scipion-pyworkflow 3.11.0__tar.gz → 3.11.2__tar.gz

{scipion_pyworkflow-3.11.0 → scipion_pyworkflow-3.11.2}/CHANGES.txt

@@ -1,3 +1,22 @@
+V3.11.2
+ users:
+  Copy (Control-C) work in log viewers too
+  Pasting a copied workflow refreshes the graph
+  Bugfix: Protocol with very fast (almost notime) steps work instead of end up finished with pending steps.
+  templates can be fetched from urls having ".json" and not json.template only.
+  Double click in a protocol in "list mode" opens the protocol
+  Double click in a collapsed node, expands it.
+
+ developers:
+  new icon
+  Executor.getGpuListStr(): Returns the assigned gpus for the step as a string (accepts sep --> separator, defaults to " ")
+  Executor.setCudaVisibleDevices(): Sets the variable CUDA_VISIBLE_DEVICES with owned information.
+  Protocol.getExecutor: returns the executor. Useful to aske for gpu information inside a step
+  __debug__ allowed: By default Project load is with -O (optimized) so __debug__ is false.
+       asserts removed, swap to if + raise AssertionError
+       if optimized, shown in project window header
+
+V3.11.1 fix packaging
 V3.11.0
 users:
   - New behaviour: Saving a protocol will unload the form and log the confirmation message. There will not be any pop up message.

{scipion_pyworkflow-3.11.0/scipion_pyworkflow.egg-info → scipion_pyworkflow-3.11.2}/PKG-INFO

@@ -1,7 +1,7 @@
 Metadata-Version: 2.4
 Name: scipion-pyworkflow
-Version: 3.11.0
-Summary: Workflow platform used in scientific applications, initially developed
+Version: 3.11.2
+Summary: Workflow platform used in scientific applications, initially developed within the Scipion framework for image processing in Electron Microscopy but generic by design to be applied to any domain.
 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

{scipion_pyworkflow-3.11.0 → scipion_pyworkflow-3.11.2}/pyproject.toml

@@ -14,9 +14,7 @@ authors = [
     {name = "Grigory Sharov", email = "sharov.grigory@gmail.com"},
     {name = "Josue Gomez Blanco", email = "josue.gomez-blanco@mcgill.ca"},
 ]
-description = """Workflow platform used in scientific applications, initially developed
-            within the Scipion framework for image processing in Electron Microscopy but
-            generic by design to be applied to any domain."""
+description = """Workflow platform used in scientific applications, initially developed within the Scipion framework for image processing in Electron Microscopy but generic by design to be applied to any domain."""
 
 readme = "README.rst"
 requires-python = ">=3.8"
@@ -28,8 +26,10 @@ Homepage = "https://scipion.i2pc.es"
 Repository = "https://github.com/scipion-em/scipion-pyworkflow"
 Issues = "https://github.com/scipion-em/scipion-pyworkflow/issues"
 
-[tool.setuptools]
-packages = ["pyworkflow", "pyworkflowtests"]
+[tool.setuptools.packages.find]
+where = ["."]
+include = ["pyworkflow*"]
+namespaces = false
 
 [tool.setuptools.package-data]
 "pyworkflow" = ["resources/*", "project/scripts/*"]

scipion_pyworkflow-3.11.2/pyworkflow/apps/__init__.py

@@ -0,0 +1,29 @@
+# **************************************************************************
+# *
+# * 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
+"""
+

scipion_pyworkflow-3.11.2/pyworkflow/apps/pw_manager.py

@@ -0,0 +1,37 @@
+#!/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()

scipion_pyworkflow-3.11.2/pyworkflow/apps/pw_plot.py

@@ -0,0 +1,51 @@
+#!/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()

scipion_pyworkflow-3.11.2/pyworkflow/apps/pw_project.py

@@ -0,0 +1,130 @@
+#!/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 subprocess import Popen
+
+from pyworkflow import Config, PYTHON
+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):
+
+        # This opens the project in the same process as the launcher. This is good for directly debugging code
+        # but  does not allow -O or not execution (usage of __debug__ flag).
+        # All we can do is to go straight to loading the project if debug is active or running optimized.
+        if Config.debugOn() or not __debug__:
+
+
+            # This may or may not be run Optimized (-O). It depends on the call to scipion last (launcher)
+            print("Launching project in debug or optimized...")
+            projWindow = ProjectWindow(projPath)
+            projWindow.show()
+        else:
+
+            # Run this same  script optimized: Defined in scipion module under scipion-app: Circular definition. To fix! Bad design.
+            print("Launching project optimized...")
+            Popen([PYTHON, "-O", "-m","scipion", "project", projectName])
+
+
+    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))

scipion_pyworkflow-3.11.2/pyworkflow/apps/pw_protocol_list.py

@@ -0,0 +1,143 @@
+#!/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()))

scipion_pyworkflow-3.11.2/pyworkflow/apps/pw_protocol_run.py

@@ -0,0 +1,51 @@
+#!/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)