Jj deprecate re3 and improve warns

CHANGES.txt

@@ -1,4 +1,10 @@
-v3.3.0:
+v4.0.0:
+  Users:
+    - Adapted to scipion-em-relion deprecation of relion3.
+    - Add warning preventing to set the box size and the cropped box size to the same value as it may cause an
+      internal error in relion (Thanks to DSheperd).
+v3.4.0:
+  Note: this was supposed to be 3.3.0, but was published as 3.4.0
   Users:
     - After having performed a refine or classification of particles, fields _rlnLogLikeliContribution,
       _rlnMaxValueProbDistribution and _rlnNrOfSignificantSamples are registered, so they can be plotted versus the

reliontomo/__init__.py

@@ -24,13 +24,12 @@
 # **************************************************************************
 _logo = "relion_logo.jpg"
 _references = ['Scheres2012a', 'Scheres2012b', 'Kimanius2016', 'Zivanov2018']
-__version__ = '3.4.0'
+__version__ = '4.0.0'
 
 try:
     import pwem
     from reliontomo.constants import RELIONTOMO_HOME, RELIONTOMO_DEFAULT, RELION, RELIONTOMO_CUDA_LIB, V4_0
     import relion
-    from relion import V3_1
 
     class Plugin(relion.Plugin):
         _supportedVersions = [V4_0]
@@ -44,8 +43,7 @@ def _defineVariables(cls):
 
         @staticmethod
         def isRe40():
-            """We only allow one version older than 4.0, which is 3.1"""
-            return False if Plugin.getHome().endswith(V3_1) else True
+            return True if Plugin.getHome().endswith(V4_0) else False
 
         @classmethod
         def runRelionTomo(cls, protocol, program, args, cwd=None, numberOfMpi=1):

reliontomo/protocols/protocol_base_make_pseusosubtomos_and_rec_particle.py

@@ -77,6 +77,17 @@ def createOutputStep(self):
         return self.genRelionParticles(binningFactor=self.binningFactor.get(), boxSize=self.croppedBoxSize.get())
 
     # -------------------------- INFO functions -------------------------------
+    def _warnings(self):
+        warnMsg = []
+        boxSize = self.boxSize.get()
+        croppedBoxSize = self.croppedBoxSize.get()
+        if boxSize == croppedBoxSize:
+            warnMsg.append('Setting the same value to the Box size and the Cropped box size may cause errors in '
+                           'later steps of the refinement cycle.')
+        elif boxSize < croppedBoxSize:
+            warnMsg.append(f"The Box size [{boxSize} px] should be lower than the Cropped box size [{croppedBoxSize} "
+                           f"px]. Please check these parameters' help to get more detailed information.")
+        return warnMsg
 
     # --------------------------- UTILS functions -----------------------------
     def _genCommonCmd(self):