hail.init() fails with Python 3.11

[dlcotter]

What happened?

The following fails:

import hail as hl
hl.init()

with the error:

ImportError: cannot import name 'getargspec' from 'inspect' (/usr/local/Cellar/python@3.11/3.11.2_1/Frameworks/Python.framework/Versions/3.11/lib/python3.11/inspect.py)

when running Python 3.11.

The code importing getargspec is the Parsimonious library (see stacktrace below).

Version

0.2.109

Relevant log output

---------------------------------------------------------------------------
ImportError                               Traceback (most recent call last)
Cell In[1], line 1
----> 1 import hail as hl
      2 hl.init()

File /usr/local/Cellar/jupyterlab/3.6.1/libexec/lib/python3.11/site-packages/hail/__init__.py:33
     14 __doc__ = r"""
     15     __  __     <>__
     16    / /_/ /__  __/ /
   (...)
     27 To report a bug, please open an issue: https://github.com/hail-is/hail/issues
     28 """
     30 # F403 'from .expr import *' used; unable to detect undefined names
     31 # F401 '.expr.*' imported but unused
     32 # E402 module level import not at top of file
---> 33 from .table import Table, GroupedTable, asc, desc  # noqa: E402
     34 from .matrixtable import MatrixTable, GroupedMatrixTable  # noqa: E402
     35 from .expr import *  # noqa: F401,F403,E402

File /usr/local/Cellar/jupyterlab/3.6.1/libexec/lib/python3.11/site-packages/hail/table.py:8
      5 import pyspark
      6 from typing import Optional, Dict, Callable, Sequence
----> 8 from hail.expr.expressions import Expression, StructExpression, \
      9     BooleanExpression, expr_struct, expr_any, expr_bool, analyze, Indices, \
     10     construct_reference, to_expr, construct_expr, extract_refs_by_indices, \
     11     ExpressionException, TupleExpression, unify_all, NumericExpression, \
     12     StringExpression, CallExpression, CollectionExpression, DictExpression, \
     13     IntervalExpression, LocusExpression, NDArrayExpression, expr_stream
     14 from hail.expr.types import hail_type, tstruct, types_match, tarray, tset, dtypes_from_pandas
     15 from hail.expr.table_type import ttable

File /usr/local/Cellar/jupyterlab/3.6.1/libexec/lib/python3.11/site-packages/hail/expr/__init__.py:1
----> 1 from .types import (dtype, HailType, hail_type, is_container, is_compound, is_numeric, is_primitive,
      2                     types_match, tint, tint32, tint64, tfloat, tfloat32, tfloat64, tstr, tbool, tarray, tstream,
      3                     tndarray, tset, tdict, tstruct, tunion, ttuple, tinterval, tlocus, tcall, tvoid, tvariable,
      4                     hts_entry_schema)
      5 from .table_type import ttable
      6 from .matrix_type import tmatrix

File /usr/local/Cellar/jupyterlab/3.6.1/libexec/lib/python3.11/site-packages/hail/expr/types.py:17
     14 from hailtop.hail_frozenlist import frozenlist
     16 from .nat import NatBase, NatLiteral
---> 17 from .type_parsing import type_grammar, type_node_visitor
     18 from .. import genetics
     19 from ..typecheck import typecheck, typecheck_method, oneof, transformed

File /usr/local/Cellar/jupyterlab/3.6.1/libexec/lib/python3.11/site-packages/hail/expr/type_parsing.py:1
----> 1 from parsimonious import Grammar, NodeVisitor
      2 from hail.expr.nat import NatVariable
      3 from . import types

File /usr/local/Cellar/jupyterlab/3.6.1/libexec/lib/python3.11/site-packages/parsimonious/__init__.py:9
      1 """Parsimonious's public API. Import from here.
      2 
      3 Things may move around in modules deeper than this one.
      4 
      5 """
      6 from parsimonious.exceptions import (ParseError, IncompleteParseError,
      7                                      VisitationError, UndefinedLabel,
      8                                      BadGrammar)
----> 9 from parsimonious.grammar import Grammar, TokenGrammar
     10 from parsimonious.nodes import NodeVisitor, VisitationError, rule

File /usr/local/Cellar/jupyterlab/3.6.1/libexec/lib/python3.11/site-packages/parsimonious/grammar.py:14
     11 from six import (text_type, itervalues, iteritems, python_2_unicode_compatible, PY2)
     13 from parsimonious.exceptions import BadGrammar, UndefinedLabel
---> 14 from parsimonious.expressions import (Literal, Regex, Sequence, OneOf,
     15     Lookahead, Optional, ZeroOrMore, OneOrMore, Not, TokenMatcher,
     16     expression)
     17 from parsimonious.nodes import NodeVisitor
     18 from parsimonious.utils import evaluate_string

File /usr/local/Cellar/jupyterlab/3.6.1/libexec/lib/python3.11/site-packages/parsimonious/expressions.py:9
      1 """Subexpressions that make up a parsed grammar
      2 
      3 These do the parsing.
      4 
      5 """
      6 # TODO: Make sure all symbol refs are local--not class lookups or
      7 # anything--for speed. And kill all the dots.
----> 9 from inspect import getargspec
     10 import re
     12 from six import integer_types, python_2_unicode_compatible

ImportError: cannot import name 'getargspec' from 'inspect' (/usr/local/Cellar/python@3.11/3.11.2_1/Frameworks/Python.framework/Versions/3.11/lib/python3.11/inspect.py)

[danking]

Hey @dlcotter ! Thanks for the report. I anticipate a fix in the next version of Hail. For now, I think you can fix with pip3 install 'parsimonious>=0.9' or downgrading to Python 3.10