Merge pull request #167 from scipion-em/devel

releasing devel

CHANGES.txt

@@ -1,3 +1,15 @@
+
+v3.1.0
+users:
+ - Fixing an error related with the Plugin Manager when clicking the plugin treeview
+ - Fix workflow tutorial intro.
+ - New variable (flag) to define if binaries are installed by default or not --> SCIPION_DONT_INSTALL_BINARIES (any value will deactivate installation of binaries
+ - scipion3 config -p <relion> (or any other): shows plugin url too
+ - SetOfVolumes and SetOfParticles have DataViewer as the default one.
+
+developers:
+    Update the methods checkLib and addPackage to improve the installation of plugins with libraries dependencies.
+
 v3.0.12
 users:
   old config file is now backed up (at backup/scipion.conf.YYmmDDHHMMSS) always after any scipion config command that updates the config files.

requirements.txt

@@ -1,2 +1,2 @@
 scipion-em
-outdated==0.2.1
+outdated==0.2.2

scipion/__init__.py

@@ -1,2 +1,2 @@
-__version__ = '3.0.12'
+__version__ = '3.1.0'
 

scipion/__main__.py

@@ -249,6 +249,8 @@ def main():
         defaultViewers.append('"SetOfLandmarkModels":["imod.viewers.ImodViewer"]')
         defaultViewers.append('"SetOfTomograms":["imod.viewers.ImodViewer"]')
         defaultViewers.append('"SetOfSubTomograms":["pwem.viewers.DataViewer"]')
+        defaultViewers.append('"SetOfVolumes":["pwem.viewers.DataViewer"]')
+        defaultViewers.append('"SetOfParticles":["pwem.viewers.DataViewer"]')
 
         os.environ["VIEWERS"] = '{%s}' % ','.join(defaultViewers)
 

scipion/install/install_plugin.py

@@ -31,7 +31,7 @@
 
 from scipion.constants import MODE_INSTALL_PLUGIN, MODE_UNINSTALL_PLUGIN
 from scipion.install import Environment
-from scipion.install.plugin_funcs import PluginRepository, PluginInfo
+from scipion.install.plugin_funcs import PluginRepository, PluginInfo, installBinsDefault
 from pyworkflow.utils import redStr
 
 #  ************************************************************************
@@ -68,6 +68,7 @@ def installPluginMethods():
     #                               Install parser                             #
     ############################################################################
 
+
     installParser = subparsers.add_parser(MODE_INSTALL_PLUGIN[1], aliases=[MODE_INSTALL_PLUGIN[0]], formatter_class=argparse.RawTextHelpFormatter,
                                           usage="%s  [-h] [--noBin] [-p pluginName [pipVersion ...]]" %
                                                 invokeCmd,
@@ -171,6 +172,7 @@ def installPluginMethods():
     parserUsed = modeToParser[mode]
     exitWithErrors = False
 
+
     if parsedArgs.help or (mode in [MODE_INSTALL_BINS, MODE_UNINSTALL_BINS]
                            and len(parsedArgs.binName) == 0):
 
@@ -212,7 +214,7 @@ def installPluginMethods():
                     plugin = PluginInfo(pipName=pluginName, pluginSourceUrl=pluginSrc, remote=False)
                     numberProcessor = parsedArgs.j
                     installed = plugin.installPipModule()
-                    if installed and not parsedArgs.noBin:
+                    if installed and installBinsDefault() and not parsedArgs.noBin:
                         plugin.getPluginClass()._defineVariables()
                         plugin.installBin({'args': ['-j', numberProcessor]})
         else:
@@ -229,22 +231,27 @@ def installPluginMethods():
                     plugin = pluginDict.get(pluginName, None)
                     if plugin:
                         installed = plugin.installPipModule(version=pluginVersion)
-                        if installed and not parsedArgs.noBin:
+                        if installed and installBinsDefault() and not parsedArgs.noBin:
+                            plugin.getPluginClass()._defineVariables()
                             plugin.installBin({'args': ['-j', numberProcessor]})
                     else:
                         print("WARNING: Plugin %s does not exist." % pluginName)
                         exitWithErrors = True
 
     elif parsedArgs.mode in MODE_UNINSTALL_PLUGIN:
 
-        for pluginName in parsedArgs.plugin:
-            plugin = PluginInfo(pluginName, pluginName, remote=False)
-            if plugin.isInstalled():
-                if not parsedArgs.noBin:
-                    plugin.uninstallBins()
-                plugin.uninstallPip()
-            else:
-                print("WARNING: Plugin %s is not installed." % pluginName)
+        if parsedArgs.plugin:
+            for pluginName in parsedArgs.plugin:
+                plugin = PluginInfo(pluginName, pluginName, remote=False)
+                if plugin.isInstalled():
+                    if installBinsDefault() and not parsedArgs.noBin:
+                        plugin.uninstallBins()
+                    plugin.uninstallPip()
+                else:
+                    print("WARNING: Plugin %s is not installed." % pluginName)
+        else:
+            print("Incorrect usage of command 'uninstallp'. Execute 'scipion3 uninstallp --help' or "
+                  "'scipion3 help' for more details.")
 
