scipion-pyworkflow 3.10.5__py3-none-any.whl → 3.11.0__py3-none-any.whl

pyworkflow/config.py

@@ -97,12 +97,15 @@ class Variable:
         self.value = new_value
         self.isDefault= self._isValueDefault()
     def _isValueDefault(self):
-        return self.value==self.default
+        return self.value == self.default
+
+
 class VariablesRegistry:
-    _variables={}
+    _variables = {}
 
     def __init__(self):
         raise RuntimeError("Variables class doesn't need to be instantiated.")
+
     @classmethod
     def register(cls, variable: Variable):
         cls._variables[variable.name] = variable
@@ -146,7 +149,7 @@ class Config:
 
         if key in os.environ:
             value = os.environ.get(key)
-            isDefault = (value==default)
+            isDefault = (value == default)
         else:
             isDefault = True
             value = default
@@ -154,10 +157,10 @@ class Config:
         # If the caster is passed do the casting, if fails go back to default
         if caster:
             try:
-                value=caster(value)
+                value = caster(value)
             except:
                 logger.warning("Variable %s has this value %s that can't be casted to the right type (%s). Using %s (default value)" %
-                               (key,value, caster, default))
+                               (key, value, caster, default))
                 value = default
         # If empty use default value
         if value == "" != default:
@@ -168,10 +171,23 @@ class Config:
         if isinstance(value, str):
             value = os.path.expandvars(os.path.expanduser(value))
 
-        # Register the variable
+        # Register the variable. Boolean variables are converted to booleans after this call. May not be accurate.
+        # 1 turns into False in the Config
         VariablesRegistry.register(Variable(key,description, source, value, default, var_type=var_type, isDefault=isDefault))
         return value
 
+    @staticmethod
+    def __notFalse(value):
+        return value != FALSE_STR
+
+    @staticmethod
+    def __notTrue(value):
+        return value != TRUE_STR
+
+    @staticmethod
+    def __bool(value):
+        return value.lower() in TRUE_YES_ON_
+
     class Root:
         """ Simple helper to return path from a root. """
 
@@ -185,13 +201,17 @@ class Config:
             # join will not join if expanded is absolute
             return os.path.join(self._root, expanded)
 
-    # Home for scipion
     _get = __get.__func__
-    SCIPION_HOME = os.path.abspath(_get(SCIPION_HOME_VAR, '',
-    "Path where Scipion is installed. Other paths are based on this like SCIPION_SOFTWARE, SCIPION_TESTS,... unless specified"))
+    _notFalse = __notFalse.__func__
+    __bool = __bool.__func__
+
+    # Home for scipion
+    _home_var = _get(SCIPION_HOME_VAR, '',
+                     "Path where Scipion is installed. Other paths are based on this like SCIPION_SOFTWARE, SCIPION_TESTS,... unless specified")
+    SCIPION_HOME = os.path.abspath(_home_var)
 
     # False if SCIPION_HOME is not found in the environment. To distinguish API documentation generation execution.
-    SCIPION_HOME_DEFINED = SCIPION_HOME != ''
+    SCIPION_HOME_DEFINED = _home_var != ''
 
     _root = Root(str(SCIPION_HOME))
     _join = _root.join
@@ -201,68 +221,75 @@ class Config:
     __defaultSpritesFile = _join(getResourcesPath(),'sprites.png')
 
     CONDA_ACTIVATION_CMD = _get(CONDA_ACTIVATION_CMD_VAR,'',
-    "str: Command to activate/initialize conda itself. Do not confuse it with 'conda activate'. It should be defined at installation time. It looks like this: eval \"$(/extra/miniconda3/bin/conda shell.bash hook)\"")
+                                "str: Command to activate/initialize conda itself. Do not confuse it with 'conda activate'. It should be defined at installation time. It looks like this: eval \"$(/extra/miniconda3/bin/conda shell.bash hook)\"")
 
     # SCIPION PATHS
     SCIPION_SOFTWARE = _get('SCIPION_SOFTWARE', _join('software'),
-    "Path where Scipion will install the software. Defaults to SCIPION_HOME/software.", var_type=VarTypes.FOLDER)
+                            "Path where Scipion will install the software. Defaults to SCIPION_HOME/software.", var_type=VarTypes.FOLDER)
 
