nltools 0.6.0.dev0__py3-none-any.whl

nltools/templates/registry.py

@@ -0,0 +1,25 @@
+"""Static registry of supported MNI templates."""
+
+from typing import Literal
+
+TemplateName = Literal["default", "nilearn", "fmriprep"]
+"""Which MNI template a brain space is built from."""
+
+Resolution = Literal[1, 2, 3]
+"""Voxel size of a template, in millimetres."""
+
+VERSION_MAP: dict[str, str] = {
+    "default": "fsl",
+    "nilearn": "a",
+    "fmriprep": "c",
+}
+
+VERSION_TO_TEMPLATE: dict[str, str] = {v: k for k, v in VERSION_MAP.items()}
+
+SUPPORTED_RESOLUTIONS: dict[str, list[int]] = {
+    "default": [2, 3],
+    "nilearn": [1, 2, 3],
+    "fmriprep": [1, 2],
+}
+
+TEMPLATE_PRIORITY: list[str] = ["default", "nilearn", "fmriprep"]

nltools/utils.py

@@ -0,0 +1,230 @@
+"""Cross-cutting utilities used across the nltools package."""
+
+__all__ = ["DesignMatrixWarning", "ResamplingWarning"]
+
+import contextlib
+import inspect
+import re
+from os.path import dirname, join, sep as pathsep
+
+import polars as pl
+
+
+# ---------------------------------------------------------------------------
+# polars compatibility
+# ---------------------------------------------------------------------------
+
+
+def _polars_version_tuple(text: str) -> tuple[int, ...]:
+    """Read the leading `(major, minor, patch)` numbers out of a version string.
+
+    polars ships a beta of every minor release and reports it in a dashed form
+    (`'1.36.0-beta.2'`), so splitting on `'.'` and calling `int` on the pieces
+    raises. Only the numeric prefix matters for a feature check.
+
+    Args:
+        text (str): A version string, e.g. `'1.33.1'` or `'1.36.0-beta.2'`.
+
+    Returns:
+        tuple[int, ...]: Up to three leading integers, e.g. `(1, 36, 0)`.
+    """
+    return tuple(int(part) for part in re.findall(r"\d+", text)[:3])
+
+
+# polars 1.42.1 renamed the classic equal-height horizontal concat to
+# ``horizontal_extend`` and deprecated the old ``horizontal`` spelling, which
+# will start padding to the tallest frame in the next breaking release. Below
+# 1.42.1 only ``horizontal`` exists. Every nltools call site concatenates
+# frames of equal height, so the two names are interchangeable there, and
+# picking by version lets the package run on the polars 1.33.1 that Pyodide
+# bundles as well as on current releases.
+_HORIZONTAL_CONCAT = (
+    "horizontal_extend"
+    if _polars_version_tuple(pl.__version__) >= (1, 42, 1)
+    else "horizontal"
+)
+
+
+# ---------------------------------------------------------------------------
+# Warnings: attribution and library-wide categories
+# ---------------------------------------------------------------------------
+
+_PACKAGE_DIR = dirname(__file__) + pathsep
+_TESTS_DIR = join(_PACKAGE_DIR, "tests") + pathsep
+# ``@_coalesced_gc()`` (a contextmanager used as a decorator) wraps facade
+# methods in a stdlib contextlib frame; it is nltools plumbing, not user code.
+_PLUMBING_FILES = frozenset({contextlib.__file__})
+
+
+def _is_library_frame(filename: str) -> bool:
+    if filename in _PLUMBING_FILES:
+        return True
+    return filename.startswith(_PACKAGE_DIR) and not filename.startswith(_TESTS_DIR)
+
+
+def _find_stack_level() -> int:
+    """Return the ``stacklevel`` that attributes a warning to the caller's code.
+
+    Walks up from the caller until the first frame outside the nltools package
+    (``nltools/tests/`` counts as outside: tests are the library's users; the
+    stdlib ``contextlib`` frame that ``@_coalesced_gc()`` inserts counts as
+    inside), so a ``warnings.warn`` deep inside a facade lands on the user's
+    line rather than on nltools internals — the same pattern nilearn and pandas
+    use. Every ``warnings.warn`` in the library passes
+    ``stacklevel=_find_stack_level()``; a source-scan test enforces it.
+
+    Returns:
+        int: Value for the ``stacklevel`` argument of ``warnings.warn``.
+
+    Examples:
+        ```python
+        warnings.warn("message", UserWarning, stacklevel=_find_stack_level())
+        ```
+    """
+    frame = inspect.currentframe()
+    level = 0
+    try:
+        while frame is not None and _is_library_frame(inspect.getfile(frame)):
+            frame = frame.f_back
+            level += 1
+    finally:
+        del frame
+    return level
+
+
+class ResamplingWarning(UserWarning):
+    """Data is (or will be) resampled to a different space than it arrived in.
+
+    Raised when a data image does not match the mask/template it is loaded
+    against — a detected template at another resolution, or a mask in a
+    different space — and nltools resamples to reconcile them. Subclasses
+    ``UserWarning`` so it participates in default filtering while staying
+    individually silenceable:
+    ``warnings.filterwarnings("ignore", category=ResamplingWarning)``.
+    """
+
+
+class DesignMatrixWarning(UserWarning):
