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skips are not honored since isort 5.9.x #1762

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pums974 opened this issue Jun 22, 2021 · 15 comments
Closed

skips are not honored since isort 5.9.x #1762

pums974 opened this issue Jun 22, 2021 · 15 comments
Labels
bug Something isn't working repo_needed Can't currently reproduce, if reproduction steps are added we will resivit this issue.

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@pums974
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pums974 commented Jun 22, 2021

I'm using isort with my project for some time now, thank you for this project !

Everything was working well with 5.8.0 but with 5.9.0 I have the error

OSError: [Errno 7] Argument list too long: 'git'

And with the version 5.9.1, extend_skip and skip_gitignore are not honored and isort goes into my venv folder where it shouldn't go.

Thank you for looking into this

@grant-zietsman
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I have noticed the same thing happening this side.

@timothycrosley
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Member

@pums974 and @grant-zietsman I'm so sorry this broke for both of you! Can you try the latest version from github and see if it is still an issue? pip install git+https://github.com/PyCQA/isort.git. Additionally, are either of you willing to share more information about how your settings are set providing the output of isort . --show-config?

@timothycrosley timothycrosley added bug Something isn't working repo_needed Can't currently reproduce, if reproduction steps are added we will resivit this issue. labels Jun 23, 2021
@pums974
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pums974 commented Jun 23, 2021

