Binder notebook does not work

[soleti]

Hello,

first of all, very cool project :) I tried to run the Binder notebook but I got this error, which happens after the test stage:

Installing headers in /home/jovyan/software/include/nuSQuIDS
Installing libraries in /home/jovyan/software/lib
Installing config information in /home/jovyan/software/lib/pkgconfig
g++ -O3 -fPIC -std=c++11 -I/srv/conda/envs/notebook/include/python3.9 -fpermissive -I/home/jovyan/software/include -Wno-abi -I/srv/conda/envs/notebook/include -I/srv/conda/envs/notebook/include -I../include/ -I/srv/conda/envs/notebook//include -I/srv/conda/envs/notebook/lib/python3.9/site-packages/numpy/core/include -I/home/jovyan/resources/python/src/../../..//include -I/home/jovyan/resources/python/src/..//inc -c nuSQUIDSpy.cpp -o nuSQUIDSpy.o
In file included from /srv/conda/envs/notebook/include/boost/python/detail/is_xxx.hpp:8:0,
                 from /srv/conda/envs/notebook/include/boost/python/detail/is_auto_ptr.hpp:9,
                 from /srv/conda/envs/notebook/include/boost/python/detail/copy_ctor_mutates_rhs.hpp:8,
                 from /srv/conda/envs/notebook/include/boost/python/detail/value_arg.hpp:7,
                 from /srv/conda/envs/notebook/include/boost/python/object/forward.hpp:10,
                 from /srv/conda/envs/notebook/include/boost/python/object/pointer_holder.hpp:16,
                 from /srv/conda/envs/notebook/include/boost/python/to_python_indirect.hpp:10,
                 from /srv/conda/envs/notebook/include/boost/python/converter/arg_to_python.hpp:10,
                 from /srv/conda/envs/notebook/include/boost/python/call.hpp:15,
                 from /srv/conda/envs/notebook/include/boost/python/object_core.hpp:14,
                 from /srv/conda/envs/notebook/include/boost/python/args.hpp:22,
                 from /srv/conda/envs/notebook/include/boost/python.hpp:11,
                 from nuSQUIDSpy.h:36,
                 from nuSQUIDSpy.cpp:24:
/srv/conda/envs/notebook/include/boost/python/detail/is_auto_ptr.hpp:17:40: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 BOOST_PYTHON_IS_XXX_DEF(auto_ptr, std::auto_ptr, 1)
                                        ^
/srv/conda/envs/notebook/include/boost/detail/is_xxx.hpp:20:4: note: in definition of macro ‘BOOST_DETAIL_IS_XXX_DEF’
    qualified_name< BOOST_PP_ENUM_PARAMS_Z(1, nargs, T) >        \
    ^~~~~~~~~~~~~~
/srv/conda/envs/notebook/include/boost/python/detail/is_auto_ptr.hpp:17:1: note: in expansion of macro ‘BOOST_PYTHON_IS_XXX_DEF’
 BOOST_PYTHON_IS_XXX_DEF(auto_ptr, std::auto_ptr, 1)
 ^~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /srv/conda/envs/notebook/include/boost/function/function_base.hpp:16,
                 from /srv/conda/envs/notebook/include/boost/function/detail/prologue.hpp:17,
                 from /srv/conda/envs/notebook/include/boost/function/function_template.hpp:13,
                 from /srv/conda/envs/notebook/include/boost/function/detail/maybe_include.hpp:15,
                 from /srv/conda/envs/notebook/include/boost/function/function0.hpp:11,
                 from /srv/conda/envs/notebook/include/boost/python/errors.hpp:13,
                 from /srv/conda/envs/notebook/include/boost/python/handle.hpp:11,
                 from /srv/conda/envs/notebook/include/boost/python/args_fwd.hpp:10,
                 from /srv/conda/envs/notebook/include/boost/python/args.hpp:10,
                 from /srv/conda/envs/notebook/include/boost/python.hpp:11,
                 from nuSQUIDSpy.h:36,
                 from nuSQUIDSpy.cpp:24:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /srv/conda/envs/notebook/include/boost/python/wrapper.hpp:8:0,
                 from /srv/conda/envs/notebook/include/boost/python/object/value_holder.hpp:15,
                 from /srv/conda/envs/notebook/include/boost/python/object/class_metadata.hpp:14,
                 from /srv/conda/envs/notebook/include/boost/python/class.hpp:23,
                 from /srv/conda/envs/notebook/include/boost/python.hpp:18,
                 from nuSQUIDSpy.h:36,
                 from nuSQUIDSpy.cpp:24:
/srv/conda/envs/notebook/include/boost/python/override.hpp: In member function ‘boost::python::detail::method_result boost::python::override::operator()() const’:
/srv/conda/envs/notebook/include/boost/python/override.hpp:103:13: warning: ‘PyObject* PyEval_CallFunction(PyObject*, const char*,...)’ is deprecated [-Wdeprecated-declarations]
             ));
             ^
In file included from /srv/conda/envs/notebook/include/python3.9/Python.h:145:0,
                 from /srv/conda/envs/notebook/include/boost/python/detail/wrap_python.hpp:178,
                 from /srv/conda/envs/notebook/include/boost/python/detail/prefix.hpp:13,
                 from /srv/conda/envs/notebook/include/boost/python/args.hpp:8,
                 from /srv/conda/envs/notebook/include/boost/python.hpp:11,
                 from nuSQUIDSpy.h:36,
                 from nuSQUIDSpy.cpp:24:
/srv/conda/envs/notebook/include/python3.9/ceval.h:26:43: note: declared here
 Py_DEPRECATED(3.9) PyAPI_FUNC(PyObject *) PyEval_CallFunction(
                                           ^~~~~~~~~~~~~~~~~~~
In file included from /srv/conda/envs/notebook/include/boost/python/exception_translator.hpp:10:0,
                 from /srv/conda/envs/notebook/include/boost/python.hpp:28,
                 from nuSQUIDSpy.h:36,
                 from nuSQUIDSpy.cpp:24:
/srv/conda/envs/notebook/include/boost/bind.hpp: At global scope:
/srv/conda/envs/notebook/include/boost/bind.hpp:41:1: note: #pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use <boost/bind/bind.hpp> + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.
 )
 ^
In file included from /srv/conda/envs/notebook/include/boost/python/object/iterator.hpp:28:0,
                 from /srv/conda/envs/notebook/include/boost/python/iterator.hpp:12,
                 from /srv/conda/envs/notebook/include/boost/python.hpp:37,
                 from nuSQUIDSpy.h:36,
                 from nuSQUIDSpy.cpp:24:
/srv/conda/envs/notebook/include/boost/detail/iterator.hpp:13:37: note: #pragma message: This header is deprecated. Use <iterator>instead.
 BOOST_HEADER_DEPRECATED("<iterator>")
                                     ^
Linking /home/jovyan/resources/python/src/..//bindings/nuSQUIDSpy.a
Linking /home/jovyan/resources/python/src/..//bindings/nuSQUIDSpy.so
g++: error: libpython3.9.a: No such file or directory
g++: error: libpython3.9.a: No such file or directory
Makefile:56: recipe for target '/home/jovyan/resources/python/src/..//bindings/nuSQUIDSpy.so' failed
make: *** [/home/jovyan/resources/python/src/..//bindings/nuSQUIDSpy.so] Error 1
Removing intermediate container ce95417b036c
The command '/bin/sh -c ./binder/postBuild' returned a non-zero code: 2

Kind regards,
Roberto

[cnweaver]

Hi Roberto, thanks for your interest in our project!
It looks like most of the output you got was not critical, just deprecation warnings (that I think aren't our fault, but we should figure out a way to clean them up at some point), with the fatal bit being that we're trying to link the wrong python library.
Over the last couple of months we've made some major changes to our python build system on a branch which we are almost, but not quite ready to merge. It's stable enough, though, that if you want to try things out, I would suggest taking a look at the v1.11-dev branch, which should now work for this use since I just applied some fixes in 5473a78.