Investigate graphviz breakage

[sklam]

See #37

The environment.yml requires a post-install fix to reinstall graphviz.

The error is:

E           graphviz.backend.execute.CalledProcessError: Command '[PosixPath('dot'), '-Kdot', '-Tsvg']' died with <Signals.SIGABRT: 6>. [stderr: b'Error: segment [(270.89, 357.85),(265.24,361.05)] does not intersect box ll=(265,319),ur=(343,361)\nAssertion failed: (0), function boxIntersectf, file compound.c, line 67.\n']

full traceback

tests/test_ch04_1.py:7:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
tests/autotests.py:33: in autotest_notebook
    exec_with_linecache(code, synthetic_filename, ns, ns)
tests/autotests.py:118: in exec_with_linecache
    exec(compiled_code, globals_dict, locals_dict)
<ch04_1_typeinfer_ifelse_main_block_6>:13: in <module>
    cres = _ch03_compiler_pipeline(
utils/pipeline.py:235: in __call__
    result = func(**filtered_kwargs)
             ^^^^^^^^^^^^^^^^^^^^^^^
ch03_egraph_program_rewrites.py:61: in egraph_saturation
    pipeline_report.append("EGraph Saturated", egraph)
utils/report.py:237: in append
    content = egraph_to_svg(content)
              ^^^^^^^^^^^^^^^^^^^^^^
utils/report.py:36: in egraph_to_svg
    svg_raw = content.pipe(format="svg", quiet=True)
              ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
temp_env/lib/python3.12/site-packages/graphviz/piping.py:104: in pipe
    return self._pipe_legacy(format,
temp_env/lib/python3.12/site-packages/graphviz/_tools.py:185: in wrapper
    return func(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^
temp_env/lib/python3.12/site-packages/graphviz/piping.py:121: in _pipe_legacy
    return self._pipe_future(format,
temp_env/lib/python3.12/site-packages/graphviz/piping.py:161: in _pipe_future
    return self._pipe_lines(*args, input_encoding=self.encoding, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
temp_env/lib/python3.12/site-packages/graphviz/backend/piping.py:161: in pipe_lines
    proc = execute.run_check(cmd, capture_output=True, quiet=quiet, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _

cmd = [PosixPath('dot'), '-Kdot', '-Tsvg'], input_lines = <generator object pipe_lines.<locals>.<genexpr> at 0x1245549e0>
encoding = None, quiet = True, kwargs = {'startupinfo': None, 'stderr': -1, 'stdout': -1}
proc = CompletedProcess(args=[PosixPath('dot'), '-Kdot', '-Tsvg'], returncode=-6, stdout=b'', stderr=b'Error: segment [(270.8...t intersect box ll=(265,319),ur=(343,361)\nAssertion failed: (0), function boxIntersectf, file compound.c, line 67.\n')

    def run_check(cmd: typing.Sequence[typing.Union[os.PathLike, str]], *,
                  input_lines: typing.Optional[BytesOrStrIterator] = None,
                  encoding: typing.Optional[str] = None,
                  quiet: bool = False,
                  **kwargs) -> subprocess.CompletedProcess:
        """Run the command described by ``cmd``
            with ``check=True`` and return its completed process.

        Raises:
            CalledProcessError: if the returncode of the subprocess is non-zero.
        """
        log.debug('run %r', cmd)
        if not kwargs.pop('check', True):  # pragma: no cover
            raise NotImplementedError('check must be True or omited')

        if encoding is not None:
            kwargs['encoding'] = encoding

        kwargs.setdefault('startupinfo', _compat.get_startupinfo())

        try:
            if input_lines is not None:
                assert kwargs.get('input') is None
                assert iter(input_lines) is input_lines
                if kwargs.pop('capture_output'):
                    kwargs['stdout'] = kwargs['stderr'] = subprocess.PIPE
                proc = _run_input_lines(cmd, input_lines, kwargs=kwargs)
            else:
                proc = subprocess.run(cmd, **kwargs)
        except OSError as e:
            if e.errno == errno.ENOENT:
                raise ExecutableNotFound(cmd) from e
            raise

        if not quiet and proc.stderr:
            _write_stderr(proc.stderr)

        try:
            proc.check_returncode()
        except subprocess.CalledProcessError as e:
>           raise CalledProcessError(*e.args)
E           graphviz.backend.execute.CalledProcessError: Command '[PosixPath('dot'), '-Kdot', '-Tsvg']' died with <Signals.SIGABRT: 6>. [stderr: b'Error: segment [(270.89, 357.85),(265.24,361.05)] does not intersect box ll=(265,319),ur=(343,361)\nAssertion failed: (0), function boxIntersectf, file compound.c, line 67.\n']

temp_env/lib/python3.12/site-packages/graphviz/backend/execute.py:90: CalledProcessError