Yeah no problem

`isort . --show-config`:
{
    "_known_patterns": null,
    "_section_comments": null,
    "_skips": null,
    "_skip_globs": null,
    "_sorting_function": null,
    "py_version": "py3",
    "force_to_top": [],
    "skip": [
        ".hg",
        "__pypackages__",
        "buck-out",
        ".pants.d",
        ".eggs",
        "_build",
        "dist",
        ".mypy_cache",
        ".venv",
        ".tox",
        ".svn",
        ".direnv",
        ".git",
        "venv",
        "node_modules",
        "build",
        ".bzr",
        ".nox"
    ],
    "extend_skip": [
        "tmp",
        "ext_bin",
        "venv",
        "ext"
    ],
    "skip_glob": [],
    "extend_skip_glob": [],
    "skip_gitignore": true,
    "line_length": 100,
    "wrap_length": 0,
    "line_ending": "",
    "sections": [
        "FUTURE",
        "STDLIB",
        "THIRDPARTY",
        "FIRSTPARTY",
        "LOCALFOLDER"
    ],
    "no_sections": false,
    "known_future_library": [
        "__future__"
    ],
    "known_third_party": [],
    "known_first_party": [],
    "known_local_folder": [],
    "known_standard_library": [
        "mmap",
        "tarfile",
        "hmac",
        "pwd",
        "shelve",
        "audioop",
        "getopt",
        "macpath",
        "uuid",
        "runpy",
        "optparse",
        "pkgutil",
        "formatter",
        "ensurepip",
        "test",
        "dbm",
        "hashlib",
        "encodings",
        "wave",
        "winreg",
        "pickletools",
        "decimal",
        "imaplib",
        "trace",
        "posixpath",
        "heapq",
        "chunk",
        "array",
        "selectors",
        "curses",
        "html",
        "tempfile",
        "statistics",
        "modulefinder",
        "mailbox",
        "dummy_threading",
        "copyreg",
        "cmd",
        "sqlite3",
        "zipfile",
        "enum",
        "winsound",
        "rlcompleter",
        "token",
        "xml",
        "time",
        "nis",
        "pyclbr",
        "netrc",
        "aifc",
        "syslog",
        "tokenize",
        "imghdr",
        "concurrent",
        "platform",
        "lzma",
        "fileinput",
        "fpectl",
        "resource",
        "crypt",
        "copy",
        "subprocess",
        "dataclasses",
        "reprlib",
        "turtledemo",
        "site",
        "xmlrpc",
        "binascii",
        "keyword",
        "pty",
        "faulthandler",
        "wsgiref",
        "abc",
        "builtins",
        "pathlib",
        "symbol",
        "gc",
        "sre_compile",
        "functools",
        "unicodedata",
        "doctest",
        "logging",
        "marshal",
        "queue",
        "ctypes",
        "types",
        "urllib",
        "glob",
        "typing",
        "multiprocessing",
        "asyncore",
        "ipaddress",
        "gzip",
        "codecs",
        "secrets",
        "filecmp",
        "_thread",
        "json",
        "calendar",
        "quopri",
        "base64",
        "pydoc",
        "numbers",
        "errno",
        "locale",
        "fcntl",
        "inspect",
        "codeop",
        "itertools",
        "fnmatch",
        "getpass",
        "_dummy_thread",
        "fractions",
        "tty",
        "contextvars",
        "sndhdr",
        "plistlib",
        "difflib",
        "posix",
        "bdb",
        "math",
        "distutils",
        "http",
        "grp",
        "dis",
        "profile",
        "cmath",
        "pdb",
        "pprint",
        "socket",
        "telnetlib",
        "ntpath",
        "graphlib",
        "py_compile",
        "symtable",
        "timeit",
        "asynchat",
        "cgitb",
        "smtpd",
        "gettext",
        "nntplib",
        "turtle",
        "ftplib",
        "uu",
        "sre_constants",
        "signal",
        "readline",
        "struct",
        "poplib",
        "mailcap",
        "termios",
        "spwd",
        "sys",
        "compileall",
        "configparser",
        "textwrap",
        "io",
        "operator",
        "linecache",
        "smtplib",
        "stat",
        "sysconfig",
        "os",
        "sre",
        "select",
        "code",
        "parser",
        "bisect",
        "tracemalloc",
        "socketserver",
        "webbrowser",
        "binhex",
        "colorsys",
        "ssl",
        "sunau",
        "asyncio",
        "cProfile",
        "mimetypes",
        "ast",
        "threading",
        "zlib",
        "lib2to3",
        "contextlib",
        "random",
        "sre_parse",
        "zoneinfo",
        "bz2",
        "zipapp",
        "xdrlib",
        "string",
        "collections",
        "atexit",
        "msilib",
        "weakref",
        "stringprep",
        "imp",
        "re",
        "pickle",
        "warnings",
        "importlib",
        "tabnanny",
        "sched",
        "shlex",
        "tkinter",
        "zipimport",
        "cgi",
        "ossaudiodev",
        "msvcrt",
        "pipes",
        "shutil",
        "csv",
        "datetime",
        "email",
        "pstats",
        "venv",
        "unittest",
        "traceback",
        "argparse"
    ],
    "extra_standard_library": [],
    "known_other": {},
    "multi_line_output": "VERTICAL_HANGING_INDENT",
    "forced_separate": [],
    "indent": "    ",
    "comment_prefix": "  #",
    "length_sort": false,
    "length_sort_straight": false,
    "length_sort_sections": [],
    "add_imports": [],
    "remove_imports": [],
    "append_only": false,
    "reverse_relative": false,
    "force_single_line": false,
    "single_line_exclusions": [],
    "default_section": "THIRDPARTY",
    "import_headings": {},
    "balanced_wrapping": false,
    "use_parentheses": true,
    "order_by_type": true,
    "atomic": false,
    "lines_after_imports": -1,
    "lines_between_sections": 1,
    "lines_between_types": 0,
    "combine_as_imports": false,
    "combine_star": false,
    "include_trailing_comma": true,
    "from_first": false,
    "verbose": false,
    "quiet": false,
    "force_adds": false,
    "force_alphabetical_sort_within_sections": false,
    "force_alphabetical_sort": false,
    "force_grid_wrap": 0,
    "force_sort_within_sections": false,
    "lexicographical": false,
    "group_by_package": false,
    "ignore_whitespace": false,
    "no_lines_before": [],
    "no_inline_sort": false,
    "ignore_comments": false,
    "case_sensitive": false,
    "sources": [
        {
            "py_version": "py3",
            "force_to_top": [],
            "skip": [
                ".hg",
                "__pypackages__",
                "buck-out",
                ".pants.d",
                ".eggs",
                "_build",
                "dist",
                ".mypy_cache",
                ".venv",
                ".tox",
                ".svn",
                ".direnv",
                ".git",
                "venv",
                "node_modules",
                "build",
                ".bzr",
                ".nox"
            ],
            "extend_skip": [],
            "skip_glob": [],
            "extend_skip_glob": [],
            "skip_gitignore": false,
            "line_length": 79,
            "wrap_length": 0,
            "line_ending": "",
            "sections": [
                "FUTURE",
                "STDLIB",
                "THIRDPARTY",
                "FIRSTPARTY",
                "LOCALFOLDER"
            ],
            "no_sections": false,
            "known_future_library": [
                "__future__"
            ],
            "known_third_party": [],
            "known_first_party": [],
            "known_local_folder": [],
            "known_standard_library": [
                "mmap",
                "tarfile",
                "hmac",
                "pwd",
                "shelve",
                "audioop",
                "getopt",
                "macpath",
                "uuid",
                "runpy",
                "optparse",
                "pkgutil",
                "formatter",
                "ensurepip",
                "test",
                "dbm",
                "hashlib",
                "encodings",
                "wave",
                "winreg",
                "pickletools",
                "decimal",
                "imaplib",
                "trace",
                "posixpath",
                "heapq",
                "chunk",
                "array",
                "selectors",
                "curses",
                "html",
                "tempfile",
                "statistics",
                "modulefinder",
                "mailbox",
                "dummy_threading",
                "copyreg",
                "cmd",
                "sqlite3",
                "zipfile",
                "enum",
                "winsound",
                "rlcompleter",
                "token",
                "xml",
                "time",
                "nis",
                "pyclbr",
                "netrc",
                "aifc",
                "syslog",
                "tokenize",
                "imghdr",
                "concurrent",
                "platform",
                "lzma",
                "fileinput",
                "fpectl",
                "resource",
                "crypt",
                "copy",
                "subprocess",
                "dataclasses",
                "reprlib",
                "turtledemo",
                "site",
                "xmlrpc",
