Fixed documentation

Doc/README.md

@@ -9,9 +9,9 @@ Then, all of the elements from within SignalIntegrity are accessible using si as
 
     si.dev.CurrentAmplifier()
 
-All of the namespaces for these packages are listed at [Packages](http://teledynelecroy.github.io/SignalIntegrity/Doc/xhtml/namespaces.xhtml).
+All of the namespaces for these packages are listed at [Packages](http://nubis-communications.github.io/SignalIntegrity/Doc/xhtml/namespaces.xhtml).
 
-All of the classes available to you are located at [Class List](http://teledynelecroy.github.io/SignalIntegrity/Doc/xhtml/annotated.xhtml) along with the [Class Hierarchy](http://teledynelecroy.github.io/SignalIntegrity/Doc/xhtml/inherits.xhtml).
+All of the classes available to you are located at [Class List](http://nubis-communications.github.io/SignalIntegrity/Doc/xhtml/annotated.xhtml) along with the [Class Hierarchy](http://nubis-communications.github.io/SignalIntegrity/Doc/xhtml/inherits.xhtml).
 
 The table of codes corresponding to each namespace is:
 
@@ -51,7 +51,7 @@ si.wl | SignalIntegrity.Lib.Wavelets | Wavelets
 The package documentation is generated using a tool called [Doxygen](http://www.doxygen.nl/).
 Unfortunately, Doxygen is a tool made for C++ and Java and is not perfect for Python.  I chose it originally because it is capable of creating [LaTeX](https://www.latex-project.org/) documentation that was originally intended with my book - that idea was abandoned.  But still, it produces a very good documentation system.
 
-When properly set up, it is invoked from the [Doc](https://github.com/TeledyneLeCroy/SignalIntegrity/tree/master/Doc) directory using:
+When properly set up, it is invoked from the [Doc](https://github.com/Nubis-Communications/SignalIntegrity/tree/master/Doc) directory using:
 
     doxygen SignalIntegrityWindows
 
@@ -64,7 +64,7 @@ or:
 
 depending on which platform you're on.
 
-This uses the configuration provided in the [SignalIntegrityWindows](https://github.com/TeledyneLeCroy/SignalIntegrity/tree/master/Doc/SignalIntegrityWindows) or [SignalIntegrityLinux](https://github.com/TeledyneLeCroy/SignalIntegrity/tree/master/Doc/SignalIntegrityLinux) configuration file and creates a directory called xhtml with the web documentation.  Both need to use a hack of [doxypy.py](https://github.com/TeledyneLeCroy/SignalIntegrity/tree/master/Doc/doxypy.py) that strips the triple quoted header required at the top of each Python file prior to processing.  This filter is specified in the [SignalIntegrityLinux](https://github.com/TeledyneLeCroy/SignalIntegrity/tree/master/Doc/SignalIntegrityLinux) as:
+This uses the configuration provided in the [SignalIntegrityWindows](https://github.com/Nubis-Communications/SignalIntegrity/tree/master/Doc/SignalIntegrityWindows) or [SignalIntegrityLinux](https://github.com/Nubis-Communications/SignalIntegrity/tree/master/Doc/SignalIntegrityLinux) configuration file and creates a directory called xhtml with the web documentation.  Both need to use a hack of [doxypy.py](https://github.com/Nubis-Communications/SignalIntegrity/tree/master/Doc/doxypy.py) that strips the triple quoted header required at the top of each Python file prior to processing.  This filter is specified in the [SignalIntegrityLinux](https://github.com/Nubis-Communications/SignalIntegrity/tree/master/Doc/SignalIntegrityLinux) as:
 
     # The INPUT_FILTER tag can be used to specify a program that doxygen should
     # invoke to filter for each input file. Doxygen will invoke the filter program
@@ -89,11 +89,11 @@ This uses the configuration provided in the [SignalIntegrityWindows](https://git
 
 Usually, Doxygen can find the hacked doxypy.py in the /SignalIntegrity/Doc/ directory - if it can't you might need to specify the path to this file directly.
 
-In [SignalIntegrityWindows](https://github.com/TeledyneLeCroy/SignalIntegrity/tree/master/Doc/SignalIntegrityWindows) this needs to be specified as:
+In [SignalIntegrityWindows](https://github.com/Nubis-Communications/SignalIntegrity/tree/master/Doc/SignalIntegrityWindows) this needs to be specified as:
 
     INPUT_FILTER           = doxypy.bat
 
-Which uses the local [doxypy.bat](https://github.com/TeledyneLeCroy/SignalIntegrity/tree/master/Doc/doxypy.bat), which simply calls the input filter file.
+Which uses the local [doxypy.bat](https://github.com/Nubis-Communications/SignalIntegrity/tree/master/Doc/doxypy.bat), which simply calls the input filter file.
 
 In order to render any equations in the documentation, you must have [GhostScript](https://www.ghostscript.com/download/gsdnld.html) installed.
 

SignalIntegrity/Lib/Devices/TLineTwoPortCOM.py

@@ -29,7 +29,7 @@ def TLineTwoPortCOM(f,gamma_0,a_1,a_2,tau,Zc,d,Z0=50.):
     @param a_1 float transmission line parameter in units sqrt(ns)/mm
     @param a_2 float transmission line parameter in units ns/mm
     @param tau float transmission line parameter in units ns/mm
-    @param Z_c float differential mode characterisitic impedance in units of ohms
+    @param Zc float differential mode characterisitic impedance in units of ohms
     @param d float length in units mm 
     @param Z0 (optional) float or complex reference impedance Z0 (defaults to 50 ohms).
     @return the s-parameter matrix of a COM defined two-port transmission line  

SignalIntegrity/Lib/Eye/EyeDiagramBitmap.py

@@ -123,7 +123,7 @@ def __init__(self,callback=None,
                  EnhancementSteps=10, # ignored unless EnhancementMode is Fixed
                  BitsPerSymbol=1, # 1 for NRZ, 2 for PAM-4  (3 for PAM-8!?)
                  recover_clock=False, # whether to recover the clock
-                 clock_recovery_trim_left_right=20 # points to trim from left and right of resampled, clock recovered waveform
+                 clock_recovery_trim_left_right=20 # points to trim from left and right
                  ):
         """Constructor
         Attempts to generate an eye diagram bitmap from the definition provided.  The bitmap generated here is

SignalIntegrity/Lib/Measurement/CalKit/Standards/Offset.py

@@ -36,6 +36,7 @@ def __init__(self,fList,offsetDelay,offsetZ0,offsetLoss,f0=1e9,Z0=50.):
         @param offsetZ0 (optional) float real characteristic impedance of offset (defaults to 50 ohms)
         @param offsetLoss (optional) float loss due to skin-effect defined in ohms/s at f0 (defaults to 0).
         @param f0 (optional) float frequency where the offset loss is defined (defaults to 1e9).
+        @param Z0 float (optional, defaults to 50.) reference impedance for the calculation.
         The result is that the class becomes the base-class SParameters with the s-parameters
         of an offset, which is a common portion of a calibration standard.
         """

SignalIntegrity/Lib/Measurement/CalKit/Standards/ThruStandard.py

@@ -31,6 +31,7 @@ def __init__(self,f,offsetDelay=0.0,offsetZ0=50.0,offsetLoss=0.0,f0=1e9,Z0=50.):
         @param offsetZ0 (optional) float real characteristic impedance of offset (defaults to 50 ohms)
         @param offsetLoss (optional) float loss due to skin-effect defined in ohms/s at f0 (defaults to 0).
         @param f0 (optional) float frequency where the offset loss is defined (defaults to 1e9).
+        @param Z0 float (optional, defaults to 50.) reference impedance for the calculation.
         The result is that the class becomes the base-class SParameters with the s-parameters
         of a thru standard."""
         Offset.__init__(self,f,offsetDelay,offsetZ0,offsetLoss,f0,Z0=50.)

SignalIntegrity/Lib/Parsers/Devices/DeviceParser.py

@@ -264,14 +264,20 @@ def MakeDevice(self,ports,callback, argsList, f, Z0=50.):
         of the class SParameters.  Otherwise, they are list of list matrices.
 
         @param ports integer number of ports
+        @param callback function ptr (optional, defaults to None) callback function.
         @param argsList list of arguments.  The name of the device is the first argument.
         If the device has no keyword for the argument, then that argument is next.  Otherwise, besides
         the name and the argument with no keyword, the remaining arguments come in keyword/value pairs where the
         keyword is a string and the value is the value of the keyword.
         @param f list of frequencies
         @param Z0 float (optional, defaults to 50.) reference impedance for the calculation
         @return boolean whether the device was created.
-        @throw SignalIntegrityExceptionDeviceParser if the device cannot be created.
+        @throw SignalIntegrityExceptionDeviceParser if the device cannot be created.  
+
+        The callback function is used to pass down into s-parameter files that are actually
+        SignalIntegrity projects so that progress can be tracked and the UI thread can be kept
+        updated.  The callback function should have a signature like Callback(self,number,name=None),
+        where the number is the progress in percent and the name is the name of the file being processed. 
         """
         # pragma: silent exclude
         from SignalIntegrity.Lib.SParameters import SParameterFile

SignalIntegrity/Lib/SParameters/Devices/TLineTwoPortCOM.py

@@ -31,7 +31,7 @@ def __init__(self,f,gamma_0,a_1,a_2,tau,Zc,d,Z0=50.):
         @param a_1 float transmission line parameter in units sqrt(ns)/mm
         @param a_2 float transmission line parameter in units ns/mm
         @param tau float transmission line parameter in units ns/mm
-        @param Z_c float differential mode characterisitic impedance in units of ohms
+        @param Zc float differential mode characterisitic impedance in units of ohms
         @param d float length in units mm 
         @param Z0 (optional) float or complex reference impedance Z0 (defaults to 50 ohms).
         @return the s-parameter matrix of a COM defined two-port transmission line  

Test/TestSignalIntegrity/TestProbeOnOff/ProbeCircuit.si

@@ -518,6 +518,7 @@
 						</Bathtub>
 						<ClockRecovery>
 							<Recover>False</Recover>
+							<TrimLeftRight>20</TrimLeftRight>
 						</ClockRecovery>
 						<Color>#f8f59a</Color>
 						<Columns>100</Columns>
@@ -649,6 +650,7 @@
 						</Bathtub>
 						<ClockRecovery>
 							<Recover>False</Recover>
+							<TrimLeftRight>20</TrimLeftRight>
 						</ClockRecovery>
 						<Color>#f8f59a</Color>
 						<Columns>100</Columns>
@@ -780,6 +782,7 @@
 						</Bathtub>
 						<ClockRecovery>
 							<Recover>False</Recover>
+							<TrimLeftRight>20</TrimLeftRight>
 						</ClockRecovery>
 						<Color>#f8f59a</Color>
 						<Columns>200</Columns>