scipion-pyworkflow 3.10.6__py3-none-any.whl → 3.11.0__py3-none-any.whl

pyworkflow/viewer.py

@@ -133,6 +133,22 @@ class Viewer(object):
         self._keyPressed = args.get('keyPressed', None)
         self._tkRoot = self.formWindow.root if self.formWindow else None
 
+    @classmethod
+    def can_handle_this(cls, classHierarchy, instance=None):
+        """ Returns none if it cannot handle the instance, otherwise returns which of the
+        classes of the hierarchy it targets (used for establishing priority"""
+
+        for t in cls._targets:
+            if t in classHierarchy:
+
+                if instance is not None and not cls.can_handle_this_instance(instance):
+                    return None
+                else:
+                    return t
+
+    @classmethod
+    def can_handle_this_instance(cls, instance):
+        return True
     def getKeyPressed(self):
         return self._keyPressed
 
@@ -222,6 +238,8 @@ class ProtocolViewer(Viewer, pwprot.Protocol):
     If should provide a mapping between form params and the corresponding
     functions that will return the corresponding Views.
     """
+
+    _label ="Protocol viewer"
     def __init__(self, **kwargs):
         # Here we are going to intercept the original _defineParams function
         # and replace by an empty one, this is to postpone the definition of 
@@ -241,7 +259,11 @@ class ProtocolViewer(Viewer, pwprot.Protocol):
         
     def getWindow(self):
         return self.formWindow
-    
+
+    @classmethod
+    def getName(cls):
+        return cls._label
+
     def getTkRoot(self):
         return self._tkRoot
     

pyworkflowtests/protocols.py

@@ -69,9 +69,7 @@ class ParallelSleepingProtocol(SleepingProtocol):
 class ConcurrencyProtocol(SleepingProtocol):
     """ Protocol to test concurrency access to sets"""
 
-    def __init__(self, **kwargs):
-        super().__init__(**kwargs)
-        self.stepsExecutionMode = pwprot.STEPS_PARALLEL
+    stepsExecutionMode = pwprot.STEPS_PARALLEL
 
     def _defineParams(self, form):
         form.addParallelSection(threads=2, mpi=0)

{scipion_pyworkflow-3.10.6.dist-info → scipion_pyworkflow-3.11.0.dist-info}/METADATA

@@ -1,22 +1,15 @@
 Metadata-Version: 2.4
 Name: scipion-pyworkflow
-Version: 3.10.6
-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
-Author-email: delarosatrevin@scilifelab.se, roberto@cnb.csic.es, gsharov@mrc-lmb.cam.ac.uk, josue.gomez-blanco@mcgill.ca, pconesa@cnb.csic.es, fonsecareyna@cnb.csic.es
-Project-URL: Bug Reports, https://github.com/scipion-em/scipion-pyworkflow/issues
-Project-URL: Source, https://github.com/scipion-em/scipion-pyworkflow/
-Keywords: workflows science electron-microscopy cryo-em structural-biology image-processing scipion
-Classifier: Development Status :: 5 - Production/Stable
-Classifier: Intended Audience :: Science/Research
-Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
-Classifier: Programming Language :: Python :: 3.8
-Classifier: Programming Language :: Python :: 3.9
-Classifier: Programming Language :: Python :: 3.10
-Classifier: Programming Language :: Python :: 3.11
-Classifier: Programming Language :: Python :: 3.12
-Classifier: Topic :: Scientific/Engineering
+Version: 3.11.0
+Summary: Workflow platform used in scientific applications, initially developed
+Author-email: Pablo Conesa <pconesa@cnb.csic.es>, Yunior Fonseca <cfonseca@cnb.csic.es>, "J.M. De la Rosa Trevin" <josemiguel.delarosatrevin@stjude.org>, Roberto Marabini <roberto@cnb.csic.es>, Grigory Sharov <sharov.grigory@gmail.com>, Josue Gomez Blanco <josue.gomez-blanco@mcgill.ca>
+License: GNU General Public License v3 (GPLv3)
+Project-URL: Homepage, https://scipion.i2pc.es
+Project-URL: Repository, https://github.com/scipion-em/scipion-pyworkflow
+Project-URL: Issues, https://github.com/scipion-em/scipion-pyworkflow/issues
+Keywords: scipion,electron-microscopy,cryo-em,structural-biology,generic-workflow-engine,image-processing,scipion-3.0
+Requires-Python: >=3.8
+Description-Content-Type: text/x-rst
 License-File: LICENSE.txt
 Requires-Dist: bibtexparser<=1.4.1
 Requires-Dist: psutil<=5.9.6
@@ -27,19 +20,12 @@ Requires-Dist: pillow==10.1.0; python_version >= "3.8"
 Requires-Dist: numpy==1.24.4; python_version == "3.8"
 Requires-Dist: numpy==1.26.1; python_version >= "3.9"
 Requires-Dist: requests==2.31.0; python_version >= "3.8"
-Requires-Dist: tkcolorpicker
+Requires-Dist: tkcolorpicker2
 Requires-Dist: distro<=1.8
 Requires-Dist: importlib-metadata<=6.8.0
-Dynamic: author
-Dynamic: author-email
-Dynamic: classifier
-Dynamic: description
-Dynamic: home-page
-Dynamic: keywords
+Requires-Dist: setuptools>=62.6
+Requires-Dist: pyperclip==1.9.0
 Dynamic: license-file
-Dynamic: project-url
-Dynamic: requires-dist
-Dynamic: summary
 
