fix issue with parsing explicit edge lists for edge group definition;…

… now brackets must be used rather than parentheses to define edges

docs/configfile.md

@@ -77,9 +77,9 @@ title: Tabnetviz configuration options
       An arbitrary number of further node groups can be defined. When a group is defined, it is added to the node table as a Boolean column so it can be used in the definition of subsequent groups. For this reason, node group names cannot be identical to existing node table column names.
 * **edgegroups:**\
   Groups of edges can be defined; optional.
-    * _**groupname: columnexpression**_ | **[(_source1, target1_), (_source2, target2_), ...]**\
-      Edge group name and a Boolean expression to define the edge group, or an explicit edge list. The expression can use edge table column names and simple numerical or string operations on them. Examples: `myedgegroup1: abs(c) > 3`, `myedgegroup2: interaction.str.lower() >= 'p'`.  Edges can also be explicitly listed by listing **(_source, target_)** pairs, e.g. `[(node1, node23), (node45, node57)]`
-    * _**groupname: columnexpression**_ | **[(_source1, target1_), (_source2, target2_), ...]**\
+    * _**groupname: columnexpression**_ | **[[_source1, target1_], [_source2, target2_], ...]**\
+      Edge group name and a Boolean expression to define the edge group, or an explicit edge list. The expression can use edge table column names and simple numerical or string operations on them. Examples: `myedgegroup1: abs(c) > 3`, `myedgegroup2: interaction.str.lower() >= 'p'`.  Edges can also be explicitly listed by listing **[_source, target_]** pairs, e.g. `[[node1, node23], [node45, node57]]`
+    * _**groupname: columnexpression**_ | **[[_source1, target1_], [_source2, target2_], ...]**\
       An arbitrary number of further edge groups can be defined. When a group is defined, it is added to the edge table as a Boolean column so it can be used in the definition of subsequent groups. For this reason, edge group names cannot be identical to existing edge table column names.
 * **clusters:** **_nodegroup1_** | **[_nodegroup1, nodegroup2, ..._]**\
   Define clusters as node groups (simple form without style specifications). Node groups should be listed in brackets (which can be omitted if there is only one cluster). The **dot** and **fdp** layout algorithms will draw a box around the nodes belonging to a cluster. Only node groups defined above under the **nodegroups** keyword can be used. If you simply list the node groups corresponding to clusters, they will be drawn with the default cluster styles. Otherwise, you can specify styles for each cluster, see below.

docs/userguide.md

@@ -346,8 +346,8 @@ Boolean table column defining the group than to list it in the
 tabnetviz configuration file. A node list is a comma-separated list of
 node names (space after the comma is necessary!) in square brackets:
 `[node1, node23, node57]`. An edge list is specified by providing a
-list of **(source, target)** pairs, e.g `[(node1, node3), (node5,
-node7), (node8, node13)]`.
+list of **[source, target]** pairs, e.g `[[node1, node3], [node5,
+node7], [node8, node13]]`.
 
 Groups are added to the node/edge table as new Boolean columns. As
 group definitions are processed in the order they appear in the

setup.py

@@ -6,7 +6,7 @@
 
 setup(
   name='tabnetviz',
-  version='1.2',
+  version='1.3',
   description='Table-based network visualizer',
   long_description=README,
   long_description_content_type='text/markdown',

tabnetviz/__init__.py

@@ -5,9 +5,9 @@
 # See https://www.gnu.org/licenses/gpl-3.0.html
 
 __author__ = "Andras Szilagyi"
-__copyright__ = "Copyright 2023 Andras Szilagyi"
+__copyright__ = "Copyright 2024 Andras Szilagyi"
 __license__ = "GPLv3"
-__version__ = "1.2"
+__version__ = "1.3"
 __maintainer__ = "Andras Szilagyi"
 __email__ = "[email protected]"
 __status__ = "Production"

tabnetviz/__main__.py

@@ -379,7 +379,7 @@ def table2net(args):
                 edgetab[egname] = edgetab.eval(groupdef, engine='python')
             elif type(groupdef) == list: # explicit edge list given
                 edges = list(zip(edgetab[sourcecolumn], edgetab[targetcolumn]))
-                ES = set(groupdef)
+                ES = set(tuple(e) for e in groupdef)
                 U = ES-set(edges)
                 if U: # there are unknown edges given
                     raise ValueError('unknown edges specified in edge group definition: '+str(U))

tabnetviz/configtemplate.py

@@ -62,12 +62,14 @@
 nodegroups:                # optional; define node groups using boolean queries
   group1: expr1            # node group name: boolean expression with node table column names
   group2: expr2          
+  group3: [node1, node2, node3] # explicit node list
 #
 # Define edge groups
 #
 edgegroups:                # optional; define edge groups using boolean queries
   group1: expr1            # edge group name: expression with edge table column names as query
   group2: expr2
+  group3: [[node1, node2], [node3, node4]] # explicit edge list
 #
 # Define clusters (note: layout must be dot or fdp)
 # (clusters are node groups with a box drawn around them)