Merge pull request #449 from yarikoptic/enh-codespell

Add codespell support (config, workflow to detect/not fix) and make it fix few typos

.github/workflows/codespell.yml

@@ -0,0 +1,25 @@
+# Codespell configuration is within pyproject.toml
+---
+name: Codespell
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+
+permissions:
+  contents: read
+
+jobs:
+  codespell:
+    name: Check for spelling errors
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+      - name: Annotate locations with typos
+        uses: codespell-project/codespell-problem-matcher@v1
+      - name: Codespell
+        uses: codespell-project/actions-codespell@v2

.pre-commit-config.yaml

@@ -31,3 +31,10 @@ repos:
         language: system
         exclude: ^docs
         types_or: [cython, pyi, python]
+  - repo: https://github.com/codespell-project/codespell
+    # Configuration for codespell is in pyproject.toml
+    rev: v2.2.6
+    hooks:
+    - id: codespell
+      additional_dependencies:
+      - tomli

README.md

@@ -14,7 +14,7 @@ Snakebids is a Python package that extends [Snakemake](https://snakemake.github.
 
 Snakebids includes all of the features of Snakemake, including flexible configuration, parallel execution, and Docker/Singularity support, plus:
 
-- **Built-in support for BIDS datasets**: Seamless workflow functionality with a wide range of BIDS datasets, accomodating various levels of complexity.
+- **Built-in support for BIDS datasets**: Seamless workflow functionality with a wide range of BIDS datasets, accommodating various levels of complexity.
 - **BIDS App Creation**: Provide command-line invocations of your workflow following BIDS App guidelines, ensuring reproducibility and enhancing accessibility of your workflow.
 - **BIDS Path Construction**: Easy, flexible construction of valid BIDS paths following BIDS guiding principles, promoting data organization and sharing.
 - **Plugin System**: Extend the functionality of Snakebids by creating and using plugins to meet your workflow's needs.

docs/api/paths.rst

@@ -16,7 +16,7 @@ Specs
 
 .. py:currentmodule:: snakebids.paths.specs
 
-BIDS specs control the formatting of paths produced by the :func:`~snakebids.bids` function. They specify the order of recognized entities, placing ``ses-X`` after ``sub-Y``, for instance, no matter what order they are specified in the function. Unrecognized entitites are placed in the order specified in the function call.
+BIDS specs control the formatting of paths produced by the :func:`~snakebids.bids` function. They specify the order of recognized entities, placing ``ses-X`` after ``sub-Y``, for instance, no matter what order they are specified in the function. Unrecognized entities are placed in the order specified in the function call.
 
 Because of this, each addition of entities to the spec presents a potentially breaking change. Suppose an entity called ``foo`` were added to the spec. Calls to :func:`~snakebids.bids` with ``foo`` as an argument would place the entity at the end of the path:
 

docs/migration/0.11_to_0.12.md

@@ -1,7 +1,7 @@
 (migrate-to-bidsapp)=
 # 0.11 to 0.12+
 
-Snakebids 0.12 introduces a [new, more flexible module](#snakebids.bidsapp) for creating bidsapps. This affects the syntax of the `run.py` file. Older versions used the {class}`snakebids.app.SnakeBidsApp` class to initialize the bidsapp, and this method will still work for the forseeable future. Switching to the new syntax will give access to new plugins and integrations and ensure long term support.
+Snakebids 0.12 introduces a [new, more flexible module](#snakebids.bidsapp) for creating bidsapps. This affects the syntax of the `run.py` file. Older versions used the {class}`snakebids.app.SnakeBidsApp` class to initialize the bidsapp, and this method will still work for the foreseeable future. Switching to the new syntax will give access to new plugins and integrations and ensure long term support.
 
 If you haven't heavily modified your `run.py` file, you can transition simply by replacing it with the following:
 

docs/migration/0.7_to_0.8.md

@@ -19,7 +19,7 @@ Be sure to also [migrate](0.11_to_0.12.md) your `run.py` file to the new snakebi
 