 .. image:: https://img.shields.io/pypi/v/scipion-pyworkflow.svg
         :target: https://pypi.python.org/pypi/scipion-pyworkflow

scipion_pyworkflow-3.11.0.dist-info/RECORD

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{scipion_pyworkflow-3.10.6.dist-info → scipion_pyworkflow-3.11.0.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (78.1.0)
+Generator: setuptools (80.9.0)
 Root-Is-Purelib: true
 Tag: py3-none-any
 

pyworkflow/apps/__init__.py

@@ -1,29 +0,0 @@
-# **************************************************************************
-# *
-# * Authors:     J.M. De la Rosa Trevin (jmdelarosa@cnb.csic.es)
-# *
-# * Unidad de  Bioinformatica of Centro Nacional de Biotecnologia , CSIC
-# *
-# * This program is free software; you can redistribute it and/or modify
-# * it under the terms of the GNU General Public License as published by
-# * the Free Software Foundation; either version 3 of the License, or
-# * (at your option) any later version.
-# *
-# * This program is distributed in the hope that it will be useful,
-# * but WITHOUT ANY WARRANTY; without even the implied warranty of
-# * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-# * GNU General Public License for more details.
-# *
-# * You should have received a copy of the GNU General Public License
-# * along with this program; if not, write to the Free Software
-# * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA
-# * 02111-1307  USA
-# *
-# *  All comments concerning this program package may be sent to the
-# *  e-mail address 'scipion@cnb.csic.es'
-# *
-# **************************************************************************
-"""
-Configuration sub-package
-"""
-

pyworkflow/apps/pw_manager.py

@@ -1,37 +0,0 @@
-#!/usr/bin/env python
-
-# **************************************************************************
-# *
-# * Authors:     J.M. De la Rosa Trevin (jmdelarosa@cnb.csic.es)
-# *
-# * Unidad de  Bioinformatica of Centro Nacional de Biotecnologia , CSIC
-# *
-# * This program is free software; you can redistribute it and/or modify
-# * it under the terms of the GNU General Public License as published by
-# * the Free Software Foundation; either version 3 of the License, or
-# * (at your option) any later version.
-# *
-# * This program is distributed in the hope that it will be useful,
-# * but WITHOUT ANY WARRANTY; without even the implied warranty of
-# * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-# * GNU General Public License for more details.
-# *
-# * You should have received a copy of the GNU General Public License
-# * along with this program; if not, write to the Free Software
-# * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA
-# * 02111-1307  USA
-# *
-# *  All comments concerning this program package may be sent to the
-# *  e-mail address 'scipion@cnb.csic.es'
-# *
-# **************************************************************************
-"""
-Launch the windows with all Projects.
-"""
-          
-from pyworkflow.gui.project import ProjectManagerWindow
-
-
-if __name__ == '__main__':
-    
-    ProjectManagerWindow().show()

