Merge remote-tracking branch 'origin/master' into explicit-config-opt…

…ions

.appveyor.yml

@@ -0,0 +1,36 @@
+
+#branches:
+#  only:
+#    - master
+
+environment:
+  global:
+      PYTHON: "C:\\miniconda"
+      PYTHON_ARCH: "64" # needs to be set for CMD_IN_ENV to succeed. If a mix
+                        # of 32 bit and 64 bit builds are needed, move this
+                        # to the matrix section.
+
+platform:
+    -x64
+
+install:
+    - "powershell %APPVEYOR_BUILD_FOLDER%\\tools\\setup_conda_windows.ps1"
+    - "SET PATH=%PYTHON%;%PYTHON%\\Scripts;%PATH%"
+    - 'conda env remove --yes --name qudi || exit 0'
+    - "conda env create -f %APPVEYOR_BUILD_FOLDER%\\tools\\conda-env-win8-qt5.yml"
+    - "activate qudi"
+    - "python %APPVEYOR_BUILD_FOLDER%\\tools\\qudikernel.py install"
+
+# Not a .NET project, we build in the install step instead
+build: false
+
+test_script:
+    - sh "%APPVEYOR_BUILD_FOLDER%\\tools\\test.sh"
+
+artifacts:
+  - path: qudi.log
+    name: Qudi log file
+
+  - path: notebooks
+    name: test notebooks
+    type: zip

README.md

@@ -17,7 +17,7 @@ Originally built around a confocal fluorescence microscope experiments, it has g
 
 ## Citation
 If you are publishing scientific results, mentioning Qudi in your methods decscription is the least you can do as good scientific practice.
-A paper about Qudi has been accepted for publication in [SoftwareX](https://www.journals.elsevier.com/softwarex/). Until it is officailly published, you should cite the preprint [arXiv:1611.09146](https://arxiv.org/abs/1611.09146) \[quant-ph\] for this purpose.
+You should cite our paper [Qudi: A modular python suite for experiment control and data processing](http://doi.org/10.1016/j.softx.2017.02.001) for this purpose.
 
 ## Documentation
 User and code documentation about Qudi is located at http://ulm-iqo.github.io/qudi-generated-docs/html-docs/ .

config/example/default.cfg

@@ -112,6 +112,7 @@ logic:
     sequencegeneratorlogic:
         module.Class: 'sequence_generator_logic.SequenceGeneratorLogic'
         #overhead_bytes: 4294967296  Not properly implemented yet
+        #additional_methods_dir: 'C:\\Custom_dir\\Methods' optional
 
     pulseextractionlogic:
         module.Class: 'pulse_extraction_logic.PulseExtractionLogic'

core/__main__.py

@@ -71,6 +71,14 @@
 # define a global variable for the manager
 man = None
 
+# Until here every module is in the python standard library.
+# Check vital packages for qudi, otherwise qudi will not even start.
+from core.util.helpers import import_check
+err_code = import_check()
+
+if err_code != 0:
+    sys.exit(err_code)
+
 
 # install logging facility for Qt errors
 import qtpy
@@ -180,7 +188,7 @@ def setupParentPoller(self, manager):
             self.poller.start()
         else:
             logger.warning('Qudi running unsupervised, restart wiill not work.')
-            
+
 
     def quitProxy(self, obj):
         """ Helper function to emit doQuit signal

core/manager.py

@@ -266,10 +266,10 @@ def readConfig(self, configFile):
         logger.info("Starting Manager configuration from {0}".format(
             configFile))
         cfg = config.load(configFile)
+        self.configFile = configFile
         # Read modules, devices, and stylesheet out of config
         self.configure(cfg)
 
-        self.configFile = configFile
         print("\n============= Manager configuration complete =================\n")
         logger.info('Manager configuration complete.')
 