+    """A ``DesignMatrix`` operation was skipped, or the design itself is suspect.
+
+    Raised by regressor builders (``add_poly``, ``add_dct_basis``,
+    ``convolve``) when the requested columns already exist and are skipped,
+    and by ``BrainData.fit()`` when the design it receives is rank deficient.
+    Subclasses ``UserWarning`` so it participates in default filtering while
+    staying individually silenceable:
+    ``warnings.filterwarnings("ignore", category=DesignMatrixWarning)``.
+    """
+
+
+# ---------------------------------------------------------------------------
+# Cross-cutting helpers (used by multiple subsystems)
+# ---------------------------------------------------------------------------
+
+
+def _attempt_to_import(dependency, fromlist=None):
+    """Attempt to import an optional dependency, returning None if unavailable.
+
+    This function is used to handle optional dependencies gracefully. If the
+    import fails, the function returns None rather than raising an error,
+    allowing the calling code to check and handle missing dependencies.
+
+    Args:
+        dependency (str): The module name to import (e.g. `'torch'`, `'cupy'`).
+        fromlist (list[str], optional): Names to import from the module (passed to
+            `__import__`).
+
+    Returns:
+        ModuleType | None: The imported module, or None if the import failed.
+
+    Examples:
+        ```python
+        torch = _attempt_to_import("torch")
+        if torch is not None:
+            ...  # use torch
+        ```
+    """
+    try:
+        mod = __import__(dependency, fromlist=fromlist)
+    except ImportError:
+        mod = None
+    return mod
+
+
+# ---------------------------------------------------------------------------
+# Progress bars — the single library-wide mechanism
+# ---------------------------------------------------------------------------
+
+
+class _NullProgressBar:
+    """No-op stand-in for `tqdm` used when `progress_bar=False`.
+
+    Supports the subset of the tqdm interface nltools relies on, so call sites
+    that drive a bar manually need no branching.
+    """
+
+    def update(self, n: int = 1) -> None:
+        pass
+
+    def close(self) -> None:
+        pass
+
+    def __enter__(self) -> "_NullProgressBar":
+        return self
+
+    def __exit__(self, *exc_info) -> bool:
+        return False
+
+
+def _maybe_tqdm(iterable, *, progress_bar: bool, **tqdm_kwargs):
+    """Wrap `iterable` in a tqdm progress bar only when `progress_bar` is True.
+
+    tqdm writes to stderr, so an unconditional bar makes functions noisy when
+    called in a loop (a 100-iteration calibration study would emit 100 bars).
+    Importing tqdm lazily also keeps it off the import path when unused. Uses
+    `tqdm.auto`, so notebooks get widget bars and terminals get text bars.
+
+    Args:
+        iterable (Iterable): The iterable to wrap.
+        progress_bar (bool): Whether to display a progress bar.
+        **tqdm_kwargs (dict): Forwarded to `tqdm` (e.g. `desc`, `unit`, `total`).
+
+    Returns:
+        Iterable: The original iterable, or a `tqdm`-wrapped version of it.
+
+    Examples:
+        ```python
+        for i in _maybe_tqdm(range(n_permute), progress_bar=progress_bar,
+                            desc="CPU parallel perms", unit="perm"):
+            ...
+        ```
+    """
+    if not progress_bar:
+        return iterable
+
+    from tqdm.auto import tqdm
+
+    return tqdm(iterable, **tqdm_kwargs)
+
+
+def _make_progress_bar(*, progress_bar: bool, **tqdm_kwargs):
+    """Build a progress bar, or a no-op stand-in when `progress_bar` is False.
+
+    Use this for call sites that drive the bar manually via `.update()` rather
+    than by iteration. Uses `tqdm.auto`, so notebooks get widget bars and
+    terminals get text bars.
+
+    Args:
+        progress_bar (bool): Whether to display a progress bar.
+        **tqdm_kwargs (dict): Forwarded to `tqdm` (e.g. `total`, `desc`, `unit`).
+
+    Returns:
+        tqdm | _NullProgressBar: A `tqdm` instance, or a `_NullProgressBar` exposing
+            the same subset of its interface (`update`, `close`, and the
+            context-manager protocol).
+    """
+    if not progress_bar:
+        return _NullProgressBar()
+
+    from tqdm.auto import tqdm
+
+    return tqdm(**tqdm_kwargs)

nltools/version.py

@@ -0,0 +1,13 @@
+"""Expose the installed nltools version. Single source of truth: pyproject.toml.
+
+`__version__` is read from the installed package metadata (populated by hatchling
+from the `version` field in pyproject.toml), so the release bump in pyproject.toml
+flows through automatically — there is no version string to keep in sync here.
+"""
+
+from importlib.metadata import PackageNotFoundError, version
+
+try:
+    __version__ = version("nltools")
+except PackageNotFoundError:  # running from a source tree without an install
+    __version__ = "0.0.0+unknown"

nltools-0.6.0.dev0.dist-info/METADATA

@@ -0,0 +1,95 @@
+Metadata-Version: 2.5
+Name: nltools
+Version: 0.6.0.dev0
+Summary: A Python package to analyze neuroimaging data
+Project-URL: Homepage, https://nltools.org
+Author-email: "Luke J. Chang" <luke.j.chang@dartmouth.edu>, Eshin Jolly <eshin.jolly@gmail.com>
+License: MIT
+License-File: LICENSE
+Keywords: analysis,machine-learning,neuroimaging,preprocessing
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Requires-Python: >=3.11
+Requires-Dist: anywidget>=0.9
+Requires-Dist: h5py>=3.13
+Requires-Dist: himalaya<0.5,>=0.4.11
+Requires-Dist: huggingface-hub>=0.30
+Requires-Dist: joblib>=1.5.3
+Requires-Dist: matplotlib>=3.8.0
+Requires-Dist: nibabel>=5.2.0
+Requires-Dist: nilearn>=0.14.1
+Requires-Dist: numpy>=2.0.2
+Requires-Dist: pandas>=2.3.0
+Requires-Dist: polars>=1.33.1
+Requires-Dist: pynv>=0.3
+Requires-Dist: scikit-learn>=1.8
+Requires-Dist: scipy>=1.11.1
+Requires-Dist: seaborn>=0.13.2
+Requires-Dist: tqdm>=4.67.1
+Provides-Extra: all
+Requires-Dist: h5py>=3.13; extra == 'all'
+Requires-Dist: ipywidgets>=8.1.7; extra == 'all'
+Requires-Dist: networkx>=3.5; extra == 'all'
+Provides-Extra: graph
+Requires-Dist: networkx>=3.5; extra == 'graph'
+Provides-Extra: h5
+Requires-Dist: h5py>=3.13; extra == 'h5'
+Provides-Extra: interactive-plots
+Requires-Dist: ipywidgets>=8.1.7; extra == 'interactive-plots'
+Description-Content-Type: text/markdown
+
+[![Package versioning](https://img.shields.io/pypi/v/nltools.svg)](https://pypi.org/project/nltools/)
+[![CI](https://github.com/cosanlab/nltools/actions/workflows/ci.yml/badge.svg)](https://github.com/cosanlab/nltools/actions/workflows/ci.yml)
+[![codecov](https://codecov.io/gh/cosanlab/nltools/branch/master/graph/badge.svg)](https://codecov.io/gh/cosanlab/nltools)
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.2229813.svg)](https://doi.org/10.5281/zenodo.2229813)
+![Python Versions](https://img.shields.io/badge/python-3.11%20%7C%203.12%20%7C%203.13-blue)
+![Platforms](https://img.shields.io/badge/platform-linux%20%7C%20osx%20%7C%20win-blue)
+
+# NLTools
+
+Python toolbox for analyzing neuroimaging data, with a focus on multivariate analyses. It grew out of Tor Wager's object-oriented Matlab [CANlab core tools](http://wagerlab.colorado.edu/tools) and builds on [nilearn](https://nilearn.github.io) and [scikit-learn](https://scikit-learn.org). Requires Python 3.11+.
+
+## Documentation
+
+Documentation and tutorials are available at https://nltools.org
+
+## Installation
+
+With [uv](https://docs.astral.sh/uv/) (recommended, for use in a project):
+
+```
+uv add nltools
+```
+
+Or with pip:
+
+```
+pip install nltools
+```
+
+## Development
+
+`uv` manages the whole workflow — it creates the virtual environment, installs core and development dependencies, and installs `nltools` into it in editable mode.
+
+```
+git clone https://github.com/cosanlab/nltools
+cd nltools
+uv sync
+```
+
+Common tasks (run via [poe](https://poethepoet.natn.io/), all prefixed with `uv run`):
+
+| Command | What it does |
+|---|---|
+| `uv run poe lint` | Fix, format, and type-check (ruff + ty) |
+| `uv run poe test` | Run the fast test suite in parallel |
+| `uv run pytest -k test_name` | Run a specific test |
+| `uv run poe docs-serve` | Live-preview the docs site at localhost:8000 (executes tutorials via the cache) |
+| `uv run poe docs-build` | Full docs build (API reference + executed tutorials) |
+| `uv run poe tutorials` | Run every tutorial notebook end-to-end |
+| `uv build` | Build the package locally |
+| `uv add/remove [--dev] pkg` | Add or remove a (dev) dependency |

nltools-0.6.0.dev0.dist-info/RECORD

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nltools-0.6.0.dev0.dist-info/licenses/LICENSE

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+The MIT License (MIT)
+
+Copyright (c) 2015-2026 Cosan Lab & SciMinds Research Studio
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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+SOFTWARE.