dmypy: ValueError: value is not in list when running a second time

[zzzeek]

I've had problems with this situation on and off for many weeks now, with 0.941 and now 0.950. sometimes it isn't happening at all, and other times, like at the moment, I get this stack trace reliably on any second run of dympy. Typically, once I get the files I'm typing in better shape, the error goes away. But to get there my process is greatly slowed by dmypy crashing on every non-initial run making it mostly not useful compared to running plain mypy.

reproduction steps follow below. the crash is:

$ dmypy  check lib
Daemon crashed!
Traceback (most recent call last):
  File "mypy/dmypy_server.py", line 230, in serve
  File "mypy/dmypy_server.py", line 273, in run_command
  File "mypy/dmypy_server.py", line 341, in cmd_check
  File "mypy/dmypy_server.py", line 394, in check
  File "mypy/dmypy_server.py", line 569, in fine_grained_increment_follow_imports
  File "mypy/server/update.py", line 245, in update
  File "mypy/server/update.py", line 328, in update_one
  File "mypy/server/update.py", line 393, in update_module
  File "mypy/server/update.py", line 615, in update_module_isolated
  File "mypy/build.py", line 2192, in type_check_first_pass
  File "mypy/checker.py", line 319, in check_first_pass
  File "mypy/checker.py", line 427, in accept
  File "mypy/errors.py", line 902, in report_internal_error
  File "mypy/checker.py", line 425, in accept
  File "mypy/nodes.py", line 1021, in accept
  File "mypy/checker.py", line 1810, in visit_class_def
  File "mypy/checker.py", line 427, in accept
  File "mypy/errors.py", line 902, in report_internal_error
  File "mypy/checker.py", line 425, in accept
  File "mypy/nodes.py", line 1092, in accept
  File "mypy/checker.py", line 2174, in visit_block
  File "mypy/checker.py", line 427, in accept
  File "mypy/errors.py", line 902, in report_internal_error
  File "mypy/checker.py", line 425, in accept
  File "mypy/nodes.py", line 740, in accept
  File "mypy/checker.py", line 776, in visit_func_def
  File "mypy/checker.py", line 780, in _visit_func_def
  File "mypy/checker.py", line 842, in check_func_item
  File "mypy/checker.py", line 1027, in check_func_def
  File "mypy/checker.py", line 427, in accept
  File "mypy/errors.py", line 902, in report_internal_error
  File "mypy/checker.py", line 425, in accept
  File "mypy/nodes.py", line 1092, in accept
  File "mypy/checker.py", line 2174, in visit_block
  File "mypy/checker.py", line 427, in accept
  File "mypy/errors.py", line 902, in report_internal_error
  File "mypy/checker.py", line 425, in accept
  File "mypy/nodes.py", line 1316, in accept
  File "mypy/checker.py", line 3581, in visit_if_stmt
  File "mypy/checkexpr.py", line 3983, in accept
  File "mypy/errors.py", line 902, in report_internal_error
  File "mypy/checkexpr.py", line 3981, in accept
  File "mypy/nodes.py", line 1897, in accept
  File "mypy/checkexpr.py", line 2244, in visit_comparison_expr
  File "mypy/checkexpr.py", line 3983, in accept
  File "mypy/errors.py", line 902, in report_internal_error
  File "mypy/checkexpr.py", line 3981, in accept
  File "mypy/nodes.py", line 1653, in accept
  File "mypy/checkexpr.py", line 197, in visit_name_expr
  File "mypy/checkexpr.py", line 224, in analyze_ref_expr
  File "mypy/checkmember.py", line 969, in type_object_type
ValueError: value is not in list

steps to reproduce:

1. using Python 3.10.0 in case that's important
2. dmypy 0.950 - this is a straight install from pypi, though ive had the issue in the past running from a source install also
3. git clone SQLAlchemy from gerrit and cd into new directory:

$ git clone https://gerrit.sqlalchemy.org/sqlalchemy/sqlalchemy
$ cd sqlalchemy

4. download a specific patch that is reproducing the issue:

$ git fetch https://gerrit.sqlalchemy.org/sqlalchemy/sqlalchemy refs/changes/25/3825/2 && git checkout FETCH_HEAD