                "binascii",
                "keyword",
                "pty",
                "faulthandler",
                "wsgiref",
                "abc",
                "builtins",
                "pathlib",
                "symbol",
                "gc",
                "sre_compile",
                "functools",
                "unicodedata",
                "doctest",
                "logging",
                "marshal",
                "queue",
                "ctypes",
                "types",
                "urllib",
                "glob",
                "typing",
                "multiprocessing",
                "asyncore",
                "ipaddress",
                "gzip",
                "codecs",
                "secrets",
                "filecmp",
                "_thread",
                "json",
                "calendar",
                "quopri",
                "base64",
                "pydoc",
                "numbers",
                "errno",
                "locale",
                "fcntl",
                "inspect",
                "codeop",
                "itertools",
                "fnmatch",
                "getpass",
                "_dummy_thread",
                "fractions",
                "tty",
                "contextvars",
                "sndhdr",
                "plistlib",
                "difflib",
                "posix",
                "bdb",
                "math",
                "distutils",
                "http",
                "grp",
                "dis",
                "profile",
                "cmath",
                "pdb",
                "pprint",
                "socket",
                "telnetlib",
                "ntpath",
                "graphlib",
                "py_compile",
                "symtable",
                "timeit",
                "asynchat",
                "cgitb",
                "smtpd",
                "gettext",
                "nntplib",
                "turtle",
                "ftplib",
                "uu",
                "sre_constants",
                "signal",
                "readline",
                "struct",
                "poplib",
                "mailcap",
                "termios",
                "spwd",
                "sys",
                "compileall",
                "configparser",
                "textwrap",
                "io",
                "operator",
                "linecache",
                "smtplib",
                "stat",
                "sysconfig",
                "os",
                "sre",
                "select",
                "code",
                "parser",
                "bisect",
                "tracemalloc",
                "socketserver",
                "webbrowser",
                "binhex",
                "colorsys",
                "ssl",
                "sunau",
                "asyncio",
                "cProfile",
                "mimetypes",
                "ast",
                "threading",
                "zlib",
                "lib2to3",
                "contextlib",
                "random",
                "sre_parse",
                "zoneinfo",
                "bz2",
                "zipapp",
                "xdrlib",
                "string",
                "collections",
                "atexit",
                "msilib",
                "weakref",
                "stringprep",
                "imp",
                "re",
                "pickle",
                "warnings",
                "importlib",
                "tabnanny",
                "sched",
                "shlex",
                "tkinter",
                "zipimport",
                "cgi",
                "ossaudiodev",
                "msvcrt",
                "pipes",
                "shutil",
                "csv",
                "datetime",
                "email",
                "pstats",
                "venv",
                "unittest",
                "traceback",
                "argparse"
            ],
            "extra_standard_library": [],
            "known_other": {},
            "multi_line_output": "GRID",
            "forced_separate": [],
            "indent": "    ",
            "comment_prefix": "  #",
            "length_sort": false,
            "length_sort_straight": false,
            "length_sort_sections": [],
            "add_imports": [],
            "remove_imports": [],
            "append_only": false,
            "reverse_relative": false,
            "force_single_line": false,
            "single_line_exclusions": [],
            "default_section": "THIRDPARTY",
            "import_headings": {},
            "balanced_wrapping": false,
            "use_parentheses": false,
            "order_by_type": true,
            "atomic": false,
            "lines_after_imports": -1,
            "lines_between_sections": 1,
            "lines_between_types": 0,
            "combine_as_imports": false,
            "combine_star": false,
            "include_trailing_comma": false,
            "from_first": false,
            "verbose": false,
            "quiet": false,
            "force_adds": false,
            "force_alphabetical_sort_within_sections": false,
            "force_alphabetical_sort": false,
            "force_grid_wrap": 0,
            "force_sort_within_sections": false,
            "lexicographical": false,
            "group_by_package": false,
            "ignore_whitespace": false,
            "no_lines_before": [],
            "no_inline_sort": false,
            "ignore_comments": false,
            "case_sensitive": false,
            "sources": [],
            "virtual_env": "",
            "conda_env": "",
            "ensure_newline_before_comments": false,
            "directory": "",
            "profile": "",
            "honor_noqa": false,
            "src_paths": [],
            "old_finders": false,
            "remove_redundant_aliases": false,
            "float_to_top": false,
            "filter_files": false,
            "formatter": "",
            "formatting_function": null,
            "color_output": false,
            "treat_comments_as_code": [],
            "treat_all_comments_as_code": false,
            "supported_extensions": [
                "pxd",
                "pyi",
                "py",
                "pyx"
            ],
            "blocked_extensions": [
                "pex"
            ],
            "constants": [],
            "classes": [],
            "variables": [],
            "dedup_headings": false,
            "only_sections": false,
            "only_modified": false,
            "combine_straight_imports": false,
            "auto_identify_namespace_packages": true,
            "namespace_packages": [],
            "follow_links": true,
            "indented_import_headings": true,
            "honor_case_in_force_sorted_sections": false,
            "sort_relative_in_force_sorted_sections": false,
            "overwrite_in_place": false,
            "reverse_sort": false,
            "star_first": false,
            "git_ignore": {},
            "format_error": "{error}: {message}",
            "format_success": "{success}: {message}",
            "sort_order": "natural",
            "source": "defaults"
        },
        {
            "multi_line_output": 3,
            "include_trailing_comma": true,
            "force_grid_wrap": 0,
            "use_parentheses": true,
            "ensure_newline_before_comments": true,
            "line_length": 88,
            "source": "black profile"
        },
        {
            "profile": "black",
            "multi_line_output": "VERTICAL_HANGING_INDENT",
            "line_length": 100,
            "extend_skip": [
                "tmp",
                "ext_bin",
                "ext"
            ],
            "src_paths": [
                "pymcac"
            ],
            "skip_gitignore": true,
            "source": "/Data/WORK/Projets/SRC/MCAC/pyproject.toml"
        }
    ],
    "virtual_env": "",
    "conda_env": "",
    "ensure_newline_before_comments": true,
    "directory": "/Data/WORK/Projets/SRC/MCAC",
    "profile": "black",
    "honor_noqa": false,
    "src_paths": [
        "/Data/WORK/Projets/SRC/MCAC/pymcac"
    ],
    "old_finders": false,
    "remove_redundant_aliases": false,
    "float_to_top": false,
    "filter_files": false,
    "formatter": "",
    "formatting_function": null,
    "color_output": false,
    "treat_comments_as_code": [],
    "treat_all_comments_as_code": false,
    "supported_extensions": [
        "pxd",
        "pyi",
        "py",
        "pyx"
    ],
    "blocked_extensions": [
        "pex"
    ],
    "constants": [],
    "classes": [],
    "variables": [],
    "dedup_headings": false,
    "only_sections": false,
    "only_modified": false,
    "combine_straight_imports": false,
    "auto_identify_namespace_packages": true,
    "namespace_packages": [],
    "follow_links": true,
    "indented_import_headings": true,
    "honor_case_in_force_sorted_sections": false,
    "sort_relative_in_force_sorted_sections": false,
    "overwrite_in_place": false,
    "reverse_sort": false,
    "star_first": false,
    "git_ignore": {},
    "format_error": "{error}: {message}",
    "format_success": "{success}: {message}",
    "sort_order": "natural"
}
`pyproject.toml`:
[tool.isort]
profile = "black"
multi_line_output = 3
line_length = 100
extend_skip = [
    "tmp",
    "ext",
    "ext_bin",
    ]
skip_gitignore = true

