Merge pull request #77 from AdriaanRol/develop

PR for release 0.3.5 - Included call funtion kwargs (#75, PR by @jorgemfm27 ) - Fixed networkx 2.x compatibility issues #73. - Updated example notebook. - Made SVG file location a property of the graph to solve a bug caused by reading and writing files. - updated version tag to 0.3.5. - Fixed a bug that caused the PyPI shield to show the wrong version.
AdriaanRol · Aug 12, 2020 · 93efb54 · 93efb54
2 parents 36d3ac3 + dd08a4e
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diff --git a/README.md b/README.md
@@ -1,12 +1,12 @@
-# AutoDepGraph 
+# AutoDepGraph
 
-[![PyPI](https://img.shields.io/pypi/v/adaptive.svg)](https://pypi.python.org/pypi/autodepgraph)
+[![PyPI](https://img.shields.io/pypi/v/autodepgraph.svg)](https://pypi.python.org/pypi/autodepgraph)
 [![Build Status](https://travis-ci.org/AdriaanRol/AutoDepGraph.svg?branch=master)](https://travis-ci.org/AdriaanRol/AutoDepGraph)
-[![Codacy Badge](https://api.codacy.com/project/badge/Grade/ae46c58617ff45df9ac98446b3dc34ac)](https://www.codacy.com/app/adriaan-rol/AutoDepGraph?utm_source=github.com&amp;utm_medium=referral&amp;utm_content=AdriaanRol/AutoDepGraph&amp;utm_campaign=Badge_Grade) 
+[![Codacy Badge](https://api.codacy.com/project/badge/Grade/ae46c58617ff45df9ac98446b3dc34ac)](https://www.codacy.com/app/adriaan-rol/AutoDepGraph?utm_source=github.com&amp;utm_medium=referral&amp;utm_content=AdriaanRol/AutoDepGraph&amp;utm_campaign=Badge_Grade)
 [![Coverage Status](https://coveralls.io/repos/github/AdriaanRol/AutoDepGraph/badge.svg?branch=master)](https://coveralls.io/github/AdriaanRol/AutoDepGraph?branch=master)
 [![DOI](https://zenodo.org/badge/85987885.svg)](https://zenodo.org/badge/latestdoi/85987885)
 
-AutoDepGraph is a framework for using dependency graphs to calibrate a system. It is heavily inspired by ["Physical qubit calibration on a directed acyclic graph"](https://arxiv.org/abs/1803.03226). 
+AutoDepGraph is a framework for using dependency graphs to calibrate a system. It is heavily inspired by ["Physical qubit calibration on a directed acyclic graph"](https://arxiv.org/abs/1803.03226).
 
 ## Overview
 AutoDepGraph consists of two main classes, the CalibrationNode and the Graph.
@@ -21,11 +21,11 @@ A CalibrationNode contains:
         + Bad (red): calibration or check has failed
         + unknown (grayed): checks of the node should be run
         + active (blue): calibration or check in progress
-    - parents: the nodes it depends on 
+    - parents: the nodes it depends on
     - children: nodes that depend on this node
     - check_function : name of function to be executed when check is called. This can be a method of another instrument.
     - calibrate_function : name of function to be executed when calibrate is called. This can be a method of another instrument.
-    - calibration_timeout: time in (s) after which a calibration times out. 
+    - calibration_timeout: time in (s) after which a calibration times out.
 
 - function
     - execute or call
@@ -35,8 +35,8 @@ A CalibrationNode contains:
     - calibrate
         + Executes the calibration routines of the node
 
-A Graph is a container of nodes, it is used for: 
-- new graphs can be created by instantiating a graph and then using the add_node method to define new nodes. 
+A Graph is a container of nodes, it is used for:
+- new graphs can be created by instantiating a graph and then using the add_node method to define new nodes.
 - loading and saving the graph
 - real-time visualization using pyqtgraph
     - state of the node determines color of a node
@@ -45,7 +45,7 @@ A Graph is a container of nodes, it is used for:
 
 ![Example calibration graph](docs/example_graph.png)
 
-## Examples 
+## Examples
 For an introductory example see the example notebook. If you want to see how to use a specific function, see the tests located in the autodepgraph/tests folder.
 
 ## Installation
@@ -54,8 +54,8 @@ For an introductory example see the example notebook. If you want to see how to
 - navigate to the repository and run `pip install -e .`
 - verify success of installation by running `py.test`
 
-#### N.B. windows can be "problematic" 
-Installation on windows is a bit more difficult, this relates mostly to the installation of pygraphviz. To install graphviz and pygraphviz on windows follow these steps: 
+#### N.B. windows can be "problematic"
+Installation on windows is a bit more difficult, this relates mostly to the installation of pygraphviz. To install graphviz and pygraphviz on windows follow these steps:
 
 - get the 64 bit version of ![graphviz for windows](https://github.com/mahkoCosmo/GraphViz_x64/), copy it to e.g., program files and add the bin folder to the system path.
 - the 64 bit version lacks the libxml2.dll, you most likely have this from some other program. You can find this by searching for `libxml2.dll` in the program files folder. After that just copy paste it to the bin folder of graphviz.
@@ -69,4 +69,4 @@ python setup.py install --include-path="C:\Program Files\graphviz-2.38_x64\inclu
 - then install autodepgraph and test the installation using `py.test`
 