5. start dmypy and run an initial check against lib. there's about 50 typing errors generated as expected

$ dmypy start
$ dmypy check lib
... output follows ...
Found 50 errors in 1 file (checked 700 source files)

6. make any change, like adding a blank line, to lib/sqlalchemy/orm/decl_api.py:

$ printf "\n" >> lib/sqlalchemy/orm/decl_api.py

7. run "dmypy recheck". crash

$ dympy recheck

... stack trace...
  File "mypy/checkexpr.py", line 197, in visit_name_expr
  File "mypy/checkexpr.py", line 224, in analyze_ref_expr
  File "mypy/checkmember.py", line 969, in type_object_type
ValueError: value is not in list

I'm able to reproduce this from running the steps above in a brand new directory.

I fully expect there is something in my code making it do this which I am sure is some horrible mistake I'm making, however, dmypy should tell me what the mistake is rather than crashing. Thanks and sorry for the complex reproduction instructions

[zzzeek]

Here's a better error message from 0.960 in current master, from the daemon log file

lib/sqlalchemy/orm/decl_api.py:183: error: Call to untyped function "Synonym" in typed context  [no-untyped-call]
lib/sqlalchemy/orm/decl_api.py:273: error: Function is missing a type annotation  [no-untyped-def]
lib/sqlalchemy/orm/decl_api.py:276: error: Function is missing a return type annotation  [no-untyped-def]
lib/sqlalchemy/orm/decl_api.py:279: error: Function is missing a type annotation for one or more arguments  [no-untyped-def]
lib/sqlalchemy/orm/decl_api.py:315: error: Incompatible return value type (got "Union[Mapped[_T], SQLCoreOperations[_T]]", expected "Union[InstrumentedAttribute[_T], _T]")  [return-value]
lib/sqlalchemy/orm/decl_api.py:319: error: Incompatible return value type (got "Union[Mapped[_T], SQLCoreOperations[_T]]", expected "Union[InstrumentedAttribute[_T], _T]")  [return-value]
lib/sqlalchemy/orm/decl_api.py:328: error: Returning Any from function declared to return "Union[InstrumentedAttribute[_T], _T]"  [no-any-return]
lib/sqlalchemy/orm/decl_api.py:331: error: Incompatible return value type (got "Union[Mapped[_T], SQLCoreOperations[_T]]", expected "Union[InstrumentedAttribute[_T], _T]")  [return-value]
lib/sqlalchemy/orm/decl_api.py:334: error: Function is missing a type annotation  [no-untyped-def]
lib/sqlalchemy/orm/decl_api.py:335: error: Call to untyped function "_stateful_declared_attr" in typed context  [no-untyped-call]
lib/sqlalchemy/orm/decl_api.py:338: error: Function is missing a return type annotation  [no-untyped-def]
lib/sqlalchemy/orm/decl_api.py:400: error: Missing type parameters for generic type "declared_attr"  [type-arg]
lib/sqlalchemy/orm/decl_api.py:401: error: Function is missing a type annotation  [no-untyped-def]
lib/sqlalchemy/orm/decl_api.py:404: error: Function is missing a type annotation  [no-untyped-def]
lib/sqlalchemy/orm/decl_api.py:407: error: Call to untyped function "_stateful_declared_attr" in typed context  [no-untyped-call]
lib/sqlalchemy/orm/decl_api.py:409: error: Function is missing a type annotation  [no-untyped-def]
lib/sqlalchemy/orm/decl_api.py:413: error: Function is missing a return type annotation  [no-untyped-def]
lib/sqlalchemy/orm/decl_api.py:455: error: Function is missing a return type annotation  [no-untyped-def]
lib/sqlalchemy/orm/decl_api.py:455: note: Use "-> None" if function does not return a value
lib/sqlalchemy/orm/decl_api.py:493: error: Missing type parameters for generic type "Mapper"  [type-arg]
lib/sqlalchemy/orm/decl_api.py:506: error: Variable "sqlalchemy.orm.decl_api.DeclarativeBaseNoMeta.registry" is not valid as a type  [valid-type]
lib/sqlalchemy/orm/decl_api.py:506: note: See https://mypy.readthedocs.io/en/stable/common_issues.html#variables-vs-type-aliases
lib/sqlalchemy/orm/decl_api.py:508: error: Missing type parameters for generic type "Mapper"  [type-arg]
lib/sqlalchemy/orm/decl_api.py:524: error: Name "InstanceState" is not defined  [name-defined]
lib/sqlalchemy/orm/decl_api.py:586: error: Variable "sqlalchemy.orm.decl_api.DeclarativeBase.registry" is not valid as a type  [valid-type]
lib/sqlalchemy/orm/decl_api.py:586: note: See https://mypy.readthedocs.io/en/stable/common_issues.html#variables-vs-type-aliases
lib/sqlalchemy/orm/decl_api.py:588: error: Missing type parameters for generic type "Mapper"  [type-arg]