I just realize that with skip_gitignore = false, everything seems to be working OK

And I have the same results the current git version (15234f8)

@grant-zietsman
Copy link

I ran this with the latest version (installed from git) and these are the results that I am seeing.

isort --check .
ERROR: /mnt/jenkins-data/workspace/branch/.local/lib/python3.6/site-packages/appdirs.py Imports are incorrectly sorted and/or formatted.
ERROR: /mnt/jenkins-data/workspace/branch/.local/lib/python3.6/site-packages/dataclasses.py Imports are incorrectly sorted and/or formatted.
ERROR: /mnt/jenkins-data/workspace/branch/.local/lib/python3.6/site-packages/mypy_extensions.py Imports are incorrectly sorted and/or formatted.
ERROR: /mnt/jenkins-data/workspace/branch/.local/lib/python3.6/site-packages/coverage/parser.py Imports are incorrectly sorted and/or formatted.
...
isort . --show-config
{
    "_known_patterns": null,
    "_section_comments": null,
    "_skips": null,
    "_skip_globs": null,
    "_sorting_function": null,
    "py_version": "py3",
    "force_to_top": [],
    "skip": [
        "dist",
        ".venv",
        ".pants.d",
        "build",
        ".hg",
        "node_modules",
        ".mypy_cache",
        ".nox",
        "_build",
        ".direnv",
        ".eggs",
        "__pypackages__",
        ".bzr",
        ".git",
        ".svn",
        "venv",
        ".tox",
        "buck-out"
    ],
    "extend_skip": [],
    "skip_glob": [],
    "extend_skip_glob": [],
    "skip_gitignore": true,
    "line_length": 88,
    "wrap_length": 0,
    "line_ending": "",
    "sections": [
        "FUTURE",
        "STDLIB",
        "THIRDPARTY",
        "FIRSTPARTY",
        "LOCALFOLDER"
    ],
    "no_sections": false,
    "known_future_library": [
        "__future__"
    ],
    "known_third_party": [],
    "known_first_party": [],
    "known_local_folder": [],
    "known_standard_library": [
        "ssl",
        "hashlib",
        "cmd",
        "profile",
        "contextvars",
        "readline",
        "cmath",
        "runpy",
        "errno",
        "colorsys",
        "re",
        "zipfile",
        "time",
        "graphlib",
        "binascii",
        "uuid",
        "secrets",
        "datetime",
        "doctest",
        "termios",
        "ipaddress",
        "rlcompleter",
        "traceback",
        "heapq",
        "signal",
        "wsgiref",
        "textwrap",
        "posixpath",
        "pkgutil",
        "_dummy_thread",
        "stat",
        "itertools",
        "sre_parse",
        "crypt",
        "smtplib",
        "tty",
        "tempfile",
        "importlib",
        "bisect",
        "smtpd",
        "site",
        "winreg",
        "io",
        "sysconfig",
        "fnmatch",
        "ftplib",
        "multiprocessing",
        "dis",
        "symbol",
        "gzip",
        "ast",
        "array",
        "quopri",
        "getopt",
        "cgi",
        "pipes",
        "contextlib",
        "subprocess",
        "tabnanny",
        "posix",
        "tkinter",
        "netrc",
        "imghdr",
        "nntplib",
        "numbers",
        "tokenize",
        "pyclbr",
        "plistlib",
        "email",
        "mailbox",
        "audioop",
        "stringprep",
        "sys",
        "dataclasses",
        "os",
        "concurrent",
        "zlib",
        "gc",
        "decimal",
        "filecmp",
        "bdb",
        "telnetlib",
        "imaplib",
        "aifc",
        "encodings",
        "macpath",
        "shelve",
        "queue",
        "mmap",
        "csv",
        "typing",
        "optparse",
        "turtle",
        "venv",
        "compileall",
        "sched",
        "pprint",
        "shlex",
        "webbrowser",
        "ntpath",
        "sre_compile",
        "xdrlib",
        "imp",
        "socketserver",
        "sre",
        "urllib",
        "pydoc",
        "http",
        "socket",
        "tarfile",
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        "wave",
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        "difflib",
        "turtledemo",
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        "sndhdr",
        "json",
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        "inspect",
        "xmlrpc",
        "dbm",
        "calendar",
        "msilib",
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        "modulefinder",
        "ossaudiodev",
        "winsound",
        "statistics",
        "zoneinfo",
        "threading",
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        "locale",
        "pdb",
        "symtable",
        "mailcap",
        "weakref",
        "lib2to3",
        "lzma",
        "functools",
        "unicodedata",
        "cProfile",
        "grp",
        "trace",
        "distutils",
        "pickle",
        "enum",
        "poplib",
        "pwd",
        "pathlib",
        "operator",
        "ensurepip",
        "argparse",
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        "nis",
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        "ctypes",
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        "codeop"
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    "forced_separate": [],
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    "append_only": false,
    "reverse_relative": false,
    "force_single_line": false,
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    "default_section": "THIRDPARTY",
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    "use_parentheses": true,
    "order_by_type": true,
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    "group_by_package": false,
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    "ignore_comments": false,
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            "force_to_top": [],
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                "sunau",
                "html",
                "wave",
                "linecache",
                "fcntl",
                "fileinput",
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                "py_compile",
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                "codecs",
                "syslog",
                "configparser",
                "asyncore",
                "code",
                "abc",
                "zipimport",
                "copyreg",
                "reprlib",
                "timeit",
                "difflib",
                "turtledemo",
                "curses",
                "sre_constants",
                "msvcrt",
                "_thread",
                "sndhdr",
                "json",
                "binhex",
                "getpass",
                "logging",
                "test",
                "types",
                "tracemalloc",
                "inspect",
                "xmlrpc",
                "dbm",
                "calendar",
                "msilib",
                "math",
                "modulefinder",
                "ossaudiodev",
                "winsound",
                "statistics",
                "zoneinfo",
                "threading",
                "parser",
                "locale",
                "pdb",
                "symtable",
                "mailcap",
                "weakref",
                "lib2to3",
                "lzma",
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                "unicodedata",
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                "grp",
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                "enum",
                "poplib",
                "pwd",
                "pathlib",
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            "verbose": false,
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            "force_adds": false,
            "force_alphabetical_sort_within_sections": false,
            "force_alphabetical_sort": false,
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            "lexicographical": false,
            "group_by_package": false,
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            "case_sensitive": false,
            "sources": [],
            "virtual_env": "",
            "conda_env": "",
            "ensure_newline_before_comments": false,
            "directory": "",
            "profile": "",
            "honor_noqa": false,
            "src_paths": [],
            "old_finders": false,
            "remove_redundant_aliases": false,
            "float_to_top": false,
            "filter_files": false,
            "formatter": "",
            "formatting_function": null,
            "color_output": false,
            "treat_comments_as_code": [],
            "treat_all_comments_as_code": false,
            "supported_extensions": [
                "pyi",
                "pyx",
                "pxd",
                "py"
            ],
            "blocked_extensions": [
                "pex"
            ],
            "constants": [],
            "classes": [],
            "variables": [],
            "dedup_headings": false,
            "only_sections": false,
            "only_modified": false,
            "combine_straight_imports": false,
            "auto_identify_namespace_packages": true,
            "namespace_packages": [],
            "follow_links": true,
            "indented_import_headings": true,
            "honor_case_in_force_sorted_sections": false,
            "sort_relative_in_force_sorted_sections": false,
            "overwrite_in_place": false,
            "reverse_sort": false,
            "star_first": false,
            "git_ignore": {},
            "format_error": "{error}: {message}",
            "format_success": "{success}: {message}",
            "sort_order": "natural",
            "source": "defaults"
        },
        {
            "multi_line_output": "VERTICAL_HANGING_INDENT",
            "include_trailing_comma": true,
            "force_grid_wrap": 0,
            "use_parentheses": true,
            "ensure_newline_before_comments": true,
            "line_length": 88,
            "skip_gitignore": true,
            "source": "/mnt/jenkins-data/workspace/branch/.isort.cfg"
        }
    ],
    "virtual_env": "",
    "conda_env": "",
    "ensure_newline_before_comments": true,
    "directory": "/mnt/jenkins-data/workspace/branch",
    "profile": "",
    "honor_noqa": false,
    "src_paths": [
        "/mnt/jenkins-data/workspace/branch/src",
        "/mnt/jenkins-data/workspace/branch"
    ],
    "old_finders": false,
    "remove_redundant_aliases": false,
    "float_to_top": false,
    "filter_files": false,
    "formatter": "",
    "formatting_function": null,
    "color_output": false,
    "treat_comments_as_code": [],
    "treat_all_comments_as_code": false,
    "supported_extensions": [
        "pyi",
        "pyx",
        "pxd",
        "py"
    ],
    "blocked_extensions": [
        "pex"
    ],
    "constants": [],
    "classes": [],
    "variables": [],
    "dedup_headings": false,
    "only_sections": false,
    "only_modified": false,
    "combine_straight_imports": false,
    "auto_identify_namespace_packages": true,
    "namespace_packages": [],
    "follow_links": true,
    "indented_import_headings": true,
    "honor_case_in_force_sorted_sections": false,
    "sort_relative_in_force_sorted_sections": false,
    "overwrite_in_place": false,
    "reverse_sort": false,
    "star_first": false,
    "git_ignore": {},
    "format_error": "{error}: {message}",
    "format_success": "{success}: {message}",
    "sort_order": "natural"
}
cat .gitignore
...

