Add --ignore CLI option and ignore_files config field (#60)

* Add --ignore CLI option and ignore_files config option

* Add configuration reference

* Fix logic in `_load_configuration`

* Fix outstanding warnings and errors

* Vendor glob.translate from Python 3.13.4

because it isn't available in earlier versions.

* Fix typo

* Type vendored glob function

* Vendor fnmatch._translate too

* Skip glob_patterns_to_regex doctests

Windows uses different path separators of course, so there is no easy
way to get this doctest working on both platforms. Instead let's just
skip this...

* Use Debian's Machine-readable format for license file

* Include vendored license in license field

See for reference:
https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license
https://spdx.github.io/spdx-spec/v2.3/SPDX-license-expressions/#:~:text=Conjunctive%20%22AND%22%20operator

* Refactor name to field

Should be a bit more expressive.

Author: lagru

LICENSE

@@ -0,0 +1,88 @@
+Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Source: https://github.com/scientific-python/docstub
+
+Files: *
+Copyright: 2025, Scientific Python Developers
+           2024, Lars Grüter
+License: BSD 3-Clause
+
+Files: src/docstub/_vendored/stdlib.py
+Copyright: 2001-2025, Python Software Foundation
+License: PSF-2.0
+
+License: BSD-3-Clause
+  All rights reserved.
+  .
+  Redistribution and use in source and binary forms, with or without
+  modification, are permitted provided that the following conditions are met:
+  .
+  * Redistributions of source code must retain the above copyright notice, this
+    list of conditions and the following disclaimer.
+  .
+  * Redistributions in binary form must reproduce the above copyright notice,
+    this list of conditions and the following disclaimer in the documentation
+    and/or other materials provided with the distribution.
+  .
+  * Neither the name of the vector package developers nor the names of its
+    contributors may be used to endorse or promote products derived from
+    this software without specific prior written permission.
+  .
+  THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+  AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+  IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+  DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+  FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+  DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+  SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+  CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+  OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+  OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
+
+License: PSF-2.0
+  PYTHON SOFTWARE FOUNDATION LICENSE VERSION 2
+  --------------------------------------------
+  .
+  1. This LICENSE AGREEMENT is between the Python Software Foundation
+  ("PSF"), and the Individual or Organization ("Licensee") accessing and
+  otherwise using this software ("Python") in source or binary form and
+  its associated documentation.
+  .
+  2. Subject to the terms and conditions of this License Agreement, PSF hereby
+  grants Licensee a nonexclusive, royalty-free, world-wide license to reproduce,
+  analyze, test, perform and/or display publicly, prepare derivative works,
+  distribute, and otherwise use Python alone or in any derivative version,
+  provided, however, that PSF's License Agreement and PSF's notice of copyright,
+  i.e., "Copyright (c) 2001 Python Software Foundation; All Rights Reserved"
+  are retained in Python alone or in any derivative version prepared by Licensee.
+  .
+  3. In the event Licensee prepares a derivative work that is based on
+  or incorporates Python or any part thereof, and wants to make
+  the derivative work available to others as provided herein, then
+  Licensee hereby agrees to include in any such work a brief summary of
+  the changes made to Python.
+  .
+  4. PSF is making Python available to Licensee on an "AS IS"
+  basis.  PSF MAKES NO REPRESENTATIONS OR WARRANTIES, EXPRESS OR
+  IMPLIED.  BY WAY OF EXAMPLE, BUT NOT LIMITATION, PSF MAKES NO AND
+  DISCLAIMS ANY REPRESENTATION OR WARRANTY OF MERCHANTABILITY OR FITNESS
+  FOR ANY PARTICULAR PURPOSE OR THAT THE USE OF PYTHON WILL NOT
+  INFRINGE ANY THIRD PARTY RIGHTS.
+  .
+  5. PSF SHALL NOT BE LIABLE TO LICENSEE OR ANY OTHER USERS OF PYTHON
+  FOR ANY INCIDENTAL, SPECIAL, OR CONSEQUENTIAL DAMAGES OR LOSS AS
+  A RESULT OF MODIFYING, DISTRIBUTING, OR OTHERWISE USING PYTHON,
+  OR ANY DERIVATIVE THEREOF, EVEN IF ADVISED OF THE POSSIBILITY THEREOF.
+  .
+  6. This License Agreement will automatically terminate upon a material
+  breach of its terms and conditions.
+  .
+  7. Nothing in this License Agreement shall be deemed to create any
+  relationship of agency, partnership, or joint venture between PSF and
+  Licensee.  This License Agreement does not grant permission to use PSF
+  trademarks or trade name in a trademark sense to endorse or promote
+  products or services of Licensee, or any third party.
+  .
+  8. By copying, installing or otherwise using Python, Licensee
+  agrees to be bound by the terms and conditions of this License
+  Agreement.

