ALE project root for Python

Question

I use ALE to run linters while editing Python code in vim. When working on code in a package, I can't get ALE to respect the pylint configuration in the project root. I've had it in .pylintrc as well as in pyproject.toml, both in the root directory of the project. Digging in a bit more, I find this is because ALE isn't correctly identifying the root directory of the project. I think this is because ALE uses vim's alternate file rather than the current file in finding the project root. (i.e., # rather than %.)

Actual behavior: In terms of the package structure described below, I use vim to open config.py, which contains this line: from . import error as err. ALE's pylint flags it as a "relative-beyond-top-level", which it's not - the package works fine with the Python interpreter. Using :ALEInfo shows me that pylint was run from top/src/package/ rather than top/. No custom ~/.vimrc is installed.

Expected behavior: ALE runs pylint from the correct directory and this line is not flagged as an error.

My question: Is this an ALE bug or am I using it wrong? I don't understand why you would use the alternate file rather than the current file in finding the project root.

Here's the project structure:

top/
    [config files including setup.py, setup.cfg, pyproject.toml]
    [other directories]
    src/
        __init__.py
        package/
            __init__.py
            config.py
            error.py
            [other files]

Complete :ALEInfo output:

 Current Filetype: python                                                                                                                                    
Available Linters: ['flake8', 'mypy', 'prospector', 'pycodestyle', 'pyflakes', 'pylint', 'pyls', 'pyre', 'vulture']
  Enabled Linters: ['flake8', 'mypy', 'pylint']
 Suggested Fixers:
  'add_blank_lines_for_python_control_statements' - Add blank lines before control statements.
  'autopep8' - Fix PEP8 issues with autopep8.
  'black' - Fix PEP8 issues with black.
  'isort' - Sort Python imports with isort.
  'remove_trailing_lines' - Remove all blank lines at the end of a file.
  'trim_whitespace' - Remove all trailing whitespace characters at the end of every line.
  'yapf' - Fix Python files with yapf.
 Linter Variables:
let g:ale_python_flake8_change_directory = 1
let g:ale_python_flake8_executable = 'flake8'
let g:ale_python_flake8_options = ''
let g:ale_python_flake8_use_global = 0
let g:ale_python_mypy_executable = 'mypy'
let g:ale_python_mypy_ignore_invalid_syntax = 0
let g:ale_python_mypy_options = ''
let g:ale_python_mypy_use_global = 0
let g:ale_python_pylint_change_directory = 1
let g:ale_python_pylint_executable = 'pylint'
let g:ale_python_pylint_options = ''
let g:ale_python_pylint_use_global = 0
 Global Variables:
let g:ale_cache_executable_check_failures = v:null
let g:ale_change_sign_column_color = 0
let g:ale_command_wrapper = ''
let g:ale_completion_delay = v:null
let g:ale_completion_enabled = 0
let g:ale_completion_max_suggestions = v:null
let g:ale_echo_cursor = 1
let g:ale_echo_msg_error_str = 'Error'
let g:ale_echo_msg_format = '%code: %%s'
let g:ale_echo_msg_info_str = 'Info'
let g:ale_echo_msg_warning_str = 'Warning'
let g:ale_enabled = 1
let g:ale_fix_on_save = 0
let g:ale_fixers = {}
let g:ale_history_enabled = 1
let g:ale_history_log_output = 1
let g:ale_keep_list_window_open = 0
let g:ale_lint_delay = 200
let g:ale_lint_on_enter = 1
let g:ale_lint_on_filetype_changed = 1
let g:ale_lint_on_save = 1
let g:ale_lint_on_text_changed = 'always'
let g:ale_lint_on_insert_leave = 0
let g:ale_linter_aliases = {}
let g:ale_linters = {}
let g:ale_linters_explicit = 0
let g:ale_list_window_size = 10
let g:ale_list_vertical = 0
let g:ale_loclist_msg_format = '%code: %%s'
let g:ale_max_buffer_history_size = 20
let g:ale_max_signs = -1
let g:ale_maximum_file_size = v:null
let g:ale_open_list = 0
let g:ale_pattern_options = v:null
let g:ale_pattern_options_enabled = v:null
let g:ale_set_balloons = 0
let g:ale_set_highlights = 1
let g:ale_set_loclist = 1
let g:ale_set_quickfix = 0
let g:ale_set_signs = 1
let g:ale_sign_column_always = 0
let g:ale_sign_error = '>>'
let g:ale_sign_info = '--'
let g:ale_sign_offset = 1000000
let g:ale_sign_style_error = '>>'
let g:ale_sign_style_warning = '--'
let g:ale_sign_warning = '--'
let g:ale_statusline_format = v:null
let g:ale_type_map = {}
let g:ale_use_global_executables = v:null
let g:ale_warn_about_trailing_blank_lines = 1
let g:ale_warn_about_trailing_whitespace = 1
  Command History:
(executable check - failure) flake8
(executable check - failure) mypy
(executable check - success) /Users/will/github/top/env/bin/pylint
(finished - exit code 2) ['/opt/homebrew/bin/bash', '-c', 'cd ''/Users/will/github/top/src/package'' && ''/Users/will/github/top/env/bin/pylint''  --output-format text --msg-
template="{path}:{line}:{column}: {msg_id} ({symbol}) {msg}" --reports n ''/Users/will/github/top/src/package/config.py''']
<<<OUTPUT STARTS>>>
[various style complaints omitted]