pyworkflow/apps/pw_plot.py

@@ -1,51 +0,0 @@
-#!/usr/bin/env python
-
-
-import argparse
-from pwem.viewers import EmPlotter
-from pyworkflow.gui.plotter import Plotter
-
-
-def main():
-    parser = argparse.ArgumentParser(prog='Scipion Plot')
-    parser.add_argument('--file', help='File to visualize', required=True)
-    parser.add_argument('--block', help='Block to visualize')
-    parser.add_argument('--type', help='Plot type')
-    parser.add_argument('--columns', help='Columns to plot')
-    parser.add_argument('--xcolumn', help='X Column to plot')
-    parser.add_argument('--orderColumn', help='Column to order')
-    parser.add_argument('--orderDir', help='Order direction(ASC, DESC)')
-    parser.add_argument('--bins', help='If plot type is histogram, number of bins')
-    parser.add_argument('--colors', help='Colors to plot columns')
-    parser.add_argument('--styles', help='Styles to plot columns')
-    parser.add_argument('--markers', help='Markers to plot columns')
-    parser.add_argument('--title', help='Plot title', default='')
-    parser.add_argument('--ytitle', help='Y axis title', default='')
-    parser.add_argument('--xtitle', help='X axis title', default='')
-
-    args = parser.parse_args()
-    plotfile = args.file
-    block = args.block if args.block else '' 
-    type = args.type
-    columns = args.columns
-    xcolumn = args.xcolumn
-    orderColumn = args.orderColumn
-    orderDir = args.orderDir
-    
-    bins = args.bins
-    colors = args.colors
-    styles = args.styles
-    markers = args.markers
-    title = args.title
-    xtitle = args.xtitle
-    ytitle = args.ytitle
-    
-    Plotter.setBackend('TkAgg')
-    plotter = EmPlotter.createFromFile(
-        plotfile, block, type, columns, colors, styles, markers, xcolumn,
-        ytitle, xtitle, title, bins, orderColumn, orderDir)
-    plotter.show(block=True)
-
-
-if __name__ == '__main__':
-    main()

pyworkflow/apps/pw_project.py

@@ -1,113 +0,0 @@
-#!/usr/bin/env python
-# **************************************************************************
-# *
-# * Authors:     J.M. De la Rosa Trevin (jmdelarosa@cnb.csic.es)
-# *
-# * Unidad de  Bioinformatica of Centro Nacional de Biotecnologia , CSIC
-# *
-# * This program is free software; you can redistribute it and/or modify
-# * it under the terms of the GNU General Public License as published by
-# * the Free Software Foundation; either version 3 of the License, or
-# * (at your option) any later version.
-# *
-# * This program is distributed in the hope that it will be useful,
-# * but WITHOUT ANY WARRANTY; without even the implied warranty of
-# * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-# * GNU General Public License for more details.
-# *
-# * You should have received a copy of the GNU General Public License
-# * along with this program; if not, write to the Free Software
-# * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA
-# * 02111-1307  USA
-# *
-# *  All comments concerning this program package may be sent to the
-# *  e-mail address 'scipion@cnb.csic.es'
-# *
-# **************************************************************************
-"""
-Launch main project window 
-"""
-
-import sys
-import os
-
-from pyworkflow import Config
-from pyworkflow.project import Manager
-from pyworkflow.gui.project import ProjectWindow
-import pyworkflow.utils as pwutils
-
-HERE = 'here'
-LAST = 'last'
-LIST = 'list'
-
-def openProject(projectName):
-    """ Opens a scipion project:
-
-    :param projectName: Name of an existing project to open,
-            or "here" to create a project in the current working dir,
-            or "last" to open the most recent project
-
-    """
-    manager = Manager()
-    projName = os.path.basename(projectName)
-
-
-    if projName == LIST:
-        showProjectList(manager)
-        return
-    # Handle special name 'here' to create a project
-    # from the current directory
-    elif projName == HERE:
-        cwd = Config.SCIPION_CWD
-
-        if " " in cwd:
-            print("Projects can't have spaces in the name: %s" % cwd)
-            sys.exit(1)
-
-        print("\nYou are trying to create a project here:",
-              pwutils.cyan(cwd))
-
-        if os.listdir(cwd):
-            print(pwutils.red('\nWARNING: this folder is not empty!!!'))
-        key = input("\nDo you want to create a project here? [y/N]?")
-
-        if key.lower().strip() != 'y':
-            print("\nAborting...")
-            sys.exit(0)
-        else:
-            print("\nCreating project....")
-            projName = os.path.basename(cwd)
-            projDir = os.path.dirname(cwd)
-            manager.createProject(projName, location=projDir)
-
-    elif projName == LAST:  # Get last project
-        projects = manager.listProjects()
-        if not projects:
-            sys.exit("No projects yet, cannot open the last one.")
-        projName = projects[0].projName
-
-    projPath = manager.getProjectPath(projName)
-
-    if os.path.exists(projPath):
-        projWindow = ProjectWindow(projPath)
-        projWindow.show()
-    else:
-        print("Can't open project %s. It does not exist" % projPath)
-
-        #Show the list of projects
-        showProjectList(manager)
-
-def showProjectList(manager):
-
-    projects = manager.listProjects()
-
-    print("\n******** LIST OF PROJECTS *******\n")
-    for project in projects:
-        print(project.projName)
-    print("\n")
-if __name__ == '__main__':
-
-    if len(sys.argv) > 1:
-        openProject(sys.argv[1])
-    else:
-        print("usage: pw_project.py PROJECT_NAME or %s or %s or %s" % (HERE, LAST, LIST))

pyworkflow/apps/pw_protocol_list.py

@@ -1,143 +0,0 @@
-#!/usr/bin/env python
-# **************************************************************************
-# *
-# * Authors:     J.M. De la Rosa Trevin (jmdelarosa@cnb.csic.es)
-# *
-# * Unidad de  Bioinformatica of Centro Nacional de Biotecnologia , CSIC
-# *
-# * This program is free software; you can redistribute it and/or modify
-# * it under the terms of the GNU General Public License as published by
-# * the Free Software Foundation; either version 3 of the License, or
-# * (at your option) any later version.
-# *
-# * This program is distributed in the hope that it will be useful,
-# * but WITHOUT ANY WARRANTY; without even the implied warranty of
-# * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-# * GNU General Public License for more details.
-# *
-# * You should have received a copy of the GNU General Public License
-# * along with this program; if not, write to the Free Software
-# * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA
-# * 02111-1307  USA
-# *
-# *  All comments concerning this program package may be sent to the
-# *  e-mail address 'scipion@cnb.csic.es'
-# *
-# **************************************************************************
-###
-"""
-List all existing protocols within Scipion
-"""
-
-import sys
-
-from pwem.protocols import (ProtImport, ProtMicrographs, ProtParticles, Prot2D,
-                            Prot3D)
-from pyworkflow import Config
-from pyworkflow.viewer import Viewer
-from pyworkflow.protocol.protocol import Protocol
-
-
-def getFirstLine(doc):
-    """ Get the first non empty line from doc. """
-    if doc:
-        for lines in doc.split('\n'):
-            l = lines.strip()
-            if l:
-                return l
-    return ''
-
-
-def hasDoubleInheritance(classRef):
-    # loop while class has single parent
-    numParents = len(classRef.__bases__)
-    while numParents == 1 and classRef is not Protocol:
-        classRef = classRef.__bases__[0]
-        numParents = len(classRef.__bases__)
-    if numParents > 1:
-        return True
-    else:
-        return False
-
-
-if __name__ == '__main__':
-    count = 0
-    withDoc = '--with-doc' in sys.argv
-    extended = '--extended' in sys.argv
-    ai = '--ai' in sys.argv
-
-    emProtocolsDict = Config.getDomain().getProtocols()
-
-    protDict = {}
-
-    # Group protocols by package name
-    for k, v in emProtocolsDict.items():
-        packageName = v.getClassPackageName()
-
-        if packageName not in protDict:
-            protDict[packageName] = []
-
-        if not issubclass(v, Viewer) and not v.isBase():
-            if extended:
-                protTuple = (k, v, hasDoubleInheritance(v),
-                             v().allowMpi, v().numberOfMpi,
-                             v().allowThreads, v().numberOfThreads,
-                             v().stepsExecutionMode)
-            else:
-                protTuple = (k, v)
-            protDict[packageName].append(protTuple)
-
-    def iterGroups(protDict):
-        groups = list(protDict.keys())
-        groups.sort(key=lambda x: 1000-len(protDict[x]))
-
-        for g in groups:
-            yield g, protDict[g]
-
-    def printProtocols(prots):
-        protList = [(p[0], p[1], p[1].getClassLabel()) for p in prots]
-        protList.sort(key=lambda x: x[2])
-
-        for k, v, l in protList:
-            doc = getFirstLine(v.__doc__) if withDoc else ''
-            print("* link:%s[%s]: %s" % (k, l, doc))
-
-
-    if withDoc:
-        for group, prots in iterGroups(protDict):
-            print("Package: ", group, "(%d protocols)" % len(prots))
-            for p in prots:
-                print("   %s ( %s ):" % (p[1].getClassLabel(), p[0]))
-                print("    ", p[1].__doc__)
-            print("-" * 100)
-
-    else:
-        if extended:
-            formatStr = "{:<15}\t{:<35}\t{:<35}" + "\t{:<20}" * 6
-            print(formatStr.format("PACKAGE", "PROTOCOL",
-                                   "LABEL", "DOUBLE_INHERITANCE",
-                                   "ALLOWS_MPI", "NUM_MPI",
-                                   "ALLOWS_THREADS", "NUM_THREADS",
-                                   "STEPS_EXEC_MODE"))
-            for group, prots in iterGroups(protDict):
-                for p in prots:
-                    print(formatStr.format(group, p[0],
-                                           p[1].getClassLabel(), *p[2:]))
-        elif ai:
-            for group, prots in iterGroups(protDict):
-                for protClassName, protClass in prots:
-                    print("\nThe protocol named \"%s\" can be found in the %s plugin." %(protClass._label, group))
-                    print("\"%s\" protocol help is as follows:\n %s." % (protClass._label, protClass.__doc__))
-                    instance = protClass()
-
-                    for name, param in instance._definition.iterParams():
-                        print("\"%s\" has a \"%s\" parameter that is explained as: %s" % (protClass._label, param.label, param.help))
-
-
-
-        else:
-            formatStr = "{:<15}\t{:<35}\t{:<35}"
-            print(formatStr.format("PACKAGE", "PROTOCOL", "LABEL"))
-            for group, prots in iterGroups(protDict):
-                for k, v in prots:
-                    print(formatStr.format(group, k, v.getClassLabel()))

