# Looking for support for adding new features of clustering algorithms in python-igraph **URL:** \ **Category:** Development\ **Tags:** Python\ **Created:** [30 October 2020 22:48 UTC](https://igraph.discourse.group/t/looking-for-support-for-adding-new-features-of-clustering-algorithms-in-python-igraph/498 "2020-10-30T22:48:10Z")\ **Posts on this page:** 10\ **Page:** 1
**Author:** ![Sofia](https://avatars.discourse-cdn.com/v4/letter/s/35a633/32.png) [@Sofia](https://igraph.discourse.group/u/Sofia)\ **Post date:** [30 October 2020 22:48 UTC](https://igraph.discourse.group/t/looking-for-support-for-adding-new-features-of-clustering-algorithms-in-python-igraph/498/1 "2020-10-30T22:48:10Z")
Dear all, I am currently implementing new features based on an existing clustering algorithm in python-igraph. As I want to test and compare with original algorithm, I have to modify the python-igraph package. I have added new c++ clustering function in vender/source/igraph/src and in vendor/source/igraph/include/igraph\_community.h, but I am having problems with the graphobject.c file by adding new clustering function there. Can I get any help regarding to wrapping c++ files into python-igraph package and any other files are linking python object with igraph object besides graphobject.c? Thank you very much in advance. Sofia ---
**Author:** ![vtraag](https://yyz2.discourse-cdn.com/free1/user_avatar/igraph.discourse.group/vtraag/32/38_2.png) [@vtraag](https://igraph.discourse.group/u/vtraag)\ **Post date:** [31 October 2020 09:39 UTC](https://igraph.discourse.group/t/looking-for-support-for-adding-new-features-of-clustering-algorithms-in-python-igraph/498/2 "2020-10-31T09:39:15Z")
In principle you could copy and edit other clustering functions in `graphobject.c`. is there anything specific that is unclear in this file? Note that new functions should also be included in the header. Finally, functions are exposed in the actual graph object in ` __init__.py`. ---
**Author:** ![Sofia](https://avatars.discourse-cdn.com/v4/letter/s/35a633/32.png) [@Sofia](https://igraph.discourse.group/u/Sofia)\ **Post date:** [3 November 2020 12:45 UTC](https://igraph.discourse.group/t/looking-for-support-for-adding-new-features-of-clustering-algorithms-in-python-igraph/498/4 "2020-11-03T12:45:24Z")
Thank you for your answer vtraag. My question is not so clearly to the problem that I face with, one issue is that I have a `PyObject *a = Py_False` (a can be taken as `False` or `True` in Python function) and I want to change it into a `igraph_bool_t` object in `graphobject.c`, I don’t know how I can change `Py_False`/`Py_True` objects into `igraph_bool_t`; another issue is that when the python function takes `None` as an input as a `ATTRIBUTE_TYPE_VERTEX`, then I got the error ```auto python3: ../../../source/igraph/src/vector.pmt:923: igraph_vector_resize: Assertion `v != NULL' failed. ``` ---
**Author:** ![vtraag](https://yyz2.discourse-cdn.com/free1/user_avatar/igraph.discourse.group/vtraag/32/38_2.png) [@vtraag](https://igraph.discourse.group/u/vtraag)\ **Post date:** [3 November 2020 13:11 UTC](https://igraph.discourse.group/t/looking-for-support-for-adding-new-features-of-clustering-algorithms-in-python-igraph/498/5 "2020-11-03T13:11:22Z")
It might be useful to look at how to program C extensions for Python: see [https://docs.python.org/3/c-api/index.html](https://docs.python.org/3/c-api/index.html) for the full reference. There is no wrapper being used to wrap C code in Python; the C code is all manually integrated in Python. This may change in the future, but for now, it all has to be manually programmed. As said, most of it is in `graphobject.c`, but there are also some other files that you need to change. `igraph_bool_t` is defined to be an `int`, so you need to use `PyLong_AsLong` to convert from a Python object to a `long` (and cast to `igraph_bool_t`). It might be more suitable to actually use `PyBool_Check`. Note that `python-igraph` also defines `PyLong_AsInt`, which explicitly checks whether the result fits an `int`, and if not raises an overflow error. If it is just argument passing, you may simply specify an `int` using `i`, see [https://docs.python.org/3/c-api/arg.html](https://docs.python.org/3/c-api/arg.html). I don’t fully understand your question regarding `ATTRIBUTE_TYPE_VERTEX`. It is defined to be `1`: it is simply an argument to the attribute interface to either get/set vertex attributes or edge attributes. ---