     SCIPION_TESTS = _get('SCIPION_TESTS', _join('data', 'tests'),
-    "Path where to find/download test data. Defaults to SCIPION_HOME/data/tests.", var_type=VarTypes.FOLDER)
+                         "Path where to find/download test data. Defaults to SCIPION_HOME/data/tests.", var_type=VarTypes.FOLDER)
 
     # User dependent paths
     SCIPION_USER_DATA = _get('SCIPION_USER_DATA', '~/ScipionUserData',
-    "Path where Scipion projects are or will be created. Defaults to ~/ScipionUserData", var_type=VarTypes.FOLDER)
+                             "Path where Scipion projects are or will be created. Defaults to ~/ScipionUserData", var_type=VarTypes.FOLDER)
 
     # LOGGING variables
     SCIPION_LOGS = _get('SCIPION_LOGS', _join(SCIPION_USER_DATA, 'logs'),
-    "Folder for Scipion logs used by the GUI. Defaults to SCIPION_USER_DATA/logs.", var_type=VarTypes.FOLDER)
+                        "Folder for Scipion logs used by the GUI. Defaults to SCIPION_USER_DATA/logs.", var_type=VarTypes.FOLDER)
 
     SCIPION_LOG_CONFIG = _get('SCIPION_LOG_CONFIG', None,
-    "Optional. Path to a python logging configuration file to fine tune the logging.", var_type=VarTypes.PATH)
+                              "Optional. Path to a python logging configuration file to fine tune the logging.", var_type=VarTypes.PATH)
 
     SCIPION_LOG = _get('SCIPION_LOG', _join(SCIPION_LOGS, 'scipion.log'),
-    "Path to the file where scipion will write GUI logging messages. Defaults to SCIPION_LOGS/scipion.log", var_type=VarTypes.PATH)
+                       "Path to the file where scipion will write GUI logging messages. Defaults to SCIPION_LOGS/scipion.log", var_type=VarTypes.PATH)
 
     SCIPION_LOG_FORMAT = _get('SCIPION_LOG_FORMAT', "%(message)s",
-    "str: Format for all the log lines, defaults to %(message)s. To compose the format see https://docs.python.org/3/library/logging.html#logrecord-attributes")
+                              "str: Format for all the log lines, defaults to %(message)s. To compose the format see https://docs.python.org/3/library/logging.html#logrecord-attributes")
 
     SCIPION_LOG_LEVEL = _get(SCIPION_LOG_LEVEL, 'INFO',
-    "Default logging level. String among CRITICAL, ERROR, WARNING, INFO, DEBUG, NOTSET. Default value is INFO.")
+                             "Default logging level. String among CRITICAL, ERROR, WARNING, INFO, DEBUG, NOTSET. Default value is INFO.")
 
     NO_COLOR = _get('NO_COLOR', '',
-    "str: Comply with https://no-color.org/ initiative. Set it to something different than '' to deactivate colors in the output.")
+                    "str: Comply with https://no-color.org/ initiative. Set it to something different than '' to deactivate colors in the output.")
 
     SCIPION_SCRATCH = _get(SCIPION_SCRATCH, None,
-    "Optional. Path to a location mounted in a scratch drive (SSD,...)")
+                           "Optional. Path to a location mounted in a scratch drive (SSD,...)")
 
     SCIPION_TESTS_OUTPUT = _get('SCIPION_TESTS_OUTPUT', _join(SCIPION_USER_DATA, 'Tests'),
-    "Path to a folder where the output of the tests will be written. Defaults to SCIPION_USER_DATA/Tests.", var_type=VarTypes.FOLDER)
+                                "Path to a folder where the output of the tests will be written. Defaults to SCIPION_USER_DATA/Tests.", var_type=VarTypes.FOLDER)
 
     SCIPION_TEST_NOSYNC = _get('SCIPION_TEST_NOSYNC', FALSE_STR,
-    "Set it to 1, True, Yes or y to cancel test dataset synchronization. Needed when updating files in a dataset.") != FALSE_STR
+                               "Set it to any value except False to cancel test dataset synchronization."
+                               " Needed when updating files in a dataset.", caster=_notFalse)
 
     SCIPION_SUPPORT_EMAIL = 'scipion@cnb.csic.es'
 