.local

...

@tahmidmehdi
Copy link

I also have this issue with isort 5.9.1. I installed the latest version ( 23d708e ) from git & the issue persisted.

isort . --show-config

{
    "_known_patterns": null,
    "_section_comments": null,
    "_skips": null,
    "_skip_globs": null,
    "_sorting_function": null,
    "py_version": "py3",
    "force_to_top": [],
    "skip": [
        "environment.py"
    ],
    "extend_skip": [],
    "skip_glob": [],
    "extend_skip_glob": [],
    "skip_gitignore": true,
    "line_length": 88,
    "wrap_length": 0,
    "line_ending": "",
    "sections": [
        "FUTURE",
        "STDLIB",
        "THIRDPARTY",
        "FIRSTPARTY",
        "LOCALFOLDER"
    ],
    "no_sections": false,
    "known_future_library": [
        "__future__"
    ],
    "known_third_party": [],
    "known_first_party": [],
    "known_local_folder": [],
    "known_standard_library": [
        "zoneinfo",
        "syslog",
        "lib2to3",
        "getpass",
        "xml",
        "imghdr",
        "turtle",
        "graphlib",
        "time",
        "tkinter",
        "binhex",
        "rlcompleter",
        "xdrlib",
        "datetime",
        "socketserver",
        "mimetypes",
        "keyword",
        "array",
        "lzma",
        "select",
        "sunau",
        "chunk",
        "functools",
        "imaplib",
        "venv",
        "bz2",
        "types",
        "sched",
        "getopt",
        "stringprep",
        "gzip",
        "codeop",
        "gettext",
        "traceback",
        "webbrowser",
        "io",
        "ensurepip",
        "bisect",
        "curses",
        "sre_compile",
        "os",
        "copyreg",
        "ast",
        "poplib",
        "py_compile",
        "bdb",
        "hashlib",
        "base64",
        "struct",
        "linecache",
        "pkgutil",
        "queue",
        "hmac",
        "asyncio",
        "xmlrpc",
        "cmd",
        "dataclasses",
        "cmath",
        "string",
        "code",
        "math",
        "spwd",
        "pyclbr",
        "grp",
        "inspect",
        "sre",
        "encodings",
        "itertools",
        "wave",
        "termios",
        "shutil",
        "codecs",
        "ssl",
        "plistlib",
        "mailcap",
        "reprlib",
        "fpectl",
        "multiprocessing",
        "subprocess",
        "pstats",
        "shelve",
        "asynchat",
        "configparser",
        "pipes",
        "aifc",
        "doctest",
        "msilib",
        "fnmatch",
        "tempfile",
        "fractions",
        "logging",
        "contextvars",
        "tty",
        "builtins",
        "random",
        "contextlib",
        "decimal",
        "distutils",
        "ftplib",
        "trace",
        "winsound",
        "dis",
        "symbol",
        "smtplib",
        "signal",
        "optparse",
        "html",
        "readline",
        "zipapp",
        "netrc",
        "ossaudiodev",
        "posix",
        "numbers",
        "sndhdr",
        "concurrent",
        "http",
        "typing",
        "marshal",
        "sre_parse",
        "uu",
        "fcntl",
        "pickle",
        "token",
        "argparse",
        "smtpd",
        "stat",
        "tabnanny",
        "dbm",
        "gc",
        "pty",
        "formatter",
        "json",
        "filecmp",
        "importlib",
        "fileinput",
        "macpath",
        "quopri",
        "nntplib",
        "sysconfig",
        "compileall",
        "urllib",
        "dummy_threading",
        "difflib",
        "email",
        "site",
        "symtable",
        "uuid",
        "csv",
        "sys",
        "cProfile",
        "zlib",
        "statistics",
        "colorsys",
        "glob",
        "copy",
        "faulthandler",
        "resource",
        "wsgiref",
        "nis",
        "locale",
        "crypt",
        "pathlib",
        "tracemalloc",
        "audioop",
        "cgi",
        "enum",
        "tokenize",
        "sre_constants",
        "asyncore",
        "winreg",
        "mailbox",
        "secrets",
        "ctypes",
        "atexit",
        "calendar",
        "ipaddress",
        "warnings",
        "abc",
        "tarfile",
        "cgitb",
        "pdb",
        "msvcrt",
        "pwd",
        "runpy",
        "zipimport",
        "modulefinder",
        "sqlite3",
        "pydoc",
        "textwrap",
        "_thread",
        "heapq",
        "test",
        "timeit",
        "unicodedata",
        "turtledemo",
        "ntpath",
        "telnetlib",
        "unittest",
        "errno",
        "zipfile",
        "operator",
        "posixpath",
        "pprint",
        "re",
        "profile",
        "selectors",
        "_dummy_thread",
        "platform",
        "pickletools",
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        "socket",
        "collections",
        "binascii",
        "mmap",
        "shlex",
        "threading",
        "weakref",
        "imp"
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    "forced_separate": [],
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    "length_sort": false,
    "length_sort_straight": false,
    "length_sort_sections": [],
    "add_imports": [],
    "remove_imports": [],
    "append_only": false,
    "reverse_relative": false,
    "force_single_line": false,
    "single_line_exclusions": [],
    "default_section": "THIRDPARTY",
    "import_headings": {},
    "balanced_wrapping": false,
    "use_parentheses": true,
    "order_by_type": true,
    "atomic": false,
    "lines_after_imports": -1,
    "lines_between_sections": 1,
    "lines_between_types": 0,
    "combine_as_imports": false,
    "combine_star": false,
    "include_trailing_comma": true,
    "from_first": false,
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    "force_alphabetical_sort_within_sections": false,
    "force_alphabetical_sort": false,
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                "build",
                ".bzr",
                ".eggs",
                ".mypy_cache",
                "buck-out",
                ".hg",
                "_build",
                ".nox",
                ".tox"
            ],
            "extend_skip": [],
            "skip_glob": [],
            "extend_skip_glob": [],
            "skip_gitignore": false,
            "line_length": 79,
            "wrap_length": 0,
            "line_ending": "",
            "sections": [
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                "STDLIB",
                "THIRDPARTY",
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                "LOCALFOLDER"
            ],
            "no_sections": false,
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                "__future__"
            ],
            "known_third_party": [],
            "known_first_party": [],
            "known_local_folder": [],
            "known_standard_library": [
                "zoneinfo",
                "syslog",
                "lib2to3",
                "getpass",
                "xml",
                "imghdr",
                "turtle",
                "graphlib",
                "time",
                "tkinter",
                "binhex",
                "rlcompleter",
                "xdrlib",
                "datetime",
                "socketserver",
                "mimetypes",
                "keyword",
                "array",
                "lzma",
                "select",
                "sunau",
                "chunk",
                "functools",
                "imaplib",
                "venv",
                "bz2",
                "types",
                "sched",
                "getopt",
                "stringprep",
                "gzip",
                "codeop",
                "gettext",
                "traceback",
                "webbrowser",
                "io",
                "ensurepip",
                "bisect",
                "curses",
                "sre_compile",
                "os",
                "copyreg",
                "ast",
                "poplib",
                "py_compile",
                "bdb",
                "hashlib",
                "base64",
                "struct",
                "linecache",
                "pkgutil",
                "queue",
                "hmac",
                "asyncio",
                "xmlrpc",
                "cmd",
                "dataclasses",
                "cmath",
                "string",
                "code",
                "math",
                "spwd",
                "pyclbr",
                "grp",
                "inspect",
                "sre",
                "encodings",
                "itertools",
                "wave",
                "termios",
                "shutil",
                "codecs",
                "ssl",
                "plistlib",
                "mailcap",
                "reprlib",
                "fpectl",
                "multiprocessing",
                "subprocess",
                "pstats",
                "shelve",
                "asynchat",
                "configparser",
                "pipes",
                "aifc",
                "doctest",
                "msilib",
                "fnmatch",
                "tempfile",
                "fractions",
                "logging",
                "contextvars",
                "tty",
                "builtins",
                "random",
                "contextlib",
                "decimal",
                "distutils",
                "ftplib",
                "trace",
                "winsound",
                "dis",
                "symbol",
                "smtplib",
                "signal",
                "optparse",
                "html",
                "readline",
                "zipapp",
                "netrc",
                "ossaudiodev",
                "posix",
                "numbers",
                "sndhdr",
                "concurrent",
                "http",
                "typing",
                "marshal",
                "sre_parse",
                "uu",
                "fcntl",
                "pickle",
                "token",
                "argparse",
                "smtpd",
                "stat",
                "tabnanny",
                "dbm",
                "gc",
                "pty",
                "formatter",
                "json",
                "filecmp",
                "importlib",
                "fileinput",
                "macpath",
                "quopri",
                "nntplib",
                "sysconfig",
                "compileall",
                "urllib",
                "dummy_threading",
                "difflib",
                "email",
                "site",
                "symtable",
                "uuid",
                "csv",
                "sys",
                "cProfile",
                "zlib",
                "statistics",
                "colorsys",
                "glob",
                "copy",
                "faulthandler",
                "resource",
                "wsgiref",
                "nis",
                "locale",
                "crypt",
                "pathlib",
                "tracemalloc",
                "audioop",
                "cgi",
                "enum",
                "tokenize",
                "sre_constants",
                "asyncore",
                "winreg",
                "mailbox",
                "secrets",
                "ctypes",
                "atexit",
                "calendar",
                "ipaddress",
                "warnings",
                "abc",
                "tarfile",
                "cgitb",
                "pdb",
                "msvcrt",
                "pwd",
                "runpy",
                "zipimport",
                "modulefinder",
                "sqlite3",
                "pydoc",
                "textwrap",
                "_thread",
                "heapq",
                "test",
                "timeit",
                "unicodedata",
                "turtledemo",
                "ntpath",
                "telnetlib",
                "unittest",
                "errno",
                "zipfile",
                "operator",
                "posixpath",
                "pprint",
                "re",
                "profile",
                "selectors",
                "_dummy_thread",
                "platform",
                "pickletools",
                "parser",
                "socket",
                "collections",
                "binascii",
                "mmap",
                "shlex",
                "threading",
                "weakref",
                "imp"
            ],
            "extra_standard_library": [],
            "known_other": {},
            "multi_line_output": "GRID",
            "forced_separate": [],
            "indent": "    ",
            "comment_prefix": "  #",
            "length_sort": false,
            "length_sort_straight": false,
            "length_sort_sections": [],
            "add_imports": [],
            "remove_imports": [],
            "append_only": false,
            "reverse_relative": false,
            "force_single_line": false,
            "single_line_exclusions": [],
            "default_section": "THIRDPARTY",
            "import_headings": {},
            "balanced_wrapping": false,
            "use_parentheses": false,
            "order_by_type": true,
            "atomic": false,
            "lines_after_imports": -1,
            "lines_between_sections": 1,
            "lines_between_types": 0,
            "combine_as_imports": false,
            "combine_star": false,
            "include_trailing_comma": false,
            "from_first": false,
            "verbose": false,
            "quiet": false,
            "force_adds": false,
            "force_alphabetical_sort_within_sections": false,
            "force_alphabetical_sort": false,
            "force_grid_wrap": 0,
            "force_sort_within_sections": false,
            "lexicographical": false,
            "group_by_package": false,
            "ignore_whitespace": false,
            "no_lines_before": [],
            "no_inline_sort": false,
            "ignore_comments": false,
            "case_sensitive": false,
            "sources": [],
            "virtual_env": "",
            "conda_env": "",
            "ensure_newline_before_comments": false,
            "directory": "",
            "profile": "",
            "honor_noqa": false,
            "src_paths": [],
            "old_finders": false,
            "remove_redundant_aliases": false,
            "float_to_top": false,
            "filter_files": false,
            "formatter": "",
            "formatting_function": null,
            "color_output": false,
            "treat_comments_as_code": [],
            "treat_all_comments_as_code": false,
            "supported_extensions": [
                "py",
                "pxd",
                "pyi",
                "pyx"
            ],
            "blocked_extensions": [
                "pex"
            ],
            "constants": [],
            "classes": [],
            "variables": [],
            "dedup_headings": false,
            "only_sections": false,
            "only_modified": false,
            "combine_straight_imports": false,
            "auto_identify_namespace_packages": true,
            "namespace_packages": [],
            "follow_links": true,
            "indented_import_headings": true,
            "honor_case_in_force_sorted_sections": false,
            "sort_relative_in_force_sorted_sections": false,
            "overwrite_in_place": false,
            "reverse_sort": false,
            "star_first": false,
            "git_ignore": {},
            "format_error": "{error}: {message}",
            "format_success": "{success}: {message}",
            "sort_order": "natural",
            "source": "defaults"
        },
        {
            "multi_line_output": "VERTICAL_HANGING_INDENT",
            "include_trailing_comma": true,
            "force_grid_wrap": 0,
            "use_parentheses": true,
            "line_length": 88,
            "skip": [
                "environment.py"
            ],
            "skip_gitignore": true,
            "source": "C:\\Users\\tfmehdi\\PycharmProjects\\api\\.isort.cfg"
        }
    ],
    "virtual_env": "",
    "conda_env": "",
    "ensure_newline_before_comments": false,
    "directory": "C:\\Users\\tfmehdi\\PycharmProjects\\api",
    "profile": "",
    "honor_noqa": false,
    "src_paths": [
        "C:\\Users\\tfmehdi\\PycharmProjects\\api\\src",
        "C:\\Users\\tfmehdi\\PycharmProjects\\api"
    ],
    "old_finders": false,
    "remove_redundant_aliases": false,
    "float_to_top": false,
    "filter_files": false,
    "formatter": "",
    "formatting_function": null,
    "color_output": false,
    "treat_comments_as_code": [],
    "treat_all_comments_as_code": false,
    "supported_extensions": [
        "py",
        "pxd",
        "pyi",
        "pyx"
    ],
    "blocked_extensions": [
        "pex"
    ],
    "constants": [],
    "classes": [],
    "variables": [],
    "dedup_headings": false,
    "only_sections": false,
    "only_modified": false,
    "combine_straight_imports": false,
    "auto_identify_namespace_packages": true,
    "namespace_packages": [],
    "follow_links": true,
    "indented_import_headings": true,
    "honor_case_in_force_sorted_sections": false,
    "sort_relative_in_force_sorted_sections": false,
    "overwrite_in_place": false,
    "reverse_sort": false,
    "star_first": false,
    "git_ignore": {},
    "format_error": "{error}: {message}",
    "format_success": "{success}: {message}",
    "sort_order": "natural"
}