 ## Default return of {func}`~snakebids.generate_inputs()`
 
-V0.8 switches the default return value of {func}`~snakebids.generate_inputs()` from {class}`~snakebids.BidsDatasetDict` to {class}`~snakebids.BidsDataset`. Legacy code still relying on the old dictionary can avoid the update by setting the `use_bids_inputs` pararmeter in {func}`~snakebids.generate_inputs()` to `False`:
+V0.8 switches the default return value of {func}`~snakebids.generate_inputs()` from {class}`~snakebids.BidsDatasetDict` to {class}`~snakebids.BidsDataset`. Legacy code still relying on the old dictionary can avoid the update by setting the `use_bids_inputs` parameter in {func}`~snakebids.generate_inputs()` to `False`:
 
 ```python
 config.update(generate_inputs(

pyproject.toml

@@ -49,7 +49,7 @@ pvandyken-deprecated = "0.0.4"
 # Need this until py39
 importlib-resources = ">=5.12.0"
 
-#  Below are non-direct dependencies (i.e. dependencies of other depenencies)
+#  Below are non-direct dependencies (i.e. dependencies of other dependencies)
 #  specified to ensure a version with a pre-built wheel is installed depending
 #  on the python version being used.
 numpy = [
@@ -83,7 +83,7 @@ pytest = "^8"
 pytest-mock = "^3.7.0"
 poethepoet = "^0.27"
 pre-commit = "^3.0.0"
-# a mkinit dep has the 'platform_system == "Windows"' as a marker on an incompatible dependeny
+# a mkinit dep has the 'platform_system == "Windows"' as a marker on an incompatible dependency
 #   (pydantic<2.0 cf copier), so set the inverse as a marker here so mkinit can
 #   still be resolved
 mkinit = { version="^1.1.0", markers = "platform_system != 'Windows'" }
@@ -308,3 +308,10 @@ more_itertools = "itx"
 
 [tool.ruff.lint.flake8-pytest-style]
 fixture-parentheses = false
+
+[tool.codespell]
+# Ref: https://github.com/codespell-project/codespell#using-a-config-file
+skip = '.git*,*.lock,*.css,./typings'
+check-hidden = true
+# ignore-regex = ''
+# ignore-words-list = ''

scripts/update_bids.py

@@ -22,7 +22,7 @@ def generate_stub(mod: ModuleType, imports: list[str], funcs: Iterable[str]):
     mod
         module for which stub file should be written
     imports
-        list of imports and other statemets to appear at the beginning of the file
+        list of imports and other statements to appear at the beginning of the file
     funcs
         list of function declarations
     """

snakebids/app.py

@@ -119,7 +119,7 @@ def _check_deprecations(self):
         if self.version is not None:
             msg = (
                 "`SnakeBidsApp.version` is deprecated and no longer has any effect. To "
-                "explcitly set the app version, use the `snakebids.plugins.Version` "
+                "explicitly set the app version, use the `snakebids.plugins.Version` "
                 "plugin"
             )
             warnings.warn(msg, stacklevel=3)

snakebids/bidsapp/hookspecs.py

@@ -72,7 +72,7 @@ def update_cli_namespace(namespace: dict[str, Any], config: dict[str, Any]):
     :meth:`~argparse.ArgumentParser.parse_args` (equivalent to
     :class:`vars(Namespace) <argparse.Namespace>`). Any modifications made to this
     :class:`dict` will be carried forward in app initialization. For instance, if
-    an entry is deleleted from ``namespace``, it will not be available to downstream
+    an entry is deleted from ``namespace``, it will not be available to downstream
     plugins or be copied into ``config``.
 
     Parameters

snakebids/cli.py

@@ -14,7 +14,7 @@ def add_dynamic_args(
 ) -> None:
     """Do nothing.
 
-    Originally added --filter-<comp> and --wildcards-<comp> argumets to the CLI. Kept
+    Originally added --filter-<comp> and --wildcards-<comp> arguments to the CLI. Kept
     as a placeholder for apps that relied on it for generating documentation. This
     functionality is now native to `SnakeBidsApp`.
     """

snakebids/core/datasets.py

@@ -363,7 +363,7 @@ def expand(
         """Safely expand over given paths with component wildcards.
 
         Uses the entity-value combinations found in the dataset to expand over the given
-        paths. Extra wildcards can be specifed as keyword arguments.
+        paths. Extra wildcards can be specified as keyword arguments.
 
         By default, expansion over paths with extra wildcards not accounted for by the
         component causes an error. This prevents accidental partial expansion. To allow
@@ -430,8 +430,8 @@ def filter(
 
         This method allows you to expand over a subset of your wildcards. This could be
         useful for extracting subjects from a specific patient group, running different
-        rules on different aquisitions, and any other reason you may need to filter your
-        data after the workflow has already started.
+        rules on different acquisitions, and any other reason you may need to filter
+        your data after the workflow has already started.
 