lib/sqlalchemy/orm/decl_api.py:831: error: Missing type parameters for generic type "Type"  [type-arg]
lib/sqlalchemy/orm/decl_api.py:831: error: Missing type parameters for generic type "TypeEngine"  [type-arg]
lib/sqlalchemy/orm/decl_api.py:517: error: INTERNAL ERROR -- Please try using mypy master on GitHub:
https://mypy.readthedocs.io/en/stable/common_issues.html#using-a-development-mypy-build
Please report a bug at https://github.com/python/mypy/issues
version: 0.960+dev.269adee09330f6f1836b0ae13e20450c9f708c2a
lib/sqlalchemy/orm/decl_api.py:517: error: INTERNAL ERROR -- Please try using mypy master on GitHub:
https://mypy.readthedocs.io/en/stable/common_issues.html#using-a-development-mypy-build
Please report a bug at https://github.com/python/mypy/issues
version: 0.960+dev.269adee09330f6f1836b0ae13e20450c9f708c2a
lib/sqlalchemy/orm/decl_api.py:517: error: INTERNAL ERROR -- Please try using mypy master on GitHub:
https://mypy.readthedocs.io/en/stable/common_issues.html#using-a-development-mypy-build
Please report a bug at https://github.com/python/mypy/issues
version: 0.960+dev.269adee09330f6f1836b0ae13e20450c9f708c2a
lib/sqlalchemy/orm/decl_api.py:516: error: INTERNAL ERROR -- Please try using mypy master on GitHub:
https://mypy.readthedocs.io/en/stable/common_issues.html#using-a-development-mypy-build
Please report a bug at https://github.com/python/mypy/issues
version: 0.960+dev.269adee09330f6f1836b0ae13e20450c9f708c2a
lib/sqlalchemy/orm/decl_api.py:516: error: INTERNAL ERROR -- Please try using mypy master on GitHub:
https://mypy.readthedocs.io/en/stable/common_issues.html#using-a-development-mypy-build
Please report a bug at https://github.com/python/mypy/issues
version: 0.960+dev.269adee09330f6f1836b0ae13e20450c9f708c2a
lib/sqlalchemy/orm/decl_api.py:493: error: INTERNAL ERROR -- Please try using mypy master on GitHub:
https://mypy.readthedocs.io/en/stable/common_issues.html#using-a-development-mypy-build
Please report a bug at https://github.com/python/mypy/issues
version: 0.960+dev.269adee09330f6f1836b0ae13e20450c9f708c2a
lib/sqlalchemy/orm/decl_api.py:493: error: INTERNAL ERROR -- Please try using mypy master on GitHub:
https://mypy.readthedocs.io/en/stable/common_issues.html#using-a-development-mypy-build
Please report a bug at https://github.com/python/mypy/issues
version: 0.960+dev.269adee09330f6f1836b0ae13e20450c9f708c2a
lib/sqlalchemy/orm/decl_api.py: error: INTERNAL ERROR -- Please try using mypy master on GitHub:
https://mypy.readthedocs.io/en/stable/common_issues.html#using-a-development-mypy-build
Please report a bug at https://github.com/python/mypy/issues
version: 0.960+dev.269adee09330f6f1836b0ae13e20450c9f708c2a
Traceback (most recent call last):
  File "/home/classic/dev/mypy/mypy/dmypy_server.py", line 230, in serve
    resp = self.run_command(command, data)
  File "/home/classic/dev/mypy/mypy/dmypy_server.py", line 273, in run_command
    return method(self, **data)
  File "/home/classic/dev/mypy/mypy/dmypy_server.py", line 341, in cmd_check
    return self.check(sources, is_tty, terminal_width)
  File "/home/classic/dev/mypy/mypy/dmypy_server.py", line 394, in check
    messages = self.fine_grained_increment_follow_imports(sources)
  File "/home/classic/dev/mypy/mypy/dmypy_server.py", line 569, in fine_grained_increment_follow_imports
    messages = fine_grained_manager.update(changed, [])
  File "/home/classic/dev/mypy/mypy/server/update.py", line 245, in update
    result = self.update_one(changed_modules, initial_set, removed_set, blocking_error)
  File "/home/classic/dev/mypy/mypy/server/update.py", line 328, in update_one
    result = self.update_module(next_id, next_path, next_id in removed_set)
  File "/home/classic/dev/mypy/mypy/server/update.py", line 392, in update_module
    result = update_module_isolated(module, path, manager, previous_modules, graph,
  File "/home/classic/dev/mypy/mypy/server/update.py", line 618, in update_module_isolated
    state.type_check_first_pass()
  File "/home/classic/dev/mypy/mypy/build.py", line 2206, in type_check_first_pass
    self.type_checker().check_first_pass()
  File "/home/classic/dev/mypy/mypy/checker.py", line 315, in check_first_pass
    self.accept(d)
  File "/home/classic/dev/mypy/mypy/checker.py", line 423, in accept
    report_internal_error(err, self.errors.file, stmt.line, self.errors, self.options)
  File "/home/classic/dev/mypy/mypy/errors.py", line 962, in report_internal_error