.isort.cfg

[settings]
multi_line_output=3
include_trailing_comma=True
force_grid_wrap=0
use_parentheses=True
line_length=88
skip=environment.py
skip_gitignore=True

The file specified with skip= is skipped as expected but the files & folders in .gitignore aren't skipped.

.gitignore

.venv/
.vscode/
.idea/
.pytest_cache/
__pycache__/
.env

@jaidisido
Copy link

jaidisido commented Jun 29, 2021

Same issue here when using 5.9.0 or 5.9.1 with a pyproject.toml:

[tool.isort]
multi_line_output = 3
include_trailing_comma = true
force_grid_wrap = 0
use_parentheses = true
ensure_newline_before_comments = true
line_length = 120
src_paths = ["setup.py", "awswrangler"]
py_version = 37
skip_gitignore = true

my entire .env Python environment is scanned by isort when it was previously ignore. Worked fine with 5.8.0

@johnthagen
Copy link

johnthagen commented Jul 2, 2021

I also experienced this as well with 5.9.1, and as a user it was very difficult to pin down what was going on because isort simply took a very long time to complete, but I couldn't figure out why. Specifically, I think isort was processing the .tox and venv folders that are ignored in Git which have thousands of .py files in them.

I observed this behavior on Windows and macOS. Reverting to 5.8.0 fixed this issue.

pyproject.toml:

[tool.isort]
profile = "black"
line_length = 99
force_sort_within_sections = true
skip_gitignore = true

.gitignore:

# See https://help.github.com/articles/ignoring-files/ for more about ignoring files.

# Dependencies
/node_modules
/.pnp
.pnp.js

# Testing
/coverage*
/Backend.Tests/coverage*

# Production
/build

# Generated Docker files for development use
docker-compose.yml
.env.*
.env*.local
nginx/scripts
/backups
/restore
script_conf.json
backup_conf.json

# Misc
.DS_Store
.eslintcache
Session.vim
scripts/*.js
!scripts/printVersion.js

npm-debug.log*
yarn-debug.log*
yarn-error.log*

# Visual Studio
.vs/*

# Backend
Backend/.vs/**/*
Backend/bin
Backend/obj
Backend/build
/**/obj/**/*
Backend.Tests/bin
Backend.Tests/obj
Backend/BackendFramework.csproj.user
BackendFramework.sln.DotSettings.user
Backend/.vscode/**/*
Backend/SIL.Lift/**/*
Backend/ql-database
/**/*.xml
/**/*.lift
/**/*.orig
Backend.Tests/bin/Audio/*.mp3
/**/*.~un
/**/*.swp
Backend.Tests/bin/Avatars/*
mongo_database

# User Guide
docs/user_guide/site

# Vagrant instances
.vagrant/

# Python
.tox
.mypy_cache
__pycache__
*.pyc
venv

# Host file to be used for ad hoc testing/development
deploy/*.hosts.yml

# YAML files for ad hoc testing/development
_*.yml

# Emacs backup files (this is Jim's fault)
*~
\#*#

# JetBrains Rider
.idea

@timothycrosley
Copy link
Member

I'm sorry everyone is continuing to experience this! There have been 2 major fixes against the git ignore behavior in the main branch since this was last experienced (I myself have not been able to get this to happen). Can someone who is experiencing this issue try against latest main and see if it is resolved?

@jaidisido
Copy link

Tested pip install from current main and it seems to have fixed it for me, thanks

@timothycrosley
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Member

@jaidisido thanks for testing! 5.9.2 has been pushed which should resolve this issue.

@pums974
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Author

pums974 commented Jul 8, 2021

Hi,
I still have the issue with the version 5.9.2, although it is a bit different.
fatal: Pathspec '/some/path/other_project/setup.py' is in submodule 'other_project

where other_project is a git submodule, not in .gitignore but in extend_skip

If I put my venv in extend_skip and turn off skip_gitignore, everything seems to be working fine

