@ class xsfSile(Sile):
 
     def _setup(self, *args, **kwargs):
         """ Setup the `xsfSile` after initialization """
+        super()._setup(*args, **kwargs)
         self._comment = ['#']
 
     def _write_key(self, key):