LICENSE.txt

@@ -43,6 +43,8 @@ Options:
   --config PATH       Set one or more configuration file(s) explicitly.
                       Otherwise, it will look for a `pyproject.toml` or
                       `docstub.toml` in the current directory.
+  --ignore GLOB       Ignore files matching this glob-style pattern. Can be
+                      used multiple times.
   --group-errors      Group identical errors together and list where they
                       occurred. Will delay showing errors until all files have
                       been processed. Otherwise, simply report errors as the

docs/command_line.md

@@ -0,0 +1,95 @@
+# Configuration reference
+
+Docstub will automatically look for configuration in files named
+
+- `pyproject.toml`, and
+- `docstub.toml`
+
+in the current working directory.
+If config files are explicitly passed to the command line interface via the `--config` option, docstub won't look implicitly look for files in the current directory.
+Multiple configuration files can be used, whose content will be merged.
+
+Out of the box, docstub makes use of an internal configuration file [`numpy_config.toml`](../src/docstub/numpy_config.toml) which provides defaults to use NumPy types.
+
+
+## Configuration fields in `[tool.docstub]`
+
+All configuration must be declared inside a `[tool.docstub]` table.
+
+
+### `ignore_files`
+
+- [TOML type](https://toml.io/en/latest): array of string(s)
+
+Ignore files and directories matching these [glob-style patterns](https://docs.python.org/3/library/glob.html#glob.translate).
+Patterns that don't start with "/" are interpreted as relative to the
+directory that contains the Python package for which stubs are generated.
+
+Example:
+
+```toml
+[tool.docstub]
+ignore_files = [
+    "**/tests",
+]
+```
+
+- Will ignore any directory anywhere that is named `tests`.
+
+
+### `types`
+
+- [TOML type](https://toml.io/en/latest): table, mapping string to string
+
+Types and their external modules to use in docstrings.
+Docstub can't yet automatically discover where to import types from other packages from.
+Instead, you can provide this information explicitly.
+Any type on the left side will be associated with the given "module" on the right side.
+
+Example:
+
+```toml
+[tool.docstub.types]
+Path = "pathlib"
+NDArray = "numpy.typing"
+```
+
+- Will allow using `Path` in docstrings and will use `from pathlib import Path` to import the type.
+- Will allow using `NDarray` in docstrings and will use `from numpy.typing import NDArray` to import the type.
+
+
+### `type_prefixes`
+
+- [TOML type](https://toml.io/en/latest): table, mapping string to string
+
+Prefixes for external modules to match types in docstrings.
+Docstub can't yet automatically discover where to import types from other packages from.
+Instead, you can provide this information explicitly.
+Any type in a docstring whose prefix matches the name given on the left side, will be associated with the given "module" on the right side.
+
+Example:
+
+```toml
+[tool.docstub.type_prefixes]
+np = "numpy"
+plt = "matplotlib.pyplot
+```
+
+- Will match `np.uint8` and `np.typing.NDarray` and use `import numpy as np`.
+- Will match `plt.Figure` use `import matplotlib.pyplot as plt`.
+
+
+### `type_nicknames`
+
+- [TOML type](https://toml.io/en/latest): table, mapping string to string
+
+Nicknames for types that can be used in docstrings to describe valid Python types or annotations.
+
+Example:
+
+```toml
+[tool.docstub.type_nicknames]
+func = "Callable"
+```
+
+- Will map `func` to the `Callable` type from the `typing` module.

docs/configuration.md

@@ -9,8 +9,11 @@ maintainers = [
 ]
 description = "Generate Python stub files from docstrings"
 readme = "README.md"
-license = "BSD-3-Clause"
-license-files = ["LICENSE"]
+
+# Need to include license of vendored code as well
+license = "BSD-3-Clause AND PSF-2.0"
+license-files = ["LICENSE.txt"]
+
 requires-python = ">=3.12"
 keywords = ["typing", "stub files", "docstings", "numpydoc"]
 classifiers = [
@@ -120,6 +123,7 @@ run.source = ["docstub"]
 Path = "pathlib"
 
 [tool.docstub.type_prefixes]
+re = "re"
 cst = "libcst"
 lark = "lark"
 numpydoc = "numpydoc"

pyproject.toml

@@ -15,13 +15,12 @@
 )
 from ._cache import FileCache
 from ._config import Config
-from ._stubs import (
+from ._path_utils import (
     STUB_HEADER_COMMENT,
-    Py2StubTransformer,
-    try_format_stub,
     walk_python_package,
     walk_source_and_targets,
 )
+from ._stubs import Py2StubTransformer, try_format_stub
 from ._utils import ErrorReporter, GroupedErrorReporter
 from ._version import __version__
 
@@ -43,22 +42,24 @@ def _load_configuration(config_paths=None):
     numpy_config = Config.from_toml(Config.NUMPY_PATH)
     config = config.merge(numpy_config)
 
-    pyproject_toml = Path.cwd() / "pyproject.toml"
-    if pyproject_toml.is_file():
-        logger.info("using %s", pyproject_toml)
-        add_config = Config.from_toml(pyproject_toml)
-        config = config.merge(add_config)
-
-    docstub_toml = Path.cwd() / "docstub.toml"
-    if docstub_toml.is_file():
-        logger.info("using %s", docstub_toml)
-        add_config = Config.from_toml(docstub_toml)
-        config = config.merge(add_config)
-
-    for path in config_paths:
-        logger.info("using %s", path)
-        add_config = Config.from_toml(path)
-        config = config.merge(add_config)
+    if config_paths:
+        for path in config_paths:
+            logger.info("using %s", path)
+            add_config = Config.from_toml(path)
+            config = config.merge(add_config)
+
+    else:
+        pyproject_toml = Path.cwd() / "pyproject.toml"
+        if pyproject_toml.is_file():
+            logger.info("using %s", pyproject_toml)
+            add_config = Config.from_toml(pyproject_toml)
+            config = config.merge(add_config)
+
+        docstub_toml = Path.cwd() / "docstub.toml"
+        if docstub_toml.is_file():
+            logger.info("using %s", docstub_toml)
+            add_config = Config.from_toml(docstub_toml)
+            config = config.merge(add_config)
 
     return config
 
@@ -78,12 +79,17 @@ def _setup_logging(*, verbose):
     )
 
 
-def _collect_types(root_path):
+def _collect_types(root_path, *, ignore=()):
     """Collect types.
 
     Parameters
     ----------
     root_path : Path
+    ignore : Sequence[str], optional
+        Don't yield files matching these glob-like patterns. The pattern is
+        interpreted relative to the root of the Python package unless it starts
+        with "/". See :ref:`glob.translate(..., recursive=True, include_hidden=True)`
+        for more details on the precise implementation.
 
     Returns
     -------
@@ -98,7 +104,7 @@ def _collect_types(root_path):
         name=f"{__version__}/collected_types",
     )
     if root_path.is_dir():
-        for source_path in walk_python_package(root_path):
+        for source_path in walk_python_package(root_path, ignore=ignore):
             logger.info("collecting types in %s", source_path)
             types_in_source = collect_cached_types(source_path)
             types.update(types_in_source)
@@ -162,6 +168,13 @@ def cli():
     "Otherwise, it will look for a `pyproject.toml` or `docstub.toml` in the "
     "current directory.",
 )
+@click.option(
+    "--ignore",
+    type=str,
+    multiple=True,
+    metavar="GLOB",
+    help="Ignore files matching this glob-style pattern. Can be used multiple times.",
+)
 @click.option(
     "--group-errors",
     is_flag=True,
@@ -182,7 +195,7 @@ def cli():
 @click.option("-v", "--verbose", count=True, help="Print more details (repeatable).")
 @click.help_option("-h", "--help")
 @report_execution_time()
-def run(root_path, out_dir, config_paths, group_errors, allow_errors, verbose):
+def run(root_path, out_dir, config_paths, ignore, group_errors, allow_errors, verbose):
     """Generate Python stub files.
 
     Given a `PACKAGE_PATH` to a Python package, generate stub files for it.
@@ -194,7 +207,8 @@ def run(root_path, out_dir, config_paths, group_errors, allow_errors, verbose):
     ----------
     root_path : Path
     out_dir : Path
-    config_paths : list[Path]
+    config_paths : Sequence[Path]
+    ignore : Sequence[str]
     group_errors : bool
     allow_errors : int
     verbose : str
@@ -212,9 +226,10 @@ def run(root_path, out_dir, config_paths, group_errors, allow_errors, verbose):
         )
 
     config = _load_configuration(config_paths)
+    config = config.merge(Config(ignore_files=list(ignore)))
 
     types = common_known_types()
-    types |= _collect_types(root_path)
+    types |= _collect_types(root_path, ignore=config.ignore_files)
     types |= {
         type_name: KnownImport(import_path=module, import_name=type_name)
         for type_name, module in config.types.items()
@@ -245,7 +260,9 @@ def run(root_path, out_dir, config_paths, group_errors, allow_errors, verbose):
 
     # Stub generation ---------------------------------------------------------
 
-    for source_path, stub_path in walk_source_and_targets(root_path, out_dir):
+    for source_path, stub_path in walk_source_and_targets(
+        root_path, out_dir, ignore=config.ignore_files
+    ):
         if source_path.suffix.lower() == ".pyi":
             logger.debug("using existing stub file %s", source_path)
             with source_path.open() as fo: