scipion-pyworkflow 3.7.0__py3-none-any.whl → 3.8.0__py3-none-any.whl

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())

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.

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:

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. "

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.dist-info → scipion_pyworkflow-3.8.0.dist-info}/METADATA

@@ -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
@@ -18,18 +18,18 @@ Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
 Classifier: Topic :: Scientific/Engineering
 License-File: LICENSE.txt
-Requires-Dist: bibtexparser <=1.4.1
-Requires-Dist: psutil <=5.9.6
+Requires-Dist: bibtexparser<=1.4.1
+Requires-Dist: psutil<=5.9.6
 Requires-Dist: tkcolorpicker
-Requires-Dist: distro <=1.8
-Requires-Dist: importlib-metadata <=6.8.0
-Requires-Dist: matplotlib ==3.7.3 ; python_version == "3.8"
-Requires-Dist: numpy ==1.24.4 ; python_version == "3.8"
-Requires-Dist: configparser ==6.0.0 ; python_version >= "3.8"
-Requires-Dist: pillow ==10.1.0 ; python_version >= "3.8"
-Requires-Dist: requests ==2.31.0 ; python_version >= "3.8"
-Requires-Dist: matplotlib ==3.8.1 ; python_version >= "3.9"
-Requires-Dist: numpy ==1.26.1 ; python_version >= "3.9"
+Requires-Dist: distro<=1.8
+Requires-Dist: importlib-metadata<=6.8.0
+Requires-Dist: matplotlib==3.7.3; python_version == "3.8"
+Requires-Dist: numpy==1.24.4; python_version == "3.8"
+Requires-Dist: configparser==6.0.0; python_version >= "3.8"
+Requires-Dist: pillow==10.1.0; python_version >= "3.8"
+Requires-Dist: requests==2.31.0; python_version >= "3.8"
+Requires-Dist: matplotlib==3.8.1; python_version >= "3.9"
+Requires-Dist: numpy==1.26.1; python_version >= "3.9"
 
 .. image:: https://img.shields.io/pypi/v/scipion-pyworkflow.svg
         :target: https://pypi.python.org/pypi/scipion-pyworkflow

{scipion_pyworkflow-3.7.0.dist-info → scipion_pyworkflow-3.8.0.dist-info}/RECORD

@@ -1,9 +1,9 @@
 pyworkflow/__init__.py,sha256=Wr-MVKMQJy_Cy-rpPPB0-pyv8-8tx7GPPaLSNBrV1AI,1246
-pyworkflow/config.py,sha256=dItVwjylh8Affxq4Q488d7cnDcFrh9lVocTN8gF5IZA,21347
-pyworkflow/constants.py,sha256=0pphRj5jaz9dst7TiC3hWUoGmhmHEai8ZOlLc7OKy28,7244
+pyworkflow/config.py,sha256=a6TyBwKFvq79dQMamA4D5dPULWfSKfIBbsRT4NdlA94,22048
+pyworkflow/constants.py,sha256=LEuEXv7rXBSl2YyTQ27X4iK4-NJYPHWi3ibLXkt4F1k,7319
 pyworkflow/exceptions.py,sha256=3VFxuNJHcIWxRnLPR0vYg0RFAQMmxPBJZLZSi87VI8E,507
-pyworkflow/object.py,sha256=0kOnViuAzqERaGh95eKSSuli7T11e5R494ntgKLp6ZA,54415
-pyworkflow/plugin.py,sha256=O9SLpltE_inmRea0uh7OiJ1eUTbgIHN54Kqpv0UwZto,28520
+pyworkflow/object.py,sha256=D5pLvHezEIXB1J_Lxc1CXF_s5ZEZ1r-pj1QAI1CQL24,55070
+pyworkflow/plugin.py,sha256=wl1n-qxBZitm5CHm6uiUIp99eOv6TxxRKLxygxcK1KM,28805
 pyworkflow/template.py,sha256=JtdK2AKgaAdu-SuovqNqn5W-ojmtw3SfaP2bOzSy_IA,10460
 pyworkflow/viewer.py,sha256=vA6VxYuxmCwMjIxCIdrp_G-R-nVo-0TA8p1rSl24EOY,11386
 pyworkflow/wizard.py,sha256=nXuk_qMUVlQNa6nB6GCt0CoFQ_P2dnJbGWdwtpDG2tQ,2633
@@ -72,7 +72,7 @@ pyworkflow/protocol/hosts.py,sha256=B9ENNclqYe75CPqAMOoPjwn-r3ST6HxTewXtsK_zWks,
 pyworkflow/protocol/launch.py,sha256=7WKAiHma2tSuhqK4xVnxD_SnVt7Y5qyDFdQwTo8BLF0,11267
 pyworkflow/protocol/package.py,sha256=L6x3HHKtbrhDQRJHD07SG3DQKNMGaRQ0ROoLEY3SuRQ,1444
 pyworkflow/protocol/params.py,sha256=DRpeNIi_uQQ_JbqORq8A7P7yMBQpoj8r-8oBfroNtYI,26338
-pyworkflow/protocol/protocol.py,sha256=X_1BdzZlju1a8rG8w1QeB3I5dtUYSYEbWyirtwb6UQo,96195
+pyworkflow/protocol/protocol.py,sha256=xlq3_K7RmuatL-KM9m2K364P6Ft0dPG5r9Fgt0-pI0U,96993
 pyworkflow/resources/Imagej.png,sha256=nU2nWI1wxZB_xlOKsZzdUjj-qiCTjO6GwEKYgZ5Risg,14480
 pyworkflow/resources/chimera.png,sha256=AKCuwMqmZo0Cg2sddMUjBWUhmAq-nPsAVCBpVrYNeiQ,815
 pyworkflow/resources/fa-exclamation-triangle_alert.png,sha256=31_XvRu0CkJ2dvHSpcBAR43378lIJTWwiag_A7SuUQc,585
@@ -131,10 +131,10 @@ pyworkflowtests/tests/test_protocol_export.py,sha256=z18nKPkOnrYLMU8KqcnVsF6-ylQ
 pyworkflowtests/tests/test_protocol_output.py,sha256=8gnIFMRNmwPnIBRCG29WHJB6mqK4FLGn1jiXHtTD6pY,5980
 pyworkflowtests/tests/test_streaming.py,sha256=vOH-bKCM-fVUSsejqNnCX5TPXhdUayk9ZtJHsNVcfCY,1615
 pyworkflowtests/tests/test_utils.py,sha256=_pTYGCuXC7YNMdCBzUYNfSBCR3etrHsxHfIhsQi4VPc,7465
-scipion_pyworkflow-3.7.0.dist-info/LICENSE.txt,sha256=ixuiBLtpoK3iv89l7ylKkg9rs2GzF9ukPH7ynZYzK5s,35148
-scipion_pyworkflow-3.7.0.dist-info/METADATA,sha256=W5giQ4auiU1eB9GaHYFFIC9jYpDWrBgRZKPQdqBwxgU,4699
-scipion_pyworkflow-3.7.0.dist-info/WHEEL,sha256=R0nc6qTxuoLk7ShA2_Y-UWkN8ZdfDBG2B6Eqpz2WXbs,91
-scipion_pyworkflow-3.7.0.dist-info/dependency_links.txt,sha256=D7r_CPRjYRtBb3q_OBocTdsaeXI5TwnYMu5ri0JFtzs,84
-scipion_pyworkflow-3.7.0.dist-info/entry_points.txt,sha256=oR-zwsOICjEPINm-FWVPp-RfnpXZanVal4_XG6BWkkQ,127
-scipion_pyworkflow-3.7.0.dist-info/top_level.txt,sha256=PzyJteyenJwLjAeSFP7oYrTN_U71GABQwET8oLZkh9k,27
-scipion_pyworkflow-3.7.0.dist-info/RECORD,,
+scipion_pyworkflow-3.8.0.dist-info/LICENSE.txt,sha256=ixuiBLtpoK3iv89l7ylKkg9rs2GzF9ukPH7ynZYzK5s,35148
+scipion_pyworkflow-3.8.0.dist-info/METADATA,sha256=A-juSUF4DN1a1bGPKIfEBkhU8HJTaNa2Bo-y6CvoG_Q,4681
+scipion_pyworkflow-3.8.0.dist-info/WHEEL,sha256=UvcQYKBHoFqaQd6LKyqHw9fxEolWLQnlzP0h_LgJAfI,91
+scipion_pyworkflow-3.8.0.dist-info/dependency_links.txt,sha256=D7r_CPRjYRtBb3q_OBocTdsaeXI5TwnYMu5ri0JFtzs,84
+scipion_pyworkflow-3.8.0.dist-info/entry_points.txt,sha256=oR-zwsOICjEPINm-FWVPp-RfnpXZanVal4_XG6BWkkQ,127
+scipion_pyworkflow-3.8.0.dist-info/top_level.txt,sha256=PzyJteyenJwLjAeSFP7oYrTN_U71GABQwET8oLZkh9k,27
+scipion_pyworkflow-3.8.0.dist-info/RECORD,,

{scipion_pyworkflow-3.7.0.dist-info → scipion_pyworkflow-3.8.0.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (72.1.0)
+Generator: setuptools (74.0.0)
 Root-Is-Purelib: true
 Tag: py3-none-any