scipion-pyworkflow 3.7.0__tar.gz → 3.8.0__tar.gz

{scipion_pyworkflow-3.7.0 → scipion_pyworkflow-3.8.0}/CHANGES.txt

@@ -1,3 +1,10 @@
+V3.8.0
+users:
+  - Inform when a plugin does not import properly
+developers:
+  - Handling the name and the suffix to be used for a new output
+  - New method: Config.isCondaInstallation
+
 V3.7.0
 users:
   - Add protocol is an icon.
@@ -27,6 +34,7 @@ developers:
      New variable: SCIPION_MAPPER_USE_TEMPLATE. By default uses the template as it was now. If deacivated, instantiation happens on each iteration (less performant) but dev friendly
   - Adding a parameter to launch jobs (e.g: bash)
   - Handling item-click event in the treeview dialog
+  - Method copyAttributes expanded to manage the complex sets properly
 
 V3.6.0
 users:

{scipion_pyworkflow-3.7.0/scipion_pyworkflow.egg-info → scipion_pyworkflow-3.8.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: scipion-pyworkflow
-Version: 3.7.0
+Version: 3.8.0
 Summary: Simple workflow platform used in scientific applications, initially developed within the Scipion framework for image processing in Electron Microscopy.
 Home-page: https://github.com/scipion-em/scipion-pyworkflow
 Author: J.M. De la Rosa Trevin, Roberto Marabini, Grigory Sharov, Josue Gomez Blanco, Pablo Conesa, Yunior Fonseca Reyna

{scipion_pyworkflow-3.7.0 → scipion_pyworkflow-3.8.0}/pyworkflow/config.py

@@ -527,6 +527,25 @@ class Config:
         like registering FileHandlers or other stuff not needed when just importing modules."""
         return cls.SCIPION_HOME_DEFINED != False
 
+    @classmethod
+    def isCondaInstallation(cls):
+        """ Returns true if the scipion installation is done using conda"""
+
+        # Get the CONDA_PYTHON_EXE
+        # NOTE: This will not work when calling scipion python directly! But should works using the launcher.
+        envFolder = os.environ.get("CONDA_PREFIX", None)
+
+        # No conda variable... virtualenv installation!!
+        if envFolder is None:
+            return False
+        else:
+            from pyworkflow.utils import getPython
+            # Conda available.... let's check if it is active the same scipion env
+            condaExe = os.path.join(envFolder, "bin", "python")
+            return condaExe == getPython()
+
+
+
 
 # Add bindings folder to sys.path
 sys.path.append(Config.getBindingsFolder())

{scipion_pyworkflow-3.7.0 → scipion_pyworkflow-3.8.0}/pyworkflow/constants.py

@@ -37,12 +37,13 @@ from enum import Enum
 # will break existing plugins, this number needs to be incremented.
 CORE_VERSION = '3.0.0'
 
+# To be removed once consumers (app, some plugins) do not make use of them
 # Versions
 VERSION_1 = '1.0.0'
 VERSION_1_1 = '1.1.0'
 VERSION_1_2 = '1.2.0'
 VERSION_2_0 = '2.0.0'
-VERSION_3_0 = '3.7.0'
+VERSION_3_0 = '3.8.0'
 
 # For a new release, define a new constant and assign it to LAST_VERSION
 # The existing one has to be added to OLD_VERSIONS list.

{scipion_pyworkflow-3.7.0 → scipion_pyworkflow-3.8.0}/pyworkflow/object.py

@@ -366,10 +366,18 @@ class Object(object):
             elif isinstance(attr, PointerList):
                 for pointer in otherAttr:
                     attr.append(pointer)
-            elif isinstance(attr, Scalar) and otherAttr.hasPointer():
-                attr.copy(otherAttr)
+            elif isinstance(attr, Scalar):
+                if otherAttr.hasPointer():
+                    attr.copy(otherAttr)
+                else:
+                    attr.set(otherAttr.get())
             else:
-                attr.set(otherAttr.get())
+                # Necessary for the correct storage of complex attributes (such as Acquisition or Transform) in
+                # heterogeneous sets of sets, like the sets of tilt-series. Those sets imply append to the intermediate
+                # level + append to the upper level + update the upper level, passing in the previous method version
+                # through the line attr.set(otherAttr.get()), resulting in a None and copying the acquisition of the
+                # set to all the elements of the set and losing the transformation info
+                setattr(self, name, otherAttr.clone())
             
     def __getObjDict(self, prefix, objDict, includeClass, includePointers=True):
         if prefix:

{scipion_pyworkflow-3.7.0 → scipion_pyworkflow-3.8.0}/pyworkflow/plugin.py

@@ -112,9 +112,13 @@ class Domain:
             cls._plugins[name] = m  # Register the name to as a plugin
 
         # Catch any import exception, warn about it but continue.
-        except ModuleNotFoundError:
-            # This is probably due to a priority package like pwchem not being installed
-            pass
+        except ModuleNotFoundError as e:
+            if e.name == name:
+                # This is probably due to a priority package like pwchem not being installed
+                pass
+            else:
+                logger.warning("Plugin '%s' has import errors: %s. Maybe a missing dependency?. "
+                               "Is it devel mode and need to be reinstalled?. Ignoring it and continuing." % (name, str(e)))
         except Exception as e:
 
             (pwutils.yellow("WARNING!!: Plugin containing module %s does not import properly. "

{scipion_pyworkflow-3.7.0 → scipion_pyworkflow-3.8.0}/pyworkflow/protocol/protocol.py

@@ -328,7 +328,6 @@ class Protocol(Step):
     """
 
     # Version where protocol appeared first time
-    _lastUpdateVersion = pw.VERSION_1
     _stepsCheckSecs = pw.Config.getStepsCheckSeconds()
     # Protocol develop status: PROD, BETA, NEW
     _devStatus = pw.PROD
@@ -916,6 +915,27 @@ class Protocol(Step):
 
         return s
 
+    def getOutputSuffix(self, outputPrefix):
+        """ Return the suffix to be used for a new output.
+        For example: output3DCoordinates7.
+        It should take into account previous outputs
+        and number with a higher value.
+        """
+        maxCounter = -1
+        for attrName, _ in self.iterOutputAttributes():
+            suffix = attrName.replace(outputPrefix, '')
+            try:
+                counter = int(suffix)
+            except:
+                counter = 1  # when there is not number assume 1
+            maxCounter = max(counter, maxCounter)
+
+        return str(maxCounter + 1) if maxCounter > 0 else ''  # empty if not output
+
+    def getNextOutputName(self, outputPrefix):
+        """Return the name to be used for a new output."""
+        return outputPrefix + self.getOutputSuffix(outputPrefix)
+
     def copyDefinitionAttributes(self, other):
         """ Copy definition attributes to other protocol. """
         for paramName, _ in self.iterDefinitionAttributes():

{scipion_pyworkflow-3.7.0 → scipion_pyworkflow-3.8.0/scipion_pyworkflow.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: scipion-pyworkflow
-Version: 3.7.0
+Version: 3.8.0
 Summary: Simple workflow platform used in scientific applications, initially developed within the Scipion framework for image processing in Electron Microscopy.
 Home-page: https://github.com/scipion-em/scipion-pyworkflow
 Author: J.M. De la Rosa Trevin, Roberto Marabini, Grigory Sharov, Josue Gomez Blanco, Pablo Conesa, Yunior Fonseca Reyna