pyworkflow/apps/pw_protocol_run.py

@@ -1,51 +0,0 @@
-#!/usr/bin/env python
-# **************************************************************************
-# *
-# * Authors:     J.M. De la Rosa Trevin (jmdelarosa@cnb.csic.es)
-# *
-# * Unidad de  Bioinformatica of Centro Nacional de Biotecnologia , CSIC
-# *
-# * This program is free software; you can redistribute it and/or modify
-# * it under the terms of the GNU General Public License as published by
-# * the Free Software Foundation; either version 3 of the License, or
-# * (at your option) any later version.
-# *
-# * This program is distributed in the hope that it will be useful,
-# * but WITHOUT ANY WARRANTY; without even the implied warranty of
-# * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-# * GNU General Public License for more details.
-# *
-# * You should have received a copy of the GNU General Public License
-# * along with this program; if not, write to the Free Software
-# * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA
-# * 02111-1307  USA
-# *
-# *  All comments concerning this program package may be sent to the
-# *  e-mail address 'scipion@cnb.csic.es'
-# *
-# **************************************************************************
-"""
-This module is responsible for launching protocol executions.
-"""
-import sys
-from pyworkflow.utils import LoggingConfigurator
-
-if __name__ == '__main__':
-
-    if len(sys.argv) == 6:
-        projPath = sys.argv[1]
-        dbPath = sys.argv[2]
-        protId = int(sys.argv[3])
-        stdOut = sys.argv[4]
-        stdErr = sys.argv[5]
-
-        LoggingConfigurator.setUpProtocolRunLogging(stdOut, stdErr)
-
-        from pyworkflow.protocol import runProtocolMain
-        runProtocolMain(projPath, dbPath, protId)
-        
-    else:
-        from os.path import basename
-        print("usage: %s projPath dbPath protocolID pathToStdoutLog pathToStdErrLog." % basename(sys.argv[0]))
-        print("sys.argv: %s" % sys.argv)
-        sys.exit(1)