Merge pull request I2PC#198 from I2PC/master-stable

reverting master changes not in v1.0, now master should be the stable…

.gitignore

@@ -72,5 +72,5 @@ gmon.out
 # Configuration for servers
 /pyworkflow/web/pages/resources/js/templates_libs/config.js
 /config.log
-/Debug/
+/Debug
 /bin/

config/templates/protocols.template

@@ -24,7 +24,6 @@ Protocols SPA = [
         {"tag": "protocol", "value": "XmippProtPreprocessMicrographs", "text": "default"},
         {"tag": "protocol_group", "text": "CTF estimation", "openItem": "False", "children": [
             {"tag": "protocol", "value": "ProtCTFFind",   "text": "default"},
-            {"tag": "protocol", "value": "ProtGctf",   "text": "default"},
             {"tag": "protocol", "value": "XmippProtCTFMicrographs",   "text": "default"},
             {"tag": "section", "text": "more", "openItem": "False", "children": [
                 {"tag": "protocol", "value": "ProtCTFAssign",           "text": "default"},
@@ -137,18 +136,13 @@ Protocols SPA = [
             {"tag": "protocol", "value": "ProtResMap",   "text": "default"},
             {"tag": "protocol", "value": "XmippProtResolution3D",  "text": "default"},
             {"tag": "protocol", "value": "XmippProtValidateNonTilt",    "text": "default"},
-<<<<<<< HEAD
-            {"tag": "protocol", "value": "XmippProtValidateOverfitting",    "text": "default"},
-=======
             {"tag": "protocol", "value": "XmippProtCompareReprojections", "text": "default"},
->>>>>>> master
             {"tag": "section", "text": "more", "openItem": "False", "children": [
                 {"tag": "protocol", "value": "XmippProtConvertToPseudoAtoms", "text": "default"},
                 {"tag": "protocol", "value": "XmippProtAlignmentNMA", "text": "default"},
                 {"tag": "protocol", "value": "XmippProtDimredNMA", "text": "default"},
                 {"tag": "protocol", "value": "AtsasProtConvertPdbToSAXS", "text": "default"},
-				{"tag": "protocol", "value": "XmippProtVolumeStrain", "text": "default"},
-				{"tag": "protocol", "value": "XmippProtNormalizeStrain", "text": "default"}
+				{"tag": "protocol", "value": "XmippProtVolumeStrain", "text": "default"}
             ]}
          ]},     
         {"tag": "protocol_group", "text": "Reconstruct", "openItem": "False", "children": [

config/templates/scipion.template

@@ -28,8 +28,6 @@ FREALIGN_HOME = %(EM_ROOT)s/frealign
 GEMPICKER_HOME = %(EM_ROOT)s/gEMpicker_v1.1
 GEMPICKER = gEMpicker_nocuda_Ubuntu_14.04.x64
 GEMPICKER_CUDA = None # gEMpicker_cuda_55.x64
-GCTF_HOME = %(EM_ROOT)s/gctf
-GCTF = Gctf-v0.38_sm_30_cu5.5_x86_64
 MATLAB_BINDIR = None
 MATLAB_LIBDIR = None
 MOTIONCORR_HOME = %(EM_ROOT)s/motioncorr

install/script.py

@@ -473,8 +473,5 @@
                tar='gEMpicker_v1.1.tgz',
                default=False)
 
-env.addPackage('Gctf_v0.38',
-               tar='Gctf_v0.38.tgz',
-               default=False)
 
 env.execute()

pyworkflow/em/metadata/classes.py

@@ -86,9 +86,6 @@ def readFromMd(self, md, objId):
         for label in md.getActiveLabels():
             self._labelDict[label] = md.getValue(label, objId)
 
-    def addToMd(self, md):
-        self.writeToMd(md, md.addObject())
-
     def writeToMd(self, md, objId):
         """ Set back row values to a metadata row. """
         for label, value in self._labelDict.iteritems():