         Takes entities as keyword arguments assigned to values or list of values to
         select from the component. Only columns containing the provided entity-values
@@ -468,7 +468,7 @@ class BidsComponent(BidsPartialComponent):
 
     A component is a set of data entries all corresponding to the same type of object.
     Entries vary over a set of entities. For example, a component may represent all the
-    unprocessed, T1-weighted anatomical images aqcuired from a group of 100 subjects,
+    unprocessed, T1-weighted anatomical images acquired from a group of 100 subjects,
     across 2 sessions, with three runs per session. Here, the subject, session, and run
     are the entities over which the component varies. Each entry in the component has
     a single value assigned for each of the three entities (e.g subject 002, session
@@ -791,7 +791,7 @@ def input_wildcards(self) -> dict[str, MultiSelectDict[str, str]]:
     def as_dict(self) -> BidsDatasetDict:
         """Get the layout as a legacy dict.
 
-        Included primarily for backward compatability with older versions of snakebids,
+        Included primarily for backward compatibility with older versions of snakebids,
         where generate_inputs() returned a dict rather than the `BidsDataset` class
 
         Returns

snakebids/core/input_generation.py

@@ -423,7 +423,7 @@ def _gen_bids_layout(
         existing database.
 
     index_metadata
-        A boolen that determines whether to parse and index metadata
+        A boolean that determines whether to parse and index metadata
 
     validate
         A boolean that determines whether to validate the bids dataset

snakebids/io/printing.py

@@ -106,7 +106,7 @@ def new_col(val: str):
 
 
 def _find_elision(widths: list[int], excluded: slice, overflow: int) -> slice:
-    # Add 4 to overflow to account for elipses
+    # Add 4 to overflow to account for ellipses
     if max(sum(widths[excluded]) - 4, 0) >= overflow:
         return excluded
     span = excluded.stop - excluded.start
@@ -118,7 +118,7 @@ def _find_elision(widths: list[int], excluded: slice, overflow: int) -> slice:
     mid = floor(num_vals / 2)
 
     # need different rules for handling exclusions of even length depending on whether
-    # theres an even or odd total number of values.
+    # there's an even or odd total number of values.
     left_bias = floor if num_vals % 2 else ceil
     right_bias = ceil if num_vals % 2 else floor
 

snakebids/jinja2_ext/snakebids_version.py

@@ -9,7 +9,7 @@
 
 
 class SnakebidsVersionExtension(Extension):
-    """Retrieve the latest snakebids vesion from pypi.
+    """Retrieve the latest snakebids version from pypi.
 
     Stores value in the ``snakebids_version`` global variable.
     """

snakebids/plugins/base.py

@@ -112,7 +112,7 @@ def add_argument(
         *name_or_flags: str,
         **kwargs: Unpack[AnyArgumentArgs],
     ) -> argparse.Action | None:
-        """Add argument to parser, applying prefix to dest as necesary."""
+        """Add argument to parser, applying prefix to dest as necessary."""
         if self.PREFIX and not kwargs["dest"].startswith(self.PREFIX):
             kwargs["dest"] = f"{self.PREFIX}.{kwargs['dest']}"
         return parser.add_argument(*name_or_flags, **kwargs)

snakebids/plugins/bidsargs.py

@@ -70,7 +70,7 @@ class BidsArgs(PluginBase):
     CLI Arguments
     ~~~~~~~~~~~~~
     All arguments are added by default, but can be disabled using their respective
-    parameters. Additinally, arguments can be directly overriden by adding arguments
+    parameters. Additionally, arguments can be directly overridden by adding arguments
     to the parser before the plugin runs, using the following ``dests``:
 
     - ``bids_dir``: The input bids directory
@@ -93,7 +93,7 @@ class BidsArgs(PluginBase):
 
         Overriding just one or two of the positional arguments may alter the order,
         preventing the app from being called correctly. Thus, if any of the positional
-        args are being overriden, they all should be.
+        args are being overridden, they all should be.
 
 
     Analysis levels

snakebids/plugins/component_edit.py

@@ -122,7 +122,7 @@ class ComponentEdit(PluginBase):
     4. ``ENTITY:none`` selects all paths without the entity.
     5. ``ENTITY:any`` removes filters for the entity.
 
-    CLI arguments created by this plugin cannot be overriden.
+    CLI arguments created by this plugin cannot be overridden.
 
     Parameters
     ----------

snakebids/plugins/pybidsdb.py

@@ -27,7 +27,7 @@ class Pybidsdb(PluginBase):
 
     CLI Arguments
     ~~~~~~~~~~~~~
-    Two arguments are added to the CLI. These can be overriden by adding arguments
+    Two arguments are added to the CLI. These can be overridden by adding arguments
     with corresponding ``dests`` before this plugin is run:
 
     - ``plugins.pybidsdb.dir``: (:class:`~pathlib.Path`) Path of the database