     # Config variables
     SCIPION_CONFIG = _get('SCIPION_CONFIG', _join('config','scipion.conf'),
-    "Path to the scipion configuration file where all this variables could be defined.", var_type=VarTypes.PATH)
+                          "Path to the scipion configuration file where all this variables could be defined.", var_type=VarTypes.PATH)
 
     SCIPION_LOCAL_CONFIG = _get('SCIPION_LOCAL_CONFIG', SCIPION_CONFIG,
-    "Path to an optional/extra/user configuration file meant to overwrite default variables.", var_type=VarTypes.PATH)
+                                "Path to an optional/extra/user configuration file meant to overwrite default variables.", var_type=VarTypes.PATH)
 
     SCIPION_HOSTS = _get('SCIPION_HOSTS', _join('config','hosts.conf'),
-    "Path to the host.cof file to allow scipion to use queue engines and run in HPC environments.")
+                         "Path to the host.cof file to allow scipion to use queue engines and run in HPC environments.")
 
     SCIPION_PROTOCOLS = _get('SCIPION_PROTOCOLS', _join('config','protocols.conf'),
-    "Custom conf file to extend the protocols tree view panel (panel on the left)")
+                             "Custom conf file to extend the protocols tree view panel (panel on the left)")
 
     SCIPION_PLUGIN_JSON = _get('SCIPION_PLUGIN_JSON', None,
-    "Optional. Path to get the json file with all the plugins available for Scipion.")
+                               "Optional. Path to get the json file with all the plugins available for Scipion.")
+
+    SCIPION_SITE = _get('SCIPION_SITE', 'https://scipion.i2pc.es',
+                        "Scipion site URL.")
+    SCIPION_SITE_API = SCIPION_SITE + '/report_protocols/api/v2'
+    SCIPION_STATS_WORKFLOW_APP = SCIPION_SITE_API + '/workflow/'
+    SCIPION_STATS_SUGGESTION = SCIPION_SITE_API + '/nextprotocol/suggestion/%s'
 
     SCIPION_PLUGIN_REPO_URL = _get('SCIPION_PLUGIN_REPO_URL',
-                                   'https://scipion.i2pc.es/getplugins/',
-    "Url from where to get the list of plugins.")
+                                   SCIPION_SITE + '/getplugins/',
+                                   "Url from where to get the list of plugins.")
 
     # REMOTE Section
     SCIPION_URL = 'https://scipion.cnb.csic.es/downloads/scipion'
@@ -271,65 +298,69 @@ class Config:
 
     # Scipion Notes
     SCIPION_NOTES_FILE = _get(SCIPION_NOTES_FILE, 'notes.txt',
-    "Name of the file where to write per project notes.")
+                              "Name of the file where to write per project notes.")
 
     SCIPION_NOTES_PROGRAM = _get(SCIPION_NOTES_PROGRAM, None,
-    "Command or program to use to open the notes file. Otherwise system will extension association will take place.")
+                                 "Command or program to use to open the notes file. Otherwise system will extension association will take place.")
 
     SCIPION_NOTES_ARGS = _get(SCIPION_NOTES_ARGS, None)
 
     # External text editor:
     SCIPION_TEXT_EDITOR = _get(SCIPION_TEXT_EDITOR, '',
-    "Preferred text editor executable.", caster=str)
+                               "Preferred text editor executable.", caster=str)
 
     # Aspect
     SCIPION_FONT_NAME = _get('SCIPION_FONT_NAME', "Helvetica",
-    "Name of the font to use in Scipion GUI. Defaults to Helvetica.")
+                             "Name of the font to use in Scipion GUI. Defaults to Helvetica.")
 