**Author:** ![Sofia](https://avatars.discourse-cdn.com/v4/letter/s/35a633/32.png) [@Sofia](https://igraph.discourse.group/u/Sofia)\ **Post date:** [4 November 2020 13:52 UTC](https://igraph.discourse.group/t/looking-for-support-for-adding-new-features-of-clustering-algorithms-in-python-igraph/498/6 "2020-11-04T13:52:46Z")
Thanks for your reply vtraag. I am changing the clustering algorithm. I have done the changes in function c files and its related files also changed igraph\_community.h and graphobject.c + **init**.py. After I changed those files, I still have some issue with graphobject.c, one is that I added an new input parameter as `PyObject *a = Py_False` changed it into a `igraph_bool_t`, when I am debugging it in gdb, I have error in terms of `igraph_vector_resize()`, but it seems a bit weird for me, casting the `igraph_bool_t` into an `igraph_vector_t`. Maybe there are some files that I haven’t changed properly, I cannot figure it out. May I have some support on which functions are needed to modify for any changing the python-igraph? I have done the same with igraph R package, my clustering function is working as expected. I think my problem with python-igraph is really on how the python interface is done which is still not clear to me. ---
**Author:** ![vtraag](https://yyz2.discourse-cdn.com/free1/user_avatar/igraph.discourse.group/vtraag/32/38_2.png) [@vtraag](https://igraph.discourse.group/u/vtraag)\ **Post date:** [4 November 2020 14:36 UTC](https://igraph.discourse.group/t/looking-for-support-for-adding-new-features-of-clustering-algorithms-in-python-igraph/498/7 "2020-11-04T14:36:12Z")
Perhaps it would be useful if you point me to the exact code that you use? If you have it in GitHub (or another git repo) somewhere, that might make it easier to take a closer look. Indeed, casting an `igraph_bool_t` to an `igraph_vector_t` is not expected to work. ---
**Author:** ![Sofia](https://avatars.discourse-cdn.com/v4/letter/s/35a633/32.png) [@Sofia](https://igraph.discourse.group/u/Sofia)\ **Post date:** [8 November 2020 22:13 UTC](https://igraph.discourse.group/t/looking-for-support-for-adding-new-features-of-clustering-algorithms-in-python-igraph/498/8 "2020-11-08T22:13:46Z")
I am still not very clear about how igraph c core files are linked with python interface. I have made changes on the C files in `python-igraph/vendor/build/igraph` and run make to compile all the `igraph` C files successfully. 1st question is after compiled igraph C source files, how to check and make sure that the python interface is linked with the latest compiled igraph files? 2nd question is regarding the debug of `python-igraph`. I have also changed the python calling functions in ` __init__.py`, `graphobject.c`. I am running into errors shown in `gdb python3`, but I want to further debug in the C level, I am not sure what I should change in `Makefile` in `/vendor/build/igraph/`, `"CFLAGS = -fPIC -I/usr/include/libxml2 -O3"` or `"CXXFLAGS = -fPIC -O3"` or others for further showing errors of functions written in C or C++ in igraph. 3rd question is for re-build and re-install the modified python-igraph package, I just want to make sure I have the command correctly, I am using `python3 setup.py build`, and `python3 setup.py install --user`. Thank you for your suggestions and help on my questions. ---
