An error in line 2655 refers to this part of the code in flowmapper.py
#SaveDirectory = os.path.realpath(SaveShpName)
SaveDirectory = SaveShpName
flowpyv07.shapefilemaker(FlowType,CreateShpNodes,IncludeNodeNames,str(SaveDirectory), str(SaveShpName),str(SaveShpNameNodes),str(InputMatrixName),str(InputNodesName),str(InputNodeNamesName),str(combotext))
and it appears because SaveShpName
was incorrectly initialized in flowpyv07.py via the function
def shapefilemaker(typeofcalculation,CreateShpNodes,IncludeNodeNames,fulldirectorystring,outputfilename,outputfilenamenodes,fulldirODinput,fulldirPTinput,fulldirPTNamesinput,combotext):
where some(or all) variables fulldirODinput,fulldirPTinput,fulldirPTNamesinput
can not be created with a built-in function open(filename, 'r')
probably due to issues in the input file content or a path to each of them.
So, there are several solutions I may suggest:
A short-time solution
I could get the desired flows in QGIS Wien 2.8.9, see image below.

When I opened your initial file "stud-steden-matrix.txt"
in Notepad++ I see this

but when I open the same file in simple Windows's Notepad the result is different

So, all text files have to be formatted appropriately.
This is a FlowMapper's working window:

A long-time solution
I assume that the Plugin's developer (@cempro) will highly appreciate if you can assist with FlowMapper Plugin migration to QGIS 3.
Using a Virtual Layer, implementation was described in this article.
Setting a new workflow for QGIS 3 and putting as a possible solution here. For instance, I just implemented a workflow with native QGIS tools.
Import a text file with points

Generating all possible line connections between all points, you can use one of the possible approach described in this thread.
For example, I used solution with a Virtual Layer with the following query
select a.id || '_' || b.id as keyf, a.id as fromp, b.id as top, makeline(a.geometry, b.geometry) as geometry
from "stud-steden-locaties" a, "stud-steden-locaties" b
where a.id <> b.id
Note: Here I created a special field with a.id || '_' || b.id
this will play a key role in joining attributes from "stud-steden-matrix-list.csv"

Drag&Drop "stud-steden-matrix-list.csv"
into QGIS and apply a simple join between lines and .csv
-file.

Apply some visualization techniques to get flows, see image below

It is possibly a complicated solution, so you may find a smarter one.
References: