Sagemath and binder do not work together (neither docker nor conda) about sage-binder-env HOT 8 CLOSED

Visiting https://github.com/flatsurf/ipyvue-flatsurf and clicking
the "launch binder" button gives a working Sage 9.6 in Binder.

from sage-binder-env.

It works, I copied the environment.yml file. I get 9.5 instead of 9.6; it complains about missing matplotlib. If I want to see an output I need to use print or show, it is not enough to write the variable at the last line of the cell.
By some reason, cocalc's docker works today

from sage-binder-env.

it complains about missing matplotlib

could you elaborate?

from sage-binder-env.

The environment.yml we use at ipyvue-flatsurf uses sagelib 9.5 because some of the dependencies (surface-dynamics) have not been built for 9.6 yet.

from sage-binder-env.

I indeed noticed that sage-binder-env was broken currently. I tried a month ago reverting to 9.2 in 98ed8d1,
but to no avail. My best bet was an incompatibility with SageMath packaged with conda with recent underlying
os image. Upon starting Sage, there is a failure:

ImportError: libgsl.so.25: cannot open shared object file: No such file or directory

I did not get however to investigate further, or even report upstream.

from sage-binder-env.

it complains about missing matplotlib

could you elaborate?

Both in the terminal and in jupyter. If I type print(1+1) i get the answer, and also with show(1+1). But with 1+1 i get:

ModuleNotFoundError Traceback (most recent call last)
/tmp/ipykernel_486/225133317.py in
----> 1 Integer(1)+Integer(1)

/srv/conda/envs/notebook/lib/python3.7/site-packages/IPython/core/displayhook.py in call(self, result)
260 self.start_displayhook()
261 self.write_output_prompt()
--> 262 format_dict, md_dict = self.compute_format_data(result)
263 self.update_user_ns(result)
264 self.fill_exec_result(result)

/srv/conda/envs/notebook/lib/python3.7/site-packages/IPython/core/displayhook.py in compute_format_data(self, result)
149
150 """
--> 151 return self.shell.display_formatter.format(result)
152
153 # This can be set to True by the write_output_prompt method in a subclass

/srv/conda/envs/notebook/lib/python3.7/site-packages/sage/repl/display/formatter.py in format(self, obj, include, exclude)
184 # use Sage rich output for any except those native to IPython, but only
185 # if it is not plain and dull
--> 186 if (not isinstance(obj, (IPYTHON_NATIVE_TYPES, Figure)) and
187 not set(sage_format.keys()).issubset([PLAIN_TEXT])):
188 return sage_format, sage_metadata

/srv/conda/envs/notebook/lib/python3.7/site-packages/sage/misc/lazy_import.pyx in sage.misc.lazy_import.LazyImport.instancecheck (build/cythonized/sage/misc/lazy_import.c:7695)()
914 True
915 """
--> 916 return isinstance(x, self.get_object())
917
918 def subclasscheck(self, x):

/srv/conda/envs/notebook/lib/python3.7/site-packages/sage/misc/lazy_import.pyx in sage.misc.lazy_import.LazyImport.get_object (build/cythonized/sage/misc/lazy_import.c:2612)()
215 if likely(self._object is not None):
216 return self._object
--> 217 return self._get_object()
218
219 cpdef _get_object(self):

/srv/conda/envs/notebook/lib/python3.7/site-packages/sage/misc/lazy_import.pyx in sage.misc.lazy_import.LazyImport._get_object (build/cythonized/sage/misc/lazy_import.c:3073)()
255 if self._feature:
256 raise FeatureNotPresentError(self._feature, reason=f'Importing {self._name} failed: {e}')
--> 257 raise
258
259 name = self._as_name

/srv/conda/envs/notebook/lib/python3.7/site-packages/sage/misc/lazy_import.pyx in sage.misc.lazy_import.LazyImport._get_object (build/cythonized/sage/misc/lazy_import.c:2935)()
251
252 try:
--> 253 self._object = getattr(import(self._module, {}, {}, [self._name]), self._name)
254 except ImportError as e:
255 if self._feature:

ModuleNotFoundError: No module named 'matplotlib'

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@enriqueartal do you have a link to the repository that does not work for you?

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@enriqueartal do you have a link to the repository that does not work for you?

The repository was https://github.com/enriqueartal/TorsionDivisorsCubicZariskiPairs, branch sagedev. With your new environment.yml it works. I got errors in some notebooks since they were built for previous versions of sage. Actually it would be helpful for me to install optional packages for sage (sirocco and for other notebooks gap_packages). Sorry for a newby question, how can it be done? Anyway, thanks for the solution!

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