     elif parsedArgs.mode == MODE_INSTALL_BINS:
         binToInstallList = parsedArgs.binName

scipion/install/plugin_funcs.py

@@ -334,6 +334,8 @@ def getInstallenv(self, envArgs=None):
                 plugin.defineBinaries(env)
             except Exception as e:
                 print("Couldn't get binaries definition of %s plugin: %s" % (self.name, e))
+                import traceback
+                traceback.print_exc()
             return env
         else:
             return None
@@ -523,3 +525,10 @@ def ansi(n):
         else:
             printStr = "List of available plugins in plugin repository inaccessible at this time."
         return printStr
+
+
+def installBinsDefault():
+    """ Returns the default behaviour for installing binaries
+    By default it is TRUE, define "SCIPION_DONT_INSTALL_BINARIES" to anything to deactivate binaries installation"""
+
+    return os.environ.get("SCIPION_DONT_INSTALL_BINARIES", True) == True

scipion/install/plugin_manager.py

@@ -673,22 +673,23 @@ def _onPluginTreeClick(self, event):
             self.popup_menu.unpost()
             x, y, widget = event.x, event.y, event.widget
             elem = widget.identify("element", x, y)
-            self.tree.selectedItem = self.tree.identify_row(y)
-            if "image" in elem:
-                # a box was clicked
-                self._treeOperation()
-            else:
-                if self.tree.selectedItem is not None:
-                    if self.isPlugin(self.tree.item(self.tree.selectedItem,
-                                                    "values")[0]):
-                        self.showPluginInformation(self.tree.selectedItem)
-                    else:
-                        parent = self.tree.parent(self.tree.selectedItem)
-                        self.showPluginInformation(parent)
-            if len(self.operationList.getOperations(None)):
-                self.executeOpsBtn.config(state='normal')
-            else:
-                self.executeOpsBtn.config(state='disable')
+            if elem:
+                self.tree.selectedItem = self.tree.identify_row(y)
+                if "image" in elem:
+                    # a box was clicked
+                    self._treeOperation()
+                else:
+                    if self.tree.selectedItem is not None:
+                        item = self.tree.selectedItem
+                        if not self.isPlugin(self.tree.item(item, "values")[0]):
+                            item = self.tree.parent(item)
+
+                        self.showPluginInformation(item)
+
+                if len(self.operationList.getOperations(None)):
+                    self.executeOpsBtn.config(state='normal')
+                else:
+                    self.executeOpsBtn.config(state='disable')
 
     def _deleteSelectedOperation(self, e=None):
         """
@@ -887,7 +888,7 @@ def showPluginInformation(self, pluginName):
                                  plugin.latestRelease + ' available. Right-click on the '
                                                         'plugin to update it)')
                 self.topPanelTree.tag_configure('pluginVersion',
-                                                foreground=Color.RED_COLOR)
+                                                foreground=Config.SCIPION_MAIN_COLOR)
             else:
                 self.topPanelTree.tag_configure('pluginVersion', foreground='black')
             self.topPanelTree.insert('', 'end', pluginVersion,

scipion/scripts/config.py

@@ -103,6 +103,12 @@ def main(args=None):
                 print("%s = %s" % (k, v))
             print("\nThese variables can be added/edited in '%s'"
                   % os.environ[SCIPION_CONFIG])
+            url = plugin.getUrl()
+
+            if url != "":
+                print("\nMore information these variables might be found at '%s'"
+                  % url)
+
         else:
             print("No plugin found with name '%s'. Module name is expected,\n"
                   "i.e. 'scipion3 config -p xmipp3' shows the config variables "
@@ -466,92 +472,6 @@ def compareConfigVariable(section, variableName, valueInConfig, valueInTemplate)
                                 yellow(valueInTemplate)))
 