-    SCIPION_FONT_SIZE = _get('SCIPION_FONT_SIZE', SCIPION_DEFAULT_FONT_SIZE,
-    "Size of the 'normal' font to be used in Scipion GUI. Defaults to 10.", caster=int)
+    SCIPION_FONT_SIZE = _get('SCIPION_FONT_SIZE', str(SCIPION_DEFAULT_FONT_SIZE),
+                             "Size of the 'normal' font to be used in Scipion GUI. "
+                             "Defaults to 10.", caster=int)
 
     SCIPION_MAIN_COLOR = _get('SCIPION_MAIN_COLOR', Color.MAIN_COLOR,
-    "str: Main color of the GUI. Background will be white, so for better contrast choose a dark color. Probably any name here will work: https://matplotlib.org/stable/gallery/color/named_colors.html",
+                              "str: Main color of the GUI. Background will be white, so for better contrast choose a dark color. Probably any name here will work: https://matplotlib.org/stable/gallery/color/named_colors.html",
                               caster=validColor)
 
     SCIPION_BG_COLOR = _get('SCIPION_BG_COLOR', Color.BG_COLOR,
-    "str: Main background color of the GUI. Default is white, chose a light one. Probably any name here will work: https://matplotlib.org/stable/gallery/color/named_colors.html",
+                            "str: Main background color of the GUI. Default is white, chose a light one. Probably any name here will work: https://matplotlib.org/stable/gallery/color/named_colors.html",
                             validColor)
 
-    SCIPION_CONTRAST_COLOR = _get('SCIPION_CONTRAST_COLOR', 'cyan',
-    "Color used to highlight features over grayscaled images.", caster=validColor)
+    SCIPION_CONTRAST_COLOR = _get('SCIPION_CONTRAST_COLOR', 'cyan', "Color used to highlight features over "
+                                                                    "gray-scaled images.", caster=validColor)
 
     SCIPION_SPRITES_FILE = _get('SCIPION_SPRITES_FILE', __defaultSpritesFile,
-    "File (png) with the icons in a collage. Default is found at pyworkflow/resources/sprites.png. And a GIMP file could be found at the same folder in the github repo.")
+                                "File (png) with the icons in a collage. Default is found at "
+                                "pyworkflow/resources/sprites.png. And a GIMP file could be found at the same "
+                                "folder in the github repo.")
 
-    SCIPION_SHOW_TEXT_IN_TOOLBAR = _get('SCIPION_SHOW_TEXT_IN_TOOLBAR', TRUE_STR,
-    "Define it to anything else except False to show the label of the icons. It will take more space.") == TRUE_STR
+    SCIPION_SHOW_TEXT_IN_TOOLBAR = _get('SCIPION_SHOW_TEXT_IN_TOOLBAR', TRUE_STR, "Define it to anything else except "
+                                                                                  "%s to hide labels. It will take less space." % TRUE_YES_ON_, caster=__bool)
 
-    SCIPION_ICON_ZOOM = _get('SCIPION_ICON_ZOOM', 50,
-    "Define it to anything else except False to show the label of the icons. It will take more space.", var_type=VarTypes.INTEGER, caster=int)
+    SCIPION_ICON_ZOOM = _get('SCIPION_ICON_ZOOM', "50",
+                             "Define it to any integer value(percentage) to increase/decrease the size of the icons.",
+                             var_type=VarTypes.INTEGER, caster=int)
 
     # Notification
-    SCIPION_NOTIFY = _get('SCIPION_NOTIFY', TRUE_STR,
-    "If set to False, Scipion developers will know almost nothing about Scipion usage and will have less information to improve it.") == TRUE_STR
+    SCIPION_NOTIFY = _get('SCIPION_NOTIFY', TRUE_STR, "If set to anything except %s Scipion developers will know "
+                                                      "nothing abut Scipion usage and will have less information to improve it." % TRUE_YES_ON_,
+                          caster=__bool)
 
     # *** Execution variables ***
-    SCIPION_CWD = _get('SCIPION_CWD', os.path.abspath(os.getcwd()),
-    "Directory when scipion was launched")
+    SCIPION_CWD = _get('SCIPION_CWD', os.path.abspath(os.getcwd()), "Directory when scipion was launched")
 
     SCIPION_GUI_REFRESH_IN_THREAD = _get('SCIPION_GUI_REFRESH_IN_THREAD', FALSE_STR,
-    "True to refresh the runs graph with a thread. Unstable.") != FALSE_STR
+                                         "True to refresh the runs graph with a thread. Unstable.") != FALSE_STR
 
     SCIPION_GUI_REFRESH_INITIAL_WAIT = _get("SCIPION_GUI_REFRESH_INITIAL_WAIT", 5,
-    "Seconds to wait after a manual refresh", caster=int)
+                                            "Seconds to wait after a manual refresh", caster=int)
 