@@ -326,7 +326,55 @@ def configure(self, cfg):
                 # global config
                 elif key == 'global' and cfg['global'] is not None:
                     for m in cfg['global']:
-                        if m == 'startup':
+                        if (m == 'extensions'):
+                            # deal with str, list and unknown types
+                            if (isinstance(cfg['global'][m], str)):
+                                dirnames = [cfg['global'][m]]
+                            elif (isinstance(cfg['global'][m], list)):
+                                dirnames = cfg['global'][m]
+                            else:
+                                logger.warning('Global ''path'' '
+                                               'configuration is neither str '
+                                               ' nor list. Ignoring.')
+                                continue
+                            # add specified directories
+                            for ii in range(len(dirnames)):
+                                path = ''
+                                # absolute or relative path? Existing?
+                                if (os.path.isabs(dirnames[ii]) and
+                                        os.path.isdir(dirnames[ii])):
+                                    path = dirnames[ii]
+                                else:
+                                    # relative path?
+                                    path = os.path.abspath(
+                                        '{0}/{1}'.format(
+                                            os.path.dirname(self.configFile),
+                                            dirnames[ii]))
+                                    if (not os.path.isdir(path)):
+                                        path = ''
+                                if (path == ''):
+                                    logger.warning(
+                                        'Error while adding qudi '
+                                        'extension: Directory \'{0}\' '
+                                        'does not exist.'
+                                        ''.format(
+                                            cfg['global'][m][ii]))
+                                    continue
+                                # check for __init__.py files within extension
+                                # and issue warning if existing
+                                for paths, dirs, files in os.walk(path):
+                                    if ('__init__.py' in files):
+                                        logger.warning(
+                                            'Warning: Extension {0} contains '
+                                            '__init__.py. Expect unexpected '
+                                            'behaviour. Hope you know what '
+                                            'you are doing.'.format(path))
+                                        break
+                                # add directory to search path
+                                logger.debug('Adding extension path: {0}'
+                                             ''.format(path))
+                                sys.path.insert(1+ii, path)
+                        elif m == 'startup':
                             self.tree['global']['startup'] = cfg[
                                 'global']['startup']
                         elif m == 'stylesheet' and self.hasGui:
@@ -607,9 +655,9 @@ def connectModule(self, base, mkey):
                 destmod = connections[c]
             destbase = ''
             # check if module exists at all
-            if (not destmod in self.tree['loaded']['gui'] and
-                    not destmod in self.tree['loaded']['hardware'] and
-                    not destmod in self.tree['loaded']['logic']):
+            if (destmod not in self.tree['loaded']['gui'] and
+                    destmod not in self.tree['loaded']['hardware'] and
+                    destmod not in self.tree['loaded']['logic']):
                 logger.error('Cannot connect {0}.{1}.{2} to module {3}. '
                              'Module does not exist.'.format(
                              base, mkey, c, destmod))
@@ -1038,7 +1086,7 @@ def startModule(self, base, key):
 
         for mkey in sorteddeps:
             for mbase in ('hardware', 'logic', 'gui'):
-                if mkey in self.tree['defined'][mbase] and not mkey in self.tree['loaded'][mbase]:
+                if mkey in self.tree['defined'][mbase] and mkey not in self.tree['loaded'][mbase]:
                     success = self.loadConfigureModule(mbase, mkey)
                     if success < 0:
                         logger.warning('Stopping module loading after loading failure.')
@@ -1109,7 +1157,7 @@ def restartModuleRecursive(self, base, key):
 
         for mkey in reversed(unloaded_mods):
             mbase = self.findBase(mkey)
-            if mkey in self.tree['defined'][mbase] and not mkey in self.tree['loaded'][mbase]:
+            if mkey in self.tree['defined'][mbase] and mkey not in self.tree['loaded'][mbase]:
                 success = self.loadConfigureModule(mbase, mkey)
                 if success < 0:
                     logger.warning('Stopping loading module {0}.{1} after '

core/util/helpers.py

@@ -34,6 +34,10 @@
 except ImportError:
     pass
 
+import importlib
+import logging
+logger = logging.getLogger(__name__)
+
 # Optional function for exiting immediately (with some manual teardown)
 