 
-# def guessJava():
-#     """Guess the system's Java installation, return a dict with the Java keys"""
-#
-#     options = {}
-#     candidates = []
-#
-#     # First check if the system has a favorite one.
-#     if 'JAVA_HOME' in os.environ:
-#         candidates.append(os.environ['JAVA_HOME'])
-#
-#     # Add also all the ones related to a "javac" program.
-#     for d in os.environ.get('PATH', '').split(':'):
-#         if not os.path.isdir(d) or 'javac' not in os.listdir(d):
-#             continue
-#         javaBin = os.path.realpath(join(d, 'javac'))
-#         if javaBin.endswith('/bin/javac'):
-#             javaHome = javaBin[:-len('/bin/javac')]
-#             candidates.append(javaHome)
-#             if javaHome.endswith('/jre'):
-#                 candidates.append(javaHome[:-len('/jre')])
-#
-#     # Check in order if for any of our candidates, all related
-#     # directories and files exist. If they do, that'd be our best guess.
-#     for javaHome in candidates:
-#         allExist = True
-#         for path in ['include', join('bin', 'javac'), join('bin', 'jar')]:
-#             if not exists(join(javaHome, path)):
-#                 allExist = False
-#         if allExist:
-#             options['JAVA_HOME'] = javaHome
-#             break
-#             # We could instead check individually for JAVA_BINDIR, JAVAC
-#             # and so on, as we do with MPI options, but we go for an
-#             # easier and consistent case instead: everything must be under
-#             # JAVA_HOME, which is the most common case for Java.
-#
-#     if not options:
-#         print(red("Warning: could not detect a suitable JAVA_HOME."))
-#         if candidates:
-#             print(red("Our candidates were:\n  %s" % '\n  '.join(candidates)))
-#
-#     return options
-#
-#
-# def guessMPI():
-#     """Guess the system's MPI installation, return a dict with MPI keys"""
-#     # Returns MPI_LIBDIR, MPI_INCLUDE and MPI_BINDIR as a dictionary.
-#
-#     options = {}
-#     candidates = []
-#
-#     # First check if the system has a favorite one.
-#     for prefix in ['MPI_', 'MPI', 'OPENMPI_', 'OPENMPI']:
-#         if '%sHOME' % prefix in os.environ:
-#             candidates.append(os.environ['%sHOME' % prefix])
-#
-#     # Add also all the ones related to a "mpicc" program.
-#     for d in os.environ.get('PATH', '').split(':'):
-#         if not os.path.isdir(d) or 'mpicc' not in os.listdir(d):
-#             continue
-#         mpiBin = os.path.realpath(join(d, 'mpicc'))
-#         if 'MPI_BINDIR' not in options:
-#             options['MPI_BINDIR'] = os.path.dirname(mpiBin)
-#         if mpiBin.endswith('/bin/mpicc'):
-#             mpiHome = mpiBin[:-len('/bin/mpicc')]
-#             candidates.append(mpiHome)
-#
-#     # Add some extra directories that are commonly around.
-#     candidates += ['/usr/lib/openmpi', '/usr/lib64/mpi/gcc/openmpi']
-#
-#     # Check in order if for any of our candidates, all related
-#     # directories and files exist. If they do, that'd be our best guess.
-#     for mpiHome in candidates:
-#         if (exists(join(mpiHome, 'include', 'mpi.h')) and
-#                 'MPI_INCLUDE' not in options):
-#             options['MPI_INCLUDE'] = join(mpiHome, 'include')
-#         if (exists(join(mpiHome, 'lib', 'libmpi.so')) and
-#                 'MPI_LIBDIR' not in options):
-#             options['MPI_LIBDIR'] = join(mpiHome, 'lib')
-#         if (exists(join(mpiHome, 'bin', 'mpicc')) and
-#                 'MPI_BINDIR' not in options):
-#             options['MPI_BINDIR'] = join(mpiHome, 'bin')
-#
-#     return options
-#
-
 def getConfigPathFromConfigFile(scipionConfigFile, configFile):
     """
     :param scipionConfigFile path to the config file to derive the folder name from

scipion/scripts/kickoff.py

@@ -252,7 +252,7 @@ def _addPair(self, text, title, r, lf, widget=ENTRY, traceCallback=None,
             elif widget == CHECKBUTTON:
                 var.set(YES if value else NO)
                 widget = tk.Checkbutton(lf, text="", font=self.bigFont, variable=var,
-                                        onvalue=YES, offvalue=NO, bg="white")
+                                        onvalue=YES, offvalue=NO, bg=pw.Config.SCIPION_BG_COLOR)
 
             widget.grid(row=r, column=1, sticky='news', padx=(5, 10), pady=pady)
 
@@ -438,9 +438,9 @@ def importTemplate(template, window):
     workflow = createTemplateFile(template)
     if workflow is not None:
         try:
-            window.getViewWidget().info('Importing the workflow...')
+            window.getViewWidget().info('Importing workflow %s' % workflow)
             window.project.loadProtocols(workflow)
-            window.getViewWidget().updateRunsGraph(True, reorganize=False)
+            window.getViewWidget().updateRunsGraph(True)
             window.getViewWidget().cleanInfo()
         except Exception as ex:
             window.showError(str(ex), exception=ex)