    raise err
  File "/home/classic/dev/mypy/mypy/checker.py", line 421, in accept
    stmt.accept(self)
  File "/home/classic/dev/mypy/mypy/nodes.py", line 1028, in accept
    return visitor.visit_class_def(self)
  File "/home/classic/dev/mypy/mypy/checker.py", line 1806, in visit_class_def
    self.accept(defn.defs)
  File "/home/classic/dev/mypy/mypy/checker.py", line 423, in accept
    report_internal_error(err, self.errors.file, stmt.line, self.errors, self.options)
  File "/home/classic/dev/mypy/mypy/errors.py", line 962, in report_internal_error
    raise err
  File "/home/classic/dev/mypy/mypy/checker.py", line 421, in accept
    stmt.accept(self)
  File "/home/classic/dev/mypy/mypy/nodes.py", line 1099, in accept
    return visitor.visit_block(self)
  File "/home/classic/dev/mypy/mypy/checker.py", line 2168, in visit_block
    self.accept(s)
  File "/home/classic/dev/mypy/mypy/checker.py", line 423, in accept
    report_internal_error(err, self.errors.file, stmt.line, self.errors, self.options)
  File "/home/classic/dev/mypy/mypy/errors.py", line 962, in report_internal_error
    raise err
  File "/home/classic/dev/mypy/mypy/checker.py", line 421, in accept
    stmt.accept(self)
  File "/home/classic/dev/mypy/mypy/nodes.py", line 747, in accept
    return visitor.visit_func_def(self)
  File "/home/classic/dev/mypy/mypy/checker.py", line 772, in visit_func_def
    self._visit_func_def(defn)
  File "/home/classic/dev/mypy/mypy/checker.py", line 776, in _visit_func_def
    self.check_func_item(defn, name=defn.name)
  File "/home/classic/dev/mypy/mypy/checker.py", line 838, in check_func_item
    self.check_func_def(defn, typ, name)
  File "/home/classic/dev/mypy/mypy/checker.py", line 1023, in check_func_def
    self.accept(item.body)
  File "/home/classic/dev/mypy/mypy/checker.py", line 423, in accept
    report_internal_error(err, self.errors.file, stmt.line, self.errors, self.options)
  File "/home/classic/dev/mypy/mypy/errors.py", line 962, in report_internal_error
    raise err
  File "/home/classic/dev/mypy/mypy/checker.py", line 421, in accept
    stmt.accept(self)
  File "/home/classic/dev/mypy/mypy/nodes.py", line 1099, in accept
    return visitor.visit_block(self)
  File "/home/classic/dev/mypy/mypy/checker.py", line 2168, in visit_block
    self.accept(s)
  File "/home/classic/dev/mypy/mypy/checker.py", line 423, in accept
    report_internal_error(err, self.errors.file, stmt.line, self.errors, self.options)
  File "/home/classic/dev/mypy/mypy/errors.py", line 962, in report_internal_error
    raise err
  File "/home/classic/dev/mypy/mypy/checker.py", line 421, in accept
    stmt.accept(self)
  File "/home/classic/dev/mypy/mypy/nodes.py", line 1323, in accept
    return visitor.visit_if_stmt(self)
  File "/home/classic/dev/mypy/mypy/checker.py", line 3575, in visit_if_stmt
    t = get_proper_type(self.expr_checker.accept(e))
  File "/home/classic/dev/mypy/mypy/checkexpr.py", line 3943, in accept
    report_internal_error(err, self.chk.errors.file,
  File "/home/classic/dev/mypy/mypy/errors.py", line 962, in report_internal_error
    raise err
  File "/home/classic/dev/mypy/mypy/checkexpr.py", line 3941, in accept
    typ = node.accept(self)
  File "/home/classic/dev/mypy/mypy/nodes.py", line 1904, in accept
    return visitor.visit_comparison_expr(self)
  File "/home/classic/dev/mypy/mypy/checkexpr.py", line 2215, in visit_comparison_expr
    left_type = self.accept(left)
  File "/home/classic/dev/mypy/mypy/checkexpr.py", line 3943, in accept
    report_internal_error(err, self.chk.errors.file,
  File "/home/classic/dev/mypy/mypy/errors.py", line 962, in report_internal_error
    raise err
  File "/home/classic/dev/mypy/mypy/checkexpr.py", line 3941, in accept
    typ = node.accept(self)
  File "/home/classic/dev/mypy/mypy/nodes.py", line 1660, in accept
    return visitor.visit_name_expr(self)
  File "/home/classic/dev/mypy/mypy/checkexpr.py", line 206, in visit_name_expr
    result = self.analyze_ref_expr(e)
  File "/home/classic/dev/mypy/mypy/checkexpr.py", line 233, in analyze_ref_expr
    result = type_object_type(node, self.named_type)
  File "/home/classic/dev/mypy/mypy/checkmember.py", line 970, in type_object_type
    init_index = info.mro.index(init_method.node.info)
ValueError: <TypeInfo sqlalchemy.orm.decl_api.DeclarativeBaseNoMeta> is not in list