 ## Acknowledgements
-I would like to thank Julian Kelly for the idea of using a dependency graph for calibrations and for early discussions. I would like to thank Joe Weston for discussions and help in working out the initial design. I would like to acknowledge Livio Ciorciaro for disucssions and as a coauthor of this project. 
+I would like to thank Julian Kelly for the idea of using a dependency graph for calibrations and for early discussions. I would like to thank Joe Weston for discussions and help in working out the initial design. I would like to acknowledge Livio Ciorciaro for disucssions and as a coauthor of this project.
diff --git a/autodepgraph/graph.py b/autodepgraph/graph.py
@@ -26,12 +26,12 @@
 
 class AutoDepGraph_DAG(nx.DiGraph):
     """
-    
+
     Attributes:
         node_states: Allowed states for the nodes
         matplotlib_edge_properties: Properties passed to networkx plotting of edges
         matplotlib_label_properties: Properties passed to networkx plotting of labels
-        
+
     """
     node_states : List[str] = ['good', 'needs calibration',
                          'bad', 'unknown', 'active']
@@ -52,9 +52,6 @@ def __init__(self, name, cfg_plot_mode='svg',
         self.cfg_plot_mode = cfg_plot_mode
         self.cfg_plot_mode_args = {'fig': None}
 
-        _path_name = split(__file__)[:-1][0]
-        self.cfg_svg_filename = join(_path_name, 'svg_viewer', 'adg_graph.svg')
-
         super().__init__(incoming_graph_data, **attr)
 
         # internal attributes
@@ -66,7 +63,15 @@ def __init__(self, name, cfg_plot_mode='svg',
         self._exec_cnt = 0
         self._calib_cnt = 0
         self._check_cnt = 0
-
+
+
+    @property
+    def cfg_svg_filename(self):
+        """
+        Default location for storing svg based visualizations of the DAG.
+        """
+        _path_name = split(__file__)[:-1][0]
+        return join(_path_name, 'svg_viewer', 'adg_graph.svg')
 
     def fresh_copy(self):
         return AutoDepGraph_DAG(name=self.name,
@@ -96,9 +101,6 @@ def add_node(self, node_for_adding, **attr):
             'autodepgraph.node_functions.calibration_functions' +
             '.NotImplementedCalibration')
 
-        attr.setdefault('calibrate_function_kwargs', {})
-            'calibrate_function_kwargs', {})
-
         attr['check_function'] = attr.get(
             'check_function',
             'autodepgraph.node_functions.check_functions' +
@@ -283,10 +285,8 @@ def calibrate_node(self, node : str, verbose : bool =False):
         self.set_node_state(node, 'active')
 
         func = _get_function(self.nodes[node]['calibrate_function'])
-        func_kwargs = self.nodes[node]['calibrate_function_kwargs']
-
         try:
-            result = func(**func_kwargs)
+            result = func()
         except Exception as e:
             self.set_node_state(node, 'bad')
             logging.warning(e)
@@ -311,8 +311,6 @@ def set_all_node_states(self, state):
     def update_monitor(self):
         if self.cfg_plot_mode == 'matplotlib':
             self.update_monitor_mpl()
-        # elif self.cfg_plot_mode == 'pyqtgraph':
-        #     self.draw_pg()
         elif self.cfg_plot_mode == 'svg':
             self.draw_svg()
         elif self.cfg_plot_mode is None or self.cfg_plot_mode == 'None':
@@ -337,8 +335,7 @@ def _generate_node_positions(self, node_positions : Optional[dict] = None):
         nodes=self.nodes()
 
         if node_positions is None:
-            node_positions = {}             
-
+            node_positions = {}
         def position_generator(N=10, centre=[0,5]):
             """ Generate circle of positions around centre """
             idx=0
@@ -350,9 +347,8 @@ def position_generator(N=10, centre=[0,5]):
 
         positions=position_generator(len(nodes))
         pos=dict([ (node, node_positions.get(node, next(positions)) ) for node in nodes] )
-        return pos        
-
-
+        return pos
+
     def draw_mpl(self, ax=None):
         if ax is None:
             f, ax = plt.subplots()
@@ -376,17 +372,6 @@ def _format_mpl_plot(ax):
         ax.set_xticks([])
         ax.set_yticks([])
 
-    # def draw_pg(self, DiGraphWindow=None):
-    #     """
-    #     draws the graph using an interactive pyqtgraph window
-    #     """
-    #     if DiGraphWindow is None:
-    #         DiGraphWindow = self._DiGraphWindow
-    #     self._DiGraphWindow = vis.draw_graph_pyqt(
-    #         self, DiGraphWindow=DiGraphWindow,
-    #         window_title=self.name)
-    #     return self._DiGraphWindow
-
     def draw_svg(self, filename: str=None):
         """
         """
@@ -446,7 +431,7 @@ def set_node_description(self, node, description):
 
     def calibration_state(self):
         """ Return dictionary with current calibration state """
-        return dict(self.node)
+        return dict(self.nodes)
 
     def _update_drawing_attrs(self):
         for node_name, node_attrs in self.nodes(True):