     SCIPION_GUI_CANCEL_AUTO_REFRESH = _get("SCIPION_GUI_CANCEL_AUTO_REFRESH",FALSE_STR,
-    "Set it to True to cancel automatic refresh of the runs.") != FALSE_STR
+                                           "Set it to True to cancel automatic refresh of the runs.") != FALSE_STR
 
     # Cancel shutil fast copy. In GPFS, shutil.copy does fail when trying a fastcopy and does not
     # fall back on the slow copy. For legacy reasons None is also False.
     SCIPION_CANCEL_FASTCOPY = _get('SCIPION_CANCEL_FASTCOPY', FALSE_STR,
-    "Cancel fast copy done by shutil (copying files) when it fails. Has happened in GPFS environments. Defaults to False. None is also False otherwise fastcopy is cancelled."
+                                   "Cancel fast copy done by shutil (copying files) when it fails. Has happened in GPFS environments. Defaults to False. None is also False otherwise fastcopy is cancelled."
                                    ) not in [NONE_STR, FALSE_STR]
 
     # Priority package list: This variable is used in the view protocols in
@@ -339,26 +370,40 @@ class Config:
     SCIPION_PRIORITY_PACKAGE_LIST = _get('SCIPION_PRIORITY_PACKAGE_LIST', EMPTY_STR)
 
     SCIPION_STEPS_CHECK_SEC = _get('SCIPION_STEPS_CHECK_SEC', 5,
-    "Number of seconds to wait before checking if new input is available in streamified protocols.", caster=int)
+                                   "Number of seconds to wait before checking if new input is available in "
+                                   "streamified protocols.", caster=int)
 
     SCIPION_UPDATE_SET_ATTEMPTS = _get('SCIPION_UPDATE_SET_ATTEMPTS', 3,
-    "Number of attempts to modify the protocol output before failing. The default value is 3", caster=int)
+                                       "Number of attempts to modify the protocol output before failing. "
+                                       "The default value is 3", caster=int)
 
     SCIPION_UPDATE_SET_ATTEMPT_WAIT = _get('SCIPION_UPDATE_SET_ATTEMPT_WAIT', 2,
-    "Time in seconds to wait until the next attempt when checking new outputs. The default value is 2 seconds", caster=int)
+                                           "Time in seconds to wait until the next attempt when checking new outputs. "
+                                           "The default value is 2 seconds", caster=int)
+
+    SCIPION_UNLOAD_FORM_ON_SAVE = _get('SCIPION_UNLOAD_FORM_ON_SAVE', TRUE_STR,
+                                       "When a protocol is saved it is unloaded if all goes fine. Set it to false "
+                                       "otherwise to rescue old behaviour.", caster=__bool)
 
     SCIPION_USE_QUEUE = _get("SCIPION_USE_QUEUE", FALSE_STR,
-    "Default value for using the queue. By default is False. ANY value will be True except and empty value. \"False\" or \"0\" will be True too.")!= FALSE_STR
+                             "Default value for using the queue. By default is False. "
+                             "ANY value will be True except and empty value. \"False\" or \"0\" "
+                             "will be True too.") != FALSE_STR
 
     SCIPION_DEFAULT_EXECUTION_ACTION = _get('SCIPION_DEFAULT_EXECUTION_ACTION', DEFAULT_EXECUTION_ACTION_ASK,
-    """Ask if you want to launch a single protocol or a sub-workflow. The default value is 1
-       1: Scipion always ask
-       2: Run a single protocol
-       3: Run a sub-workflow """, caster=int)
+                                            """Ask if you want to launch a single protocol or a sub-workflow. The default value is 1
+                                               1: Scipion always ask
+                                               2: Run a single protocol
+                                               3: Run a sub-workflow """, caster=int)
 