`isort . --show-config`:
{
    "_known_patterns": null,
    "_section_comments": null,
    "_skips": null,
    "_skip_globs": null,
    "_sorting_function": null,
    "py_version": "py3",
    "force_to_top": [],
    "skip": [
        "__pypackages__",
        ".tox",
        "dist",
        ".nox",
        ".venv",
        "build",
        ".mypy_cache",
        ".direnv",
        ".bzr",
        "venv",
        ".eggs",
        "buck-out",
        ".git",
        "node_modules",
        ".hg",
        ".svn",
        "_build",
        ".pants.d"
    ],
    "extend_skip": [
        "other_project"
    ],
    "skip_glob": [],
    "extend_skip_glob": [],
    "skip_gitignore": true,
    "line_length": 100,
    "wrap_length": 0,
    "line_ending": "",
    "sections": [
        "FUTURE",
        "STDLIB",
        "THIRDPARTY",
        "FIRSTPARTY",
        "LOCALFOLDER"
    ],
    "no_sections": false,
    "known_future_library": [
        "__future__"
    ],
    "known_third_party": [],
    "known_first_party": [],
    "known_local_folder": [],
    "known_standard_library": [
        "shelve",
        "formatter",
        "struct",
        "pstats",
        "sys",
        "imp",
        "imaplib",
        "pkgutil",
        "trace",
        "pprint",
        "fcntl",
        "symtable",
        "rlcompleter",
        "msilib",
        "tempfile",
        "tarfile",
        "json",
        "msvcrt",
        "pickle",
        "uu",
        "grp",
        "statistics",
        "keyword",
        "cmd",
        "difflib",
        "string",
        "hashlib",
        "argparse",
        "site",
        "itertools",
        "pipes",
        "tokenize",
        "faulthandler",
        "tracemalloc",
        "cmath",
        "smtplib",
        "datetime",
        "ast",
        "winreg",
        "aifc",
        "netrc",
        "pydoc",
        "ntpath",
        "subprocess",
        "zipimport",
        "importlib",
        "zipapp",
        "curses",
        "_dummy_thread",
        "resource",
        "multiprocessing",
        "bdb",
        "email",
        "gettext",
        "fractions",
        "tkinter",
        "gc",
        "select",
        "unittest",
        "warnings",
        "timeit",
        "sqlite3",
        "encodings",
        "zoneinfo",
        "reprlib",
        "math",
        "chunk",
        "readline",
        "pyclbr",
        "binascii",
        "binhex",
        "inspect",
        "random",
        "zipfile",
        "imghdr",
        "xmlrpc",
        "operator",
        "sre",
        "typing",
        "atexit",
        "pty",
        "stat",
        "ctypes",
        "compileall",
        "urllib",
        "wsgiref",
        "asyncio",
        "html",
        "macpath",
        "sre_compile",
        "csv",
        "crypt",
        "copyreg",
        "abc",
        "types",
        "zlib",
        "lib2to3",
        "linecache",
        "shlex",
        "dataclasses",
        "poplib",
        "mimetypes",
        "io",
        "smtpd",
        "colorsys",
        "pwd",
        "dbm",
        "contextlib",
        "glob",
        "unicodedata",
        "concurrent",
        "array",
        "hmac",
        "asyncore",
        "graphlib",
        "time",
        "venv",
        "profile",
        "builtins",
        "ensurepip",
        "sunau",
        "bz2",
        "mmap",
        "sched",
        "http",
        "queue",
        "sre_parse",
        "posix",
        "uuid",
        "contextvars",
        "mailcap",
        "cgitb",
        "telnetlib",
        "mailbox",
        "token",
        "marshal",
        "doctest",
        "wave",
        "functools",
        "copy",
        "nntplib",
        "ossaudiodev",
        "fnmatch",
        "termios",
        "selectors",
        "pathlib",
        "tabnanny",
        "tty",
        "sndhdr",
        "fileinput",
        "posixpath",
        "locale",
        "webbrowser",
        "enum",
        "dis",
        "quopri",
        "codeop",
        "numbers",
        "threading",
        "secrets",
        "calendar",
        "ssl",
        "base64",
        "heapq",
        "collections",
        "turtledemo",
        "getpass",
        "stringprep",
        "ftplib",
        "xdrlib",
        "lzma",
        "_thread",
        "test",
        "xml",
        "sre_constants",
        "asynchat",
        "socketserver",
        "pdb",
        "nis",
        "symbol",
        "codecs",
        "os",
        "filecmp",
        "textwrap",
        "code",
        "getopt",
        "re",
        "logging",
        "plistlib",
        "parser",
        "cProfile",
        "dummy_threading",
        "bisect",
        "shutil",
        "py_compile",
        "socket",
        "configparser",
        "sysconfig",
        "distutils",
        "gzip",
        "pickletools",
        "optparse",
        "turtle",
        "runpy",
        "syslog",
        "fpectl",
        "ipaddress",
        "errno",
        "modulefinder",
        "winsound",
        "cgi",
        "weakref",
        "spwd",
        "audioop",
        "traceback",
        "signal",
        "decimal",
        "platform"
    ],
    "extra_standard_library": [],
    "known_other": {},
    "multi_line_output": "VERTICAL_HANGING_INDENT",
    "forced_separate": [],
    "indent": "    ",
    "comment_prefix": "  #",
    "length_sort": false,
    "length_sort_straight": false,
    "length_sort_sections": [],
    "add_imports": [],
    "remove_imports": [],
    "append_only": false,
    "reverse_relative": false,
    "force_single_line": false,
    "single_line_exclusions": [],
    "default_section": "THIRDPARTY",
    "import_headings": {},
    "balanced_wrapping": false,
    "use_parentheses": true,
    "order_by_type": true,
    "atomic": false,
    "lines_after_imports": -1,
    "lines_between_sections": 1,
    "lines_between_types": 0,
    "combine_as_imports": false,
    "combine_star": false,
    "include_trailing_comma": true,
    "from_first": false,
    "verbose": false,
    "quiet": false,
    "force_adds": false,
    "force_alphabetical_sort_within_sections": false,
    "force_alphabetical_sort": false,
    "force_grid_wrap": 0,
    "force_sort_within_sections": false,
    "lexicographical": false,
    "group_by_package": false,
    "ignore_whitespace": false,
    "no_lines_before": [],
    "no_inline_sort": false,
    "ignore_comments": false,
    "case_sensitive": false,
    "sources": [
        {
            "py_version": "py3",
            "force_to_top": [],
            "skip": [
                "__pypackages__",
                ".tox",
                "dist",
                ".nox",
                ".venv",
                "build",
                ".mypy_cache",
                ".direnv",
                ".bzr",
                "venv",
                ".eggs",
                "buck-out",
                ".git",
                "node_modules",
                ".hg",
                ".svn",
                "_build",
                ".pants.d"
            ],
            "extend_skip": [],
            "skip_glob": [],
            "extend_skip_glob": [],
            "skip_gitignore": false,
            "line_length": 79,
            "wrap_length": 0,
            "line_ending": "",
            "sections": [
                "FUTURE",
                "STDLIB",
                "THIRDPARTY",
                "FIRSTPARTY",
                "LOCALFOLDER"
            ],
            "no_sections": false,
            "known_future_library": [
                "__future__"
            ],
            "known_third_party": [],
            "known_first_party": [],
            "known_local_folder": [],
            "known_standard_library": [
                "shelve",
                "formatter",
                "struct",
                "pstats",
                "sys",
                "imp",
                "imaplib",
                "pkgutil",
                "trace",
                "pprint",
                "fcntl",
                "symtable",
                "rlcompleter",
                "msilib",
                "tempfile",
                "tarfile",
                "json",
                "msvcrt",
                "pickle",
                "uu",
                "grp",
                "statistics",
                "keyword",
                "cmd",
                "difflib",
                "string",
                "hashlib",
                "argparse",
                "site",
                "itertools",
                "pipes",
                "tokenize",
                "faulthandler",
                "tracemalloc",
                "cmath",
                "smtplib",
                "datetime",
                "ast",
                "winreg",
                "aifc",
                "netrc",
                "pydoc",
                "ntpath",
                "subprocess",
                "zipimport",
                "importlib",
                "zipapp",
                "curses",
                "_dummy_thread",
                "resource",
                "multiprocessing",
                "bdb",
                "email",
                "gettext",
                "fractions",
                "tkinter",
                "gc",
                "select",
                "unittest",
                "warnings",
                "timeit",
                "sqlite3",
                "encodings",
                "zoneinfo",
                "reprlib",
                "math",
                "chunk",
                "readline",
                "pyclbr",
                "binascii",
                "binhex",
                "inspect",
                "random",
                "zipfile",
                "imghdr",
                "xmlrpc",
                "operator",
                "sre",
                "typing",
                "atexit",
                "pty",
                "stat",
                "ctypes",
                "compileall",
                "urllib",
                "wsgiref",
                "asyncio",
                "html",
                "macpath",
                "sre_compile",
                "csv",
                "crypt",
                "copyreg",
                "abc",
                "types",
                "zlib",
                "lib2to3",
                "linecache",
                "shlex",
                "dataclasses",
                "poplib",
                "mimetypes",
                "io",
                "smtpd",
                "colorsys",
                "pwd",
                "dbm",
                "contextlib",
                "glob",
                "unicodedata",
                "concurrent",
                "array",
                "hmac",
                "asyncore",
                "graphlib",
                "time",
                "venv",
                "profile",
                "builtins",
                "ensurepip",
                "sunau",
                "bz2",
                "mmap",
                "sched",
                "http",
                "queue",
                "sre_parse",
                "posix",
                "uuid",
                "contextvars",
                "mailcap",
                "cgitb",
                "telnetlib",
                "mailbox",
                "token",
                "marshal",
                "doctest",
                "wave",
                "functools",
                "copy",
                "nntplib",
                "ossaudiodev",
                "fnmatch",
                "termios",
                "selectors",
                "pathlib",
                "tabnanny",
                "tty",
                "sndhdr",
                "fileinput",
                "posixpath",
                "locale",
                "webbrowser",
                "enum",
                "dis",
                "quopri",
                "codeop",
                "numbers",
                "threading",
                "secrets",
                "calendar",
                "ssl",
                "base64",
                "heapq",
                "collections",
                "turtledemo",
                "getpass",
                "stringprep",
                "ftplib",
                "xdrlib",
                "lzma",
                "_thread",
                "test",
                "xml",
                "sre_constants",
                "asynchat",
                "socketserver",
                "pdb",
                "nis",
                "symbol",
                "codecs",
                "os",
                "filecmp",
                "textwrap",
                "code",
                "getopt",
                "re",
                "logging",
                "plistlib",
                "parser",
                "cProfile",
                "dummy_threading",
                "bisect",
                "shutil",
                "py_compile",
                "socket",
                "configparser",
                "sysconfig",
                "distutils",
                "gzip",
                "pickletools",
                "optparse",
                "turtle",
                "runpy",
                "syslog",
                "fpectl",
                "ipaddress",
                "errno",
                "modulefinder",
                "winsound",
                "cgi",
                "weakref",
                "spwd",
                "audioop",
                "traceback",
                "signal",
                "decimal",
                "platform"
            ],
            "extra_standard_library": [],
            "known_other": {},
            "multi_line_output": "GRID",
            "forced_separate": [],
            "indent": "    ",
            "comment_prefix": "  #",
            "length_sort": false,
            "length_sort_straight": false,
            "length_sort_sections": [],
            "add_imports": [],
            "remove_imports": [],
            "append_only": false,
            "reverse_relative": false,
            "force_single_line": false,
            "single_line_exclusions": [],
            "default_section": "THIRDPARTY",
            "import_headings": {},
            "balanced_wrapping": false,
            "use_parentheses": false,
            "order_by_type": true,
            "atomic": false,
            "lines_after_imports": -1,
            "lines_between_sections": 1,
            "lines_between_types": 0,
            "combine_as_imports": false,
            "combine_star": false,
            "include_trailing_comma": false,
            "from_first": false,
            "verbose": false,
            "quiet": false,
            "force_adds": false,
            "force_alphabetical_sort_within_sections": false,
            "force_alphabetical_sort": false,
            "force_grid_wrap": 0,
            "force_sort_within_sections": false,
            "lexicographical": false,
            "group_by_package": false,
            "ignore_whitespace": false,
            "no_lines_before": [],
            "no_inline_sort": false,
            "ignore_comments": false,
            "case_sensitive": false,
            "sources": [],
            "virtual_env": "",
            "conda_env": "",
            "ensure_newline_before_comments": false,
            "directory": "",
            "profile": "",
            "honor_noqa": false,
            "src_paths": [],
            "old_finders": false,
            "remove_redundant_aliases": false,
            "float_to_top": false,
            "filter_files": false,
            "formatter": "",
            "formatting_function": null,
            "color_output": false,
            "treat_comments_as_code": [],
            "treat_all_comments_as_code": false,
            "supported_extensions": [
                "py",
                "pyi",
                "pxd",
                "pyx"
            ],
            "blocked_extensions": [
                "pex"
            ],
            "constants": [],
            "classes": [],
            "variables": [],
            "dedup_headings": false,
            "only_sections": false,
            "only_modified": false,
            "combine_straight_imports": false,
            "auto_identify_namespace_packages": true,
            "namespace_packages": [],
            "follow_links": true,
            "indented_import_headings": true,
            "honor_case_in_force_sorted_sections": false,
            "sort_relative_in_force_sorted_sections": false,
            "overwrite_in_place": false,
            "reverse_sort": false,
            "star_first": false,
            "git_ignore": {},
            "format_error": "{error}: {message}",
            "format_success": "{success}: {message}",
            "sort_order": "natural",
            "source": "defaults"
        },
        {
            "multi_line_output": 3,
            "include_trailing_comma": true,
            "force_grid_wrap": 0,
            "use_parentheses": true,
            "ensure_newline_before_comments": true,
            "line_length": 88,
            "source": "black profile"
        },
        {
            "profile": "black",
            "multi_line_output": "VERTICAL_HANGING_INDENT",
            "line_length": 100,
            "extend_skip": [
                "other_project"
            ],
            "skip_gitignore": true,
            "source": "/some/path/pyproject.toml"
        }
    ],
    "virtual_env": "",
    "conda_env": "",
    "ensure_newline_before_comments": true,
    "directory": "/some/path",
    "profile": "black",
    "honor_noqa": false,
    "src_paths": [
        "/some/path/src",
        "/some/path"
    ],
    "old_finders": false,
    "remove_redundant_aliases": false,
    "float_to_top": false,
    "filter_files": false,
    "formatter": "",
    "formatting_function": null,
    "color_output": false,
    "treat_comments_as_code": [],
    "treat_all_comments_as_code": false,
    "supported_extensions": [
        "py",
        "pyi",
        "pxd",
        "pyx"
    ],
    "blocked_extensions": [
        "pex"
    ],
    "constants": [],
    "classes": [],
    "variables": [],
    "dedup_headings": false,
    "only_sections": false,
    "only_modified": false,
    "combine_straight_imports": false,
    "auto_identify_namespace_packages": true,
    "namespace_packages": [],
    "follow_links": true,
    "indented_import_headings": true,
    "honor_case_in_force_sorted_sections": false,
    "sort_relative_in_force_sorted_sections": false,
    "overwrite_in_place": false,
    "reverse_sort": false,
    "star_first": false,
    "git_ignore": {},
    "format_error": "{error}: {message}",
    "format_success": "{success}: {message}",
    "sort_order": "natural"
}
`pyproject.toml`:
[tool.isort]
profile = "black"
multi_line_output = 3
line_length = 100
extend_skip = [
    "other_project",
    ]
skip_gitignore = true