snakebids/plugins/validator.py

@@ -29,7 +29,7 @@ class BidsValidator(PluginBase):
     InvalidBidsError is raised.
 
     An argument --skip-bids-validation is added to the CLI. This argument can be
-    overriden by adding an argument with dest ``plugins.validator.skip`` before this
+    overridden by adding an argument with dest ``plugins.validator.skip`` before this
     plugin runs.
 
     Two entries are added to config:

snakebids/project_template/{{name_slug}}/config/snakebids.yml

@@ -9,7 +9,7 @@ targets_by_analysis_level:
     - 'all'  # if '', then the first rule is run
 
 # Configure components:
-# Each entry creates a new component that can be retreived within the workflow
+# Each entry creates a new component that can be retrieved within the workflow
 # via `generate_inputs`.
 # Filters are used to select paths: each filter has an `entity` key and a
 # single value or list of values to select.

snakebids/tests/test_datasets.py

@@ -355,7 +355,7 @@ class TestBidsComponentExpand:
     """
     `extension` is generally excluded from the generated components because its wildcard
     is immediately adjacent to the previous wildcard (e.g.
-    sub-{subject}_{suffix}{extenions}), making it impossible to correctly parse using
+    sub-{subject}_{suffix}{extension}), making it impossible to correctly parse using
     `glob_wildcards`. Its absence does not affect the spirit of the tests.
 
     We also exclude extra_entities from the generated Components for the same reason:

snakebids/tests/test_generate_inputs.py

@@ -994,7 +994,7 @@ def path_entities(draw: st.DrawFn):
     valid_chars = st.characters(
         min_codepoint=48, max_codepoint=122, whitelist_categories=["Ll", "Lu"]
     )
-    # We need to explicitely exclude keywords here because the current implementation
+    # We need to explicitly exclude keywords here because the current implementation
     # of glob_wildcards uses a named tuple, which doesn't allow keywords as attributes.
     path_text = st.text(valid_chars, min_size=1).filter(
         lambda s: not keyword.iskeyword(s)
@@ -1821,9 +1821,9 @@ def test_exclude_participant_does_not_make_all_other_filters_regex(
             for comp in dataset.values()
         )
 
-        # Create an extra set of paths by modifing one of the existing components to put
-        # foo after a set of entity values. If that filter gets changed to a regex, all
-        # of the suffixed decoys will get picked up by pybids
+        # Create an extra set of paths by modifying one of the existing components to
+        # put foo after a set of entity values. If that filter gets changed to a regex,
+        # all of the suffixed decoys will get picked up by pybids
         ziplist = dict(itx.first(rooted.values()).zip_lists)
         mut_entity = itx.first(
             filter(lambda e: e not in {"subject", "extension"}, ziplist)

snakebids/utils/containers.py

@@ -50,7 +50,7 @@ class ImmutableList(Sequence[_T_co], Generic[_T_co]):
 
     Unlike tuples, only a single type parameter is supported. In other words,
     ``ImmutableList`` cannot be specified via type hints as a fixed length sequence
-    containing heterogenous items. A tuple specified as ``tuple[str, int, str]`` would
+    containing heterogeneous items. A tuple specified as ``tuple[str, int, str]`` would
     be specified as ``ImmutableList[str | int]``
     """
 

snakebids/utils/output.py

@@ -77,8 +77,8 @@ def write_output_mode(dotfile: Path, mode: Mode) -> None:
 def _get_snakebids_file(outputdir: Path) -> dict[str, str] | None:
     """Ensure populated dir contains .snakebids file, retrieving it if it does.
 
-    First checks if outputdir doesn't exist or is completely empty, returing None if so.
-    If it does have data, it checks for a .snakebids file, returning its contents if
+    First checks if outputdir doesn't exist or is completely empty, returning None if
+    so. If it does have data, it checks for a .snakebids file, returning its contents if
     found. If no .snakebids file is found, it raises an exception.
 
     Parameters
@@ -89,7 +89,7 @@ def _get_snakebids_file(outputdir: Path) -> dict[str, str] | None:
     Returns
     -------
     Dict or None
-        None if output dir is nonexistant or empty, otherwise the contents
+        None if output dir is nonexistent or empty, otherwise the contents
         of the .snakebids file
 
     Raises

snakebids/utils/snakemake_io.py

@@ -25,7 +25,7 @@ def regex(filepattern: str) -> str:
             if match.group("constraint"):
                 msg = (
                     "Constraint regex must be defined only in the first "
-                    "occurence of the wildcard in a string."
+                    "occurrence of the wildcard in a string."
                 )
                 raise ValueError(msg)
             regex_list.append(f"(?P={wildcard})")