Merge pull request #180 from scipion-em/devel

release 3.3.0

CHANGES.txt

@@ -1,4 +1,11 @@
-
+V3.3.0
+developers:
+ - Exist code is not masked when running xmipp, relion etc commands
+ - CommandDef and CondaCommandDef assist in the definition of commands for the binaries
+V3.2.0
+ - Update message is green now
+ - SCIPION_DONT_INSTALL_BINARIES is used in the plugin manager to initialize "Skip binaries" check box
+ - Do not raise error when one of the CUDA env vars is not set
 v3.1.0
 users:
  - Fixing an error related with the Plugin Manager when clicking the plugin treeview

requirements.txt

@@ -1,2 +1,3 @@
 scipion-em
 outdated==0.2.2
+typing_extensions

scipion/__init__.py

@@ -1,2 +1,2 @@
-__version__ = '3.1.0'
+__version__ = '3.3.0'
 

scipion/__main__.py

@@ -30,6 +30,7 @@
 """
 Main entry point to scipion. It launches the gui, tests, etc.
 """
+import subprocess
 import sys
 import os
 from os.path import join, exists, expanduser, expandvars
@@ -104,10 +105,9 @@ def runCmd(cmd, args=''):
     cmd = '%s %s' % (cmd, args)
 
     os.environ.update(VARS)
-    # sys.stdout.write(">>>>> %s\n" % cmd)
-    result = os.system(cmd)
-    if not -256 < result < 256:
-        result = 1  # because if not, 256 is confused with 0 !
+    # result = os.system(cmd)
+    # Replacement of os.system with subprocess.call(cmd, shell=True)
+    result = subprocess.call(cmd, shell=True)
     sys.exit(result)
 
 
@@ -278,7 +278,16 @@ def main():
         from pyworkflow.utils.log import LoggingConfigurator
         LoggingConfigurator.setUpGUILogging()
         from pyworkflow.apps.pw_project import openProject
-        arg = sys.argv[2] if mode == MODE_PROJECT else mode
+
+        if mode == MODE_PROJECT:
+            if len(sys.argv)==3:
+                arg = sys.argv[2]
+
+            else:
+                arg = "list" #TODO, import LIST from pyworkflow.apps.pw_project
+        else:
+            arg = mode
+
         openProject(arg)
 
     elif mode == MODE_TESTS or mode == MODE_TEST:

scipion/install/plugin_manager.py

@@ -27,12 +27,11 @@
 from tkinter import *
 import threading
 
-from pyworkflow import Config
 from pyworkflow.gui.project import ProjectManagerWindow
 from pyworkflow.project import MenuConfig
 from pyworkflow.gui import *
 import pyworkflow.gui.dialog as pwgui
-from scipion.install.plugin_funcs import PluginRepository, PluginInfo, NULL_VERSION
+from scipion.install.plugin_funcs import PluginRepository, PluginInfo, NULL_VERSION, installBinsDefault
 
 from pyworkflow.utils.properties import *
 from pyworkflow.utils import redStr, makeFilePath
@@ -434,7 +433,7 @@ def _fillToolbar(self, frame):
         # Add option to cancel binaries installation
         self._col += 1
         self.skipBinaries = tk.BooleanVar()
-        self.skipBinaries.set(False)
+        self.skipBinaries.set(not installBinsDefault())
         installBinsEntry = tk.Checkbutton(frame, variable=self.skipBinaries,
                                           font=getDefaultFont(), text="Skip binaries")
         installBinsEntry.grid(row=0, column=self._col, sticky='ew', padx=5)

scipion/install/update_manager.py

@@ -92,7 +92,7 @@ def getPackagesStatus(cls, printAll=True):
             if needToUpdate:
                 outdatedPackages.append((package[0], version))
                 print(
-                    redStr('The package %s is out of date. Your version is %s, '
+                    greenStr('The package %s is out of date. Your version is %s, '
                            'the latest is %s.' % (package[0], package[1],
                                                   version)))
             elif printAll:

scipion/scripts/kickoff.py

@@ -147,7 +147,7 @@ def _onClosing(self):
 
 
 class KickoffView(tk.Frame):
-    def __init__(self, parent, windows, template=None, argsList=[],
+    def __init__(self, parent, windows, template:Template=None, argsList=[],
                  showScheduleOption=True, schedule=True, showProjectOption=True,
                  showProject=True, showProjectName=True, **kwargs):
 
@@ -282,9 +282,12 @@ def _onReadDataFromTemplateForm(self, e=None):
         for field in self.template.params.values():
             newValue = self._getValue(field.getTitle())
             field.setValue(newValue)
-            if not field.validate():
-                errors.append("%s value does not validate. Value: %s, Type: %s"
-                              % (field.getTitle(), field.getValue(),
+
+            validationMsg = field.validate()
+
+            if validationMsg:
+                errors.append("%s value does not validate: %s. Value: %s, Type: %s."
+                              % (field.getTitle(), validationMsg, field.getValue(),
                                  field.getType()))
 
         # Do more checks only if there are no previous errors

scipion/tests/installation.py

@@ -0,0 +1,24 @@
+import unittest
+from scipion.install.funcs import CommandDef, CondaCommandDef
+
+class TestCommands(unittest.TestCase):
+    def test_command_class(self):
+
+        myCmd = CommandDef("ls -l", "lolo")\
+            .append("cd ..", ["one", "two"])\
+            .append("cd .", sep="?")
+
+        self.assertEqual(myCmd.getCommands()[0][0], "ls -l && cd .. ? cd .")
+        self.assertEqual(myCmd.getCommands()[0][1], ["lolo", "one", "two"])
+
+        cmds = CondaCommandDef("modelangelo-3.0")
+        cmds.create('python=3.9').activate().cd('model-angelo')\
+            .pipInstall('-r requirements.txt')\
+            .condaInstall('-y torchvision torchaudio cudatoolkit=11.3 -c pytorch')\
+            .pipInstall('-e .').touch('../env-installed.txt')
+
+        print(cmds.getCommands())
+
+
+if __name__ == '__main__':
+    unittest.main()