[ilevkivskyi]

A simple test case to repro

[case testSqlalchemyCrash]
import m
[file m.py]
import typing
from typing import Any

class DeclarativeBaseNoMeta:
    if True:
        def __init__(self, **kw: Any):
            ...

DeclarativeBaseNoMeta
[file m.py.2]
import typing
from typing import Any

class DeclarativeBaseNoMeta:
    if True:
        def __init__(self, **kw: Any):
            ...

DeclarativeBaseNoMeta
# change
[builtins fixtures/dict.pyi]
[out]
==

It looks like original_def in this case points to the function itself, and this interferes with replace_object_state(). Probably not hard to fix, I will give it a try later today.

[ilevkivskyi]

Oh wow, it is actually worse. Because of a bug in visit_block() in astmerge, function/method definitions that appear in all nested positions (if, try, with, etc), will never get processed correctly by the daemon, their stale versions will persist. I guess this may be a major source of daemon bugs/crashes, will submit a PR in few minutes.

cc @JukkaL

[zzzeek]

my dmypy use is totally different since this bug was fixed, I can now leave it running and "dmypy check lib" doesn't crash even when I check out different branches. Previously, any code changes beyond a dozen lines would guaranteed crash every time. looks like it was all the same thing, thanks for fixing!

[ilevkivskyi]

Glad to hear it helped!