datajoint-python Error with`dj.Diagram()` and new release of `pydot==3.0.*`

Error with`dj.Diagram()` and new release of `pydot==3.0.*`

Open MilagrosMarin opened this issue 1 year ago • 0 comments

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Bug Report

One month ago, pydot released version 3.0, which introduced breaking changes (reference). These changes appear to be causing issues with dj.Diagram.

One of the breaking changes in the new version of pydot is Breaking change: Remove .create_attribute_methods() from classes, and the error I received breaks in dj.Diagram using create_*(). The datajoint-python unit tests cover the import and table attributes but not the create attributes reference.

Downgrading to pydot==2.0 resolves these issues and restores plotting functionality for dj.Diagram.

Description

dj.Diagram(probe)

{
	"name": "AssertionError",
	"message": "\"dot\" with args ['-Tsvg', '/var/folders/h8/_lx50k3d6qx586662kr066h40000gn/T/tmp2kxf9kd7'] returned code: 1",
	"stack": "---------------------------------------------------------------------------
AssertionError                            Traceback (most recent call last)
File ~/miniconda/envs/utah_organoids/lib/python3.10/site-packages/IPython/core/formatters.py:347, in BaseFormatter.__call__(self, obj)
    345     method = get_real_method(obj, self.print_method)
    346     if method is not None:
--> 347         return method()
    348     return None
    349 else:

File ~/miniconda/envs/utah_organoids/lib/python3.10/site-packages/datajoint/diagram.py:436, in Diagram._repr_svg_(self)
    435 def _repr_svg_(self):
--> 436     return self.make_svg()._repr_svg_()

File ~/miniconda/envs/utah_organoids/lib/python3.10/site-packages/datajoint/diagram.py:424, in Diagram.make_svg(self)
    421 def make_svg(self):
    422     from IPython.display import SVG
--> 424     return SVG(self.make_dot().create_svg())

File ~/miniconda/envs/utah_organoids/lib/python3.10/site-packages/pydot/core.py:169, in __generate_format_methods.<locals>.__create_method(self, f, prog, encoding)
    167 def __create_method(self, f=frmt, prog=None, encoding=None):
    168     \"\"\"Refer to docstring of method `create`.\"\"\"
--> 169     return self.create(format=f, prog=prog, encoding=encoding)

File ~/miniconda/envs/utah_organoids/lib/python3.10/site-packages/pydot/core.py:1825, in Dot.create(self, prog, format, encoding)
   1819     code = process.returncode
   1820     print(
   1821         f'\"{prog}\" with args {arguments} returned code: {code}\
\
'
   1822         f\"stdout, stderr:\
 {stdout_data}\
{stderr_data}\
\"
   1823     )
-> 1825 assert process.returncode == 0, (
   1826     f'\"{prog}\" with args {arguments} '
   1827     f\"returned code: {process.returncode}\"
   1828 )
   1830 return stdout_data

AssertionError: \"dot\" with args ['-Tsvg', '/var/folders/h8/_lx50k3d6qx586662kr066h40000gn/T/tmp2kxf9kd7'] returned code: 1"
}