**Author:** ![vtraag](https://yyz2.discourse-cdn.com/free1/user_avatar/igraph.discourse.group/vtraag/32/38_2.png) [@vtraag](https://igraph.discourse.group/u/vtraag)\ **Post date:** [11 November 2020 14:36 UTC](https://igraph.discourse.group/t/looking-for-support-for-adding-new-features-of-clustering-algorithms-in-python-igraph/498/9 "2020-11-11T14:36:39Z")
There are two ways to compile the Python interface for `igraph`: 1. You compiled using the vendored `igraph` source files (i.e. located in `vendor/source/igraph`), which is the default. When you run `python setup.py build` it automatically builds the `igraph` library from the vendored `igraph` source files in the background. 2. You compile the `igraph` library separately yourself, and then build the `python-igraph` library separately and link it to the separate `igraph` library. If you compiled and installed the `igraph` library separately (using the typical `./configure`, `make` and `make install` steps) you should be able to build `python-igraph` by running `python setup.py build --use-pkg-config`. This force the Python interface to link to the provided library using `pkg-config` (assuming you have this installed). It might make sense to first make sure that you are able to compile the provided source packages yourself, before seeing how you can make changes to this package? It is difficult to answer your second question with a bit more details. But first making sure that you compile/build the source package, might clarify a number of these issues. ---
**Author:** ![Sofia](https://avatars.discourse-cdn.com/v4/letter/s/35a633/32.png) [@Sofia](https://igraph.discourse.group/u/Sofia)\ **Post date:** [17 November 2020 10:03 UTC](https://igraph.discourse.group/t/looking-for-support-for-adding-new-features-of-clustering-algorithms-in-python-igraph/498/11 "2020-11-17T10:03:57Z")
Following @vtraag instruction for the installation. Here I write down a bit more detailed steps for those who may be interested in locally installation without changing anything in the shared environment for the development: Step 1. C source compilation on local stored python package directory: ./configure --exec-prefix=/loc/dir/python-packages --prefix=/loc/dir/python-packages make make install Step 2. export PKG\_CONFIG\_PATH=/loc/dir/python-packages/lib/pkgconfig pkg-config --cflags --libs igraph (make sure you have a folder called lib/pkgconfig under the local python package directory) Step 3. build python-igraph python3 setup.py build --use-pkg-config python3 setup.py install --user (not sudo user) ---
**Author:** ![Sofia](https://avatars.discourse-cdn.com/v4/letter/s/35a633/32.png) [@Sofia](https://igraph.discourse.group/u/Sofia)\ **Post date:** [18 November 2020 10:01 UTC](https://igraph.discourse.group/t/looking-for-support-for-adding-new-features-of-clustering-algorithms-in-python-igraph/498/12 "2020-11-18T10:01:50Z")
Thank you for the detailed information on the igraph C compilation and python-igraph building. It is very helpful. Finally, I managed to successfully install both C source and python-igraph. Now, it comes to the questions about debug. When I added new parameters of a clustering algorithm in graphobject.c file, how to check if the input parameters have been interpreted from Python interface to C objects used in igraph C source file? For example, I am trying to print out the igraph\_vector\_t \*v\_ws values in graphobject.c: PyObject \*v\_weights = Py\_None; igraph\_vector\_t \*v\_ws = NULL; for (int i= 0; i \< igraph\_vcount(&self-\>g); i++){ printf(VECTOR(\*v\_ws)[i]); } if (igraphmodule\_attrib\_to\_vector\_t(v\_weights, self, &v\_ws, ATTRIBUTE\_TYPE\_VERTEX)){ igraph\_vector\_destroy(&membership); igraphmodule\_handle\_igraph\_error(); return NULL; } I got an error of “/igraph\_vector\_pmt.h:61:19: error: incompatible type for argument 1 of ‘printf’ #define VECTOR(v) ((v).stor\_begin)”; It would be very helpful to have any suggestions or information on the process of debugging.