     SCIPION_MAPPER_USE_TEMPLATE = _get('SCIPION_MAPPER_USE_TEMPLATE', TRUE_STR,
-    "Set it to False to force instantiation for each item during sets iterations. Experimental. This penalize the iteration but avoids"
-    "the use of .clone() ot the items.") == TRUE_STR
+                                       "Set it to False to force instantiation for each item during sets iterations. Experimental. This penalize the iteration but avoids"
+                                       "the use of .clone() ot the items.") == TRUE_STR
+
+    CUDA_DEVICE_ORDER = _get('CUDA_DEVICE_ORDER', 'PCI_BUS_ID',
+                             "To make GPU ID match what you see in nvidia-smi, that is the PCI ID."
+                             " Use FASTEST_FIRST for default behaviour but this may not match what is returned by nvidia-smi."
+                             " See https://docs.nvidia.com/cuda/cuda-c-programming-guide/#:~:text=in%20device%20memory.-,CUDA_DEVICE_ORDER,-FASTEST_FIRST%2C%20PCI_BUS_ID%2C%20(default ")
 
     try:
         VIEWERS = ast.literal_eval(_get('VIEWERS', "{}", "Json string to define which viewer are the default ones per output type."))
@@ -377,7 +422,8 @@ class Config:
         :return: Folder where libraries must be placed in case a binding needs them
         """
         lib = cls._join(cls.SCIPION_SOFTWARE, 'lib')
-        os.makedirs(lib, exist_ok=True)
+        if cls.SCIPION_HOME_DEFINED:
+            os.makedirs(lib, exist_ok=True)
         return lib
 
     @classmethod
@@ -388,7 +434,8 @@ class Config:
         :return:   The bindings folder
         """
         bindings = cls._join(cls.SCIPION_SOFTWARE, 'bindings')
-        os.makedirs(bindings, exist_ok=True)
+        if cls.SCIPION_HOME_DEFINED:
+            os.makedirs(bindings, exist_ok=True)
         return bindings
 
     @classmethod
@@ -397,7 +444,8 @@ class Config:
         Folder where scipion logs must be placed. The folder is created         
         """
         logsFolder = cls.SCIPION_LOGS
-        os.makedirs(logsFolder, exist_ok=True)
+        if cls.SCIPION_HOME_DEFINED:
+            os.makedirs(logsFolder, exist_ok=True)
         return logsFolder
 
     @classmethod
@@ -455,8 +503,13 @@ class Config:
         debugOn = not Config.debugOn()
         os.environ[SCIPION_DEBUG] = str(debugOn)
         os.environ[SCIPION_DEBUG_NOCLEAN] = str(debugOn)
-        os.environ[SCIPION_LOG_LEVEL] = "INFO" if not debugOn else "DEBUG"
 
+        newLevel = "DEBUG" if debugOn else "INFO"
+        os.environ[SCIPION_LOG_LEVEL] = newLevel
+
+        from pyworkflow.utils import changeLogLevel
+        changeLogLevel(newLevel)
+        logger.info("Log level set to %s" % newLevel)
     @staticmethod
     def debugSQLOn():
         from .utils import envVarOn
@@ -545,6 +598,17 @@ class Config:
             condaExe = os.path.join(envFolder, "bin", "python")
             return condaExe == getPython()
 
+    @classmethod
+    def getEnvName(cls):
+        """ Returns Scipion's environment name(conda or venv)"""
+        if cls.isCondaInstallation():
+            envPath = os.environ['CONDA_PREFIX']
+        else:  # Virtualenv
+            envPath = os.environ['VIRTUAL_ENV']
+
+        return os.path.basename(envPath)
+
+
     @classmethod
     def getSpritesFile(cls):
         if not os.path.exists(Config.SCIPION_SPRITES_FILE):

pyworkflow/constants.py

@@ -43,7 +43,7 @@ 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 = '3.10.5'
+VERSION_3_0 = '3.11.0'
 
 # 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.
@@ -73,6 +73,16 @@ SCIPION_HOME_VAR = 'SCIPION_HOME'
 SCIPION_TESTS = 'SCIPION_TESTS'
 SCIPION_SCRATCH = 'SCIPION_SCRATCH'
 
+# VARIABLE names in host.conf
+PARALLEL_COMMAND_VAR = 'PARALLEL_COMMAND'
+PLUGIN_MODULE_VAR = 'PLUGIN_MODULE'
+QUEUE_FOR_JOBS = 'QUEUE_FOR_JOBS'
+
+
+# Launching constants
+RUN_JOB_GPU_PARAM = 'GPU' # Param name to "place" GPU ids used to build a run command.
+RUN_JOB_GPU_PARAM_SEARCH = "%("+ RUN_JOB_GPU_PARAM +")s"
+
 # FONT
 SCIPION_DEFAULT_FONT_SIZE = 10
 