 
@@ -77,3 +81,48 @@ def exit(exitcode=0):
         os.closerange(3, 4096)
 
     os._exit(exitcode)
+
+
+
+def import_check():
+    """ Checks whether all the necessary modules are present upon start of qudi.
+    
+    @return: int, error code either 0 or 4.
+    
+    Check also whether some recommended packages exists. Return err_code=0 if
+    all vital packages are installed and err_code=4 if vital packages are
+    missing. Make a warning about missing packages.
+    """
+    err_code = 0
+
+    # encode like: (python-package-name, repository-name)
+    vital_pkg = [('ruamel.yaml','ruamel.yaml'), ('rpyc','rpyc'), ('fysom','fysom')]
+    opt_pkg = [('pyqtgraph','pyqtgraph'), ('git','gitpython')]
+
+    for pkg_name, repo_name in vital_pkg:
+        try:
+            importlib.import_module(pkg_name)
+        except ImportError:
+            logger.error('No Package "{0}" installed! Perform e.g.\n\n'
+                         '    pip install {1}\n\n'
+                         'in the console to install the missing package.'.format(pkg_name, repo_name))
+            err_code = err_code | 4
+
+    try:
+        from qtpy.QtCore import Qt
+    except ImportError:
+        logger.error('No Qt bindungs detected! Perform e.g.\n\n'
+                     '    pip install PyQt5\n\n'
+                     'in the console to install the missing package.')
+        err_code = err_code | 4
+
+    for pkg_name, repo_name in opt_pkg:
+        try:
+            importlib.import_module(pkg_name)
+        except ImportError:
+            logger.warning('No Package "{0}" installed! It is recommended to '
+                           'have this package installed. Perform e.g.\n\n'
+                           '    pip install {1}\n\n'
+                           'in the console to install the missing package.'.format(pkg_name, repo_name))
+
+    return err_code

documentation/changelog.md

@@ -1,5 +1,62 @@
 # Changelog {#changelog}
 
+## Release 0.8
+
+Released on 2 Mar 2017.
+Available at https://github.com/Ulm-IQO/qudi/releases/tag/v0.8
+
+Caution: fits need to be configured in the respective settings dialog and
+may not include printed results or may be just broken.
+If you find a defective fit, consider fixing it and submitting a pull request.
+
+Changes/New features:
+
+ * The Qudi paper was published: http://doi.org/10.1016/j.softx.2017.02.001
+ * Move everything to Qt5 only (no more Qt4 support) and pyqtgraph 0.10.0
+ * Re-usable/configurable fit GUI components
+ * Scienific notation input for PID GUI
+ * Support for [Extensions](@ref extensions) (out-of-tree modules) 
+ * Removed the fysom event parameter (usually called e) from on_activae and on_deactivate functions
+ * Swabian Instruments TimeTagger / PulseStreamer hardware modules
+ * Much faster savelogic
+ * Remove 'Out' connectors, connection is now by module name only
+ * Pulse analysis supports multiple methods
+ * Predefined pulse sequences can now be imported from a custom path 
+ (in addition to /logic/predefined_methods)
+ * Module loading and unloading now definitely happens in the correct order
+ * Locked modules are only deactivated after prompting the user
+
+Config changes:
+ * New optional parameter "additional_methods_dir" for SequenceGeneratorLogic
+ * No more 'Out' connectors:
+
+ Old style, produces lots of warnings:
+
+ logic:
+    counter:
+        module.Class: 'counter_logic.CounterLogic'
+        connect:
+            counter1: 'mynicard.counter'
+            savelogic: 'savelogic.savelogic'
+    save:
+        module.Class: 'save_logic.SaveLogic'
+        win_data_directory: 'C:/Data'
+        unix_data_directory: 'Data/'
+
+ New style:
+
+ logic:
+    counter:
+        module.Class: 'counter_logic.CounterLogic'
+        connect:
+            counter1: 'mynicard'
+            savelogic: 'save'
+    save:
+        module.Class: 'save_logic.SaveLogic'
+        win_data_directory: 'C:/Data'
+        unix_data_directory: 'Data/'
+
+
 ## Release 0.7
 
 Released on 01 Feb 2017.