@johnthagen
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johnthagen commented Jul 8, 2021

@timothycrosley 5.9.2 seemed to fix the issue for me. Though when I ran with -v I was surprised to see no mention of skip_gitignore. Each of the skipped folders below is actually skipped because they are listed in .gitignore.

.tox was skipped as it's listed in 'skip' setting or matches a glob in 'skip_glob' setting
dist was skipped as it's listed in 'skip' setting or matches a glob in 'skip_glob' setting
.mypy_cache was skipped as it's listed in 'skip' setting or matches a glob in 'skip_glob' setting
venv was skipped as it's listed in 'skip' setting or matches a glob in 'skip_glob' setting
_build was skipped as it's listed in 'skip' setting or matches a glob in 'skip_glob' setting
Skipped 5 files

My config:

[tool.isort]
profile = "black"
line_length = 99
force_sort_within_sections = true
src_paths = ["config", "api"]
skip_gitignore = true

Let me know if you think I should open a separate issue about this.

@timothycrosley
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@johnthagen, good call out! Currently, that message isn't aware of why a skip happened. I've done the minimal thing of updating it to mention the gitignore possibility: 6c1ec9a but making it know why a file was skipped would require a bit more of a refactoring if it is needed.

@pums974
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pums974 commented Jul 8, 2021

Hi,
I still have the issue with the version 5.9.2, although it is a bit different.
fatal: Pathspec '/some/path/other_project/setup.py' is in submodule 'other_project

where other_project is a git submodule, not in .gitignore but in extend_skip

If I put my venv in extend_skip and turn off skip_gitignore, everything seems to be working fine

Do you want me to open a different issue ?

@johnthagen
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johnthagen commented Jul 8, 2021

I've done the minimal thing of updating it to mention the gitignore possibility: 6c1ec9a

To me that makes it clear enough (just knowing that it could be possibility). I don't think there is huge value is trying to track why each item was skipped. Thanks for the quick response and fix. isort is awesome.

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