@@ -131,6 +141,7 @@ PROJECT_SETTINGS = 'settings.sqlite'
 FALSE_STR = str(False)
 TRUE_STR = str(True)
 NONE_STR = str(None)
+TRUE_YES_ON_ = ['true', 'yes', 'on', '1']
 EMPTY_STR = ""
 
 # GUI colors
@@ -215,4 +226,3 @@ DEFAULT_EXECUTION_ACTION_ALL = 3
 # Id field/attribute constants
 ID_COLUMN='id'
 ID_ATTRIBUTE='_objId'
-

pyworkflow/object.py

@@ -1233,12 +1233,13 @@ class Set(Object):
         return self._getMapper().exists(itemId)
 
     def iterItems(self, orderBy='id', direction='ASC', where=None,
-                  limit=None, iterate=True):
+                  limit=None, iterate=True, rowFilter=None):
         return self._getMapper().selectAll(orderBy=orderBy,
                                            direction=direction,
                                            where=where,
                                            limit=limit,
-                                           iterate=iterate)  # has flat mapper, iterate is true
+                                           iterate=iterate,
+                                           rowFilter=rowFilter)  # has flat mapper, iterate is true
 
     def getFirstItem(self):
         """ Return the first item in the Set. """

pyworkflow/plugin.py

@@ -28,6 +28,7 @@
 # **************************************************************************
 import logging
 import sys
+from functools import lru_cache
 
 from pyworkflow import Variable, VariablesRegistry, VarTypes
 from .protocol import Protocol
@@ -79,6 +80,9 @@ class Domain:
     _viewers = {}
     _wizards = {}
 
+    # Preferred viewers:
+    _preferred_viewers = None
+
     @classmethod
     def registerPlugin(cls, name):
         """ Register a new plugin. This function should only be called when
@@ -113,15 +117,17 @@ class Domain:
 
         # Catch any import exception, warn about it but continue.
         except ModuleNotFoundError as e:
+
+            logger.debug("Module %s not found: %s" %(name, e))
             if e.name == name:
                 # This is probably due to a priority package like pwchem not being installed
-                pass
+                logger.debug("Name is different!!: e.name='%s', name='%s'" %( e.name , name))
             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. "
+            logger.info(pwutils.yellow("WARNING!!: Plugin containing module %s does not import properly. "
                                  "All its content will be missing in this execution." % name))
             logger.info("Please, contact developers at %s and send this ugly information below. They'll understand it!." % DOCSITEURLS.CONTACTUS)
             logger.info("Error message: %s"% str(e))
@@ -390,56 +396,99 @@ class Domain:
     @classmethod
     def getPreferredViewers(cls, className):
         """ Find and import the preferred viewers for this class. """
-        viewerNames = pw.Config.VIEWERS.get(className, [])
-        if not isinstance(viewerNames, list):
-            viewerNames = [viewerNames]
-        viewers = []  # we will try to import them and store here
-        for prefViewerStr in viewerNames:
-            try:
-                viewerModule, viewerClassName = prefViewerStr.rsplit('.', 1)
-                prefViewer = cls.importFromPlugin(viewerModule,
-                                                  viewerClassName,
-                                                  doRaise=True)
-                viewers.append(prefViewer)
-            except Exception as e:
-                logger.error("Couldn't load \"%s\" as preferred viewer for %s.\n"
-                      "There might be a typo in your VIEWERS variable "
-                      "or an error in the viewer's plugin installation"
-                      % (prefViewerStr, className), exc_info=e)
-        return viewers
+
+        if cls._preferred_viewers is None:
+            logger.info("Caching preferred viewers from VIEWERS config variable.")
+            cls._preferred_viewers = dict()
+
+            for target, viewerNames in pw.Config.VIEWERS.items():
+                viewers = []
+                for prefViewerStr in viewerNames:
+                    try:
+                        viewerModule, viewerClassName = prefViewerStr.rsplit('.', 1)
+                        prefViewer = cls.importFromPlugin(viewerModule,
+                                                          viewerClassName,
+                                                          doRaise=True)
+                        viewers.append(prefViewer)
+                    except Exception as e:
+                        logger.error("Couldn't load \"%s\" as preferred viewer for %s.\n"
+                              "There might be a typo in your VIEWERS variable "
+                              "or an error in the viewer's plugin installation"
+                              % (prefViewerStr, className), exc_info=e)
+
+                cls._preferred_viewers[target] = viewers
+
+        return cls._preferred_viewers.get(className, [])
 
     @classmethod
-    def findViewers(cls, className, environment):
-        """ Find the available viewers in this Domain for this class. """
+    @lru_cache
+    def getViewersSorted(cls):
+        """ Returns all viewers sorted by its class name"""
+
+        viewers = cls.getViewers()
+        return [viewers[key] for key in sorted(viewers)]
+
+    @classmethod
+    def findViewers(cls, target, environment):
+        """ Find the available viewers in this Domain for this target.
+
+        Sorting criteria:
+
+        1st Will appear those viewers in VIEWERS variable (preferred viewers) in appearance order
+        2nd Viewers targeting specifically the target and not any super class of it
+        3rd rest.
+
+        In 2nd and 3rd case the order viewers are added depends on the alphabetical order the viewer when discovered.
+        This usually matches the viewer class name, but could be fine tune using import aliases like:
+
+        from my_viewer import MyViewer as AAAMyViewer in the viewers folder of the plugin.
+
+        In case viewers is a file and not a folder with an __init__, I'm afraid class name is what is taken into account
+
+        The import order is not possible to use since python sort them automatically.
+
+        """
         viewers = []
         try:
-            clazz = cls.findClass(className)
+            instance = None
+            if isinstance(target, str):
+                logger.warning("DEVELOPERS: pass the instance/object instead of the class. This mode will be deprecated soon")
+                className = target
+                clazz = cls.findClass(className)
+            else:
+                className = target.__class__.__name__
+                clazz = target.__class__
+                instance = target
+
             baseClasses = clazz.mro()
-            preferredViewers = cls.getPreferredViewers(className)
-            preferedFlag = 0
 
-            for viewer in cls.getViewers().values():
-                viewerAdded=False
+            # Add preferred viewers
+            preferred_viewers = []
+            available_preferred_viewers = cls.getPreferredViewers(className)
+            for prefViewer in available_preferred_viewers:
+                if prefViewer.can_handle_this(baseClasses, instance=instance):
+                    preferred_viewers.append(prefViewer)
+
+
+            specific_viewers = []
+            other_viewers=[]
+            # get all the viewers available
+
+            for viewer in cls.getViewersSorted():
+
                 if environment in viewer._environments:
-                    for t in viewer._targets:
-                        if t in baseClasses:
-                            for prefViewer in preferredViewers:
-                                if viewer is prefViewer:
-                                    viewers.insert(0, viewer)
-                                    viewerAdded=True
-                                    preferedFlag = 1
-                                    break
+
+                    if viewer not in preferred_viewers:
+
+                        t = viewer.can_handle_this(baseClasses, target)
+                        if t is not None:
+                            if t == clazz:
+                                specific_viewers.append(viewer)
+
                             else:
-                                if t == clazz:
-                                    viewers.insert(preferedFlag, viewer)
-                                    viewerAdded = True
-                                else:
-                                    viewers.append(viewer)
-                                    viewerAdded = True
-                                break
+                                other_viewers.append(viewer)
 
-                        if viewerAdded:
-                            break
+            viewers = preferred_viewers + specific_viewers + other_viewers
 
         except Exception as e:
             # Catch if there is a missing plugin, we will get Legacy which triggers and Exception
@@ -508,7 +557,7 @@ class Domain:
 
         raiseMsg = "%s\n %s\n%s\n" % (msgStr, calling, hint)
         if doRaise:
-            raise Exception("\n\n" + raiseMsg)
+            raise ImportError("\n\n" + raiseMsg)
         else:
             logger.info(raiseMsg)
 

pyworkflow/project/scripts/fix_links.py

@@ -3,12 +3,15 @@
 import sys
 import os
 import logging
-logging.basicConfig(level="INFO")
 
+from pyworkflow.config import Config
 from pyworkflow.project import Manager
 import pyworkflow.utils as pwutils
 
 
+logging.basicConfig(level=Config.SCIPION_LOG_LEVEL, format=Config.SCIPION_LOG_FORMAT)
+
+
 def usage(error):
     print("""
     ERROR: %s